PMID- 39612613 OWN - NLM STAT- MEDLINE DCOM- 20250126 LR - 20250126 IS - 1879-0380 (Electronic) IS - 0959-437X (Linking) VI - 90 DP - 2025 Feb TI - Inferring human phenotypes using ancient DNA: from molecules to populations. PG - 102283 LID - S0959-437X(24)00132-1 [pii] LID - 10.1016/j.gde.2024.102283 [doi] AB - The increasing availability of ancient DNA (aDNA) from human groups across space and time has yielded deep insights into the movements of our species. However, given the challenges of mapping from genotype to phenotype, aDNA has revealed less about the phenotypes of ancient individuals. In this review, we highlight recent advances in inferring ancient phenotypes - from the molecular to population scale - with a focus on applications enabled by new machine learning approaches. The genetic architecture of complex traits across human groups suggests that the prediction of individual-level complex traits, like behavior or disease risk, is often challenging across the relevant evolutionary distances. Thus, we propose an approach that integrates predictions of molecular phenotypes, whose mechanisms are more conserved, with nongenetic data. CI - Copyright © 2024. Published by Elsevier Ltd. FAU - Ferrando-Bernal, Manuel AU - Ferrando-Bernal M AD - Bakar Computational Health Science Institute, University of California San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA. Electronic address: manuel.ferrandobernal@ucsf.edu. FAU - Brand, Colin M AU - Brand CM AD - Bakar Computational Health Science Institute, University of California San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA. Electronic address: colin.brand@ucsf.edu. FAU - Capra, John A AU - Capra JA AD - Bakar Computational Health Science Institute, University of California San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA. Electronic address: tony@capralab.org. LA - eng PT - Journal Article PT - Review DEP - 20241129 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - *Phenotype MH - Genetics, Population MH - Machine Learning MH - Genotype MH - Evolution, Molecular COIS- Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: John A. Capra reports financial support was provided by National Institutes of Health. Colin M. Brand reports that financial support was provided by National Institutes of Health. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. EDAT- 2024/11/30 11:16 MHDA- 2025/01/27 00:20 CRDT- 2024/11/29 18:06 PHST- 2024/08/17 00:00 [received] PHST- 2024/10/04 00:00 [revised] PHST- 2024/11/04 00:00 [accepted] PHST- 2025/01/27 00:20 [medline] PHST- 2024/11/30 11:16 [pubmed] PHST- 2024/11/29 18:06 [entrez] AID - S0959-437X(24)00132-1 [pii] AID - 10.1016/j.gde.2024.102283 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2025 Feb;90:102283. doi: 10.1016/j.gde.2024.102283. Epub 2024 Nov 29. PMID- 37438988 OWN - NLM STAT- MEDLINE DCOM- 20250103 LR - 20250106 IS - 1755-0998 (Electronic) IS - 1755-098X (Linking) VI - 25 IP - 2 DP - 2025 Feb TI - More than dirt: Sedimentary ancient DNA and Indigenous Australia. PG - e13835 LID - 10.1111/1755-0998.13835 [doi] AB - The rise of sedimentary ancient DNA (sedaDNA) studies has opened new possibilities for studying past environments. This groundbreaking area of genomics uses sediments to identify organisms, even in cases where macroscopic remains no longer exist. Managing this substrate in Indigenous Australian contexts, however, requires special considerations. Sediments and soils are often considered as waste by-products during archaeological and paleontological excavations and are not typically regulated by the same ethics guidelines utilised in mainstream 'western' research paradigms. Nevertheless, the product of sedaDNA work-genetic information from past fauna, flora, microbial communities and human ancestors-is likely to be of cultural significance and value for Indigenous peoples. This article offers an opinion on the responsibilities of researchers in Australia who engage in research related to this emerging field, particularly when it involves Indigenous communities. One aspect that deserves consideration in such research is the concept of benefit sharing. Benefit sharing refers to the practice of ensuring that the benefits that arise from research are shared equitably with the communities from which the research data were derived. This practice is particularly relevant in research that involves Indigenous communities, who may have unique cultural and spiritual connections to the research material. We argue that the integration of Traditional Knowledges into sedaDNA research would add enormous value to research and its outcomes by providing genomic outputs alongside and within the rich context of multimillennia oral histories. CI - © 2023 John Wiley & Sons Ltd. FAU - Lewis, Dawn A AU - Lewis DA AUID- ORCID: 0000-0003-2257-7161 AD - Australian Centre for Ancient DNA, School of Biological Sciences and Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. AD - ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia. FAU - Simpson, Rebecca AU - Simpson R AUID- ORCID: 0000-0002-4225-7790 AD - National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australia. AD - Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia. FAU - Hermes, Azure AU - Hermes A AUID- ORCID: 0000-0001-9142-2580 AD - National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australia. FAU - Brown, Alex AU - Brown A AUID- ORCID: 0000-0003-2112-3918 AD - National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australia. AD - Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia. FAU - Llamas, Bastien AU - Llamas B AUID- ORCID: 0000-0002-5550-9176 AD - Australian Centre for Ancient DNA, School of Biological Sciences and Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. AD - ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia. AD - National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australia. AD - Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia. LA - eng GR - 2011277/National Health and Medical Research Council/ GR - 1137563/National Health and Medical Research Council/ PT - Journal Article DEP - 20230712 PL - England TA - Mol Ecol Resour JT - Molecular ecology resources JID - 101465604 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Archaeology/methods MH - Australia MH - *DNA, Ancient/analysis MH - *Geologic Sediments/chemistry MH - *Indigenous Peoples/genetics OTO - NOTNLM OT - Australia OT - Indigenous OT - sedimentary ancient DNA OT - traditional knowledge EDAT- 2023/07/13 06:42 MHDA- 2025/01/03 06:21 CRDT- 2023/07/13 02:08 PHST- 2023/04/03 00:00 [revised] PHST- 2022/10/31 00:00 [received] PHST- 2023/07/04 00:00 [accepted] PHST- 2025/01/03 06:21 [medline] PHST- 2023/07/13 06:42 [pubmed] PHST- 2023/07/13 02:08 [entrez] AID - 10.1111/1755-0998.13835 [doi] PST - ppublish SO - Mol Ecol Resour. 2025 Feb;25(2):e13835. doi: 10.1111/1755-0998.13835. Epub 2023 Jul 12. PMID- 39715432 OWN - NLM STAT- MEDLINE DCOM- 20241223 LR - 20250115 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 122 IP - 1 DP - 2025 Jan 7 TI - Family relations of Moche elite burials on the North Coast of Peru (~500 CE): Analyses of the Señora de Cao and relatives. PG - e2416321121 LID - 10.1073/pnas.2416321121 [doi] LID - e2416321121 AB - The Moche archaeological culture flourished along Peru's North Coast between the 4th and 10th centuries CE and was characterized by a complex social hierarchy dominated by political and religious elites. Previous archaeological evidence suggests kinship was a key factor in maintaining political authority within Moche society. To test this hypothesis, we applied archaeological, genetic, and isotopic methods to examine familial relationships between six individuals, including the prominent Señora de Cao (~500 CE), buried together in a pyramid-like, painted temple, Huaca Cao Viejo, in the Chicama Valley, Peru. Our findings reveal that all six individuals were biologically related, with varying degrees of kinship. The Señora de Cao was interred with a sacrificed juvenile, identified as a possible niece, and at least one, and potentially two siblings and a grandparent in separate tombs nearby. One of the male siblings was accompanied in death by his sacrificed son. Isotopic analysis indicates that while most individuals had diets rich in maize and animal protein and spent their childhoods in or near the Chicama Valley, the sacrificed juvenile accompanying the Señora had a distinct diet and geographic origin. These results demonstrate that Moche elites were interred with family members, including some raised far from their parental homes. This supports the hypothesis that kinship was central to transmitting status and authority. Moreover, sacrificing family members to accompany deceased elites underscores the significance of ritual sacrifice in reinforcing familial ties and linking the deceased to both ancestors and the divine. FAU - Quilter, Jeffrey AU - Quilter J AUID- ORCID: 0000-0001-9069-2116 AD - Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA 02138. FAU - Harkins, Kelly AU - Harkins K AD - UCSC Paleogenomics, Department of Anthropology, University of California, Santa Cruz, CA 95064. FAU - Fanco Jordan, Régulo AU - Fanco Jordan R AD - Régulo Franco Jordán, Parque Arqueológico Nacional de Machupicchu, Ministerio de Cultura, Cusco, Peru. FAU - Marsh, Erik AU - Marsh E AUID- ORCID: 0000-0003-2355-5415 AD - CONICET, Laboratorio de Paleoecología Humana, Instituto Interdisciplinario de Ciencias Baásicas, Universidad Nacional de Cuyo, Mendoza M5500, Argentina. FAU - Prieto, Gabriel AU - Prieto G AUID- ORCID: 0000-0001-6229-986X AD - Department of Anthropology, University of Florida, Gainesville, FL 32611. FAU - Verano, John AU - Verano J AUID- ORCID: 0000-0002-0263-5611 AD - Department of Anthropology, Tulane University, New Orleans, LA 70118. FAU - LeBlanc, Steven AU - LeBlanc S AUID- ORCID: 0000-0001-9201-1070 AD - Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA 02138. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - UCSC Paleogenomics, Department of Anthropology, University of California, Santa Cruz, CA 95064. FAU - Krigbaum, John AU - Krigbaum J AUID- ORCID: 0000-0003-3113-7061 AD - Department of Anthropology, University of Florida, Gainesville, FL 32611. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AUID- ORCID: 0000-0001-5510-1114 AD - UCSC Paleogenomics, Department of Anthropology, University of California, Santa Cruz, CA 95064. AD - UCSC Genomics Institute, University of California, Santa Cruz, CA 95064. LA - eng GR - NGS- HJ-142R-17/National Geographic Society (NGS)/ GR - NGS-52945R-19/National Geographic Society (NGS)/ GR - NGS-7844-05/National Geographic Society (NGS)/ GR - NGS-7961-05/National Geographic Society (NGS)/ PT - Historical Article PT - Journal Article DEP - 20241223 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Peru MH - Humans MH - *Burial/history MH - Male MH - *Archaeology MH - Female MH - Family Relations MH - History, Medieval MH - Family MH - History, Ancient PMC - PMC11725780 OTO - NOTNLM OT - Moche OT - Peru OT - ancient DNA OT - isotopes OT - kinship COIS- Competing interests statement:The authors declare no competing interest. EDAT- 2024/12/23 22:58 MHDA- 2024/12/23 22:59 PMCR- 2024/12/23 CRDT- 2024/12/23 15:03 PHST- 2024/12/23 22:59 [medline] PHST- 2024/12/23 22:58 [pubmed] PHST- 2024/12/23 15:03 [entrez] PHST- 2024/12/23 00:00 [pmc-release] AID - 202416321 [pii] AID - 10.1073/pnas.2416321121 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2025 Jan 7;122(1):e2416321121. doi: 10.1073/pnas.2416321121. Epub 2024 Dec 23. PMID- 39613690 OWN - NLM STAT- MEDLINE DCOM- 20250108 LR - 20250114 IS - 1878-4380 (Electronic) IS - 0966-842X (Linking) VI - 33 IP - 1 DP - 2025 Jan TI - Historical plague pandemics: perspectives from ancient DNA. PG - 7-10 LID - S0966-842X(24)00282-8 [pii] LID - 10.1016/j.tim.2024.10.008 [doi] AB - Ancient DNA research has provided important insights into the evolutionary history of Yersinia pestis during the historical plague pandemics. Future work should prioritise a more diversified approach to sampling, to ensure a broader understanding of the factors underlying pandemic onset, spread, and impact across different regions and hosts. CI - Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Gaul, Emily AU - Gaul E AD - Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany. FAU - Spyrou, Maria A AU - Spyrou MA AD - Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. Electronic address: maria.spyrou@ifu.uni-tuebingen.de. LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20241129 PL - England TA - Trends Microbiol JT - Trends in microbiology JID - 9310916 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - *Plague/history/microbiology/epidemiology MH - *Yersinia pestis/genetics MH - *DNA, Ancient/analysis MH - Humans MH - *Pandemics/history MH - Evolution, Molecular MH - Animals MH - DNA, Bacterial/genetics MH - History, Ancient OTO - NOTNLM OT - Black Death OT - Justinianic Plague OT - Yersinia pestis OT - ancient pathogen genomics OT - pathogen evolution COIS- Declaration of interests None are declared by the authors. EDAT- 2024/11/30 11:16 MHDA- 2025/01/09 00:22 CRDT- 2024/11/29 22:35 PHST- 2024/07/18 00:00 [received] PHST- 2024/10/29 00:00 [revised] PHST- 2024/10/30 00:00 [accepted] PHST- 2025/01/09 00:22 [medline] PHST- 2024/11/30 11:16 [pubmed] PHST- 2024/11/29 22:35 [entrez] AID - S0966-842X(24)00282-8 [pii] AID - 10.1016/j.tim.2024.10.008 [doi] PST - ppublish SO - Trends Microbiol. 2025 Jan;33(1):7-10. doi: 10.1016/j.tim.2024.10.008. Epub 2024 Nov 29. PMID- 39567757 OWN - NLM STAT- MEDLINE DCOM- 20250110 LR - 20250116 IS - 2397-334X (Electronic) IS - 2397-334X (Linking) VI - 9 IP - 1 DP - 2025 Jan TI - Inferring DNA methylation in non-skeletal tissues of ancient specimens. PG - 153-165 LID - 10.1038/s41559-024-02571-w [doi] AB - Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes. CI - © 2024. The Author(s). FAU - Mathov, Yoav AU - Mathov Y AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. AD - Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Nissim-Rafinia, Malka AU - Nissim-Rafinia M AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Leibson, Chen AU - Leibson C AUID- ORCID: 0000-0002-1333-1381 AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Galun, Nir AU - Galun N AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Marques-Bonet, Tomas AU - Marques-Bonet T AUID- ORCID: 0000-0002-5597-3075 AD - Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain. AD - Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain. AD - CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. AD - Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain. FAU - Kandel, Arye AU - Kandel A AD - Orthopedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel. FAU - Liebergal, Meir AU - Liebergal M AD - Orthopedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel. FAU - Meshorer, Eran AU - Meshorer E AUID- ORCID: 0000-0003-4777-986X AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. eran.meshorer@mail.huji.ac.il. AD - Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel. eran.meshorer@mail.huji.ac.il. FAU - Carmel, Liran AU - Carmel L AUID- ORCID: 0000-0003-0225-8550 AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. liran.carmel@huji.ac.il. LA - eng GR - R01 HG010898/HG/NHGRI NIH HHS/United States GR - 61739/John Templeton Foundation (JTF)/ PT - Journal Article DEP - 20241120 PL - England TA - Nat Ecol Evol JT - Nature ecology & evolution JID - 101698577 RN - 0 (DNA, Ancient) SB - IM MH - *DNA Methylation MH - Humans MH - *DNA, Ancient/analysis MH - Algorithms MH - Animals MH - Fossils PMC - PMC11726462 COIS- Competing interests: The authors declare no competing interests. EDAT- 2024/11/21 00:22 MHDA- 2025/01/11 14:00 PMCR- 2024/11/20 CRDT- 2024/11/20 23:46 PHST- 2023/05/07 00:00 [received] PHST- 2024/10/01 00:00 [accepted] PHST- 2025/01/11 14:00 [medline] PHST- 2024/11/21 00:22 [pubmed] PHST- 2024/11/20 23:46 [entrez] PHST- 2024/11/20 00:00 [pmc-release] AID - 10.1038/s41559-024-02571-w [pii] AID - 2571 [pii] AID - 10.1038/s41559-024-02571-w [doi] PST - ppublish SO - Nat Ecol Evol. 2025 Jan;9(1):153-165. doi: 10.1038/s41559-024-02571-w. Epub 2024 Nov 20. PMID- 39432055 OWN - NLM STAT- MEDLINE DCOM- 20241215 LR - 20250104 IS - 1755-0998 (Electronic) IS - 1755-098X (Print) IS - 1755-098X (Linking) VI - 25 IP - 1 DP - 2025 Jan TI - Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage. PG - e14029 LID - 10.1111/1755-0998.14029 [doi] LID - e14029 AB - One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data. CI - © 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd. FAU - Zhao, Lei AU - Zhao L AUID- ORCID: 0000-0002-6551-2707 AD - School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China. AD - Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen K, Denmark. FAU - Henriksen, Rasmus Amund AU - Henriksen RA AUID- ORCID: 0000-0003-3657-1983 AD - Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen K, Denmark. FAU - Ramsøe, Abigail AU - Ramsøe A AUID- ORCID: 0000-0001-5132-007X AD - Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen K, Denmark. FAU - Nielsen, Rasmus AU - Nielsen R AUID- ORCID: 0000-0003-0513-6591 AD - Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen K, Denmark. AD - Department of Integrative Biology and Department of Statistics, University of California, Berkeley, California, USA. FAU - Korneliussen, Thorfinn Sand AU - Korneliussen TS AUID- ORCID: 0000-0001-7576-5380 AD - Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen K, Denmark. LA - eng SI - RefSeq/PRJEB26349 SI - RefSeq/ERP107300 SI - RefSeq/PRJEB64656 SI - RefSeq/PRJEB9021 SI - RefSeq/PRJEB37976 GR - CF19-0712/Carlsberg Foundation/ GR - CF20-0071/Carlsberg Foundation/ GR - R302-2018-2155/Lundbeck Foundation/ PT - Evaluation Study PT - Journal Article DEP - 20241021 PL - England TA - Mol Ecol Resour JT - Molecular ecology resources JID - 101465604 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient/analysis MH - DNA Damage MH - Sequence Analysis, DNA/methods MH - Likelihood Functions MH - High-Throughput Nucleotide Sequencing/methods MH - Computational Biology/methods MH - Humans PMC - PMC11646307 OTO - NOTNLM OT - DNA deamination OT - ancient DNA OT - high‐throughput data OT - maximum likelihood estimation OT - posterior ancient probability OT - statistical inference COIS- The authors declare no conflicts of interest. EDAT- 2024/10/21 12:49 MHDA- 2024/12/16 11:29 PMCR- 2024/12/15 CRDT- 2024/10/21 11:05 PHST- 2024/09/13 00:00 [revised] PHST- 2023/11/21 00:00 [received] PHST- 2024/09/20 00:00 [accepted] PHST- 2024/12/16 11:29 [medline] PHST- 2024/10/21 12:49 [pubmed] PHST- 2024/10/21 11:05 [entrez] PHST- 2024/12/15 00:00 [pmc-release] AID - MEN14029 [pii] AID - 10.1111/1755-0998.14029 [doi] PST - ppublish SO - Mol Ecol Resour. 2025 Jan;25(1):e14029. doi: 10.1111/1755-0998.14029. Epub 2024 Oct 21. PMID- 39383567 OWN - NLM STAT- MEDLINE DCOM- 20241130 LR - 20241130 IS - 1879-1506 (Electronic) IS - 0003-9969 (Linking) VI - 169 DP - 2025 Jan TI - Familial hypodontia in bronze age Northwest China (1046-771BC). PG - 106104 LID - S0003-9969(24)00225-5 [pii] LID - 10.1016/j.archoralbio.2024.106104 [doi] AB - OBJECTIVE: This research aimed to report hypodontia cases in a Middle Bronze Age high-tier cemetery in China and test the possible hereditary behind hypodontia by performing kinship tests on those individuals. DESIGN: In this study, dental anomalies were observed on a human skeletal sample (n = 45) uncovered from Yaoheyuan, China. Ancient DNA analysis was subsequently employed on a subsample of the Yaoheyuan individuals (n = 15), including individuals observed hypodontia and individuals randomly sampled from the cemetery for preliminary investigation on the cemetery demography. Kinship estimation tests (READ, TKGWV2, KIN, and F3 test) were subsequently employed. RESULTS: The Yaoheyuan elite population had a prevalence (n = 7, 15 %) of tooth agenesis in either the maxilla or mandible, with one to two teeth missing. All missing teeth were incisors, except for one individual missing maxillary second molar. Preliminary ancient DNA results indicate that several kinship groups existed among interred individuals, including those with hypodontia, indicating the hereditary origin of these cases. CONCLUSIONS: The prevalence of hypodontia observed on site is high compared to that in both modern East Asian populations and archaeological samples in the Chinese population. The preliminary kinship analysis suggests a case of familial hypodontia. Ancient DNA analysis should be thoroughly conducted in future studies to understand the genetic markers contributing to those hypodontia cases among the Yaoheyuan individuals. CI - Copyright © 2024 Elsevier Ltd. All rights reserved. FAU - Wu, Yaohan AU - Wu Y AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Department of Anthropology, University of California San Diego, La Jolla, CA 92093, USA. FAU - Ma, Qiang AU - Ma Q AD - Ningxia Institute of Cultural Relics and Archaeology, Yinchuan 750001, China. FAU - Han, Baiwei AU - Han B AD - Ningxia Institute of Cultural Relics and Archaeology, Yinchuan 750001, China. FAU - Shen, Yuanyuan AU - Shen Y AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Wen, Shaoqing AU - Wen S AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China; Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai 200433, China. Electronic address: wenshaoqing@fudan.edu.cn. LA - eng PT - Historical Article PT - Journal Article DEP - 20241002 PL - England TA - Arch Oral Biol JT - Archives of oral biology JID - 0116711 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - China/epidemiology MH - *Anodontia/genetics/epidemiology MH - Male MH - History, Ancient MH - Female MH - DNA, Ancient/analysis MH - Cemeteries MH - Prevalence OTO - NOTNLM OT - Ancient DNA OT - Bronze age China OT - Familial hypodontia OT - Kinship estimation COIS- Declaration of Competing Interest The authors declare no conflict of interests. EDAT- 2024/10/10 04:18 MHDA- 2024/12/01 15:22 CRDT- 2024/10/09 18:02 PHST- 2024/06/26 00:00 [received] PHST- 2024/09/05 00:00 [revised] PHST- 2024/10/01 00:00 [accepted] PHST- 2024/12/01 15:22 [medline] PHST- 2024/10/10 04:18 [pubmed] PHST- 2024/10/09 18:02 [entrez] AID - S0003-9969(24)00225-5 [pii] AID - 10.1016/j.archoralbio.2024.106104 [doi] PST - ppublish SO - Arch Oral Biol. 2025 Jan;169:106104. doi: 10.1016/j.archoralbio.2024.106104. Epub 2024 Oct 2. PMID- 37548135 OWN - NLM STAT- MEDLINE DCOM- 20250128 LR - 20250128 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 186 IP - 1 DP - 2025 Jan TI - Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone. PG - e24822 LID - 10.1002/ajpa.24822 [doi] AB - OBJECTIVES: The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia. MATERIALS AND METHODS: Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network. RESULTS: The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established. DISCUSSION: The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought. CI - © 2023 Wiley Periodicals LLC. FAU - Arencibia, Valeria AU - Arencibia V AUID- ORCID: 0000-0002-5360-2457 AD - Equipo de Antropología Biológica, CCNAA, Universidad Maimónides, Buenos Aires, Argentina. AD - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina. FAU - Muñoz, Marianne AU - Muñoz M AD - Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina. AD - Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina. FAU - Crespo, Cristian M AU - Crespo CM AUID- ORCID: 0000-0003-3796-8472 AD - Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA), Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina. FAU - Russo, M Gabriela AU - Russo MG AD - Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Grupo de Investigación en Biología Evolutiva (GIBE), Universidad de Buenos Aires, Buenos Aires, Argentina. FAU - Vera, Pablo AU - Vera P AD - Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina. AD - Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina. FAU - Lia, Verónica V AU - Lia VV AD - Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina. AD - Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Buenos Aires, Argentina. FAU - García Guraieb, Solana AU - García Guraieb S AD - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina. AD - Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), Buenos Aires, Argentina. AD - Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina. FAU - Goñi, Rafael A AU - Goñi RA AD - Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), Buenos Aires, Argentina. AD - Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina. FAU - Avena, Sergio AU - Avena S AD - Equipo de Antropología Biológica, CCNAA, Universidad Maimónides, Buenos Aires, Argentina. AD - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina. AD - Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina. FAU - Puebla, Andrea AU - Puebla A AD - Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina. AD - Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina. FAU - Dejean, Cristina B AU - Dejean CB AUID- ORCID: 0000-0002-3642-1945 AD - Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina. AD - Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina. AD - Facultad de Filosofía y Letras, Instituto de Ciencias Antropológicas, Sección Antropología Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina. LA - eng GR - PICT 2014-3012/Agencia Nacional de Promoción Científica y Tecnológica/ GR - Fundación Científica Felipe Fiorellino/ GR - Fundación de Historia Natural Félix Azara/ GR - UBACyT 20020150200233BA/Universidad de Buenos Aires/ GR - UBACyT 20020170200363BA/Universidad de Buenos Aires/ GR - CONICET/ PT - Journal Article DEP - 20230807 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 RN - 0 (DNA, Ancient) SB - IM CIN - Am J Biol Anthropol. 2024 Aug;184(4):e24934. doi: 10.1002/ajpa.24934. PMID: 38577959 MH - Humans MH - *Haplotypes MH - Argentina MH - *Phylogeny MH - *Genome, Mitochondrial/genetics MH - Human Migration/history MH - Male MH - DNA, Ancient/analysis MH - Indians, South American/genetics/history OTO - NOTNLM OT - B2 OT - Patagonia OT - ancient DNA OT - mitogenomes EDAT- 2023/08/07 06:42 MHDA- 2025/01/28 12:33 CRDT- 2023/08/07 05:33 PHST- 2023/05/23 00:00 [revised] PHST- 2023/01/20 00:00 [received] PHST- 2023/07/09 00:00 [accepted] PHST- 2025/01/28 12:33 [medline] PHST- 2023/08/07 06:42 [pubmed] PHST- 2023/08/07 05:33 [entrez] AID - 10.1002/ajpa.24822 [doi] PST - ppublish SO - Am J Biol Anthropol. 2025 Jan;186(1):e24822. doi: 10.1002/ajpa.24822. Epub 2023 Aug 7. PMID- 39701966 OWN - NLM STAT- MEDLINE DCOM- 20241220 LR - 20250104 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 25 IP - 1 DP - 2024 Dec 19 TI - Unraveling the ancient fungal DNA from the Iceman gut. PG - 1225 LID - 10.1186/s12864-024-11123-2 [doi] LID - 1225 AB - BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria). METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples. RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples. CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples. CI - © 2024. The Author(s). FAU - Oskolkov, Nikolay AU - Oskolkov N AD - Department of Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden. nikolay.oskolkov@scilifelab.se. FAU - Sandionigi, Anna AU - Sandionigi A AD - Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy. AD - Quantia Consulting Srl, Milan, Italy. FAU - Götherström, Anders AU - Götherström A AD - Centre for Palaeogenetics, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Canini, Fabiana AU - Canini F AD - Department of Ecological and Biological Sciences, University of Tuscia, 01100, Viterbo, Italy. FAU - Turchetti, Benedetta AU - Turchetti B AD - Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy. FAU - Zucconi, Laura AU - Zucconi L AD - Department of Ecological and Biological Sciences, University of Tuscia, 01100, Viterbo, Italy. FAU - Mimmo, Tanja AU - Mimmo T AD - Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Piazza Università 5, Bolzano, Italy. FAU - Buzzini, Pietro AU - Buzzini P AD - Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy. FAU - Borruso, Luigimaria AU - Borruso L AD - Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Piazza Università 5, Bolzano, Italy. luigimaria.borruso@unibz.it. LA - eng PT - Journal Article DEP - 20241219 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (DNA, Ancient) RN - 0 (DNA, Fungal) SB - IM MH - *DNA, Ancient/analysis MH - Humans MH - *DNA, Fungal/genetics MH - Metagenomics/methods MH - Gastrointestinal Microbiome/genetics MH - Gastrointestinal Tract/microbiology MH - Mummies/microbiology MH - Computational Biology/methods MH - Fungi/genetics/classification PMC - PMC11660557 OTO - NOTNLM OT - Pseudogymnoascus OT - Ancient DNA (aDNA) OT - Ancient metagenomics OT - Fungi OT - Iceman COIS- Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests. EDAT- 2024/12/20 06:23 MHDA- 2024/12/20 06:24 PMCR- 2024/12/19 CRDT- 2024/12/20 00:05 PHST- 2024/10/21 00:00 [received] PHST- 2024/12/03 00:00 [accepted] PHST- 2024/12/20 06:24 [medline] PHST- 2024/12/20 06:23 [pubmed] PHST- 2024/12/20 00:05 [entrez] PHST- 2024/12/19 00:00 [pmc-release] AID - 10.1186/s12864-024-11123-2 [pii] AID - 11123 [pii] AID - 10.1186/s12864-024-11123-2 [doi] PST - epublish SO - BMC Genomics. 2024 Dec 19;25(1):1225. doi: 10.1186/s12864-024-11123-2. PMID- 39666807 OWN - NLM STAT- MEDLINE DCOM- 20241212 LR - 20241216 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 386 IP - 6727 DP - 2024 Dec 13 TI - Study reveals kinship among first modern humans in Europe. PG - 1207 LID - 10.1126/science.adv2424 [doi] AB - Ancient DNA links people across hundreds of kilometers. FAU - Curry, Andrew AU - Curry A LA - eng PT - News DEP - 20241212 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Czech Republic MH - *DNA, Ancient/analysis MH - History, Ancient MH - *Human Migration/history MH - Pedigree MH - Female MH - Neanderthals/genetics MH - Animals EDAT- 2024/12/12 18:23 MHDA- 2024/12/12 18:24 CRDT- 2024/12/12 14:03 PHST- 2024/12/12 18:24 [medline] PHST- 2024/12/12 18:23 [pubmed] PHST- 2024/12/12 14:03 [entrez] AID - 10.1126/science.adv2424 [doi] PST - ppublish SO - Science. 2024 Dec 13;386(6727):1207. doi: 10.1126/science.adv2424. Epub 2024 Dec 12. PMID- 39674265 OWN - NLM STAT- MEDLINE DCOM- 20241214 LR - 20250104 IS - 1477-4054 (Electronic) IS - 1467-5463 (Print) IS - 1467-5463 (Linking) VI - 26 IP - 1 DP - 2024 Nov 22 TI - Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping. LID - 10.1093/bib/bbae646 [doi] LID - bbae646 AB - Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses. CI - © The Author(s) 2024. Published by Oxford University Press. FAU - Ravishankar, Shyamsundar AU - Ravishankar S AUID- ORCID: 0000-0003-3006-6134 AD - Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. FAU - Perez, Vilma AU - Perez V AD - Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia. FAU - Davidson, Roberta AU - Davidson R AD - Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. FAU - Roca-Rada, Xavier AU - Roca-Rada X AD - Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. AD - Faculty of Arts and Humanities, University of Coimbra, Coimbra, Portugal. FAU - Lan, Divon AU - Lan D AD - Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. AD - Genozip Limited, Hong Kong. FAU - Souilmi, Yassine AU - Souilmi Y AUID- ORCID: 0000-0001-7543-4864 AD - Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. AD - National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia. AD - Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia. AD - National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia. AD - Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia. LA - eng GR - CE170100015/Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage/ GR - GA204260/NHMRC SYNERGY/ GR - Australian Government Research Training Program Scholarship/ GR - Portuguese National Funds/ PT - Journal Article PL - England TA - Brief Bioinform JT - Briefings in bioinformatics JID - 100912837 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient/analysis MH - *Metagenomics/methods MH - *Sequence Analysis, DNA/methods MH - Humans MH - High-Throughput Nucleotide Sequencing/methods MH - Metagenome MH - Workflow MH - DNA Contamination PMC - PMC11646131 OTO - NOTNLM OT - Kraken2 OT - ancient DNA OT - contamination OT - filtering, metagenomic classifiers EDAT- 2024/12/15 00:42 MHDA- 2024/12/15 00:43 PMCR- 2024/12/14 CRDT- 2024/12/14 19:13 PHST- 2024/07/18 00:00 [received] PHST- 2024/11/03 00:00 [revised] PHST- 2024/11/28 00:00 [accepted] PHST- 2024/12/15 00:43 [medline] PHST- 2024/12/15 00:42 [pubmed] PHST- 2024/12/14 19:13 [entrez] PHST- 2024/12/14 00:00 [pmc-release] AID - 7923980 [pii] AID - bbae646 [pii] AID - 10.1093/bib/bbae646 [doi] PST - ppublish SO - Brief Bioinform. 2024 Nov 22;26(1):bbae646. doi: 10.1093/bib/bbae646. PMID- 39567978 OWN - NLM STAT- MEDLINE DCOM- 20241121 LR - 20241218 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 25 IP - 1 DP - 2024 Nov 21 TI - The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy. PG - 292 LID - 10.1186/s13059-024-03430-4 [doi] LID - 292 AB - BACKGROUND: The Italic Iron Age is characterized by the presence of various ethnic groups partially examined from a genomic perspective. To explore the evolution of Iron Age Italic populations and the genetic impact of Romanization, we focus on the Picenes, one of the most fascinating pre-Roman civilizations, who flourished on the Middle Adriatic side of Central Italy between the 9(th) and the 3(rd) century BCE, until the Roman colonization. RESULTS: More than 50 samples are reported, spanning more than 1000 years of history from the Iron Age to Late Antiquity. Despite cultural diversity, our analysis reveals no major differences between the Picenes and other coeval populations, suggesting a shared genetic history of the Central Italian Iron Age ethnic groups. Nevertheless, a slight genetic differentiation between populations along the Adriatic and Tyrrhenian coasts can be observed, possibly due to different population dynamics in the two sides of Italy and/or genetic contacts across the Adriatic Sea. Additionally, we identify several individuals with ancestries deviating from their general population. Lastly, in our Late Antiquity site, we observe a drastic change in the genetic landscape of the Middle Adriatic region, indicating a relevant influx from the Near East, possibly as a consequence of Romanization. CONCLUSIONS: Our findings, consistently with archeological hypotheses, suggest genetic interactions across the Adriatic Sea during the Bronze/Iron Age and a high level of individual mobility typical of cosmopolitan societies. Finally, we highlight the role of the Roman Empire in shaping genetic and phenotypic changes that greatly impact the Italian peninsula. CI - © 2024. The Author(s). FAU - Ravasini, Francesco AU - Ravasini F AD - Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy. FAU - Kabral, Helja AU - Kabral H AD - Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Solnik, Anu AU - Solnik A AD - Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - de Gennaro, Luciana AU - de Gennaro L AD - Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy. FAU - Montinaro, Francesco AU - Montinaro F AD - Institute of Genomics, University of Tartu, Tartu, Estonia. AD - Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy. FAU - Hui, Ruoyun AU - Hui R AD - Alan Turing Institute, London, UK. AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK. FAU - Delpino, Chiara AU - Delpino C AD - Superintendence Archaeology, Fine Arts and Landscape for the Provinces of Frosinone and Latina, Ministry of Cultural Heritage, Rome, Italy. FAU - Finocchi, Stefano AU - Finocchi S AD - Superintendence Archaeology, Fine Arts and Landscape of Ancona, Ministry of Cultural Heritage, Ancona, Italy. FAU - Giroldini, Pierluigi AU - Giroldini P AD - Superintendence Archaeology, Fine Arts and Landscape for the Metropolitan City of Florence and the Provinces of Pistoia and Prato, Ministry of Cultural Heritage, Florence, Italy. FAU - Mei, Oscar AU - Mei O AD - Department of Communication Sciences, Humanities and International Studies, University of Urbino, Urbino, Italy. FAU - Beck De Lotto, Michael Allen AU - Beck De Lotto MA AD - Department of Cardiac, Vascular Sciences and Public Health, University of Padova, Padua, Italy. FAU - Cilli, Elisabetta AU - Cilli E AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. FAU - Hajiesmaeil, Mogge AU - Hajiesmaeil M AD - Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy. FAU - Pistacchia, Letizia AU - Pistacchia L AD - Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy. FAU - Risi, Flavia AU - Risi F AD - Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy. FAU - Giacometti, Chiara AU - Giacometti C AD - Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy. FAU - Scheib, Christiana Lyn AU - Scheib CL AD - Department of Zoology, University of Cambridge and St John's College, University of Cambridge, Cambridge, UK. FAU - Tambets, Kristiina AU - Tambets K AD - Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Metspalu, Mait AU - Metspalu M AD - Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Cruciani, Fulvio AU - Cruciani F AD - Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy. AD - Institute of Molecular Biology and Pathology, CNR, Rome, Italy. FAU - D'Atanasio, Eugenia AU - D'Atanasio E AD - Institute of Molecular Biology and Pathology, CNR, Rome, Italy. eugenia.datanasio@cnr.it. FAU - Trombetta, Beniamino AU - Trombetta B AUID- ORCID: 0000-0001-8245-9437 AD - Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy. beniamino.trombetta@uniroma1.it. LA - eng PT - Historical Article PT - Journal Article DEP - 20241121 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (DNA, Ancient) SB - IM MH - Italy MH - Humans MH - History, Ancient MH - *Roman World/history MH - DNA, Ancient/analysis MH - Genome, Human MH - Ethnicity/genetics MH - Genetics, Population MH - Genomics PMC - PMC11580440 OTO - NOTNLM OT - Adriatic cultures OT - Ancient DNA OT - Ancient Italy OT - Archaeogenomics OT - Iron Age OT - Late Antiquity OT - Novilara necropolis OT - Picenes OT - Proto-history OT - Roman Empire COIS- Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare that they have no competing interests. EDAT- 2024/11/21 00:22 MHDA- 2024/11/21 06:21 PMCR- 2024/11/21 CRDT- 2024/11/20 23:55 PHST- 2024/03/19 00:00 [received] PHST- 2024/10/29 00:00 [accepted] PHST- 2024/11/21 06:21 [medline] PHST- 2024/11/21 00:22 [pubmed] PHST- 2024/11/20 23:55 [entrez] PHST- 2024/11/21 00:00 [pmc-release] AID - 10.1186/s13059-024-03430-4 [pii] AID - 3430 [pii] AID - 10.1186/s13059-024-03430-4 [doi] PST - epublish SO - Genome Biol. 2024 Nov 21;25(1):292. doi: 10.1186/s13059-024-03430-4. PMID- 39567925 OWN - NLM STAT- MEDLINE DCOM- 20241121 LR - 20241218 IS - 1741-7007 (Electronic) IS - 1741-7007 (Linking) VI - 22 IP - 1 DP - 2024 Nov 20 TI - Ancient genomes from the Tang Dynasty capital reveal the genetic legacy of trans-Eurasian communication at the eastern end of Silk Road. PG - 267 LID - 10.1186/s12915-024-02068-9 [doi] LID - 267 AB - BACKGROUND: Ancient Chang'an in the Tang Dynasty (618-907 AD) was one of the world's largest and most populated cities and acted as the eastern end of the world-famous Silk Road. However, little is known about the genetics of Chang'an people and whether the Western Regions-related gene flows have been prevalent in this cosmopolitan city. RESULTS: Here, we present seven genomes from Xingfulindai (XFLD) sites dating to the Tang Dynasty in Chang'an. We observed that four of seven XFLD individuals (XFLD_1) were genetically homogenous with the Late Neolithic Wadian, Pingliangtai, and Haojiatai populations from the middle reaches of the Yellow River Basin (YR_LN), with no genetic influence from the Western Eurasian or other non-Yellow River-related lineages. The remaining three XFLD individuals were a mixture of YR_LN-related ancestry and ~ 3-15% Western Eurasian-related ancestry. Mixtures of XFLD_1 and Western Eurasian-related ancestry drove the main gradient of genetic variation in northern and central Shaanxi Province today. CONCLUSIONS: Our study underlined the widespread distribution of the YR_LN-related ancestry alongside the Silk Road within the territory of China during the historical era and provided direct evidence of trans-Eurasian communication in Chang'an from a genetic perspective. CI - © 2024. The Author(s). FAU - Lv, Minglei AU - Lv M AD - School of Archaeology and Cultural Heritage, Zhengzhou University, Zhengzhou , Henan, 450001, China. FAU - Ma, Hao AU - Ma H AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - Wang, Rui AU - Wang R AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. 17786126601@163.com. FAU - Li, Hui AU - Li H AD - School of Archaeology and Cultural Heritage, Zhengzhou University, Zhengzhou , Henan, 450001, China. FAU - Zhang, Xiangyu AU - Zhang X AD - Institute of Antiquities and Archaeology, Xi'an 710064, Shaanxi, China. FAU - Zhang, Wenbo AU - Zhang W AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - Zeng, Yuding AU - Zeng Y AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - Qin, Ziwei AU - Qin Z AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - Zhai, Hongbo AU - Zhai H AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - Lou, Yiqiang AU - Lou Y AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - Lin, Yukai AU - Lin Y AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - Tao, Le AU - Tao L AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - He, Haifeng AU - He H AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - Yang, Xiaomin AU - Yang X AD - Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China. FAU - Zhu, Kongyang AU - Zhu K AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China. FAU - Zhou, Yawei AU - Zhou Y AD - School of Archaeology and Cultural Heritage, Zhengzhou University, Zhengzhou , Henan, 450001, China. zhouyawei469@163.com. FAU - Wang, Chuan-Chao AU - Wang CC AD - Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China. wang@xmu.edu.cn. LA - eng PT - Historical Article PT - Journal Article DEP - 20241120 PL - England TA - BMC Biol JT - BMC biology JID - 101190720 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - China MH - *Genome, Human MH - DNA, Ancient/analysis MH - History, Ancient MH - Asian People/genetics MH - Gene Flow MH - Genetic Variation MH - Human Migration/history PMC - PMC11577736 OTO - NOTNLM OT - Ancient Chang’an OT - Ancient DNA OT - East Asia OT - Neolithic middle Yellow River-related ancestry OT - Population history OT - Silk Road OT - Tang Dynasty OT - Western-Eastern admixture COIS- Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests. EDAT- 2024/11/21 00:22 MHDA- 2024/11/21 06:21 PMCR- 2024/11/20 CRDT- 2024/11/20 23:52 PHST- 2024/06/25 00:00 [received] PHST- 2024/11/12 00:00 [accepted] PHST- 2024/11/21 06:21 [medline] PHST- 2024/11/21 00:22 [pubmed] PHST- 2024/11/20 23:52 [entrez] PHST- 2024/11/20 00:00 [pmc-release] AID - 10.1186/s12915-024-02068-9 [pii] AID - 2068 [pii] AID - 10.1186/s12915-024-02068-9 [doi] PST - epublish SO - BMC Biol. 2024 Nov 20;22(1):267. doi: 10.1186/s12915-024-02068-9. PMID- 39515325 OWN - NLM STAT- MEDLINE DCOM- 20241119 LR - 20241211 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 34 IP - 22 DP - 2024 Nov 18 TI - Ancient DNA challenges prevailing interpretations of the Pompeii plaster casts. PG - 5307-5318.e7 LID - S0960-9822(24)01361-7 [pii] LID - 10.1016/j.cub.2024.10.007 [doi] AB - The eruption of Somma-Vesuvius in 79 CE buried several nearby Roman towns, killing the inhabitants and burying under pumice lapilli and ash deposits a unique set of civil and private buildings, monuments, sculptures, paintings, and mosaics that provide a rich picture of life in the empire. The eruption also preserved the forms of many of the dying as the ash compacted around their bodies. Although the soft tissue decayed, the outlines of the bodies remained and were recovered by excavators centuries later by filling the cavities with plaster. From skeletal material embedded in the casts, we generated genome-wide ancient DNA and strontium isotopic data to characterize the genetic relationships, sex, ancestry, and mobility of five individuals. We show that the individuals' sexes and family relationships do not match traditional interpretations, exemplifying how modern assumptions about gendered behaviors may not be reliable lenses through which to view data from the past. For example, an adult wearing a golden bracelet with a child on their lap-often interpreted as mother and child-is genetically an adult male biologically unrelated to the child. Similarly, a pair of individuals who were thought to have died in an embrace-often interpreted as sisters-included at least one genetic male. All Pompeiians with genome-wide data consistently derive their ancestry largely from recent immigrants from the eastern Mediterranean, as has also been seen in contemporaneous ancient genomes from the city of Rome, underscoring the cosmopolitanism of the Roman Empire in this period. CI - Copyright © 2024 Elsevier Inc. All rights reserved. FAU - Pilli, Elena AU - Pilli E AD - Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy. FAU - Vai, Stefania AU - Vai S AD - Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy. FAU - Moses, Victoria C AU - Moses VC AD - Department of History, Harvard University, Cambridge, MA 02138, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Morelli, Stefania AU - Morelli S AD - Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy. FAU - Lari, Martina AU - Lari M AD - Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy. FAU - Modi, Alessandra AU - Modi A AD - Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy. FAU - Diroma, Maria Angela AU - Diroma MA AD - Dipartimento di Biologia, Università di Firenze, 50019 Florence, Italy. FAU - Amoretti, Valeria AU - Amoretti V AD - Parco Archeologico di Pompei, 80045 Naples, Italy. FAU - Zuchtriegel, Gabriel AU - Zuchtriegel G AD - Parco Archeologico di Pompei, 80045 Naples, Italy. FAU - Osanna, Massimo AU - Osanna M AD - Ministry of Cultural Heritage and Activities and Tourism, 00197 Rome, Italy. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA. FAU - George, Richard J AU - George RJ AD - Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA. FAU - Krigbaum, John AU - Krigbaum J AD - Department of Anthropology, University of Florida, Gainesville, FL 32611, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. FAU - Caramelli, David AU - Caramelli D AD - Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy. Electronic address: david.caramelli@unifi.it. FAU - Reich, David AU - Reich D AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 04103 Leipzig, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA. Electronic address: reich@genetics.med.harvard.edu. FAU - Mittnik, Alissa AU - Mittnik A AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 04103 Leipzig, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. Electronic address: alissa_mittnik@eva.mpg.de. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States GR - R01 HG012287/HG/NHGRI NIH HHS/United States PT - Historical Article PT - Journal Article DEP - 20241107 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - Male MH - Female MH - History, Ancient MH - Archaeology MH - Roman World/history MH - Adult PMC - PMC11627482 MID - NIHMS2034971 OTO - NOTNLM OT - Pompeii OT - Roman Empire OT - ancient DNA OT - bioarchaeology OT - mobility OT - relatedness OT - stable isotopes OT - strontium COIS- Declaration of interests The authors declare no competing interests. EDAT- 2024/11/13 13:49 MHDA- 2024/11/20 00:21 PMCR- 2024/12/09 CRDT- 2024/11/08 18:42 PHST- 2024/06/14 00:00 [received] PHST- 2024/09/13 00:00 [revised] PHST- 2024/10/01 00:00 [accepted] PHST- 2024/11/20 00:21 [medline] PHST- 2024/11/13 13:49 [pubmed] PHST- 2024/11/08 18:42 [entrez] PHST- 2024/12/09 00:00 [pmc-release] AID - S0960-9822(24)01361-7 [pii] AID - 10.1016/j.cub.2024.10.007 [doi] PST - ppublish SO - Curr Biol. 2024 Nov 18;34(22):5307-5318.e7. doi: 10.1016/j.cub.2024.10.007. Epub 2024 Nov 7. PMID- 39532856 OWN - NLM STAT- MEDLINE DCOM- 20241112 LR - 20241116 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 15 IP - 1 DP - 2024 Nov 12 TI - Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift. PG - 9772 LID - 10.1038/s41467-024-53852-8 [doi] LID - 9772 AB - Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture. CI - © 2024. The Author(s). FAU - Pandey, Devansh AU - Pandey D AUID- ORCID: 0009-0005-6490-517X AD - Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA. FAU - Harris, Mariana AU - Harris M AD - Department of Computational Medicine, University of California, Los Angeles, CA, USA. FAU - Garud, Nandita R AU - Garud NR AUID- ORCID: 0000-0003-4217-4407 AD - Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA. ngarud@ucla.edu. AD - Department of Human Genetics, University of California, Los Angeles, CA, USA. ngarud@ucla.edu. FAU - Narasimhan, Vagheesh M AU - Narasimhan VM AUID- ORCID: 0000-0001-8651-8844 AD - Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA. vagheesh@utexas.edu. AD - Department of Statistics and Data Science, The University of Texas at Austin, Austin, TX, USA. vagheesh@utexas.edu. LA - eng PT - Journal Article DEP - 20241112 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) RN - EC 3.2.1.108 (Lactase) SB - IM MH - *DNA, Ancient/analysis MH - *Selection, Genetic MH - Humans MH - Europe MH - *Genetic Drift MH - *Gene Frequency MH - Haplotypes/genetics MH - Animals MH - Lactase/genetics MH - Genetics, Population/methods MH - Evolution, Molecular MH - Genotype PMC - PMC11557891 COIS- Competing interests The authors declare no competing interests. EDAT- 2024/11/13 13:48 MHDA- 2024/11/13 13:49 PMCR- 2024/11/12 CRDT- 2024/11/12 23:27 PHST- 2023/04/11 00:00 [received] PHST- 2024/10/23 00:00 [accepted] PHST- 2024/11/13 13:49 [medline] PHST- 2024/11/13 13:48 [pubmed] PHST- 2024/11/12 23:27 [entrez] PHST- 2024/11/12 00:00 [pmc-release] AID - 10.1038/s41467-024-53852-8 [pii] AID - 53852 [pii] AID - 10.1038/s41467-024-53852-8 [doi] PST - epublish SO - Nat Commun. 2024 Nov 12;15(1):9772. doi: 10.1038/s41467-024-53852-8. PMID- 39509486 OWN - NLM STAT- MEDLINE DCOM- 20241107 LR - 20241108 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 386 IP - 6722 DP - 2024 Nov 8 TI - India looks to ancient DNA to track migrations. PG - 607 LID - 10.1126/science.adu4090 [doi] AB - Findings from analyses of human bones could be politically sensitive. FAU - Chandrashekhar, Vaishnavi AU - Chandrashekhar V LA - eng PT - News DEP - 20241107 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) RN - Indian people SB - IM MH - Humans MH - Bone and Bones MH - *DNA, Ancient/analysis MH - *Human Migration/history MH - India MH - *South Asian People/history EDAT- 2024/11/13 13:48 MHDA- 2024/11/13 13:49 CRDT- 2024/11/07 14:03 PHST- 2024/11/13 13:49 [medline] PHST- 2024/11/13 13:48 [pubmed] PHST- 2024/11/07 14:03 [entrez] AID - 10.1126/science.adu4090 [doi] PST - ppublish SO - Science. 2024 Nov 8;386(6722):607. doi: 10.1126/science.adu4090. Epub 2024 Nov 7. PMID- 39292210 OWN - NLM STAT- MEDLINE DCOM- 20241106 LR - 20241108 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 228 IP - 3 DP - 2024 Nov 6 TI - An explanation for the sister repulsion phenomenon in Patterson's f-statistics. LID - 10.1093/genetics/iyae144 [doi] LID - iyae144 AB - Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f3- and f4-statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behavior of f-statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbors, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern "sister repulsion". We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity toward Bronze Age Greece rather than each other. This is observed both using f3- and f4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using principal components analysis or multidimensional scaling on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculate f3- and f4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from 1 region can create sister repulsion in f-statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, multidimensional scaling analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f-statistics. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. FAU - Atağ, Gözde AU - Atağ G AD - Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey. AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Waldman, Shamam AU - Waldman S AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Carmi, Shai AU - Carmi S AUID- ORCID: 0000-0002-0188-2610 AD - Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel. FAU - Somel, Mehmet AU - Somel M AUID- ORCID: 0000-0002-3138-1307 AD - Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey. LA - eng GR - 772390/H2020 ERC Consolidator/ GR - 952317/H2020-WIDESPREAD-05-2020 TWINNING/ GR - Scientific and Technological Research Council of Turkey (TÜBİTAK)/ PT - Journal Article PL - United States TA - Genetics JT - Genetics JID - 0374636 SB - IM MH - Humans MH - *Models, Genetic MH - *Gene Flow MH - *Gene Frequency MH - Genetics, Population MH - Genome, Human MH - Greece PMC - PMC11538414 OTO - NOTNLM OT - f-statistics OT - admixture OT - ancient DNA OT - deep ancestry OT - demographic inference COIS- Conflicts of interest The author(s) declare no conflicts of interest. EDAT- 2024/09/18 12:50 MHDA- 2024/11/06 06:21 PMCR- 2024/09/18 CRDT- 2024/09/18 10:48 PHST- 2024/06/29 00:00 [received] PHST- 2024/08/19 00:00 [accepted] PHST- 2024/11/06 06:21 [medline] PHST- 2024/09/18 12:50 [pubmed] PHST- 2024/09/18 10:48 [entrez] PHST- 2024/09/18 00:00 [pmc-release] AID - 7760116 [pii] AID - iyae144 [pii] AID - 10.1093/genetics/iyae144 [doi] PST - ppublish SO - Genetics. 2024 Nov 6;228(3):iyae144. doi: 10.1093/genetics/iyae144. PMID- 39300260 OWN - NLM STAT- MEDLINE DCOM- 20241107 LR - 20241109 IS - 2397-334X (Electronic) IS - 2397-334X (Linking) VI - 8 IP - 11 DP - 2024 Nov TI - 9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter. PG - 2121-2134 LID - 10.1038/s41559-024-02532-3 [doi] AB - Southern Africa has one of the longest records of fossil hominins and harbours the largest human genetic diversity in the world. Yet, despite its relevance for human origins and spread around the globe, the formation and processes of its gene pool in the past are still largely unknown. Here, we present a time transect of genome-wide sequences from nine individuals recovered from a single site in South Africa, Oakhurst Rockshelter. Spanning the whole Holocene, the ancient DNA of these individuals allows us to reconstruct the demographic trajectories of the indigenous San population and their ancestors during the last 10,000 years. We show that, in contrast to most regions around the world, the population history of southernmost Africa was not characterized by several waves of migration, replacement and admixture but by long-lasting genetic continuity from the early Holocene to the end of the Later Stone Age. Although the advent of pastoralism and farming substantially transformed the gene pool in most parts of southern Africa after 1,300 BP, we demonstrate using allele-frequency and identity-by-descent segment-based methods that the ‡Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers, a pattern obscured by recent, extensive non-Southern African admixture. Yet, some southern San in South Africa still preserve this ancient, Pleistocene-derived genetic signature, extending the period of genetic continuity until today. CI - © 2024. The Author(s). FAU - Gretzinger, Joscha AU - Gretzinger J AD - Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany. FAU - Gibbon, Victoria E AU - Gibbon VE AUID- ORCID: 0000-0001-7875-3297 AD - Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa. victoria.gibbon@uct.ac.za. FAU - Penske, Sandra E AU - Penske SE AD - Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany. FAU - Sealy, Judith C AU - Sealy JC AUID- ORCID: 0000-0001-5071-8211 AD - Department of Archaeology, University of Cape Town, Cape Town, South Africa. FAU - Rohrlach, Adam B AU - Rohrlach AB AUID- ORCID: 0000-0002-4204-5018 AD - Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany. AD - School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Salazar-García, Domingo C AU - Salazar-García DC AD - Department of Geological Sciences, University of Cape Town, Cape Town, South Africa. AD - Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany. FAU - Schiffels, Stephan AU - Schiffels S AUID- ORCID: 0000-0002-1017-9150 AD - Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany. stephan_schiffels@eva.mpg.de. LA - eng PT - Journal Article DEP - 20240919 PL - England TA - Nat Ecol Evol JT - Nature ecology & evolution JID - 101698577 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - South Africa MH - *DNA, Ancient/analysis MH - Genetic Variation PMC - PMC11541196 COIS- The authors declare no competing interests. EDAT- 2024/09/20 01:06 MHDA- 2024/11/12 04:45 PMCR- 2024/09/19 CRDT- 2024/09/19 23:38 PHST- 2024/01/31 00:00 [received] PHST- 2024/08/02 00:00 [accepted] PHST- 2024/11/12 04:45 [medline] PHST- 2024/09/20 01:06 [pubmed] PHST- 2024/09/19 23:38 [entrez] PHST- 2024/09/19 00:00 [pmc-release] AID - 10.1038/s41559-024-02532-3 [pii] AID - 2532 [pii] AID - 10.1038/s41559-024-02532-3 [doi] PST - ppublish SO - Nat Ecol Evol. 2024 Nov;8(11):2121-2134. doi: 10.1038/s41559-024-02532-3. Epub 2024 Sep 19. PMID- 39215552 OWN - NLM STAT- MEDLINE DCOM- 20241002 LR - 20241002 IS - 1755-0998 (Electronic) IS - 1755-098X (Linking) VI - 24 IP - 8 DP - 2024 Nov TI - Deep estimation of the intensity and timing of natural selection from ancient genomes. PG - e14015 LID - 10.1111/1755-0998.14015 [doi] AB - Leveraging past allele frequencies has proven to be key for identifying the impact of natural selection across time. However, this approach suffers from imprecise estimations of the intensity (s) and timing (T) of selection, particularly when ancient samples are scarce in specific epochs. Here, we aimed to bypass the computation of allele frequencies across arbitrarily defined past epochs and refine the estimations of selection parameters by implementing convolutional neural networks (CNNs) algorithms that directly use ancient genotypes sampled across time. Using computer simulations, we first show that genotype-based CNNs consistently outperform an approximate Bayesian computation (ABC) approach based on past allele frequency trajectories, regardless of the selection model assumed and the number of available ancient genotypes. When applying this method to empirical data from modern and ancient Europeans, we replicated the reported increased number of selection events in post-Neolithic Europe, independently of the continental subregion studied. Furthermore, we substantially refined the ABC-based estimations of s and T for a set of positively and negatively selected variants, including iconic cases of positive selection and experimentally validated disease-risk variants. Our CNN predictions support a history of recent positive and negative selection targeting variants associated with host defence against pathogens, aligning with previous work that highlights the significant impact of infectious diseases, such as tuberculosis, in Europe. These findings collectively demonstrate that detecting the footprints of natural selection on ancient genomes is crucial for unravelling the history of severe human diseases. CI - © 2024 John Wiley & Sons Ltd. FAU - Laval, Guillaume AU - Laval G AUID- ORCID: 0000-0003-0845-1909 AD - Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France. FAU - Patin, Etienne AU - Patin E AD - Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France. FAU - Quintana-Murci, Lluis AU - Quintana-Murci L AD - Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France. AD - Chair of Human Genomics and Evolution, Collège de France, Paris, France. FAU - Kerner, Gaspard AU - Kerner G AD - Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France. LA - eng PT - Journal Article DEP - 20240831 PL - England TA - Mol Ecol Resour JT - Molecular ecology resources JID - 101465604 RN - 0 (DNA, Ancient) SB - IM MH - *Selection, Genetic MH - Humans MH - *DNA, Ancient/analysis MH - Gene Frequency MH - Europe MH - Computer Simulation MH - Genotype MH - Neural Networks, Computer OTO - NOTNLM OT - ancient DNA OT - approximate bayesian computation OT - convolutional neural network OT - deep learning OT - negative selection OT - positive selection EDAT- 2024/08/31 09:53 MHDA- 2024/10/02 12:42 CRDT- 2024/08/31 03:52 PHST- 2024/07/22 00:00 [revised] PHST- 2024/04/24 00:00 [received] PHST- 2024/08/15 00:00 [accepted] PHST- 2024/10/02 12:42 [medline] PHST- 2024/08/31 09:53 [pubmed] PHST- 2024/08/31 03:52 [entrez] AID - 10.1111/1755-0998.14015 [doi] PST - ppublish SO - Mol Ecol Resour. 2024 Nov;24(8):e14015. doi: 10.1111/1755-0998.14015. Epub 2024 Aug 31. PMID- 38177408 OWN - NLM STAT- MEDLINE DCOM- 20241120 LR - 20241211 IS - 1476-5438 (Electronic) IS - 1018-4813 (Print) IS - 1018-4813 (Linking) VI - 32 IP - 11 DP - 2024 Nov TI - Koban culture genome-wide and archeological data open the bridge between Bronze and Iron Ages in the North Caucasus. PG - 1483-1491 LID - 10.1038/s41431-023-01524-4 [doi] AB - The North Caucasus played a key role during the ancient colonization of Eurasia and the formation of its cultural and genetic ancestry. Previous archeogenetic studies described a relative genetic and cultural continuity of ancient Caucasus societies, since the Eneolithic period. The Koban culture, which formed in the Late Bronze Age on the North Caucasian highlands, is considered as a cultural "bridge" between the ancient and modern autochthonous peoples of the Caucasus. Here, we discuss the place of this archeological culture and its representatives in the genetic orbit of Caucasian cultures using genome-wide SNP data from five individuals of the Koban culture and one individual of the early Alanic culture as well as previously published genomic data of ancient and modern North Caucasus individuals. Ancient DNA analysis shows that an ancient individual from Klin-Yar III, who was previously described as male, was in fact a female. Additional studies on well-preserved ancient human specimens are necessary to determine the level of local mobility and kinship between individuals in ancient societies of North Caucasus. Further studies with a larger sample size will allow us gain a deeper understanding of this topic. CI - © 2023. The Author(s), under exclusive licence to European Society of Human Genetics. FAU - Sharko, Fedor S AU - Sharko FS AD - European University at St. Petersburg, 6/1A Gagarinskaya Street, 191187, St. Petersburg, Russia. AD - Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences. 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia. AD - National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia. FAU - Boulygina, Eugenia S AU - Boulygina ES AD - National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia. FAU - Tsygankova, Svetlana V AU - Tsygankova SV AD - National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia. FAU - Slobodova, Natalia V AU - Slobodova NV AD - National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia. AD - HSE University, Profsoyuznaya st. 33, bld. 4, Moscow, 117418, Russia. FAU - Rastorguev, Sergey M AU - Rastorguev SM AUID- ORCID: 0000-0002-0095-0255 AD - N. I. Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation Ostrovityanova st. 1, Moscow, 117997, Russia. FAU - Krasivskaya, Anna A AU - Krasivskaya AA AD - Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia. FAU - Belinsky, Andrej B AU - Belinsky AB AD - Limited liability company Nasledie, K. Marx av., 56, Stavropol', 355017, Russia. FAU - Härke, Heinrich AU - Härke H AUID- ORCID: 0000-0002-2226-618X AD - Centre for Classical and Oriental Archaeology, National Research University Higher School of Economics, ul. Staraya Basmannaya 21/4c1, Moscow, 105066, Russia. AD - Department of Medieval Archaeology, University of Tübingen, Schloss Hohentübingen, D-72070, Tübingen, Germany. FAU - Kadieva, Anna A AU - Kadieva AA AD - Department of Archaeology, State Historical Museum, Krasnaya pl., 1, Moscow, 109012, Russia. FAU - Demidenko, Sergej V AU - Demidenko SV AUID- ORCID: 0000-0002-6462-0132 AD - Department of Scythian and Sarmatian Archaeology, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia. FAU - Malashev, Vladimir Yu AU - Malashev VY AD - Department of Scythian and Sarmatian Archaeology, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia. FAU - Shvedchikova, Tatiana Yu AU - Shvedchikova TY AD - Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia. FAU - Dobrovolskaya, Maria V AU - Dobrovolskaya MV AD - Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia. FAU - Reshetova, Irina K AU - Reshetova IK AUID- ORCID: 0000-0002-3425-3212 AD - Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia. FAU - Korobov, Dmitry S AU - Korobov DS AUID- ORCID: 0000-0002-9571-0405 AD - Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia. dkorobov@mail.ru. FAU - Nedoluzhko, Artem V AU - Nedoluzhko AV AUID- ORCID: 0000-0001-7040-0892 AD - European University at St. Petersburg, 6/1A Gagarinskaya Street, 191187, St. Petersburg, Russia. nedoluzhko@gmail.com. LA - eng PT - Historical Article PT - Journal Article DEP - 20240104 PL - England TA - Eur J Hum Genet JT - European journal of human genetics : EJHG JID - 9302235 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - Female MH - Male MH - *Genome, Human MH - Archaeology MH - History, Ancient MH - White People/genetics MH - Polymorphism, Single Nucleotide MH - Russia PMC - PMC11576754 COIS- Competing interests The authors declare no competing interests. Ethical approval This research was carried out under the ethics guidelines for DNA research on human remains described previously: Alpaslan-Roodenberg S, Anthony D, Babiker H, Bánffy E, Booth T, Capone P et al. Ethics of DNA research on human remains: five globally applicable guidelines. Nature 2021; 599: 41–46. EDAT- 2024/01/05 00:42 MHDA- 2024/11/20 11:04 PMCR- 2025/11/01 CRDT- 2024/01/04 23:25 PHST- 2022/05/05 00:00 [received] PHST- 2023/12/07 00:00 [accepted] PHST- 2023/10/05 00:00 [revised] PHST- 2025/11/01 00:00 [pmc-release] PHST- 2024/11/20 11:04 [medline] PHST- 2024/01/05 00:42 [pubmed] PHST- 2024/01/04 23:25 [entrez] AID - 10.1038/s41431-023-01524-4 [pii] AID - 1524 [pii] AID - 10.1038/s41431-023-01524-4 [doi] PST - ppublish SO - Eur J Hum Genet. 2024 Nov;32(11):1483-1491. doi: 10.1038/s41431-023-01524-4. Epub 2024 Jan 4. PMID- 39326418 OWN - NLM STAT- MEDLINE DCOM- 20241018 LR - 20241018 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 187 IP - 21 DP - 2024 Oct 17 TI - Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history. PG - 5891-5900.e8 LID - S0092-8674(24)00899-7 [pii] LID - 10.1016/j.cell.2024.08.008 [doi] AB - Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors. CI - Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Liu, Yichen AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Miao, Bo AU - Miao B AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China. FAU - Li, Wenying AU - Li W AD - Xinjiang Cultural Relics and Archaeology Institute, Ürümchi 830000, China. FAU - Hu, Xingjun AU - Hu X AD - Research Center for Governance of China's Northwest Frontier in the Historical Periods, School of History, Xinjiang University, Ürümqi 830046, China. FAU - Bai, Fan AU - Bai F AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Abuduresule, Yidilisi AU - Abuduresule Y AD - Xinjiang Cultural Relics and Archaeology Institute, Ürümchi 830000, China. FAU - Liu, Yalin AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Zheng, Zequan AU - Zheng Z AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Wang, Wenjun AU - Wang W AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; Science and Technology Archaeology, National Centre for Archaeology, Beijing 100013, China. FAU - Chen, Zehui AU - Chen Z AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Zhu, Shilun AU - Zhu S AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China. FAU - Ping, Wanjing AU - Ping W AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China. FAU - Yang, Ruowei AU - Yang R AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China. FAU - Dai, Qingyan AU - Dai Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China. FAU - Liu, Feng AU - Liu F AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China. FAU - Tian, Chan AU - Tian C AD - Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China. FAU - Yang, Yimin AU - Yang Y AD - Department of Archaeology and Anthropology, University of the Chinese Academy of Sciences, Beijing 100049, China. Electronic address: yiminyang@ucas.ac.cn. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng PT - Historical Article PT - Journal Article DEP - 20240925 PL - United States TA - Cell JT - Cell JID - 0413066 SB - IM MH - Humans MH - *Cheese/microbiology MH - *Lactobacillus/genetics MH - Kefir/microbiology MH - History, Ancient MH - Phylogeny MH - China MH - Biological Evolution MH - Fermentation MH - Asia, Eastern OTO - NOTNLM OT - Lactobacillus OT - Xiaohe cemetery OT - ancient DNA OT - ancient fermented dairy OT - horizontal gene transfer OT - kefir cheese OT - microbial evolution OT - paleomicrobiome COIS- Declaration of interests The authors declare no competing interests. EDAT- 2024/09/27 00:42 MHDA- 2024/10/19 16:22 CRDT- 2024/09/26 18:41 PHST- 2024/02/09 00:00 [received] PHST- 2024/06/01 00:00 [revised] PHST- 2024/08/07 00:00 [accepted] PHST- 2024/10/19 16:22 [medline] PHST- 2024/09/27 00:42 [pubmed] PHST- 2024/09/26 18:41 [entrez] AID - S0092-8674(24)00899-7 [pii] AID - 10.1016/j.cell.2024.08.008 [doi] PST - ppublish SO - Cell. 2024 Oct 17;187(21):5891-5900.e8. doi: 10.1016/j.cell.2024.08.008. Epub 2024 Sep 25. PMID- 39390557 OWN - NLM STAT- MEDLINE DCOM- 20241011 LR - 20241013 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 25 IP - 1 DP - 2024 Oct 10 TI - Improved detection of methylation in ancient DNA. PG - 261 LID - 10.1186/s13059-024-03405-5 [doi] LID - 261 AB - Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA. CI - © 2024. The Author(s). FAU - Sawyer, Susanna AU - Sawyer S AUID- ORCID: 0000-0002-8477-6089 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. susanna.sawyer@univie.ac.at. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. susanna.sawyer@univie.ac.at. FAU - Gelabert, Pere AU - Gelabert P AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Yakir, Benjamin AU - Yakir B AD - Department of Statistics, The Faculty of Social Science, The Hebrew University Mount Scopus, Jerusalem, Israel. FAU - Llanos-Lizcano, Alejandro AU - Llanos-Lizcano A AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Facultad de Química y Farmacia, Universidad del Atlántico, Barranquilla, Colombia. FAU - Sperduti, Alessandra AU - Sperduti A AD - Museo Delle Civiltà, Servizio Di Bioarcheologia, Rome, Italy. AD - Dipartimento di Asia, Africa e Mediterraneo, Università degli Studi di Napoli "L'Orientale", Naples, Italy. FAU - Bondioli, Luca AU - Bondioli L AD - Università Di Padova, Dipartimento Dei Beni Culturali, Padua, Italy. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Neugebauer-Maresch, Christine AU - Neugebauer-Maresch C AD - Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria. AD - Institute of Prehistory and Early History, University of Vienna, Vienna, Austria. FAU - Teschler-Nicola, Maria AU - Teschler-Nicola M AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Department of Anthropology, Natural History Museum Vienna, Vienna, Austria. FAU - Novak, Mario AU - Novak M AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. AD - Department of Archaeology and Heritage, Faculty of Humanities, University of Primorska, Koper, Slovenia. FAU - Pap, Ildikó AU - Pap I AD - Department of Biological Anthropology, Institute of Biology, University of Szeged, Szeged, Hungary. AD - Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary. AD - Department of Biological Anthropology, Eötvös Loránd University, Budapest, Hungary. FAU - Szikossy, Ildikó AU - Szikossy I AD - , Budapest, Hungary. FAU - Hajdu, Tamás AU - Hajdu T AD - Department of Biological Anthropology, Eötvös Loránd University, Budapest, Hungary. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), RAS, Saint Petersburg, Russia. FAU - Gromov, Andrey AU - Gromov A AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), RAS, Saint Petersburg, Russia. FAU - Zariņa, Gunita AU - Zariņa G AD - Institute of Latvian History, University of Latvia, Riga, Latvia. FAU - Meshorer, Eran AU - Meshorer E AD - The Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel. AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Carmel, Liran AU - Carmel L AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at. LA - eng PT - Journal Article DEP - 20241010 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (DNA, Ancient) RN - 0 (Sulfites) RN - OJ9787WBLU (hydrogen sulfite) SB - IM MH - *DNA Methylation MH - *DNA, Ancient/analysis MH - Humans MH - *Sulfites MH - Sequence Analysis, DNA/methods PMC - PMC11465500 OTO - NOTNLM OT - Ancient DNA OT - Bisulfite treatment OT - Enzymatic methylation treatment OT - Methylation OT - Paleogenomics COIS- The authors declare no competing interests. EDAT- 2024/10/11 00:33 MHDA- 2024/10/11 06:23 PMCR- 2024/10/10 CRDT- 2024/10/10 23:51 PHST- 2023/12/20 00:00 [received] PHST- 2024/09/26 00:00 [accepted] PHST- 2024/10/11 06:23 [medline] PHST- 2024/10/11 00:33 [pubmed] PHST- 2024/10/10 23:51 [entrez] PHST- 2024/10/10 00:00 [pmc-release] AID - 10.1186/s13059-024-03405-5 [pii] AID - 3405 [pii] AID - 10.1186/s13059-024-03405-5 [doi] PST - epublish SO - Genome Biol. 2024 Oct 10;25(1):261. doi: 10.1186/s13059-024-03405-5. PMID- 39360904 OWN - NLM STAT- MEDLINE DCOM- 20241003 LR - 20241003 IS - 1541-0420 (Electronic) IS - 0006-341X (Linking) VI - 80 IP - 4 DP - 2024 Oct 3 TI - Composite dyadic models for spatio-temporal data. LID - ujae107 [pii] LID - 10.1093/biomtc/ujae107 [doi] AB - Mechanistic statistical models are commonly used to study the flow of biological processes. For example, in landscape genetics, the aim is to infer spatial mechanisms that govern gene flow in populations. Existing statistical approaches in landscape genetics do not account for temporal dependence in the data and may be computationally prohibitive. We infer mechanisms with a Bayesian hierarchical dyadic model that scales well with large data sets and that accounts for spatial and temporal dependence. We construct a fully connected network comprising spatio-temporal data for the dyadic model and use normalized composite likelihoods to account for the dependence structure in space and time. We develop a dyadic model to account for physical mechanisms commonly found in physical-statistical models and apply our methods to ancient human DNA data to infer the mechanisms that affected human movement in Bronze Age Europe. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of The International Biometric Society. FAU - Schwob, Michael R AU - Schwob MR AUID- ORCID: 0000-0001-6367-2013 AD - Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, TX 78712, United States. FAU - Hooten, Mevin B AU - Hooten MB AD - Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, TX 78712, United States. FAU - Narasimhan, Vagheesh AU - Narasimhan V AD - Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, TX 78712, United States. AD - Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, United States. AD - Department of Population Health, Dell Medical School, Austin, TX 78712, United States. LA - eng GR - NSF 2222525/National Science Foundation/ PT - Journal Article PL - England TA - Biometrics JT - Biometrics JID - 0370625 RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - *Bayes Theorem MH - *Spatio-Temporal Analysis MH - *Models, Statistical MH - Europe MH - Gene Flow MH - Likelihood Functions MH - Genetics, Population/statistics & numerical data MH - Human Migration/statistics & numerical data MH - DNA/genetics OTO - NOTNLM OT - Bayesian OT - advection OT - diffusion OT - landscape genomics OT - potential surface EDAT- 2024/10/03 16:18 MHDA- 2024/10/03 16:19 CRDT- 2024/10/03 09:34 PHST- 2023/11/01 00:00 [received] PHST- 2024/08/10 00:00 [revised] PHST- 2024/09/11 00:00 [accepted] PHST- 2024/10/03 16:19 [medline] PHST- 2024/10/03 16:18 [pubmed] PHST- 2024/10/03 09:34 [entrez] AID - 7808592 [pii] AID - 10.1093/biomtc/ujae107 [doi] PST - ppublish SO - Biometrics. 2024 Oct 3;80(4):ujae107. doi: 10.1093/biomtc/ujae107. PMID- 39294129 OWN - NLM STAT- MEDLINE DCOM- 20240918 LR - 20241103 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 14 IP - 1 DP - 2024 Sep 18 TI - Towards predicting the geographical origin of ancient samples with metagenomic data. PG - 21794 LID - 10.1038/s41598-023-40246-x [doi] LID - 21794 AB - Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples. CI - © 2024. The Author(s). FAU - Bozzi, Davide AU - Bozzi D AD - Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland. davide.bozzi@unil.ch. AD - Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland. davide.bozzi@unil.ch. FAU - Neuenschwander, Samuel AU - Neuenschwander S AD - Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland. AD - Vital-IT, SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland. FAU - Cruz Dávalos, Diana Ivette AU - Cruz Dávalos DI AD - Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland. FAU - Sousa da Mota, Bárbara AU - Sousa da Mota B AD - Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland. FAU - Schroeder, Hannes AU - Schroeder H AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Moreno-Mayar, J Víctor AU - Moreno-Mayar JV AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Allentoft, Morten E AU - Allentoft ME AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia. FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland. annasapfo.malaspinas@unil.ch. AD - Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland. annasapfo.malaspinas@unil.ch. LA - eng PT - Journal Article DEP - 20240918 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - *Metagenomics/methods MH - *Metagenome MH - Geography MH - Microbiota/genetics PMC - PMC11411106 COIS- The authors declare no competing interests. EDAT- 2024/09/19 00:53 MHDA- 2024/09/19 00:54 PMCR- 2024/09/18 CRDT- 2024/09/18 23:14 PHST- 2023/03/10 00:00 [received] PHST- 2023/08/07 00:00 [accepted] PHST- 2024/09/19 00:54 [medline] PHST- 2024/09/19 00:53 [pubmed] PHST- 2024/09/18 23:14 [entrez] PHST- 2024/09/18 00:00 [pmc-release] AID - 10.1038/s41598-023-40246-x [pii] AID - 40246 [pii] AID - 10.1038/s41598-023-40246-x [doi] PST - epublish SO - Sci Rep. 2024 Sep 18;14(1):21794. doi: 10.1038/s41598-023-40246-x. PMID- 39146937 OWN - NLM STAT- MEDLINE DCOM- 20240910 LR - 20240911 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 34 IP - 17 DP - 2024 Sep 9 TI - Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic. PG - 3996-4006.e11 LID - S0960-9822(24)01002-9 [pii] LID - 10.1016/j.cub.2024.07.063 [doi] AB - The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities. CI - Copyright © 2024 Elsevier Inc. All rights reserved. FAU - Du, Panxin AU - Du P AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Zhu, Kongyang AU - Zhu K AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Wang, Minghui AU - Wang M AD - Institute of Archaeology, Academy of Social Sciences, Beijing 100101, China. FAU - Sun, Zhaofeng AU - Sun Z AD - Yantai Municipal Museum, Yantai 264001, China. FAU - Tan, Jingze AU - Tan J AD - Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Sun, Bo AU - Sun B AD - Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China. FAU - Sun, Bo AU - Sun B AD - Linyi Museum, Linyi 276000, China. FAU - Wang, Peixiao AU - Wang P AD - Linyi Museum, Linyi 276000, China. FAU - He, Guanglin AU - He G AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China; Center for Archaeological Science, Sichuan University, Chengdu 610000, China. FAU - Xiong, Jianxue AU - Xiong J AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Huang, Zixiao AU - Huang Z AD - Department of History, Fudan University, Shanghai 200433, China. FAU - Meng, Hailiang AU - Meng H AD - Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Sun, Chang AU - Sun C AD - Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Xie, Shouhua AU - Xie S AD - Department of History, Fudan University, Shanghai 200433, China. FAU - Wang, Bangyan AU - Wang B AD - State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China. FAU - Ge, Dong AU - Ge D AD - Shanghai Natural History Museum, Branch of the Shanghai Science & Technology Museum, Shanghai 200041, China. FAU - Ma, Yongqiang AU - Ma Y AD - Nanjing Museum, Nanjing 210000, China. FAU - Sheng, Pengfei AU - Sheng P AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Ren, Xiaoying AU - Ren X AD - State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China. FAU - Tao, Yichen AU - Tao Y AD - Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Xu, Yiran AU - Xu Y AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Qin, Xiaoli AU - Qin X AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Allen, Edward AU - Allen E AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Zhang, Baoshuai AU - Zhang B AD - USTC Archaeometry Laboratory, University of Science and Technology of China, Hefei 230026, China. FAU - Chang, Xin AU - Chang X AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Wang, Ke AU - Wang K AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Bao, Haoquan AU - Bao H AD - Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Yu, Yao AU - Yu Y AD - Department of History, Fudan University, Shanghai 200433, China. FAU - Wang, Lingxiang AU - Wang L AD - MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China. FAU - Ma, Xiaolin AU - Ma X AD - State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China. FAU - Du, Zhenyuan AU - Du Z AD - Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China. FAU - Guo, Jianxin AU - Guo J AD - Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China. FAU - Yang, Xiaomin AU - Yang X AD - Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China. FAU - Wang, Rui AU - Wang R AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Ma, Hao AU - Ma H AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Li, Dapeng AU - Li D AD - Yantai Municipal Museum, Yantai 264001, China. FAU - Pan, Yiling AU - Pan Y AD - Shanghai Natural History Museum, Branch of the Shanghai Science & Technology Museum, Shanghai 200041, China. FAU - Li, Bicheng AU - Li B AD - Shanghai Natural History Museum, Branch of the Shanghai Science & Technology Museum, Shanghai 200041, China. FAU - Zhang, Yunfei AU - Zhang Y AD - Shanghai Natural History Museum, Branch of the Shanghai Science & Technology Museum, Shanghai 200041, China. FAU - Zheng, Xiaoqu AU - Zheng X AD - School of Cultural Heritage and Information Management, Shanghai University, Shanghai 200444, China. FAU - Han, Sheng AU - Han S AD - Department of History, Fudan University, Shanghai 200433, China. FAU - Jin, Li AU - Jin L AD - Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. Electronic address: lijin@fudan.edu.cn. FAU - Chen, Gang AU - Chen G AD - Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China. Electronic address: chengangcs@gmail.com. FAU - Li, Hui AU - Li H AD - Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. Electronic address: lhca@fudan.edu.cn. FAU - Wang, Chuan-Chao AU - Wang CC AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China. Electronic address: wang@xmu.edu.cn. FAU - Wen, Shaoqing AU - Wen S AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China; Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai 200433, China. Electronic address: wenshaoqing@fudan.edu.cn. LA - eng PT - Historical Article PT - Journal Article DEP - 20240814 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - China MH - *Genome, Human MH - History, Ancient MH - DNA, Ancient/analysis MH - Human Migration/history MH - Rivers MH - Genetics, Population MH - Archaeology MH - Genetic Variation MH - Genomics OTO - NOTNLM OT - Dawenkou OT - Neolithic Yellow River farmers OT - Shandong OT - ancient DNA COIS- Declaration of interests The authors declare no competing interests. EDAT- 2024/08/16 01:19 MHDA- 2024/09/11 00:43 CRDT- 2024/08/15 18:53 PHST- 2022/07/01 00:00 [received] PHST- 2024/04/05 00:00 [revised] PHST- 2024/07/17 00:00 [accepted] PHST- 2024/09/11 00:43 [medline] PHST- 2024/08/16 01:19 [pubmed] PHST- 2024/08/15 18:53 [entrez] AID - S0960-9822(24)01002-9 [pii] AID - 10.1016/j.cub.2024.07.063 [doi] PST - ppublish SO - Curr Biol. 2024 Sep 9;34(17):3996-4006.e11. doi: 10.1016/j.cub.2024.07.063. Epub 2024 Aug 14. PMID- 39268685 OWN - NLM STAT- MEDLINE DCOM- 20240913 LR - 20241001 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 41 IP - 9 DP - 2024 Sep 4 TI - Low Genetic Impact of the Roman Occupation of Britain in Rural Communities. LID - 10.1093/molbev/msae168 [doi] LID - msae168 AB - The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored. Here, using genome-wide data from 52 ancient individuals from eight sites in Cambridgeshire covering the period of Roman occupation, we show low levels of genetic ancestry differentiation between Romano-British sites and indications of larger populations than in the Bronze Age and Neolithic. We find no evidence of long-distance migration from elsewhere in the Empire, though we do find one case of possible temporary mobility within a family unit during the Late Romano-British period. We also show that the present-day patterns of genetic ancestry composition in Britain emerged after the Roman period. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Scheib, Christiana L AU - Scheib CL AUID- ORCID: 0000-0003-4158-8296 AD - Estonian Biocentre, Institute of Genomics, University of Tartu  Tartu 51010, Estonia. AD - St John's College, University of Cambridge, Cambridge CB2 1TP, UK. AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK. FAU - Hui, Ruoyun AU - Hui R AUID- ORCID: 0000-0002-5689-7131 AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK. AD - Alan Turing Institute, British Library, London NW1 2DB, UK. FAU - Rose, Alice K AU - Rose AK AUID- ORCID: 0000-0003-1755-7174 AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK. FAU - D'Atanasio, Eugenia AU - D'Atanasio E AUID- ORCID: 0000-0002-4965-246X AD - Institute of Molecular Biology and Pathology, IBPM CNR, Rome 00185, Italy. FAU - Inskip, Sarah A AU - Inskip SA AUID- ORCID: 0000-0001-7424-2094 AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK. AD - School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK. FAU - Dittmar, Jenna AU - Dittmar J AUID- ORCID: 0000-0003-3514-1869 AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK. FAU - Cessford, Craig AU - Cessford C AUID- ORCID: 0000-0001-7291-7828 AD - Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK. FAU - Griffith, Samuel J AU - Griffith SJ AUID- ORCID: 0009-0001-2335-9054 AD - Estonian Biocentre, Institute of Genomics, University of Tartu  Tartu 51010, Estonia. FAU - Solnik, Anu AU - Solnik A AD - Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Wiseman, Rob AU - Wiseman R AUID- ORCID: 0000-0001-8947-5624 AD - Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Neil, Benjamin AU - Neil B AUID- ORCID: 0000-0002-7183-4622 AD - Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Biers, Trish AU - Biers T AUID- ORCID: 0000-0002-1467-7667 AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK. FAU - Harknett, Sarah-Jane AU - Harknett SJ AUID- ORCID: 0009-0004-9922-6364 AD - Museum of Archaeology and Anthropology, Cambridge CB2 3DZ, UK. FAU - Sasso, Stefania AU - Sasso S AUID- ORCID: 0009-0008-1090-5731 AD - Estonian Biocentre, Institute of Genomics, University of Tartu  Tartu 51010, Estonia. FAU - Biagini, Simone A AU - Biagini SA AUID- ORCID: 0000-0002-4488-3162 AD - Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain. AD - Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium. FAU - Runfeldt, Göran AU - Runfeldt G AUID- ORCID: 0000-0002-1313-3123 AD - FamilyTreeDNA, Gene by Gene, Houston, TX 77008, USA. FAU - Duhig, Corinne AU - Duhig C AD - Wolfson College, University of Cambridge, Cambridge CB3 9BB, UK. FAU - Evans, Christopher AU - Evans C AUID- ORCID: 0000-0001-9203-1354 AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK. FAU - Metspalu, Mait AU - Metspalu M AUID- ORCID: 0000-0003-3099-9161 AD - Estonian Biocentre, Institute of Genomics, University of Tartu  Tartu 51010, Estonia. FAU - Millett, Martin J AU - Millett MJ AUID- ORCID: 0000-0003-4073-3260 AD - Faculty of Classics, University of Cambridge, Cambridge CB3 9DA, UK. FAU - O'Connell, Tamsin C AU - O'Connell TC AUID- ORCID: 0000-0002-4744-0332 AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK. FAU - Robb, John E AU - Robb JE AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK. FAU - Kivisild, Toomas AU - Kivisild T AUID- ORCID: 0000-0002-6297-7808 AD - Estonian Biocentre, Institute of Genomics, University of Tartu  Tartu 51010, Estonia. AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK. AD - Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium. LA - eng GR - 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom GR - St John's College, Cambridge/ GR - 2014-2020.4.01.15-0012/European Regional Development Fund/ GR - PRG243/Estonian Research Council/ GR - 2014-2020.4.01.16-0030/European Union through the European Regional Development Fund/ GR - WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - United Kingdom MH - *Human Migration MH - *Rural Population MH - History, Ancient MH - DNA, Ancient/analysis MH - Genetics, Population PMC - PMC11393495 OTO - NOTNLM OT - Roman OT - United Kingdom OT - ancient DNA OT - genomics OT - kinship OT - population genomics COIS- Conflict of Interest The authors declare no conflicting interests. EDAT- 2024/09/15 21:16 MHDA- 2024/09/15 21:17 PMCR- 2024/09/12 CRDT- 2024/09/13 05:33 PHST- 2023/09/04 00:00 [received] PHST- 2024/07/25 00:00 [revised] PHST- 2024/08/07 00:00 [accepted] PHST- 2024/09/15 21:17 [medline] PHST- 2024/09/15 21:16 [pubmed] PHST- 2024/09/13 05:33 [entrez] PHST- 2024/09/12 00:00 [pmc-release] AID - 7741671 [pii] AID - msae168 [pii] AID - 10.1093/molbev/msae168 [doi] PST - ppublish SO - Mol Biol Evol. 2024 Sep 4;41(9):msae168. doi: 10.1093/molbev/msae168. PMID- 39013011 OWN - NLM STAT- MEDLINE DCOM- 20240904 LR - 20240906 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 228 IP - 1 DP - 2024 Sep 4 TI - Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA. LID - 10.1093/genetics/iyae110 [doi] LID - iyae110 AB - Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches-firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes-and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudohaploidization. We observe that population differentiation is the primary factor driving qpAdm performance. Notably, while complex gene flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible among a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. FAU - Williams, Matthew P AU - Williams MP AUID- ORCID: 0000-0001-7117-193X AD - Department of Biology, Pennsylvania State University, University Park, PA 16802, USA. FAU - Flegontov, Pavel AU - Flegontov P AUID- ORCID: 0000-0001-9759-4981 AD - Department of Biology and Ecology, University of Ostrava, Ostrava 701 03, Czechia. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Maier, Robert AU - Maier R AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Huber, Christian D AU - Huber CD AUID- ORCID: 0000-0002-2267-2604 AD - Department of Biology, Pennsylvania State University, University Park, PA 16802, USA. LA - eng GR - R35GM146886/National Institute of Health/ GR - CZ.10.03.01/00/22_003/0000003/European Union/ GR - R35 GM146886/GM/NIGMS NIH HHS/United States GR - CZ.10.03.01/00/22_003/0000003/European Union Operational Programme/ GR - 61220/John Templeton Foundation/ GR - 21-27624S/Czech Science Foundation/ GR - LL2103/Czech Ministry of Education, Youth and Sports/ PT - Journal Article PL - United States TA - Genetics JT - Genetics JID - 0374636 RN - 0 (DNA, Ancient) SB - IM UOF - bioRxiv. 2023 Nov 15:2023.11.13.566841. doi: 10.1101/2023.11.13.566841. PMID: 38014190 MH - *DNA, Ancient/analysis MH - Humans MH - *Models, Genetic MH - Genetics, Population/methods MH - Gene Flow MH - Polymorphism, Single Nucleotide MH - Genome, Human MH - Evolution, Molecular PMC - PMC11373510 OTO - NOTNLM OT - f-statistics OT - aDNA OT - admixture OT - ancient DNA OT - archaeogenetics OT - paleogenomics OT - qpAdm COIS- Conflicts of interest: The authors declare no conflicts of interest. EDAT- 2024/07/16 18:41 MHDA- 2024/09/04 18:42 PMCR- 2024/07/16 CRDT- 2024/07/16 14:23 PHST- 2024/04/08 00:00 [received] PHST- 2024/06/11 00:00 [accepted] PHST- 2024/09/04 18:42 [medline] PHST- 2024/07/16 18:41 [pubmed] PHST- 2024/07/16 14:23 [entrez] PHST- 2024/07/16 00:00 [pmc-release] AID - 7714968 [pii] AID - iyae110 [pii] AID - 10.1093/genetics/iyae110 [doi] PST - ppublish SO - Genetics. 2024 Sep 4;228(1):iyae110. doi: 10.1093/genetics/iyae110. PMID- 39261607 OWN - NLM STAT- MEDLINE DCOM- 20240912 LR - 20240912 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 633 IP - 8029 DP - 2024 Sep TI - Rapa Nui's population history rewritten using ancient DNA. PG - 290-291 LID - 10.1038/d41586-024-02620-1 [doi] FAU - Schiffels, Stephan AU - Schiffels S FAU - Nägele, Kathrin AU - Nägele K LA - eng PT - Historical Article PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - *Genetics, Population/history MH - History, Ancient MH - Reproducibility of Results MH - Polynesia MH - Colonialism/history OTO - NOTNLM OT - Culture OT - Genomics OT - History EDAT- 2024/09/12 00:42 MHDA- 2024/09/12 08:42 CRDT- 2024/09/11 23:35 PHST- 2024/09/12 08:42 [medline] PHST- 2024/09/12 00:42 [pubmed] PHST- 2024/09/11 23:35 [entrez] AID - 10.1038/d41586-024-02620-1 [pii] AID - 10.1038/d41586-024-02620-1 [doi] PST - ppublish SO - Nature. 2024 Sep;633(8029):290-291. doi: 10.1038/d41586-024-02620-1. PMID- 39098141 OWN - NLM STAT- MEDLINE DCOM- 20240816 LR - 20240816 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 362 DP - 2024 Sep TI - Searching for alternative high DNA-yielding bone types for DNA analysis of aged skeletal remains. PG - 112184 LID - S0379-0738(24)00265-2 [pii] LID - 10.1016/j.forsciint.2024.112184 [doi] AB - The petrous bone contains significantly higher amounts of DNA than any other human bone. Because of highly destructive sampling and because it is not always part of the recovered remains, the need for alternative sources of DNA is important. To identify additional optimal bone types, petrous bones were compared to femurs, tali, and calcanei sampled from 66 adult skeletons from two distinct modern-era Christian cemeteries. An extraction method employing full demineralization was used to obtain DNA, real-time PCR quantification to ascertain DNA quantity and degradation, and a commercial forensic short tandem repeats (STR) PCR amplification kit to determine genetic profiles. Statistical analysis was performed to explore the differences in DNA yield, DNA degradation, and success of STR amplification. A systematic studies exploring intra-skeletal variability in DNA preservation including various excavation sites differing by time period and geographical position are rare, and the second part of the investigation was based on a comparison of both archaeological sites, which allowed us to compare the effect of different post-mortem intervals and environmental conditions on DNA preservation. The older burial site in Črnomelj was active between the 13th and 18th century, whereas the more recent Polje burial was in use from the 16th to 19th century, creating different temporal and geographical environments. Results for the Črnomelj burial site revealed that the petrous bone outperformed all other bone types studied, except the calcaneus. At the Polje archeological site calcanei, tali, and femurs yielded the same STR typing success as petrous bones. The results obtained highlight the importance of careful bone sample selection for DNA analysis of aged skeletal remains. In addition to petrous bones, calcanei were found to be an alternative source of DNA when older burial sites are investigated. When more recent burial sites are processed, calcanei, tali, and femurs should be sampled besides petrous bones, not only because they exhibited good performance, but also because of easier sampling and easier grinding in the case of trabecular bones. This study contributes valuable insights into the potential use of various skeletal types as a source of DNA for investigation of aged skeletal remains, and it offers practical implications for forensic and archaeological investigations. CI - Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved. FAU - Golob, Aja AU - Golob A AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia. FAU - Kravanja, Pia AU - Kravanja P AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia. FAU - Concato, Monica AU - Concato M AD - Department of Medicine, Surgery, and Health, University of Trieste, Trieste 34137, Italy. FAU - Leskovar, Tamara AU - Leskovar T AD - Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia. FAU - Zupanič Pajnič, Irena AU - Zupanič Pajnič I AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia. Electronic address: irena.zupanic@mf.uni-lj.si. LA - eng PT - Journal Article DEP - 20240802 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - *Microsatellite Repeats MH - *DNA Fingerprinting/methods MH - Male MH - *Real-Time Polymerase Chain Reaction MH - *DNA/analysis/isolation & purification MH - Adult MH - Middle Aged MH - Female MH - Body Remains MH - DNA Degradation, Necrotic MH - Aged MH - Femur/chemistry/anatomy & histology MH - History, Medieval MH - Bone and Bones/chemistry MH - Petrous Bone/chemistry/anatomy & histology MH - Aged, 80 and over MH - Forensic Anthropology/methods MH - Young Adult MH - Calcaneus/anatomy & histology OTO - NOTNLM OT - Aged skeletal remains OT - Ancient DNA OT - DNA preservation OT - STR typing OT - Sampling strategy COIS- Declaration of Competing Interest The authors declare that they have no conflict of interest. EDAT- 2024/08/05 00:42 MHDA- 2024/08/17 15:42 CRDT- 2024/08/04 21:58 PHST- 2024/06/22 00:00 [received] PHST- 2024/07/24 00:00 [revised] PHST- 2024/08/01 00:00 [accepted] PHST- 2024/08/17 15:42 [medline] PHST- 2024/08/05 00:42 [pubmed] PHST- 2024/08/04 21:58 [entrez] AID - S0379-0738(24)00265-2 [pii] AID - 10.1016/j.forsciint.2024.112184 [doi] PST - ppublish SO - Forensic Sci Int. 2024 Sep;362:112184. doi: 10.1016/j.forsciint.2024.112184. Epub 2024 Aug 2. PMID- 39028337 OWN - NLM STAT- MEDLINE DCOM- 20240816 LR - 20240816 IS - 1432-1777 (Electronic) IS - 0938-8990 (Linking) VI - 35 IP - 3 DP - 2024 Sep TI - Evaluation of genotype imputation using Glimpse tools on low coverage ancient DNA. PG - 461-473 LID - 10.1007/s00335-024-10053-4 [doi] AB - Ancient DNA provides a unique frame for directly studying human population genetics in time and space. Still, since most of the ancient genomic data is low coverage, analysis is confronted with a low number of SNPs, genotype uncertainties, and reference-bias. Here, we for the first time benchmark the two distinct versions of Glimpse tools on 120 ancient human genomes from Eurasia including those largely from previously under-evaluated regions and compare the performance of genotype imputation with de facto analysis approaches for low coverage genomic data analysis. We further investigate the impact of two distinct reference panels on imputation accuracy for low coverage genomic data. We compute accuracy statistics and perform PCA and f(4)-statistics to explore the behaviour of genotype imputation on low coverage data regarding (i)two versions of Glimpse, (ii)two reference panels, (iii)four post-imputation filters and coverages, as well as (iv)data type and geographical origin of the samples on the analyses. Our results reveal that even for 0.1X coverage ancient human genomes, genotype imputation using Glimpse-v2 is suitable. Additionally, using the 1000 Genomes merged with Human Genome Diversity Panel improves the accuracy of imputation for the rare variants with low MAF, which might be important not only for ancient genomics but also for modern human genomic studies based on low coverage data and for haplotype-based analysis. Most importantly, we reveal that genotype imputation of low coverage ancient human genomes reduces the genetic affinity of the samples towards human reference genome. Through solving one of the most challenging biases in data analysis, so-called reference bias, genotype imputation using Glimpse v2 is promising for low coverage ancient human genomic data analysis and for rare-variant-based and haplotype-based analysis. CI - © 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature. FAU - Çubukcu, Hande AU - Çubukcu H AD - Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey. FAU - Kılınç, Gülşah Merve AU - Kılınç GM AD - Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey. gulsahkilinc@hacettepe.edu.tr. LA - eng PT - Journal Article DEP - 20240719 PL - United States TA - Mamm Genome JT - Mammalian genome : official journal of the International Mammalian Genome Society JID - 9100916 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - *Genome, Human MH - *Polymorphism, Single Nucleotide MH - *Genotype MH - Genetics, Population/methods MH - Software MH - Genomics/methods OTO - NOTNLM OT - Ancient DNA OT - Genotype imputation OT - Glimpse2 OT - Low coverage OT - Reference bias EDAT- 2024/07/19 12:42 MHDA- 2024/08/16 13:41 CRDT- 2024/07/19 11:03 PHST- 2024/03/22 00:00 [received] PHST- 2024/07/12 00:00 [accepted] PHST- 2024/08/16 13:41 [medline] PHST- 2024/07/19 12:42 [pubmed] PHST- 2024/07/19 11:03 [entrez] AID - 10.1007/s00335-024-10053-4 [pii] AID - 10.1007/s00335-024-10053-4 [doi] PST - ppublish SO - Mamm Genome. 2024 Sep;35(3):461-473. doi: 10.1007/s00335-024-10053-4. Epub 2024 Jul 19. PMID- 38963678 OWN - NLM STAT- MEDLINE DCOM- 20240814 LR - 20240814 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 185 IP - 1 DP - 2024 Sep TI - A morphological and molecular approach to investigating infectious disease in early medieval Iberia: The necropolis of La Olmeda (Palencia, Spain). PG - e24994 LID - 10.1002/ajpa.24994 [doi] AB - OBJECTIVE: Here we investigate infectious diseases that potentially contribute to osteological lesions in individuals from the early medieval necropolis of La Olmeda (6th-11th c. CE) in North Iberia. MATERIALS AND METHODS: We studied a minimum number of 268 individuals (33 adult females; 38 adult males, 77 unknown/indeterminate sex; and 120 non-adults), including articulated and commingled remains. Individuals with differential diagnoses suggesting chronic systemic infectious diseases were sampled and bioinformatically screened for ancient pathogen DNA. RESULTS: Five non-adults (and no adults) presented skeletal evidence of chronic systemic infectious disease (1.87% of the population; 4.67% of non-adults). The preferred diagnoses for these individuals included tuberculosis, brucellosis, and malaria. Ancient DNA fragments assigned to the malaria-causing pathogen, Plasmodium spp., were identified in three of the five individuals. Observed pathology includes lesions generally consistent with malaria; however, additional lesions in two of the individuals may represent hitherto unknown variation in the skeletal manifestation of this disease or co-infection with tuberculosis or brucellosis. Additionally, spondylolysis was observed in one individual with skeletal lesions suggestive of infectious disease. CONCLUSIONS: This study sheds light on the pathological landscape in Iberia during a time of great social, demographic, and environmental change. Genetic evidence challenges the hypothesis that malaria was absent from early medieval Iberia and demonstrates the value of combining osteological and archaeogenetic methods. Additionally, all of the preferred infectious diagnoses for the individuals included in this study (malaria, tuberculosis, and brucellosis) could have contributed to the febrile cases described in historical sources from this time. CI - © 2024 The Author(s). American Journal of Biological Anthropology published by Wiley Periodicals LLC. FAU - Coppola Bove, L AU - Coppola Bove L AUID- ORCID: 0000-0002-1420-5061 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain. FAU - Kirkpatrick, C L AU - Kirkpatrick CL AUID- ORCID: 0000-0001-9755-6459 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Anthropology, University of Western Ontario, London, Canada. FAU - Vigil-Escalera Guirado, A AU - Vigil-Escalera Guirado A AD - Department of Humanities: History, Geography and Art, University Carlos III de Madrid, Madrid, Spain. FAU - Botella López, M C AU - Botella López MC AD - Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain. FAU - Bos, K I AU - Bos KI AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. LA - eng GR - Erasmus+ Traineeship Program Scholarship/ GR - Junta de Andalucía and SEPIE/ GR - 756-2023-0246/Social Sciences and Humanities Research Council of Canada Postdoctoral Fellowship/ GR - 805268/ERC_/European Research Council/International PT - Historical Article PT - Journal Article DEP - 20240704 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Male MH - History, Medieval MH - Spain MH - Female MH - Adult MH - Middle Aged MH - *Malaria/history MH - Young Adult MH - Adolescent MH - Child MH - DNA, Ancient/analysis MH - Child, Preschool MH - Infant MH - Bone and Bones/pathology/microbiology MH - Communicable Diseases/history MH - Paleopathology MH - Brucellosis/history MH - Tuberculosis/history OTO - NOTNLM OT - ancient DNA OT - brucellosis OT - malaria OT - spondylolysis OT - tuberculosis EDAT- 2024/07/04 12:43 MHDA- 2024/08/14 06:42 CRDT- 2024/07/04 11:42 PHST- 2024/04/30 00:00 [revised] PHST- 2023/07/21 00:00 [received] PHST- 2024/06/19 00:00 [accepted] PHST- 2024/08/14 06:42 [medline] PHST- 2024/07/04 12:43 [pubmed] PHST- 2024/07/04 11:42 [entrez] AID - 10.1002/ajpa.24994 [doi] PST - ppublish SO - Am J Biol Anthropol. 2024 Sep;185(1):e24994. doi: 10.1002/ajpa.24994. Epub 2024 Jul 4. PMID- 39169089 OWN - NLM STAT- MEDLINE DCOM- 20240821 LR - 20241211 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 14 IP - 1 DP - 2024 Aug 20 TI - Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach. PG - 19388 LID - 10.1038/s41598-024-69741-5 [doi] LID - 19388 AB - In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth. CI - © 2024. The Author(s). FAU - Oberreiter, Victoria AU - Oberreiter V AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. FAU - Gelabert, Pere AU - Gelabert P AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. pere.gelabert@univie.ac.at. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. pere.gelabert@univie.ac.at. AD - Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Bellaterra, Spain. pere.gelabert@univie.ac.at. FAU - Brück, Florian AU - Brück F AD - Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria. FAU - Franz, Stefan AU - Franz S AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Zelger, Evelyn AU - Zelger E AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Szedlacsek, Sophie AU - Szedlacsek S AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. FAU - Cano, Fernanda Tenorio AU - Cano FT AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Exler, Florian AU - Exler F AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. AD - Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. FAU - Zagorc, Brina AU - Zagorc B AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. FAU - Karavanić, Ivor AU - Karavanić I AD - Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Banda, Marko AU - Banda M AD - Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Gasparyan, Boris AU - Gasparyan B AD - Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia. FAU - Straus, Lawrence Guy AU - Straus LG AD - Department of Anthropology, University of New Mexico, Albuquerque, USA. AD - EvoAdapta Group Universidad de Cantabria, Santander, Spain. FAU - Gonzalez Morales, Manuel R AU - Gonzalez Morales MR AD - Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Gobierno de Cantabria, Banco Santander, Spain. FAU - Kappelman, John AU - Kappelman J AD - Department of Anthropology and Department of Earth and Planetary Sciences, The University of Texas, Austin, TX, USA. FAU - Stahlschmidt, Mareike AU - Stahlschmidt M AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. FAU - Rattei, Thomas AU - Rattei T AD - Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. FAU - Kraemer, Stephan M AU - Kraemer SM AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. AD - Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. AD - Institut für Analytische Chemie, University of Vienna, Vienna, Austria. AD - Forschungsverbund Umwelt und Klima, University of Vienna, Vienna, Austria. FAU - Sawyer, Susanna AU - Sawyer S AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. susanna.sawyer@univie.ac.at. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. susanna.sawyer@univie.ac.at. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at. LA - eng GR - 1111111/Research Platform MINERVA, University of Vienna/ GR - M 3108/FWF_/Austrian Science Fund FWF/Austria GR - CA19141-8d068698/COST iNEAL STSM Grant/ GR - No. 101042570/European Research Council (ERC) MicroStratDNA project/ GR - M3108-G/Austrian Science Fund/ GR - NECEM, HRZZ-IP-2019-04-6649/Hrvatska Zaklada za Znanost/ PT - Journal Article DEP - 20240820 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient/analysis MH - *Geologic Sediments MH - Humans MH - Animals MH - Archaeology/methods MH - Fossils MH - High-Throughput Nucleotide Sequencing/methods MH - Hominidae/genetics MH - Europe MH - Africa PMC - PMC11339378 COIS- The authors declare no competing interests. EDAT- 2024/08/22 00:42 MHDA- 2024/08/22 00:43 PMCR- 2024/08/20 CRDT- 2024/08/21 23:34 PHST- 2024/01/12 00:00 [received] PHST- 2024/08/08 00:00 [accepted] PHST- 2024/08/22 00:43 [medline] PHST- 2024/08/22 00:42 [pubmed] PHST- 2024/08/21 23:34 [entrez] PHST- 2024/08/20 00:00 [pmc-release] AID - 10.1038/s41598-024-69741-5 [pii] AID - 69741 [pii] AID - 10.1038/s41598-024-69741-5 [doi] PST - epublish SO - Sci Rep. 2024 Aug 20;14(1):19388. doi: 10.1038/s41598-024-69741-5. PMID- 39135108 OWN - NLM STAT- MEDLINE DCOM- 20240813 LR - 20240815 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 25 IP - 1 DP - 2024 Aug 12 TI - READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics. PG - 216 LID - 10.1186/s13059-024-03350-3 [doi] LID - 216 AB - The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures. CI - © 2024. The Author(s). FAU - Alaçamlı, Erkin AU - Alaçamlı E AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. AD - Present Address: Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Naidoo, Thijessen AU - Naidoo T AD - Ancient DNA Unit, Science for Life Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. AD - Centre for Palaeogenetics, Stockholm, Sweden. FAU - Güler, Merve N AU - Güler MN AD - Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey. FAU - Sağlıcan, Ekin AU - Sağlıcan E AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Aktürk, Şevval AU - Aktürk Ş AD - Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey. FAU - Mapelli, Igor AU - Mapelli I AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Vural, Kıvılcım Başak AU - Vural KB AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Somel, Mehmet AU - Somel M AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Malmström, Helena AU - Malmström H AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. Helena.Malmstrom@ebc.uu.se. FAU - Günther, Torsten AU - Günther T AUID- ORCID: 0000-0001-9460-390X AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. torsten.gunther@ebc.uu.se. AD - Ancient DNA Unit, Science for Life Laboratory, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. torsten.gunther@ebc.uu.se. LA - eng GR - P21-0266/Riksbankens Jubileumsfond/ GR - 772390/HORIZON EUROPE European Research Council/ PT - Journal Article DEP - 20240812 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - *Software MH - *Archaeology/methods MH - Genomics/methods MH - Pedigree PMC - PMC11318251 OTO - NOTNLM OT - Ancient DNA OT - Archaeogenomics OT - Kinship OT - Relatedness OT - Software COIS- The authors declare that they have no competing interests. EDAT- 2024/08/13 00:42 MHDA- 2024/08/13 06:42 PMCR- 2024/08/12 CRDT- 2024/08/12 23:45 PHST- 2024/01/25 00:00 [received] PHST- 2024/07/24 00:00 [accepted] PHST- 2024/08/13 06:42 [medline] PHST- 2024/08/13 00:42 [pubmed] PHST- 2024/08/12 23:45 [entrez] PHST- 2024/08/12 00:00 [pmc-release] AID - 10.1186/s13059-024-03350-3 [pii] AID - 3350 [pii] AID - 10.1186/s13059-024-03350-3 [doi] PST - epublish SO - Genome Biol. 2024 Aug 12;25(1):216. doi: 10.1186/s13059-024-03350-3. PMID- 38916350 OWN - NLM STAT- MEDLINE DCOM- 20240808 LR - 20240808 IS - 2165-0497 (Electronic) IS - 2165-0497 (Linking) VI - 12 IP - 8 DP - 2024 Aug 6 TI - Exploring antimicrobial resistance determinants in the Neanderthal microbiome. PG - e0266223 LID - 10.1128/spectrum.02662-23 [doi] LID - e02662-23 AB - This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history. IMPORTANCE: The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices. FAU - Sankaranarayanan, Gomathinayagam AU - Sankaranarayanan G AUID- ORCID: 0000-0002-4657-9041 AD - School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India. FAU - Kodiveri Muthukaliannan, Gothandam AU - Kodiveri Muthukaliannan G AUID- ORCID: 0000-0003-1576-5324 AD - School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India. LA - eng GR - 20/2022-ECR-II/Indian Council of Medical Research (ICMR)/ PT - Journal Article DEP - 20240625 PL - United States TA - Microbiol Spectr JT - Microbiology spectrum JID - 101634614 RN - 0 (DNA, Ancient) RN - 0 (Anti-Bacterial Agents) SB - IM MH - Animals MH - *Microbiota/genetics/drug effects MH - *Neanderthals/genetics/microbiology MH - *DNA, Ancient/analysis MH - *Metagenomics MH - *Bacteria/genetics/drug effects/classification/isolation & purification MH - *Anti-Bacterial Agents/pharmacology MH - Drug Resistance, Bacterial/genetics MH - Humans MH - Feces/microbiology MH - Metagenome MH - Drug Resistance, Microbial/genetics MH - Europe MH - Fossils/microbiology PMC - PMC11302244 OTO - NOTNLM OT - Neanderthal microbiome OT - ancient DNA OT - antimicrobial resistance OT - fecal microbiome OT - metagenomics COIS- The authors declare no conflict of interest. EDAT- 2024/06/25 12:43 MHDA- 2024/08/08 06:42 PMCR- 2024/06/25 CRDT- 2024/06/25 09:03 PHST- 2024/08/08 06:42 [medline] PHST- 2024/06/25 12:43 [pubmed] PHST- 2024/06/25 09:03 [entrez] PHST- 2024/06/25 00:00 [pmc-release] AID - spectrum02662-23 [pii] AID - spectrum.02662-23 [pii] AID - 10.1128/spectrum.02662-23 [doi] PST - ppublish SO - Microbiol Spectr. 2024 Aug 6;12(8):e0266223. doi: 10.1128/spectrum.02662-23. Epub 2024 Jun 25. PMID- 39078618 OWN - NLM STAT- MEDLINE DCOM- 20240813 LR - 20240815 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 41 IP - 8 DP - 2024 Aug 2 TI - Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA. LID - 10.1093/molbev/msae156 [doi] LID - msae156 AB - We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Vaughn, Andrew H AU - Vaughn AH AUID- ORCID: 0000-0003-3113-2981 AD - Center for Computational Biology, University of California, Berkeley, CA 94720, USA. FAU - Nielsen, Rasmus AU - Nielsen R AUID- ORCID: 0000-0003-0513-6591 AD - Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720, USA. AD - Center for GeoGenetics, University of Copenhagen, Copenhagen DK-1350, Denmark. LA - eng PT - Journal Article PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) SB - IM MH - *Selection, Genetic MH - Humans MH - *DNA, Ancient/analysis MH - *Models, Genetic MH - *Gene Frequency MH - Likelihood Functions MH - Markov Chains MH - Algorithms MH - Evolution, Molecular MH - Alleles MH - Computer Simulation PMC - PMC11321360 OTO - NOTNLM OT - ARGs OT - HMMs OT - ancient DNA OT - lactase persistence OT - selection EDAT- 2024/07/30 12:43 MHDA- 2024/08/13 18:42 PMCR- 2024/07/30 CRDT- 2024/07/30 11:23 PHST- 2023/12/16 00:00 [received] PHST- 2024/07/02 00:00 [revised] PHST- 2024/07/10 00:00 [accepted] PHST- 2024/08/13 18:42 [medline] PHST- 2024/07/30 12:43 [pubmed] PHST- 2024/07/30 11:23 [entrez] PHST- 2024/07/30 00:00 [pmc-release] AID - 7724092 [pii] AID - msae156 [pii] AID - 10.1093/molbev/msae156 [doi] PST - ppublish SO - Mol Biol Evol. 2024 Aug 2;41(8):msae156. doi: 10.1093/molbev/msae156. PMID- 39191285 OWN - NLM STAT- MEDLINE DCOM- 20240827 LR - 20240924 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 291 IP - 2029 DP - 2024 Aug TI - Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France. PG - rspb20241215 LID - 10.1098/rspb.2024.1215 [doi] LID - rspb.2024.1215 AB - The Aven de la Boucle (Corconne, Gard, southern France) is a karst shaft used as a collective burial between 3600 and 2800 cal BCE. The site encompasses the skeletal remains of approximately 75 individuals comprising a large majority of adult individuals, represented by scattered and commingled remains. To date, few studies have explored the potential of ancient DNA to tackle the documentation of Neolithic collective burials, and the funerary selection rules within such structures remain largely debated. In this study, we combine genomic analysis of 37 individuals with archaeo-anthropological data and Bayesian modelling of radiocarbon dates. Through this multidisciplinary approach, we aim to characterize the identity of the deceased and their relationships, as well as untangle the genetic diversity and funerary dynamics of this community. Genomic results identify 76% of male Neolithic individuals, suggesting a marked sex-biased selection. Available data emphasize the importance of biological relatedness and a male-mediated transmission of social status, as the affiliation to a specific male-lineage appears as a preponderant selection factor. The genomic results argue in favour of 'continuous' deposits between 3600 and 2800 BCE, carried out by the same community, despite cultural changes reflected by the ceramic material. FAU - Arzelier, Ana AU - Arzelier A AD - Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France. FAU - De Belvalet, Harmony AU - De Belvalet H AD - Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France. FAU - Pemonge, Marie-Hélène AU - Pemonge MH AD - Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France. FAU - Garberi, Pauline AU - Garberi P AUID- ORCID: 0009-0000-8991-5351 AD - Université Côte d'Azur, CNRS, Cultures, Environnements. Préhistoire, Antiquité, Moyen-Âge (CEPAM UMR 7264) , Nice 06300, France. FAU - Binder, Didier AU - Binder D AD - Université Côte d'Azur, CNRS, Cultures, Environnements. Préhistoire, Antiquité, Moyen-Âge (CEPAM UMR 7264) , Nice 06300, France. FAU - Duday, Henri AU - Duday H AD - Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France. FAU - Pruvost, Mélanie AU - Pruvost M AUID- ORCID: 0000-0001-7824-2155 AD - Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France. LA - eng GR - DFG-HA-5407/4-1/Deutsche Forschungsgemeinschaft/ GR - ANR22-CE27-0012, ANR15-CE27-0001, ANR17-FRAL-0010/Agence Nationale de la Recherche/ PT - Historical Article PT - Journal Article DEP - 20240828 PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient/analysis MH - France MH - Humans MH - *Burial/history MH - *Archaeology MH - Male MH - Bayes Theorem MH - Female MH - History, Ancient PMC - PMC11349438 OTO - NOTNLM OT - Neolithic OT - ancient DNA OT - funerary practice OT - past society COIS- We declare we have no competing interests. EDAT- 2024/08/28 02:29 MHDA- 2024/08/28 02:30 PMCR- 2025/08/28 CRDT- 2024/08/27 19:13 PHST- 2025/08/28 00:00 [pmc-release] PHST- 2024/08/28 02:30 [medline] PHST- 2024/08/28 02:29 [pubmed] PHST- 2024/08/27 19:13 [entrez] AID - rspb20241215 [pii] AID - 10.1098/rspb.2024.1215 [doi] PST - ppublish SO - Proc Biol Sci. 2024 Aug;291(2029):rspb20241215. doi: 10.1098/rspb.2024.1215. Epub 2024 Aug 28. PMID- 38996465 OWN - NLM STAT- MEDLINE DCOM- 20240712 LR - 20241008 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 111 IP - 7 DP - 2024 Jul 11 TI - Charting a landmark-driven path forward for population genetics and ancient DNA research in Africa. PG - 1243-1251 LID - S0002-9297(24)00182-4 [pii] LID - 10.1016/j.ajhg.2024.05.019 [doi] AB - Population history-focused DNA and ancient DNA (aDNA) research in Africa has dramatically increased in the past decade, enabling increasingly fine-scale investigations into the continent's past. However, while international interest in human genomics research in Africa grows, major structural barriers limit the ability of African scholars to lead and engage in such research and impede local communities from partnering with researchers and benefitting from research outcomes. Because conversations about research on African people and their past are often held outside Africa and exclude African voices, an important step for African DNA and aDNA research is moving these conversations to the continent. In May 2023 we held the DNAirobi workshop in Nairobi, Kenya and here we synthesize what emerged most prominently in our discussions. We propose an ideal vision for population history-focused DNA and aDNA research in Africa in ten years' time and acknowledge that to realize this future, we need to chart a path connecting a series of "landmarks" that represent points of consensus in our discussions. These include effective communication across multiple audiences, reframed relationships and capacity building, and action toward structural changes that support science and beyond. We concluded there is no single path to creating an equitable and self-sustaining research ecosystem, but rather many possible routes linking these landmarks. Here we share our diverse perspectives as geneticists, anthropologists, archaeologists, museum curators, and educators to articulate challenges and opportunities for African DNA and aDNA research and share an initial map toward a more inclusive and equitable future. CI - Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Sawchuk, Elizabeth A AU - Sawchuk EA AD - Cleveland Museum of Natural History, Cleveland, OH, USA; Department of Anthropology, University of Alberta, Edmonton, AB, Canada; Department of Anthropology, Stony Brook University, Stony Brook, NY, USA. Electronic address: esawchuk@cmnh.org. FAU - Sirak, Kendra A AU - Sirak KA AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA. Electronic address: kendra_sirak@fas.harvard.edu. FAU - Manthi, Fredrick K AU - Manthi FK AD - National Museums of Kenya, Nairobi, Kenya. FAU - Ndiema, Emmanuel K AU - Ndiema EK AD - National Museums of Kenya, Nairobi, Kenya. FAU - Ogola, Christine A AU - Ogola CA AD - National Museums of Kenya, Nairobi, Kenya. FAU - Prendergast, Mary E AU - Prendergast ME AD - Department of Anthropology, Rice University, Houston, TX, USA. FAU - Reich, David AU - Reich D AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Aluvaala, Eva AU - Aluvaala E AD - Kenya Medical Research Institute, Nairobi, Kenya. FAU - Ayodo, George AU - Ayodo G AD - Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya. FAU - Badji, Lamine AU - Badji L AD - Cultural Engineering Research Unit (URICA) of IFAN-University Cheikh Anta Diop, Dakar, Senegal. FAU - Bird, Nancy AU - Bird N AD - UCL Genetics Institute and Research Department of Genetics, Evolution, and Environment, University College London, London, UK. FAU - Black, Wendy AU - Black W AD - Archaeology Unit, Department of Research & Exhibitions, Iziko Museums of South Africa, Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa. FAU - Fregel, Rosa AU - Fregel R AD - Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain. FAU - Gachihi, Njeri AU - Gachihi N AD - National Museums of Kenya, Nairobi, Kenya. FAU - Gibbon, Victoria E AU - Gibbon VE AD - Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - Gidna, Agness AU - Gidna A AD - Department of Cultural Heritage, Ngorongoro Conservation Area Authority, Arusha, Tanzania. FAU - Goldstein, Steven T AU - Goldstein ST AD - Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA. FAU - Hamad, Reem AU - Hamad R AD - Diversity and Diseases Group, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan. FAU - Hassan, Hisham Y AU - Hassan HY AD - Bahrain Defence Force Hospital, Royal Medical Services, Riffa, Kingdom of Bahrain. FAU - Hayes, Vanessa M AU - Hayes VM AD - School of Medical Sciences, University of Sydney, Sydney, NSW, Australia; School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa. FAU - Hellenthal, Garrett AU - Hellenthal G AD - UCL Genetics Institute and Research Department of Genetics, Evolution, and Environment, University College London, London, UK. FAU - Kebede, Solomon AU - Kebede S AD - Authority for Research and Conservation of Cultural Heritage Ethiopia, Addis Ababa, Ethiopia. FAU - Kurewa, Abdikadir AU - Kurewa A AD - National Museums of Kenya, Nairobi, Kenya; Department of Anthropology, University of Florida, Gainesville, FL, USA. FAU - Kusimba, Chapurukha AU - Kusimba C AD - Department of Anthropology, University of South Florida, Tampa, FL, USA. FAU - Kyazike, Elizabeth AU - Kyazike E AD - Department of History, Archaeology and Heritage Studies, Faculty of Arts and Humanities, Kyambogo University, Kampala, Uganda. FAU - Lane, Paul J AU - Lane PJ AD - Department of Archaeology, University of Cambridge, Cambridge, UK; School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa. FAU - MacEachern, Scott AU - MacEachern S AD - Department of Archaeology and Anthropology, Duke Kunshan University, Kunshan, China. FAU - Massilani, Diyendo AU - Massilani D AD - Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA. FAU - Mbua, Emma AU - Mbua E AD - National Museums of Kenya, Nairobi, Kenya. FAU - Morris, Alan G AU - Morris AG AD - Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - Mutinda, Christina AU - Mutinda C AD - National Museums of Kenya, Nairobi, Kenya. FAU - M'Mbogori, Freda Nkirote AU - M'Mbogori FN AD - National Museums of Kenya, Nairobi, Kenya. FAU - Reynolds, Austin W AU - Reynolds AW AD - Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA. FAU - Tishkoff, Sarah AU - Tishkoff S AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA; Penn Center for Global Genomics & Health Equity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. FAU - Vilar, Miguel AU - Vilar M AD - Department of Anthropology, University of Maryland, College Park, MD, USA. FAU - Yimer, Getnet AU - Yimer G AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA; Penn Center for Global Genomics & Health Equity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - *Genetics, Population MH - Africa MH - Genomics MH - Black People/genetics PMC - PMC11267517 OTO - NOTNLM OT - Africa OT - capacity building OT - community engagement OT - genetics research OT - population history COIS- Declaration of interests The authors declare no competing interests. EDAT- 2024/07/13 07:48 MHDA- 2024/07/13 07:49 PMCR- 2024/07/11 CRDT- 2024/07/12 19:39 PHST- 2024/03/26 00:00 [received] PHST- 2024/05/20 00:00 [revised] PHST- 2024/05/21 00:00 [accepted] PHST- 2024/07/13 07:49 [medline] PHST- 2024/07/13 07:48 [pubmed] PHST- 2024/07/12 19:39 [entrez] PHST- 2024/07/11 00:00 [pmc-release] AID - S0002-9297(24)00182-4 [pii] AID - 10.1016/j.ajhg.2024.05.019 [doi] PST - ppublish SO - Am J Hum Genet. 2024 Jul 11;111(7):1243-1251. doi: 10.1016/j.ajhg.2024.05.019. PMID- 38987254 OWN - NLM STAT- MEDLINE DCOM- 20240710 LR - 20240911 IS - 2052-4463 (Electronic) IS - 2052-4463 (Linking) VI - 11 IP - 1 DP - 2024 Jul 10 TI - Improving data archiving practices in ancient genomics. PG - 754 LID - 10.1038/s41597-024-03563-y [doi] LID - 754 AB - Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data. CI - © 2024. The Author(s). FAU - Bergström, Anders AU - Bergström A AUID- ORCID: 0000-0002-4096-9268 AD - School of Biological Sciences, University of East Anglia, Norwich, UK. a.bergstrom@uea.ac.uk. LA - eng PT - Dataset PT - Journal Article DEP - 20240710 PL - England TA - Sci Data JT - Scientific data JID - 101640192 RN - 0 (DNA, Ancient) SB - IM MH - *Genomics MH - Humans MH - *DNA, Ancient/analysis MH - Animals MH - Metadata PMC - PMC11236975 COIS- The author declares no competing interests. EDAT- 2024/07/11 00:42 MHDA- 2024/07/11 00:43 PMCR- 2024/07/10 CRDT- 2024/07/10 23:14 PHST- 2024/02/19 00:00 [received] PHST- 2024/06/21 00:00 [accepted] PHST- 2024/07/11 00:43 [medline] PHST- 2024/07/11 00:42 [pubmed] PHST- 2024/07/10 23:14 [entrez] PHST- 2024/07/10 00:00 [pmc-release] AID - 10.1038/s41597-024-03563-y [pii] AID - 3563 [pii] AID - 10.1038/s41597-024-03563-y [doi] PST - epublish SO - Sci Data. 2024 Jul 10;11(1):754. doi: 10.1038/s41597-024-03563-y. PMID- 38742634 OWN - NLM STAT- MEDLINE DCOM- 20240704 LR - 20240706 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 52 IP - W1 DP - 2024 Jul 5 TI - DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data. PG - W54-W60 LID - 10.1093/nar/gkae373 [doi] AB - The ability to sequence ancient genomes has revolutionized the way we study evolutionary history by providing access to the most important aspect of evolution-time. Until recently, studying human demography, ecology, biology, and history using population genomic inference relied on contemporary genomic datasets. Over the past decade, the availability of human ancient DNA (aDNA) has increased rapidly, almost doubling every year, opening the way for spatiotemporal studies of ancient human populations. However, the multidimensionality of aDNA, with genotypes having temporal, spatial and genomic coordinates, and integrating multiple sources of data, poses a challenge for developing meta-analyses pipelines. To address this challenge, we developed a publicly-available interactive tool, DORA, which integrates multiple data types, genomic and non-genomic, in a unified interface. This web-based tool enables browsing sample metadata alongside additional layers of information, such as population structure, climatic data, and unpublished samples. Users can perform analyses on genotypes of these samples, or export sample subsets for external analyses. DORA integrates analyses and visualizations in a single intuitive interface, resolving the technical issues of combining datasets from different sources and formats, and allowing researchers to focus on the scientific questions that can be addressed through analysis of aDNA datasets. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research. FAU - Harris, Keith D AU - Harris KD AUID- ORCID: 0000-0003-2162-9652 AD - Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Givat Ram, 9190401 Jerusalem, Israel. FAU - Greenbaum, Gili AU - Greenbaum G AD - Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Givat Ram, 9190401 Jerusalem, Israel. LA - eng PT - Journal Article PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - *Software MH - Genomics/methods MH - Genome, Human MH - Genotype MH - User-Computer Interface MH - Genetics, Population/methods PMC - PMC11223807 EDAT- 2024/05/15 05:44 MHDA- 2024/07/05 05:42 PMCR- 2024/05/14 CRDT- 2024/05/14 06:53 PHST- 2024/04/25 00:00 [accepted] PHST- 2024/04/17 00:00 [revised] PHST- 2024/02/28 00:00 [received] PHST- 2024/07/05 05:42 [medline] PHST- 2024/05/15 05:44 [pubmed] PHST- 2024/05/14 06:53 [entrez] PHST- 2024/05/14 00:00 [pmc-release] AID - 7671306 [pii] AID - gkae373 [pii] AID - 10.1093/nar/gkae373 [doi] PST - ppublish SO - Nucleic Acids Res. 2024 Jul 5;52(W1):W54-W60. doi: 10.1093/nar/gkae373. PMID- 38965340 OWN - NLM STAT- MEDLINE DCOM- 20240704 LR - 20241219 IS - 2399-3642 (Electronic) IS - 2399-3642 (Linking) VI - 7 IP - 1 DP - 2024 Jul 4 TI - Informed proxy consent for ancient DNA research. PG - 815 LID - 10.1038/s42003-024-06413-0 [doi] LID - 815 AB - We argue for implementation of informed proxy or relational autonomy consent in human aDNA research, where the deceased may be represented by living people the research affects. Embracing the underlying principles and process of informed proxy consent has the potential to transform research by (1) enriching outcomes by learning from and collaborating with interested and affected persons; (2) empowering people potentially impacted by research to stipulate evidence for information flow; (3) guarding researchers against actual or perceived violations by providing a common set of guidelines; and (4) highlighting the essential nature of long-term consultation and community partnerships to research outcome success. FAU - Gibbon, Victoria E AU - Gibbon VE AUID- ORCID: 0000-0001-7875-3297 AD - Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Observatory 7935, Cape Town, South Africa. victoria.gibbon@uct.ac.za. FAU - Thompson, Jessica C AU - Thompson JC AUID- ORCID: 0000-0003-1627-4949 AD - Department of Anthropology, Yale University, 10 Sachem Street, New Haven, CT, 06511, USA. AD - Yale Peabody Museum, Yale University, 170 Whitney Avenue, New Haven, CT, 06511, USA. FAU - Alves, Sianne AU - Alves S AD - Office for Inclusivity & Change, Office of the Deputy Vice Chancellor for Transformation: University of Cape Town, Ivan Toms Building, 28 Rhodes Avenue Mowbray, Cape Town, South Africa. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240704 PL - England TA - Commun Biol JT - Communications biology JID - 101719179 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Informed Consent MH - *DNA, Ancient/analysis PMC - PMC11224335 OAB - Embracing the underlying principles and processes of informed proxy consent or relational autonomy consent in human ancient DNA research can transform research. OABL- eng COIS- The authors declare no competing interests. EDAT- 2024/07/05 00:42 MHDA- 2024/07/05 00:43 PMCR- 2024/07/04 CRDT- 2024/07/04 23:32 PHST- 2023/03/27 00:00 [received] PHST- 2024/06/05 00:00 [accepted] PHST- 2024/07/05 00:43 [medline] PHST- 2024/07/05 00:42 [pubmed] PHST- 2024/07/04 23:32 [entrez] PHST- 2024/07/04 00:00 [pmc-release] AID - 10.1038/s42003-024-06413-0 [pii] AID - 6413 [pii] AID - 10.1038/s42003-024-06413-0 [doi] PST - epublish SO - Commun Biol. 2024 Jul 4;7(1):815. doi: 10.1038/s42003-024-06413-0. PMID- 38885310 OWN - NLM STAT- MEDLINE DCOM- 20240710 LR - 20241015 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 41 IP - 7 DP - 2024 Jul 3 TI - Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage. LID - 10.1093/molbev/msae122 [doi] LID - msae122 AB - Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Wang, Mengge AU - Wang M AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - Center for Archaeological Science, Sichuan University, Chengdu 610000, China. AD - Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China. FAU - Huang, Yuguo AU - Huang Y AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. FAU - Liu, Kaijun AU - Liu K AD - School of International Tourism and Culture, Guizhou Normal University, Guiyang 550025, China. AD - MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, Sichuan 610042, China. FAU - Wang, Zhiyong AU - Wang Z AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - School of Forensic Medicine, Kunming Medical University, Kunming 650500, China. FAU - Zhang, Menghan AU - Zhang M AUID- ORCID: 0000-0002-3505-862X AD - Institute of Modern Languages and Linguistics, Fudan University, Shanghai 200433, China. AD - Research Institute of Intelligent Complex Systems, Fudan University, Shanghai 200433, China. FAU - Yuan, Haibing AU - Yuan H AD - Center for Archaeological Science, Sichuan University, Chengdu 610000, China. FAU - Duan, Shuhan AU - Duan S AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - School of Basic Medical Sciences, North Sichuan Medical College, Nanchong 637100, China. FAU - Wei, Lanhai AU - Wei L AD - School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot 010022, China. FAU - Yao, Hongbing AU - Yao H AD - Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou 730000, China. FAU - Sun, Qiuxia AU - Sun Q AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China. FAU - Zhong, Jie AU - Zhong J AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. FAU - Tang, Renkuan AU - Tang R AD - Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China. FAU - Chen, Jing AU - Chen J AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - School of Forensic Medicine, Shanxi Medical University, Jinzhong 030001, China. FAU - Sun, Yuntao AU - Sun Y AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China. FAU - Li, Xiangping AU - Li X AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - School of Forensic Medicine, Kunming Medical University, Kunming 650500, China. FAU - Su, Haoran AU - Su H AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - School of Laboratory Medicine and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China. FAU - Yang, Qingxin AU - Yang Q AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - School of Forensic Medicine, Kunming Medical University, Kunming 650500, China. FAU - Hu, Liping AU - Hu L AD - School of Forensic Medicine, Kunming Medical University, Kunming 650500, China. FAU - Yun, Libing AU - Yun L AD - Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China. FAU - Yang, Junbao AU - Yang J AD - Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China. FAU - Nie, Shengjie AU - Nie S AD - School of Forensic Medicine, Kunming Medical University, Kunming 650500, China. FAU - Cai, Yan AU - Cai Y AD - School of Laboratory Medicine and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China. FAU - Yan, Jiangwei AU - Yan J AD - School of Forensic Medicine, Shanxi Medical University, Jinzhong 030001, China. FAU - Zhou, Kun AU - Zhou K AD - MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, Sichuan 610042, China. FAU - Wang, Chuanchao AU - Wang C AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, China. CN - 10K_CPGDP Consortium FAU - Zhu, Bofeng AU - Zhu B AD - Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China. AD - Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China. FAU - Liu, Chao AU - Liu C AD - Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China. AD - Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China. FAU - He, Guanglin AU - He G AUID- ORCID: 0000-0002-6614-5267 AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China. AD - Center for Archaeological Science, Sichuan University, Chengdu 610000, China. LA - eng GR - 82202078/National Natural Science Foundation of China/ GR - 23&ZD203/Major Project of the National Social Science Foundation of China/ PT - Journal Article PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Human Migration MH - China MH - Male MH - *Chromosomes, Human, Y/genetics MH - DNA, Ancient/analysis MH - Paternal Inheritance MH - Phylogeny MH - East Asian People PMC - PMC11232699 OTO - NOTNLM OT - Y-chromosome phylogeny OT - YanHuang cohort OT - evolutionary history OT - founding lineage COIS- Conflict of Interest The authors declare that they have no competing interests. FIR - He, Guanglin IR - He G FIR - Liu, Chao IR - Liu C FIR - Wang, Mengge IR - Wang M FIR - Tang, Renkuan IR - Tang R FIR - Yun, Libing IR - Yun L FIR - Yang, Junbao IR - Yang J FIR - Wang, Chuan-Chao IR - Wang CC FIR - Yan, Jiangwei IR - Yan J FIR - Zhu, Bofeng IR - Zhu B FIR - Hu, Liping IR - Hu L FIR - Nie, Shengjie IR - Nie S FIR - Yao, Hongbing IR - Yao H EDAT- 2024/06/17 18:43 MHDA- 2024/07/10 06:41 PMCR- 2024/06/17 CRDT- 2024/06/17 14:03 PHST- 2023/08/29 00:00 [received] PHST- 2024/05/30 00:00 [revised] PHST- 2024/06/13 00:00 [accepted] PHST- 2024/07/10 06:41 [medline] PHST- 2024/06/17 18:43 [pubmed] PHST- 2024/06/17 14:03 [entrez] PHST- 2024/06/17 00:00 [pmc-release] AID - 7695223 [pii] AID - msae122 [pii] AID - 10.1093/molbev/msae122 [doi] PST - ppublish SO - Mol Biol Evol. 2024 Jul 3;41(7):msae122. doi: 10.1093/molbev/msae122. PMID- 38913897 OWN - NLM STAT- MEDLINE DCOM- 20240624 LR - 20250104 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 121 IP - 27 DP - 2024 Jul 2 TI - Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders. PG - e2406734121 LID - 10.1073/pnas.2406734121 [doi] LID - e2406734121 AB - The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation. FAU - Sasso, Stefania AU - Sasso S AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Saag, Lehti AU - Saag L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Spros, Rachèl AU - Spros R AD - Research Unit: Archaeology, Environmental Changes and Geo-Chemistry (AMGC), Vrije Universiteit Brussel, 1050 Brussels, Belgium. AD - Research Unit: Social History of Capitalism, Vrije Universiteit Brussel, 1050 Brussels, Belgium. FAU - Beneker, Owyn AU - Beneker O AUID- ORCID: 0000-0003-3553-1672 AD - Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium. FAU - Molinaro, Ludovica AU - Molinaro L AD - Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium. FAU - Biagini, Simone A AU - Biagini SA AUID- ORCID: 0000-0002-4488-3162 AD - Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium. AD - Institut de Biologia Evolutiva, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain. FAU - Lehouck, Alexander AU - Lehouck A AD - Abdijmuseum Ten Duinen, 8670 Koksijde, Belgium. FAU - Van De Vijver, Katrien AU - Van De Vijver K AUID- ORCID: 0000-0002-5188-9749 AD - Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium. FAU - Hui, Ruoyun AU - Hui R AD - Alan Turing Institute, NW1 2DB London, United Kingdom. FAU - D'Atanasio, Eugenia AU - D'Atanasio E AD - Institute of Molecular Biology and Pathology, Italian National Research Council, Rome, Italy. FAU - Kushniarevich, Alena AU - Kushniarevich A AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Kabral, Helja AU - Kabral H AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Metspalu, Ene AU - Metspalu E AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Guellil, Meriam AU - Guellil M AUID- ORCID: 0000-0002-7235-4604 AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Ali, Muhammad Q A AU - Ali MQA AD - Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium. FAU - Geypen, Jan AU - Geypen J AUID- ORCID: 0000-0003-1766-2038 AD - Histories vzw, 1000 Brussels, Belgium. FAU - Hoebreckx, Maxim AU - Hoebreckx M AD - Aron bv, 3740 Bilzen, Belgium. FAU - Berk, Birgit AU - Berk B AD - Birgit Berk Fysische Anthropologie, 6231EC Meerssen, Netherlands. FAU - De Winter, Natasja AU - De Winter N AD - Aron bv, 3740 Bilzen, Belgium. FAU - Driesen, Petra AU - Driesen P AD - Aron bv, 3740 Bilzen, Belgium. FAU - Pijpelink, April AU - Pijpelink A AD - Crematie en Inhumatie Analyse (CRINA) Fysische Antropologie, 5237 JG 's-Hertogenbosch, Netherlands. FAU - Van Damme, Philip AU - Van Damme P AUID- ORCID: 0000-0002-4010-2357 AD - Department of Neurology, KU Leuven and Center for Brain & Disease Research Vlaamse Instituut voor Biotechnologie, 3000 Leuven, Belgium. AD - Department of Neurosciences, KU Leuven and Center for Brain & Disease Research VIB, 3000 Leuven, Belgium. FAU - Scheib, Christiana L AU - Scheib CL AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. AD - Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdom. AD - Department of Archaeology, University of Cambridge, CB2 3DZ Cambridge, United Kingdom. AD - St John's College, University of Cambridge, CB2 1TP Cambridge, United Kingdom. FAU - Deschepper, Ewoud AU - Deschepper E AUID- ORCID: 0000-0003-2568-0391 AD - Historical Archaeology Research Group, Department of Archaeology, Ghent University, 9000 Ghent, Belgium. FAU - Deckers, Pieterjan AU - Deckers P AUID- ORCID: 0000-0002-7033-516X AD - Research Unit: Archaeology, KU Leuven, 3000 Leuven, Belgium. FAU - Snoeck, Christophe AU - Snoeck C AUID- ORCID: 0000-0003-3770-4055 AD - Research Unit: Archaeology, Environmental Changes and Geo-Chemistry (AMGC), Vrije Universiteit Brussel, 1050 Brussels, Belgium. FAU - Dewilde, Marc AU - Dewilde M AD - Flanders Heritage Agency, 1000 Brussels, Belgium. FAU - Ervynck, Anton AU - Ervynck A AUID- ORCID: 0000-0002-2016-8041 AD - Flanders Heritage Agency, 1000 Brussels, Belgium. FAU - Tambets, Kristiina AU - Tambets K AUID- ORCID: 0000-0002-8173-6380 AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Larmuseau, Maarten H D AU - Larmuseau MHD AD - Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium. FAU - Kivisild, Toomas AU - Kivisild T AUID- ORCID: 0000-0002-6297-7808 AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. AD - Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium. LA - eng GR - NA/agentschap Onroerend Erfgoed Archeologie syntheseproject/ GR - G0A4521N/Fonds Wetenschappelijk Onderzoek (FWO)/ GR - STG/18/021/KU Leuven start-up grant/ GR - ZKD6488 C24M/19/075/KU Leuven BOF-C24/ GR - NA/EWI-Vlaanderen citizien science project "MamaMito"/ GR - PRG1027/Estonian Research fundation grant/ GR - NA/Sapienza University Rome fellowship/ PT - Historical Article PT - Journal Article DEP - 20240624 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - History, Medieval MH - *Pedigree MH - Belgium MH - Burial/history MH - Genetics, Population/methods MH - Female MH - Male MH - DNA, Ancient/analysis MH - England MH - Human Migration MH - Archaeology MH - Netherlands MH - Genome, Human PMC - PMC11228521 OTO - NOTNLM OT - Merovingian OT - ancestry OT - ancient DNA OT - kinship COIS- Competing interests statement:The authors declare no competing interest. EDAT- 2024/06/24 18:42 MHDA- 2024/06/24 18:43 PMCR- 2024/12/24 CRDT- 2024/06/24 15:03 PHST- 2024/06/24 18:43 [medline] PHST- 2024/06/24 18:42 [pubmed] PHST- 2024/06/24 15:03 [entrez] PHST- 2024/12/24 00:00 [pmc-release] AID - 202406734 [pii] AID - 10.1073/pnas.2406734121 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2024 Jul 2;121(27):e2406734121. doi: 10.1073/pnas.2406734121. Epub 2024 Jun 24. PMID- 38960861 OWN - NLM STAT- MEDLINE DCOM- 20240717 LR - 20240912 IS - 1367-4811 (Electronic) IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 40 IP - 7 DP - 2024 Jul 1 TI - Unravelling reference bias in ancient DNA datasets. LID - 10.1093/bioinformatics/btae436 [doi] LID - btae436 AB - MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths. RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings. AVAILABILITY AND IMPLEMENTATION: AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts). CI - © The Author(s) 2024. Published by Oxford University Press. FAU - Dolenz, Stephanie AU - Dolenz S AD - Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden. AD - Department of Geological Sciences, Stockholm University, Stockholm, SE-106 91, Sweden. FAU - van der Valk, Tom AU - van der Valk T AUID- ORCID: 0000-0001-6582-3452 AD - Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden. AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden. AD - Science for Life Laboratory, Stockholm, SE-171 65, Sweden. FAU - Jin, Chenyu AU - Jin C AUID- ORCID: 0000-0002-2392-7090 AD - Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden. AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden. AD - Department of Zoology, Stockholm University, Stockholm, SE-106 91, Sweden. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, United States. FAU - Sharif, Muhammad Bilal AU - Sharif MB AD - Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden. AD - Department of Zoology, Stockholm University, Stockholm, SE-106 91, Sweden. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for Anthropobiology and Genomics of Toulouse (CAGT, CNRS UMR5288), University Paul Sabatier, Faculté de Santé, Toulouse, 31000, France. FAU - Shapiro, Beth AU - Shapiro B AD - Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, United States. AD - Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, United States. FAU - Dalén, Love AU - Dalén L AD - Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden. AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden. AD - Department of Zoology, Stockholm University, Stockholm, SE-106 91, Sweden. FAU - Heintzman, Peter D AU - Heintzman PD AUID- ORCID: 0000-0002-6449-0219 AD - Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden. AD - Department of Geological Sciences, Stockholm University, Stockholm, SE-106 91, Sweden. LA - eng GR - 2021.0048/Knut and Alice Wallenberg Foundation/ PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient/analysis MH - Humans MH - *Sequence Analysis, DNA/methods MH - Software MH - Animals MH - Sequence Alignment/methods MH - Computational Biology/methods MH - Algorithms PMC - PMC11254355 COIS- None declared. EDAT- 2024/07/04 00:43 MHDA- 2024/07/18 05:42 PMCR- 2024/07/03 CRDT- 2024/07/03 22:02 PHST- 2023/07/24 00:00 [received] PHST- 2024/03/22 00:00 [revised] PHST- 2024/07/02 00:00 [accepted] PHST- 2024/07/18 05:42 [medline] PHST- 2024/07/04 00:43 [pubmed] PHST- 2024/07/03 22:02 [entrez] PHST- 2024/07/03 00:00 [pmc-release] AID - 7705522 [pii] AID - btae436 [pii] AID - 10.1093/bioinformatics/btae436 [doi] PST - ppublish SO - Bioinformatics. 2024 Jul 1;40(7):btae436. doi: 10.1093/bioinformatics/btae436. PMID- 38813936 OWN - NLM STAT- MEDLINE DCOM- 20240615 LR - 20240615 IS - 1932-8494 (Electronic) IS - 1932-8486 (Linking) VI - 307 IP - 7 DP - 2024 Jul TI - How the Sima de los Huesos was won. PG - 2225-2245 LID - 10.1002/ar.25509 [doi] AB - Although the first discovery of a human fossil in the Sima de los Huesos took place in 1976, systematic excavations did not begin there until 1984. Since then, this site has been continuously excavated in month-long camps. The site is dated by different radiometric techniques to between 430,000 and 300,000 years ago. Until the 2023 campaign, just over 7000 human fossils have been recovered, constituting the largest collection of fossils prior to Homo sapiens ever discovered. The fossils correspond to a minimum of 29 individuals of both sexes and different ages at death, from preadolescents to a specimen of advanced age. Comparative anatomy and ancient DNA studies both suggest that this is a population closely related to Homo neanderthalensis. The great variety and extraordinary quality of the fossils recovered have allowed us to carry out a series of investigations that have greatly increased our knowledge about the evolution of Homo in the Middle Pleistocene. Among the most important discoveries, it has been possible to establish body size and proportions, the confirmation that the origin of the accumulation of human fossils was of an anthropic nature, that those past humans took care of disabled individuals and who were capable of having an oral language almost as complex and efficient as that of our own species. CI - © 2024 The Author(s). The Anatomical Record published by Wiley Periodicals LLC on behalf of American Association for Anatomy. FAU - Arsuaga, Juan-Luis AU - Arsuaga JL AD - Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain. AD - Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain. FAU - Martínez, Ignacio AU - Martínez I AUID- ORCID: 0000-0002-1835-9199 AD - Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Universidad de Alcalá, Alcalá de Henares, Spain. FAU - Gracia-Téllez, Ana AU - Gracia-Téllez A AD - Departamento de Geología, Geografía y Medio Ambiente, Área de Paleontología, Facultad de Ciencias, Universidad de Alcalá, Madrid, Spain. FAU - Carretero, José-Miguel AU - Carretero JM AUID- ORCID: 0000-0003-0409-8087 AD - Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain. AD - Laboratorio de Evolución Humana, Universidad de Burgos, Burgos, Spain. AD - Unidad Asociada de I+D+i al CSIC Vidrio y Materiales del Patrimonio Cultural (VIMPAC), Burgos, Spain. FAU - Esquivel, Alfonso AU - Esquivel A AD - Fundación Ciudad de la Energía - CIUDEN, F.S.P. Cl. de la Energía, Ponferrada, Spain. FAU - García, Nuria AU - García N AD - Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain. AD - Grupo UCM Ecosistemas Cuaternarios Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain. FAU - Lorenzo, Carlos AU - Lorenzo C AD - Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Àrea de Prehistòria, Tarragona, Spain. AD - Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain. FAU - Quam, Rolf AU - Quam R AUID- ORCID: 0000-0002-1140-5615 AD - Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain. AD - Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Universidad de Alcalá, Alcalá de Henares, Spain. AD - Department of Anthropology, Binghamton University (SUNY), New York, New York, USA. AD - Division of Anthropology, American Museum of Natural History, New York, New York, USA. FAU - Aramburu, Arantza AU - Aramburu A AD - Departamento de Geología, Área de Mineralogía y Petrología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-/Euskal Herriko Unibertsitatea, Leioa, Spain. FAU - Sala, Nohemi AU - Sala N AD - Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain. AD - Centro Nacional de Investigación sobre Evolución Humana-CENIEH, Burgos, Spain. FAU - Trueba, Javier AU - Trueba J AD - Madrid Scientific Films, Villanueva de la Cañada, Spain. LA - eng GR - PID2021-122355NB-C31 supported by MCIN/AEI/10.1303/Government of Spain/ GR - Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá)/ GR - EPU-INV-UAH/2022/006/Universidad de Alcalá/ PT - Historical Article PT - Journal Article DEP - 20240530 PL - United States TA - Anat Rec (Hoboken) JT - Anatomical record (Hoboken, N.J. : 2007) JID - 101292775 SB - IM MH - Humans MH - *Fossils MH - Animals MH - *Biological Evolution MH - Female MH - Male MH - Hominidae/anatomy & histology MH - Spain OTO - NOTNLM OT - Atapuerca OT - history of the discoveries OT - homo OT - human evolution OT - middle Pleistocene EDAT- 2024/05/30 12:44 MHDA- 2024/06/15 10:45 CRDT- 2024/05/30 07:43 PHST- 2024/04/22 00:00 [revised] PHST- 2024/03/29 00:00 [received] PHST- 2024/05/09 00:00 [accepted] PHST- 2024/06/15 10:45 [medline] PHST- 2024/05/30 12:44 [pubmed] PHST- 2024/05/30 07:43 [entrez] AID - 10.1002/ar.25509 [doi] PST - ppublish SO - Anat Rec (Hoboken). 2024 Jul;307(7):2225-2245. doi: 10.1002/ar.25509. Epub 2024 May 30. PMID- 38796876 OWN - NLM STAT- MEDLINE DCOM- 20240616 LR - 20240616 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 71 DP - 2024 Jul TI - Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes. PG - 103060 LID - S1872-4973(24)00054-1 [pii] LID - 10.1016/j.fsigen.2024.103060 [doi] AB - In the Battle of Crete during the World War II occupation of Greece, the German forces faced substantial civilian resistance. To retribute the numerous German losses, a series of mass executions took place in numerous places in Crete; a common practice reported from Greece and elsewhere. In Adele, a village in the regional unit of Rethymnon, 18 male civilians were executed and buried in a burial pit at the Sarakina site. In this study, the first one conducted for a conflict that occurred in Greece, we identified for humanitarian purposes the 18 skulls of the Sarakina victims, following a request from the local community of Adele. The molecular identification of historical human remains via ancient DNA approaches and low coverage whole genome sequencing has only recently been introduced. Here, we performed genome skimming on the living relatives of the victims, as well as high throughput historical DNA analysis on the skulls to infer the kinship degrees among the victims via genetic relatedness analyses. We also conducted targeted anthropological analysis to successfully complete the identification of all Sarakina victims. We demonstrate that our methodological approach constitutes a potentially highly informative forensic tool to identify war victims. It can hence be applied to analogous studies on degraded DNA, thus, paving the path for systematic war victim identification in Greece and beyond. CI - Copyright © 2024 Elsevier B.V. All rights reserved. FAU - Psonis, Nikolaos AU - Psonis N AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece. Electronic address: nikos.psonis@gmail.com. FAU - Vassou, Despoina AU - Vassou D AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece. FAU - Nafplioti, Argyro AU - Nafplioti A AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece. FAU - Tabakaki, Eugenia AU - Tabakaki E AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece. FAU - Pavlidis, Pavlos AU - Pavlidis P AD - Institute of Computer Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Irakleio 70013, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio 70013, Greece. FAU - Stamatakis, Alexandros AU - Stamatakis A AD - Institute of Computer Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Irakleio 70013, Greece; Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany. FAU - Poulakakis, Nikos AU - Poulakakis N AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece; Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio 70013, Greece. LA - eng PT - Historical Article PT - Journal Article DEP - 20240514 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - *World War II MH - Male MH - Greece MH - *DNA Fingerprinting MH - Skull MH - Genome, Human MH - Forensic Anthropology MH - Whole Genome Sequencing OTO - NOTNLM OT - Ancient DNA OT - Genome skimming OT - Kinship relationships OT - Next Generation Sequencing OT - Relatedness analysis COIS- Declaration of Competing Interest The authors have no conflict of interest to declare EDAT- 2024/05/27 00:42 MHDA- 2024/06/17 00:42 CRDT- 2024/05/26 18:01 PHST- 2023/11/07 00:00 [received] PHST- 2024/04/22 00:00 [revised] PHST- 2024/05/05 00:00 [accepted] PHST- 2024/06/17 00:42 [medline] PHST- 2024/05/27 00:42 [pubmed] PHST- 2024/05/26 18:01 [entrez] AID - S1872-4973(24)00054-1 [pii] AID - 10.1016/j.fsigen.2024.103060 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2024 Jul;71:103060. doi: 10.1016/j.fsigen.2024.103060. Epub 2024 May 14. PMID- 38676702 OWN - NLM STAT- MEDLINE DCOM- 20240603 LR - 20240603 IS - 1755-0998 (Electronic) IS - 1755-098X (Linking) VI - 24 IP - 5 DP - 2024 Jul TI - Benchmarking kinship estimation tools for ancient genomes using pedigree simulations. PG - e13960 LID - 10.1111/1755-0998.13960 [doi] AB - There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F(1) scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F(1) > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes. CI - © 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. FAU - Aktürk, Şevval AU - Aktürk Ş AUID- ORCID: 0000-0003-4157-6551 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Mapelli, Igor AU - Mapelli I AUID- ORCID: 0000-0001-9814-7884 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Güler, Merve N AU - Güler MN AUID- ORCID: 0000-0001-7766-9333 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Gürün, Kanat AU - Gürün K AUID- ORCID: 0000-0002-0433-2593 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Katırcıoğlu, Büşra AU - Katırcıoğlu B AUID- ORCID: 0009-0006-4095-9728 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Vural, Kıvılcım Başak AU - Vural KB AUID- ORCID: 0000-0003-3964-3065 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Sağlıcan, Ekin AU - Sağlıcan E AUID- ORCID: 0000-0001-8646-1163 AD - Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey. FAU - Çetin, Mehmet AU - Çetin M AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Yaka, Reyhan AU - Yaka R AUID- ORCID: 0000-0002-9359-4391 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. AD - Centre for Palaeogenetics, Stockholm, Sweden. AD - Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Sürer, Elif AU - Sürer E AUID- ORCID: 0000-0002-0738-6669 AD - Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey. FAU - Atağ, Gözde AU - Atağ G AUID- ORCID: 0000-0001-6173-3126 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Çokoğlu, Sevim Seda AU - Çokoğlu SS AUID- ORCID: 0000-0002-1055-3966 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Sevkar, Arda AU - Sevkar A AUID- ORCID: 0000-0003-4573-6778 AD - Department of Anthropology, Hacettepe University, Ankara, Turkey. FAU - Altınışık, N Ezgi AU - Altınışık NE AUID- ORCID: 0000-0003-0653-4292 AD - Department of Anthropology, Hacettepe University, Ankara, Turkey. FAU - Koptekin, Dilek AU - Koptekin D AUID- ORCID: 0000-0003-2664-5774 AD - Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey. FAU - Somel, Mehmet AU - Somel M AUID- ORCID: 0000-0002-3138-1307 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. LA - eng PT - Evaluation Study PT - Journal Article DEP - 20240427 PL - England TA - Mol Ecol Resour JT - Molecular ecology resources JID - 101465604 RN - 0 (DNA, Ancient) SB - IM MH - *Pedigree MH - *Benchmarking/methods MH - *Polymorphism, Single Nucleotide MH - Humans MH - Gene Frequency MH - DNA, Ancient/analysis MH - Computer Simulation MH - Genetics, Population/methods MH - Computational Biology/methods OTO - NOTNLM OT - ancient DNA OT - inbreeding OT - kinship coefficient estimation OT - low coverage OT - pedigree simulation EDAT- 2024/04/28 07:23 MHDA- 2024/06/03 06:42 CRDT- 2024/04/27 09:53 PHST- 2024/03/19 00:00 [revised] PHST- 2023/11/25 00:00 [received] PHST- 2024/03/28 00:00 [accepted] PHST- 2024/06/03 06:42 [medline] PHST- 2024/04/28 07:23 [pubmed] PHST- 2024/04/27 09:53 [entrez] AID - 10.1111/1755-0998.13960 [doi] PST - ppublish SO - Mol Ecol Resour. 2024 Jul;24(5):e13960. doi: 10.1111/1755-0998.13960. Epub 2024 Apr 27. PMID- 38926415 OWN - NLM STAT- MEDLINE DCOM- 20240626 LR - 20240814 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 14 IP - 1 DP - 2024 Jun 26 TI - Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool. PG - 14720 LID - 10.1038/s41598-024-64818-7 [doi] LID - 14720 AB - Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution's Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of Treponema pallidum subsp. pallidum and Mycobacterium tuberculosis complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of T. p. pallidum DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections. CI - © 2024. The Author(s). FAU - Austin, Rita M AU - Austin RM AD - Frontiers in Evolutionary Zoology Research Group, Natural History Museum of Oslo, University of Oslo, Oslo, 0562, Norway. austinrmca@gmail.com. AD - Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA. austinrmca@gmail.com. AD - Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA. austinrmca@gmail.com. AD - Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA. austinrmca@gmail.com. FAU - Honap, Tanvi P AU - Honap TP AD - Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA. AD - Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA. FAU - Mann, Allison E AU - Mann AE AD - Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA. FAU - Hübner, Alexander AU - Hübner A AD - Department Archaeogenetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. FAU - DeGaglia, Cassandra M S AU - DeGaglia CMS AD - Department of Anthropology, Tulane University, New Orleans, LA, 70118, USA. FAU - Warinner, Christina AU - Warinner C AD - Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA. FAU - Zuckerman, Molly K AU - Zuckerman MK AD - Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Mississippi State, MS, 39762, USA. mkz12@msstate.edu. FAU - Hofman, Courtney A AU - Hofman CA AD - Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA. courtney.hofman@ou.edu. AD - Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA. courtney.hofman@ou.edu. AD - Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA. courtney.hofman@ou.edu. LA - eng GR - Pre-doctoral Fellowship/Smithsonian Institution, National Museum of Natural History, United States/ GR - NSF BCS-1643318/National Science Foundation, United States/ GR - NSF BCS-1643318/National Science Foundation, United States/ GR - NSF BCS-1643318/National Science Foundation, United States/ PT - Historical Article PT - Journal Article DEP - 20240626 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Bacterial) SB - IM EIN - Sci Rep. 2024 Aug 12;14(1):18723. doi: 10.1038/s41598-024-69609-8. PMID: 39134606 MH - *Dental Calculus/microbiology/history MH - Humans MH - *Metagenomics/methods MH - *Paleopathology/methods MH - *Tuberculosis/diagnosis/microbiology MH - *Mycobacterium tuberculosis/genetics/isolation & purification MH - DNA, Bacterial/genetics MH - Male MH - Treponema pallidum/genetics/isolation & purification MH - Syphilis/diagnosis/microbiology/history MH - Female MH - Adult MH - Metagenome/genetics MH - Middle Aged PMC - PMC11208530 OTO - NOTNLM OT - Ancient DNA OT - Dental calculus OT - Interdisciplinary OT - Pathogen identification OT - Robert J. Terry Collection OT - Tuberculosis COIS- The authors declare no competing interests. EDAT- 2024/06/27 00:42 MHDA- 2024/06/27 00:43 PMCR- 2024/06/26 CRDT- 2024/06/26 23:28 PHST- 2024/01/27 00:00 [received] PHST- 2024/06/13 00:00 [accepted] PHST- 2024/06/27 00:43 [medline] PHST- 2024/06/27 00:42 [pubmed] PHST- 2024/06/26 23:28 [entrez] PHST- 2024/06/26 00:00 [pmc-release] AID - 10.1038/s41598-024-64818-7 [pii] AID - 64818 [pii] AID - 10.1038/s41598-024-64818-7 [doi] PST - epublish SO - Sci Rep. 2024 Jun 26;14(1):14720. doi: 10.1038/s41598-024-64818-7. PMID- 38691462 OWN - NLM STAT- MEDLINE DCOM- 20240625 LR - 20240625 IS - 2666-1667 (Electronic) IS - 2666-1667 (Linking) VI - 5 IP - 2 DP - 2024 Jun 21 TI - Protocol for a comprehensive pipeline to study ancient human genomes. PG - 102985 LID - S2666-1667(24)00150-3 [pii] LID - 10.1016/j.xpro.2024.102985 [doi] LID - 102985 AB - Ancient genomics has revolutionized our understanding of human evolution and migration history in recent years. Here, we present a protocol to prepare samples for ancient genomics research. We describe steps for releasing DNA from human remains, DNA library construction, hybridization capture, quantification, and sequencing. We then detail procedures for mapping sequence reads and population genetics analysis. This protocol also outlines challenges in extracting ancient DNA samples and authenticating ancient DNA to uncover the genetic history and diversity of ancient populations. For complete details on the use and execution of this protocol, please refer to Tao et al.(1). CI - Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Zhu, Kongyang AU - Zhu K AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - He, Haifeng AU - He H AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Tao, Le AU - Tao L AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Ma, Hao AU - Ma H AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Yang, Xiaomin AU - Yang X AD - Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China. FAU - Wang, Rui AU - Wang R AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Guo, Jianxin AU - Guo J AD - Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China. Electronic address: jxguo@xmu.edu.cn. FAU - Wang, Chuan-Chao AU - Wang CC AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen, Fujian 361005, China. Electronic address: wang@xmu.edu.cn. LA - eng PT - Journal Article DEP - 20240430 PL - United States TA - STAR Protoc JT - STAR protocols JID - 101769501 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Genome, Human/genetics MH - *DNA, Ancient/analysis MH - *Genomics/methods MH - Sequence Analysis, DNA/methods MH - Gene Library MH - Genetics, Population/methods PMC - PMC11070629 OTO - NOTNLM OT - Genetics OT - Genomics OT - Sequence analysis OT - Sequencing COIS- Declaration of interests The authors declare no competing interests. EDAT- 2024/05/01 18:52 MHDA- 2024/06/25 06:42 PMCR- 2024/04/30 CRDT- 2024/05/01 12:36 PHST- 2023/10/12 00:00 [received] PHST- 2023/11/19 00:00 [revised] PHST- 2024/03/11 00:00 [accepted] PHST- 2024/06/25 06:42 [medline] PHST- 2024/05/01 18:52 [pubmed] PHST- 2024/05/01 12:36 [entrez] PHST- 2024/04/30 00:00 [pmc-release] AID - S2666-1667(24)00150-3 [pii] AID - 102985 [pii] AID - 10.1016/j.xpro.2024.102985 [doi] PST - ppublish SO - STAR Protoc. 2024 Jun 21;5(2):102985. doi: 10.1016/j.xpro.2024.102985. Epub 2024 Apr 30. PMID- 38781957 OWN - NLM STAT- MEDLINE DCOM- 20240618 LR - 20240620 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 34 IP - 12 DP - 2024 Jun 17 TI - Ancient genomes revealed the complex human interactions of the ancient western Tibetans. PG - 2594-2605.e7 LID - S0960-9822(24)00581-5 [pii] LID - 10.1016/j.cub.2024.04.068 [doi] AB - The western Tibetan Plateau is the crossroad between the Tibetan Plateau, Central Asia, and South Asia, and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500-300 years before present (BP) in the Ngari prefecture. The ancient western Tibetan Plateau populations share the majority of their genetic components with the southern Tibetan Plateau populations and have maintained genetic continuity since 3,500 BP while maintaining interactions with populations within and outside the Tibetan Plateau. Within the Tibetan Plateau, the ancient western Tibetan Plateau populations were influenced by the additional expansion from the south to the southwest plateau before 1,800 BP. Outside the Tibetan Plateau, the western Tibetan Plateau populations interacted with both South and Central Asian populations at least 2,000 years ago, and the South Asian-related genetic influence, despite being very limited, was from the Indus Valley Civilization (IVC) migrants in Central Asia instead of the IVC populations from the Indus Valley. In light of the new genetic data, our study revealed the complex population interconnections across and within the Tibetan Plateau. CI - Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Bai, Fan AU - Bai F AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Liu, Yichen AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Wangdue, Shargan AU - Wangdue S AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China. FAU - Wang, Tianyi AU - Wang T AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China. FAU - He, Wei AU - He W AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China. FAU - Xi, Lin AU - Xi L AD - Shaanxi Academy of Archaeology, Xi'an 710054, China. FAU - Tsho, Yang AU - Tsho Y AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China. FAU - Tsering, Tashi AU - Tsering T AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. FAU - Dai, Qingyan AU - Dai Q AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. FAU - Liu, Feng AU - Liu F AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. FAU - Zhang, Ming AU - Zhang M AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. FAU - Ran, Jingkun AU - Ran J AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Ping, Wanjing AU - Ping W AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. FAU - Payon, Danzin AU - Payon D AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China. FAU - Mao, Xiaowei AU - Mao X AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. FAU - Tong, Yan AU - Tong Y AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China. FAU - Tsring, Tinley AU - Tsring T AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China. FAU - Chen, Zehui AU - Chen Z AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng PT - Journal Article DEP - 20240522 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - Tibetan people SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - East Asian People/genetics MH - Genetics, Population MH - *Genome, Human MH - *Human Migration/history MH - Tibet OTO - NOTNLM OT - Indus Valley Civilization OT - ancient DNA OT - ancient population history OT - ancient population interactions OT - descent practice OT - southern Tibetan Plateau OT - western Tibetan Plateau COIS- Declaration of interests The authors declare no competing interests. EDAT- 2024/05/24 00:42 MHDA- 2024/06/19 00:43 CRDT- 2024/05/23 18:42 PHST- 2023/09/21 00:00 [received] PHST- 2023/12/21 00:00 [revised] PHST- 2024/04/29 00:00 [accepted] PHST- 2024/06/19 00:43 [medline] PHST- 2024/05/24 00:42 [pubmed] PHST- 2024/05/23 18:42 [entrez] AID - S0960-9822(24)00581-5 [pii] AID - 10.1016/j.cub.2024.04.068 [doi] PST - ppublish SO - Curr Biol. 2024 Jun 17;34(12):2594-2605.e7. doi: 10.1016/j.cub.2024.04.068. Epub 2024 May 22. PMID- 38870299 OWN - NLM STAT- MEDLINE DCOM- 20240613 LR - 20240621 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 384 IP - 6701 DP - 2024 Jun 14 TI - Sacrificed Maya boys tied to myth of 'Hero Twins'. PG - 1160-1161 LID - 10.1126/science.adr0288 [doi] AB - Ancient DNA shows continuity between living and ancient Maya communities. FAU - Curry, Andrew AU - Curry A LA - eng PT - Historical Article PT - News DEP - 20240613 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Female MH - Humans MH - Male MH - *DNA, Ancient MH - History, Ancient MH - *Twins/history MH - Child MH - *Ceremonial Behavior MH - *Civilization/history EDAT- 2024/06/13 18:42 MHDA- 2024/06/13 18:43 CRDT- 2024/06/13 14:03 PHST- 2024/06/13 18:43 [medline] PHST- 2024/06/13 18:42 [pubmed] PHST- 2024/06/13 14:03 [entrez] AID - 10.1126/science.adr0288 [doi] PST - ppublish SO - Science. 2024 Jun 14;384(6701):1160-1161. doi: 10.1126/science.adr0288. Epub 2024 Jun 13. PMID- 38284317 OWN - NLM STAT- MEDLINE DCOM- 20240515 LR - 20240603 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 81 IP - 3 DP - 2024 Jun 3 TI - Suggested mechanism of CCR5Δ32, CCR2-64I and SDF 1-3'A allele frequency change in Polish and Lithuanian gene pools from the perspective of passing time. PG - 261-280 AB - The study aimed to determine the frequency of the alleles associated with hereditary immune response in 16 historical populations and assess which evolutionary forces may have contributed to the observed frequency fluctuation. The analysed polymorphic sites are located in three genes - CCR5, CCR2 and SDF 1 (CXCL12). Protein products are involved in the innate immune response and are also involved in various types of infections, autoimmune diseases and tumours. The frequency of the alleles found in the DNA of the studied individuals was determined by the Sanger methodology and was compared with the data obtained for modern populations. To confirm the authenticity of the obtained results, mtDNA HVRI haplotypes of all the studied samples were obtained and compared with the genetic database of the laboratory personnel who came into contact with the studied material. Based on the variability of allele frequency, advanced biostatistical analysis was used to distinguish the effect of natural selection from genetic drift, i.e. the forces operating on the polymorphic sites studied. All procedures were performed according to the guidelines for working with ancient DNA to avoid contamination with modern DNA molecules. 681 samples from 39 archaeological sites in Poland and Lithuania dated to the 40(th) century BC and the 19(th) century were studied. The biostatistical analysis showed that the fluctuations in the frequency of CCR5Δ32 in the analysed time interval could be mainly the effect of genetic drift. Nevertheless, for CCR2-64I and SDF 1-3'A, the results confirm the suggestion of negative selection as the mechanism involved. Since all the polymorphic sites encode the elements of innate immune response that are indirectly associated with the process of an HPV infection and the development of cervical cancer, the human papillomavirus may be a good candidate for a selection coefficient affecting the frequency of CCR2-64I and SDF 1-3'A. However, for CCR5Δ32, selection was not detected despite its proven role in the molecular mechanism involved in the response to an HPV infection. The presented work seems to be the first in which the problem of the pattern of CCR5Δ32, CCR2-64I and SDF 1-3'A frequency fluctuations in a temporal perspective was discussed, proposing HPV as a factor influencing the occurrence of the CCR2 and SDF1 alleles. FAU - Śledziński, Łukasz J AU - Śledziński ŁJ AD - Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland. AD - Department of Molecular Biology, Medical University of Lodz, Lodz, Poland. FAU - Zamerska, Alicja AU - Zamerska A AD - Department of Molecular Biology, Medical University of Lodz, Lodz, Poland. FAU - Jędrychowska-Dańska, Krystyna AU - Jędrychowska-Dańska K AD - Department of Molecular Biology, Medical University of Lodz, Lodz, Poland. FAU - Strózik, Tadeusz AU - Strózik T AD - Department of Molecular Biology, Medical University of Lodz, Lodz, Poland. FAU - Wasiak, Tomasz AU - Wasiak T AD - Department of Molecular Biology, Medical University of Lodz, Lodz, Poland. FAU - Płoszaj, Tomasz AU - Płoszaj T AD - Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland. AD - Department of Molecular Biology, Medical University of Lodz, Lodz, Poland. FAU - Witas, Piotr AU - Witas P AD - Department of Molecular Biology, Medical University of Lodz, Lodz, Poland. FAU - Witas, Henryk W AU - Witas HW AD - Department of Molecular Biology, Medical University of Lodz, Lodz, Poland. FAU - Borowiec, Maciej AU - Borowiec M AD - Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland. FAU - Agier, Justyna AU - Agier J AD - Department of Microbiology, Genetics and Experimental Immunology, Medical University of Lodz, Lodz, Poland. LA - eng PT - Journal Article PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 SB - IM MH - Humans MH - Lithuania MH - *Receptors, CCR5/genetics MH - *Receptors, CCR2/genetics MH - Poland MH - *Gene Frequency MH - *Chemokine CXCL12/genetics MH - Haplotypes MH - DNA, Mitochondrial/genetics MH - Polymorphism, Genetic EDAT- 2024/01/29 06:43 MHDA- 2024/05/15 06:42 CRDT- 2024/01/29 05:42 PHST- 2022/04/07 00:00 [received] PHST- 2023/11/08 00:00 [revised] PHST- 2023/11/16 00:00 [accepted] PHST- 2024/05/15 06:42 [medline] PHST- 2024/01/29 06:43 [pubmed] PHST- 2024/01/29 05:42 [entrez] AID - 10.1127/anthranz/2024/1637 [doi] PST - ppublish SO - Anthropol Anz. 2024 Jun 3;81(3):261-280. doi: 10.1127/anthranz/2024/1637. PMID- 38986104 OWN - NLM STAT- MEDLINE DCOM- 20240710 LR - 20240917 IS - 1958-5381 (Electronic) IS - 0767-0974 (Linking) VI - 40 IP - 6-7 DP - 2024 Jun-Jul TI - [Ancient DNA speaks]. PG - 563-565 LID - 10.1051/medsci/2024070 [doi] AB - Many human DNA sequences have been obtained from ancient remains dating back from several millennia. However, these have low coverage and may contain many errors; this has limited their usefulness for many analyses, in particular the search for Identical By Descent (IBD) segments that is very powerful for detection of kinship. A new method, using imputation from database data and sophisticated statistical analysis, proves able to detect IBD segments (and thus parenthood) in low-quality DNA sequences from individuals linked only by sixth degree parenthood, opening a whole new field of investigation using ancient DNA. CI - © 2024 médecine/sciences – Inserm. FAU - Jordan, Bertrand AU - Jordan B AD - Biologiste, généticien et immunologiste, Président d'Aprogène (Association pour la promotion de la Génomique), 13007 Marseille, France. LA - fre PT - News TT - L’ADN ancien parle de plus en plus. DEP - 20240708 PL - France TA - Med Sci (Paris) JT - Medecine sciences : M/S JID - 8710980 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - Sequence Analysis, DNA/methods MH - Pedigree EDAT- 2024/07/10 18:42 MHDA- 2024/07/10 18:43 CRDT- 2024/07/10 16:42 PHST- 2024/07/10 18:43 [medline] PHST- 2024/07/10 18:42 [pubmed] PHST- 2024/07/10 16:42 [entrez] AID - msc240090 [pii] AID - 10.1051/medsci/2024070 [doi] PST - ppublish SO - Med Sci (Paris). 2024 Jun-Jul;40(6-7):563-565. doi: 10.1051/medsci/2024070. Epub 2024 Jul 8. PMID- 38447923 OWN - NLM STAT- MEDLINE DCOM- 20240422 LR - 20240422 IS - 1095-9513 (Electronic) IS - 1055-7903 (Linking) VI - 195 DP - 2024 Jun TI - Origin and dispersal of the Mycobacterium tuberculosis Haarlem genotype: Clues from its phylogeographic landscape and human migration. PG - 108045 LID - S1055-7903(24)00037-X [pii] LID - 10.1016/j.ympev.2024.108045 [doi] AB - The Haarlem family belongs to the Euro-American phylogenetic lineage of Mycobacterium tuberculosis and is one of the globally spread genotypes of this important human pathogen. In spite of the sporadic observations on drug resistance and peculiar virulence profile, Haarlem remains in the shade of other M. tuberculosis genotypes. I analyzed genotyping data of the Haarlem genotype in light of its pathogenic properties and relevant human migration, to gain insight into its origin, evolutionary history, and current spread. Central Europe is marked with a very high prevalence of both major Haarlem subclades ancestral H3/SIT50 and derived H1, jointly making 33-41% in Czechia, Austria, and Hungary. There is a declining gradient of Haarlem beyond central Europe with 10-18% in Italy, France, Belgium, 10-13% in the Balkan countries and Turkey. Placing the available genetic diversity and ancient DNA data within the historical context, I hypothesize that M. tuberculosis Haarlem genotype likely originated in Central Europe and its primary long-term circulation occurred within the area of the former Austria/Austria-Hungary Empire in the 14th-19th centuries. The genotype is not highly transmissible and its spread was driven by long-term human migration. The European colonial expansion (when accompanied by a sufficient volume of migration) was a vehicle of its secondary dissemination. I conclude that human migration and its lack thereof (but not strain pathobiology) was a major driving force that shaped the population structure of this global lineage of M. tuberculosis. At the same time, Haarlem strains appear over-represented in some ethnic groups which warrants in-depth experimental research. CI - Copyright © 2024 Elsevier Inc. All rights reserved. FAU - Mokrousov, Igor AU - Mokrousov I AD - Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia; Henan International Joint Laboratory of Children's Infectious Diseases, Henan Children's Hospital, Children's Hospital, Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China. Electronic address: imokrousov@mail.ru. LA - eng PT - Journal Article DEP - 20240304 PL - United States TA - Mol Phylogenet Evol JT - Molecular phylogenetics and evolution JID - 9304400 SB - IM MH - Humans MH - *Mycobacterium tuberculosis/genetics MH - Phylogeny MH - *Tuberculosis/microbiology MH - Human Migration MH - Genotype OTO - NOTNLM OT - Austria-Hungary state OT - Euro-American lineage OT - Haarlem genotype OT - Mycobacterium tuberculosis OT - Phylogeography OT - VNTR COIS- Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. EDAT- 2024/03/07 00:42 MHDA- 2024/04/22 06:44 CRDT- 2024/03/06 19:20 PHST- 2023/07/11 00:00 [received] PHST- 2024/01/04 00:00 [revised] PHST- 2024/02/27 00:00 [accepted] PHST- 2024/04/22 06:44 [medline] PHST- 2024/03/07 00:42 [pubmed] PHST- 2024/03/06 19:20 [entrez] AID - S1055-7903(24)00037-X [pii] AID - 10.1016/j.ympev.2024.108045 [doi] PST - ppublish SO - Mol Phylogenet Evol. 2024 Jun;195:108045. doi: 10.1016/j.ympev.2024.108045. Epub 2024 Mar 4. PMID- 38308451 OWN - NLM STAT- MEDLINE DCOM- 20240516 LR - 20240716 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 184 IP - 2 DP - 2024 Jun TI - Bioanthropological analysis of human remains from the archaic and classic period discovered in Puyil cave, Mexico. PG - e24903 LID - 10.1002/ajpa.24903 [doi] AB - OBJECTIVES: Determine the geographic place of origin and maternal lineage of prehistoric human skeletal remains discovered in Puyil Cave, Tabasco State, Mexico, located in a region currently populated by Olmec, Zoque and Maya populations. MATERIALS AND METHODS: All specimens were radiocarbon ((14)C) dated (beta analytic), had dental modifications classified, and had an analysis of 13 homologous reference points conducted to evaluate artificial cranial deformation (ACD). Following DNA purification, hypervariable region I (HVR-1) of the mitogenome was amplified and Sanger sequenced. Finally, Next Generation Sequencing (NGS) was performed for total DNA. Mitochondrial DNA (mtDNA) variants and haplogroups were determined using BioEdit 7.2 and IGV software and confirmed with MITOMASTER and WebHome softwares. RESULTS: Radiocarbon dating ((14)C) demonstrated that the inhabitants of Puyil Cave lived during the Archaic and Classic Periods and displayed tabular oblique and tabular mimetic ACD. These pre-Hispanic remains exhibited five mtDNA lineages: A, A2, C1, C1c and D4. Network analysis revealed a close genetic affinity between pre-Hispanic Puyil Cave inhabitants and contemporary Maya subpopulations from Mexico and Guatemala, as well as individuals from Bolivia, Brazil, the Dominican Republic, and China. CONCLUSIONS: Our results elucidate the dispersal of pre-Hispanic Olmec and Maya ancestors and suggest that ACD practices are closely related to Olmec and Maya practices. Additionally, we conclude that ACD has likely been practiced in the region since the Middle-Archaic Period. CI - © 2024 The Authors. American Journal of Biological Anthropology published by Wiley Periodicals LLC. FAU - Navarro-Romero, María Teresa AU - Navarro-Romero MT AUID- ORCID: 0000-0002-4824-6363 AD - Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico. FAU - Muñoz, María de Lourdes AU - Muñoz ML AUID- ORCID: 0000-0002-4185-2205 AD - Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AUID- ORCID: 0000-0001-9435-2872 AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Cervini-Silva, Javiera AU - Cervini-Silva J AUID- ORCID: 0000-0002-1661-5961 AD - Department of Process and Technology, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico. FAU - Alcalá-Castañeda, Enrique AU - Alcalá-Castañeda E AD - Department of Archaeological Studies, Instituto Nacional de Antropología e Historia, Mexico City, Mexico. FAU - David, Randy E AU - David RE AUID- ORCID: 0000-0003-0659-2492 AD - Department of Population Health and Disease Prevention, University of California, Irvine, Irvine, California, USA. LA - eng GR - 2015-Marzo 2016-290936/Consejo Nacional de Ciencia y Tecnología/ GR - 2014_Primer Periodo-380118/Consejo Nacional de Ciencia y Tecnología/ PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240202 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 SB - IM MH - Humans MH - Mexico MH - *Caves MH - *DNA, Mitochondrial/genetics MH - *Body Remains/chemistry/anatomy & histology MH - Radiometric Dating MH - Male MH - History, Ancient MH - Female MH - Anthropology, Physical MH - Archaeology OTO - NOTNLM OT - Mesoamerica OT - ancient DNA (aDNA) OT - artificial cranial deformation (ACD) OT - mitochondrial DNA (mtDNA) OT - pre‐Hispanic EDAT- 2024/02/03 10:42 MHDA- 2024/05/16 12:42 CRDT- 2024/02/03 02:11 PHST- 2023/12/19 00:00 [revised] PHST- 2023/05/08 00:00 [received] PHST- 2024/01/13 00:00 [accepted] PHST- 2024/05/16 12:42 [medline] PHST- 2024/02/03 10:42 [pubmed] PHST- 2024/02/03 02:11 [entrez] AID - 10.1002/ajpa.24903 [doi] PST - ppublish SO - Am J Biol Anthropol. 2024 Jun;184(2):e24903. doi: 10.1002/ajpa.24903. Epub 2024 Feb 2. PMID- 38806487 OWN - NLM STAT- MEDLINE DCOM- 20240528 LR - 20240531 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 14 IP - 1 DP - 2024 May 28 TI - Bioarchaeology aids the cultural understanding of six characters in search of their agency (Tarquinia, ninth-seventh century BC, central Italy). PG - 11895 LID - 10.1038/s41598-024-61052-z [doi] LID - 11895 AB - Etruria contained one of the great early urban civilisations in the Italian peninsula during the first millennium BC, much studied from a cultural, humanities-based, perspective, but relatively little with scientific data, and rarely in combination. We have addressed the unusual location of twenty inhumations found in the sacred heart of the Etruscan city of Tarquinia, focusing on six of these as illustrative, contrasting with the typical contemporary cremations found in cemeteries on the edge of the city. The cultural evidence suggests that the six skeletons were also distinctive in their ritualization and memorialisation. Focusing on the six, as a representative sample, the scientific evidence of osteoarchaeology, isotopic compositions, and ancient DNA has established that these appear to show mobility, diversity and violence through an integrated bioarchaeological approach. The combination of multiple lines of evidence makes major strides towards a deeper understanding of the role of these extraordinary individuals in the life of the early city of Etruria. CI - © 2024. The Author(s). FAU - Bagnasco, G AU - Bagnasco G AD - Dipartimento di Beni Culturali e Ambientali, CRC "Progetto Tarquinia", Università degli Studi di Milano, Milan, Italy. giovanna.bagnasco@unimi.it. FAU - Marzullo, M AU - Marzullo M AD - Dipartimento di Beni Culturali e Ambientali, CRC "Progetto Tarquinia", Università degli Studi di Milano, Milan, Italy. FAU - Cattaneo, C AU - Cattaneo C AD - LABANOF (Laboratorio di Antropologia e Odontologia Forense), Università degli Studi di Milano, Milan, Italy. FAU - Biehler-Gomez, L AU - Biehler-Gomez L AD - LABANOF (Laboratorio di Antropologia e Odontologia Forense), Università degli Studi di Milano, Milan, Italy. FAU - Mazzarelli, D AU - Mazzarelli D AD - LABANOF (Laboratorio di Antropologia e Odontologia Forense), Università degli Studi di Milano, Milan, Italy. FAU - Ricciardi, V AU - Ricciardi V AD - LABANOF (Laboratorio di Antropologia e Odontologia Forense), Università degli Studi di Milano, Milan, Italy. FAU - Müller, W AU - Müller W AD - Institute of Geosciences, Goethe University, Frankfurt, Frankfurt am Main, Germany. AD - Frankfurt Isotope and Element Research Center (FIERCE), Goethe University, Frankfurt, Frankfurt am Main, Germany. FAU - Coppa, A AU - Coppa A AD - Dipartimento di Storia Antropologia Religioni Arte Spettacolo, Sapienza Università di Roma, Rome, Italy. FAU - McLaughlin, R AU - McLaughlin R AD - Hamilton Institute, Maynooth University, Maynooth, Ireland. FAU - Motta, L AU - Motta L AD - Department of Classical Studies and Program in the Environment, University of Michigan, Ann Arbor, USA. FAU - Prato, O AU - Prato O AD - Institute of Archaeology, UCL University College London, London, UK. FAU - Schmidt, F AU - Schmidt F AD - Magdalene College, Cambridge, UK. FAU - Gaveriaux, F AU - Gaveriaux F AD - Kelsey Museum of Archaeology, University of Michigan, Ann Arbor, USA. FAU - Marras, G B AU - Marras GB AD - Magdalene College, Cambridge, UK. FAU - Millet, M A AU - Millet MA AD - School of Earth and Environmental Sciences, Cardiff University, Cardiff, CF10 3AT, UK. FAU - Madgwick, R AU - Madgwick R AD - Cardiff School of History, Archaeology and Religion, Cardiff University, Cardiff, UK. FAU - Ballantyne, R AU - Ballantyne R AD - School of Archaeology, University of Oxford, Oxford, UK. AD - Department of Archaeology, University of Cambridge, Cambridge, UK. FAU - Makarewicz, C A AU - Makarewicz CA AD - Institut für Ur- und Frühgeschichte, Christian-Albrechts-Universität zu Kiel, Kiel, Germany. FAU - Trentacoste, A AU - Trentacoste A AD - Institut für Ur- und Frühgeschichte, Christian-Albrechts-Universität zu Kiel, Kiel, Germany. FAU - Reimer, P AU - Reimer P AD - School of Natural and Built Environment, Queen's University Belfast, Belfast, BT7 1NN, UK. FAU - Mattiangeli, V AU - Mattiangeli V AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin2, Ireland. FAU - Bradley, D G AU - Bradley DG AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin2, Ireland. FAU - Malone, C AU - Malone C AD - School of Natural and Built Environment, Queen's University Belfast, Belfast, BT7 1NN, UK. FAU - Esposito, C AU - Esposito C AD - Dipartimento di Beni Culturali, Alma Mater Studiorum, Università di Bologna, Ravenna, Italy. FAU - Breslin, E M AU - Breslin EM AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin2, Ireland. FAU - Stoddart, S AU - Stoddart S AD - Magdalene College, Cambridge, UK. ss16@cam.ac.uk. LA - eng GR - WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article DEP - 20240528 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Italy MH - Humans MH - *Archaeology MH - History, Ancient MH - Male MH - DNA, Ancient/analysis MH - Female PMC - PMC11133411 COIS- The authors declare no competing interests. EDAT- 2024/05/29 00:49 MHDA- 2024/05/29 00:50 PMCR- 2024/05/28 CRDT- 2024/05/28 23:16 PHST- 2023/10/20 00:00 [received] PHST- 2024/04/30 00:00 [accepted] PHST- 2024/05/29 00:50 [medline] PHST- 2024/05/29 00:49 [pubmed] PHST- 2024/05/28 23:16 [entrez] PHST- 2024/05/28 00:00 [pmc-release] AID - 10.1038/s41598-024-61052-z [pii] AID - 61052 [pii] AID - 10.1038/s41598-024-61052-z [doi] PST - epublish SO - Sci Rep. 2024 May 28;14(1):11895. doi: 10.1038/s41598-024-61052-z. PMID- 38932149 OWN - NLM STAT- MEDLINE DCOM- 20240627 LR - 20240629 IS - 1999-4915 (Electronic) IS - 1999-4915 (Linking) VI - 16 IP - 6 DP - 2024 May 27 TI - Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data. LID - 10.3390/v16060856 [doi] LID - 856 AB - DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10(-5) to 10(-8) substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment. FAU - Ferreira, Renata C AU - Ferreira RC AD - Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP 04039-032, Brazil. AD - Epigene LLC, São Paulo, SP 04537-080, Brazil. FAU - Alves, Gustavo V AU - Alves GV AD - Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP 04039-032, Brazil. FAU - Ramon, Marcello AU - Ramon M AD - Computique LLC, São Paulo, SP 04545-006, Brazil. FAU - Antoneli, Fernando AU - Antoneli F AUID- ORCID: 0000-0001-9179-4632 AD - Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP 04039-032, Brazil. FAU - Briones, Marcelo R S AU - Briones MRS AUID- ORCID: 0000-0001-8045-2477 AD - Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP 04039-032, Brazil. LA - eng GR - 20/08943-5/Fundação de Amparo à Pesquisa do Estado de São Paulo/ GR - 311154/2021-2/National Council for Scientific and Technological Development/ PT - Journal Article DEP - 20240527 PL - Switzerland TA - Viruses JT - Viruses JID - 101509722 RN - 0 (DNA, Ancient) RN - 0 (DNA, Viral) SB - IM MH - Animals MH - *Neanderthals/genetics/virology MH - *Genome, Viral MH - *DNA, Ancient/analysis MH - Evolution, Molecular MH - DNA, Viral/genetics MH - Sequence Analysis, DNA/methods MH - Humans MH - Phylogeny MH - DNA Viruses/genetics/classification/isolation & purification MH - Fossils/virology PMC - PMC11209150 OTO - NOTNLM OT - Neanderthal genome OT - adenovirus OT - ancient viruses OT - genome assembly OT - herpesvirus OT - papillomavirus OT - sequence data COIS- Author Renata C. Ferreira was employed by the company Epigene LLC. Author Marcello Ramon was employed by the company Computique LLC. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. EDAT- 2024/06/27 06:42 MHDA- 2024/06/27 06:43 PMCR- 2024/05/27 CRDT- 2024/06/27 01:27 PHST- 2024/03/13 00:00 [received] PHST- 2024/05/20 00:00 [revised] PHST- 2024/05/24 00:00 [accepted] PHST- 2024/06/27 06:43 [medline] PHST- 2024/06/27 06:42 [pubmed] PHST- 2024/06/27 01:27 [entrez] PHST- 2024/05/27 00:00 [pmc-release] AID - v16060856 [pii] AID - viruses-16-00856 [pii] AID - 10.3390/v16060856 [doi] PST - epublish SO - Viruses. 2024 May 27;16(6):856. doi: 10.3390/v16060856. PMID- 38769390 OWN - NLM STAT- MEDLINE DCOM- 20240520 LR - 20240523 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 14 IP - 1 DP - 2024 May 20 TI - Phylogenetic insights into the genetic legacies of Hungarian-speaking communities in the Carpathian Basin. PG - 11480 LID - 10.1038/s41598-024-61978-4 [doi] LID - 11480 AB - This study focuses on exploring the uniparental genetic lineages of Hungarian-speaking minorities residing in rural villages of Baranja (Croatia) and the Zobor region (Slovakia). We aimed to identify ancestral lineages by examining genetic markers distributed across the entire mitogenome and on the Y-chromosome. This allowed us to discern disparities in regional genetic structures within these communities. By integrating our newly acquired genetic data from a total of 168 participants with pre-existing Eurasian and ancient DNA datasets, our goal was to enrich the understanding of the genetic history trajectories of Carpathian Basin populations. Our findings suggest that while population-based analyses may not be sufficiently robust to detect fine-scale uniparental genetic patterns with the sample sizes at hand, phylogenetic analysis of well-characterized Y-chromosomal Short Tandem Repeat (STR) data and entire mitogenome sequences did uncover multiple lineage ties to far-flung regions and eras. While the predominant portions of both paternal and maternal DNA align with the East-Central European spectrum, rarer subhaplogroups and lineages have unveiled ancient ties to both prehistoric and historic populations spanning Europe and Eastern Eurasia. This research augments the expansive field of phylogenetics, offering critical perspectives on the genetic constitution and heritage of the communities in East-Central Europe. CI - © 2024. The Author(s). FAU - Borbély, Noémi AU - Borbély N AUID- ORCID: 0000-0002-1488-5298 AD - Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary. AD - Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary. FAU - Dudás, Dániel AU - Dudás D AD - Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Gyorskocsi u. 25, Budapest, 1027, Hungary. FAU - Tapasztó, Attila AU - Tapasztó A AD - Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Gyorskocsi u. 25, Budapest, 1027, Hungary. FAU - Dudás-Boda, Eszter AU - Dudás-Boda E AUID- ORCID: 0000-0003-1895-2133 AD - Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Gyorskocsi u. 25, Budapest, 1027, Hungary. FAU - Csáky, Veronika AU - Csáky V AUID- ORCID: 0000-0002-7225-7265 AD - Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary. FAU - Szeifert, Bea AU - Szeifert B AUID- ORCID: 0000-0003-0786-1690 AD - Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary. FAU - Mende, Balázs Gusztáv AU - Mende BG AUID- ORCID: 0000-0001-7667-8633 AD - Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary. FAU - Egyed, Balázs AU - Egyed B AUID- ORCID: 0000-0003-3960-2052 AD - Department of Genetics, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AUID- ORCID: 0000-0003-2095-738X AD - Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary. szecsenyi-nagy.anna@abtk.hu. FAU - Pamjav, Horolma AU - Pamjav H AUID- ORCID: 0000-0002-1719-9154 AD - Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Gyorskocsi u. 25, Budapest, 1027, Hungary. phorolma@hotmail.com. LA - eng GR - FK 127938/Hungarian National Research, Development, and Innovation Office/ PT - Journal Article DEP - 20240520 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Humans MH - *Phylogeny MH - *Chromosomes, Human, Y/genetics MH - Hungary MH - *Genome, Mitochondrial MH - Male MH - Genetics, Population MH - Female MH - DNA, Mitochondrial/genetics MH - DNA, Ancient/analysis MH - Microsatellite Repeats/genetics MH - Haplotypes PMC - PMC11106325 COIS- The authors declare no competing interests. EDAT- 2024/05/21 00:42 MHDA- 2024/05/21 00:43 PMCR- 2024/05/20 CRDT- 2024/05/20 23:31 PHST- 2024/01/31 00:00 [received] PHST- 2024/05/13 00:00 [accepted] PHST- 2024/05/21 00:43 [medline] PHST- 2024/05/21 00:42 [pubmed] PHST- 2024/05/20 23:31 [entrez] PHST- 2024/05/20 00:00 [pmc-release] AID - 10.1038/s41598-024-61978-4 [pii] AID - 61978 [pii] AID - 10.1038/s41598-024-61978-4 [doi] PST - epublish SO - Sci Rep. 2024 May 20;14(1):11480. doi: 10.1038/s41598-024-61978-4. PMID- 38703773 OWN - NLM STAT- MEDLINE DCOM- 20240521 LR - 20240523 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 34 IP - 10 DP - 2024 May 20 TI - Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host. PG - 2221-2230.e8 LID - S0960-9822(24)00446-9 [pii] LID - 10.1016/j.cub.2024.04.006 [doi] AB - Leprosy, one of the oldest recorded diseases in human history, remains prevalent in Asia, Africa, and South America, with over 200,000 cases every year.(1)(,)(2) Although ancient DNA (aDNA) approaches on the major causative agent, Mycobacterium leprae, have elucidated the disease's evolutionary history,(3)(,)(4)(,)(5) the role of animal hosts and interspecies transmission in the past remains unexplored. Research has uncovered relationships between medieval strains isolated from archaeological human remains and modern animal hosts such as the red squirrel in England.(6)(,)(7) However, the time frame, distribution, and direction of transmissions remains unknown. Here, we studied 25 human and 12 squirrel samples from two archaeological sites in Winchester, a medieval English city well known for its leprosarium and connections to the fur trade. We reconstructed four medieval M. leprae genomes, including one from a red squirrel, at a 2.2-fold average coverage. Our analysis revealed a phylogenetic placement of all strains on branch 3 as well as a close relationship between the squirrel strain and one newly reconstructed medieval human strain. In particular, the medieval squirrel strain is more closely related to some medieval human strains from Winchester than to modern red squirrel strains from England, indicating a yet-undetected circulation of M. leprae in non-human hosts in the Middle Ages. Our study represents the first One Health approach for M. leprae in archaeology, which is centered around a medieval animal host strain, and highlights the future capability of such approaches to understand the disease's zoonotic past and current potential. CI - Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Urban, Christian AU - Urban C AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland; Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. FAU - Blom, Alette A AU - Blom AA AD - Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland; Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK; School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK. FAU - Avanzi, Charlotte AU - Avanzi C AD - Department of Microbiology, Immunology and Pathology, Colorado State University, 401 W Pitkin St, Fort Collins, CO 80523, USA. FAU - Walker-Meikle, Kathleen AU - Walker-Meikle K AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland; Science Museum Group, Science Museum, Exhibition Road, South Kensington, London SW7 2DD, UK. FAU - Warren, Alaine K AU - Warren AK AD - Department of Microbiology, Immunology and Pathology, Colorado State University, 401 W Pitkin St, Fort Collins, CO 80523, USA. FAU - White-Iribhogbe, Katie AU - White-Iribhogbe K AD - School of Oriental and African Studies (SOAS), University of London, 10 Thornaugh Street, London WC1H 0XG, UK. FAU - Turle, Ross AU - Turle R AD - Hampshire Cultural Trust, Chilcomb House, Chilcomb Lane, Winchester SO23 8RB, UK. FAU - Marter, Phil AU - Marter P AD - School of History, Archaeology and Philosophy, University of Winchester, Medecroft Building, Sparkford Road, Winchester SO22 4NH, UK. FAU - Dawson-Hobbis, Heidi AU - Dawson-Hobbis H AD - School of History, Archaeology and Philosophy, University of Winchester, Medecroft Building, Sparkford Road, Winchester SO22 4NH, UK. FAU - Roffey, Simon AU - Roffey S AD - School of History, Archaeology and Philosophy, University of Winchester, Medecroft Building, Sparkford Road, Winchester SO22 4NH, UK. FAU - Inskip, Sarah A AU - Inskip SA AD - School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK. Electronic address: s.inskip@le.ac.uk. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland; Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. Electronic address: verena.schuenemann@iem.uzh.ch. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240503 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Animals MH - *Mycobacterium leprae/genetics/isolation & purification MH - *Sciuridae/microbiology MH - *Leprosy/microbiology/history MH - Humans MH - *Genome, Bacterial MH - *Phylogeny MH - England MH - DNA, Ancient/analysis MH - Archaeology MH - History, Medieval OTO - NOTNLM OT - Mycobacterium leprae OT - One Health across time OT - ancient DNA OT - ancient pathogen genomics OT - animal hosts of diseases OT - medieval leprosy COIS- Declaration of interests We have no competing interests. EDAT- 2024/05/05 07:47 MHDA- 2024/05/22 01:52 CRDT- 2024/05/04 18:42 PHST- 2023/10/13 00:00 [received] PHST- 2024/02/15 00:00 [revised] PHST- 2024/04/02 00:00 [accepted] PHST- 2024/05/22 01:52 [medline] PHST- 2024/05/05 07:47 [pubmed] PHST- 2024/05/04 18:42 [entrez] AID - S0960-9822(24)00446-9 [pii] AID - 10.1016/j.cub.2024.04.006 [doi] PST - ppublish SO - Curr Biol. 2024 May 20;34(10):2221-2230.e8. doi: 10.1016/j.cub.2024.04.006. Epub 2024 May 3. PMID- 38750053 OWN - NLM STAT- MEDLINE DCOM- 20240515 LR - 20240518 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 14 IP - 1 DP - 2024 May 15 TI - New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages. PG - 11150 LID - 10.1038/s41598-024-61731-x [doi] LID - 11150 AB - Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands. CI - © 2024. The Author(s). FAU - Cabrera, Vicente M AU - Cabrera VM AD - Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, 38200, San Cristobal de La Laguna, Spain. Vicente.vca811@gmail.com. LA - eng PT - Journal Article DEP - 20240515 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Humans MH - *DNA, Mitochondrial/genetics MH - *DNA, Ancient/analysis MH - *Phylogeography MH - Spain MH - Phylogeny MH - Genetics, Population MH - Indigenous Peoples/genetics MH - Archaeology MH - Human Migration MH - History, Ancient MH - High-Throughput Nucleotide Sequencing PMC - PMC11096394 COIS- The author declares no competing interests. EDAT- 2024/05/16 00:43 MHDA- 2024/05/16 00:44 PMCR- 2024/05/15 CRDT- 2024/05/15 23:17 PHST- 2023/08/26 00:00 [received] PHST- 2024/05/09 00:00 [accepted] PHST- 2024/05/16 00:44 [medline] PHST- 2024/05/16 00:43 [pubmed] PHST- 2024/05/15 23:17 [entrez] PHST- 2024/05/15 00:00 [pmc-release] AID - 10.1038/s41598-024-61731-x [pii] AID - 61731 [pii] AID - 10.1038/s41598-024-61731-x [doi] PST - epublish SO - Sci Rep. 2024 May 15;14(1):11150. doi: 10.1038/s41598-024-61731-x. PMID- 38458749 OWN - NLM STAT- MEDLINE DCOM- 20240510 LR - 20240805 IS - 1468-3288 (Electronic) IS - 0017-5749 (Linking) VI - 73 IP - 6 DP - 2024 May 10 TI - PNPLA3 fatty liver allele was fixed in Neanderthals and segregates neutrally in humans. PG - 1008-1014 LID - 10.1136/gutjnl-2023-331594 [doi] AB - OBJECTIVE: Fat deposition is modulated by environmental factors and genetic predisposition. Genome-wide association studies identified PNPLA3 p.I148M (rs738409) as a common variant that increases risk of developing liver steatosis. When and how this variant evolved in humans has not been studied to date. DESIGN: Here we analyse ancient DNA to track the history of this allele throughout human history. In total, 6444 published ancient (modern humans, Neanderthal, Denisovan) and 3943 published present day genomes were used for analysis after extracting genotype calls for PNPLA3 p.I148M. To quantify changes through time, logistic and, by grouping individuals according to geography and age, linear regression analyses were performed. RESULTS: We find that archaic human individuals (Neanderthal, Denisovan) exclusively carried a fixed PNPLA3 risk allele, whereas allele frequencies in modern human populations range from very low in Africa to >50% in Mesoamerica. Over the last 15 000 years, distributions of ancestral and derived alleles roughly match the present day distribution. Logistic regression analyses did not yield signals of natural selection during the last 10 000 years. CONCLUSION: Archaic human individuals exclusively carried a fixed PNPLA3 allele associated with fatty liver, whereas allele frequencies in modern human populations are variable even in the oldest samples. Our observation might underscore the advantage of fat storage in cold climate and particularly for Neanderthal under ice age conditions. The absent signals of natural selection during modern human history does not support the thrifty gene hypothesis in case of PNPLA3 p.I148M. CI - © Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ. FAU - Geier, Andreas AU - Geier A AUID- ORCID: 0000-0002-9626-5083 AD - Department of Medicine II, Division of Hepatology, University Hospital Wurzburg, Würzburg, Germany geier_a2@ukw.de stephan_schiffels@eva.mpg.de. FAU - Trost, Jonas AU - Trost J AD - Department of Medicine II, Division of Hepatology, University Hospital Wurzburg, Würzburg, Germany. FAU - Wang, Ke AU - Wang K AUID- ORCID: 0000-0003-3935-8344 AD - Department Archaeogenetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. AD - School of Life Sciences, Fudan University, Shanghai, China. FAU - Schmid, Clemens AU - Schmid C AUID- ORCID: 0000-0003-3448-5715 AD - Department Archaeogenetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. AD - International Max Planck Research School for the Science of Human History, Max Planck Institute for Geoanthropology, Jena, Germany. FAU - Krawczyk, Marcin AU - Krawczyk M AUID- ORCID: 0000-0002-0113-0777 AD - Department of Medicine II, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany. AD - Laboratory of Metabolic Liver Diseases, Center for Preclinical Research, Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland. FAU - Schiffels, Stephan AU - Schiffels S AUID- ORCID: 0000-0002-1017-9150 AD - Department Archaeogenetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany geier_a2@ukw.de stephan_schiffels@eva.mpg.de. LA - eng GR - 851511/ERC_/European Research Council/International PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240510 PL - England TA - Gut JT - Gut JID - 2985108R RN - EC 2.3.- (Acyltransferases) RN - 0 (DNA, Ancient) RN - EC 3.1.1.4 (Phospholipases A2, Calcium-Independent) RN - EC 3.1.1.3 (PNPLA3 protein, human) SB - IM MH - Animals MH - Humans MH - *Acyltransferases/genetics MH - *Alleles MH - DNA, Ancient/analysis MH - *Fatty Liver/genetics MH - Gene Frequency MH - Genetic Predisposition to Disease MH - Genome-Wide Association Study MH - Genotype MH - *Neanderthals/genetics MH - *Phospholipases A2, Calcium-Independent/genetics OTO - NOTNLM OT - fatty liver OT - genetics OT - lipid metabolism OT - nutrition COIS- Competing interests: None declared. EDAT- 2024/03/09 10:43 MHDA- 2024/05/11 08:42 CRDT- 2024/03/08 21:03 PHST- 2023/11/21 00:00 [received] PHST- 2024/02/19 00:00 [accepted] PHST- 2024/05/11 08:42 [medline] PHST- 2024/03/09 10:43 [pubmed] PHST- 2024/03/08 21:03 [entrez] AID - gutjnl-2023-331594 [pii] AID - 10.1136/gutjnl-2023-331594 [doi] PST - epublish SO - Gut. 2024 May 10;73(6):1008-1014. doi: 10.1136/gutjnl-2023-331594. PMID- 38739117 OWN - NLM STAT- MEDLINE DCOM- 20240513 LR - 20240613 IS - 2057-5858 (Electronic) IS - 2057-5858 (Linking) VI - 10 IP - 5 DP - 2024 May TI - Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes. LID - 10.1099/mgen.0.001251 [doi] LID - 001251 AB - The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era. FAU - Dahlquist-Axe, Gwyn AU - Dahlquist-Axe G AD - School of Chemistry and Biosciences, University of Bradford, Bradford, UK. FAU - Standeven, Francesca J AU - Standeven FJ AD - School of Chemistry and Biosciences, University of Bradford, Bradford, UK. FAU - Speller, Camilla F AU - Speller CF AD - Department of Anthropology, University of British Columbia, Vancouver, Canada. FAU - Tedder, Andrew AU - Tedder A AD - School of Chemistry and Biosciences, University of Bradford, Bradford, UK. FAU - Meehan, Conor J AU - Meehan CJ AD - Department of Biosciences, Nottingham Trent University, Nottingham, UK. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Microb Genom JT - Microbial genomics JID - 101671820 RN - 0 (Anti-Bacterial Agents) SB - IM MH - Humans MH - *Microbiota MH - *Mouth/microbiology MH - *Anti-Bacterial Agents/pharmacology MH - History, Ancient MH - Diet MH - Bacteria/genetics/classification/drug effects MH - Drug Resistance, Microbial/genetics MH - Drug Resistance, Bacterial/genetics MH - History, Medieval MH - History, 17th Century MH - History, 18th Century MH - History, 16th Century PMC - PMC11165619 OTO - NOTNLM OT - ancient DNA OT - antibiotic resistance OT - evolution COIS- The authors declare no competing interests. EDAT- 2024/05/13 12:53 MHDA- 2024/05/13 12:54 PMCR- 2024/05/13 CRDT- 2024/05/13 10:53 PHST- 2024/05/13 12:54 [medline] PHST- 2024/05/13 12:53 [pubmed] PHST- 2024/05/13 10:53 [entrez] PHST- 2024/05/13 00:00 [pmc-release] AID - 001251 [pii] AID - 10.1099/mgen.0.001251 [doi] PST - ppublish SO - Microb Genom. 2024 May;10(5):001251. doi: 10.1099/mgen.0.001251. PMID- 38658749 OWN - NLM STAT- MEDLINE DCOM- 20240508 LR - 20240511 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 629 IP - 8011 DP - 2024 May TI - Network of large pedigrees reveals social practices of Avar communities. PG - 376-383 LID - 10.1038/s41586-024-07312-4 [doi] AB - From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years(1). Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies(2). Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment. CI - © 2024. The Author(s). FAU - Gnecchi-Ruscone, Guido Alberto AU - Gnecchi-Ruscone GA AUID- ORCID: 0000-0002-6490-8101 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. guido_gnecchi@eva.mpg.de. FAU - Rácz, Zsófia AU - Rácz Z AUID- ORCID: 0000-0001-5116-2235 AD - Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary. FAU - Samu, Levente AU - Samu L AD - Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary. FAU - Szeniczey, Tamás AU - Szeniczey T AD - Department of Biological Anthropology, ELTE - Eötvös Loránd University, Budapest, Hungary. FAU - Faragó, Norbert AU - Faragó N AUID- ORCID: 0000-0002-0351-1223 AD - Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary. FAU - Knipper, Corina AU - Knipper C AD - Curt Engelhorn Center for Archaeometry gGmbH, Mannheim, Germany. FAU - Friedrich, Ronny AU - Friedrich R AUID- ORCID: 0000-0001-5199-1957 AD - Curt Engelhorn Center for Archaeometry gGmbH, Mannheim, Germany. FAU - Zlámalová, Denisa AU - Zlámalová D AD - Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czechia. FAU - Traverso, Luca AU - Traverso L AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Liccardo, Salvatore AU - Liccardo S AD - Department of History, University of Vienna, Vienna, Austria. AD - Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria. FAU - Wabnitz, Sandra AU - Wabnitz S AD - Department of History, University of Vienna, Vienna, Austria. AD - Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria. FAU - Popli, Divyaratan AU - Popli D AD - Department of Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Wang, Ke AU - Wang K AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China. FAU - Radzeviciute, Rita AU - Radzeviciute R AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Gulyás, Bence AU - Gulyás B AD - Hungarian National Museum, Budapest, Hungary. FAU - Koncz, István AU - Koncz I AUID- ORCID: 0000-0002-8113-5753 AD - Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary. FAU - Balogh, Csilla AU - Balogh C AUID- ORCID: 0000-0002-9161-1653 AD - Department of Art History, Istanbul Medeniyet University, Istanbul, Turkey. FAU - Lezsák, Gabriella M AU - Lezsák GM AD - Institute of History, HUN-REN Research Centre for the Humanities, Budapest, Hungary. FAU - Mácsai, Viktor AU - Mácsai V AD - Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary. FAU - Bunbury, Magdalena M E AU - Bunbury MME AUID- ORCID: 0000-0003-3114-3138 AD - ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society and Education, James Cook University, Cairns, Queensland, Australia. FAU - Spekker, Olga AU - Spekker O AD - Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary. AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - le Roux, Petrus AU - le Roux P AUID- ORCID: 0000-0002-5930-4995 AD - Department of Geological Sciences, University of Cape Town, Rondebosch, South Africa. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AUID- ORCID: 0000-0003-2095-738X AD - Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary. FAU - Mende, Balázs Gusztáv AU - Mende BG AD - Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary. FAU - Colleran, Heidi AU - Colleran H AUID- ORCID: 0000-0002-2126-8116 AD - BirthRites Lise Meitner Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Hajdu, Tamás AU - Hajdu T AD - Department of Biological Anthropology, ELTE - Eötvös Loránd University, Budapest, Hungary. FAU - Geary, Patrick AU - Geary P AUID- ORCID: 0000-0002-3971-2588 AD - Institute for Advanced Study, Princeton, NJ, USA. FAU - Pohl, Walter AU - Pohl W AD - Department of History, University of Vienna, Vienna, Austria. AD - Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria. FAU - Vida, Tivadar AU - Vida T AUID- ORCID: 0000-0002-0588-1906 AD - Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary. vida.tivadar@btk.elte.hu. AD - Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary. vida.tivadar@btk.elte.hu. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. krause@eva.mpg.de. FAU - Hofmanová, Zuzana AU - Hofmanová Z AUID- ORCID: 0000-0003-1336-4455 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. zuzana_hofmanova@eva.mpg.de. AD - Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czechia. zuzana_hofmanova@eva.mpg.de. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240424 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Adult MH - Female MH - Humans MH - Male MH - *Archaeology/methods MH - Asia/ethnology MH - Cemeteries/history MH - Consanguinity MH - *DNA, Ancient/analysis MH - Europe/ethnology MH - *Family Characteristics/ethnology/history MH - Genomics MH - *Grassland MH - History, Medieval MH - *Pedigree MH - Politics MH - Adolescent MH - Young Adult PMC - PMC11078744 COIS- The authors declare no competing interests. EDAT- 2024/04/25 00:55 MHDA- 2024/05/09 00:47 PMCR- 2024/04/24 CRDT- 2024/04/24 23:36 PHST- 2023/04/13 00:00 [received] PHST- 2024/03/13 00:00 [accepted] PHST- 2024/05/09 00:47 [medline] PHST- 2024/04/25 00:55 [pubmed] PHST- 2024/04/24 23:36 [entrez] PHST- 2024/04/24 00:00 [pmc-release] AID - 10.1038/s41586-024-07312-4 [pii] AID - 7312 [pii] AID - 10.1038/s41586-024-07312-4 [doi] PST - ppublish SO - Nature. 2024 May;629(8011):376-383. doi: 10.1038/s41586-024-07312-4. Epub 2024 Apr 24. PMID- 38658715 OWN - NLM STAT- MEDLINE DCOM- 20240503 LR - 20240508 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 629 IP - 8011 DP - 2024 May TI - Ancient DNA traces family lines and political shifts in the Avar empire. PG - 287-288 LID - 10.1038/d41586-024-01020-9 [doi] FAU - Cassidy, Lara M AU - Cassidy LM LA - eng PT - Historical Article PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient/analysis MH - Humans MH - *Politics MH - History, Ancient MH - Female OTO - NOTNLM OT - Archaeology OT - Genomics OT - History OT - Society EDAT- 2024/04/25 00:54 MHDA- 2024/05/04 11:50 CRDT- 2024/04/24 23:35 PHST- 2024/05/04 11:50 [medline] PHST- 2024/04/25 00:54 [pubmed] PHST- 2024/04/24 23:35 [entrez] AID - 10.1038/d41586-024-01020-9 [pii] AID - 10.1038/d41586-024-01020-9 [doi] PST - ppublish SO - Nature. 2024 May;629(8011):287-288. doi: 10.1038/d41586-024-01020-9. PMID- 38530148 OWN - NLM STAT- MEDLINE DCOM- 20240426 LR - 20240426 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 76 IP - 5 DP - 2024 May TI - Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples. PG - 216-223 LID - 10.2144/btn-2023-0107 [doi] AB - Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results. FAU - Yaka, Reyhan AU - Yaka R AUID- ORCID: 0000-0002-9359-4391 AD - Centre for Palaeogenetics, Stockholm, Sweden. AD - Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden. AD - Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey. FAU - Maja Krzewińska AU - Maja Krzewińska AD - Centre for Palaeogenetics, Stockholm, Sweden. AD - Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Lagerholm, Vendela Kempe AU - Lagerholm VK AD - Centre for Palaeogenetics, Stockholm, Sweden. AD - Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Linderholm, Anna AU - Linderholm A AD - Centre for Palaeogenetics, Stockholm, Sweden. AD - Department of Geological Sciences, Stockholm University, Stockholm, Sweden. FAU - Özer, Füsun AU - Özer F AD - Department of Anthropology, Hacettepe University, Ankara, Turkey. FAU - Somel, Mehmet AU - Somel M AD - Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey. FAU - Götherström, Anders AU - Götherström A AD - Centre for Palaeogenetics, Stockholm, Sweden. AD - Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden. LA - eng GR - STF 7909/EMBO (short-term fellowship)/ GR - 772390/ERC (consolidator grant)/ GR - 117Z229/TUBITAK of Turkey/ GR - NAISS 2023/22-504, NAISS 2023/23-262/Uppsala Multidisciplinary Center for Advanced Computational Science/ PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240326 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Ancient) RN - 7631-86-9 (Silicon Dioxide) SB - IM MH - *DNA, Ancient/analysis/isolation & purification MH - Humans MH - *Genome, Human/genetics MH - Gene Library MH - Sequence Analysis, DNA/methods MH - Silicon Dioxide/chemistry OTO - NOTNLM OT - DNA extraction OT - aDNA library OT - ancient DNA OT - optimization OT - whole genome capture EDAT- 2024/03/26 12:48 MHDA- 2024/04/26 18:53 CRDT- 2024/03/26 10:03 PHST- 2024/04/26 18:53 [medline] PHST- 2024/03/26 12:48 [pubmed] PHST- 2024/03/26 10:03 [entrez] AID - 10.2144/btn-2023-0107 [doi] PST - ppublish SO - Biotechniques. 2024 May;76(5):216-223. doi: 10.2144/btn-2023-0107. Epub 2024 Mar 26. PMID- 38462159 OWN - NLM STAT- MEDLINE DCOM- 20240509 LR - 20240509 IS - 1872-8278 (Electronic) IS - 1567-7249 (Linking) VI - 76 DP - 2024 May TI - Ancient mitogenomes suggest complex maternal history of one of the oldest settlements of western India. PG - 101871 LID - S1567-7249(24)00029-1 [pii] LID - 10.1016/j.mito.2024.101871 [doi] AB - The ancient township of Vadnagar tells a story of a long chain of cultural diversity and exchange. Vadnagar has been continuously habituated and shows a presence of rich cultural amalgamation and continuous momentary sequences between the 2th century BCE and present-day. Seven cultural periods developed a complex and enriched settlement at Vadnagar in spatio-temporality. Although archaeological studies done on this oldest settlement suggested a rich cultural heritage, the genetic studies to pinpoint the genetic ancestry was lacking till date. In our current study we have for the first time reconstructed the complete mitogenomes of medieval individuals of the Vadnagar archaeological site in Gujarat. The study aimed to investigate the cosmopolitan nature of the present population as well as the migratory pattern and the inflow of different groups through trade, cultural and religious practices. Our analysis suggests heterogeneous nature of the medieval population of Vadnagar with presence of deeply rooted local ancestral components as well as central Asian genetic ancestry. This Central Asian component associated with mitochondrial haplotype U2e was not shared with any individual from India, but rather with individuals from the Bronze Age of Tajikistan and with an earlier age of coalescence. In summary, we propose that the medieval site of Vadnagar in western India was rich in cultural and genetic aspects, with both local and western Eurasian components. CI - Copyright © 2024 Elsevier B.V. and Mitochondria Research Society. All rights reserved. FAU - Ahlawat, Bhavna AU - Ahlawat B AD - Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Department of Anthropology, Panjab University, Chandigarh 160014, India. FAU - Kumar, Lomous AU - Kumar L AD - Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India. FAU - Ambekar, Abhijit AU - Ambekar A AD - Science Branch, Archaeological Survey of India, India. FAU - Singh Sehrawat, Jagmahender AU - Singh Sehrawat J AD - Department of Anthropology, Panjab University, Chandigarh 160014, India. FAU - Rawat, Yadubir Singh AU - Rawat YS AD - Archaeological Survey of India, India. FAU - Rai, Niraj AU - Rai N AD - Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India. Electronic address: nirajrai@bsip.res.in. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240309 PL - Netherlands TA - Mitochondrion JT - Mitochondrion JID - 100968751 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - India MH - *Genome, Mitochondrial MH - DNA, Ancient/analysis MH - History, Medieval MH - Human Migration MH - Archaeology MH - Female MH - DNA, Mitochondrial/genetics MH - Haplotypes MH - History, Ancient OTO - NOTNLM OT - Ancient DNA OT - Archaeology OT - Mitogenome OT - South Asia OT - West Eurasia COIS- Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. EDAT- 2024/03/11 00:42 MHDA- 2024/05/10 00:43 CRDT- 2024/03/10 20:18 PHST- 2024/01/14 00:00 [received] PHST- 2024/03/05 00:00 [revised] PHST- 2024/03/07 00:00 [accepted] PHST- 2024/05/10 00:43 [medline] PHST- 2024/03/11 00:42 [pubmed] PHST- 2024/03/10 20:18 [entrez] AID - S1567-7249(24)00029-1 [pii] AID - 10.1016/j.mito.2024.101871 [doi] PST - ppublish SO - Mitochondrion. 2024 May;76:101871. doi: 10.1016/j.mito.2024.101871. Epub 2024 Mar 9. PMID- 38417515 OWN - NLM STAT- MEDLINE DCOM- 20240320 LR - 20240320 IS - 1879-1026 (Electronic) IS - 0048-9697 (Linking) VI - 922 DP - 2024 Apr 20 TI - Sedimentary ancient DNA reveals the impact of anthropogenic land use disturbance and ecological shifts on fish community structure in small lowland lake. PG - 171266 LID - S0048-9697(24)01405-0 [pii] LID - 10.1016/j.scitotenv.2024.171266 [doi] AB - Freshwater fish biodiversity and abundance are decreasing globally. The drivers of decline are primarily anthropogenic; however, the causative links between disturbances and fish community change are complex and challenging to investigate. We used a suite of sedimentary DNA methods (droplet digital PCR and metabarcoding) and traditional paleolimnological approaches, including pollen and trace metal analysis, ITRAX X-ray fluorescence and hyperspectral core scanning to explore changes in fish abundance and drivers over 1390 years in a small lake. This period captured a disturbance trajectory from pre-human settlement through subsistence living to intensive agriculture. Generalized additive mixed models explored the relationships between catchment inputs, internal drivers, and fish community structure. Fish community composition distinctly shifted around 1350 CE, with the decline of a sensitive Galaxias species concomitant with early land use changes. Total fish abundance significantly declined around 1950 CE related to increases in ruminant bacterial DNA (a proxy for ruminant abundance) and cadmium flux (a proxy for phosphate fertilizers), implicating land use intensification as a key driver. Concurrent shifts in phytoplankton and zooplankton suggested that fish communities were likely impacted by food web dynamics. This study highlights the potential of sedDNA to elucidate the long-term disturbance impacts on biological communities in lakes. CI - Copyright © 2024. Published by Elsevier B.V. FAU - Thomson-Laing, Georgia AU - Thomson-Laing G AD - Cawthron Institute, 98 Halifax Street, The Wood, Nelson 7010, New Zealand; School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand. Electronic address: Georgia.Thomson-Laing@cawthron.org.nz. FAU - Howarth, Jamie D AU - Howarth JD AD - School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand. FAU - Atalah, Javier AU - Atalah J AD - Cawthron Institute, 98 Halifax Street, The Wood, Nelson 7010, New Zealand. FAU - Vandergoes, Marcus J AU - Vandergoes MJ AD - GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5011, New Zealand. FAU - Li, Xun AU - Li X AD - GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5011, New Zealand. FAU - Pearman, John K AU - Pearman JK AD - School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand. FAU - Fitzsimons, Sean AU - Fitzsimons S AD - School of Geography, University of Otago, 360 Leith Street, North Dunedin, Dunedin 9054, New Zealand. FAU - Moy, Chris AU - Moy C AD - Department of Geology, University of Otago, 360 Leith Street, North Dunedin, Dunedin 9054, New Zealand. FAU - Moody, Adelaine AU - Moody A AD - School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand. FAU - Shepherd, Claire AU - Shepherd C AD - GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5011, New Zealand. FAU - McKay, Nicholas AU - McKay N AD - School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA. FAU - Wood, Susanna A AU - Wood SA AD - Cawthron Institute, 98 Halifax Street, The Wood, Nelson 7010, New Zealand. LA - eng PT - Journal Article DEP - 20240228 PL - Netherlands TA - Sci Total Environ JT - The Science of the total environment JID - 0330500 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Humans MH - *DNA, Ancient MH - *Lakes MH - Biodiversity MH - DNA MH - Fishes MH - Ruminants MH - Ecosystem OTO - NOTNLM OT - Digital droplet PCR OT - Environmental DNA OT - Fish OT - Freshwater ecology OT - Lakes OT - Metabarcoding COIS- Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. EDAT- 2024/02/29 00:43 MHDA- 2024/03/20 06:45 CRDT- 2024/02/28 19:14 PHST- 2023/12/20 00:00 [received] PHST- 2024/01/29 00:00 [revised] PHST- 2024/02/23 00:00 [accepted] PHST- 2024/03/20 06:45 [medline] PHST- 2024/02/29 00:43 [pubmed] PHST- 2024/02/28 19:14 [entrez] AID - S0048-9697(24)01405-0 [pii] AID - 10.1016/j.scitotenv.2024.171266 [doi] PST - ppublish SO - Sci Total Environ. 2024 Apr 20;922:171266. doi: 10.1016/j.scitotenv.2024.171266. Epub 2024 Feb 28. PMID- 38552628 OWN - NLM STAT- MEDLINE DCOM- 20240411 LR - 20240523 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 34 IP - 7 DP - 2024 Apr 8 TI - Ancient genome of the Chinese Emperor Wu of Northern Zhou. PG - 1587-1595.e5 LID - S0960-9822(24)00240-9 [pii] LID - 10.1016/j.cub.2024.02.059 [doi] AB - Emperor Wu (, Wudi) of the Xianbei-led Northern Zhou dynasty, named Yuwen Yong (, 543-578 CE), was a highly influential emperor who reformed the system of regional troops, pacified the Turks, and unified the northern part of the country. His genetic profile and physical characteristics, including his appearance and potential diseases, have garnered significant interest from the academic community and the public. In this study, we have successfully generated a 0.343×-coverage genome of Wudi with 1,011,419 single-nucleotide polymorphisms (SNPs) on the 1240k panel. By analyzing pigmentation-relevant SNPs and conducting cranial CT-based facial reconstruction, we have determined that Wudi possessed a typical East or Northeast Asian appearance. Furthermore, pathogenic SNPs suggest Wudi faced an increased susceptibility to certain diseases, such as stroke. Wudi shared the closest genetic relationship with ancient Khitan and Heishui Mohe samples and modern Daur and Mongolian populations but also showed additional affinity with Yellow River (YR) farmers. We estimated that Wudi derived 61% of his ancestry from ancient Northeast Asians (ANAs) and nearly one-third from YR farmer-related groups. This can likely be attributed to continuous intermarriage between Xianbei royal families, and local Han aristocrats.(1)(,)(2) Furthermore, our study has revealed genetic diversities among available ancient Xianbei individuals from different regions, suggesting that the formation of the Xianbei was a dynamic process influenced by admixture with surrounding populations. CI - Copyright © 2024 Elsevier Inc. All rights reserved. FAU - Du, Panxin AU - Du P AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Zhu, Kongyang AU - Zhu K AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Qiao, Hui AU - Qiao H AD - State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Zhang, Jianlin AU - Zhang J AD - Shaanxi Academy of Archaeology, Xi'an 710054, China. FAU - Meng, Hailiang AU - Meng H AD - Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Huang, Zixiao AU - Huang Z AD - Department of History, Fudan University, Shanghai 200433, China. FAU - Yu, Yao AU - Yu Y AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Xie, Shouhua AU - Xie S AD - Department of History, Fudan University, Shanghai 200433, China. FAU - Allen, Edward AU - Allen E AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Xiong, Jianxue AU - Xiong J AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Zhang, Baoshuai AU - Zhang B AD - USTC Archaeometry Laboratory, University of Science and Technology of China, Hefei 230026, China. FAU - Chang, Xin AU - Chang X AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Ren, Xiaoying AU - Ren X AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Xu, Yiran AU - Xu Y AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. FAU - Zhou, Qi AU - Zhou Q AD - Shanghai Federation of Social Science Associations, Shanghai 200020, China. FAU - Han, Sheng AU - Han S AD - Department of History, Fudan University, Shanghai 200433, China. FAU - Jin, Li AU - Jin L AD - State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China. Electronic address: lijin@fudan.edu.cn. FAU - Wei, Pianpian AU - Wei P AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China. Electronic address: weipianpian@fudan.edu.cn. FAU - Wang, Chuan-Chao AU - Wang CC AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China. Electronic address: wang@xmu.edu.cn. FAU - Wen, Shaoqing AU - Wen S AD - Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China; Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai 200433, China. Electronic address: wenshaoqing@fudan.edu.cn. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240328 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - *DNA, Mitochondrial/genetics MH - *Asian People/genetics MH - Genome MH - Polymorphism, Single Nucleotide MH - China MH - Genetics, Population OTO - NOTNLM OT - Emperor Wu OT - Xianbei OT - ancient DNA OT - facial reconstruction COIS- Declaration of interests The authors declare no competing interests. EDAT- 2024/03/30 11:45 MHDA- 2024/04/11 06:43 CRDT- 2024/03/29 19:42 PHST- 2023/02/03 00:00 [received] PHST- 2023/12/23 00:00 [revised] PHST- 2024/02/23 00:00 [accepted] PHST- 2024/04/11 06:43 [medline] PHST- 2024/03/30 11:45 [pubmed] PHST- 2024/03/29 19:42 [entrez] AID - S0960-9822(24)00240-9 [pii] AID - 10.1016/j.cub.2024.02.059 [doi] PST - ppublish SO - Curr Biol. 2024 Apr 8;34(7):1587-1595.e5. doi: 10.1016/j.cub.2024.02.059. Epub 2024 Mar 28. PMID- 38526010 OWN - NLM STAT- MEDLINE DCOM- 20240409 LR - 20240704 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 16 IP - 4 DP - 2024 Apr 2 TI - Reconstructing the Genetic Relationship between Ancient and Present-Day Siberian Populations. LID - 10.1093/gbe/evae063 [doi] LID - evae063 AB - Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here, we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 yr ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Gill, Haechan AU - Gill H AUID- ORCID: 0000-0002-6679-5331 AD - School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea. FAU - Lee, Juhyeon AU - Lee J AUID- ORCID: 0000-0001-7008-4471 AD - School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea. FAU - Jeong, Choongwon AU - Jeong C AUID- ORCID: 0000-0003-3049-2352 AD - School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea. LA - eng GR - RS-2023-00212640/National Research Foundation of Korea/ PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 RN - Nganasan people SB - IM MH - Humans MH - Siberia MH - *Genome, Human MH - *Genetics, Population MH - *North Asian People PMC - PMC10999361 OTO - NOTNLM OT - Baikal OT - Siberian ancestry OT - Syalakh–Belkachi cultures OT - Yakutia OT - ancient genome COIS- The authors declare no competing interests. EDAT- 2024/03/25 12:47 MHDA- 2024/04/09 06:45 PMCR- 2024/03/25 CRDT- 2024/03/25 08:24 PHST- 2024/03/21 00:00 [accepted] PHST- 2024/04/09 06:45 [medline] PHST- 2024/03/25 12:47 [pubmed] PHST- 2024/03/25 08:24 [entrez] PHST- 2024/03/25 00:00 [pmc-release] AID - 7634480 [pii] AID - evae063 [pii] AID - 10.1093/gbe/evae063 [doi] PST - ppublish SO - Genome Biol Evol. 2024 Apr 2;16(4):evae063. doi: 10.1093/gbe/evae063. PMID- 38348756 OWN - NLM STAT- MEDLINE DCOM- 20240304 LR - 20240716 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 183 IP - 4 DP - 2024 Apr TI - Female biased adult sex ratio in the Bronze Age cemetery of Shahr-i Sokhta (Iran) as an indicator of long distance trade and matrilocality. PG - e24911 LID - 10.1002/ajpa.24911 [doi] AB - OBJECTIVES: This paper starts from the unusual observation of the overrepresentation of females among adults in the cemetery of Bronze Age Shahr-i Sokhta (Seistan, Iran) and explores the post marital residence pattern. By integrating taphonomical (skeletal preservation), anthropological (sex ratio [SR], sexual dimorphism, stress indicators, age at death), archeological (long distance trade indicators, habitation floor area, social role of women), and ancient DNA (heterozygosity levels in X chromosomes) data we test the hypothesis of post marital matrilocality in the site. METHODS: We computed the SR (pelvis-based sex determination) in a random unpublished adult sample from the cemetery of Shahr-i Sokhta and in two samples previously published by other authors. We used comparative data on SR from: a large Supra Regional multi-chronological sample of sites, n = 47, with 8808 adult sexed individuals, from Southern Europe, Egypt, Middle East, Southern Russia; a Regional Bronze Age sample of sites (n = 10) from Bactria Margiana and Indus Valley with 1324 adult sexed individuals. We estimated the heterozygosity levels in X chromosomes compared with the rest of the autosomes on the assumption that in a matrilocal society females should show lower variability than men. RESULTS: Adult SR in a sample (n = 549) from Shahr-i Sokhta is 70.5, the overrepresentation of females is shared with Regional Bronze Age sites from Bactria Margiana (SR = 72.09) and Indus Valley (SR = 67.54). On the contrary, in a larger Supra Regional multi-chronological sample of sites, mean SR ranges between 112.7 (Bronze Age) and 163.1 (Middle Ages). Taphonomical and anthropological indicators do not explain the overrepresentation of female skeletons. Archeological indicators suggest a high social status of women and that the society was devoted to long range trade activities. heterozygosity levels in X chromosomes are in agreement with a matrilocal society. CONCLUSIONS: Indicators suggest that Bronze Age Shahr-ì Sokhta was a matrilocal society and that long distance trade was an important economic factor producing an overrepresentation of adult female skeletons in the cemetery. CI - © 2024 Wiley Periodicals LLC. FAU - Vincenti, Giorgia AU - Vincenti G AUID- ORCID: 0000-0002-5382-1932 AD - MAIPS, Multidisciplinary Archaeological Italian Project at Shahr-i Sokhta - Dipartimento Beni Culturali, Laboratorio di Antropologia Fisica, Università del Salento, Lecce, Italy. FAU - Molinaro, Ludovica AU - Molinaro L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia. AD - Department of Human Genetics, KU Leuven, Leuven, Belgium. FAU - Sajjadi, Seyed Mansur Seyed AU - Sajjadi SMS AD - Iranian Center for Archaeological Research, Tehran, Iran. FAU - Moradi, Hossein AU - Moradi H AD - Independent Researcher, Tehran, Iran. FAU - Pagani, Luca AU - Pagani L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia. AD - Department of Biology, University of Padova, Padova, Italy. FAU - Fabbri, Pier Francesco AU - Fabbri PF AUID- ORCID: 0000-0003-3633-0178 AD - MAIPS, Multidisciplinary Archaeological Italian Project at Shahr-i Sokhta, Università del Salento, Lecce, Italy. AD - Museo Fiorentino di Preistoria, Firenze, Italy. LA - eng GR - Ministero degli Affari Esteri e della Cooperazione Internazionale/ GR - University of Salento/ PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240213 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 SB - IM MH - Adult MH - Male MH - Middle Aged MH - Humans MH - Female MH - Iran MH - *Cemeteries MH - Sex Ratio MH - Middle East MH - Anthropology MH - *Polygonaceae OTO - NOTNLM OT - Bronze Age OT - Shahr-i Sokhta OT - adult sex ratio OT - ancient DNA OT - bioarcheology OT - long distance trade OT - matrilocality EDAT- 2024/02/13 06:45 MHDA- 2024/03/04 06:42 CRDT- 2024/02/13 05:37 PHST- 2024/01/18 00:00 [revised] PHST- 2023/06/11 00:00 [received] PHST- 2024/01/22 00:00 [accepted] PHST- 2024/03/04 06:42 [medline] PHST- 2024/02/13 06:45 [pubmed] PHST- 2024/02/13 05:37 [entrez] AID - 10.1002/ajpa.24911 [doi] PST - ppublish SO - Am J Biol Anthropol. 2024 Apr;183(4):e24911. doi: 10.1002/ajpa.24911. Epub 2024 Feb 13. PMID- 38173222 OWN - NLM STAT- MEDLINE DCOM- 20240306 LR - 20240306 IS - 1755-0998 (Electronic) IS - 1755-098X (Linking) VI - 24 IP - 3 DP - 2024 Apr TI - Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data. PG - e13913 LID - 10.1111/1755-0998.13913 [doi] AB - The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non-model organisms. CI - © 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. FAU - Caduff, Madleina AU - Caduff M AUID- ORCID: 0000-0001-8941-4274 AD - Department of Biology, University of Fribourg, Fribourg, Switzerland. AD - Swiss Institute of Bioinformatics, Fribourg, Switzerland. FAU - Eckel, Raphael AU - Eckel R AD - Department of Biology, University of Fribourg, Fribourg, Switzerland. AD - Swiss Institute of Bioinformatics, Fribourg, Switzerland. FAU - Leuenberger, Christoph AU - Leuenberger C AD - Department of Biology, University of Fribourg, Fribourg, Switzerland. AD - Swiss Institute of Bioinformatics, Fribourg, Switzerland. FAU - Wegmann, Daniel AU - Wegmann D AUID- ORCID: 0000-0003-2866-6739 AD - Department of Biology, University of Fribourg, Fribourg, Switzerland. AD - Swiss Institute of Bioinformatics, Fribourg, Switzerland. LA - eng GR - 310030_200420/Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ PT - Journal Article DEP - 20240103 PL - England TA - Mol Ecol Resour JT - Molecular ecology resources JID - 101465604 SB - IM MH - Humans MH - Bayes Theorem MH - *Sex Chromosomes/genetics MH - *Genomics MH - Genetic Testing MH - Karyotype OTO - NOTNLM OT - ancient DNA OT - aneuploidy OT - low-depth sequencing OT - molecular sexing OT - sex chromosomes EDAT- 2024/01/04 11:43 MHDA- 2024/03/06 06:44 CRDT- 2024/01/04 01:24 PHST- 2023/11/27 00:00 [revised] PHST- 2023/09/16 00:00 [received] PHST- 2023/11/30 00:00 [accepted] PHST- 2024/03/06 06:44 [medline] PHST- 2024/01/04 11:43 [pubmed] PHST- 2024/01/04 01:24 [entrez] AID - 10.1111/1755-0998.13913 [doi] PST - ppublish SO - Mol Ecol Resour. 2024 Apr;24(3):e13913. doi: 10.1111/1755-0998.13913. Epub 2024 Jan 3. PMID- 38612593 OWN - NLM STAT- MEDLINE DCOM- 20240415 LR - 20240425 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 25 IP - 7 DP - 2024 Mar 28 TI - Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals. LID - 10.3390/ijms25073785 [doi] LID - 3785 AB - The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes. FAU - Ferreira, Renata C AU - Ferreira RC AD - Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil. FAU - Rodrigues, Camila R AU - Rodrigues CR AD - Graduate Program in Microbiology and Immunology, Federal University of São Paulo, São Paulo 04039032, SP, Brazil. FAU - Broach, James R AU - Broach JR AUID- ORCID: 0000-0003-1197-0312 AD - Department of Biochemistry, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA. FAU - Briones, Marcelo R S AU - Briones MRS AUID- ORCID: 0000-0001-8045-2477 AD - Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil. LA - eng GR - 20/08943-5/Fundação de Amparo à Pesquisa do Estado de São Paulo/ GR - 311154/2021-2/National Council for Scientific and Technological Development/ PT - Journal Article DEP - 20240328 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (Nucleotides) SB - IM MH - Humans MH - Animals MH - *Neanderthals/genetics MH - *Genome, Mitochondrial MH - Mutation MH - *Alzheimer Disease MH - Nucleotides PMC - PMC11012180 OTO - NOTNLM OT - SNPs OT - ancient DNA OT - human genome OT - mitochondrial genome OT - neanderthal admixture COIS- The authors declare no conflicts of interest. EDAT- 2024/04/13 10:43 MHDA- 2024/04/15 06:42 PMCR- 2024/03/28 CRDT- 2024/04/13 01:14 PHST- 2024/01/25 00:00 [received] PHST- 2024/03/12 00:00 [revised] PHST- 2024/03/13 00:00 [accepted] PHST- 2024/04/15 06:42 [medline] PHST- 2024/04/13 10:43 [pubmed] PHST- 2024/04/13 01:14 [entrez] PHST- 2024/03/28 00:00 [pmc-release] AID - ijms25073785 [pii] AID - ijms-25-03785 [pii] AID - 10.3390/ijms25073785 [doi] PST - epublish SO - Int J Mol Sci. 2024 Mar 28;25(7):3785. doi: 10.3390/ijms25073785. PMID- 38517967 OWN - NLM STAT- MEDLINE DCOM- 20240325 LR - 20240325 IS - 2375-2548 (Electronic) IS - 2375-2548 (Linking) VI - 10 IP - 12 DP - 2024 Mar 22 TI - Isotopic biographies reveal horse rearing and trading networks in medieval London. PG - eadj5782 LID - 10.1126/sciadv.adj5782 [doi] LID - eadj5782 AB - This paper reports a high-resolution isotopic study of medieval horse mobility, revealing their origins and in-life mobility both regionally and internationally. The animals were found in an unusual horse cemetery site found within the City of Westminster, London, England. Enamel strontium, oxygen, and carbon isotope analysis of 15 individuals provides information about likely place of birth, diet, and mobility during the first approximately 5 years of life. Results show that at least seven horses originated outside of Britain in relatively cold climates, potentially in Scandinavia or the Western Alps. Ancient DNA sexing data indicate no consistent sex-specific mobility patterning, although three of the five females came from exceptionally highly radiogenic regions. Another female with low mobility is suggested to be a sedentary broodmare. Our results provide direct and unprecedented evidence for a variety of horse movement and trading practices in the Middle Ages and highlight the importance of international trade in securing high-quality horses for medieval London elites. FAU - Pryor, Alexander J E AU - Pryor AJE AUID- ORCID: 0000-0002-1669-3513 AD - Department of Archaeology and History, University of Exeter, Exeter, UK. FAU - Ameen, Carly AU - Ameen C AUID- ORCID: 0000-0002-4580-2125 AD - Department of Archaeology and History, University of Exeter, Exeter, UK. FAU - Liddiard, Robert AU - Liddiard R AUID- ORCID: 0009-0005-6944-3971 AD - School of History, University of East Anglia, Norwich, UK. FAU - Baker, Gary AU - Baker G AUID- ORCID: 0009-0005-8767-3914 AD - Department of History, University of Southampton, Southampton, UK. FAU - Kanne, Katherine S AU - Kanne KS AUID- ORCID: 0000-0003-0808-3501 AD - Department of Archaeology and History, University of Exeter, Exeter, UK. AD - School of Archaeology, University College Dublin, Dublin, Ireland. FAU - Milton, J Andy AU - Milton JA AUID- ORCID: 0000-0003-4245-5532 AD - School of Ocean and Earth Sciences, University of Southampton, Southampton, UK. FAU - Standish, Christopher D AU - Standish CD AUID- ORCID: 0000-0002-9726-295X AD - School of Ocean and Earth Sciences, University of Southampton, Southampton, UK. FAU - Hambach, Bastian AU - Hambach B AUID- ORCID: 0000-0003-4546-5672 AD - School of Ocean and Earth Sciences, University of Southampton, Southampton, UK. FAU - Orlando, Ludovic AU - Orlando L AUID- ORCID: 0000-0003-3936-1850 AD - Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Toulouse, France. FAU - Chauvey, Lorelei AU - Chauvey L AUID- ORCID: 0000-0002-5015-3924 AD - Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Toulouse, France. FAU - Schiavinato, Stephanie AU - Schiavinato S AUID- ORCID: 0000-0001-9007-6305 AD - Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Toulouse, France. FAU - Calvière-Tonasso, Laure AU - Calvière-Tonasso L AUID- ORCID: 0000-0001-5140-074X AD - Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Toulouse, France. FAU - Tressières, Gaetan AU - Tressières G AUID- ORCID: 0000-0001-5827-5398 AD - Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Toulouse, France. FAU - Wagner, Stefanie AU - Wagner S AUID- ORCID: 0000-0003-1737-9021 AD - Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Toulouse, France. FAU - Southon, John AU - Southon J AUID- ORCID: 0000-0001-6168-6235 AD - Department of Earth System Science, University of California Irvine, Irvine, CA, USA. FAU - Shapiro, Beth AU - Shapiro B AUID- ORCID: 0000-0002-2733-7776 AD - Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA. FAU - Pipe, Alan AU - Pipe A AUID- ORCID: 0009-0007-8522-4386 AD - Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA. FAU - Creighton, Oliver H AU - Creighton OH AD - Department of Archaeology and History, University of Exeter, Exeter, UK. FAU - Outram, Alan K AU - Outram AK AUID- ORCID: 0000-0003-3360-089X AD - Department of Archaeology and History, University of Exeter, Exeter, UK. LA - eng PT - Journal Article DEP - 20240322 PL - United States TA - Sci Adv JT - Science advances JID - 101653440 RN - 0 (Oxygen Isotopes) RN - 0 (Strontium Isotopes) SB - IM MH - Humans MH - Middle Aged MH - Male MH - Female MH - Horses MH - Animals MH - London MH - *Commerce MH - *Bone and Bones/chemistry MH - Oxygen Isotopes/analysis MH - Strontium Isotopes/analysis MH - Internationality PMC - PMC10959406 EDAT- 2024/03/22 18:44 MHDA- 2024/03/25 06:44 PMCR- 2024/03/22 CRDT- 2024/03/22 14:03 PHST- 2024/03/25 06:44 [medline] PHST- 2024/03/22 18:44 [pubmed] PHST- 2024/03/22 14:03 [entrez] PHST- 2024/03/22 00:00 [pmc-release] AID - adj5782 [pii] AID - 10.1126/sciadv.adj5782 [doi] PST - ppublish SO - Sci Adv. 2024 Mar 22;10(12):eadj5782. doi: 10.1126/sciadv.adj5782. Epub 2024 Mar 22. PMID- 37580949 OWN - NLM STAT- MEDLINE DCOM- 20240306 LR - 20240306 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 81 IP - 2 DP - 2024 Mar 21 TI - X-chromosomal STRs in aDNA kinship analysis. PG - 131-138 LID - 10.1127/anthranz/2023/1714 [doi] AB - The analysis of ancient DNA (aDNA) from human skeletal remains can provide useful insights when investigating archaeological finds. One popular application of aDNA is to examine genealogical relationships between individuals recovered at the same archaeological site. For the reconstruction of genealogical relationships, several genetic markers are commonly used: autosomal STRs, mitochondrial lineages (based on SNP-analysis) and Y-chromosomal haplotypes (based on Y-STR-analysis). In this paper, we present the additional opportunities that X-STRs provide in aDNA kinship reconstruction, especially in deficiency cases and for the examination of father-daughter relationships. Possible applications are demonstrated on a range of different kinship reconstructions: confirmation of half-siblingship in the Lichtenstein cave (Germany), exclusion of two potential father-daughter relationships in Goslar (Germany), investigation of three siblingships in Boilstädt (Germany) as well as the confirmation of a father-daughter relationship in Stolpe (Germany). This study shows that the analysis of X-STRs can contribute to the investigation of relationship constellations otherwise difficult to approach (e.g. father-daughter relationships) and that X-STRs are useful to support and complement autosomal STRs, mtDNA and Y-STR data. FAU - Bretschneider, Anna AU - Bretschneider A AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. FAU - Mazanec, Janine AU - Mazanec J AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. FAU - Wittmeier, Patrick AU - Wittmeier P AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. FAU - Flux, Anna Lena AU - Flux AL AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. FAU - Schmidt, Diane AU - Schmidt D AD - Hessisches Landeskriminalamt, Hölderlinstraße 1-5, 65187, Wiesbaden, Germany. FAU - Hummel, Susanne AU - Hummel S AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. LA - eng PT - Journal Article PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - *DNA, Ancient MH - Haplotypes/genetics MH - *DNA, Mitochondrial/genetics MH - Germany MH - Body Remains MH - Microsatellite Repeats/genetics MH - Chromosomes, Human, Y/genetics EDAT- 2023/08/15 06:42 MHDA- 2024/03/06 06:44 CRDT- 2023/08/15 02:32 PHST- 2023/03/03 00:00 [received] PHST- 2023/06/27 00:00 [revised] PHST- 2023/06/27 00:00 [accepted] PHST- 2024/03/06 06:44 [medline] PHST- 2023/08/15 06:42 [pubmed] PHST- 2023/08/15 02:32 [entrez] AID - 10.1127/anthranz/2023/1714 [doi] PST - ppublish SO - Anthropol Anz. 2024 Mar 21;81(2):131-138. doi: 10.1127/anthranz/2023/1714. PMID- 38417441 OWN - NLM STAT- MEDLINE DCOM- 20240318 LR - 20241103 IS - 2666-979X (Electronic) IS - 2666-979X (Linking) VI - 4 IP - 3 DP - 2024 Mar 13 TI - Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria. PG - 100507 LID - S2666-979X(24)00034-X [pii] LID - 10.1016/j.xgen.2024.100507 [doi] LID - 100507 AB - The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region. CI - Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Martiniano, Rui AU - Martiniano R AD - School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK. Electronic address: r.martiniano@ljmu.ac.uk. FAU - Haber, Marc AU - Haber M AD - Institute of Cancer and Genomic Sciences, University of Birmingham Dubai, Dubai, United Arab Emirates. FAU - Almarri, Mohamed A AU - Almarri MA AD - Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates. FAU - Mattiangeli, Valeria AU - Mattiangeli V AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Kuijpers, Mirte C M AU - Kuijpers MCM AD - Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA. FAU - Chamel, Berenice AU - Chamel B AD - Institut Français du Proche-Orient (MEAE/CNRS), Beirut, Lebanon. FAU - Breslin, Emily M AU - Breslin EM AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Littleton, Judith AU - Littleton J AD - School of Social Sciences, University of Auckland, Auckland, New Zealand. FAU - Almahari, Salman AU - Almahari S AD - Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain. FAU - Aloraifi, Fatima AU - Aloraifi F AD - Mersey and West Lancashire Teaching Hospitals NHS Trust, Whiston Hospital, Warrington Road, Prescot, L35 5DR Liverpool, UK. FAU - Bradley, Daniel G AU - Bradley DG AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Lombard, Pierre AU - Lombard P AD - Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain; Archéorient UMR 5133, CNRS, Université Lyon 2, Maison de l'Orient et de la Méditerranée - Jean Pouilloux, Lyon, France. FAU - Durbin, Richard AU - Durbin R AD - Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK. Electronic address: rd109@cam.ac.uk. LA - eng GR - 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom GR - 205072/WT_/Wellcome Trust/United Kingdom GR - 207492/WT_/Wellcome Trust/United Kingdom GR - 205072/Z/16/Z/WT_/Wellcome Trust/United Kingdom GR - WT_/Wellcome Trust/United Kingdom PT - Journal Article DEP - 20240227 PL - United States TA - Cell Genom JT - Cell genomics JID - 9918284260106676 RN - 0 (DNA, Ancient) RN - Arabian people SB - IM MH - Humans MH - *Arabs/genetics MH - Bahrain MH - *DNA, Ancient MH - *Genetics, Population MH - *Genome, Human PMC - PMC10943591 MID - EMS194653 OTO - NOTNLM OT - Arabia OT - ancient DNA OT - genomics OT - human genetics OT - malaria adaptation COIS- Declaration of interests The authors declare no competing interests. EDAT- 2024/02/29 00:43 MHDA- 2024/03/18 06:43 PMCR- 2024/02/27 CRDT- 2024/02/28 18:41 PHST- 2023/08/04 00:00 [received] PHST- 2023/11/01 00:00 [revised] PHST- 2024/01/31 00:00 [accepted] PHST- 2024/03/18 06:43 [medline] PHST- 2024/02/29 00:43 [pubmed] PHST- 2024/02/28 18:41 [entrez] PHST- 2024/02/27 00:00 [pmc-release] AID - S2666-979X(24)00034-X [pii] AID - 100507 [pii] AID - 10.1016/j.xgen.2024.100507 [doi] PST - ppublish SO - Cell Genom. 2024 Mar 13;4(3):100507. doi: 10.1016/j.xgen.2024.100507. Epub 2024 Feb 27. PMID- 38453993 OWN - NLM STAT- MEDLINE DCOM- 20240311 LR - 20240311 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 14 IP - 1 DP - 2024 Mar 7 TI - Identification of microbial pathogens in Neolithic Scandinavian humans. PG - 5630 LID - 10.1038/s41598-024-56096-0 [doi] LID - 5630 AB - With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts. CI - © 2024. The Author(s). FAU - Bergfeldt, Nora AU - Bergfeldt N AD - Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden. nora.bergfeldt@zoologi.su.se. AD - Department of Zoology, Stockholm University, Stockholm, Sweden. nora.bergfeldt@zoologi.su.se. AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden. nora.bergfeldt@zoologi.su.se. FAU - Kırdök, Emrah AU - Kırdök E AD - Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey. FAU - Oskolkov, Nikolay AU - Oskolkov N AD - Science for Life Laboratory, Department of Biology, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden. FAU - Mirabello, Claudio AU - Mirabello C AD - Science for Life Laboratory, Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden. FAU - Unneberg, Per AU - Unneberg P AD - Science for Life Laboratory, Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden. FAU - Malmström, Helena AU - Malmström H AD - Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden. FAU - Fraser, Magdalena AU - Fraser M AD - Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden. FAU - Sanchez-Quinto, Federico AU - Sanchez-Quinto F AD - Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden. FAU - Jorgensen, Roger AU - Jorgensen R AD - Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway. FAU - Skar, Birgitte AU - Skar B AD - Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway. FAU - Lidén, Kerstin AU - Lidén K AD - Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden. FAU - Storå, Jan AU - Storå J AD - Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Götherström, Anders AU - Götherström A AD - Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden. AD - Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. LA - eng GR - 2017-02503/Vetenskapsrådet/ GR - 2019-00849/Vetenskapsrådet/ GR - P21-0266/Riksbankens Jubileumsfond/ GR - P19.0740:1/Riksbankens Jubileumsfond/ PT - Journal Article DEP - 20240307 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - Agriculture MH - *DNA, Mitochondrial/genetics MH - Europe MH - History, Ancient MH - *Yersinia/classification/isolation & purification MH - *Microbiota PMC - PMC10920878 COIS- The authors declare no competing interests. EDAT- 2024/03/08 00:43 MHDA- 2024/03/11 06:43 PMCR- 2024/03/07 CRDT- 2024/03/07 23:41 PHST- 2023/06/01 00:00 [received] PHST- 2024/03/01 00:00 [accepted] PHST- 2024/03/11 06:43 [medline] PHST- 2024/03/08 00:43 [pubmed] PHST- 2024/03/07 23:41 [entrez] PHST- 2024/03/07 00:00 [pmc-release] AID - 10.1038/s41598-024-56096-0 [pii] AID - 56096 [pii] AID - 10.1038/s41598-024-56096-0 [doi] PST - epublish SO - Sci Rep. 2024 Mar 7;14(1):5630. doi: 10.1038/s41598-024-56096-0. PMID- 38446809 OWN - NLM STAT- MEDLINE DCOM- 20240308 LR - 20240308 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 19 IP - 3 DP - 2024 TI - Shrouded in history: Unveiling the ways of life of an early Muslim population in Santarém, Portugal (8th- 10th century AD). PG - e0299958 LID - 10.1371/journal.pone.0299958 [doi] LID - e0299958 AB - In around 716 AD, the city of Santarém, Portugal, was conquered by the Berber and Arab armies that swept the Iberian Peninsula and went on to rule the region until the 12th century. Archaeological excavations in 2007/08 discovered an Islamic necropolis (Avenida 5 de Outubro #2-8) that appears to contain the remains of an early Muslim population in Santarém (8th- 10th century). In this study, skeletal material from 58 adult individuals was analysed for stable carbon (δ13Ccol; δ13Cap), nitrogen (δ15N) and sulphur (δ34S) isotope ratios in bones, and stable oxygen (δ18O), carbon (δ13Cen) and radiogenic strontium (87Sr/86Sr) isotopes in tooth enamel. The results of this study revealed a dietary pattern of predominantly C3-plant and domestic C3-fed herbivore consumption during adulthood (δ13Ccol and δ15N, respectively) but a higher proportion of C4-plant input during childhood (δ13Cen) for some individuals-interpreted as possible childhood consumption of millet porridge, a common practice in North Africa-in those with unorthodox burial types (Groups 1 and 2) that was not practiced in the individuals with canonical burials (Group 3). In this first mobility study of a medieval Muslim population in Portugal, δ18ODW values revealed greater heterogeneity in Groups 1 and 2, consistent with diverse origins, some in more humid regions than Santarém when compared to regional precipitation δ18O data, contrasting the more homogenous Group 3, consistent with the local precipitation δ18O range. Ancient DNA analysis conducted on three individuals revealed maternal (mtDNA) and paternal (Y-chromosome) lineages compatible with a North African origin for (at least) some of the individuals. Additionally, mobility of females in this population was higher than males, potentially resulting from a patrilocal social system, practiced in Berber and Arab communities. These results serve to offer a more detailed insight into the ancestry and cultural practices of early Muslim populations in Iberia. CI - Copyright: © 2024 MacRoberts et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. FAU - MacRoberts, Rebecca Anne AU - MacRoberts RA AUID- ORCID: 0000-0003-0221-0450 AD - HERCULES Laboratory and IN2PAST, University of Évora, Évora, Portugal. FAU - Liberato, Marco AU - Liberato M AD - Centro de Estudos de Arqueologia, Artes e Ciências do Património (CEAACP), Universidade de Coimbra, Coimbra, Portugal. FAU - Roca-Rada, Xavier AU - Roca-Rada X AUID- ORCID: 0000-0001-7502-6270 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, Australia. AD - Faculdade de Letras, University of Coimbra, Coimbra, Portugal. FAU - Valente, Maria João AU - Valente MJ AUID- ORCID: 0000-0002-6137-5995 AD - Faculdade de Ciências Humanas e Sociais (FCHS), Universidade do Algarve, Faro, Portugal. FAU - Relvado, Claudia AU - Relvado C AD - Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), University of Algarve, Faro, Portugal. FAU - Matos Fernandes, Teresa AU - Matos Fernandes T AD - School of Technology Sciences, Department of Biology, University of Évora, Évora, Portugal. AD - Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal. FAU - Barrocas Dias, Cristina AU - Barrocas Dias C AD - HERCULES Laboratory and IN2PAST, University of Évora, Évora, Portugal. AD - School of Technology Sciences, Department of Chemistry and Biochemistry, University of Évora, Évora, Portugal. FAU - Llamas, Bastien AU - Llamas B AUID- ORCID: 0000-0002-5550-9176 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, Australia. FAU - Vasconcelos Vilar, Hermínia AU - Vasconcelos Vilar H AD - Escola de Ciências Sociais-CIDEHUS, University of Évora, Évora, Portugal. FAU - Schöne, Bernd R AU - Schöne BR AD - Institute of Geosciences, University of Mainz, Mainz, Germany. FAU - Ribeiro, Sara AU - Ribeiro S AUID- ORCID: 0000-0002-5074-5452 AD - Geobiotec, Department of Geosciences, University of Aveiro, Aveiro, Portugal. FAU - Santos, José Francisco AU - Santos JF AUID- ORCID: 0000-0003-4997-8264 AD - Geobiotec, Department of Geosciences, University of Aveiro, Aveiro, Portugal. FAU - Teixeira, João C AU - Teixeira JC AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, Australia. AD - Centre for Interdisciplinary Studies (CEIS20), University of Coimbra, Coimbra, Portugal. AD - Evolution of Cultural Diversity Initiative, The Australian National University, Canberra, Australia. FAU - Maurer, Anne-France AU - Maurer AF AUID- ORCID: 0000-0002-4997-5357 AD - HERCULES Laboratory and IN2PAST, University of Évora, Évora, Portugal. LA - eng PT - Journal Article DEP - 20240306 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Strontium-87) RN - 0 (Strontium-86) RN - 0 (Strontium Isotopes) RN - 7440-44-0 (Carbon) SB - IM MH - Humans MH - Adult MH - Female MH - Male MH - Portugal MH - *Islam MH - *Strontium Isotopes MH - Carbon PMC - PMC10917335 COIS- The authors declare no competing interests that are relevant to the content of this article. EDAT- 2024/03/06 18:42 MHDA- 2024/03/08 06:43 PMCR- 2024/03/06 CRDT- 2024/03/06 13:43 PHST- 2023/07/24 00:00 [received] PHST- 2024/02/19 00:00 [accepted] PHST- 2024/03/08 06:43 [medline] PHST- 2024/03/06 18:42 [pubmed] PHST- 2024/03/06 13:43 [entrez] PHST- 2024/03/06 00:00 [pmc-release] AID - PONE-D-23-22907 [pii] AID - 10.1371/journal.pone.0299958 [doi] PST - epublish SO - PLoS One. 2024 Mar 6;19(3):e0299958. doi: 10.1371/journal.pone.0299958. eCollection 2024. PMID- 38533900 OWN - NLM STAT- MEDLINE DCOM- 20240328 LR - 20241110 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 41 IP - 3 DP - 2024 Mar 1 TI - Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts. LID - 10.1093/molbev/msae017 [doi] LID - msae017 AB - Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Jackson, Iseult AU - Jackson I AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. AD - The SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway, Ireland. FAU - Woodman, Peter AU - Woodman P AD - Department of Archaeology, University College Cork, Cork, Ireland. FAU - Dowd, Marion AU - Dowd M AD - Faculty of Science, Atlantic Technological University, Sligo, Ireland. FAU - Fibiger, Linda AU - Fibiger L AD - School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK. FAU - Cassidy, Lara M AU - Cassidy LM AUID- ORCID: 0000-0001-5005-1963 AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - IRCLA/2022/126/Wellcome Trust Institutional Strategic Support Fund/ GR - 18/CRT/6214/Science Foundation Ireland Centre for Research Training in Genomics Data Science/ PT - Journal Article PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 SB - IM MH - Humans MH - Phylogeny MH - *Streptococcus mutans/genetics MH - Genomics MH - Metagenome MH - *Microbiota PMC - PMC10966897 OTO - NOTNLM OT - Streptococcus mutans OT - Tannerella forsythia OT - ancient pathogen genomics OT - microbial evolution OT - oral microbiome COIS- Conflict of Interest: The authors declare no competing interests. EDAT- 2024/03/27 12:48 MHDA- 2024/03/28 06:45 PMCR- 2024/03/27 CRDT- 2024/03/27 07:13 PHST- 2023/06/30 00:00 [received] PHST- 2024/01/19 00:00 [revised] PHST- 2024/01/26 00:00 [accepted] PHST- 2024/03/28 06:45 [medline] PHST- 2024/03/27 12:48 [pubmed] PHST- 2024/03/27 07:13 [entrez] PHST- 2024/03/27 00:00 [pmc-release] AID - 7617356 [pii] AID - msae017 [pii] AID - 10.1093/molbev/msae017 [doi] PST - ppublish SO - Mol Biol Evol. 2024 Mar 1;41(3):msae017. doi: 10.1093/molbev/msae017. PMID- 38466119 OWN - NLM STAT- MEDLINE DCOM- 20240328 LR - 20241113 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 41 IP - 3 DP - 2024 Mar 1 TI - Predicting Functional Consequences of Recent Natural Selection in Britain. LID - 10.1093/molbev/msae053 [doi] LID - msae053 AB - Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are noncoding, so we expect that a large proportion of the phenotypic effects of selection will also act through noncoding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation [JTI]) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4,500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (false discovery rate [FDR] < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-single nucleotide polymorphism (SNP) selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally, we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Poyraz, Lin AU - Poyraz L AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. AD - Department of Computational Biology, Cornell University, Ithaca, NY, USA. FAU - Colbran, Laura L AU - Colbran LL AUID- ORCID: 0000-0002-7752-6671 AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. FAU - Mathieson, Iain AU - Mathieson I AUID- ORCID: 0000-0002-4256-3982 AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. LA - eng GR - R35 GM133708/GM/NIGMS NIH HHS/United States GR - T32 HG009495/HG/NHGRI NIH HHS/United States GR - R35GM133708/GM/NIGMS NIH HHS/United States GR - grant T32HG009495/HG/NHGRI NIH HHS/United States PT - Journal Article PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) SB - IM UOF - bioRxiv. 2023 Oct 19:2023.10.16.562549. doi: 10.1101/2023.10.16.562549. PMID: 37904954 MH - Humans MH - *DNA, Ancient MH - United Kingdom MH - *Selection, Genetic MH - Genome MH - Genotype MH - Polymorphism, Single Nucleotide MH - Genome-Wide Association Study PMC - PMC10962637 OTO - NOTNLM OT - ancient DNA OT - gene expression OT - human evolution OT - time series COIS- None declared. EDAT- 2024/03/11 12:43 MHDA- 2024/03/28 06:45 PMCR- 2024/03/11 CRDT- 2024/03/11 10:12 PHST- 2023/10/16 00:00 [received] PHST- 2024/02/02 00:00 [revised] PHST- 2024/03/01 00:00 [accepted] PHST- 2024/03/28 06:45 [medline] PHST- 2024/03/11 12:43 [pubmed] PHST- 2024/03/11 10:12 [entrez] PHST- 2024/03/11 00:00 [pmc-release] AID - 7625217 [pii] AID - msae053 [pii] AID - 10.1093/molbev/msae053 [doi] PST - ppublish SO - Mol Biol Evol. 2024 Mar 1;41(3):msae053. doi: 10.1093/molbev/msae053. PMID- 38440408 OWN - NLM STAT- MEDLINE DCOM- 20240306 LR - 20240306 IS - 2167-8359 (Electronic) IS - 2167-8359 (Linking) VI - 12 DP - 2024 TI - Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities. PG - e16770 LID - 10.7717/peerj.16770 [doi] LID - e16770 AB - The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods. CI - © 2024 Eisenhofer et al. FAU - Eisenhofer, Raphael AU - Eisenhofer R AUID- ORCID: 0000-0002-3843-0749 AD - The Globe Institute, University of Copenhagen, Copenhagan, Denmark. FAU - Wright, Sterling AU - Wright S AUID- ORCID: 0000-0003-0526-9132 AD - Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States. FAU - Weyrich, Laura AU - Weyrich L AD - Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States. AD - Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States. AD - School of Biological Sciences, University of Adelaide, Adelaide, Australia. LA - eng PT - Journal Article DEP - 20240301 PL - United States TA - PeerJ JT - PeerJ JID - 101603425 RN - 0 (RNA, Ribosomal, 16S) RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - RNA, Ribosomal, 16S/genetics MH - *Benchmarking MH - Genes, rRNA MH - Dental Calculus MH - *Microbiota MH - DNA, Ancient PMC - PMC10911074 OTO - NOTNLM OT - 16S rRNA gene OT - Ancient DNA OT - Bioinformatics OT - Dental calculus OT - Hybridization capture OT - Oral microbiome OT - Paleomicrobiology OT - Shotgun metagenomics COIS- The authors declare that they have no competing interests. EDAT- 2024/03/05 06:45 MHDA- 2024/03/06 06:43 PMCR- 2024/03/01 CRDT- 2024/03/05 03:56 PHST- 2023/08/31 00:00 [received] PHST- 2023/12/16 00:00 [accepted] PHST- 2024/03/06 06:43 [medline] PHST- 2024/03/05 06:45 [pubmed] PHST- 2024/03/05 03:56 [entrez] PHST- 2024/03/01 00:00 [pmc-release] AID - 16770 [pii] AID - 10.7717/peerj.16770 [doi] PST - epublish SO - PeerJ. 2024 Mar 1;12:e16770. doi: 10.7717/peerj.16770. eCollection 2024. PMID- 38267579 OWN - NLM STAT- MEDLINE DCOM- 20240308 LR - 20241010 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 627 IP - 8002 DP - 2024 Mar TI - Redefining the treponemal history through pre-Columbian genomes from Brazil. PG - 182-188 LID - 10.1038/s41586-023-06965-x [doi] AB - The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions(1,2). Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico(3-6). However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses. CI - © 2024. The Author(s). FAU - Majander, Kerttu AU - Majander K AUID- ORCID: 0000-0002-7922-4482 AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. kerttu.majander@gmail.com. AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. kerttu.majander@gmail.com. AD - Department of Environmental Sciences, University of Basel, Basel, Switzerland. kerttu.majander@gmail.com. FAU - Pla-Díaz, Marta AU - Pla-Díaz M AD - Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain. AD - CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain. FAU - du Plessis, Louis AU - du Plessis L AUID- ORCID: 0000-0003-0352-6289 AD - Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. AD - Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, Switzerland. FAU - Arora, Natasha AU - Arora N AD - Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland. FAU - Filippini, Jose AU - Filippini J AD - Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil. FAU - Pezo-Lanfranco, Luis AU - Pezo-Lanfranco L AD - Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil. AD - Institute of Environmental Science and Technology (ICTA) and Prehistory Department, Universitat Autònoma de Barcelona, Bellaterra, Spain. FAU - Eggers, Sabine AU - Eggers S AUID- ORCID: 0000-0003-4002-0754 AD - Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil. AD - Department of Anthropology, Natural History Museum Vienna, Vienna, Austria. FAU - González-Candelas, Fernando AU - González-Candelas F AUID- ORCID: 0000-0002-0879-5798 AD - Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain. fernando.gonzalez@uv.es. AD - CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain. fernando.gonzalez@uv.es. FAU - Schuenemann, Verena J AU - Schuenemann VJ AUID- ORCID: 0000-0002-8593-3672 AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. verena.schuenemann@iem.uzh.ch. AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. verena.schuenemann@iem.uzh.ch. AD - Department of Environmental Sciences, University of Basel, Basel, Switzerland. verena.schuenemann@iem.uzh.ch. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria. verena.schuenemann@iem.uzh.ch. LA - eng PT - Journal Article DEP - 20240124 PL - England TA - Nature JT - Nature JID - 0410462 SB - IM MH - Humans MH - Brazil/epidemiology/ethnology MH - Europe/epidemiology MH - *Evolution, Molecular MH - *Genome, Bacterial/genetics MH - History, 15th Century MH - History, Ancient MH - Syphilis/epidemiology/history/microbiology/transmission MH - *Treponema pallidum/classification/genetics/isolation & purification MH - *Treponemal Infections/epidemiology/history/microbiology/transmission PMC - PMC10917687 COIS- The authors declare no competing interests. EDAT- 2024/01/25 00:42 MHDA- 2024/03/08 06:42 PMCR- 2024/01/24 CRDT- 2024/01/24 23:22 PHST- 2023/05/25 00:00 [received] PHST- 2023/12/12 00:00 [accepted] PHST- 2024/03/08 06:42 [medline] PHST- 2024/01/25 00:42 [pubmed] PHST- 2024/01/24 23:22 [entrez] PHST- 2024/01/24 00:00 [pmc-release] AID - 10.1038/s41586-023-06965-x [pii] AID - 6965 [pii] AID - 10.1038/s41586-023-06965-x [doi] PST - ppublish SO - Nature. 2024 Mar;627(8002):182-188. doi: 10.1038/s41586-023-06965-x. Epub 2024 Jan 24. PMID- 38428387 OWN - NLM STAT- MEDLINE DCOM- 20240304 LR - 20240308 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 187 IP - 5 DP - 2024 Feb 29 TI - Ancient genomes and the evolutionary path of modern humans. PG - 1042-1046 LID - S0092-8674(24)00116-8 [pii] LID - 10.1016/j.cell.2024.01.047 [doi] AB - Growing evidence from archaic and early modern human genomes brings new insights to the emergence of modern humans. We recount recent information collected from ancient DNA studies that inform us about the evolutionary pathway to modern humanity. These findings point to both individual- and population-level advantages underlying modern human expansion. CI - Copyright © 2024 Elsevier Inc. All rights reserved. FAU - Bennett, E Andrew AU - Bennett EA AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China. Electronic address: e.andrew.bennett@ivpp.ac.cn. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; University of the Chinese Academy of Sciences, Beijing 100049, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng PT - Journal Article PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Humans MH - *Biological Evolution MH - *DNA, Ancient MH - Genome, Human MH - *Hominidae/genetics COIS- Declaration of interests The authors declare no competing interests. EDAT- 2024/03/02 10:43 MHDA- 2024/03/04 06:46 CRDT- 2024/03/01 18:21 PHST- 2023/10/19 00:00 [received] PHST- 2023/12/21 00:00 [revised] PHST- 2024/01/29 00:00 [accepted] PHST- 2024/03/04 06:46 [medline] PHST- 2024/03/02 10:43 [pubmed] PHST- 2024/03/01 18:21 [entrez] AID - S0092-8674(24)00116-8 [pii] AID - 10.1016/j.cell.2024.01.047 [doi] PST - ppublish SO - Cell. 2024 Feb 29;187(5):1042-1046. doi: 10.1016/j.cell.2024.01.047. PMID- 38261973 OWN - NLM STAT- MEDLINE DCOM- 20240229 LR - 20240316 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 52 IP - 4 DP - 2024 Feb 28 TI - Reconstructing DNA methylation maps of ancient populations. PG - 1602-1612 LID - 10.1093/nar/gkad1232 [doi] AB - Studying premortem DNA methylation from ancient DNA (aDNA) provides a proxy for ancient gene activity patterns, and hence valuable information on evolutionary changes in gene regulation. Due to statistical limitations, current methods to reconstruct aDNA methylation maps are constrained to high-coverage shotgun samples, which comprise a small minority of available ancient samples. Most samples are sequenced using in-situ hybridization capture sequencing which targets a predefined set of genomic positions. Here, we develop methods to reconstruct aDNA methylation maps of samples that were not sequenced using high-coverage shotgun sequencing, by way of pooling together individuals to obtain a DNA methylation map that is characteristic of a population. We show that the resulting DNA methylation maps capture meaningful biological information and allow for the detection of differential methylation across populations. We offer guidelines on how to carry out comparative studies involving ancient populations, and how to control the rate of falsely discovered differentially methylated regions. The ability to reconstruct DNA methylation maps of past populations allows for the development of a whole new frontier in paleoepigenetic research, tracing DNA methylation changes throughout human history, using data from thousands of ancient samples. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research. FAU - Barouch, Arielle AU - Barouch A AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. AD - School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. FAU - Mathov, Yoav AU - Mathov Y AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. AD - Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. FAU - Meshorer, Eran AU - Meshorer E AUID- ORCID: 0000-0003-4777-986X AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. AD - Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. FAU - Yakir, Benjamin AU - Yakir B AD - Department of Statistics and Data Science, The Hebrew University of Jerusalem, Jerusalem 9190500, Israel. FAU - Carmel, Liran AU - Carmel L AUID- ORCID: 0000-0003-0225-8550 AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel. LA - eng GR - 2436/22/Israel Science Foundation/ GR - 61739/John Templeton Foundation/ GR - 1001584586/Israel Ministry of Innovation, Science & Technology/ PT - Journal Article PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA Methylation/genetics MH - *DNA, Ancient MH - Genome MH - Genomics MH - Sequence Analysis, DNA/methods MH - Human Genetics PMC - PMC10939417 EDAT- 2024/01/23 18:42 MHDA- 2024/02/29 06:42 PMCR- 2024/01/23 CRDT- 2024/01/23 16:03 PHST- 2024/01/19 00:00 [accepted] PHST- 2023/12/09 00:00 [revised] PHST- 2023/01/11 00:00 [received] PHST- 2024/02/29 06:42 [medline] PHST- 2024/01/23 18:42 [pubmed] PHST- 2024/01/23 16:03 [entrez] PHST- 2024/01/23 00:00 [pmc-release] AID - 7585666 [pii] AID - gkad1232 [pii] AID - 10.1093/nar/gkad1232 [doi] PST - ppublish SO - Nucleic Acids Res. 2024 Feb 28;52(4):1602-1612. doi: 10.1093/nar/gkad1232. PMID- 38363870 OWN - NLM STAT- MEDLINE DCOM- 20240219 LR - 20240304 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 121 IP - 9 DP - 2024 Feb 27 TI - The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. PG - e2312377121 LID - 10.1073/pnas.2312377121 [doi] LID - e2312377121 AB - Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets. FAU - Simon, Alexis AU - Simon A AUID- ORCID: 0000-0002-6176-5045 AD - Center for Population Biology, University of California, Davis, CA 95616. AD - Department of Evolution and Ecology, University of California, Davis, CA 95616. FAU - Coop, Graham AU - Coop G AD - Center for Population Biology, University of California, Davis, CA 95616. AD - Department of Evolution and Ecology, University of California, Davis, CA 95616. LA - eng GR - R35 GM136290/GM/NIGMS NIH HHS/United States GR - R35 GM136290/GF/NIH HHS/United States PT - Journal Article DEP - 20240216 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM UOF - bioRxiv. 2024 Jan 11:2023.07.11.548607. doi: 10.1101/2023.07.11.548607. PMID: 37503227 MH - Humans MH - *Gene Flow MH - *Selection, Genetic MH - DNA, Ancient MH - Gene Frequency MH - Genetic Drift MH - Genetics, Population PMC - PMC10907250 OTO - NOTNLM OT - ancient DNA OT - gene flow OT - human evolution OT - linked selection OT - time series COIS- Competing interests statement:The authors declare no competing interest. EDAT- 2024/02/16 18:42 MHDA- 2024/02/19 06:43 PMCR- 2024/02/16 CRDT- 2024/02/16 14:06 PHST- 2024/02/19 06:43 [medline] PHST- 2024/02/16 18:42 [pubmed] PHST- 2024/02/16 14:06 [entrez] PHST- 2024/02/16 00:00 [pmc-release] AID - 202312377 [pii] AID - 10.1073/pnas.2312377121 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2024 Feb 27;121(9):e2312377121. doi: 10.1073/pnas.2312377121. Epub 2024 Feb 16. PMID- 38378781 OWN - NLM STAT- MEDLINE DCOM- 20240222 LR - 20240224 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 15 IP - 1 DP - 2024 Feb 20 TI - Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA. PG - 1294 LID - 10.1038/s41467-024-45438-1 [doi] LID - 1294 AB - Aneuploidies, and in particular, trisomies represent the most common genetic aberrations observed in human genetics today. To explore the presence of trisomies in historic and prehistoric populations we screen nearly 10,000 ancient human individuals for the presence of three copies of any of the target autosomes. We find clear genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome), and all cases are present in infant or perinatal burials. We perform comparative osteological examinations of the skeletal remains and find overlapping skeletal markers, many of which are consistent with these syndromes. Interestingly, three cases of trisomy 21, and the case of trisomy 18 were detected in two contemporaneous sites in early Iron Age Spain (800-400 BCE), potentially suggesting a higher frequency of burials of trisomy carriers in those societies. Notably, the care with which the burials were conducted, and the items found with these individuals indicate that ancient societies likely acknowledged these individuals with trisomy 18 and 21 as members of their communities, from the perspective of burial practice. CI - © 2024. The Author(s). FAU - Rohrlach, Adam Benjamin AU - Rohrlach AB AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. adam_ben_rohrlach@eva.mpg.de. AD - School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, SA, Australia. adam_ben_rohrlach@eva.mpg.de. FAU - Rivollat, Maïté AU - Rivollat M AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - ArcheOs lab, Department of Archaeology, Ghent University, Sint-Pietersnieuwstraat 35, 9000, Gent, Belgium. AD - Archaeo-DNA lab, Department of Archaeology, Durham University, Lower Mount Joy, South Road, Durham, DH1 3LE, UK. AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, Bordeaux University, Bât. B8, Allée Geoffroy Saint Hilaire, CS50023, 33615, Pessac cedex, France. FAU - de-Miguel-Ibáñez, Patxuka AU - de-Miguel-Ibáñez P AUID- ORCID: 0000-0003-3957-3378 AD - Department of Prehistory, Archaeology, Ancient History and Greek and Latin Philology, INAPH, University of Alicante, San Vicente del Raspeig, Spain. AD - Sociedad de Ciencias Aranzadi, Donosti, Spain. AD - Hospital Verge dels Lliris, Alcoi, Alicante, Spain. FAU - Moilanen, Ulla AU - Moilanen U AUID- ORCID: 0000-0002-4213-4061 AD - Department of Biology, University of Turku, Turku, Finland. FAU - Liira, Anne-Mari AU - Liira AM AD - Department of Archaeology, University of Turku, Turku, Finland. FAU - Teixeira, João C AU - Teixeira JC AUID- ORCID: 0000-0001-6417-4702 AD - Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT, Australia. AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia. AD - CEIS.20 Centro de Estudos Interdisciplinares, Universidade de Coimbra, Coimbra, Portugal. FAU - Roca-Rada, Xavier AU - Roca-Rada X AUID- ORCID: 0000-0001-7502-6270 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. FAU - Armendáriz-Martija, Javier AU - Armendáriz-Martija J AD - Departamento de Ciencias Humanas y de la Educación, Universidad Pública de Navarra, Pamplona, Spain. FAU - Boyadzhiev, Kamen AU - Boyadzhiev K AD - National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Saborna str. 2, Sofia, Bulgaria. FAU - Boyadzhiev, Yavor AU - Boyadzhiev Y AD - National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Saborna str. 2, Sofia, Bulgaria. FAU - Llamas, Bastien AU - Llamas B AUID- ORCID: 0000-0002-5550-9176 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia. AD - National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia. AD - Telethon Kids Institute, Indigenous Genomics Research Group, Adelaide, SA, Australia. FAU - Tiliakou, Anthi AU - Tiliakou A AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Mötsch, Angela AU - Mötsch A AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. FAU - Tuke, Jonathan AU - Tuke J AD - School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, SA, Australia. FAU - Prevedorou, Eleni-Anna AU - Prevedorou EA AD - Hellenic Center for Bioarchaeology, Athens, Greece. FAU - Polychronakou-Sgouritsa, Naya AU - Polychronakou-Sgouritsa N AD - Department of History and Archaeology, National and Kapodistrian University of Athens, Athens, Greece. FAU - Buikstra, Jane AU - Buikstra J AUID- ORCID: 0000-0003-0206-0165 AD - Department of Anthropology, Arizona State University, Tempe, AZ, USA. FAU - Onkamo, Päivi AU - Onkamo P AD - Department of Biology, University of Turku, Turku, Finland. AD - Department of Biosciences, University of Helsinki, Helsinki, Finland. FAU - Stockhammer, Philipp W AU - Stockhammer PW AUID- ORCID: 0000-0003-4702-9372 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, München, Germany. FAU - Heyne, Henrike O AU - Heyne HO AD - Hasso-Plattner-Institute, University of Potsdam, Potsdam, Germany. AD - Hasso Plattner Institute, Mount Sinai School of Medicine, New York, USA. AD - Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland. FAU - Lemke, Johannes R AU - Lemke JR AUID- ORCID: 0000-0002-4435-6610 AD - Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany. AD - Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany. FAU - Risch, Roberto AU - Risch R AUID- ORCID: 0000-0001-8534-5806 AD - Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain. FAU - Schiffels, Stephan AU - Schiffels S AUID- ORCID: 0000-0002-1017-9150 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Prüfer, Kay AU - Prüfer K AUID- ORCID: 0000-0001-6242-3058 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. pruefer@eva.mpg.de. LA - eng GR - 771234/EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ PT - Journal Article DEP - 20240220 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) SB - IM MH - Pregnancy MH - Female MH - Humans MH - *Down Syndrome/genetics MH - Trisomy/genetics MH - Trisomy 18 Syndrome/genetics MH - *Chromosome Disorders/genetics MH - DNA, Ancient MH - Trisomy 13 Syndrome PMC - PMC10879165 COIS- The authors declare no competing interests. EDAT- 2024/02/21 11:15 MHDA- 2024/02/22 12:12 PMCR- 2024/02/20 CRDT- 2024/02/20 23:52 PHST- 2023/04/02 00:00 [received] PHST- 2024/01/19 00:00 [accepted] PHST- 2024/02/22 12:12 [medline] PHST- 2024/02/21 11:15 [pubmed] PHST- 2024/02/20 23:52 [entrez] PHST- 2024/02/20 00:00 [pmc-release] AID - 10.1038/s41467-024-45438-1 [pii] AID - 45438 [pii] AID - 10.1038/s41467-024-45438-1 [doi] PST - epublish SO - Nat Commun. 2024 Feb 20;15(1):1294. doi: 10.1038/s41467-024-45438-1. PMID- 38341426 OWN - NLM STAT- MEDLINE DCOM- 20240214 LR - 20240318 IS - 2052-4463 (Electronic) IS - 2052-4463 (Linking) VI - 11 IP - 1 DP - 2024 Feb 10 TI - The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. PG - 182 LID - 10.1038/s41597-024-03031-7 [doi] LID - 182 AB - More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR. CI - © 2024. The Author(s). FAU - Mallick, Swapan AU - Mallick S AUID- ORCID: 0000-0002-4531-4439 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. shop@genetics.med.harvard.edu. AD - Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. shop@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Boston, MA, 02115, USA. shop@genetics.med.harvard.edu. FAU - Micco, Adam AU - Micco A AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Boston, MA, 02115, USA. FAU - Mah, Matthew AU - Mah M AUID- ORCID: 0000-0001-8987-6436 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Boston, MA, 02115, USA. FAU - Ringbauer, Harald AU - Ringbauer H AUID- ORCID: 0000-0002-4884-9682 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. FAU - Lazaridis, Iosif AU - Lazaridis I AUID- ORCID: 0000-0002-4094-9347 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. FAU - Olalde, Iñigo AU - Olalde I AUID- ORCID: 0000-0002-2660-6807 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. reich@genetics.med.harvard.edu. LA - eng GR - R01 HG012287/HG/NHGRI NIH HHS/United States PT - Dataset PT - Journal Article DEP - 20240210 PL - England TA - Sci Data JT - Scientific data JID - 101640192 RN - 0 (DNA, Ancient) SB - IM UOF - bioRxiv. 2023 Apr 06:2023.04.06.535797. doi: 10.1101/2023.04.06.535797. PMID: 37066305 MH - Humans MH - *DNA, Ancient MH - *Genome, Human MH - *Genomics MH - Paleontology PMC - PMC10858950 COIS- The authors declare no competing interests. EDAT- 2024/02/11 07:19 MHDA- 2024/02/11 07:20 PMCR- 2024/02/10 CRDT- 2024/02/10 23:14 PHST- 2023/08/10 00:00 [received] PHST- 2024/01/31 00:00 [accepted] PHST- 2024/02/11 07:20 [medline] PHST- 2024/02/11 07:19 [pubmed] PHST- 2024/02/10 23:14 [entrez] PHST- 2024/02/10 00:00 [pmc-release] AID - 10.1038/s41597-024-03031-7 [pii] AID - 3031 [pii] AID - 10.1038/s41597-024-03031-7 [doi] PST - epublish SO - Sci Data. 2024 Feb 10;11(1):182. doi: 10.1038/s41597-024-03031-7. PMID- 38362924 OWN - NLM STAT- MEDLINE DCOM- 20240219 LR - 20240219 IS - 1473-5644 (Electronic) IS - 0022-2615 (Linking) VI - 73 IP - 2 DP - 2024 Feb TI - Bioarchaeological investigation of individuals with suspected multibacillary leprosy from the mediaeval leprosarium of St Mary Magdalen, Winchester, Hampshire, UK. LID - 10.1099/jmm.0.001806 [doi] AB - Introduction. We have examined four burials from the St Mary Magdalen mediaeval leprosarium cemetery in Winchester, Hampshire, UK. One (Sk.8) was a male child, two (Sk.45 and Sk.52) were adolescent females and the fourth (Sk.512) was an adult male. The cemetery was in use between the 10th and 12th centuries. All showed skeletal lesions of leprosy. Additionally, one of the two females (Sk.45) had lesions suggestive of multi-cystic tuberculosis and the second (Sk.52) of leprogenic odontodysplasia (LO), a rare malformation of the roots of the permanent maxillary incisors.Gap statement. Relatively little is known of the manifestations of lepromatous leprosy (LL) in younger individuals from the archaeological record.Aims and Methodology. To address this, we have used ancient DNA testing and osteological examination of the individuals, supplemented with X-ray and microcomputed tomography (micro-CT) scan as necessary to assess the disease status.Results and Conclusions. The presence of Mycobacterium leprae DNA was confirmed in both females, and genotyping showed SNP type 3I-1 strains but with a clear genotypic variation. We could not confirm Mycobacterium tuberculosis complex DNA in the female individual SK.45. High levels of M. leprae DNA were found within the pulp cavities of four maxillary teeth from the male child (Sk.8) with LO, consistent with the theory that the replication of M. leprae in alveolar bone may interfere with root formation at key stages of development. We report our biomolecular findings in these individuals and review the evidence this site has contributed to our knowledge of mediaeval leprosy. FAU - Taylor, G Michael AU - Taylor GM AD - Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, GU2 7XH, Surrey, UK. FAU - White-Iribhogbe, Katie AU - White-Iribhogbe K AD - Centre of African Studies, School of Oriental and African Studies (SOAS), University of London, Thornhaugh Street, Russell Square, London, WC1H 0XG, UK. FAU - Cole, Garrard AU - Cole G AD - UCL Institute of Archaeology, 31-34 Gordon Square, London, WC1H 0PY, UK. FAU - Ashby, David AU - Ashby D AD - School of History, Archaeology and Philosophy, University of Winchester, Sparkford Road, Winchester, Hampshire, SO22 4NR, UK. FAU - Stewart, Graham R AU - Stewart GR AD - Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, GU2 7XH, Surrey, UK. FAU - Dawson-Hobbis, Heidi AU - Dawson-Hobbis H AD - School of History, Archaeology and Philosophy, University of Winchester, Sparkford Road, Winchester, Hampshire, SO22 4NR, UK. LA - eng PT - Journal Article PL - England TA - J Med Microbiol JT - Journal of medical microbiology JID - 0224131 RN - 0 (DNA, Bacterial) SB - IM MH - Adult MH - Child MH - Humans MH - Male MH - Female MH - Adolescent MH - X-Ray Microtomography MH - *Leprosy/microbiology MH - Mycobacterium leprae/genetics MH - DNA, Bacterial/genetics MH - *Leprosy, Multibacillary MH - United Kingdom OTO - NOTNLM OT - PCR OT - aDNA OT - leprosy OT - mediaeval OT - tuberculosis EDAT- 2024/02/16 12:43 MHDA- 2024/02/19 06:42 CRDT- 2024/02/16 08:00 PHST- 2024/02/19 06:42 [medline] PHST- 2024/02/16 12:43 [pubmed] PHST- 2024/02/16 08:00 [entrez] AID - 10.1099/jmm.0.001806 [doi] PST - ppublish SO - J Med Microbiol. 2024 Feb;73(2). doi: 10.1099/jmm.0.001806. PMID- 38177452 OWN - NLM STAT- MEDLINE DCOM- 20240205 LR - 20240307 IS - 1474-1741 (Electronic) IS - 1474-1733 (Linking) VI - 24 IP - 2 DP - 2024 Feb TI - Ancient DNA reveals evolutionary origins of autoimmune diseases. PG - 85-86 LID - 10.1038/s41577-023-00983-6 [doi] FAU - Barrie, William AU - Barrie W AD - Department of Zoology, University of Cambridge, Cambridge, UK. AD - Department of Genetics, University of Cambridge, Cambridge, UK. FAU - Irving-Pease, Evan K AU - Irving-Pease EK AUID- ORCID: 0000-0003-1940-2192 AD - Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - Department of Zoology, University of Cambridge, Cambridge, UK. ewillerslev@sund.ku.dk. AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. ewillerslev@sund.ku.dk. AD - MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany. ewillerslev@sund.ku.dk. FAU - Iversen, Astrid K N AU - Iversen AKN AD - MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK. astrid.iversen@ndcn.ox.ac.uk. FAU - Fugger, Lars AU - Fugger L AUID- ORCID: 0000-0003-2883-3226 AD - MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK. lars.fugger@ndcn.ox.ac.uk. AD - Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK. lars.fugger@ndcn.ox.ac.uk. LA - eng PT - Journal Article PL - England TA - Nat Rev Immunol JT - Nature reviews. Immunology JID - 101124169 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - Biological Evolution MH - Evolution, Molecular MH - *Autoimmune Diseases/genetics EDAT- 2024/01/05 00:42 MHDA- 2024/02/05 06:42 CRDT- 2024/01/04 23:26 PHST- 2024/02/05 06:42 [medline] PHST- 2024/01/05 00:42 [pubmed] PHST- 2024/01/04 23:26 [entrez] AID - 10.1038/s41577-023-00983-6 [pii] AID - 10.1038/s41577-023-00983-6 [doi] PST - ppublish SO - Nat Rev Immunol. 2024 Feb;24(2):85-86. doi: 10.1038/s41577-023-00983-6. PMID- 38081999 OWN - NLM STAT- MEDLINE DCOM- 20240228 LR - 20240229 IS - 2397-3374 (Electronic) IS - 2397-3374 (Linking) VI - 8 IP - 2 DP - 2024 Feb TI - Socio-cultural practices may have affected sex differences in stature in Early Neolithic Europe. PG - 243-255 LID - 10.1038/s41562-023-01756-w [doi] AB - The rules and structure of human culture impact health as much as genetics or environment. To study these relationships, we combine ancient DNA (n = 230), skeletal metrics (n = 391), palaeopathology (n = 606) and dietary stable isotopes (n = 873) to analyse stature variation in Early Neolithic Europeans from North Central, South Central, Balkan and Mediterranean regions. In North Central Europe, stable isotopes and linear enamel hypoplasias indicate high environmental stress across sexes, but female stature is low, despite polygenic scores identical to males, and suggests that cultural factors preferentially supported male recovery from stress. In Mediterranean populations, sexual dimorphism is reduced, indicating male vulnerability to stress and no strong cultural preference for males. Our analysis indicates that biological effects of sex-specific inequities can be linked to cultural influences at least as early as 7,000 yr ago, and culture, more than environment or genetics, drove height disparities in Early Neolithic Europe. CI - © 2023. The Author(s), under exclusive licence to Springer Nature Limited. FAU - Cox, Samantha L AU - Cox SL AUID- ORCID: 0000-0003-2557-6711 AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. coxsl@sas.upenn.edu. AD - Physical Anthropology Section, Penn Museum, University of Pennsylvania, Philadelphia, PA, USA. coxsl@sas.upenn.edu. FAU - Nicklisch, Nicole AU - Nicklisch N AUID- ORCID: 0000-0001-7423-8343 AD - Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria. FAU - Francken, Michael AU - Francken M AUID- ORCID: 0000-0001-6336-2111 AD - State Office for Cultural Heritage Management Baden-Württemberg, Osteology, Konstanz, Germany. FAU - Wahl, Joachim AU - Wahl J AD - Paleoanthropology Section, Institute of Archaeological Sciences, Eberhard Karls University, Tübingen, Germany. FAU - Meller, Harald AU - Meller H AUID- ORCID: 0000-0002-7590-0375 AD - State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Alt, Kurt W AU - Alt KW AUID- ORCID: 0000-0001-6938-643X AD - Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria. FAU - Rosenstock, Eva AU - Rosenstock E AUID- ORCID: 0000-0002-6693-4303 AD - Bonn Center for ArchaeoSciences, Universität Bonn, Bonn, Germany. FAU - Mathieson, Iain AU - Mathieson I AUID- ORCID: 0000-0002-4256-3982 AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. mathi@pennmedicine.upenn.edu. LA - eng GR - Al 287/7-1/Deutsche Forschungsgemeinschaft (German Research Foundation)/ GR - Al 287/7-3/Deutsche Forschungsgemeinschaft (German Research Foundation)/ GR - Me 3245/1-1/Deutsche Forschungsgemeinschaft (German Research Foundation)/ GR - Me 3245/1-3/Deutsche Forschungsgemeinschaft (German Research Foundation)/ GR - RO 4148/1-1/Deutsche Forschungsgemeinschaft (German Research Foundation)/ GR - BCS2123627/National Science Foundation (NSF)/ PT - Journal Article DEP - 20231211 PL - England TA - Nat Hum Behav JT - Nature human behaviour JID - 101697750 RN - 0 (DNA, Mitochondrial) RN - 0 (Isotopes) SB - IM MH - Female MH - Male MH - Humans MH - *Genetics, Population MH - *Sex Characteristics MH - DNA, Mitochondrial MH - Europe MH - Isotopes EDAT- 2023/12/12 00:42 MHDA- 2024/02/28 06:44 CRDT- 2023/12/11 23:40 PHST- 2023/02/06 00:00 [received] PHST- 2023/10/09 00:00 [accepted] PHST- 2024/02/28 06:44 [medline] PHST- 2023/12/12 00:42 [pubmed] PHST- 2023/12/11 23:40 [entrez] AID - 10.1038/s41562-023-01756-w [pii] AID - 10.1038/s41562-023-01756-w [doi] PST - ppublish SO - Nat Hum Behav. 2024 Feb;8(2):243-255. doi: 10.1038/s41562-023-01756-w. Epub 2023 Dec 11. PMID- 38288729 OWN - NLM STAT- MEDLINE DCOM- 20240131 LR - 20241211 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 13 DP - 2024 Jan 30 TI - Stable population structure in Europe since the Iron Age, despite high mobility. LID - 10.7554/eLife.79714 [doi] LID - e79714 AB - Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000-3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire's mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history. CI - © 2024, Antonio, Weiß, Gao et al. FAU - Antonio, Margaret L AU - Antonio ML AUID- ORCID: 0000-0003-1049-211X AD - Biomedical Informatics Program, Stanford University, Stanford, United States. FAU - Weiß, Clemens L AU - Weiß CL AUID- ORCID: 0000-0003-3321-3902 AD - Department of Genetics, Stanford University, Stanford, United States. FAU - Gao, Ziyue AU - Gao Z AUID- ORCID: 0000-0001-9244-0238 AD - Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, United States. FAU - Sawyer, Susanna AU - Sawyer S AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Oberreiter, Victoria AU - Oberreiter V AUID- ORCID: 0000-0003-0766-3782 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Moots, Hannah M AU - Moots HM AD - Stanford Archaeology Center, Stanford University, Stanford, United States. AD - University of Chicago, Department of Human Genetics, Chicago, United States. FAU - Spence, Jeffrey P AU - Spence JP AUID- ORCID: 0000-0002-3199-1447 AD - Department of Genetics, Stanford University, Stanford, United States. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Zagorc, Brina AU - Zagorc B AUID- ORCID: 0000-0002-7685-1958 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Praxmarer, Elisa AU - Praxmarer E AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Özdoğan, Kadir Toykan AU - Özdoğan KT AD - Department of History and Art History, Utrecht University, Utrecht, Netherlands. FAU - Demetz, Lea AU - Demetz L AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Gelabert, Pere AU - Gelabert P AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Fernandes, Daniel AU - Fernandes D AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. AD - CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. FAU - Lucci, Michaela AU - Lucci M AD - Dipartimento di Storia Antropologia Religioni Arte Spettacolo, Sapienza University, Rome, Italy. FAU - Alihodžić, Timka AU - Alihodžić T AD - Archaeological Museum Zadar, Zadar, Croatia. FAU - Amrani, Selma AU - Amrani S AD - LBEIG, Population Genetics & Conservation Unit, Department of Cellular and Molecular Biology - Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Algiers, Algeria. FAU - Avetisyan, Pavel AU - Avetisyan P AD - National Academy of Sciences of Armenia, Institute of Archaeology and Ethnography, Yerevan, Armenia. FAU - Baillif-Ducros, Christèle AU - Baillif-Ducros C AUID- ORCID: 0000-0003-3050-3082 AD - French National Institute for Preventive Archaeological Research (INRAP)/CAGT UMR 5288, Toulouse, France. FAU - Bedić, Željka AU - Bedić Ž AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. FAU - Bertrand, Audrey AU - Bertrand A AD - Université Gustave Eiffel - Laboratoire ACP, Paris, France. FAU - Bilić, Maja AU - Bilić M AD - Palisada Ltd, Split, Croatia. FAU - Bondioli, Luca AU - Bondioli L AD - Dipartimento dei Beni Culturali, Archeologia, Storia dell'arte, del Cinema e della Musica, Università di Padova, Padova, Italy. FAU - Borówka, Paulina AU - Borówka P AD - Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland. FAU - Botte, Emmanuel AU - Botte E AD - Aix Marseille Université, CNRS, Centre Camille Jullian, Aix-en-Provence, France. FAU - Burmaz, Josip AU - Burmaz J AD - Kaducej Ltd, Split, Croatia. FAU - Bužanić, Domagoj AU - Bužanić D AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Candilio, Francesca AU - Candilio F AUID- ORCID: 0000-0002-4668-1361 AD - Bioarchaeology Service, Museum of Civilizations, Rome, Italy. FAU - Cvetko, Mirna AU - Cvetko M AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - De Angelis, Daniela AU - De Angelis D AD - Museo Archeologico Nazionale di Tarquinia, Direzione Regionale Musei Lazio, Rome, Italy. FAU - Drnić, Ivan AU - Drnić I AD - Archaeological Museum in Zagreb, Zagreb, Croatia. FAU - Elschek, Kristián AU - Elschek K AD - Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia. FAU - Fantar, Mounir AU - Fantar M AD - Département des Monuments et des Sites Antiques - Institut National du Patrimoine INP, Tunis, Tunisia. FAU - Gaspari, Andrej AU - Gaspari A AD - University of Ljubljana, Faculty of Arts, Department for Archaeology, Ljubljana, Slovenia. FAU - Gasperetti, Gabriella AU - Gasperetti G AD - Soprintendenza Archeologia, belle arti e paesaggio per le province di Sassari e Nuoro, Sassari, Italy. FAU - Genchi, Francesco AU - Genchi F AUID- ORCID: 0000-0002-7696-4207 AD - Department of Oriental Studies, Sapienza University of Rome, Rome, Italy. FAU - Golubović, Snežana AU - Golubović S AD - Institute of Archaeology Belgrade, Belgrade, Serbia. FAU - Hukeľová, Zuzana AU - Hukeľová Z AD - Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia. FAU - Jankauskas, Rimantas AU - Jankauskas R AD - Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania. FAU - Vučković, Kristina Jelinčić AU - Vučković KJ AUID- ORCID: 0000-0002-1236-734X AD - Institute of Archaeology, Zagreb, Croatia. FAU - Jeremić, Gordana AU - Jeremić G AD - Institute of Archaeology Belgrade, Belgrade, Serbia. FAU - Kaić, Iva AU - Kaić I AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Kazek, Kevin AU - Kazek K AD - Université de Lorraine, Centre de Recherche Universitaire Lorrain d' Histoire (CRULH), Nancy, France. FAU - Khachatryan, Hamazasp AU - Khachatryan H AD - Department of Archaeologi, Shirak Centere of Armenological Studies, National Academy of Sciences Republic of Armenia, Gyumri, Armenia. FAU - Khudaverdyan, Anahit AU - Khudaverdyan A AD - Institute of Archaeology and Ethnography of the National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia. FAU - Kirchengast, Sylvia AU - Kirchengast S AUID- ORCID: 0000-0002-3220-7271 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Korać, Miomir AU - Korać M AD - Institute of Archaeology Belgrade, Belgrade, Serbia. FAU - Kozlowski, Valérie AU - Kozlowski V AD - Musée Archéologique de l'Oise, Vendeuil-Caply, France. FAU - Krošláková, Mária AU - Krošláková M AD - Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia. FAU - Kušan Špalj, Dora AU - Kušan Špalj D AD - Archaeological Museum in Zagreb, Zagreb, Croatia. FAU - La Pastina, Francesco AU - La Pastina F AD - Department of Environmental Biology, Sapienza University of Rome, Rome, Italy. FAU - Laguardia, Marie AU - Laguardia M AD - UMR 7041 ArScAn / French Institute of the Near East, Beirut, Lebanon. FAU - Legrand, Sandra AU - Legrand S AD - Musée Archéologique de l'Oise, Vendeuil-Caply, France. FAU - Leleković, Tino AU - Leleković T AD - Archaeology Division, Croatian Academy of Sciences and Arts, Zagreb, Croatia. FAU - Leskovar, Tamara AU - Leskovar T AD - University of Ljubljana, Faculty of Arts, Department for Archaeology, Ljubljana, Slovenia. FAU - Lorkiewicz, Wiesław AU - Lorkiewicz W AUID- ORCID: 0000-0003-0754-5161 AD - Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland. FAU - Los, Dženi AU - Los D AD - Kaducej Ltd, Split, Croatia. FAU - Silva, Ana Maria AU - Silva AM AUID- ORCID: 0000-0002-1912-6581 AD - CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. AD - CEF - University of Coimbra, Coimbra, Portugal. AD - UNIARQ - University of Lisbon, Lisbon, Portugal. FAU - Masaryk, Rene AU - Masaryk R AD - Skupina STIK Zavod za preučevanje povezovalnih področij preteklosti in sedanjosti, Ljubljana, Slovenia. FAU - Matijević, Vinka AU - Matijević V AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Cherifi, Yahia Mehdi Seddik AU - Cherifi YMS AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Cardiolo-Oncology Research Collaborative Group (CORCG), Faculty of Medicine, Benyoucef Benkhedda University, Algiers, Algeria. AD - Molecular Pathology, University Paul Sabatier Toulouse III, Toulouse, France. FAU - Meyer, Nicolas AU - Meyer N AD - French National Institute for Preventive Archaeological Research (INRAP), Metz, France. FAU - Mikić, Ilija AU - Mikić I AD - Institute of Archaeology Belgrade, Belgrade, Serbia. FAU - Miladinović-Radmilović, Nataša AU - Miladinović-Radmilović N AD - Institute of Archaeology Belgrade, Belgrade, Serbia. FAU - Milošević Zakić, Branka AU - Milošević Zakić B AD - Museum of Croatian Archaeological Monuments, Split, Croatia. FAU - Nacouzi, Lina AU - Nacouzi L AD - L'Institut français du Proche-Orient, Beirut, Lebanon. FAU - Natuniewicz-Sekuła, Magdalena AU - Natuniewicz-Sekuła M AD - Institute of Archaeology and Ethnology Polish Academy of Sciences, Centre of Interdisciplinary Archaeological Research, Warsaw, Poland. FAU - Nava, Alessia AU - Nava A AD - Department of Odontostomatological and Maxillofacial Sciences, Sapienza University of Rome, Rome, Italy. FAU - Neugebauer-Maresch, Christine AU - Neugebauer-Maresch C AD - Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria. AD - Institute of Prehistory and Early History, University of Vienna, Vienna, Austria. FAU - Nováček, Jan AU - Nováček J AUID- ORCID: 0000-0003-2707-5347 AD - Thuringia State Service for Cultural Heritage and Archaeology Weimar, Thuringia, Germany. AD - Institute of Anatomy and Cell Biology, University Medical Centre, Georg-August University of Göttingen, Göttingen, Germany. FAU - Osterholtz, Anna AU - Osterholtz A AD - Mississippi State University, Starkville, United States. FAU - Paige, Julianne AU - Paige J AD - University of Nevada, Las Vegas, United States. FAU - Paraman, Lujana AU - Paraman L AD - Trogir Town Museum, Trogir, Croatia. FAU - Pieri, Dominique AU - Pieri D AD - Université Paris 1 Panthéon-Sorbonne, Paris, France. FAU - Pieta, Karol AU - Pieta K AD - Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia. FAU - Pop-Lazić, Stefan AU - Pop-Lazić S AD - Institute of Archaeology Belgrade, Belgrade, Serbia. FAU - Ruttkay, Matej AU - Ruttkay M AUID- ORCID: 0000-0002-6441-9914 AD - Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia. FAU - Sanader, Mirjana AU - Sanader M AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Sołtysiak, Arkadiusz AU - Sołtysiak A AUID- ORCID: 0000-0002-9040-5022 AD - Faculty of Archaeology, University of Warsaw, Warsaw, Poland. FAU - Sperduti, Alessandra AU - Sperduti A AUID- ORCID: 0000-0001-9338-5891 AD - Bioarchaeology Service, Museum of Civilizations, Rome, Italy. AD - Dipartimento Asia, Africa e Mediterraneo, Università degli Studi di Napoli "L'Orientale", Naples, Italy. FAU - Stankovic Pesterac, Tijana AU - Stankovic Pesterac T AD - Museum of Vojvodina, Novi Sad, Serbia. FAU - Teschler-Nicola, Maria AU - Teschler-Nicola M AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Department of Anthropology, Natural History Museum Vienna, Vienna, Austria. FAU - Teul, Iwona AU - Teul I AD - Chair and Department of Normal Anatomy, Faculty of Medicine and Dentistry, Pomeranian Medical University, Szczecin, Poland. FAU - Tončinić, Domagoj AU - Tončinić D AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Trapp, Julien AU - Trapp J AD - Musée de La Cour d'Or, Eurométropole de Metz, Metz, France. FAU - Vulović, Dragana AU - Vulović D AD - Institute of Archaeology Belgrade, Belgrade, Serbia. FAU - Waliszewski, Tomasz AU - Waliszewski T AUID- ORCID: 0000-0002-5793-4600 AD - Faculty of Archaeology, University of Warsaw, Warsaw, Poland. FAU - Walter, Diethard AU - Walter D AD - Thuringia State Service for Cultural Heritage and Archaeology Weimar, Thuringia, Germany. FAU - Živanović, Miloš AU - Živanović M AD - Department of Archeology, Center for Conservation and Archeology of Montenegro, Cetinje, Montenegro. FAU - Filah, Mohamed El Mostefa AU - Filah MEM AD - Insitut d'Archeologie, University Algiers 2, Algiers, Algeria. FAU - Čaušević-Bully, Morana AU - Čaušević-Bully M AD - Université de Franche Comté / UMR Chrono-Environnement, Besançon, France. FAU - Šlaus, Mario AU - Šlaus M AUID- ORCID: 0000-0002-4941-2212 AD - Anthropological Centre, Croatian Academy of Sciences and Arts, Zagreb, Croatia. FAU - Borić, Dušan AU - Borić D AUID- ORCID: 0000-0003-0166-627X AD - Department of Environmental Biology, Sapienza University of Rome, Rome, Italy. AD - Department of Anthropology, New York University, New York, United States. FAU - Novak, Mario AU - Novak M AUID- ORCID: 0000-0002-4567-8742 AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. FAU - Coppa, Alfredo AU - Coppa A AUID- ORCID: 0000-0002-7708-2484 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Department of Environmental Biology, Sapienza University of Rome, Rome, Italy. AD - Department of Genetics, Harvard Medical School, Boston, United States. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Pritchard, Jonathan K AU - Pritchard JK AUID- ORCID: 0000-0002-8828-5236 AD - Department of Genetics, Stanford University, Stanford, United States. AD - Department of Biology, Stanford University, Stanford, United States. LA - eng GR - M 3108/FWF_/Austrian Science Fund FWF/Austria GR - R01 HG011432/HG/NHGRI NIH HHS/United States GR - HG011432/NH/NIH HHS/United States PT - Journal Article DEP - 20240130 PL - England TA - Elife JT - eLife JID - 101579614 RN - 0 (DNA, Ancient) SB - IM UOF - doi: 10.1101/2022.05.15.491973 MH - Humans MH - *DNA, Ancient MH - *Genome, Human MH - Europe MH - France MH - Genetics, Population MH - Population Dynamics MH - Human Migration PMC - PMC10827293 OTO - NOTNLM OT - Roman Empire OT - ancient DNA OT - evolutionary biology OT - genetics OT - genomics OT - human OT - population structure COIS- MA, CW, SS, VO, HM, JS, OC, BZ, EP, KÖ, LD, PG, DF, ML, TA, SA, PA, CB, ŽB, AB, LB, PB, EB, DB, FC, MC, DD, ID, KE, MF, AG, GG, FG, SG, ZH, RJ, KV, GJ, IK, KK, HK, AK, SK, MK, VK, MK, DK, FL, ML, SL, TL, TL, WL, AS, VM, YC, NM, IM, NM, BM, LN, MN, AN, CN, JN, AO, JP, LP, DP, KP, SP, MR, MS, AS, AS, TS, MT, IT, DT, JT, DV, TW, DW, MŽ, MF, MČ, MŠ, DB, MN, AC, RP, JP No competing interests declared, ZG Reviewing editor, eLife, MB Affiliated with Palisada Ltd. The author has no financial interests to declare, JB, DL Affiliated with Kaducej Ltd. The author has no financial interests to declare, RM Affiliated with Skupina STIK. The author has no financial interests to declare EDAT- 2024/01/30 12:44 MHDA- 2024/01/31 06:43 PMCR- 2024/01/30 CRDT- 2024/01/30 07:55 PHST- 2022/04/23 00:00 [received] PHST- 2023/12/12 00:00 [accepted] PHST- 2024/01/31 06:43 [medline] PHST- 2024/01/30 12:44 [pubmed] PHST- 2024/01/30 07:55 [entrez] PHST- 2024/01/30 00:00 [pmc-release] AID - 79714 [pii] AID - 10.7554/eLife.79714 [doi] PST - epublish SO - Elife. 2024 Jan 30;13:e79714. doi: 10.7554/eLife.79714. PMID- 38287404 OWN - NLM STAT- MEDLINE DCOM- 20240131 LR - 20241105 IS - 1479-7364 (Electronic) IS - 1473-9542 (Print) IS - 1473-9542 (Linking) VI - 18 IP - 1 DP - 2024 Jan 29 TI - Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes. PG - 5 LID - 10.1186/s40246-024-00573-0 [doi] LID - 5 AB - BACKGROUND: Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs. METHODS: We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis. RESULTS: Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns. CONCLUSION: Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history. CI - © 2024. The Author(s). FAU - Lei, Huijun AU - Lei H AD - Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China. AD - Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China. AD - Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China. FAU - Li, Jiaheng AU - Li J AD - Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China. FAU - Zhao, Bojin AU - Zhao B AD - Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China. FAU - Kou, Si Hoi AU - Kou SH AD - Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China. FAU - Xiao, Fengxia AU - Xiao F AD - Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China. FAU - Chen, Tianhui AU - Chen T AD - Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China. chenth@zjcc.org.cn. AD - Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China. chenth@zjcc.org.cn. FAU - Wang, San Ming AU - Wang SM AD - Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China. sanmingwang@um.edu.mo. LA - eng GR - 2019YFE0198800/National Key Research-Development Program of China/ GR - 2021R52020/Ten-Thousand Talents Plan of Zhejiang Province/ GR - 085/2017/A2/Macau Science and Technology Development Fund/ GR - 0077/2019/AMJ/Macau Science and Technology Development Fund/ GR - 0032/2022/A1/Macau Science and Technology Development Fund/ GR - SRG2017-00097-FHS/University of Macau/ GR - MYRG2019-00018-FHS/University of Macau/ GR - MYRG2020-00094-FHS/University of Macau/ GR - FHSIG/SW/0007/2020P, MOE Frontiers Science Center for Precision Oncology pilot grant and a startup fund/Faculdade de Ciências da Saúde, Universidade de Macau/ PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240129 PL - England TA - Hum Genomics JT - Human genomics JID - 101202210 RN - Turcot syndrome SB - IM MH - Humans MH - *DNA Mismatch Repair/genetics MH - Phylogeny MH - *Neoplastic Syndromes, Hereditary MH - Germ-Line Mutation/genetics MH - Germ Cells MH - *Brain Neoplasms MH - *Colorectal Neoplasms PMC - PMC10823654 OTO - NOTNLM OT - Ancient genome OT - Conservation OT - DNA mismatch repair OT - Evolutionary origin OT - Pathogenic variant COIS- The authors declare that they have no competing interests. EDAT- 2024/01/30 06:42 MHDA- 2024/01/31 06:43 PMCR- 2024/01/29 CRDT- 2024/01/30 00:01 PHST- 2023/05/27 00:00 [received] PHST- 2024/01/17 00:00 [accepted] PHST- 2024/01/31 06:43 [medline] PHST- 2024/01/30 06:42 [pubmed] PHST- 2024/01/30 00:01 [entrez] PHST- 2024/01/29 00:00 [pmc-release] AID - 10.1186/s40246-024-00573-0 [pii] AID - 573 [pii] AID - 10.1186/s40246-024-00573-0 [doi] PST - epublish SO - Hum Genomics. 2024 Jan 29;18(1):5. doi: 10.1186/s40246-024-00573-0. PMID- 38273870 OWN - NLM STAT- MEDLINE DCOM- 20240129 LR - 20241023 IS - 2214-9996 (Electronic) IS - 2214-9996 (Linking) VI - 90 IP - 1 DP - 2024 TI - Genetic Predisposition of Atherosclerotic Cardiovascular Disease in Ancient Human Remains. PG - 6 LID - 10.5334/aogh.4366 [doi] LID - 6 AB - BACKGROUND: Several computed tomographic studies have shown the presence of atherosclerosis in ancient human remains. However, while it is important to understand the development of atherosclerotic cardiovascular disease (ASCVD), genetic data concerning the prevalence of the disease-associated single nucleotide polymorphisms (SNPs) in our ancestors are scarce. OBJECTIVE: For a better understanding of the role of genetics in the evolution of ASCVD, we applied an enrichment capture sequencing approach to mummified human remains from different geographic regions and time periods. METHODS: Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans. FINDINGS: Five out of 22 ancient individuals passed all filter steps for calculating a weighted polygenic risk score (PRS) based on 87 SNPs in 56 genes. PRSs were correlated to scores obtained from contemporary people from around the world and cover their complete range. The genetic results of the ancient individuals reflect their phenotypic results, given that the only two mummies showing calcified atherosclerotic arterial plaques on computed tomography scans are the ones exhibiting the highest calculated PRSs. CONCLUSIONS: These data show that alleles associated with ASCVD have been widespread for at least 5,000 years. Despite some limitations due to the nature of aDNA, our approach has the potential to lead to a better understanding of the interaction between environmental and genetic influences on the development of ASCVD. CI - Copyright: © 2024 The Author(s). FAU - Wurst, Christina AU - Wurst C AUID- ORCID: 0000-0001-5214-2615 AD - Eurac Research -Institute for Mummy Studies, Bozen/Bolzano, Italy. AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University of Mainz, Mainz, Germany. FAU - Maixner, Frank AU - Maixner F AUID- ORCID: 0000-0003-2846-8994 AD - Eurac Research -Institute for Mummy Studies, Bozen/Bolzano, Italy. FAU - Paladin, Alice AU - Paladin A AUID- ORCID: 0000-0001-5397-195X AD - Eurac Research -Institute for Mummy Studies, Bozen/Bolzano, Italy. FAU - Mussauer, Alexandra AU - Mussauer A AUID- ORCID: 0009-0002-4618-5752 AD - Eurac Research -Institute for Mummy Studies, Bozen/Bolzano, Italy. FAU - Valverde, Guido AU - Valverde G AUID- ORCID: 0000-0001-6201-6030 AD - Eurac Research -Institute for Mummy Studies, Bozen/Bolzano, Italy. FAU - Narula, Jagat AU - Narula J AUID- ORCID: 0000-0002-0280-3996 AD - Medicine & Cardiology, McGovern Medical School, Houston, Texas, USA. FAU - Thompson, Randall AU - Thompson R AUID- ORCID: 0000-0002-4048-8827 AD - Saint Luke's Mid America Heart Institute, Kansas City, MO, USA. FAU - Zink, Albert AU - Zink A AUID- ORCID: 0000-0002-1461-747X AD - Eurac Research -Institute for Mummy Studies, Bozen/Bolzano, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240125 PL - United States TA - Ann Glob Health JT - Annals of global health JID - 101620864 SB - IM MH - Humans MH - *Cardiovascular Diseases MH - Genome-Wide Association Study MH - Body Remains MH - *Atherosclerosis/genetics MH - Genetic Predisposition to Disease MH - Risk Factors MH - Risk Assessment PMC - PMC10809863 OTO - NOTNLM OT - Polygenic Risk Score (PRS) OT - ancient DNA (aDNA) OT - atherosclerosis OT - atherosclerotic cardiovascular disease (ASCVD) OT - calcified atherosclerotic plaques; targeted enrichment capture OT - mummy COIS- Professor Jagat Narula is Executive Editor of the journal Annals of Global Health. None of the other authors have any conflicts of interest. EDAT- 2024/01/26 06:43 MHDA- 2024/01/29 06:42 PMCR- 2024/01/25 CRDT- 2024/01/26 03:44 PHST- 2023/11/17 00:00 [received] PHST- 2023/12/30 00:00 [accepted] PHST- 2024/01/29 06:42 [medline] PHST- 2024/01/26 06:43 [pubmed] PHST- 2024/01/26 03:44 [entrez] PHST- 2024/01/25 00:00 [pmc-release] AID - 10.5334/aogh.4366 [doi] PST - epublish SO - Ann Glob Health. 2024 Jan 25;90(1):6. doi: 10.5334/aogh.4366. eCollection 2024. PMID- 38238372 OWN - NLM STAT- MEDLINE DCOM- 20240130 LR - 20241023 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 13 IP - 1 DP - 2024 Jan 18 TI - Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals. PG - 22125 LID - 10.1038/s41598-023-48762-6 [doi] LID - 22125 AB - Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health. CI - © 2023. The Author(s). FAU - Kırdök, Emrah AU - Kırdök E AD - Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin, Turkey. emrahkirdok@gmail.com. FAU - Kashuba, Natalija AU - Kashuba N AD - Department of Archaeology and Ancient History, Uppsala University, Engelska Parken, Thunbergsvägen 3H Box 626, 751 26, Uppsala, Sweden. FAU - Damlien, Hege AU - Damlien H AD - Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway. FAU - Manninen, Mikael A AU - Manninen MA AD - PAES, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science, University of Helsinki, Viikinkaari 1, P.O. Box 65, Helsinki, Finland. FAU - Nordqvist, Bengt AU - Nordqvist B AD - Foundation War-Booty Site Finnestorp, Klarinettvägen 75, 434 75, Kungsbacka, Sweden. FAU - Kjellström, Anna AU - Kjellström A AD - Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Organismal Biology, Human Evolution, Uppsala University, Evolutionsbiologiskt Centrum EBC Norbyvägen 18 A, Uppsala, Sweden. FAU - Lindberg, A Michael AU - Lindberg AM AD - Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Hus Vita, 44018, Kalmar, Sweden. FAU - Storå, Jan AU - Storå J AD - Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden. FAU - Persson, Per AU - Persson P AD - Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway. FAU - Andersson, Björn AU - Andersson B AD - Department of Cell and Molecular Biology (CMB), Karolinska Insitutet, P.O. Box 285, 171 77, Stockholm, Sweden. FAU - Aravena, Andrés AU - Aravena A AD - Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey. FAU - Götherström, Anders AU - Götherström A AD - Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden. AD - Department of Archaeology and Classical Studies, Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden. LA - eng GR - 2019-3-AP3-3729/Mersin University BAP project/ GR - The Research Council of Norway project no. 231305/Pioneers of NW Europe/ GR - The Research Council of Norway project no. 231305/Pioneers of NW Europe/ GR - The Research Council of Norway project no. 231305/Pioneers of NW Europe/ GR - The Research Council of Norway project no. 231305/Pioneers of NW Europe/ GR - project no. 2019-00849/The Swedish Research Council/ PT - Case Reports PT - Journal Article DEP - 20240118 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Animals MH - Humans MH - Dysbiosis/genetics MH - Metagenome MH - *Microbiota/genetics MH - Oral Health MH - *Periodontitis/genetics PMC - PMC10796427 COIS- The authors declare no competing interests. EDAT- 2024/01/19 00:42 MHDA- 2024/01/22 06:43 PMCR- 2024/01/18 CRDT- 2024/01/18 23:18 PHST- 2023/06/23 00:00 [received] PHST- 2023/11/30 00:00 [accepted] PHST- 2024/01/22 06:43 [medline] PHST- 2024/01/19 00:42 [pubmed] PHST- 2024/01/18 23:18 [entrez] PHST- 2024/01/18 00:00 [pmc-release] AID - 10.1038/s41598-023-48762-6 [pii] AID - 48762 [pii] AID - 10.1038/s41598-023-48762-6 [doi] PST - epublish SO - Sci Rep. 2024 Jan 18;13(1):22125. doi: 10.1038/s41598-023-48762-6. PMID- 38207026 OWN - NLM STAT- MEDLINE DCOM- 20240205 LR - 20240205 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 383 IP - 6679 DP - 2024 Jan 12 TI - Ancient DNA ties modern diseases to ancestry. PG - 138-139 LID - 10.1126/science.adn9644 [doi] AB - Among Europeans, risk of multiple sclerosis rises with genes from Bronze Age Yamnaya herders. FAU - Curry, Andrew AU - Curry A LA - eng PT - News DEP - 20240111 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - Europe/epidemiology MH - Genome, Human MH - *Multiple Sclerosis/epidemiology/genetics/history EDAT- 2024/01/11 18:42 MHDA- 2024/01/15 12:42 CRDT- 2024/01/11 14:05 PHST- 2024/01/15 12:42 [medline] PHST- 2024/01/11 18:42 [pubmed] PHST- 2024/01/11 14:05 [entrez] AID - 10.1126/science.adn9644 [doi] PST - ppublish SO - Science. 2024 Jan 12;383(6679):138-139. doi: 10.1126/science.adn9644. Epub 2024 Jan 11. PMID- 38212558 OWN - NLM STAT- MEDLINE DCOM- 20240115 LR - 20241020 IS - 2399-3642 (Electronic) IS - 2399-3642 (Linking) VI - 7 IP - 1 DP - 2024 Jan 11 TI - Detection of chromosomal aneuploidy in ancient genomes. PG - 14 LID - 10.1038/s42003-023-05642-z [doi] LID - 14 AB - Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits. CI - © 2024. The Author(s). FAU - Anastasiadou, Kyriaki AU - Anastasiadou K AUID- ORCID: 0000-0001-8033-6070 AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. kyriaki.anastasiadou@crick.ac.uk. FAU - Silva, Marina AU - Silva M AUID- ORCID: 0000-0002-3756-0920 AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. FAU - Booth, Thomas AU - Booth T AUID- ORCID: 0000-0002-8731-818X AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. FAU - Speidel, Leo AU - Speidel L AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. AD - Genetics Institute, University College London, London, United Kingdom. FAU - Audsley, Tony AU - Audsley T AD - Independent Scholar, Wells, United Kingdom. FAU - Barrington, Christopher AU - Barrington C AUID- ORCID: 0000-0003-1281-2658 AD - Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom. FAU - Buckberry, Jo AU - Buckberry J AD - School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom. FAU - Fernandes, Diana AU - Fernandes D AD - Network Archaeology, Lincoln, United Kingdom. FAU - Ford, Ben AU - Ford B AD - Oxford Archaeology, Oxford, United Kingdom. FAU - Gibson, Mark AU - Gibson M AD - Oxford Archaeology, Oxford, United Kingdom. FAU - Gilardet, Alexandre AU - Gilardet A AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. FAU - Glocke, Isabelle AU - Glocke I AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. FAU - Keefe, Katie AU - Keefe K AD - York Osteoarchaeology, York, United Kingdom. AD - On-Site Archaeology, York, United Kingdom. FAU - Kelly, Monica AU - Kelly M AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. FAU - Masters, Mackenzie AU - Masters M AUID- ORCID: 0000-0002-8940-5906 AD - York Osteoarchaeology, York, United Kingdom. AD - Department of Archaeology, University of York, York, United Kingdom. FAU - McCabe, Jesse AU - McCabe J AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. FAU - McIntyre, Lauren AU - McIntyre L AD - Oxford Archaeology, Oxford, United Kingdom. FAU - Ponce, Paola AU - Ponce P AD - York Osteoarchaeology, York, United Kingdom. AD - Department of Archaeology, University of York, York, United Kingdom. FAU - Rowland, Stephen AU - Rowland S AD - Oxford Archaeology, Oxford, United Kingdom. FAU - Ruiz Ventura, Jordi AU - Ruiz Ventura J AD - York Osteoarchaeology, York, United Kingdom. AD - Department of Archaeology, University of York, York, United Kingdom. FAU - Swali, Pooja AU - Swali P AUID- ORCID: 0000-0002-8301-8649 AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. FAU - Tait, Frankie AU - Tait F AUID- ORCID: 0009-0004-1864-5867 AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. FAU - Walker, David AU - Walker D AD - Wells and Mendip Museum, Wells, United Kingdom. FAU - Webb, Helen AU - Webb H AD - Oxford Archaeology, Oxford, United Kingdom. FAU - Williams, Mia AU - Williams M AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. FAU - Witkin, Annsofie AU - Witkin A AD - Oxford Archaeology, Oxford, United Kingdom. FAU - Holst, Malin AU - Holst M AD - York Osteoarchaeology, York, United Kingdom. AD - Department of Archaeology, University of York, York, United Kingdom. FAU - Loe, Louise AU - Loe L AUID- ORCID: 0009-0009-6727-3306 AD - Oxford Archaeology, Oxford, United Kingdom. FAU - Armit, Ian AU - Armit I AUID- ORCID: 0000-0001-8669-3810 AD - Department of Archaeology, University of York, York, United Kingdom. FAU - Schulting, Rick AU - Schulting R AUID- ORCID: 0000-0002-4444-766X AD - School of Archaeology, University of Oxford, Oxford, United Kingdom. FAU - Skoglund, Pontus AU - Skoglund P AUID- ORCID: 0000-0002-3021-5913 AD - Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom. pontus.skoglund@crick.ac.uk. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - FC001595/ARC_/Arthritis Research UK/United Kingdom GR - FC001595/WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20240111 PL - England TA - Commun Biol JT - Communications biology JID - 101719179 RN - 0 (DNA, Ancient) SB - IM MH - Male MH - Humans MH - *Klinefelter Syndrome/diagnosis/genetics MH - DNA, Ancient MH - Aneuploidy MH - *Down Syndrome MH - Sex Chromosomes PMC - PMC10784527 COIS- The authors declare no competing interests. EDAT- 2024/01/12 00:42 MHDA- 2024/01/15 12:43 PMCR- 2024/01/11 CRDT- 2024/01/11 23:27 PHST- 2023/06/01 00:00 [received] PHST- 2023/11/28 00:00 [accepted] PHST- 2024/01/15 12:43 [medline] PHST- 2024/01/12 00:42 [pubmed] PHST- 2024/01/11 23:27 [entrez] PHST- 2024/01/11 00:00 [pmc-release] AID - 10.1038/s42003-023-05642-z [pii] AID - 5642 [pii] AID - 10.1038/s42003-023-05642-z [doi] PST - epublish SO - Commun Biol. 2024 Jan 11;7(1):14. doi: 10.1038/s42003-023-05642-z. PMID- 38200208 OWN - NLM STAT- MEDLINE DCOM- 20240112 LR - 20240113 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 14 IP - 1 DP - 2024 Jan 10 TI - A fresh perspective on infrared spectroscopy as a prescreening method for molecular and stable isotopes analyses on ancient human bones. PG - 1028 LID - 10.1038/s41598-024-51518-5 [doi] LID - 1028 AB - Following the development of modern genome sequencing technologies, the investigation of museum osteological finds is increasingly informative and popular. Viable protocols to help preserve these collections from exceedingly invasive analyses, would allow greater access to the specimens for scientific research. The main aim of this work is to survey skeletal tissues, specifically petrous bones and roots of teeth, using infrared spectroscopy as a prescreening method to assess the bone quality for molecular analyses. This approach could overcome the major problem of identifying useful genetic material in archaeological bone collections without resorting to demanding, time consuming and expensive laboratory studies. A minimally invasive sampling of archaeological bones was developed and bone structural and compositional changes were examined, linking isotopic and genetic data to infrared spectra. The predictive model based on Infrared parameters is effective in determining the occurrence of ancient DNA (aDNA); however, the quality/quantity of aDNA cannot be determined because of the influence of environmental and local factors experienced by the examined bones during the burial period. CI - © 2024. The Author(s). FAU - Scaggion, Cinzia AU - Scaggion C AD - Department of Geosciences, University of Padova, 35131, Padova, Italy. cinzia.scaggion@phd.unipd.it. AD - INSTM, National Interuniversity Consortium of Materials Science and Technology, 50121, Firenze, Italy. cinzia.scaggion@phd.unipd.it. FAU - Marinato, Maurizio AU - Marinato M AD - Department of Cultural Heritage: Archaeology and History of Art, Cinema and Music, University of Padova, 35139, Padova, Italy. FAU - Dal Sasso, Gregorio AU - Dal Sasso G AD - Institute of Geosciences and Earth Resources, Italian National Research Council-CNR, 35131, Padova, Italy. FAU - Nodari, Luca AU - Nodari L AD - Institute of Condensed Matter Chemistry and Technologies for Energy, Italian National Research Council-CNR, 35127, Padova, Italy. FAU - Saupe, Tina AU - Saupe T AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia. FAU - Aneli, Serena AU - Aneli S AD - Department of Biology, University of Padova, 35122, Padova, Italy. AD - Department of Public Health Sciences and Pediatrics, University of Torino, 10126, Torino, Italy. FAU - Pagani, Luca AU - Pagani L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia. AD - Department of Biology, University of Padova, 35122, Padova, Italy. FAU - Scheib, Christiana L AU - Scheib CL AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia. FAU - Rigo, Manuel AU - Rigo M AD - Department of Geosciences, University of Padova, 35131, Padova, Italy. AD - Institute of Geosciences and Earth Resources, Italian National Research Council-CNR, 35131, Padova, Italy. FAU - Artioli, Gilberto AU - Artioli G AD - Department of Geosciences, University of Padova, 35131, Padova, Italy. AD - INSTM, National Interuniversity Consortium of Materials Science and Technology, 50121, Firenze, Italy. LA - eng GR - Ph.D. scholarship/Fondazione Cassa di Risparmio di Padova e Rovigo/ GR - scholarship/Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali/ PT - Journal Article DEP - 20240110 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (Isotopes) SB - IM MH - Humans MH - Spectrophotometry, Infrared MH - *Archaeology MH - *Burial MH - Chromosome Mapping MH - DNA, Ancient MH - Isotopes PMC - PMC10781948 COIS- The authors declare no competing interests. EDAT- 2024/01/11 00:42 MHDA- 2024/01/12 06:42 PMCR- 2024/01/10 CRDT- 2024/01/10 23:25 PHST- 2023/06/08 00:00 [received] PHST- 2024/01/06 00:00 [accepted] PHST- 2024/01/12 06:42 [medline] PHST- 2024/01/11 00:42 [pubmed] PHST- 2024/01/10 23:25 [entrez] PHST- 2024/01/10 00:00 [pmc-release] AID - 10.1038/s41598-024-51518-5 [pii] AID - 51518 [pii] AID - 10.1038/s41598-024-51518-5 [doi] PST - epublish SO - Sci Rep. 2024 Jan 10;14(1):1028. doi: 10.1038/s41598-024-51518-5. PMID- 38194921 OWN - NLM STAT- MEDLINE DCOM- 20240111 LR - 20240207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 34 IP - 1 DP - 2024 Jan 8 TI - Archaeogenetics: Tracing ancient migrations from the Yellow River. PG - R18-R20 LID - S0960-9822(23)01538-5 [pii] LID - 10.1016/j.cub.2023.11.024 [doi] AB - Migration from the Yellow River homeland of Sino-Tibetan languages and people has impacted humans in East Asia for more than 6,000 years. A new study of ancient DNA from southwest China reveals an important component of this migration history. CI - Copyright © 2023 Elsevier Inc. All rights reserved. FAU - Bellwood, Peter AU - Bellwood P AD - School of Archaeology and Anthropology, Australian National University, Canberra, ACT 2600, Australia. Electronic address: peter.bellwood@anu.edu.au. LA - eng PT - Journal Article PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Rivers MH - Asia, Eastern MH - China MH - *DNA, Ancient MH - Language COIS- Declaration of interests The author declares no competing interests. EDAT- 2024/01/10 00:42 MHDA- 2024/01/11 07:43 CRDT- 2024/01/09 18:22 PHST- 2024/01/11 07:43 [medline] PHST- 2024/01/10 00:42 [pubmed] PHST- 2024/01/09 18:22 [entrez] AID - S0960-9822(23)01538-5 [pii] AID - 10.1016/j.cub.2023.11.024 [doi] PST - ppublish SO - Curr Biol. 2024 Jan 8;34(1):R18-R20. doi: 10.1016/j.cub.2023.11.024. PMID- 38118448 OWN - NLM STAT- MEDLINE DCOM- 20240111 LR - 20240207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 34 IP - 1 DP - 2024 Jan 8 TI - An individual with Sarmatian-related ancestry in Roman Britain. PG - 204-212.e6 LID - S0960-9822(23)01634-2 [pii] LID - 10.1016/j.cub.2023.11.049 [doi] AB - In the second century CE the Roman Empire had increasing contact with Sarmatians, nomadic Iranian speakers occupying an area stretching from the Pontic-Caspian steppe to the Carpathian mountains, both in the Caucasus and in the Danubian borders of the empire.(1)(,)(2)(,)(3) In 175 CE, following their defeat in the Marcomannic Wars, emperor Marcus Aurelius drafted Sarmatian cavalry into Roman legions and deployed 5,500 Sarmatian soldiers to Britain, as recorded by contemporary historian Cassius Dio.(4)(,)(5) Little is known about where the Sarmatian cavalry were stationed, and no individuals connected with this historically attested event have been identified to date, leaving its impact on Britain largely unknown. Here we document Caucasus- and Sarmatian-related ancestry in the whole genome of a Roman-period individual (126-228 calibrated [cal.] CE)-an outlier without traceable ancestry related to local populations in Britain-recovered from a farmstead site in present-day Cambridgeshire, UK. Stable isotopes support a life history of mobility during childhood. Although several scenarios are possible, the historical deployment of Sarmatians to Britain provides a parsimonious explanation for this individual's extraordinary life history. Regardless of the factors behind his migrations, these results highlight how long-range mobility facilitated by the Roman Empire impacted provincial locations outside of urban centers. CI - Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Silva, Marina AU - Silva M AD - Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. Electronic address: marina.silva@crick.ac.uk. FAU - Booth, Thomas AU - Booth T AD - Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. FAU - Moore, Joanna AU - Moore J AD - Department of Archaeology, Durham University, Lower Mountjoy, South Rd, DH1 3LE, Durham, United Kingdom. FAU - Anastasiadou, Kyriaki AU - Anastasiadou K AD - Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. FAU - Walker, Don AU - Walker D AD - Museum of London Archaeology (MOLA), Mortimer Wheeler House, 46 Eagle Wharf Road, London N1 7ED, UK. FAU - Gilardet, Alexandre AU - Gilardet A AD - Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. FAU - Barrington, Christopher AU - Barrington C AD - Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. FAU - Kelly, Monica AU - Kelly M AD - Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. FAU - Williams, Mia AU - Williams M AD - Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. FAU - Henderson, Michael AU - Henderson M AD - Museum of London Archaeology (MOLA), Mortimer Wheeler House, 46 Eagle Wharf Road, London N1 7ED, UK. FAU - Smith, Alex AU - Smith A AD - Headland Archaeology, 13 Jane Street, Edinburgh EH6 5HE, UK. FAU - Bowsher, David AU - Bowsher D AD - Museum of London Archaeology (MOLA), Mortimer Wheeler House, 46 Eagle Wharf Road, London N1 7ED, UK. FAU - Montgomery, Janet AU - Montgomery J AD - Department of Archaeology, Durham University, Lower Mountjoy, South Rd, DH1 3LE, Durham, United Kingdom. Electronic address: janet.montgomery@durham.ac.uk. FAU - Skoglund, Pontus AU - Skoglund P AD - Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. Electronic address: pontus.skoglund@crick.ac.uk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20231219 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (Isotopes) SB - IM MH - Humans MH - United Kingdom MH - Iran MH - *Isotopes MH - *Roman World/history OTO - NOTNLM OT - Britain OT - Roman OT - Sarmatian OT - ancient DNA OT - archeology OT - stable isotopes COIS- Declaration of interests The authors declare no competing interests. EDAT- 2023/12/21 00:41 MHDA- 2024/01/11 07:42 CRDT- 2023/12/20 18:42 PHST- 2023/07/19 00:00 [received] PHST- 2023/10/10 00:00 [revised] PHST- 2023/11/21 00:00 [accepted] PHST- 2024/01/11 07:42 [medline] PHST- 2023/12/21 00:41 [pubmed] PHST- 2023/12/20 18:42 [entrez] AID - S0960-9822(23)01634-2 [pii] AID - 10.1016/j.cub.2023.11.049 [doi] PST - ppublish SO - Curr Biol. 2024 Jan 8;34(1):204-212.e6. doi: 10.1016/j.cub.2023.11.049. Epub 2023 Dec 19. PMID- 38227345 OWN - NLM STAT- MEDLINE DCOM- 20240205 LR - 20241023 IS - 1751-7915 (Electronic) IS - 1751-7915 (Linking) VI - 17 IP - 1 DP - 2024 Jan TI - Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities. PG - e14390 LID - 10.1111/1751-7915.14390 [doi] LID - e14390 AB - By deciphering information encoded in degraded ancient DNA extracted from up to million-years-old samples, molecular paleomicrobiology enables to objectively retrace the temporal evolution of microbial species and communities. Assembly of full-length genomes of ancient pathogen lineages allows not only to follow historical epidemics in space and time but also to identify the acquisition of genetic features that represent landmarks in the evolution of the host-microbe interaction. Analysis of microbial community DNA extracted from essentially human paleo-artefacts (paleofeces, dental calculi) evaluates the relative contribution of diet, lifestyle and geography on the taxonomic and functional diversity of these guilds in which have been identified species that may have gone extinct in today's human microbiome. As for non-host-associated environmental samples, such as stratified sediment cores, analysis of their DNA illustrates how and at which pace microbial communities are affected by local or widespread environmental disturbance. Description of pre-disturbance microbial diversity patterns can aid in evaluating the relevance and effectiveness of remediation policies. We finally discuss how recent achievements in paleomicrobiology could contribute to microbial biotechnology in the fields of medical microbiology and food science to trace the domestication of microorganisms used in food processing or to illustrate the historic evolution of food processing microbial consortia. CI - © 2024 The Authors. Microbial Biotechnology published by Applied Microbiology International and John Wiley & Sons Ltd. FAU - Grasso, Gianluca AU - Grasso G AUID- ORCID: 0000-0001-9865-0017 AD - Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi of Turin, Turin, Italy. AD - Institut Systématique Evolution, Biodiversité (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA)¸ Muséum National d'Histoire Naturelle, Paris, France. AD - Institute for Sustainable Plant Protection (IPSP), SS, National Research Council (CNR), Turin, Italy. FAU - Bianciotto, Valeria AU - Bianciotto V AUID- ORCID: 0000-0002-7409-5538 AD - Institute for Sustainable Plant Protection (IPSP), SS, National Research Council (CNR), Turin, Italy. FAU - Marmeisse, Roland AU - Marmeisse R AUID- ORCID: 0000-0003-1653-3517 AD - Institut Systématique Evolution, Biodiversité (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA)¸ Muséum National d'Histoire Naturelle, Paris, France. AD - Institute for Sustainable Plant Protection (IPSP), SS, National Research Council (CNR), Turin, Italy. LA - eng GR - Alliance Sorbonne Université/ GR - ATM 2021/Muséum National d'Histoire Naturelle/ GR - Bando Da Vinci 2022/Università Italo Francese/ PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20240116 PL - United States TA - Microb Biotechnol JT - Microbial biotechnology JID - 101316335 RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - *Microbiota MH - DNA MH - Microbial Consortia PMC - PMC10832523 COIS- The authors declare no conflict of Interest. EDAT- 2024/01/16 13:42 MHDA- 2024/02/05 06:43 PMCR- 2024/01/16 CRDT- 2024/01/16 11:34 PHST- 2023/11/04 00:00 [revised] PHST- 2023/07/28 00:00 [received] PHST- 2023/12/10 00:00 [accepted] PHST- 2024/02/05 06:43 [medline] PHST- 2024/01/16 13:42 [pubmed] PHST- 2024/01/16 11:34 [entrez] PHST- 2024/01/16 00:00 [pmc-release] AID - MBT214390 [pii] AID - 10.1111/1751-7915.14390 [doi] PST - ppublish SO - Microb Biotechnol. 2024 Jan;17(1):e14390. doi: 10.1111/1751-7915.14390. Epub 2024 Jan 16. PMID- 38216764 OWN - NLM STAT- MEDLINE DCOM- 20240125 LR - 20240125 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 625 IP - 7996 DP - 2024 Jan TI - Ancient DNA reveals first known case of sex-development disorder. PG - 639 LID - 10.1038/d41586-024-00101-z [doi] FAU - Wong, Carissa AU - Wong C LA - eng PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Disorders of Sex Development/genetics/history MH - *DNA, Ancient/analysis MH - Turner Syndrome/genetics/history MH - History, Ancient OTO - NOTNLM OT - Genomics OT - History EDAT- 2024/01/13 00:42 MHDA- 2024/01/25 06:43 CRDT- 2024/01/12 23:26 PHST- 2024/01/25 06:43 [medline] PHST- 2024/01/13 00:42 [pubmed] PHST- 2024/01/12 23:26 [entrez] AID - 10.1038/d41586-024-00101-z [pii] AID - 10.1038/d41586-024-00101-z [doi] PST - ppublish SO - Nature. 2024 Jan;625(7996):639. doi: 10.1038/d41586-024-00101-z. PMID- 38200339 OWN - NLM STAT- MEDLINE DCOM- 20240118 LR - 20240118 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 625 IP - 7995 DP - 2024 Jan TI - Ancient DNA reveals origins of multiple sclerosis in Europe. PG - 431-432 LID - 10.1038/d41586-024-00024-9 [doi] FAU - Reardon, Sara AU - Reardon S LA - eng PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Archaeology MH - *DNA, Ancient/analysis MH - Europe MH - *Multiple Sclerosis/genetics/history OTO - NOTNLM OT - Archaeology OT - Genomics OT - Neurodegeneration EDAT- 2024/01/11 00:42 MHDA- 2024/01/18 06:42 CRDT- 2024/01/10 23:30 PHST- 2024/01/18 06:42 [medline] PHST- 2024/01/11 00:42 [pubmed] PHST- 2024/01/10 23:30 [entrez] AID - 10.1038/d41586-024-00024-9 [pii] AID - 10.1038/d41586-024-00024-9 [doi] PST - ppublish SO - Nature. 2024 Jan;625(7995):431-432. doi: 10.1038/d41586-024-00024-9. PMID- 38200296 OWN - NLM STAT- MEDLINE DCOM- 20240112 LR - 20241023 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 625 IP - 7994 DP - 2024 Jan TI - Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations. PG - 321-328 LID - 10.1038/s41586-023-06618-z [doi] AB - Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated(1). Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age(2), along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment. CI - © 2024. The Author(s). FAU - Barrie, William AU - Barrie W AD - Department of Zoology, University of Cambridge, Cambridge, UK. AD - Department of Genetics, University of Cambridge, Cambridge, UK. FAU - Yang, Yaoling AU - Yang Y AUID- ORCID: 0000-0003-4905-8097 AD - Department of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK. AD - MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK. FAU - Irving-Pease, Evan K AU - Irving-Pease EK AUID- ORCID: 0000-0003-1940-2192 AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Attfield, Kathrine E AU - Attfield KE AUID- ORCID: 0000-0003-3387-521X AD - Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK. FAU - Scorrano, Gabriele AU - Scorrano G AUID- ORCID: 0000-0002-0887-4023 AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Jensen, Lise Torp AU - Jensen LT AD - Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK. AD - Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark. FAU - Armen, Angelos P AU - Armen AP AD - Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK. FAU - Dimopoulos, Evangelos Antonios AU - Dimopoulos EA AD - Pathogen Genomics and Evolution Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK. FAU - Stern, Aaron AU - Stern A AD - Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA, USA. FAU - Refoyo-Martinez, Alba AU - Refoyo-Martinez A AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Pearson, Alice AU - Pearson A AD - Department of Genetics, University of Cambridge, Cambridge, UK. FAU - Ramsøe, Abigail AU - Ramsøe A AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Gaunitz, Charleen AU - Gaunitz C AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Demeter, Fabrice AU - Demeter F AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Musée de l'Homme, Paris, France. FAU - Jørkov, Marie Louise S AU - Jørkov MLS AUID- ORCID: 0000-0002-5283-4328 AD - Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark. FAU - Møller, Stig Bermann AU - Møller SB AD - Ålborg Historiske Museum, Nordjyske Museer, Vestbjerg, Denmark. FAU - Springborg, Bente AU - Springborg B AD - Ålborg Historiske Museum, Nordjyske Museer, Vestbjerg, Denmark. FAU - Klassen, Lutz AU - Klassen L AD - Museum Østdanmark-Djursland og Randers, Randers, Denmark. FAU - Hyldgård, Inger Marie AU - Hyldgård IM AD - Museum Østdanmark-Djursland og Randers, Randers, Denmark. FAU - Wickmann, Niels AU - Wickmann N AD - Museum Vestsjælland, Holbæk, Denmark. FAU - Vinner, Lasse AU - Vinner L AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Korneliussen, Thorfinn Sand AU - Korneliussen TS AUID- ORCID: 0000-0001-7576-5380 AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Allentoft, Morten E AU - Allentoft ME AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia. FAU - Sikora, Martin AU - Sikora M AUID- ORCID: 0000-0003-2818-8319 AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Kristiansen, Kristian AU - Kristiansen K AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden. FAU - Rodriguez, Santiago AU - Rodriguez S AD - MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK. FAU - Nielsen, Rasmus AU - Nielsen R AUID- ORCID: 0000-0003-0513-6591 AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA, USA. FAU - Iversen, Astrid K N AU - Iversen AKN AUID- ORCID: 0000-0002-3507-5956 AD - Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK. astrid.iversen@ndcn.ox.ac.uk. AD - Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK. astrid.iversen@ndcn.ox.ac.uk. FAU - Lawson, Daniel J AU - Lawson DJ AUID- ORCID: 0000-0002-5311-6213 AD - Department of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK. dan.lawson@bristol.ac.uk. AD - MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK. dan.lawson@bristol.ac.uk. FAU - Fugger, Lars AU - Fugger L AUID- ORCID: 0000-0003-2883-3226 AD - Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK. lars.fugger@ndcn.ox.ac.uk. AD - Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark. lars.fugger@ndcn.ox.ac.uk. AD - MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK. lars.fugger@ndcn.ox.ac.uk. FAU - Willerslev, Eske AU - Willerslev E AUID- ORCID: 0000-0002-7081-6748 AD - Department of Zoology, University of Cambridge, Cambridge, UK. ew482@cam.ac.uk. AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. ew482@cam.ac.uk. AD - MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany. ew482@cam.ac.uk. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - MC_UU_00036/3/MRC_/Medical Research Council/United Kingdom GR - R01 GM138634/GM/NIGMS NIH HHS/United States PT - Journal Article DEP - 20240110 PL - England TA - Nature JT - Nature JID - 0410462 SB - IM MH - Humans MH - Datasets as Topic MH - Diet/ethnology/history MH - Europe/ethnology MH - *Genetic Predisposition to Disease/history MH - Genetics, Medical MH - *Genome, Human MH - *Grassland MH - History, 15th Century MH - History, Ancient MH - History, Medieval MH - Human Migration/history MH - Life Style/ethnology/history MH - *Multiple Sclerosis/genetics/history/immunology MH - Neurodegenerative Diseases/genetics/history/immunology MH - Population Density PMC - PMC10781639 COIS- The authors declare no competing interests. EDAT- 2024/01/11 00:42 MHDA- 2024/01/12 06:43 PMCR- 2024/01/10 CRDT- 2024/01/10 23:29 PHST- 2022/09/21 00:00 [received] PHST- 2023/09/06 00:00 [accepted] PHST- 2024/01/12 06:43 [medline] PHST- 2024/01/11 00:42 [pubmed] PHST- 2024/01/10 23:29 [entrez] PHST- 2024/01/10 00:00 [pmc-release] AID - 10.1038/s41586-023-06618-z [pii] AID - 6618 [pii] AID - 10.1038/s41586-023-06618-z [doi] PST - ppublish SO - Nature. 2024 Jan;625(7994):321-328. doi: 10.1038/s41586-023-06618-z. Epub 2024 Jan 10. PMID- 38123640 OWN - NLM STAT- MEDLINE DCOM- 20240115 LR - 20240621 IS - 1546-1718 (Electronic) IS - 1061-4036 (Print) IS - 1061-4036 (Linking) VI - 56 IP - 1 DP - 2024 Jan TI - Accurate detection of identity-by-descent segments in human ancient DNA. PG - 143-151 LID - 10.1038/s41588-023-01582-w [doi] AB - Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events. CI - © 2023. The Author(s). FAU - Ringbauer, Harald AU - Ringbauer H AUID- ORCID: 0000-0002-4884-9682 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. harald_ringbauer@eva.mpg.de. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. harald_ringbauer@eva.mpg.de. FAU - Huang, Yilei AU - Huang Y AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germany. FAU - Akbari, Ali AU - Akbari A AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Olalde, Iñigo AU - Olalde I AUID- ORCID: 0000-0002-2660-6807 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - BIOMICs Research Group, University of the Basque Country, Vitoria-Gasteiz, Spain. AD - Ikerbasque-Basque Foundation of Science, Bilbao, Spain. FAU - Patterson, Nick AU - Patterson N AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. LA - eng GR - R01 HG012287/HG/NHGRI NIH HHS/United States PT - Journal Article DEP - 20231220 PL - United States TA - Nat Genet JT - Nature genetics JID - 9216904 RN - 0 (DNA, Ancient) SB - IM UOF - bioRxiv. 2023 Mar 09:2023.03.08.531671. doi: 10.1101/2023.03.08.531671. PMID: 36945531 MH - Humans MH - *DNA, Ancient MH - Genotype MH - *Genome, Human/genetics MH - Polymorphism, Single Nucleotide/genetics PMC - PMC10786714 COIS- The authors declare no competing interests. EDAT- 2023/12/21 00:42 MHDA- 2024/01/15 12:43 PMCR- 2023/12/20 CRDT- 2023/12/20 23:31 PHST- 2023/03/21 00:00 [received] PHST- 2023/10/20 00:00 [accepted] PHST- 2024/01/15 12:43 [medline] PHST- 2023/12/21 00:42 [pubmed] PHST- 2023/12/20 23:31 [entrez] PHST- 2023/12/20 00:00 [pmc-release] AID - 10.1038/s41588-023-01582-w [pii] AID - 1582 [pii] AID - 10.1038/s41588-023-01582-w [doi] PST - ppublish SO - Nat Genet. 2024 Jan;56(1):143-151. doi: 10.1038/s41588-023-01582-w. Epub 2023 Dec 20. PMID- 38030719 OWN - NLM STAT- MEDLINE DCOM- 20240122 LR - 20240210 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 625 IP - 7995 DP - 2024 Jan TI - The genetic legacy of the expansion of Bantu-speaking peoples in Africa. PG - 540-547 LID - 10.1038/s41586-023-06770-6 [doi] AB - The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent(1-7). With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals(8). We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods(9) and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies(10) and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations. CI - © 2023. The Author(s). FAU - Fortes-Lima, Cesar A AU - Fortes-Lima CA AUID- ORCID: 0000-0002-9310-5009 AD - Human Evolution Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. FAU - Burgarella, Concetta AU - Burgarella C AD - Human Evolution Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. AD - AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France. FAU - Hammarén, Rickard AU - Hammarén R AUID- ORCID: 0000-0001-9017-591X AD - Human Evolution Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. FAU - Eriksson, Anders AU - Eriksson A AUID- ORCID: 0000-0003-3436-3726 AD - cGEM, Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Vicente, Mário AU - Vicente M AD - Centre for Palaeogenetics, University of Stockholm, Stockholm, Sweden. AD - Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Jolly, Cecile AU - Jolly C AD - Human Evolution Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. FAU - Semo, Armando AU - Semo A AD - CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal. AD - BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal. AD - Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal. FAU - Gunnink, Hilde AU - Gunnink H AUID- ORCID: 0000-0002-5508-8156 AD - UGent Centre for Bantu Studies (BantUGent), Department of Languages and Cultures, Ghent University, Ghent, Belgium. AD - Leiden University Centre for Linguistics, Leiden, the Netherlands. FAU - Pacchiarotti, Sara AU - Pacchiarotti S AUID- ORCID: 0000-0003-1360-5060 AD - UGent Centre for Bantu Studies (BantUGent), Department of Languages and Cultures, Ghent University, Ghent, Belgium. FAU - Mundeke, Leon AU - Mundeke L AD - University of Kinshasa, Kinshasa, Democratic Republic of Congo. FAU - Matonda, Igor AU - Matonda I AD - University of Kinshasa, Kinshasa, Democratic Republic of Congo. FAU - Muluwa, Joseph Koni AU - Muluwa JK AD - Institut Supérieur Pédagogique de Kikwit, Kikwit, Democratic Republic of Congo. FAU - Coutros, Peter AU - Coutros P AUID- ORCID: 0000-0002-4861-6432 AD - UGent Centre for Bantu Studies (BantUGent), Department of Languages and Cultures, Ghent University, Ghent, Belgium. FAU - Nyambe, Terry S AU - Nyambe TS AD - Livingstone Museum, Livingstone, Zambia. FAU - Cikomola, Justin Cirhuza AU - Cikomola JC AUID- ORCID: 0000-0002-0856-5992 AD - Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of Congo. FAU - Coetzee, Vinet AU - Coetzee V AD - Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. FAU - de Castro, Minique AU - de Castro M AD - Biotechnology Platform, Agricultural Research Council, Onderstepoort, Pretoria, South Africa. FAU - Ebbesen, Peter AU - Ebbesen P AD - Department of Health Science and Technology, University of Aalborg, Aalborg, Denmark. FAU - Delanghe, Joris AU - Delanghe J AUID- ORCID: 0000-0002-5702-6792 AD - Department of Diagnostic Sciences, Ghent University, Ghent, Belgium. FAU - Stoneking, Mark AU - Stoneking M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université Lyon 1, CNRS, Villeurbanne, France. FAU - Barham, Lawrence AU - Barham L AUID- ORCID: 0000-0002-5474-4668 AD - Department of Archaeology, Classics & Egyptology, University of Liverpool, Liverpool, UK. FAU - Lombard, Marlize AU - Lombard M AUID- ORCID: 0000-0002-0675-0414 AD - Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa. FAU - Meyer, Anja AU - Meyer A AUID- ORCID: 0000-0002-5275-9276 AD - Human Variation and Identification Research Unit, School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Steyn, Maryna AU - Steyn M AD - Human Variation and Identification Research Unit, School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Malmström, Helena AU - Malmström H AUID- ORCID: 0000-0002-6456-8055 AD - Human Evolution Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. AD - Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa. FAU - Rocha, Jorge AU - Rocha J AUID- ORCID: 0000-0001-5460-7615 AD - CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal. AD - BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal. AD - Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal. FAU - Soodyall, Himla AU - Soodyall H AD - Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. AD - Academy of Science of South Africa, Pretoria, South Africa. FAU - Pakendorf, Brigitte AU - Pakendorf B AD - Dynamique Du Langage, UMR5596, CNRS & Université de Lyon, Lyon, France. FAU - Bostoen, Koen AU - Bostoen K AUID- ORCID: 0000-0003-2284-6165 AD - UGent Centre for Bantu Studies (BantUGent), Department of Languages and Cultures, Ghent University, Ghent, Belgium. FAU - Schlebusch, Carina M AU - Schlebusch CM AUID- ORCID: 0000-0002-8160-9621 AD - Human Evolution Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. carina.schlebusch@ebc.uu.se. AD - Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa. carina.schlebusch@ebc.uu.se. AD - SciLifeLab, Uppsala, Sweden. carina.schlebusch@ebc.uu.se. LA - eng GR - WT_/Wellcome Trust/United Kingdom PT - Journal Article DEP - 20231129 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Africa, Western MH - Datasets as Topic MH - Democratic Republic of the Congo MH - *DNA, Ancient/analysis MH - *Emigration and Immigration/history MH - Founder Effect MH - Gene Flow/genetics MH - Genetic Variation/genetics MH - *Genetics, Population MH - History, Ancient MH - *Language/history MH - Linguistics/history MH - Zambia MH - Geographic Mapping PMC - PMC10794141 COIS- The authors declare no competing interests. EDAT- 2023/11/30 00:43 MHDA- 2024/01/19 06:42 PMCR- 2023/11/29 CRDT- 2023/11/29 23:31 PHST- 2023/04/03 00:00 [received] PHST- 2023/10/20 00:00 [accepted] PHST- 2024/01/19 06:42 [medline] PHST- 2023/11/30 00:43 [pubmed] PHST- 2023/11/29 23:31 [entrez] PHST- 2023/11/29 00:00 [pmc-release] AID - 10.1038/s41586-023-06770-6 [pii] AID - 6770 [pii] AID - 10.1038/s41586-023-06770-6 [doi] PST - ppublish SO - Nature. 2024 Jan;625(7995):540-547. doi: 10.1038/s41586-023-06770-6. Epub 2023 Nov 29. PMID- 37819677 OWN - NLM STAT- MEDLINE DCOM- 20231216 LR - 20231216 IS - 1755-0998 (Electronic) IS - 1755-098X (Linking) VI - 24 IP - 1 DP - 2024 Jan TI - Demogenomic inference from spatially and temporally heterogeneous samples. PG - e13877 LID - 10.1111/1755-0998.13877 [doi] AB - Modern and ancient genomes are not necessarily drawn from homogeneous populations, as they may have been collected from different places and at different times. This heterogeneous sampling can be an issue for demographic inferences and results in biased demographic parameters and incorrect model choice if not properly considered. When explicitly accounted for, it can result in very complex models and high data dimensionality that are difficult to analyse. In this paper, we formally study the impact of such spatial and temporal sampling heterogeneity on demographic inference, and we introduce a way to circumvent this problem. To deal with structured samples without increasing the dimensionality of the site frequency spectrum (SFS), we introduce a new structured approach to the existing program fastsimcoal2. We assess the efficiency and relevance of this methodological update with simulated and modern human genomic data. We particularly focus on spatial and temporal heterogeneities to evidence the interest of this new SFS-based approach, which can be especially useful when handling scattered and ancient DNA samples, as in conservation genetics or archaeogenetics. CI - © 2023 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. FAU - Marchi, Nina AU - Marchi N AD - CMPG, Institute for Ecology and Evolution, University of Berne, Berne, Switzerland. AD - Swiss Institute of Bioinformatics, Lausanne, Switzerland. FAU - Kapopoulou, Adamandia AU - Kapopoulou A AD - CMPG, Institute for Ecology and Evolution, University of Berne, Berne, Switzerland. AD - Swiss Institute of Bioinformatics, Lausanne, Switzerland. FAU - Excoffier, Laurent AU - Excoffier L AUID- ORCID: 0000-0002-7507-6494 AD - CMPG, Institute for Ecology and Evolution, University of Berne, Berne, Switzerland. AD - Swiss Institute of Bioinformatics, Lausanne, Switzerland. LA - eng GR - 310030_188883/SNSF_/Swiss National Science Foundation/Switzerland PT - Journal Article DEP - 20231011 PL - England TA - Mol Ecol Resour JT - Molecular ecology resources JID - 101465604 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Genetics, Population MH - *Genome MH - Genomics MH - DNA, Ancient MH - Models, Genetic OTO - NOTNLM OT - archaeogenetics OT - conservation genetics OT - demogenomics OT - demographic inference OT - population genetics - empirical OT - site frequency spectrum EDAT- 2023/10/11 14:42 MHDA- 2023/12/17 09:43 CRDT- 2023/10/11 11:42 PHST- 2023/09/15 00:00 [revised] PHST- 2023/04/24 00:00 [received] PHST- 2023/09/27 00:00 [accepted] PHST- 2023/12/17 09:43 [medline] PHST- 2023/10/11 14:42 [pubmed] PHST- 2023/10/11 11:42 [entrez] AID - 10.1111/1755-0998.13877 [doi] PST - ppublish SO - Mol Ecol Resour. 2024 Jan;24(1):e13877. doi: 10.1111/1755-0998.13877. Epub 2023 Oct 11. PMID- 38065079 OWN - NLM STAT- MEDLINE DCOM- 20231216 LR - 20241019 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 186 IP - 25 DP - 2023 Dec 7 TI - A genetic history of the Balkans from Roman frontier to Slavic migrations. PG - 5472-5485.e9 LID - S0092-8674(23)01135-2 [pii] LID - 10.1016/j.cell.2023.10.018 [doi] AB - The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1(st) millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between ∼250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that "barbarian" migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%-60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period. CI - Copyright © 2023 Elsevier Inc. All rights reserved. FAU - Olalde, Iñigo AU - Olalde I AD - BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Ikerbasque-Basque Foundation of Science, Bilbao, Spain; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain. Electronic address: inigo.olalde@ehu.eus. FAU - Carrión, Pablo AU - Carrión P AD - Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain. FAU - Mikić, Ilija AU - Mikić I AD - Institute of Archaeology, Belgrade, Serbia. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Lazaridis, Iosif AU - Lazaridis I AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Mah, Matthew AU - Mah M AD - Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA. FAU - Korać, Miomir AU - Korać M AD - Institute of Archaeology, Belgrade, Serbia. FAU - Golubović, Snežana AU - Golubović S AD - Institute of Archaeology, Belgrade, Serbia. FAU - Petković, Sofija AU - Petković S AD - Institute of Archaeology, Belgrade, Serbia. FAU - Miladinović-Radmilović, Nataša AU - Miladinović-Radmilović N AD - Institute of Archaeology, Belgrade, Serbia. FAU - Vulović, Dragana AU - Vulović D AD - Institute of Archaeology, Belgrade, Serbia. FAU - Alihodžić, Timka AU - Alihodžić T AD - Archaeological Museum Zadar, Zadar, Croatia. FAU - Ash, Abigail AU - Ash A AD - Department of Archaeology, Durham University, Durham, UK. FAU - Baeta, Miriam AU - Baeta M AD - BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain. FAU - Bartík, Juraj AU - Bartík J AD - Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic. FAU - Bedić, Željka AU - Bedić Ž AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. FAU - Bilić, Maja AU - Bilić M AD - Palisada Ltd., Split, Croatia. FAU - Bonsall, Clive AU - Bonsall C AD - School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, UK. FAU - Bunčić, Maja AU - Bunčić M AD - Archaeological Museum in Zagreb, Zagreb, Croatia. FAU - Bužanić, Domagoj AU - Bužanić D AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Carić, Mario AU - Carić M AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. FAU - Čataj, Lea AU - Čataj L AD - Division for Archaeological Heritage, Croatian Conservation Institute, Zagreb, Croatia. FAU - Cvetko, Mirna AU - Cvetko M AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Drnić, Ivan AU - Drnić I AD - Archaeological Museum in Zagreb, Zagreb, Croatia. FAU - Dugonjić, Anita AU - Dugonjić A AD - Archaeological Museum in Zagreb, Zagreb, Croatia. FAU - Đukić, Ana AU - Đukić A AD - Archaeological Museum in Zagreb, Zagreb, Croatia. FAU - Đukić, Ksenija AU - Đukić K AD - Center of Bone Biology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia. FAU - Farkaš, Zdeněk AU - Farkaš Z AD - Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic. FAU - Jelínek, Pavol AU - Jelínek P AD - Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic. FAU - Jovanovic, Marija AU - Jovanovic M AD - Museum of Vojvodina, Novi Sad, Serbia. FAU - Kaić, Iva AU - Kaić I AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Kalafatić, Hrvoje AU - Kalafatić H AD - Institute of Archaeology, Zagreb, Croatia. FAU - Krmpotić, Marijana AU - Krmpotić M AD - Department for Archaeology, Croatian Conservation Institute, Zagreb, Croatia. FAU - Krznar, Siniša AU - Krznar S AD - Institute of Archaeology, Zagreb, Croatia. FAU - Leleković, Tino AU - Leleković T AD - Archaeology Division, Croatian Academy of Sciences and Arts, Zagreb, Croatia. FAU - M de Pancorbo, Marian AU - M de Pancorbo M AD - BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain. FAU - Matijević, Vinka AU - Matijević V AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Milošević Zakić, Branka AU - Milošević Zakić B AD - Museum of Croatian Archaeological Monuments, Split, Croatia. FAU - Osterholtz, Anna J AU - Osterholtz AJ AD - Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Starkville, MS, USA. FAU - Paige, Julianne M AU - Paige JM AD - Department of Anthropology, University of Nevada, Las Vegas, NV, USA. FAU - Tresić Pavičić, Dinko AU - Tresić Pavičić D AD - Kaducej Ltd., Split, Croatia. FAU - Premužić, Zrinka AU - Premužić Z AD - Independent Researcher, 10000 Zagreb, Croatia. FAU - Rajić Šikanjić, Petra AU - Rajić Šikanjić P AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. FAU - Rapan Papeša, Anita AU - Rapan Papeša A AD - Vinkovci Municipal Museum, Vinkovci, Croatia. FAU - Paraman, Lujana AU - Paraman L AD - Trogir Town Museum, Trogir, Croatia. FAU - Sanader, Mirjana AU - Sanader M AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Radovanović, Ivana AU - Radovanović I AD - Department of Anthropology, University of Kansas, Lawrence, KS, USA. FAU - Roksandic, Mirjana AU - Roksandic M AD - Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada. FAU - Šefčáková, Alena AU - Šefčáková A AD - Department of Anthropology, Slovak National Museum-Natural History Museum, Bratislava, Slovak Republic. FAU - Stefanović, Sofia AU - Stefanović S AD - Laboratory for Bioarchaeology, Faculty of Philosophy, University of Belgrade, Belgrade, Serbia. FAU - Teschler-Nicola, Maria AU - Teschler-Nicola M AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; Department of Anthropology, Natural History Museum Vienna, Vienna, Austria. FAU - Tončinić, Domagoj AU - Tončinić D AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Zagorc, Brina AU - Zagorc B AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Callan, Kim AU - Callan K AD - Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Candilio, Francesca AU - Candilio F AD - Servizio di Bioarcheologia, Museo delle Civiltà, Rome, Italy. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Fernandes, Daniel AU - Fernandes D AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal. FAU - Kearns, Aisling AU - Kearns A AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Lawson, Ann Marie AU - Lawson AM AD - Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Mandl, Kirsten AU - Mandl K AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Wagner, Anna AU - Wagner A AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Zalzala, Fatma AU - Zalzala F AD - Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Zettl, Anna AU - Zettl A AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Tomanović, Željko AU - Tomanović Ž AD - Faculty of Biology, University of Belgrade, Belgrade, Serbia; Serbian Academy of Sciences and Arts, Belgrade, Serbia. FAU - Keckarević, Dušan AU - Keckarević D AD - Faculty of Biology, University of Belgrade, Belgrade, Serbia. FAU - Novak, Mario AU - Novak M AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. FAU - Harper, Kyle AU - Harper K AD - Department of Classics and Letters, University of Oklahoma, Norman, OK, USA; Santa Fe Institute, Santa Fe, NM, USA. FAU - McCormick, Michael AU - McCormick M AD - Department of History, Harvard University, Cambridge, MA, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Harvard University, Cambridge, MA, USA. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Grbić, Miodrag AU - Grbić M AD - Faculty of Biology, University of Belgrade, Belgrade, Serbia; Department of Biology, University of Western Ontario, London, ON, Canada; Department of Agriculture and Food, Universidad de La Rioja, Logroño, Spain. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain; Museu de Ciències Naturals de Barcelona, Barcelona, Spain. Electronic address: carles.lalueza.fox@gmail.com. FAU - Reich, David AU - Reich D AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States GR - R01 HG012287/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell JT - Cell JID - 0413066 SB - IM MH - Humans MH - Balkan Peninsula MH - Europe MH - *White People/genetics MH - *Human Migration PMC - PMC10752003 MID - NIHMS1944038 OTO - NOTNLM OT - Balkan Peninsula OT - Great Migration Period OT - Slavic migrations OT - ancient DNA OT - archaeogenetics OT - cosmopolitanism OT - demographic changes OT - population dynamics OT - the Roman Empire COIS- Declaration of interests The authors declare no competing interests. EDAT- 2023/12/09 05:43 MHDA- 2023/12/17 09:44 PMCR- 2023/12/27 CRDT- 2023/12/08 18:19 PHST- 2023/06/23 00:00 [received] PHST- 2023/08/22 00:00 [revised] PHST- 2023/10/18 00:00 [accepted] PHST- 2023/12/17 09:44 [medline] PHST- 2023/12/09 05:43 [pubmed] PHST- 2023/12/08 18:19 [entrez] PHST- 2023/12/27 00:00 [pmc-release] AID - S0092-8674(23)01135-2 [pii] AID - 10.1016/j.cell.2023.10.018 [doi] PST - ppublish SO - Cell. 2023 Dec 7;186(25):5472-5485.e9. doi: 10.1016/j.cell.2023.10.018. PMID- 38051947 OWN - NLM STAT- MEDLINE DCOM- 20231220 LR - 20241018 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 15 IP - 12 DP - 2023 Dec 1 TI - Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications. LID - 10.1093/gbe/evad222 [doi] LID - evad222 AB - Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations. CI - © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Wroblewski, Tadeusz H AU - Wroblewski TH AUID- ORCID: 0000-0002-8082-1997 AD - Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA. FAU - Witt, Kelsey E AU - Witt KE AUID- ORCID: 0000-0002-3242-2123 AD - Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, South Carolina, USA. FAU - Lee, Seung-Been AU - Lee SB AUID- ORCID: 0000-0001-9869-1070 AD - Precision Medicine Institute, Macrogen Inc., Seoul, Republic of Korea. FAU - Malhi, Ripan S AU - Malhi RS AD - Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Illinois, USA. FAU - Peede, David AU - Peede D AUID- ORCID: 0000-0002-4826-0464 AD - Department of Ecology, Evolution, and Organismal Biology and Center for Computational and Molecular Biology, Brown University, Providence, Rhode Island, USA. AD - Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA. FAU - Huerta-Sánchez, Emilia AU - Huerta-Sánchez E AUID- ORCID: 0000-0002-1506-5494 AD - Department of Ecology, Evolution, and Organismal Biology and Center for Computational and Molecular Biology, Brown University, Providence, Rhode Island, USA. FAU - Villanea, Fernando A AU - Villanea FA AUID- ORCID: 0000-0002-6661-0368 AD - Department of Anthropology, University of Colorado Boulder, Colorado, USA. FAU - Claw, Katrina G AU - Claw KG AUID- ORCID: 0000-0003-2239-5018 AD - Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA. LA - eng GR - 1R35GM128946-01/NH/NIH HHS/United States GR - R35 HG011319/HG/NHGRI NIH HHS/United States GR - R35 GM128946/GM/NIGMS NIH HHS/United States GR - R35HG011319/HG/NHGRI NIH HHS/United States GR - T32 GM128596/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 SB - IM MH - Animals MH - Humans MH - *Neanderthals/genetics MH - Pharmacogenetics MH - Genome, Human MH - *Hominidae/genetics MH - Biological Evolution PMC - PMC10727477 OTO - NOTNLM OT - ancient DNA OT - archaic OT - genetics OT - pharmacogenetics EDAT- 2023/12/06 03:41 MHDA- 2023/12/20 06:42 PMCR- 2023/12/05 CRDT- 2023/12/05 15:23 PHST- 2023/11/16 00:00 [accepted] PHST- 2023/12/20 06:42 [medline] PHST- 2023/12/06 03:41 [pubmed] PHST- 2023/12/05 15:23 [entrez] PHST- 2023/12/05 00:00 [pmc-release] AID - 7459155 [pii] AID - evad222 [pii] AID - 10.1093/gbe/evad222 [doi] PST - ppublish SO - Genome Biol Evol. 2023 Dec 1;15(12):evad222. doi: 10.1093/gbe/evad222. PMID- 38040695 OWN - NLM STAT- MEDLINE DCOM- 20231204 LR - 20241015 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 14 IP - 1 DP - 2023 Dec 1 TI - Haplotype-based inference of recent effective population size in modern and ancient DNA samples. PG - 7945 LID - 10.1038/s41467-023-43522-6 [doi] LID - 7945 AB - Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups. CI - © 2023. The Author(s). FAU - Fournier, Romain AU - Fournier R AUID- ORCID: 0000-0003-2790-2445 AD - Department of Statistics, University of Oxford, Oxford, UK. FAU - Tsangalidou, Zoi AU - Tsangalidou Z AD - Department of Statistics, University of Oxford, Oxford, UK. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Palamara, Pier Francesco AU - Palamara PF AUID- ORCID: 0000-0002-7999-1972 AD - Department of Statistics, University of Oxford, Oxford, UK. palamara@stats.ox.ac.uk. AD - Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. palamara@stats.ox.ac.uk. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R21 HG010748/HG/NHGRI NIH HHS/United States GR - R01 HG012287/HG/NHGRI NIH HHS/United States GR - WT_/Wellcome Trust/United Kingdom PT - Journal Article DEP - 20231201 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Haplotypes/genetics MH - *DNA, Ancient MH - Population Density MH - *Genomics MH - Linkage Disequilibrium MH - Genetics, Population MH - Polymorphism, Single Nucleotide PMC - PMC10692198 COIS- The authors declare no competing interests. EDAT- 2023/12/02 00:41 MHDA- 2023/12/04 12:43 PMCR- 2023/12/01 CRDT- 2023/12/01 23:16 PHST- 2022/07/03 00:00 [received] PHST- 2023/11/10 00:00 [accepted] PHST- 2023/12/04 12:43 [medline] PHST- 2023/12/02 00:41 [pubmed] PHST- 2023/12/01 23:16 [entrez] PHST- 2023/12/01 00:00 [pmc-release] AID - 10.1038/s41467-023-43522-6 [pii] AID - 43522 [pii] AID - 10.1038/s41467-023-43522-6 [doi] PST - epublish SO - Nat Commun. 2023 Dec 1;14(1):7945. doi: 10.1038/s41467-023-43522-6. PMID- 38012935 OWN - NLM STAT- MEDLINE DCOM- 20231129 LR - 20240328 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 143S DP - 2023 Dec TI - Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains. PG - 102392 LID - S1472-9792(23)00090-2 [pii] LID - 10.1016/j.tube.2023.102392 [doi] AB - Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of ancient pathogens remains challenging. Here, we present a first assessment of the intra-bone variability of metagenomic composition in human skeletal remains and its effect on the sampling success for Mycobacterium tuberculosis (MTB) and human endogenous DNA. For this purpose, four bone samples from published peer-reviewed studies with PCR-based evidence for ancient MTB DNA were selected. Two bone samples of a Neolithic individual from Halberstadt, Germany and two ribs of two 18th-century Hungarian church mummies were sampled at multiple locations for equal amounts, followed by DNA extraction and library construction. Shotgun sequencing data was generated for taxonomic profiling as well as quantitative and qualitative evaluation of MTB and human endogenous DNA. Despite low variance in microbial diversity within and across samples, intra-bone variability of up to 36.45- and 62.88-fold for authentic ancient MTB and human reads, respectively, was detected. This study demonstrates the variable sampling success for MTB and human endogenous DNA within single skeletal samples despite relatively consistent microbial composition and highlights how a multisampling approach can facilitate the detection of hotspots with highly concentrated pathogen and human endogenous DNA. CI - Copyright © 2023 Elsevier Ltd. All rights reserved. FAU - Jäger, Heidi Y AU - Jäger HY AD - Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy. Electronic address: heidijaeger@bundeswehr.org. FAU - Atz Zanotelli, Daniel AU - Atz Zanotelli D AD - Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy. Electronic address: daniel.atz94@gmail.com. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy. Electronic address: frank.maixner@eurac.edu. FAU - Nicklisch, Nicole AU - Nicklisch N AD - Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany. Electronic address: nicole.nicklisch@dp-uni.ac.at. FAU - Alt, Kurt W AU - Alt KW AD - Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany. Electronic address: kurt.alt@dp-uni.ac.at. FAU - Meller, Harald AU - Meller H AD - State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany. Electronic address: hmeller@lda.mk.sachsen-anhalt.de. FAU - Pap, Ildikó AU - Pap I AD - Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary; Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary. Electronic address: ildiko.pap.2@hotmail.com. FAU - Szikossy, Ildikó AU - Szikossy I AD - Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary. Electronic address: szikossy@gmail.com. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary. Electronic address: gypalfi@hotmail.com. FAU - Zink, Albert R AU - Zink AR AD - Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy. Electronic address: albert.zink@eurac.edu. LA - eng GR - 2014-2020_CALL-FESR 2017/European Regional Development Fund/ GR - FESR1078/Research and Innovation_Autonomous Province Bolzano-South Tyrol_/ GR - NKTIH K 125561/National Research Development and Innovation Office (Hungary)/ GR - 57437987/Germany Academic Exchange Service/ PT - Journal Article PT - Review DEP - 20231125 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 9007-49-2 (DNA) RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Mycobacterium tuberculosis/genetics MH - Body Remains MH - *Tuberculosis/microbiology MH - Bone and Bones MH - DNA MH - DNA, Ancient OTO - NOTNLM OT - Ancient DNA OT - Ancient pathogens OT - Metagenomics OT - Mycobacterium tuberculosis COIS- Declaration of competing interest We declare we have no competing interests. EDAT- 2023/11/28 06:42 MHDA- 2023/11/29 06:42 CRDT- 2023/11/28 00:22 PHST- 2023/01/03 00:00 [received] PHST- 2023/07/11 00:00 [revised] PHST- 2023/07/26 00:00 [accepted] PHST- 2023/11/29 06:42 [medline] PHST- 2023/11/28 06:42 [pubmed] PHST- 2023/11/28 00:22 [entrez] AID - S1472-9792(23)00090-2 [pii] AID - 10.1016/j.tube.2023.102392 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2023 Dec;143S:102392. doi: 10.1016/j.tube.2023.102392. Epub 2023 Nov 25. PMID- 38012931 OWN - NLM STAT- MEDLINE DCOM- 20231129 LR - 20240328 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 143S DP - 2023 Dec TI - Tuberculosis in mummies - New findings, perspectives and limitations. PG - 102371 LID - S1472-9792(23)00069-0 [pii] LID - 10.1016/j.tube.2023.102371 [doi] AB - The molecular analysis of ancient pathogen DNA represents a unique opportunity for the study of infectious diseases in ancient human remains. Among other diseases, paleogenetic studies have been successful in detecting tuberculous DNA in ancient human remains. In the beginning of ancient DNA (aDNA) studies, the presence of tuberculosis (TB) DNA was assessed using a PCR-based assay targeting specific regions of the Mycobacterium tuberculosis (MTB) complex, such as the repetitive element IS6110. The advent of high-throughput sequencing has enabled the reconstruction of full ancient TB genomes in the field of paleomicrobiology. However, despite the numerous paleopathological and PCR-based studies on the presence of tuberculosis in historic human remains, full genome wide reconstructions are still limited to well-preserved specimens with low environmental contamination and connected with extensive screening efforts. This has led to some controversies regarding the evolutionary history of its causative agent Mycobacterium tuberculosis. In this context, mummies have been shown to be a good source for the detection of MTB complex DNA due to a low exposure to environmental influences and the overall good state of preservation of hard and soft tissues in the human remains. Here, we present the major findings on the presence of TB infections in the 18th century naturally mummified human remains from Vác, Hungary and the current status of the detection of MTB complex DNA in mummified human remains. The future perspectives of detecting tuberculosis in mummies will be discussed in the light of methodological aspects, as well as ethical and curational challenges. CI - Copyright © 2023 Elsevier Ltd. All rights reserved. FAU - Zink, Albert AU - Zink A AD - Institute for Mummy Studies, Eurac Research, Bolzano, Italy. Electronic address: albert.zink@eurac.edu. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, Eurac Research, Bolzano, Italy. FAU - Jäger, Heidi Yoko AU - Jäger HY AD - Institute for Mummy Studies, Eurac Research, Bolzano, Italy. FAU - Szikossy, Ildikó AU - Szikossy I AD - Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary. FAU - Pap, Ildikó AU - Pap I AD - Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary; Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary; Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary. LA - eng PT - Journal Article PT - Review DEP - 20231125 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 0 (DNA, Bacterial) SB - IM MH - Humans MH - *Mycobacterium tuberculosis/genetics MH - Body Remains MH - *Mummies MH - DNA, Bacterial/genetics/analysis MH - *Tuberculosis/microbiology COIS- Declaration of competing interest None. EDAT- 2023/11/28 06:42 MHDA- 2023/11/29 06:42 CRDT- 2023/11/28 00:22 PHST- 2023/06/14 00:00 [received] PHST- 2023/06/29 00:00 [revised] PHST- 2023/07/02 00:00 [accepted] PHST- 2023/11/29 06:42 [medline] PHST- 2023/11/28 06:42 [pubmed] PHST- 2023/11/28 00:22 [entrez] AID - S1472-9792(23)00069-0 [pii] AID - 10.1016/j.tube.2023.102371 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2023 Dec;143S:102371. doi: 10.1016/j.tube.2023.102371. Epub 2023 Nov 25. PMID- 38012918 OWN - NLM STAT- MEDLINE DCOM- 20231129 LR - 20240328 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 143S DP - 2023 Dec TI - Bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century orthodox cemeteries in Irkutsk, Eastern Siberia. PG - 102368 LID - S1472-9792(23)00066-5 [pii] LID - 10.1016/j.tube.2023.102368 [doi] AB - In this study, we tested the skeletal human remains from the 18th - early 19th century Orthodox cemeteries in Irkutsk, Eastern Siberia, for tuberculosis-associated morphological alterations and Mycobacterium tuberculosis DNA. The morphologically studied bone collection included 591 individuals of mainly Caucasian origin. The molecular methods (IS6110-PCR and spoligotyping) suggested that at least four individuals (out of 15 TB-suspected, DNA-tested) were positive for the presence of M. tuberculosis DNA. All of them were males (3 maturus, 1 maturus senilis). Two of them date back to the second and third quarters of the 18th century, another to the last quarter of the 18th century, and the last one to the second half of the 19th century. The combined molecular analysis cautiously suggested presence of different strains and at least some of them represented not the currently predominant in Siberia Beijing genotype (M. tuberculosis East-Asian lineage) but strains of European origin. In conclusion, this study presented bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century Orthodox cemeteries in Irkutsk, Eastern Siberia. The samples are not M. bovis and represent human M. tuberculosis sensu stricto. Their precise phylogenetic identity is elusive but evokes the European/Russian origin of at least some isolates. CI - Copyright © 2023 Elsevier Ltd. All rights reserved. FAU - Kharlamova, Natalia AU - Kharlamova N AD - Center for Physical Anthropology, N.N. Mikloukho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119334, Russia. Electronic address: natasha_kharlamova@iea.ras.ru. FAU - Ogarkov, Oleg AU - Ogarkov O AD - Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, 664003, Russia. FAU - Berdnikov, Ivan AU - Berdnikov I AD - Scientific Research Center "Baikal Region", Irkutsk State University, Irkutsk, 664003, Russia. FAU - Berdnikova, Natalia AU - Berdnikova N AD - Scientific Research Center "Baikal Region", Irkutsk State University, Irkutsk, 664003, Russia. FAU - Galeev, Ravil AU - Galeev R AD - Laboratory of Facial Reconstruction, N.N. Mikloukho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119334, Russia. FAU - Mokrousov, Igor AU - Mokrousov I AD - Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, 197101, Russia. Electronic address: imokrousov@mail.ru. LA - eng PT - Journal Article PT - Review DEP - 20231125 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 9007-49-2 (DNA) SB - IM MH - Male MH - Humans MH - Female MH - *Mycobacterium tuberculosis/genetics MH - Siberia MH - Body Remains MH - Phylogeny MH - Cemeteries MH - *Tuberculosis/microbiology MH - Genotype MH - DNA OTO - NOTNLM OT - Ancient DNA analysis OT - Bioarcheology OT - Eastern Siberia OT - Paleopathology OT - Tuberculosis COIS- Declaration of competing interest None. EDAT- 2023/11/28 06:42 MHDA- 2023/11/29 06:43 CRDT- 2023/11/28 00:22 PHST- 2023/02/04 00:00 [received] PHST- 2023/06/20 00:00 [revised] PHST- 2023/06/25 00:00 [accepted] PHST- 2023/11/29 06:43 [medline] PHST- 2023/11/28 06:42 [pubmed] PHST- 2023/11/28 00:22 [entrez] AID - S1472-9792(23)00066-5 [pii] AID - 10.1016/j.tube.2023.102368 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2023 Dec;143S:102368. doi: 10.1016/j.tube.2023.102368. Epub 2023 Nov 25. PMID- 38006200 OWN - NLM STAT- MEDLINE DCOM- 20231127 LR - 20231212 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 182 IP - 4 DP - 2023 Dec TI - Infectious disease in the Pleistocene: Old friends or old foes? PG - 513-531 LID - 10.1002/ajpa.24737 [doi] AB - The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future. CI - © 2023 The Authors. American Journal of Biological Anthropology published by Wiley Periodicals LLC. FAU - Houldcroft, Charlotte J AU - Houldcroft CJ AUID- ORCID: 0000-0002-1833-5285 AD - Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK. FAU - Underdown, Simon AU - Underdown S AD - Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK. AD - Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. LA - eng GR - Oxford Brookes University/ PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20230330 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Humans MH - Friends MH - *Hominidae MH - *Communicable Diseases/epidemiology MH - Genome MH - DNA OTO - NOTNLM OT - ancient DNA OT - human evolution OT - infectious diseases OT - metagenomics OT - pandemics EDAT- 2023/11/25 12:42 MHDA- 2023/11/27 16:18 CRDT- 2023/11/25 01:33 PHST- 2023/03/01 00:00 [revised] PHST- 2022/03/12 00:00 [received] PHST- 2023/03/14 00:00 [accepted] PHST- 2023/11/27 16:18 [medline] PHST- 2023/11/25 12:42 [pubmed] PHST- 2023/11/25 01:33 [entrez] AID - 10.1002/ajpa.24737 [doi] PST - ppublish SO - Am J Biol Anthropol. 2023 Dec;182(4):513-531. doi: 10.1002/ajpa.24737. Epub 2023 Mar 30. PMID- 37955259 OWN - NLM STAT- MEDLINE DCOM- 20231114 LR - 20231122 IS - 1552-4833 (Electronic) IS - 1552-4825 (Linking) VI - 191 IP - 12 DP - 2023 Dec TI - Neolithic Community Revealed Using Ancient DNA Data. PG - 2797-2798 LID - 10.1002/ajmg.a.62840 [doi] LA - eng PT - Journal Article PL - United States TA - Am J Med Genet A JT - American journal of medical genetics. Part A JID - 101235741 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - *DNA, Ancient MH - *DNA, Mitochondrial/genetics MH - Haplotypes MH - Europe EDAT- 2023/11/13 12:41 MHDA- 2023/11/14 06:43 CRDT- 2023/11/13 06:38 PHST- 2023/10/13 00:00 [revised] PHST- 2023/07/22 00:00 [received] PHST- 2023/11/05 00:00 [accepted] PHST- 2023/11/14 06:43 [medline] PHST- 2023/11/13 12:41 [pubmed] PHST- 2023/11/13 06:38 [entrez] AID - 10.1002/ajmg.a.62840 [doi] PST - ppublish SO - Am J Med Genet A. 2023 Dec;191(12):2797-2798. doi: 10.1002/ajmg.a.62840. PMID- 37717498 OWN - NLM STAT- MEDLINE DCOM- 20231124 LR - 20231124 IS - 1879-9825 (Electronic) IS - 1879-9817 (Linking) VI - 43 DP - 2023 Dec TI - Holes in the Head. Double cranial surgery on an individual from the Chalcolithic burial site of Camino del Molino (SE Spain). PG - 22-30 LID - S1879-9817(23)00051-7 [pii] LID - 10.1016/j.ijpp.2023.09.003 [doi] AB - OBJECTIVE: This article analyses new prehistoric evidence of trepanation from a collective burial site in the south-eastern Iberian Peninsula. MATERIALS: The trepanned individual was documented in the Chalcolithic burial site of Camino del Molino, where 1348 individuals (30.7 % non-adults and 69.3 % adults) were deposited in two contiguous funerary phases, making it a reference site for the knowledge of Recent Prehistoric populations. METHODS: The individual has been sexed using traditional anthropological methods and ancient DNA. C14 dating has also been obtained. The lesion has been analysed macroscopically and microscopically using SEM. RESULTS: The skull under study belonged to an adult female deposited in the second burial phase (2566-2239 years cal BCE). It exhibits in the anterior region of the right temporal fossa two contiguous and partially overlapping holes that correspond to two trepanations performed using the scraping technique. CONCLUSIONS: It is a double cranial trepanation with signs of bone remodelling suggesting survival from surgery. No pathological signs were identified potentially associated with the intervention. SIGNIFICANCE: This is the second case of surgical interventions in the geographical area of study and one of the few evidences of this practice in women during prehistoric times. LIMITATIONS: So far only the articulated skeletons from this burial have been thoroughly analysed. SUGGESTIONS FOR FURTHER RESEARCH: Further intensive review of skull collection is advised to learn more about these surgical interventions in Copper Age and to go deeper into the causes that motivated their execution. CI - Copyright © 2023 Elsevier Inc. All rights reserved. FAU - Díaz-Navarro, Sonia AU - Díaz-Navarro S AD - Departamento de Prehistoria, Arqueología, Antropología Social y CC. y TT. Historiográficas, Universidad de Valladolid, Facultad de Filosofía y Letras, Plaza del Campus s/n, 47011 Valladolid, Spain. Electronic address: sonia.diaz@uva.es. FAU - Haber Uriarte, María AU - Haber Uriarte M AD - Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y CC. y TT. Historiográficas, Universidad de Murcia, Spain. FAU - García-González, Rebeca AU - García-González R AD - Laboratorio de Evolución Humana, Universidad de Burgos, Spain. LA - eng PT - Case Reports PT - Journal Article DEP - 20230915 PL - Netherlands TA - Int J Paleopathol JT - International journal of paleopathology JID - 101562474 SB - IM MH - Adult MH - Humans MH - Female MH - Spain MH - *Skull/pathology MH - *Trephining MH - Burial/methods MH - Europe OTO - NOTNLM OT - Ancient Surgery OT - Complete trepanation OT - Healed trauma OT - Iberia OT - Prehistory OT - Taphonomy EDAT- 2023/09/18 00:41 MHDA- 2023/11/24 06:42 CRDT- 2023/09/17 18:09 PHST- 2023/04/04 00:00 [received] PHST- 2023/09/06 00:00 [revised] PHST- 2023/09/10 00:00 [accepted] PHST- 2023/11/24 06:42 [medline] PHST- 2023/09/18 00:41 [pubmed] PHST- 2023/09/17 18:09 [entrez] AID - S1879-9817(23)00051-7 [pii] AID - 10.1016/j.ijpp.2023.09.003 [doi] PST - ppublish SO - Int J Paleopathol. 2023 Dec;43:22-30. doi: 10.1016/j.ijpp.2023.09.003. Epub 2023 Sep 15. PMID- 37002784 OWN - NLM STAT- MEDLINE DCOM- 20231127 LR - 20231212 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 182 IP - 4 DP - 2023 Dec TI - Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era. PG - 542-556 LID - 10.1002/ajpa.24735 [doi] AB - OBJECTIVES: Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA. MATERIALS AND METHODS: Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted. RESULTS: Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains. DISCUSSION: We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas. CI - © 2023 The Authors. American Journal of Biological Anthropology published by Wiley Periodicals LLC. FAU - Honap, Tanvi P AU - Honap TP AUID- ORCID: 0000-0001-5271-9162 AD - Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA. AD - Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA. FAU - Monroe, Cara R AU - Monroe CR AD - Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA. AD - Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA. AD - Center for the Ethics of Indigenous Genomics Research (CEIGR), University of Oklahoma, 73072, Norman, Oklahoma, USA. FAU - Johnson, Sarah J AU - Johnson SJ AD - Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA. AD - Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA. FAU - Jacobson, David K AU - Jacobson DK AD - Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA. AD - Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA. FAU - Abin, Christopher A AU - Abin CA AD - Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA. FAU - Austin, Rita M AU - Austin RM AD - Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA. AD - Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA. FAU - Sandberg, Paul AU - Sandberg P AD - Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA. AD - Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA. FAU - Levine, Marc AU - Levine M AD - Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA. AD - Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA. FAU - Sankaranarayanan, Krithivasan AU - Sankaranarayanan K AD - Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA. AD - Department of Microbiology and Plant Biology, University of Oklahoma, 73019, Norman, Oklahoma, USA. FAU - Lewis, Cecil M Jr AU - Lewis CM Jr AUID- ORCID: 0000-0002-2198-3427 AD - Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA. AD - Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA. LA - eng GR - NSF BCS-2045308/National Science Foundation/ PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20230401 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 RN - 0 (DNA, Bacterial) SB - IM MH - Humans MH - *American Indian or Alaska Native MH - Calculi/genetics MH - Chloroflexi/genetics MH - DNA, Bacterial/analysis MH - *Metagenome/genetics MH - Periodontitis/microbiology MH - Treponema denticola/genetics MH - *Mouth/microbiology OTO - NOTNLM OT - ancient DNA OT - dental calculus OT - oral microbiome OT - oral pathogens EDAT- 2023/04/02 06:00 MHDA- 2023/11/27 12:44 CRDT- 2023/04/01 04:52 PHST- 2023/03/08 00:00 [revised] PHST- 2022/03/16 00:00 [received] PHST- 2023/03/14 00:00 [accepted] PHST- 2023/11/27 12:44 [medline] PHST- 2023/04/02 06:00 [pubmed] PHST- 2023/04/01 04:52 [entrez] AID - 10.1002/ajpa.24735 [doi] PST - ppublish SO - Am J Biol Anthropol. 2023 Dec;182(4):542-556. doi: 10.1002/ajpa.24735. Epub 2023 Apr 1. PMID- 37852263 OWN - NLM STAT- MEDLINE DCOM- 20231123 LR - 20240207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 33 IP - 22 DP - 2023 Nov 20 TI - Ancient genomes reveal millet farming-related demic diffusion from the Yellow River into southwest China. PG - 4995-5002.e7 LID - S0960-9822(23)01303-9 [pii] LID - 10.1016/j.cub.2023.09.055 [doi] AB - The study of southwest China is vital for understanding the dispersal and development of farming because of the coexistence of millet and rice in this region since the Neolithic period.(1)(,)(2) However, the process of the Neolithic transition in southwest China is largely unknown, mainly due to the lack of ancient DNA from the Neolithic period. Here, we report genome-wide data from 11 human samples from the Gaoshan and Haimenkou sites with mixed farming of millet and rice dating to between 4,500 and 3,000 years before present in southwest China. The two ancient groups derived approximately 90% of their ancestry from the Neolithic Yellow River farmers, suggesting a demic diffusion of millet farming to southwest China. We inferred their remaining ancestry to be derived from a Hòabìnhian-related hunter-gatherer lineage. We did not detect rice farmer-related ancestry in the two ancient groups, which indicates that they likely adopted rice farming without genetic assimilation. We, however, observed rice farmer-related ancestry in the formation of some present-day Tibeto-Burman populations. Our results suggested the occurrence of both demic and cultural diffusion in the development of Neolithic mixed farming in some parts of southwest China. CI - Copyright © 2023 Elsevier Inc. All rights reserved. FAU - Tao, Le AU - Tao L AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Yuan, Haibing AU - Yuan H AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China. Electronic address: yuanbenhb@scu.edu.cn. FAU - Zhu, Kongyang AU - Zhu K AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Liu, Xiangyu AU - Liu X AD - Chengdu Municipal Institute of Cultural Relics and Archaeology, Chengdu 610008, China. FAU - Guo, Jianxin AU - Guo J AD - Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China. Electronic address: jxguo@xmu.edu.cn. FAU - Min, Rui AU - Min R AD - Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China. FAU - He, Haifeng AU - He H AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Cao, Doudou AU - Cao D AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK. FAU - Yang, Xiaomin AU - Yang X AD - Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China. FAU - Zhou, Zhiqing AU - Zhou Z AD - Chengdu Municipal Institute of Cultural Relics and Archaeology, Chengdu 610008, China. FAU - Wang, Rui AU - Wang R AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Zhao, Deyun AU - Zhao D AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - Ma, Hao AU - Ma H AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Chen, Jian AU - Chen J AD - Chengdu Municipal Institute of Cultural Relics and Archaeology, Chengdu 610008, China. FAU - Zhao, Jing AU - Zhao J AD - Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China. FAU - Li, Yingfu AU - Li Y AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - He, Yuanhong AU - He Y AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - Suo, Dehao AU - Suo D AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - Zhang, Ruojing AU - Zhang R AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - Li, Shuai AU - Li S AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - Li, Lan AU - Li L AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - Yang, Feng AU - Yang F AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - Li, Haichao AU - Li H AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - Zhang, Liang AU - Zhang L AD - Center for Archaeological Science, Sichuan University, Chengdu 610064, China; School of Archaeology and Museology, Sichuan University, Chengdu 610064, China; National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu 610064, China. FAU - Jin, Li AU - Jin L AD - State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Wang, Chuan-Chao AU - Wang CC AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China; Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, Fujian, China. Electronic address: wang@xmu.edu.cn. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20231017 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Millets/genetics MH - *Rivers MH - Agriculture MH - Genome MH - Farms MH - DNA, Ancient MH - Human Migration OTO - NOTNLM OT - Neolithic transition OT - ancient DNA OT - demic diffusion OT - genetic history COIS- Declaration of interests The authors declare no competing interests. EDAT- 2023/10/19 00:45 MHDA- 2023/11/23 06:42 CRDT- 2023/10/18 18:44 PHST- 2023/05/31 00:00 [received] PHST- 2023/08/12 00:00 [revised] PHST- 2023/09/22 00:00 [accepted] PHST- 2023/11/23 06:42 [medline] PHST- 2023/10/19 00:45 [pubmed] PHST- 2023/10/18 18:44 [entrez] AID - S0960-9822(23)01303-9 [pii] AID - 10.1016/j.cub.2023.09.055 [doi] PST - ppublish SO - Curr Biol. 2023 Nov 20;33(22):4995-5002.e7. doi: 10.1016/j.cub.2023.09.055. Epub 2023 Oct 17. PMID- 38002979 OWN - NLM STAT- MEDLINE DCOM- 20231127 LR - 20240620 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 14 IP - 11 DP - 2023 Nov 2 TI - Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley. LID - 10.3390/genes14112036 [doi] LID - 2036 AB - This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area. FAU - Uricoechea Patiño, Daniel AU - Uricoechea Patiño D AD - Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia. FAU - Collins, Andrew AU - Collins A AUID- ORCID: 0000-0001-7108-0771 AD - Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK. FAU - Romero García, Oscar Julián AU - Romero García OJ AD - Genetics Group, National Institute of Legal Medicine and Forensic Sciences, Bogotá 110311, Colombia. FAU - Santos Vecino, Gustavo AU - Santos Vecino G AD - Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia. FAU - Aristizábal Espinosa, Pablo AU - Aristizábal Espinosa P AD - School for Advanced Studies in the Social Sciences, Americanists Society of Paris, 75006 Paris, France. FAU - Bernal Villegas, Jaime Eduardo AU - Bernal Villegas JE AD - Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia. FAU - Benavides Benitez, Escilda AU - Benavides Benitez E AD - Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia. FAU - Vergara Muñoz, Saray AU - Vergara Muñoz S AD - Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia. FAU - Briceño Balcázar, Ignacio AU - Briceño Balcázar I AD - Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia. LA - eng GR - Convocatoria interna de 2013 (Internal Call of 2013) as per acta 809 de la comisión de asuntos generales, proyecto MED-168-2013./Universidad de La Sabana/ PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20231102 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - *DNA, Mitochondrial/genetics MH - *Genetics, Population MH - Mitochondria/genetics MH - North America MH - Human Migration PMC - PMC10670959 OTO - NOTNLM OT - Colombia OT - aburrá valley OT - ancient DNA OT - antioquia OT - haplogroup OT - mtDNA HVS-I OT - pre-hispanic COIS- The authors declare no conflict of interest. EDAT- 2023/11/25 12:47 MHDA- 2023/11/27 16:18 PMCR- 2023/11/02 CRDT- 2023/11/25 01:13 PHST- 2023/08/09 00:00 [received] PHST- 2023/09/18 00:00 [revised] PHST- 2023/10/30 00:00 [accepted] PHST- 2023/11/27 16:18 [medline] PHST- 2023/11/25 12:47 [pubmed] PHST- 2023/11/25 01:13 [entrez] PHST- 2023/11/02 00:00 [pmc-release] AID - genes14112036 [pii] AID - genes-14-02036 [pii] AID - 10.3390/genes14112036 [doi] PST - epublish SO - Genes (Basel). 2023 Nov 2;14(11):2036. doi: 10.3390/genes14112036. PMID- 37935112 OWN - NLM STAT- MEDLINE DCOM- 20231124 LR - 20240705 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 15 IP - 11 DP - 2023 Nov 1 TI - Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus). LID - 10.1093/gbe/evad198 [doi] LID - evad198 AB - To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community. CI - © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Schurr, Theodore G AU - Schurr TG AUID- ORCID: 0000-0001-9323-9237 AD - Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. FAU - Shengelia, Ramaz AU - Shengelia R AD - Department of the History of Medicine, Tbilisi State Medical University, Tbilisi, Georgia. FAU - Shamoon-Pour, Michel AU - Shamoon-Pour M AUID- ORCID: 0000-0002-2094-002X AD - First-year Research Immersion, Binghamton University, Binghamton, New York, USA. FAU - Chitanava, David AU - Chitanava D AUID- ORCID: 0000-0002-2610-2094 AD - Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia. FAU - Laliashvili, Shorena AU - Laliashvili S AD - Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia. FAU - Laliashvili, Irma AU - Laliashvili I AD - Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia. FAU - Kibret, Redate AU - Kibret R AD - Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA. FAU - Kume-Kangkolo, Yanu AU - Kume-Kangkolo Y AD - Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. FAU - Akhvlediani, Irakli AU - Akhvlediani I AUID- ORCID: 0009-0004-3098-0342 AD - Georgian and Caucasus YDNA, Family Tree DNA, Houston, Texas, USA. FAU - Bitadze, Lia AU - Bitadze L AD - Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia. FAU - Mathieson, Iain AU - Mathieson I AUID- ORCID: 0000-0002-4256-3982 AD - Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA. FAU - Yardumian, Aram AU - Yardumian A AUID- ORCID: 0009-0002-1603-8022 AD - Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA. LA - eng GR - BCS-1824826/National Science Foundation/ GR - University of Pennsylvania Museum of Archaeology and Anthropology/ GR - University of Pennsylvania Faculty Research Funds/ GR - Paul Carpenter Scholars Program/ GR - Bryn Athyn College Summer Research Funds/ PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - Male MH - Female MH - *Genetics, Population MH - Georgia (Republic) MH - *Chromosomes, Human, Y/genetics MH - DNA, Mitochondrial/genetics MH - Europe MH - Haplotypes MH - Genetic Variation PMC - PMC10665041 OTO - NOTNLM OT - Samegrelo OT - Y-chromosome OT - autosomal DNA OT - haplogroup OT - mtDNA EDAT- 2023/11/08 00:42 MHDA- 2023/11/24 06:42 PMCR- 2023/11/03 CRDT- 2023/11/07 18:13 PHST- 2023/10/28 00:00 [accepted] PHST- 2023/11/24 06:42 [medline] PHST- 2023/11/08 00:42 [pubmed] PHST- 2023/11/07 18:13 [entrez] PHST- 2023/11/03 00:00 [pmc-release] AID - 7341981 [pii] AID - evad198 [pii] AID - 10.1093/gbe/evad198 [doi] PST - ppublish SO - Genome Biol Evol. 2023 Nov 1;15(11):evad198. doi: 10.1093/gbe/evad198. PMID- 37884848 OWN - NLM STAT- MEDLINE DCOM- 20231102 LR - 20231103 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 623 IP - 7985 DP - 2023 Nov TI - Ancient DNA reveals traces of elusive first humans in Europe. PG - 11 LID - 10.1038/d41586-023-03278-x [doi] LA - eng PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Humans MH - *DNA, Ancient MH - *Hominidae MH - Europe OTO - NOTNLM OT - Genomics EDAT- 2023/10/27 00:43 MHDA- 2023/11/02 12:44 CRDT- 2023/10/26 23:45 PHST- 2023/11/02 12:44 [medline] PHST- 2023/10/27 00:43 [pubmed] PHST- 2023/10/26 23:45 [entrez] AID - 10.1038/d41586-023-03278-x [pii] AID - 10.1038/d41586-023-03278-x [doi] PST - ppublish SO - Nature. 2023 Nov;623(7985):11. doi: 10.1038/d41586-023-03278-x. PMID- 37567955 OWN - NLM STAT- MEDLINE DCOM- 20231103 LR - 20240210 IS - 1476-5438 (Electronic) IS - 1018-4813 (Print) IS - 1018-4813 (Linking) VI - 31 IP - 11 DP - 2023 Nov TI - Record-matching of STR profiles with fragmentary genomic SNP data. PG - 1283-1290 LID - 10.1038/s41431-023-01430-9 [doi] AB - In many forensic settings, identity of a DNA sample is sought from poor-quality DNA, for which the typical STR loci tabulated in forensic databases are not possible to reliably genotype. Genome-wide SNPs, however, can potentially be genotyped from such samples via next-generation sequencing, so that queries can in principle compare SNP genotypes from DNA samples of interest to STR genotype profiles that represent proposed matches. We use genetic record-matching to evaluate the possibility of testing SNP profiles obtained from poor-quality DNA samples to identify exact and relatedness matches to STR profiles. Using simulations based on whole-genome sequences, we show that in some settings, similar match accuracies to those seen with full coverage of the genome are obtained by genetic record-matching for SNP data that represent 5-10% genomic coverage. Thus, if even a fraction of random genomic SNPs can be genotyped by next-generation sequencing, then the potential may exist to test the resulting genotype profiles for matches to profiles consisting exclusively of nonoverlapping STR loci. The result has implications in relation to criminal justice, mass disasters, missing-person cases, studies of ancient DNA, and genomic privacy. CI - © 2023. The Author(s). FAU - Kim, Jaehee AU - Kim J AUID- ORCID: 0000-0002-5210-2004 AD - Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA. FAU - Rosenberg, Noah A AU - Rosenberg NA AUID- ORCID: 0000-0002-1829-8664 AD - Department of Biology, Stanford University, Stanford, CA, 94305, USA. noahr@stanford.edu. LA - eng GR - R01 HG005855/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20230811 PL - England TA - Eur J Hum Genet JT - European journal of human genetics : EJHG JID - 9302235 RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - *Polymorphism, Single Nucleotide MH - *DNA Fingerprinting/methods MH - Microsatellite Repeats MH - Genotype MH - Genomics MH - DNA MH - High-Throughput Nucleotide Sequencing/methods PMC - PMC10620386 COIS- The authors declare no competing interests. EDAT- 2023/08/12 10:41 MHDA- 2023/11/03 06:43 PMCR- 2023/08/11 CRDT- 2023/08/11 23:23 PHST- 2022/09/19 00:00 [received] PHST- 2023/07/03 00:00 [accepted] PHST- 2023/05/30 00:00 [revised] PHST- 2023/11/03 06:43 [medline] PHST- 2023/08/12 10:41 [pubmed] PHST- 2023/08/11 23:23 [entrez] PHST- 2023/08/11 00:00 [pmc-release] AID - 10.1038/s41431-023-01430-9 [pii] AID - 1430 [pii] AID - 10.1038/s41431-023-01430-9 [doi] PST - ppublish SO - Eur J Hum Genet. 2023 Nov;31(11):1283-1290. doi: 10.1038/s41431-023-01430-9. Epub 2023 Aug 11. PMID- 37423869 OWN - NLM STAT- MEDLINE DCOM- 20231012 LR - 20231017 IS - 0168-9525 (Print) IS - 0168-9525 (Linking) VI - 39 IP - 11 DP - 2023 Nov TI - Ancient DNA reveals an early adoption of horse culture by Native Americans. PG - 808-809 LID - S0168-9525(23)00156-7 [pii] LID - 10.1016/j.tig.2023.06.010 [doi] AB - Native Americans of the Plains and Rocky Mountains are renowned for their horsemanship. Taylor et al. recently used ancient DNA and other bioarcheological approaches to document how horses dispersed throughout America and transformed Native American societies following their introduction by the Spanish in 1519, well before the arrival of European settlers. CI - Copyright © 2023 Elsevier Ltd. All rights reserved. FAU - Bailey, Ernest AU - Bailey E AD - Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA. Electronic address: ebailey@uky.edu. LA - eng PT - Journal Article DEP - 20230707 PL - England TA - Trends Genet JT - Trends in genetics : TIG JID - 8507085 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Humans MH - *American Indian or Alaska Native MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - *Horses/genetics COIS- Declaration of interests None declared. EDAT- 2023/07/10 00:41 MHDA- 2023/10/12 06:43 CRDT- 2023/07/09 22:01 PHST- 2023/06/06 00:00 [received] PHST- 2023/06/26 00:00 [accepted] PHST- 2023/10/12 06:43 [medline] PHST- 2023/07/10 00:41 [pubmed] PHST- 2023/07/09 22:01 [entrez] AID - S0168-9525(23)00156-7 [pii] AID - 10.1016/j.tig.2023.06.010 [doi] PST - ppublish SO - Trends Genet. 2023 Nov;39(11):808-809. doi: 10.1016/j.tig.2023.06.010. Epub 2023 Jul 7. PMID- 37907573 OWN - NLM STAT- MEDLINE DCOM- 20231102 LR - 20240930 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 13 IP - 1 DP - 2023 Oct 31 TI - Biological and substitute parents in Beaker period adult-child graves. PG - 18765 LID - 10.1038/s41598-023-45612-3 [doi] LID - 18765 AB - Joint inhumations of adults and children are an intriguing aspect of the shift from collective to single burial rites in third millennium BC Western Eurasia. Here, we revisit two exceptional Beaker period adult-child graves using ancient DNA: Altwies in Luxembourg and Dunstable Downs in Britain. Ancestry modelling and patterns of shared IBD segments between the individuals examined, and contemporary genomes from Central and Northwest Europe, highlight the continental connections of British Beakers. Although simultaneous burials may involve individuals with no social or biological ties, we present evidence that close blood relations played a role in shaping third millennium BC social systems and burial practices, for example a biological mother and her son buried together at Altwies. Extended family, such as a paternal aunt at Dunstable Downs, could also act as 'substitute parents' in the grave. Hypotheses are explored to explain such simultaneous inhumations. Whilst intercommunity violence, infectious disease and epidemics may be considered as explanations, they fail to account for both the specific, codified nature of this particular form of inhumation, and its pervasiveness, as evidenced by a representative sample of 131 adult-child graves from 88 sites across Eurasia, all dating to the third and second millennia BC. CI - © 2023. The Author(s). FAU - Zedda, Nicoletta AU - Zedda N AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany. AD - Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy. FAU - Meheux, Katie AU - Meheux K AD - Institute of Archaeology Library, LCCOS, University College London, London, UK. FAU - Blöcher, Jens AU - Blöcher J AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany. FAU - Diekmann, Yoan AU - Diekmann Y AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany. FAU - Gorelik, Alexander V AU - Gorelik AV AD - Vor- Und Frühgeschichtliche Archäologie, Institut Für Altertumswissenschaften, Johannes Gutenberg University Mainz, Mainz, Germany. FAU - Kalle, Martin AU - Kalle M AD - Vor- Und Frühgeschichtliche Archäologie, Institut Für Altertumswissenschaften, Johannes Gutenberg University Mainz, Mainz, Germany. FAU - Klein, Kevin AU - Klein K AD - Vor- Und Frühgeschichtliche Archäologie, Institut Für Altertumswissenschaften, Johannes Gutenberg University Mainz, Mainz, Germany. FAU - Titze, Anna-Lena AU - Titze AL AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany. FAU - Winkelbach, Laura AU - Winkelbach L AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany. FAU - Naish, Elise AU - Naish E AD - The Culture Trust, Luton, UK. FAU - Brou, Laurent AU - Brou L AD - Institut National de Recherches Archéologiques (INRA), Bertrange, Luxembourg. FAU - Valotteau, François AU - Valotteau F AD - Institut National de Recherches Archéologiques (INRA), Bertrange, Luxembourg. FAU - Le Brun-Ricalens, Foni AU - Le Brun-Ricalens F AD - Institut National de Recherches Archéologiques (INRA), Bertrange, Luxembourg. FAU - Burger, Joachim AU - Burger J AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany. FAU - Brami, Maxime AU - Brami M AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany. mbrami@uni-mainz.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20231031 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Humans MH - Adult MH - Female MH - *Archaeology MH - *Burial/methods MH - Europe MH - Parents MH - Adult Children PMC - PMC10618162 COIS- The authors declare no competing interests. EDAT- 2023/11/01 06:43 MHDA- 2023/11/02 12:46 PMCR- 2023/10/31 CRDT- 2023/11/01 00:32 PHST- 2023/07/18 00:00 [received] PHST- 2023/10/21 00:00 [accepted] PHST- 2023/11/02 12:46 [medline] PHST- 2023/11/01 06:43 [pubmed] PHST- 2023/11/01 00:32 [entrez] PHST- 2023/10/31 00:00 [pmc-release] AID - 10.1038/s41598-023-45612-3 [pii] AID - 45612 [pii] AID - 10.1038/s41598-023-45612-3 [doi] PST - epublish SO - Sci Rep. 2023 Oct 31;13(1):18765. doi: 10.1038/s41598-023-45612-3. PMID- 37844237 OWN - NLM STAT- MEDLINE DCOM- 20231023 LR - 20231101 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 120 IP - 43 DP - 2023 Oct 24 TI - The impact of farming on prehistoric culinary practices throughout Northern Europe. PG - e2310138120 LID - 10.1073/pnas.2310138120 [doi] LID - e2310138120 AB - To investigate changes in culinary practices associated with the arrival of farming, we analysed the organic residues of over 1,000 pottery vessels from hunter-gatherer-fisher and early agricultural sites across Northern Europe from the Lower Rhine Basin to the Northeastern Baltic. Here, pottery was widely used by hunter-gatherer-fishers prior to the introduction of domesticated animals and plants. Overall, there was surprising continuity in the way that hunter-gatherer-fishers and farmers used pottery. Both aquatic products and wild plants remained prevalent, a pattern repeated consistently across the study area. We argue that the rapid adaptation of farming communities to exploit coastal and lagoonal resources facilitated their northerly expansion, and in some cases, hunting, gathering, and fishing became the most dominant subsistence strategy. Nevertheless, dairy products frequently appear in pottery associated with the earliest farming groups often mixed with wild plants and fish. Interestingly, we also find compelling evidence of dairy products in hunter-gatherer-fisher Ertebølle pottery, which predates the arrival of domesticated animals. We propose that Ertebølle hunter-gatherer-fishers frequently acquired dairy products through exchange with adjacent farming communities prior to the transition. The continuity observed in pottery use across the transition to farming contrasts with the analysis of human remains which shows substantial demographic change through ancient DNA and, in some cases, a reduction in marine consumption through stable isotope analysis. We postulate that farmers acquired the knowledge and skills they needed to succeed from local hunter-gatherer-fishers but without substantial admixture. FAU - Lucquin, Alexandre AU - Lucquin A AUID- ORCID: 0000-0003-4892-6323 AD - BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom. FAU - Robson, Harry K AU - Robson HK AUID- ORCID: 0000-0002-4850-692X AD - BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom. FAU - Oras, Ester AU - Oras E AUID- ORCID: 0000-0002-7212-629X AD - Institute of History and Archaeology, Institute of Chemistry, University of Tartu, Tartu 50411, Estonia. AD - Swedish Collegium for Advanced Study, Uppsala 752 38, Sweden. FAU - Lundy, Jasmine AU - Lundy J AUID- ORCID: 0000-0001-8250-7697 AD - BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom. FAU - Moretti, Giulia AU - Moretti G AUID- ORCID: 0000-0003-0208-6832 AD - The British Museum, London WC1B 3DG, United Kingdom. FAU - González Carretero, Lara AU - González Carretero L AD - BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom. FAU - Dekker, Joannes AU - Dekker J AUID- ORCID: 0000-0002-3952-4448 AD - BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom. AD - Section for Geobiology, Globe Institute, University of Copenhagen, Copenhagen 1350, Denmark. FAU - Demirci, Özge AU - Demirci Ö AD - BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom. AD - Groningen Institute of Archaeology, University of Groningen, Groningen 9712, Netherlands. FAU - Dolbunova, Ekaterina AU - Dolbunova E AD - The British Museum, London WC1B 3DG, United Kingdom. AD - Department of Archaeology of Eastern Europe and Siberia, State Hermitage Museum, Saint Petersburg 190000, Russia. FAU - McLaughlin, T Rowan AU - McLaughlin TR AUID- ORCID: 0000-0003-4923-1339 AD - The British Museum, London WC1B 3DG, United Kingdom. FAU - Piezonka, Henny AU - Piezonka H AD - Institute of Prehistoric Archaeology, Department of History and Cultural Studies, Free University, Berlin 14195, Germany. FAU - Talbot, Helen M AU - Talbot HM AUID- ORCID: 0009-0001-7402-2830 AD - BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom. FAU - Adamczak, Kamil AU - Adamczak K AUID- ORCID: 0000-0002-8847-5670 AD - Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Toruń 87-100, Poland. FAU - Czekaj-Zastawny, Agnieszka AU - Czekaj-Zastawny A AUID- ORCID: 0000-0001-6171-9930 AD - Centre for Archaeology of Hills and Uplands, Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków 00-927, Poland. FAU - Groß, Daniel AU - Groß D AUID- ORCID: 0000-0002-1328-1134 AD - Museum Lolland-Falster, Nykøbing F. 4800, Denmark. FAU - Gumiński, Witold AU - Gumiński W AD - Faculty of Archaeology, University of Warsaw, Warsaw 00-927, Poland. FAU - Hartz, Sönke AU - Hartz S AD - Stiftung Schleswig-Holsteinische Landesmuseen, Schloss Gottorf, Schleswig 24837, Germany. FAU - Kabaciński, Jacek AU - Kabaciński J AUID- ORCID: 0000-0002-2118-2005 AD - Centre for Archaeology of Hills and Uplands, Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków 00-927, Poland. FAU - Koivisto, Satu AU - Koivisto S AUID- ORCID: 0000-0002-4978-9191 AD - Department of Archaeology, University of Turku, Turku FI-20014, Finland. FAU - Linge, Trond Eilev AU - Linge TE AUID- ORCID: 0009-0000-8665-781X AD - University Museum of Bergen, Section for Cultural Heritage Management, Bergen 5007, Norway. FAU - Meyer, Ann-Katrin AU - Meyer AK AD - Institute of Prehistoric and Protohistoric Archaeology, University of Hamburg, Hamburg 20146, Germany. FAU - Mökkönen, Teemu AU - Mökkönen T AUID- ORCID: 0009-0005-8682-2850 AD - Cultural Environment Services, The Finnish Heritage Agency, Helsinki 913, Finland. FAU - Philippsen, Bente AU - Philippsen B AD - NTNU University Museum, Norwegian University of Science and Technology, Trondheim NO-7491, Norway. FAU - Piličiauskas, Gytis AU - Piličiauskas G AUID- ORCID: 0000-0002-4591-8822 AD - Lithuanian Institute of History, Vilnius 01101, Lithuania. FAU - Visocka, Vanda AU - Visocka V AD - Department of History and Archaeology, Faculty of History and Philosophy, University of Latvia, Rīga 1050, Latvia. FAU - Kriiska, Aivar AU - Kriiska A AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 50090, Estonia. FAU - Raemaekers, Daan AU - Raemaekers D AUID- ORCID: 0000-0001-8665-9065 AD - Groningen Institute of Archaeology, University of Groningen, Groningen 9712, Netherlands. FAU - Meadows, John AU - Meadows J AUID- ORCID: 0000-0002-4346-5591 AD - Centre for Baltic and Scandinavian Archaeology, Schleswig 24837, Germany. FAU - Heron, Carl AU - Heron C AUID- ORCID: 0000-0002-5206-7464 AD - The British Museum, London WC1B 3DG, United Kingdom. FAU - Craig, Oliver E AU - Craig OE AUID- ORCID: 0000-0002-4296-8402 AD - BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20231016 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Animals MH - Humans MH - *Archaeology MH - *Agriculture MH - Europe MH - Farms MH - Farmers PMC - PMC10614617 OTO - NOTNLM OT - circum-Baltic OT - early farmers OT - hunter-gatherers OT - organic residue analysis OT - pottery COIS- The authors declare no competing interest. EDAT- 2023/10/16 18:42 MHDA- 2023/10/23 01:18 PMCR- 2023/10/16 CRDT- 2023/10/16 15:23 PHST- 2023/10/23 01:18 [medline] PHST- 2023/10/16 18:42 [pubmed] PHST- 2023/10/16 15:23 [entrez] PHST- 2023/10/16 00:00 [pmc-release] AID - 202310138 [pii] AID - 10.1073/pnas.2310138120 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2023 Oct 24;120(43):e2310138120. doi: 10.1073/pnas.2310138120. Epub 2023 Oct 16. PMID- 37819893 OWN - NLM STAT- MEDLINE DCOM- 20231102 LR - 20240210 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 18 IP - 10 DP - 2023 TI - Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data. PG - e0292077 LID - 10.1371/journal.pone.0292077 [doi] LID - e0292077 AB - Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifestyles. We also analyzed DNA sequences of putative phytopathogenic fungi, likely ingested during food consumption, to further support dietary habits. Our findings show that pre-Columbian Caribbean cultures had a diverse diet consisting of maize (Zea mays), sweet potato (Ipomoea batatas), chili peppers (Capsicum annuum), peanuts (Arachis spp.), papaya (Carica papaya), tomato (Solanum lycopersicum) and, very surprisingly cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris). Modelling of putative phytopathogenic fungi and plant interactions confirmed the potential consumption of these plants as well as edible fungi, particularly Ustilago spp., which suggest the consumption of maize and huitlacoche. These findings suggest that a variety of dietary, medicinal, and hallucinogenic plants likely played an important role in ancient human subsistence and societal customs. We compared our results with coprolites found in Mexico and the United States, as well as present-day faeces from Mexico, Peru, and the United States. The results suggest that the diet of pre-Columbian cultures resembled that of present-day hunter-gatherers, while agriculturalists exhibited a transitional state in dietary lifestyles between the pre-Columbian cultures and larger scale farmers and United States individuals. Our study highlights differences in dietary patterns related to human lifestyles and provides insight into the flora present in the pre-Columbian Caribbean area. Importantly, data from ancient fecal specimens demonstrate the importance of ancient DNA studies to better understand pre-Columbian populations. CI - Copyright: © 2023 Reynoso-García et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. FAU - Reynoso-García, Jelissa AU - Reynoso-García J AUID- ORCID: 0000-0002-5285-6295 AD - Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan, Puerto Rico. FAU - Santiago-Rodriguez, Tasha M AU - Santiago-Rodriguez TM AD - Diversigen, Inc., New Brighton, Minnesota, United States of America. FAU - Narganes-Storde, Yvonne AU - Narganes-Storde Y AD - Center for Archaeological Research, University of Puerto Rico, San Juan, Puerto Rico. FAU - Cano, Raul J AU - Cano RJ AD - Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, United States of America. FAU - Toranzos, Gary A AU - Toranzos GA AD - Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan, Puerto Rico. LA - eng GR - P20 GM103475/GM/NIGMS NIH HHS/United States GR - R25 GM061151/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20231011 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - Puerto Rico MH - *Diet MH - Ethnicity MH - Fungi PMC - PMC10566737 COIS- Tasha Santiago is a current Diversigen employee, a microbiome services company. This does not alter our adherence to PLOS ONE policies on sharing data and materials. EDAT- 2023/10/11 18:43 MHDA- 2023/11/02 12:46 PMCR- 2023/10/11 CRDT- 2023/10/11 13:33 PHST- 2023/05/06 00:00 [received] PHST- 2023/09/12 00:00 [accepted] PHST- 2023/11/02 12:46 [medline] PHST- 2023/10/11 18:43 [pubmed] PHST- 2023/10/11 13:33 [entrez] PHST- 2023/10/11 00:00 [pmc-release] AID - PONE-D-23-13775 [pii] AID - 10.1371/journal.pone.0292077 [doi] PST - epublish SO - PLoS One. 2023 Oct 11;18(10):e0292077. doi: 10.1371/journal.pone.0292077. eCollection 2023. PMID- 37797024 OWN - NLM STAT- MEDLINE DCOM- 20231016 LR - 20240227 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 382 IP - 6666 DP - 2023 Oct 6 TI - Going local with ancient DNA: A review of human histories from regional perspectives. PG - 53-58 LID - 10.1126/science.adh8140 [doi] AB - Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AUID- ORCID: 0000-0003-1691-1696 AD - International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, Mexico. FAU - Raghavan, Maanasa AU - Raghavan M AUID- ORCID: 0000-0003-1997-0739 AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. FAU - Schlebusch, Carina AU - Schlebusch C AUID- ORCID: 0000-0002-8160-9621 AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. AD - Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa. AD - SciLifeLab, Uppsala, Sweden. LA - eng GR - R35 GM143094/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Review DEP - 20231005 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Africa MH - Americas MH - Asia MH - *DNA, Ancient MH - Oceania MH - *Demography/history MH - *Social Structure MH - *Health/history EDAT- 2023/10/05 18:42 MHDA- 2023/10/09 06:42 CRDT- 2023/10/05 14:07 PHST- 2023/10/09 06:42 [medline] PHST- 2023/10/05 18:42 [pubmed] PHST- 2023/10/05 14:07 [entrez] AID - 10.1126/science.adh8140 [doi] PST - ppublish SO - Science. 2023 Oct 6;382(6666):53-58. doi: 10.1126/science.adh8140. Epub 2023 Oct 5. PMID- 37525572 OWN - NLM STAT- MEDLINE DCOM- 20230918 LR - 20231012 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 182 IP - 2 DP - 2023 Oct TI - Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia. PG - 161-176 LID - 10.1002/ajpa.24821 [doi] AB - Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective. CI - © 2023 Wiley Periodicals LLC. FAU - Tamburrini, Camila AU - Tamburrini C AUID- ORCID: 0000-0001-8197-973X AD - Instituto de Diversidad y Evolución Austral (IDEAus, CCT CONICET-CENPAT), Puerto Madryn, Chubut, Argentina. FAU - Dahinten, Silvia Lucrecia AU - Dahinten SL AD - Instituto de Diversidad y Evolución Austral (IDEAus, CCT CONICET-CENPAT), Puerto Madryn, Chubut, Argentina. FAU - Saihueque, Rubén Ricardo Romero AU - Saihueque RRR AD - Dirección de Asuntos Indígenas, Subsecretaría de Derechos Humanos, Ministerio de Gobierno y Justicia del Chubut, Rawson, Chubut, Argentina. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AD - International Laboratory for Human Genome Research, Universidad Nacional Autónoma de Mexico (UNAM), Santiago de Querétaro, Mexico. FAU - Parolin, María Laura AU - Parolin ML AD - Instituto de Diversidad y Evolución Austral (IDEAus, CCT CONICET-CENPAT), Puerto Madryn, Chubut, Argentina. LA - eng PT - Journal Article PT - Review DEP - 20230731 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 SB - IM MH - Humans MH - *Genomics MH - Argentina OTO - NOTNLM OT - Chubut Province OT - Mapuche-Tehuelche communities OT - ancient DNA OT - hunter-gatherers OT - sustainable science EDAT- 2023/08/01 06:44 MHDA- 2023/09/18 12:43 CRDT- 2023/08/01 02:53 PHST- 2023/06/12 00:00 [revised] PHST- 2022/10/17 00:00 [received] PHST- 2023/07/09 00:00 [accepted] PHST- 2023/09/18 12:43 [medline] PHST- 2023/08/01 06:44 [pubmed] PHST- 2023/08/01 02:53 [entrez] AID - 10.1002/ajpa.24821 [doi] PST - ppublish SO - Am J Biol Anthropol. 2023 Oct;182(2):161-176. doi: 10.1002/ajpa.24821. Epub 2023 Jul 31. PMID- 37057308 OWN - NLM STAT- MEDLINE DCOM- 20230904 LR - 20230920 IS - 1758-2229 (Electronic) IS - 1758-2229 (Linking) VI - 15 IP - 5 DP - 2023 Oct TI - Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD. PG - 383-391 LID - 10.1111/1758-2229.13157 [doi] AB - In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms. CI - © 2023 The Authors. Environmental Microbiology Reports published by Applied Microbiology International and John Wiley & Sons Ltd. FAU - Ķimsis, Jānis AU - Ķimsis J AD - Latvian Biomedical Research and Study Centre, Laboratory of molecular microbiology, Riga, Latvia. FAU - Pokšāne, Alise AU - Pokšāne A AD - Latvian Biomedical Research and Study Centre, Laboratory of molecular microbiology, Riga, Latvia. FAU - Kazarina, Alisa AU - Kazarina A AD - Latvian Biomedical Research and Study Centre, Laboratory of molecular microbiology, Riga, Latvia. FAU - Vilcāne, Antonija AU - Vilcāne A AD - Institute of Latvian History, University of Latvia, Riga, Latvia. FAU - Petersone-Gordina, Elina AU - Petersone-Gordina E AD - Institute of Latvian History, University of Latvia, Riga, Latvia. FAU - Zayakin, Pawel AU - Zayakin P AD - Latvian Biomedical Research and Study Centre, Laboratory of molecular microbiology, Riga, Latvia. FAU - Gerhards, Guntis AU - Gerhards G AUID- ORCID: 0000-0002-3347-7775 AD - Institute of Latvian History, University of Latvia, Riga, Latvia. FAU - Ranka, Renate AU - Ranka R AUID- ORCID: 0000-0002-3716-7950 AD - Latvian Biomedical Research and Study Centre, Laboratory of molecular microbiology, Riga, Latvia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230413 PL - United States TA - Environ Microbiol Rep JT - Environmental microbiology reports JID - 101499207 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Humans MH - Latvia MH - *Microbiota/genetics MH - DNA MH - Burial PMC - PMC10472514 COIS- The authors declare no conflicts of interest. EDAT- 2023/04/15 06:00 MHDA- 2023/09/04 06:44 PMCR- 2023/04/13 CRDT- 2023/04/14 02:42 PHST- 2023/01/13 00:00 [received] PHST- 2023/03/23 00:00 [accepted] PHST- 2023/09/04 06:44 [medline] PHST- 2023/04/15 06:00 [pubmed] PHST- 2023/04/14 02:42 [entrez] PHST- 2023/04/13 00:00 [pmc-release] AID - EMI413157 [pii] AID - 10.1111/1758-2229.13157 [doi] PST - ppublish SO - Environ Microbiol Rep. 2023 Oct;15(5):383-391. doi: 10.1111/1758-2229.13157. Epub 2023 Apr 13. PMID- 36933795 OWN - NLM STAT- MEDLINE DCOM- 20240513 LR - 20240830 IS - 1673-8527 (Print) IS - 1673-8527 (Linking) VI - 50 IP - 10 DP - 2023 Oct TI - Maternal genetic history of ancient Tibetans over the past 4000 years. PG - 765-775 LID - S1673-8527(23)00071-1 [pii] LID - 10.1016/j.jgg.2023.03.007 [doi] AB - The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians vary over the past 4000 years, with a stronger matrilineal connection between the two during 4000 BP-3000 BP, and a weakened connection after 3000 BP, that are coincident with climate change, followed by a reinforced connection after the Tubo period (1400 BP-1100 BP). Besides, an over 4000-year matrilineal continuity is observed in some of the maternal lineages. We also find the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that are dynamically shaped by geography, climate changes, as well as historical events. CI - Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Zhang, Ganyu AU - Zhang G AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Cui, Can AU - Cui C AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Wangdue, Shargan AU - Wangdue S AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - Lu, Hongliang AU - Lu H AD - Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China. FAU - Chen, Honghai AU - Chen H AD - School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China. FAU - Xi, Lin AU - Xi L AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - He, Wei AU - He W AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - Yuan, Haibing AU - Yuan H AD - Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China. FAU - Tsring, Tinley AU - Tsring T AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - Chen, Zujun AU - Chen Z AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - Yang, Feng AU - Yang F AD - Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China. FAU - Tsering, Tashi AU - Tsering T AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - Li, Shuai AU - Li S AD - Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China. FAU - Tashi, Norbu AU - Tashi N AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - Yang, Tsho AU - Yang T AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - Tong, Yan AU - Tong Y AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - Wu, Xiaohong AU - Wu X AD - School of Archaeology and Museology, Peking University, Beijing 100871, China. FAU - Li, Linhui AU - Li L AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China. FAU - He, Yuanhong AU - He Y AD - Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Dai, Qingyan AU - Dai Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Liu, Feng AU - Liu F AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Wang, Tianyi AU - Wang T AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Yang, Ruowei AU - Yang R AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Ping, Wanjing AU - Ping W AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Zhang, Ming AU - Zhang M AD - School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China. FAU - Gao, Xing AU - Gao X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Liu, Yichen AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. Electronic address: yichen.liu@ivpp.ac.cn. FAU - Wang, Wenjun AU - Wang W AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Science and Technology Archaeology, National Centre for Archaeology, Beijing 100013, China. Electronic address: wangwenjun@ivpp.ac.cn. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Qi Zhi Institute, Shanghai 200232, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230316 PL - China TA - J Genet Genomics JT - Journal of genetics and genomics = Yi chuan xue bao JID - 101304616 RN - 0 (DNA, Mitochondrial) RN - Tibetan people SB - IM MH - Tibet MH - Humans MH - *Phylogeny MH - *Haplotypes/genetics MH - Female MH - Genome, Mitochondrial/genetics MH - DNA, Mitochondrial/genetics MH - History, Ancient MH - Asian People/genetics MH - Genetics, Population MH - Maternal Inheritance/genetics MH - East Asian People OTO - NOTNLM OT - Ancient DNA OT - Mitochondrial genome OT - Population history OT - Tibetans COIS- Conflict of interest The authors declare that they have no conflict of interest. EDAT- 2023/03/19 06:00 MHDA- 2024/05/13 12:53 CRDT- 2023/03/18 20:31 PHST- 2023/01/17 00:00 [received] PHST- 2023/03/14 00:00 [revised] PHST- 2023/03/14 00:00 [accepted] PHST- 2024/05/13 12:53 [medline] PHST- 2023/03/19 06:00 [pubmed] PHST- 2023/03/18 20:31 [entrez] AID - S1673-8527(23)00071-1 [pii] AID - 10.1016/j.jgg.2023.03.007 [doi] PST - ppublish SO - J Genet Genomics. 2023 Oct;50(10):765-775. doi: 10.1016/j.jgg.2023.03.007. Epub 2023 Mar 16. PMID- 37268008 OWN - NLM STAT- MEDLINE DCOM- 20231023 LR - 20231023 IS - 2327-0578 (Electronic) IS - 2327-056X (Linking) VI - 10 IP - 1 DP - 2023 Sep 29 TI - A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History. PG - 49-75 LID - 10.1146/annurev-virology-111821-123859 [doi] AB - Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis of ancient nucleic acids from diverse human remains, the identification and characterization of ancient viruses became feasible. Recent studies have provided invaluable information about past epidemics and made it possible to examine assumptions and inferences on the origin and evolution of certain viral families. In parallel, the study of ancient viruses also uncovered their importance in the evolution of the human lineage and their key roles in shaping major events in human history. In this review, we describe the strategies used for the study of ancient viruses, along with their limitations, and provide a detailed account of what past viral infections have revealed about human history. FAU - Guzmán-Solís, Axel A AU - Guzmán-Solís AA AD - Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. FAU - Navarro, Miguel Alejandro AU - Navarro MA AD - Licenciatura en Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México. AD - International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, México; email: mavila@liigh.unam.mx. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AD - International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, México; email: mavila@liigh.unam.mx. FAU - Blanco-Melo, Daniel AU - Blanco-Melo D AD - Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; email: dblancom@fredhutch.org. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20230602 PL - United States TA - Annu Rev Virol JT - Annual review of virology JID - 101625721 SB - IM MH - Humans MH - Genomics MH - *Virus Diseases/genetics MH - *Viruses/genetics MH - Disease Outbreaks MH - Genome, Viral OTO - NOTNLM OT - aDNA OT - ancient DNA OT - ancient viruses OT - historical epidemics OT - human history OT - paleogenomics OT - paleovirology EDAT- 2023/06/03 11:42 MHDA- 2023/10/23 00:43 CRDT- 2023/06/02 19:13 PHST- 2023/10/23 00:43 [medline] PHST- 2023/06/03 11:42 [pubmed] PHST- 2023/06/02 19:13 [entrez] AID - 10.1146/annurev-virology-111821-123859 [doi] PST - ppublish SO - Annu Rev Virol. 2023 Sep 29;10(1):49-75. doi: 10.1146/annurev-virology-111821-123859. Epub 2023 Jun 2. PMID- 37767965 OWN - NLM STAT- MEDLINE DCOM- 20231027 LR - 20231027 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 12 DP - 2023 Sep 28 TI - Adulis and the transshipment of baboons during classical antiquity. LID - 10.7554/eLife.87513 [doi] LID - e87513 AB - Adulis, located on the Red Sea coast in present-day Eritrea, was a bustling trading centre between the first and seventh centuries CE. Several classical geographers-Agatharchides of Cnidus, Pliny the Elder, Strabo-noted the value of Adulis to Greco-Roman Egypt, particularly as an emporium for living animals, including baboons (Papio spp.). Though fragmentary, these accounts predict the Adulite origins of mummified baboons in Ptolemaic catacombs, while inviting questions on the geoprovenance of older (Late Period) baboons recovered from Gabbanat el-Qurud ('Valley of the Monkeys'), Egypt. Dated to ca. 800-540 BCE, these animals could extend the antiquity of Egyptian-Adulite trade by as much as five centuries. Previously, Dominy et al. (2020) used stable isotope analysis to show that two New Kingdom specimens of Papio hamadryas originate from the Horn of Africa. Here, we report the complete mitochondrial genomes from a mummified baboon from Gabbanat el-Qurud and 14 museum specimens with known provenance together with published georeferenced mitochondrial sequence data. Phylogenetic assignment connects the mummified baboon to modern populations of P. hamadryas in Eritrea, Ethiopia, and eastern Sudan. This result, assuming geographical stability of phylogenetic clades, corroborates Greco-Roman historiographies by pointing toward present-day Eritrea, and by extension Adulis, as a source of baboons for Late Period Egyptians. It also establishes geographic continuity with baboons from the fabled Land of Punt (Dominy et al., 2020), giving weight to speculation that Punt and Adulis were essentially the same trading centres separated by a thousand years of history. CI - © 2023, Grathwol et al. FAU - Grathwol, Franziska AU - Grathwol F AD - Department of Biology, University of Konstanz, Konstanz, Germany. FAU - Roos, Christian AU - Roos C AUID- ORCID: 0000-0003-0190-4266 AD - Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany. FAU - Zinner, Dietmar AU - Zinner D AUID- ORCID: 0000-0003-3967-8014 AD - Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany. AD - Department of Primate Cognition, Georg-August-University of Göttingen, Göttingen, Germany. AD - Leibniz-ScienceCampus Primate Cognition, Göttingen, Germany. FAU - Hume, Benjamin AU - Hume B AD - Department of Biology, University of Konstanz, Konstanz, Germany. AD - SequAna - Sequencing Analysis Core Facility, University of Konstanz, Konstanz, Germany. FAU - Porcier, Stéphanie M AU - Porcier SM AD - Laboratoire CNRS ASM « Archéologie des Sociétés Méditerranéennes » (UMR 5140), Université Paul-Valéry, LabEx Archimede, Montpellier, France. FAU - Berthet, Didier AU - Berthet D AD - Musée des Confluences, Lyon, France. FAU - Cuisin, Jacques AU - Cuisin J AD - Muséum National d'Histoire Naturelle, Paris, France. FAU - Merker, Stefan AU - Merker S AD - Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany. FAU - Ottoni, Claudio AU - Ottoni C AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy. FAU - Van Neer, Wim AU - Van Neer W AUID- ORCID: 0000-0003-1710-3623 AD - Royal Belgian Institute of Natural Sciences, Brussels, Belgium. AD - Department of Biology, KU Leuven, Leuven, Belgium. FAU - Dominy, Nathaniel J AU - Dominy NJ AUID- ORCID: 0000-0001-5916-418X AD - Departments of Anthropology and Biological Sciences, Dartmouth College, Hanover, United States. AD - Zukunftskolleg, University of Konstanz, Konstanz, Germany. FAU - Kopp, Gisela H AU - Kopp GH AUID- ORCID: 0000-0001-8396-3264 AD - Department of Biology, University of Konstanz, Konstanz, Germany. AD - Zukunftskolleg, University of Konstanz, Konstanz, Germany. AD - Department of Migration, Max Planck Institute of Animal Behavior, Konstanz, Germany. AD - Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230928 PL - England TA - Elife JT - eLife JID - 101579614 SB - IM UOF - doi: 10.1101/2023.02.28.530428 MH - Humans MH - Animals MH - *Papio MH - Phylogeny MH - Africa MH - Egypt MH - Geography PMC - PMC10597581 OTO - NOTNLM OT - Papio OT - ancient DNA OT - ancient trade routes OT - capture enrichment OT - ecology OT - genetics OT - genomics OT - mitochondrial genome OT - museomics COIS- FG, CR, DZ, BH, SP, DB, JC, SM, CO, WV, ND, GK No competing interests declared EDAT- 2023/09/28 12:45 MHDA- 2023/10/27 06:42 PMCR- 2023/09/28 CRDT- 2023/09/28 07:53 PHST- 2023/03/07 00:00 [received] PHST- 2023/09/27 00:00 [accepted] PHST- 2023/10/27 06:42 [medline] PHST- 2023/09/28 12:45 [pubmed] PHST- 2023/09/28 07:53 [entrez] PHST- 2023/09/28 00:00 [pmc-release] AID - 87513 [pii] AID - 10.7554/eLife.87513 [doi] PST - epublish SO - Elife. 2023 Sep 28;12:e87513. doi: 10.7554/eLife.87513. PMID- 37895202 OWN - NLM STAT- MEDLINE DCOM- 20231031 LR - 20231113 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 14 IP - 10 DP - 2023 Sep 23 TI - High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia. LID - 10.3390/genes14101853 [doi] LID - 1853 AB - The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia. FAU - Uricoechea Patiño, Daniel AU - Uricoechea Patiño D AD - Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia. FAU - Collins, Andrew AU - Collins A AUID- ORCID: 0000-0001-7108-0771 AD - Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK. FAU - García, Oscar Julián Romero AU - García OJR AD - Genetics Group, National Institute of Legal Medicine and Forensic Sciences, Bogotá 110311, Colombia. FAU - Santos Vecino, Gustavo AU - Santos Vecino G AD - Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia. FAU - Cuenca, José Vicente Rodríguez AU - Cuenca JVR AD - Research Group in Biological Anthropology, Universidad Nacional de Colombia, Bogotá 111321, Colombia. FAU - Bernal, Jaime E AU - Bernal JE AD - Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia. FAU - Benavides Benítez, Escilda AU - Benavides Benítez E AD - Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia. FAU - Vergara Muñoz, Saray AU - Vergara Muñoz S AD - Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia. FAU - Briceño Balcázar, Ignacio AU - Briceño Balcázar I AD - Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230923 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - Colombia MH - *DNA, Mitochondrial/genetics/analysis MH - *Genetic Variation/genetics MH - Haplotypes/genetics MH - Indians, South American MH - Genetics, Population PMC - PMC10606881 OTO - NOTNLM OT - Colombia OT - ancient DNA OT - mtDNA HVS-I OT - native American ancestries OT - native American founding lineages OT - native American genetic history OT - pre-Hispanic COIS- The authors declare no conflict of interest. EDAT- 2023/10/28 11:46 MHDA- 2023/10/30 06:47 PMCR- 2023/09/23 CRDT- 2023/10/28 01:20 PHST- 2023/08/09 00:00 [received] PHST- 2023/08/30 00:00 [revised] PHST- 2023/09/18 00:00 [accepted] PHST- 2023/10/30 06:47 [medline] PHST- 2023/10/28 11:46 [pubmed] PHST- 2023/10/28 01:20 [entrez] PHST- 2023/09/23 00:00 [pmc-release] AID - genes14101853 [pii] AID - genes-14-01853 [pii] AID - 10.3390/genes14101853 [doi] PST - epublish SO - Genes (Basel). 2023 Sep 23;14(10):1853. doi: 10.3390/genes14101853. PMID- 37738339 OWN - NLM STAT- MEDLINE DCOM- 20230925 LR - 20231019 IS - 2375-2548 (Electronic) IS - 2375-2548 (Linking) VI - 9 IP - 38 DP - 2023 Sep 22 TI - Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry. PG - eadh3822 LID - 10.1126/sciadv.adh3822 [doi] LID - eadh3822 AB - Ancient DNA studies reveal the genetic structure of Africa before the expansion of Bantu-speaking agriculturalists; however, the impact of now extinct hunter-gatherer and herder societies on the genetic makeup of present-day African groups remains elusive. Here, we uncover the genetic legacy of pre-Bantu populations from the Angolan Namib Desert, where we located small-scale groups associated with enigmatic forager traditions, as well as the last speakers of the Khoe-Kwadi family's Kwadi branch. By applying an ancestry decomposition approach to genome-wide data from these and other African populations, we reconstructed the fine-scale histories of contact emerging from the migration of Khoe-Kwadi-speaking pastoralists and identified a deeply divergent ancestry, which is exclusively shared between groups from the Angolan Namib and adjacent areas of Namibia. The unique genetic heritage of the Namib peoples shows how modern DNA research targeting understudied regions of high ethnolinguistic diversity can complement ancient DNA studies in probing the deep genetic structure of the African continent. FAU - Oliveira, Sandra AU - Oliveira S AUID- ORCID: 0000-0002-1133-7130 AD - CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal. AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. AD - Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland. FAU - Fehn, Anne-Maria AU - Fehn AM AUID- ORCID: 0000-0003-2006-6552 AD - CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal. AD - Biopolis Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal. FAU - Amorim, Beatriz AU - Amorim B AUID- ORCID: 0000-0002-4485-2729 AD - CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal. AD - Biopolis Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal. AD - Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal. FAU - Stoneking, Mark AU - Stoneking M AUID- ORCID: 0000-0001-9044-6679 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. AD - Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558 Villeurbanne, France. FAU - Rocha, Jorge AU - Rocha J AUID- ORCID: 0000-0001-5460-7615 AD - CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal. AD - Biopolis Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal. AD - Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal. LA - eng PT - Journal Article DEP - 20230922 PL - United States TA - Sci Adv JT - Science advances JID - 101653440 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Black People/genetics MH - *DNA, Ancient MH - Namibia PMC - PMC10516492 EDAT- 2023/09/22 18:42 MHDA- 2023/09/25 06:42 PMCR- 2023/09/22 CRDT- 2023/09/22 14:04 PHST- 2023/09/25 06:42 [medline] PHST- 2023/09/22 18:42 [pubmed] PHST- 2023/09/22 14:04 [entrez] PHST- 2023/09/22 00:00 [pmc-release] AID - adh3822 [pii] AID - 10.1126/sciadv.adh3822 [doi] PST - ppublish SO - Sci Adv. 2023 Sep 22;9(38):eadh3822. doi: 10.1126/sciadv.adh3822. Epub 2023 Sep 22. PMID- 37683613 OWN - NLM STAT- MEDLINE DCOM- 20230911 LR - 20231006 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 110 IP - 9 DP - 2023 Sep 7 TI - The ancestry and geographical origins of St Helena's liberated Africans. PG - 1590-1599 LID - S0002-9297(23)00277-X [pii] LID - 10.1016/j.ajhg.2023.08.001 [doi] AB - The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition. CI - Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Sandoval-Velasco, Marcela AU - Sandoval-Velasco M AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA. Electronic address: sandoval-velascom@si.edu. FAU - Jagadeesan, Anuradha AU - Jagadeesan A AD - deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland. FAU - Ramos-Madrigal, Jazmín AU - Ramos-Madrigal J AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AD - International Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla, 76230 Santiago de Querétaro, México. FAU - Fortes-Lima, Cesar A AU - Fortes-Lima CA AD - Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden. FAU - Watson, Judy AU - Watson J AD - Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK. FAU - Johannesdóttir, Erna AU - Johannesdóttir E AD - Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK. FAU - Cruz-Dávalos, Diana I AU - Cruz-Dávalos DI AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Gopalakrishnan, Shyam AU - Gopalakrishnan S AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark. FAU - Moreno-Mayar, J Víctor AU - Moreno-Mayar JV AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark. FAU - Niemann, Jonas AU - Niemann J AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark. FAU - Renaud, Gabriel AU - Renaud G AD - Department of Health Technology Bioinformatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. FAU - Robson Brown, Katharine A AU - Robson Brown KA AD - Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK. FAU - Bennett, Helena AU - Bennett H AD - St Helena National Trust, Broadway House, Mainstreet, Jamestown, St Helena. FAU - Pearson, Andrew AU - Pearson A AD - Environmental Dimension Partnership, Atlantic Wharf, CF10 4HF Cardiff, UK. FAU - Helgason, Agnar AU - Helgason A AD - deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland. FAU - Gilbert, M Thomas P AU - Gilbert MTP AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway. FAU - Schroeder, Hannes AU - Schroeder H AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark. Electronic address: hschroeder@sund.ku.dk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Ancient) SB - IM EIN - Am J Hum Genet. 2023 Oct 5;110(10):1825. doi: 10.1016/j.ajhg.2023.09.007. PMID: 37802045 MH - Humans MH - Female MH - Male MH - *African People MH - DNA, Ancient MH - Black People/genetics MH - *Enslaved Persons MH - Genotype PMC - PMC10502851 OTO - NOTNLM OT - ancestry OT - ancient DNA OT - genomics OT - identity by state OT - next-generation sequencing OT - transatlantic slave trade COIS- Declaration of interests The authors declare no competing interests. EDAT- 2023/09/09 10:41 MHDA- 2023/09/11 06:42 PMCR- 2023/09/07 CRDT- 2023/09/08 18:17 PHST- 2022/10/27 00:00 [received] PHST- 2023/07/31 00:00 [revised] PHST- 2023/08/03 00:00 [accepted] PHST- 2023/09/11 06:42 [medline] PHST- 2023/09/09 10:41 [pubmed] PHST- 2023/09/08 18:17 [entrez] PHST- 2023/09/07 00:00 [pmc-release] AID - S0002-9297(23)00277-X [pii] AID - 10.1016/j.ajhg.2023.08.001 [doi] PST - ppublish SO - Am J Hum Genet. 2023 Sep 7;110(9):1590-1599. doi: 10.1016/j.ajhg.2023.08.001. PMID- 37541241 OWN - NLM STAT- MEDLINE DCOM- 20230911 LR - 20231002 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 110 IP - 9 DP - 2023 Sep 7 TI - Ethical considerations when co-analyzing ancient DNA and data from private genetic databases. PG - 1447-1453 LID - S0002-9297(23)00212-4 [pii] LID - 10.1016/j.ajhg.2023.06.011 [doi] AB - Ancient DNA studies have begun to explore the possibility of identifying identical DNA segments shared between historical and living people. This research requires access to large genetic datasets to maximize the likelihood of identifying previously unknown, close genetic connections. Direct-to-consumer genetic testing companies, such as 23andMe, Inc., manage by far the largest and most diverse genetic databases that can be used for this purpose. It is therefore important to think carefully about guidelines for carrying out collaborations between researchers and such companies. Such collaborations require consideration of ethical issues, including policies for sharing ancient DNA datasets, and ensuring reproducibility of research findings when access to privately controlled genetic datasets is limited. At the same time, they introduce unique possibilities for returning results to the research participants whose data are analyzed, including those who are identified as close genetic relatives of historical individuals, thereby enabling ancient DNA research to contribute to the restoration of information about ancestral connections that were lost over time, which can be particularly meaningful for families and groups where such history has not been well documented. We explore these issues by describing our experience designing and carrying out a study searching for genetic connections between 18th- and 19th-century enslaved and free African Americans who labored at Catoctin Furnace, Maryland, and 23andMe research participants. We share our experience in the hope of helping future researchers navigate similar ethical considerations, recognizing that our perspective is part of a larger conversation about best ethical practices. CI - Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Harney, Éadaoin AU - Harney É AD - 23andMe, Inc., Sunnyvale, CA 94043, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: eadaoinh@23andme.com. FAU - Sirak, Kendra AU - Sirak K AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Sedig, Jakob AU - Sedig J AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Micheletti, Steven AU - Micheletti S AD - 23andMe, Inc., Sunnyvale, CA 94043, USA. FAU - Curry, Roslyn AU - Curry R AD - 23andMe, Inc., Sunnyvale, CA 94043, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Ancona Esselmann, Samantha AU - Ancona Esselmann S AD - 23andMe, Inc., Sunnyvale, CA 94043, USA. FAU - Reich, David AU - Reich D AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States GR - R01 GM100233/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20230803 PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - *DNA, Ancient MH - Reproducibility of Results MH - *Communication MH - DNA/genetics MH - Databases, Genetic PMC - PMC10502734 MID - NIHMS1921189 COIS- Declaration of interests E.H., S.M., and S.A.E. are employees and shareholders of 23andMe, Inc. During the summer of 2021, R.C. was employed as an intern at 23andMe, Inc. EDAT- 2023/08/05 05:41 MHDA- 2023/09/11 06:42 PMCR- 2023/08/03 CRDT- 2023/08/04 18:41 PHST- 2023/04/13 00:00 [received] PHST- 2023/06/15 00:00 [revised] PHST- 2023/06/21 00:00 [accepted] PHST- 2023/09/11 06:42 [medline] PHST- 2023/08/05 05:41 [pubmed] PHST- 2023/08/04 18:41 [entrez] PHST- 2023/08/03 00:00 [pmc-release] AID - S0002-9297(23)00212-4 [pii] AID - 10.1016/j.ajhg.2023.06.011 [doi] PST - ppublish SO - Am J Hum Genet. 2023 Sep 7;110(9):1447-1453. doi: 10.1016/j.ajhg.2023.06.011. Epub 2023 Aug 3. PMID- 37673908 OWN - NLM STAT- MEDLINE DCOM- 20230908 LR - 20240923 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 14 IP - 1 DP - 2023 Sep 6 TI - Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains. PG - 5475 LID - 10.1038/s41467-023-41174-0 [doi] LID - 5475 AB - The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals. CI - © 2023. Springer Nature Limited. FAU - Hodgins, Harold P AU - Hodgins HP AD - Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada. FAU - Chen, Pengsheng AU - Chen P AD - Department of Urology, Boston Children's Hospital, Boston, MA, USA. AD - Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA. FAU - Lobb, Briallen AU - Lobb B AD - Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada. FAU - Wei, Xin AU - Wei X AD - Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada. FAU - Tremblay, Benjamin J M AU - Tremblay BJM AUID- ORCID: 0000-0002-7441-2951 AD - Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada. FAU - Mansfield, Michael J AU - Mansfield MJ AUID- ORCID: 0000-0003-4717-4721 AD - Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan. FAU - Lee, Victoria C Y AU - Lee VCY AD - Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada. FAU - Lee, Pyung-Gang AU - Lee PG AD - Department of Urology, Boston Children's Hospital, Boston, MA, USA. AD - Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA. FAU - Coffin, Jeffrey AU - Coffin J AD - Department of Anthropology, University of Waterloo, Waterloo, ON, Canada. FAU - Duggan, Ana T AU - Duggan AT AUID- ORCID: 0000-0002-2582-2954 AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada. FAU - Dolphin, Alexis E AU - Dolphin AE AD - Department of Anthropology, University of Waterloo, Waterloo, ON, Canada. FAU - Renaud, Gabriel AU - Renaud G AUID- ORCID: 0000-0002-0630-027X AD - Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark. gabre@dtu.dk. FAU - Dong, Min AU - Dong M AUID- ORCID: 0000-0002-1744-7293 AD - Department of Urology, Boston Children's Hospital, Boston, MA, USA. Min.Dong@childrens.harvard.edu. AD - Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA. Min.Dong@childrens.harvard.edu. FAU - Doxey, Andrew C AU - Doxey AC AUID- ORCID: 0000-0003-2015-099X AD - Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada. acdoxey@uwaterloo.ca. LA - eng SI - figshare/10.6084/m9.figshare.23804106 SI - figshare/10.6084/m9.figshare.21652340 SI - figshare/10.6084/m9.figshare.21498330 SI - figshare/10.6084/m9.figshare.21498222 SI - figshare/10.6084/m9.figshare.21498198 GR - R01 NS080833/NS/NINDS NIH HHS/United States GR - R01 NS117626/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20230906 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 11032-48-7 (tetanospasmin) RN - 0 (DNA, Ancient) RN - 0 (Neurotoxins) SB - IM MH - Humans MH - Animals MH - Mice MH - *DNA, Ancient MH - Neurotoxins MH - *Tetanus MH - Phylogeny MH - Clostridium MH - Chile MH - Mammals PMC - PMC10482840 COIS- The authors declare no competing interests. EDAT- 2023/09/07 00:41 MHDA- 2023/09/08 06:43 PMCR- 2023/09/06 CRDT- 2023/09/06 23:20 PHST- 2023/02/16 00:00 [received] PHST- 2023/08/23 00:00 [accepted] PHST- 2023/09/08 06:43 [medline] PHST- 2023/09/07 00:41 [pubmed] PHST- 2023/09/06 23:20 [entrez] PHST- 2023/09/06 00:00 [pmc-release] AID - 10.1038/s41467-023-41174-0 [pii] AID - 41174 [pii] AID - 10.1038/s41467-023-41174-0 [doi] PST - epublish SO - Nat Commun. 2023 Sep 6;14(1):5475. doi: 10.1038/s41467-023-41174-0. PMID- 37562011 OWN - NLM STAT- MEDLINE DCOM- 20230904 LR - 20231003 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 40 IP - 9 DP - 2023 Sep 1 TI - Interdisciplinary Analyses of Bronze Age Communities from Western Hungary Reveal Complex Population Histories. LID - 10.1093/molbev/msad182 [doi] LID - msad182 AB - In this study, we report 21 ancient shotgun genomes from present-day Western Hungary, from previously understudied Late Copper Age Baden, and Bronze Age Somogyvár-Vinkovci, Kisapostag, and Encrusted Pottery archeological cultures (3,530-1,620 cal Bce). Our results indicate the presence of high steppe ancestry in the Somogyvár-Vinkovci culture. They were then replaced by the Kisapostag group, who exhibit an outstandingly high (up to ∼47%) Mesolithic hunter-gatherer ancestry, despite this component being thought to be highly diluted by the time of the Early Bronze Age. The Kisapostag population contributed the genetic basis for the succeeding community of the Encrusted Pottery culture. We also found an elevated hunter-gatherer component in a local Baden culture-associated individual, but no connections were proven to the Bronze Age individuals. The hunter-gatherer ancestry in Kisapostag is likely derived from two main sources, one from a Funnelbeaker or Globular Amphora culture-related population and one from a previously unrecognized source in Eastern Europe. We show that this ancestry not only appeared in various groups in Bronze Age Central Europe but also made contributions to Baltic populations. The social structure of Kisapostag and Encrusted Pottery cultures is patrilocal, similarly to most contemporaneous groups. Furthermore, we developed new methods and method standards for computational analyses of ancient DNA, implemented to our newly developed and freely available bioinformatic package. By analyzing clinical traits, we found carriers of aneuploidy and inheritable genetic diseases. Finally, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin. CI - © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Gerber, Dániel AU - Gerber D AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. AD - Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary. AD - Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary. FAU - Szeifert, Bea AU - Szeifert B AUID- ORCID: 0000-0003-0786-1690 AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. AD - Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary. AD - Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary. FAU - Székely, Orsolya AU - Székely O AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. FAU - Egyed, Balázs AU - Egyed B AD - Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary. FAU - Gyuris, Balázs AU - Gyuris B AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. AD - Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary. AD - Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary. FAU - Giblin, Julia I AU - Giblin JI AD - Department of Sociology and Anthropology, Quinnipiac University, Hamden, CT, USA. FAU - Horváth, Anikó AU - Horváth A AD - Isotope Climatology and Environmental Research (ICER) Centre, Institute for Nuclear Research, Debrecen, Hungary. FAU - Köhler, Kitti AU - Köhler K AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. FAU - Kulcsár, Gabriella AU - Kulcsár G AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. FAU - Kustár, Ágnes AU - Kustár Á AD - Freelancer anthropologist, Budapest, Hungary. FAU - Major, István AU - Major I AD - Isotope Climatology and Environmental Research (ICER) Centre, Institute for Nuclear Research, Debrecen, Hungary. FAU - Molnár, Mihály AU - Molnár M AD - Isotope Climatology and Environmental Research (ICER) Centre, Institute for Nuclear Research, Debrecen, Hungary. FAU - Palcsu, László AU - Palcsu L AD - Isotope Climatology and Environmental Research (ICER) Centre, Institute for Nuclear Research, Debrecen, Hungary. FAU - Szeverényi, Vajk AU - Szeverényi V AD - Department of Archaeology, Déri Museum, Debrecen, Hungary. FAU - Fábián, Szilvia AU - Fábián S AD - Hungarian National Museum, Budapest, Hungary. FAU - Mende, Balázs Gusztáv AU - Mende BG AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. FAU - Bondár, Mária AU - Bondár M AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. FAU - Ari, Eszter AU - Ari E AUID- ORCID: 0000-0001-7774-1067 AD - Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary. AD - HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary. AD - Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary. FAU - Kiss, Viktória AU - Kiss V AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest, Hungary. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - History, Ancient MH - Hungary MH - *Human Migration MH - *Genome, Human MH - Europe MH - DNA, Ancient PMC - PMC10473862 OTO - NOTNLM OT - ancient DNA OT - archaeogenomics OT - bioinformatics OT - population genomics EDAT- 2023/08/10 18:41 MHDA- 2023/09/04 06:44 PMCR- 2023/08/10 CRDT- 2023/08/10 16:33 PHST- 2023/09/04 06:44 [medline] PHST- 2023/08/10 18:41 [pubmed] PHST- 2023/08/10 16:33 [entrez] PHST- 2023/08/10 00:00 [pmc-release] AID - 7240678 [pii] AID - msad182 [pii] AID - 10.1093/molbev/msad182 [doi] PST - ppublish SO - Mol Biol Evol. 2023 Sep 1;40(9):msad182. doi: 10.1093/molbev/msad182. PMID- 37438447 OWN - NLM STAT- MEDLINE DCOM- 20230724 LR - 20230724 IS - 1617-4623 (Electronic) IS - 1617-4623 (Linking) VI - 298 IP - 5 DP - 2023 Sep TI - The first maternal genetic study of hunter-gatherers from Vietnam. PG - 1225-1235 LID - 10.1007/s00438-023-02050-0 [doi] AB - The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam. CI - © 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. FAU - Tran, Huyen Linh AU - Tran HL AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. AD - University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam. FAU - Mai, Huong Pham AU - Mai HP AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. FAU - Le Thi, Dung AU - Le Thi D AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. AD - University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam. FAU - Thi, Nhung Doan AU - Thi ND AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. FAU - Le Tung, Lam AU - Le Tung L AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. FAU - Thanh, Tung Pham AU - Thanh TP AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. FAU - Manh, Ha Tran AU - Manh HT AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. FAU - Mau, Hung Nguyen AU - Mau HN AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. FAU - Chu, Hoang Ha AU - Chu HH AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. AD - University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam. AD - Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam. FAU - Hoang, Ha AU - Hoang H AUID- ORCID: 0000-0002-3090-8795 AD - Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam. hoanghapcb@ibt.ac.vn. LA - eng GR - DL0000.08/20-23/Vietnam Academy of Science and Technology/ PT - Journal Article DEP - 20230712 PL - Germany TA - Mol Genet Genomics JT - Molecular genetics and genomics : MGG JID - 101093320 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Vietnam MH - *Archaeology MH - *DNA, Ancient/analysis MH - Genome, Human OTO - NOTNLM OT - Ancient DNA OT - Hunter-gather OT - Mitogenome OT - Population genetics OT - Pre-Neolithic EDAT- 2023/07/13 01:06 MHDA- 2023/07/24 06:42 CRDT- 2023/07/12 23:26 PHST- 2022/02/22 00:00 [received] PHST- 2023/06/22 00:00 [accepted] PHST- 2023/07/24 06:42 [medline] PHST- 2023/07/13 01:06 [pubmed] PHST- 2023/07/12 23:26 [entrez] AID - 10.1007/s00438-023-02050-0 [pii] AID - 10.1007/s00438-023-02050-0 [doi] PST - ppublish SO - Mol Genet Genomics. 2023 Sep;298(5):1225-1235. doi: 10.1007/s00438-023-02050-0. Epub 2023 Jul 12. PMID- 37284851 OWN - NLM STAT- MEDLINE DCOM- 20230814 LR - 20230815 IS - 1437-1596 (Electronic) IS - 0937-9827 (Print) IS - 0937-9827 (Linking) VI - 137 IP - 5 DP - 2023 Sep TI - Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology. PG - 1629-1638 LID - 10.1007/s00414-023-03032-y [doi] AB - Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period. CI - © 2023. The Author(s). FAU - Zupanič Pajnič, Irena AU - Zupanič Pajnič I AUID- ORCID: 0000-0002-6704-015X AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia. irena.zupanic@mf.uni-lj.si. FAU - Leskovar, Tamara AU - Leskovar T AD - Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia. FAU - Črešnar, Matija AU - Črešnar M AD - Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia. LA - eng GR - J3-3080/Javna Agencija za Raziskovalno Dejavnost RS/ PT - Journal Article DEP - 20230607 PL - Germany TA - Int J Legal Med JT - International journal of legal medicine JID - 9101456 RN - 0 (Powders) RN - 9007-49-2 (DNA) SB - IM MH - Male MH - Humans MH - Adult MH - Middle Aged MH - Child MH - *Eye Color/genetics MH - *Hair Color/genetics MH - Powders MH - DNA/genetics MH - Bone and Bones MH - Polymorphism, Single Nucleotide PMC - PMC10421759 OTO - NOTNLM OT - Ancient DNA OT - Eye color OT - HIrisPlex OT - Hair color OT - Petrous bones OT - Skeletal remains COIS- The authors declare that they have no conflict of interest. EDAT- 2023/06/07 13:10 MHDA- 2023/08/14 06:42 PMCR- 2023/06/07 CRDT- 2023/06/07 11:04 PHST- 2023/01/13 00:00 [received] PHST- 2023/05/24 00:00 [accepted] PHST- 2023/08/14 06:42 [medline] PHST- 2023/06/07 13:10 [pubmed] PHST- 2023/06/07 11:04 [entrez] PHST- 2023/06/07 00:00 [pmc-release] AID - 10.1007/s00414-023-03032-y [pii] AID - 3032 [pii] AID - 10.1007/s00414-023-03032-y [doi] PST - ppublish SO - Int J Legal Med. 2023 Sep;137(5):1629-1638. doi: 10.1007/s00414-023-03032-y. Epub 2023 Jun 7. PMID- 37644833 OWN - NLM STAT- MEDLINE DCOM- 20230831 LR - 20240924 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 290 IP - 2005 DP - 2023 Aug 30 TI - Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia. PG - 20231262 LID - 10.1098/rspb.2023.1262 [doi] LID - 20231262 AB - An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north. FAU - Aoki, Kenichi AU - Aoki K AD - Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan. FAU - Takahata, Naoyuki AU - Takahata N AD - Graduate University for Advanced Studies, Hayama, Kanagawa 240-0116, Japan. FAU - Oota, Hiroki AU - Oota H AD - Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan. FAU - Wakano, Joe Yuichiro AU - Wakano JY AD - School of Interdisciplinary Mathematical Sciences, Meiji University, Nakano, Tokyo 164-8525, Japan. FAU - Feldman, Marcus W AU - Feldman MW AUID- ORCID: 0000-0002-0664-3803 AD - Department of Biology, Stanford University, Stanford, CA 94305, USA. LA - eng SI - figshare/10.6084/m9.figshare.c.6781088 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230830 PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Archaeology MH - Asia, Eastern MH - *Communicable Diseases MH - DNA, Ancient MH - East Asian People PMC - PMC10465978 OTO - NOTNLM OT - Qinling–Huaihe Line OT - ancient DNA OT - diffusion equation OT - infectious disease OT - microblades COIS- We declare we have no competing interests. EDAT- 2023/08/30 06:47 MHDA- 2023/08/31 06:41 PMCR- 2023/08/30 CRDT- 2023/08/30 03:09 PHST- 2023/08/31 06:41 [medline] PHST- 2023/08/30 06:47 [pubmed] PHST- 2023/08/30 03:09 [entrez] PHST- 2023/08/30 00:00 [pmc-release] AID - rspb20231262 [pii] AID - 10.1098/rspb.2023.1262 [doi] PST - ppublish SO - Proc Biol Sci. 2023 Aug 30;290(2005):20231262. doi: 10.1098/rspb.2023.1262. Epub 2023 Aug 30. PMID- 37535713 OWN - NLM STAT- MEDLINE DCOM- 20230808 LR - 20230922 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 381 IP - 6657 DP - 2023 Aug 4 TI - Community-initiated genomics. PG - 482-483 LID - 10.1126/science.adj2380 [doi] AB - Ancient DNA is used to connect enslaved African Americans to modern descendants. FAU - Jackson, Fatimah L C AU - Jackson FLC AD - Howard University and QuadGrid Data Lab, Washington, DC, USA. LA - eng PT - Journal Article DEP - 20230803 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Black or African American/genetics MH - *DNA, Ancient MH - Metagenomics MH - *Enslavement/history EDAT- 2023/08/03 19:14 MHDA- 2023/08/07 06:42 CRDT- 2023/08/03 14:03 PHST- 2023/08/07 06:42 [medline] PHST- 2023/08/03 19:14 [pubmed] PHST- 2023/08/03 14:03 [entrez] AID - 10.1126/science.adj2380 [doi] PST - ppublish SO - Science. 2023 Aug 4;381(6657):482-483. doi: 10.1126/science.adj2380. Epub 2023 Aug 3. PMID- 37589132 OWN - NLM STAT- MEDLINE DCOM- 20230818 LR - 20240318 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 75 IP - 2 DP - 2023 Aug TI - Releasing secrets bound to ancient remains with modern DNA extraction techniques: an interview with Elena Essel. PG - 42-46 LID - 10.2144/btn-2023-0067 [doi] AB - Elena Essel (Msc) spoke to Ebony Torrington, Managing Editor of BioTechniques. Essel is a molecular biologist in Matthias Meyer's Advanced DNA Sequencing Techniques group at the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany). Essel studied biology at University of Erlangen-Nuremberg (Erlangen, Germany) for her bachelor's and in Martin-Luther-University Halle-Wittenberg (Halle an der Saale, Germany) for her master's. Essel worked in Meyer's group on DNA extraction of very degraded material for her master's thesis. Meyer is an expert in developing new cutting-edge methods for researching ancient DNA, with a focus on skeletal remains, and more recently on sediment remains. Essel now focusses on DNA sampling and extraction aspects of the pipeline at Meyer's lab for the ancient DNA workflow. FAU - Essel, Elena AU - Essel E AUID- ORCID: 0000-0002-2642-8043 AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103 Leipzig, Germany. LA - eng PT - Interview DEP - 20230817 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Female MH - *DNA, Ancient MH - *Anthropology MH - Body Remains MH - Sequence Analysis, DNA MH - Universities OTO - NOTNLM OT - DNA extraction OT - Denisova OT - Paleolithic pendant OT - ancient DNA OT - molecular biology OT - temperature-controlled DNA extraction EDAT- 2023/08/17 06:42 MHDA- 2023/08/18 06:42 CRDT- 2023/08/17 05:32 PHST- 2023/08/18 06:42 [medline] PHST- 2023/08/17 06:42 [pubmed] PHST- 2023/08/17 05:32 [entrez] AID - 10.2144/btn-2023-0067 [doi] PST - ppublish SO - Biotechniques. 2023 Aug;75(2):42-46. doi: 10.2144/btn-2023-0067. Epub 2023 Aug 17. PMID- 37537290 OWN - NLM STAT- MEDLINE DCOM- 20230810 LR - 20240312 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 620 IP - 7973 DP - 2023 Aug TI - Ancient DNA reveals the living descendants of enslaved people through 23andMe. PG - 251-252 LID - 10.1038/d41586-023-02478-9 [doi] FAU - Callaway, Ewen AU - Callaway E LA - eng PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Black People/genetics/history MH - *DNA, Ancient/analysis MH - *Enslaved Persons/history MH - *Genetic Testing MH - *Genetics, Population MH - Genome, Human MH - *Genomics MH - History, 18th Century MH - History, 19th Century MH - Mass Screening OTO - NOTNLM OT - Databases OT - Genetics OT - History EDAT- 2023/08/04 01:07 MHDA- 2023/08/10 06:43 CRDT- 2023/08/03 23:25 PHST- 2023/08/10 06:43 [medline] PHST- 2023/08/04 01:07 [pubmed] PHST- 2023/08/03 23:25 [entrez] AID - 10.1038/d41586-023-02478-9 [pii] AID - 10.1038/d41586-023-02478-9 [doi] PST - ppublish SO - Nature. 2023 Aug;620(7973):251-252. doi: 10.1038/d41586-023-02478-9. PMID- 37528222 OWN - NLM STAT- MEDLINE DCOM- 20230803 LR - 20230804 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 13 IP - 1 DP - 2023 Aug 1 TI - Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas. PG - 12444 LID - 10.1038/s41598-023-39518-3 [doi] LID - 12444 AB - Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries. CI - © 2023. The Author(s). FAU - Delsol, Nicolas AU - Delsol N AD - Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. ndelsol@ufl.edu. FAU - Stucky, Brian J AU - Stucky BJ AD - Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. AD - Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD, USA. FAU - Oswald, Jessica A AU - Oswald JA AD - Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. AD - Biology Department, University of Nevada, Reno, Reno, NV, 89557, USA. AD - U.S. Fish and Wildlife Service, National Fish and Wildlife Forensic Laboratory, Ashland, OR, 97520, USA. FAU - Cobb, Charles R AU - Cobb CR AD - Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. FAU - Emery, Kitty F AU - Emery KF AD - Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. FAU - Guralnick, Robert AU - Guralnick R AD - Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20230801 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - Animals MH - Cattle/genetics MH - *DNA, Ancient MH - Phylogeny MH - Americas MH - Europe MH - Caribbean Region MH - *DNA, Mitochondrial/genetics MH - Haplotypes PMC - PMC10394069 COIS- The authors declare no competing interests. EDAT- 2023/08/02 01:07 MHDA- 2023/08/03 06:43 PMCR- 2023/08/01 CRDT- 2023/08/01 23:27 PHST- 2023/03/21 00:00 [received] PHST- 2023/07/26 00:00 [accepted] PHST- 2023/08/03 06:43 [medline] PHST- 2023/08/02 01:07 [pubmed] PHST- 2023/08/01 23:27 [entrez] PHST- 2023/08/01 00:00 [pmc-release] AID - 10.1038/s41598-023-39518-3 [pii] AID - 39518 [pii] AID - 10.1038/s41598-023-39518-3 [doi] PST - epublish SO - Sci Rep. 2023 Aug 1;13(1):12444. doi: 10.1038/s41598-023-39518-3. PMID- 37495691 OWN - NLM STAT- MEDLINE DCOM- 20230823 LR - 20230905 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 620 IP - 7974 DP - 2023 Aug TI - Extensive pedigrees reveal the social organization of a Neolithic community. PG - 600-606 LID - 10.1038/s41586-023-06350-8 [doi] AB - Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations(1-4). However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy 'les Noisats' (France), dated to the western European Neolithic around 4850-4500 BC. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality(5). Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic. CI - © 2023. The Author(s). FAU - Rivollat, Maïté AU - Rivollat M AUID- ORCID: 0000-0002-4011-2862 AD - University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France. maite.rivollat@ugent.be. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. maite.rivollat@ugent.be. AD - Department of Archaeology, Durham University, Durham, UK. maite.rivollat@ugent.be. AD - Department of Archaeology, Ghent University, Ghent, Belgium. maite.rivollat@ugent.be. FAU - Rohrlach, Adam Benjamin AU - Rohrlach AB AUID- ORCID: 0000-0002-4204-5018 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Ringbauer, Harald AU - Ringbauer H AUID- ORCID: 0000-0002-4884-9682 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Childebayeva, Ainash AU - Childebayeva A AUID- ORCID: 0000-0002-3144-6481 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Mendisco, Fanny AU - Mendisco F AD - University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France. FAU - Barquera, Rodrigo AU - Barquera R AUID- ORCID: 0000-0003-0518-4518 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Szolek, András AU - Szolek A AUID- ORCID: 0000-0003-4758-7817 AD - Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany. AD - Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany. FAU - Le Roy, Mélie AU - Le Roy M AUID- ORCID: 0000-0002-5613-3190 AD - Department of Archaeology & Anthropology, Bournemouth University, Bournemouth, UK. FAU - Colleran, Heidi AU - Colleran H AUID- ORCID: 0000-0002-2126-8116 AD - Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - BirthRites Lise Meitner Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Tuke, Jonathan AU - Tuke J AD - School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Aron, Franziska AU - Aron F AD - Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany. AD - RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany. FAU - Pemonge, Marie-Hélène AU - Pemonge MH AD - University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France. FAU - Späth, Ellen AU - Späth E AUID- ORCID: 0000-0002-3851-3931 AD - Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany. FAU - Télouk, Philippe AU - Télouk P AD - Ecole Normale Supérieure de Lyon, CNRS, UCBL, LGL-TPE, Lyon, France. FAU - Rey, Léonie AU - Rey L AD - University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France. FAU - Goude, Gwenaëlle AU - Goude G AUID- ORCID: 0000-0002-3008-3607 AD - CNRS, Aix Marseille University, Ministry of Culture, LAMPEA, Aix-en-Provence, France. FAU - Balter, Vincent AU - Balter V AUID- ORCID: 0000-0002-9236-4834 AD - Ecole Normale Supérieure de Lyon, CNRS, UCBL, LGL-TPE, Lyon, France. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Rottier, Stéphane AU - Rottier S AUID- ORCID: 0000-0002-1520-6648 AD - University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France. stephane.rottier@u-bordeaux.fr. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. wolfgang_haak@eva.mpg.de. LA - eng PT - Journal Article DEP - 20230726 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Strontium Isotopes) SB - IM MH - Adult MH - Child MH - Female MH - Humans MH - Male MH - Agriculture/history MH - *Anthropology, Cultural MH - Burial/history MH - Fathers/history MH - Fertility MH - France MH - History, Ancient MH - Mortality/history MH - *Pedigree MH - Siblings MH - Social Support/history MH - Strontium Isotopes/analysis MH - *Social Environment MH - Mothers/history PMC - PMC10432279 COIS- The authors declare no competing interests. EDAT- 2023/07/27 01:09 MHDA- 2023/08/18 06:42 PMCR- 2023/07/26 CRDT- 2023/07/26 23:24 PHST- 2022/10/20 00:00 [received] PHST- 2023/06/21 00:00 [accepted] PHST- 2023/08/18 06:42 [medline] PHST- 2023/07/27 01:09 [pubmed] PHST- 2023/07/26 23:24 [entrez] PHST- 2023/07/26 00:00 [pmc-release] AID - 10.1038/s41586-023-06350-8 [pii] AID - 6350 [pii] AID - 10.1038/s41586-023-06350-8 [doi] PST - ppublish SO - Nature. 2023 Aug;620(7974):600-606. doi: 10.1038/s41586-023-06350-8. Epub 2023 Jul 26. PMID- 37450551 OWN - NLM STAT- MEDLINE DCOM- 20230810 LR - 20230810 IS - 1520-6505 (Electronic) IS - 1060-1538 (Linking) VI - 32 IP - 4 DP - 2023 Aug TI - Deconstructing Eurocentrism in skin pigmentation research via the incorporation of diverse populations and theoretical perspectives. PG - 195-205 LID - 10.1002/evan.21993 [doi] AB - The evolution of skin pigmentation has been shaped by numerous biological and cultural shifts throughout human history. Vitamin D is considered a driver of depigmentation evolution in humans, given the deleterious health effects associated with vitamin D deficiency, which is often shaped by cultural factors. New advancements in genomics and epigenomics have opened the door to a deeper exploration of skin pigmentation evolution in both contemporary and ancient populations. Data from ancient Europeans has offered great context to the spread of depigmentation alleles via the evaluation of migration events and cultural shifts that occurred during the Neolithic. However, novel insights can further be gained via the inclusion of diverse ancient and contemporary populations. Here we present on how potential biases and limitations in skin pigmentation research can be overcome with the integration of interdisciplinary data that includes both cultural and biological elements, which have shaped the evolutionary history of skin pigmentation in humans. CI - © 2023 Wiley Periodicals LLC. FAU - Pryor, Yemko AU - Pryor Y AUID- ORCID: 0000-0002-1942-786X AD - Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA. FAU - Lindo, John AU - Lindo J AUID- ORCID: 0000-0002-2533-8505 AD - Department of Anthropology, Emory University, Atlanta, Georgia, USA. LA - eng GR - 1926075/Division of Behavioral and Cognitive Sciences/ GR - 1945046/Division of Behavioral and Cognitive Sciences/ GR - Ford Foundation Predoctoral Fellowship/ GR - 21602/National Science Foundation Graduate Research Fellowship/ PT - Journal Article PT - Review DEP - 20230714 PL - United States TA - Evol Anthropol JT - Evolutionary anthropology JID - 9306331 SB - IM MH - Animals MH - Humans MH - *Skin Pigmentation MH - Biological Evolution MH - *Hominidae MH - Genomics OTO - NOTNLM OT - ancient DNA OT - human evolution OT - skin pigmentation EDAT- 2023/07/14 19:08 MHDA- 2023/08/10 06:42 CRDT- 2023/07/14 13:44 PHST- 2023/03/29 00:00 [revised] PHST- 2022/12/11 00:00 [received] PHST- 2023/06/16 00:00 [accepted] PHST- 2023/08/10 06:42 [medline] PHST- 2023/07/14 19:08 [pubmed] PHST- 2023/07/14 13:44 [entrez] AID - 10.1002/evan.21993 [doi] PST - ppublish SO - Evol Anthropol. 2023 Aug;32(4):195-205. doi: 10.1002/evan.21993. Epub 2023 Jul 14. PMID- 37323114 OWN - NLM STAT- MEDLINE DCOM- 20230725 LR - 20230725 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 181 IP - 4 DP - 2023 Aug TI - Ancient mitochondrial genome diversity in South America: Contributions from Quebrada del Toro, Northwestern Argentina. PG - 597-610 LID - 10.1002/ajpa.24795 [doi] AB - OBJECTIVES: The objective of this study was to enhance our understanding of the population history in South America, specifically Northwestern Argentina, by analyzing complete ancient mitogenomes of individuals from the Ojo de Agua archeological site (970 BP) in Quebrada del Toro (Salta, Argentina). MATERIALS AND METHODS: We analyzed teeth from four individuals from the site Ojo de Agua (970 ± 60 BP), located in Quebrada del Toro (Andean region of Northwestern Argentina). DNA extracts were converted to double-stranded DNA libraries and indexed using unique dual-indexing primer combinations. DNA libraries were then enriched for the complete mitochondrial genome, pooled at equimolar concentrations, and sequenced on an Illumina® MiSeq™ platform. Reads from high quality libraries were trimmed, merged, and then mapped to the revised Cambridge Reference Sequence. The aDNA damage patterns were assessed and contamination estimated. Finally, variants were called, filtered, and the consensus mitogenome was constructed and used for haplogroup assignment. We also compiled available mitogenome sequences from ancient and present-day populations from the Southcentral Andes and other surrounding regions in Argentina. Maximum Likelihood and Bayesian phylogenetic reconstructions were obtained using the generated dataset. RESULTS: We successfully obtained the complete mitogenome sequence from one individual with an average depth coverage of 102X. We discovered a novel haplotype that was assigned to haplogroup D1. Phylogenetic reconstructions suggests that this haplotype falls within the sister branches of the D1j lineage, forming a well-supported clade. The estimate TMRCA of this clade that includes D1j and its sister branches ranged between 12,535 and 18,669 ya. DISCUSSION: The sequence analyzed in this study represents the first ancient mitogenome from within the valley region in Northwestern Argentina. We found that a representative of a lineage highly associated with D1j was already present approximately 1000 BP in the region. Our results agree with the proposed origin of D1j in other regions north of Patagonia and independent of the Pacific coast fast migratory route, contrary to what was originally hypothesized. This study highlights the lack of information regarding pre-Hispanic genetic diversity and contributes to the knowledge about the peopling process in South America. CI - © 2023 Wiley Periodicals LLC. FAU - Russo, María Gabriela AU - Russo MG AUID- ORCID: 0000-0002-5727-4956 AD - Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Grupo de Investigación en Biología Evolutiva, Buenos Aires, Argentina. AD - Universidad Maimónides, Centro de Ciencias Naturales, Ambientales y Antropológicas, Equipo de Antropología Biológica, Buenos Aires, Argentina. FAU - Arencibia, Valeria AU - Arencibia V AUID- ORCID: 0000-0002-5360-2457 AD - CONICET, Universidad Maimónides, Centro de Ciencias Naturales, Ambientales y Antropológicas, Equipo de Antropología Biológica, Buenos Aires, Argentina. FAU - Emery, Matthew AU - Emery M AD - School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA. AD - Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA. AD - Department of Anthropology, Binghamton University, Binghamton, New York, USA. FAU - Bettera Marcat, Gianina AU - Bettera Marcat G AD - Universidad de Buenos Aires, Facultad de Filosofía y Letras, Sección Antropología Biológica, Instituto de Ciencias Antropológicas, Buenos Aires, Argentina. FAU - Seldes, Verónica AU - Seldes V AD - CONICET, Universidad de Buenos Aires, Facultad de Filosofía y Letras, Sección Antropología Biológica, Instituto de Ciencias Antropológicas, Buenos Aires, Argentina. FAU - Mercolli, Pablo AU - Mercolli P AD - Universidad de Buenos Aires, Facultad de Filosofía y Letras, Instituto Interdisciplinario Tilcara, Tilcara, Argentina. FAU - Soria, Silvia AU - Soria S AD - Facultad de Humanidades, Universidad Nacional de Salta, ICSOH CIUNSa, Salta, Argentina. FAU - Maldonado, Lucas AU - Maldonado L AD - CONICET, Universidad de Buenos Aires, Facultad de Medicina, IMPaM, Buenos Aires, Argentina. FAU - Kamenetzky, Laura AU - Kamenetzky L AD - Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología traslacional (iB3), Buenos Aires, Argentina. FAU - Avena, Sergio AU - Avena S AD - CONICET, Universidad Maimónides, Centro de Ciencias Naturales, Ambientales y Antropológicas, Equipo de Antropología Biológica, Buenos Aires, Argentina. AD - Universidad de Buenos Aires, Facultad de Filosofía y Letras, Sección Antropología Biológica, Instituto de Ciencias Antropológicas, Buenos Aires, Argentina. FAU - Dejean, Cristina AU - Dejean C AD - Universidad Maimónides, Centro de Ciencias Naturales, Ambientales y Antropológicas, Equipo de Antropología Biológica, Buenos Aires, Argentina. AD - Universidad de Buenos Aires, Facultad de Filosofía y Letras, Sección Antropología Biológica, Instituto de Ciencias Antropológicas, Buenos Aires, Argentina. FAU - Stone, Anne C AU - Stone AC AD - School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA. AD - Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA. AD - Center for Bioarchaeological Research, Arizona State University, Tempe, Arizona, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230616 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - Argentina MH - *Genome, Mitochondrial/genetics MH - Phylogeny MH - Bayes Theorem MH - DNA, Mitochondrial/genetics MH - South America OTO - NOTNLM OT - Northwestern Argentina OT - Southcentral Andes OT - ancient DNA OT - mitogenome EDAT- 2023/06/16 06:42 MHDA- 2023/07/25 06:42 CRDT- 2023/06/16 03:53 PHST- 2023/05/23 00:00 [revised] PHST- 2022/11/09 00:00 [received] PHST- 2023/05/26 00:00 [accepted] PHST- 2023/07/25 06:42 [medline] PHST- 2023/06/16 06:42 [pubmed] PHST- 2023/06/16 03:53 [entrez] AID - 10.1002/ajpa.24795 [doi] PST - ppublish SO - Am J Biol Anthropol. 2023 Aug;181(4):597-610. doi: 10.1002/ajpa.24795. Epub 2023 Jun 16. PMID- 37491505 OWN - NLM STAT- MEDLINE DCOM- 20230727 LR - 20230728 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 13 IP - 1 DP - 2023 Jul 25 TI - First molecular data on the human roundworm Ascaris lumbricoides species complex from the Bronze and Iron Age in Hallstatt, Austria. PG - 12055 LID - 10.1038/s41598-023-38989-8 [doi] LID - 12055 AB - Palaeoparasitological studies can provide valuable information on the emergence, distribution, and elimination of parasites during a particular time in the past. In the prehistoric salt mines of Hallstatt, located in the Austrian Alps, human faeces have been conserved in salt. The aim of this study was to recover ancient DNA of intestinal parasites from these coprolites. Altogether, 35 coprolites from the Hallstatt salt mines, dating back to the Bronze Age mining phase (1158-1063 BCE) and the Iron Age mining phase (750-662 BCE), respectively, were analysed by microscopy and molecular methods. In 91% of the coprolite samples, eggs of soil-transmitted helminths (STH), namely of Trichuris and/or Ascaris were detected by light microscopy. The Ascaris eggs were exceptionally well preserved. For further analysis, DNA was extracted from the palaeofaecal samples and species-specific primers targeting different genes were designed. While amplification of Trichuris DNA remained unsuccessful, sequence data of A. lumbricoides species complex were successfully obtained from 16 coprolites from three different genes, the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), the mitochondrial cytochrome B gene (cytB) and the mitochondrial NADH dehydrogenase subunit 1 gene (nadh1). Importantly, these included two Ascaris sequences from a coprolite from the Bronze Age, which to the best of our knowledge are the first molecular data of this genus from this period. CI - © 2023. The Author(s). FAU - Barsch, Elisabeth AU - Barsch E AD - Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria. FAU - Kowarik, Kerstin AU - Kowarik K AD - Prehistoric Department, Natural History Museum Vienna, Vienna, Austria. AD - Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria. FAU - Rodler, Katharina AU - Rodler K AD - Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria. FAU - Hörweg, Christoph AU - Hörweg C AD - 3rd Zoological Department, Natural History Museum Vienna, Vienna, Austria. FAU - Reschreiter, Hans AU - Reschreiter H AD - Prehistoric Department, Natural History Museum Vienna, Vienna, Austria. FAU - Sattmann, Helmut AU - Sattmann H AD - 3rd Zoological Department, Natural History Museum Vienna, Vienna, Austria. FAU - Walochnik, Julia AU - Walochnik J AD - Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria. julia.walochnik@meduniwien.ac.at. LA - eng PT - Journal Article DEP - 20230725 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (Soil) SB - IM MH - Animals MH - Humans MH - Ascaris lumbricoides/genetics MH - Austria MH - Ascaris/genetics MH - *Ascariasis MH - *Nematode Infections MH - Trichuris/genetics MH - Feces/parasitology MH - Soil PMC - PMC10368691 COIS- The authors declare no competing interests. EDAT- 2023/07/26 01:06 MHDA- 2023/07/27 06:42 PMCR- 2023/07/25 CRDT- 2023/07/25 23:56 PHST- 2023/03/31 00:00 [received] PHST- 2023/07/18 00:00 [accepted] PHST- 2023/07/27 06:42 [medline] PHST- 2023/07/26 01:06 [pubmed] PHST- 2023/07/25 23:56 [entrez] PHST- 2023/07/25 00:00 [pmc-release] AID - 10.1038/s41598-023-38989-8 [pii] AID - 38989 [pii] AID - 10.1038/s41598-023-38989-8 [doi] PST - epublish SO - Sci Rep. 2023 Jul 25;13(1):12055. doi: 10.1038/s41598-023-38989-8. PMID- 37216609 OWN - NLM STAT- MEDLINE DCOM- 20230719 LR - 20230719 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 51 IP - W1 DP - 2023 Jul 5 TI - Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics. PG - W269-W273 LID - 10.1093/nar/gkad428 [doi] AB - Archeogenomics is a rapidly growing interdisciplinary research field driven by the development of techniques that enable the acquisition and analysis of ancient DNA (aDNA). Recent advances in aDNA studies have contributed significantly to increasing our understanding of the natural history of humans. One of the most significant challenges facing archeogenomics is the integration of highly heterogeneous genomic, archeological, and anthropological data and their comprehensive analysis, considering changes that occur in time and space. Only this complex approach can explain the relationship between past populations in the context of migration or cultural development. To address these challenges, we developed a Human AGEs web server. It focuses on creating comprehensive spatiotemporal visualizations of genomic, archeogenomic, and archeological information, which can be provided by the user or loaded from a graph database. The interactive map application at the center of Human AGEs can display multiple layers of data in various forms, such as bubble charts, pie charts, heatmaps, or tag clouds. These visualizations can be modified using various clustering, filtering, and styling options, and the map state can be exported to a high-resolution image or saved as a session file for later use. Human AGEs, along with their tutorial, are accessible at https://archeogenomics.eu/. CI - © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. FAU - Ciecierski, Lukasz AU - Ciecierski L AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. FAU - Stolarek, Ireneusz AU - Stolarek I AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. FAU - Figlerowicz, Marek AU - Figlerowicz M AUID- ORCID: 0000-0002-6392-0192 AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Genomics/methods MH - Software MH - Human Genetics MH - DNA, Ancient MH - Databases, Genetic PMC - PMC10320146 EDAT- 2023/05/22 19:11 MHDA- 2023/07/06 06:42 PMCR- 2023/05/22 CRDT- 2023/05/22 15:43 PHST- 2023/05/12 00:00 [accepted] PHST- 2023/04/26 00:00 [revised] PHST- 2023/03/15 00:00 [received] PHST- 2023/07/06 06:42 [medline] PHST- 2023/05/22 19:11 [pubmed] PHST- 2023/05/22 15:43 [entrez] PHST- 2023/05/22 00:00 [pmc-release] AID - 7175335 [pii] AID - gkad428 [pii] AID - 10.1093/nar/gkad428 [doi] PST - ppublish SO - Nucleic Acids Res. 2023 Jul 5;51(W1):W269-W273. doi: 10.1093/nar/gkad428. PMID- 37528780 OWN - NLM STAT- MEDLINE DCOM- 20231102 LR - 20231102 IS - 0026-8984 (Print) IS - 0026-8984 (Linking) VI - 57 IP - 4 DP - 2023 Jul-Aug TI - [DNA Phenotyping of Remains from Elite Burials of the Khazar Period of Southern Russia]. PG - 597-608 AB - Ancient DNA analyses help to solve the problems related to the genogeographic origin and migration patterns of populations. The Khazar Khaganate is a subject of controversy among researchers. Its complex historical development, lack of a sufficient number of artistic and written sources, the disappearance of representatives of Khazar culture leaves open the question of the appearance of the Khazars. DNA phenotyping of bone remains from elite burials of the Khazar period of Southern Russia was carried out with respect to eye color, hair color, skin color, and AB0 blood groups. Eight out of 10 individuals had brown eyes, dark hair (to varying degrees), and a predominantly dark skin during their lifetime. Individuals from two burials had gray-blue eyes, and one individual had blond hair. The most probable AB0 blood group was identified in eight people, of which five blood group 0 (I) group, four had blood group A (II), and one had blood group B (III). The allele frequency distribution was assessed for ten population-specific autosomal markers and suggested high heterogeneity for the ethnogeographic origin of the Khazars examined. The results are evidence for ethnocultural, genetic, and phenotypic diversity of the Khazar Khaganate. FAU - Fesenko, D O AU - Fesenko DO AD - Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia. FAU - Aramova, O Yu AU - Aramova OY AD - Southern Research Center, Russian Academy of Sciences, Rostov-on-Don, 344006 Russia. AD - Ivanovsky Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344090 Russia. FAU - Vdovchenkov, E V AU - Vdovchenkov EV AD - Ivanovsky Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344090 Russia. FAU - Ivanovsky, I D AU - Ivanovsky ID AD - DNA Research Center, LLC, Hkimki, Moscow Oblast, 141402 Russia. FAU - Fesenko, O E AU - Fesenko OE AD - Institute of Physics, Southern Federal University, Rostov-on-Don, 344090 Russia. FAU - Polyakov, S A AU - Polyakov SA AD - Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia. FAU - Faleeva, T G AU - Faleeva TG AD - St. Petersburg Forensic Bureau, St. Petersburg, 195067 Russia. AD - Mechnikov North-Western State Medical University, St. Petersburg, 191015 Russia. FAU - Filippova, M A AU - Filippova MA AD - Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia. FAU - Florinskaya, V S AU - Florinskaya VS AD - Ivanovsky Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344090 Russia. FAU - Kornienko, I V AU - Kornienko IV AD - Southern Research Center, Russian Academy of Sciences, Rostov-on-Don, 344006 Russia. AD - Ivanovsky Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344090 Russia. AD - ikornienko@yandex.ru. LA - rus PT - English Abstract PT - Journal Article PL - Russia (Federation) TA - Mol Biol (Mosk) JT - Molekuliarnaia biologiia JID - 0105454 RN - 9007-49-2 (DNA) RN - 0 (Blood Group Antigens) SB - IM MH - Humans MH - *Eye Color MH - DNA/genetics MH - Burial MH - Russia MH - *Blood Group Antigens OTO - NOTNLM OT - AB0 blood group OT - DNA phenotyping OT - Khazars OT - Y-chromosome haplogroup OT - ancient DNA OT - biochip OT - burial mounds EDAT- 2023/08/02 06:42 MHDA- 2023/08/02 06:43 CRDT- 2023/08/02 03:42 PHST- 2022/10/18 00:00 [received] PHST- 2022/12/28 00:00 [accepted] PHST- 2023/08/02 06:43 [medline] PHST- 2023/08/02 06:42 [pubmed] PHST- 2023/08/02 03:42 [entrez] PST - ppublish SO - Mol Biol (Mosk). 2023 Jul-Aug;57(4):597-608. PMID- 37379890 OWN - NLM STAT- MEDLINE DCOM- 20230712 LR - 20230718 IS - 1872-8278 (Electronic) IS - 1567-7249 (Linking) VI - 71 DP - 2023 Jul TI - Maternal ancestry of first Parsi settlers of India using ancient mitogenome. PG - 104-111 LID - S1567-7249(23)00055-7 [pii] LID - 10.1016/j.mito.2023.06.004 [doi] AB - The rich cultural and genetic diversity of South Asia emerged from multiple migrations and cultural assimilation of multiple waves of migrants. The Parsi community of North-western India were one of those who migrated from West Eurasia in the aftermath of 7th century CE and assimilated into the local cultural framework. Earlier genetic studies further strengthened this notion with the finding that they harbour both Middle Eastern and South Asian genetic components. Although these studies covered both autosomal and uniparental markers, still maternal ancestry was not covered in depth and with good resolution of mitochondrial markers. Hence in our current study, we have first time generated a complete mitogenome of 19 ancient samples of the first Parsi settlers excavated from the archaeological site of Sanjan and performed detailed phylogenetic analysis to infer their maternal genetic affinity. In our analysis, we found that the Parsi mitogenome with mtDNA haplogroup M3a1 + 204 shares clade with both Middle Eastern and South Asian modern individuals in both the Maximum Likelihood tree and Bayesian phylogenetic tree. This haplogroup was also prevalent among the medieval Swat valley population of present-day Northern Pakistan and was also observed in two Roopkund A individuals. In the phylogenetic network this sample share haplotype with both South Asian and Middle Eastern samples. So conclusively, the first Parsi settlers' maternal ancestry encompasses both South Asian and Middle Eastern genetic composition. CI - Copyright © 2023 Elsevier B.V. and Mitochondria Research Society. All rights reserved. FAU - Kumar, Lomous AU - Kumar L AD - Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India. FAU - Ahlawat, Bhavna AU - Ahlawat B AD - Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Department of Anthropology, Panjab University, Chandigarh 160014, India. FAU - Kumar, Sachin AU - Kumar S AD - Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India. FAU - Mushrif-Tripathy, Veena AU - Mushrif-Tripathy V AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune, Maharashtra 411006, India. FAU - Rai, Niraj AU - Rai N AD - Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India. Electronic address: nirajrai@bsip.res.in. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230626 PL - Netherlands TA - Mitochondrion JT - Mitochondrion JID - 100968751 RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - *Genetics, Population MH - Ethnicity/genetics MH - Phylogeny MH - Bayes Theorem MH - *Genome, Mitochondrial MH - India MH - DNA, Mitochondrial/genetics MH - Haplotypes MH - Genetic Variation OTO - NOTNLM OT - Haplogroup OT - Middle Eastern OT - Mitogenome OT - Parsi OT - Phylogenetic OT - aDNA COIS- Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. EDAT- 2023/06/29 01:08 MHDA- 2023/07/12 06:42 CRDT- 2023/06/28 19:12 PHST- 2023/02/27 00:00 [received] PHST- 2023/06/18 00:00 [revised] PHST- 2023/06/25 00:00 [accepted] PHST- 2023/07/12 06:42 [medline] PHST- 2023/06/29 01:08 [pubmed] PHST- 2023/06/28 19:12 [entrez] AID - S1567-7249(23)00055-7 [pii] AID - 10.1016/j.mito.2023.06.004 [doi] PST - ppublish SO - Mitochondrion. 2023 Jul;71:104-111. doi: 10.1016/j.mito.2023.06.004. Epub 2023 Jun 26. PMID- 37141673 OWN - NLM STAT- MEDLINE DCOM- 20230616 LR - 20230618 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 65 DP - 2023 Jul TI - A fast and highly efficient automated DNA extraction method from small quantities of bone powder from aged bone samples. PG - 102882 LID - S1872-4973(23)00057-1 [pii] LID - 10.1016/j.fsigen.2023.102882 [doi] AB - An efficient extraction method is important for obtaining high-quality DNA from degraded aged bone samples. An automated full-demineralization method using the EDTA and DNA Investigator Kit (Qiagen) combined with Qiagen's biorobots was optimized in our laboratory in the past to extract the DNA from 500 mg of aged bone samples. The purpose of this research was to further improve the method with the aim of reducing the required sample material, shortening the extraction time, and achieving higher throughput. To process extremely small samples, the amount of bone powder was reduced to 75 mg, EDTA was replaced with reagents from the Bone DNA Extraction Kit (Promega), and decalcification was shortened from overnight to 2.5 h. Instead of 50 ml tubes, 2 ml tubes were used, which allows higher throughput. The DNA Investigator Kit (Qiagen) and EZ1 Advanced XL biorobot (Qiagen) was used for DNA purification. A comparison between both extraction methods was made on 29 Second World War bones and 22 archaeological bone samples. The differences between both methods were explored by measuring nuclear DNA yield and STR typing success. After cleaning the samples, 500 mg of bone powder was processed using EDTA, and 75 mg of powder from the same bone was processed using the Bone DNA Extraction Kit (Promega). DNA content and DNA degradation were determined using PowerQuant (Promega), and the PowerPlex ESI 17 Fast System (Promega) was used for STR typing. The results showed that the full-demineralization protocol using 500 mg of bone was efficient for Second World War and archaeological samples, and the partial-demineralization protocol using 75 mg of bone powder was only efficient for the Second World War bones. The improved extraction method-for which significantly lower amounts of bone powder can be used, the extraction process is faster, and higher throughput of bone samples is possible-is applicable for genetic identification of relatively well-preserved aged bone samples in routine forensic analyses. CI - Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved. FAU - Zupanič Pajnič, Irena AU - Zupanič Pajnič I AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia. Electronic address: irena.zupanic@mf.uni-lj.si. FAU - Leskovar, Tamara AU - Leskovar T AD - Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia. FAU - Zupanc, Tomaž AU - Zupanc T AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia. FAU - Podovšovnik, Eva AU - Podovšovnik E AD - Orthopedic Hospital of Valdoltra, Ankaran, Slovenia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230429 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (Powders) RN - 9G34HU7RV0 (Edetic Acid) RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - Aged MH - Powders MH - Edetic Acid MH - *DNA Fingerprinting/methods MH - *Microsatellite Repeats MH - DNA OTO - NOTNLM OT - Ancient DNA OT - Bone DNA extraction OT - Missing person identification OT - STR typing OT - Second World War COIS- Declaration of Competing Interest The authors declare that they have no conflict of interest. EDAT- 2023/05/04 18:42 MHDA- 2023/06/16 06:42 CRDT- 2023/05/04 18:01 PHST- 2022/08/18 00:00 [received] PHST- 2023/03/20 00:00 [revised] PHST- 2023/04/26 00:00 [accepted] PHST- 2023/06/16 06:42 [medline] PHST- 2023/05/04 18:42 [pubmed] PHST- 2023/05/04 18:01 [entrez] AID - S1872-4973(23)00057-1 [pii] AID - 10.1016/j.fsigen.2023.102882 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2023 Jul;65:102882. doi: 10.1016/j.fsigen.2023.102882. Epub 2023 Apr 29. PMID- 37137206 OWN - NLM STAT- MEDLINE DCOM- 20230616 LR - 20230618 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 65 DP - 2023 Jul TI - Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site. PG - 102886 LID - S1872-4973(23)00061-3 [pii] LID - 10.1016/j.fsigen.2023.102886 [doi] AB - The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity. CI - Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved. FAU - Zupanič Pajnič, Irena AU - Zupanič Pajnič I AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia. Electronic address: irena.zupanic@mf.uni-lj.si. FAU - Geršak, Živa Miriam AU - Geršak ŽM AD - Institute of Radiology, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, Slovenia. FAU - Leskovar, Tamara AU - Leskovar T AD - Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia. FAU - Črešnar, Matija AU - Črešnar M AD - Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia. LA - eng PT - Case Reports PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230429 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (Powders) RN - 9007-49-2 (DNA) SB - IM MH - Female MH - Child MH - Humans MH - Male MH - Middle Aged MH - Powders MH - *DNA Fingerprinting MH - *DNA/genetics MH - Bone and Bones MH - Microsatellite Repeats MH - Chromosomes, Human, Y MH - Indigenous Peoples MH - Haplotypes OTO - NOTNLM OT - Ancient DNA OT - Archaeology OT - Kinship analysis OT - Multiple burial OT - Petrous bones OT - STR typing COIS- Declaration of Competing Interest The authors declare that they have no conflict of interest. EDAT- 2023/05/04 00:42 MHDA- 2023/06/16 06:42 CRDT- 2023/05/03 18:02 PHST- 2022/12/15 00:00 [received] PHST- 2023/03/31 00:00 [revised] PHST- 2023/04/27 00:00 [accepted] PHST- 2023/06/16 06:42 [medline] PHST- 2023/05/04 00:42 [pubmed] PHST- 2023/05/03 18:02 [entrez] AID - S1872-4973(23)00061-3 [pii] AID - 10.1016/j.fsigen.2023.102886 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2023 Jul;65:102886. doi: 10.1016/j.fsigen.2023.102886. Epub 2023 Apr 29. PMID- 37127762 OWN - NLM STAT- MEDLINE DCOM- 20230609 LR - 20230609 IS - 1437-1596 (Electronic) IS - 0937-9827 (Linking) VI - 137 IP - 4 DP - 2023 Jul TI - Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology. PG - 1007-1015 LID - 10.1007/s00414-023-03003-3 [doi] AB - In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 10(7) (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed. CI - © 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. FAU - Zupanič Pajnič, Irena AU - Zupanič Pajnič I AUID- ORCID: 0000-0002-6704-015X AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia. irena.zupanic@mf.uni-lj.si. FAU - Leskovar, Tamara AU - Leskovar T AD - Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia. FAU - Črešnar, Matija AU - Črešnar M AD - Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia. LA - eng PT - Journal Article DEP - 20230502 PL - Germany TA - Int J Legal Med JT - International journal of legal medicine JID - 9101456 RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - *Polymorphism, Single Nucleotide MH - *DNA Fingerprinting MH - High-Throughput Nucleotide Sequencing MH - Microsatellite Repeats MH - DNA MH - Skeleton MH - Probability MH - Sequence Analysis, DNA OTO - NOTNLM OT - Ancient DNA OT - Identity SNP typing OT - Kinship analysis OT - Massive parallel sequencing OT - Petrous bones OT - STR typing EDAT- 2023/05/02 00:42 MHDA- 2023/06/09 06:42 CRDT- 2023/05/01 23:25 PHST- 2023/02/02 00:00 [received] PHST- 2023/04/17 00:00 [accepted] PHST- 2023/06/09 06:42 [medline] PHST- 2023/05/02 00:42 [pubmed] PHST- 2023/05/01 23:25 [entrez] AID - 10.1007/s00414-023-03003-3 [pii] AID - 10.1007/s00414-023-03003-3 [doi] PST - ppublish SO - Int J Legal Med. 2023 Jul;137(4):1007-1015. doi: 10.1007/s00414-023-03003-3. Epub 2023 May 2. PMID- 37339987 OWN - NLM STAT- MEDLINE DCOM- 20230622 LR - 20240921 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 14 IP - 1 DP - 2023 Jun 20 TI - Imputation of ancient human genomes. PG - 3660 LID - 10.1038/s41467-023-39202-0 [doi] LID - 3660 AB - Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies. CI - © 2023. The Author(s). FAU - Sousa da Mota, Bárbara AU - Sousa da Mota B AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland. FAU - Rubinacci, Simone AU - Rubinacci S AUID- ORCID: 0000-0002-7725-4813 AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland. FAU - Cruz Dávalos, Diana Ivette AU - Cruz Dávalos DI AUID- ORCID: 0000-0002-5309-6937 AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland. FAU - G Amorim, Carlos Eduardo AU - G Amorim CE AD - Department of Biology, California State University, Northridge, California, USA. FAU - Sikora, Martin AU - Sikora M AUID- ORCID: 0000-0003-2818-8319 AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Johannsen, Niels N AU - Johannsen NN AD - Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark. FAU - Szmyt, Marzena H AU - Szmyt MH AD - Institute for Eastern Research, Adam Mickiewicz University in Poznań, Poznań, Poland. FAU - Włodarczak, Piotr AU - Włodarczak P AUID- ORCID: 0000-0003-0359-7386 AD - Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland. FAU - Szczepanek, Anita AU - Szczepanek A AD - Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland. AD - Department of Anatomy, Jagiellonian University, Medical College, Kraków, Poland. FAU - Przybyła, Marcin M AU - Przybyła MM AD - Institute of Archaeology, Jagiellonian University, Kraków, Poland. FAU - Schroeder, Hannes AU - Schroeder H AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Allentoft, Morten E AU - Allentoft ME AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Bentley, WA, Australia. FAU - Willerslev, Eske AU - Willerslev E AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. AD - Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK. AD - MARUM, University of Bremen, Bremen, Germany. FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. annasapfo.malaspinas@unil.ch. AD - Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland. annasapfo.malaspinas@unil.ch. FAU - Delaneau, Olivier AU - Delaneau O AUID- ORCID: 0000-0002-3906-8446 AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. olivier.delaneau@unil.ch. AD - Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland. olivier.delaneau@unil.ch. LA - eng GR - R35 GM142939/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20230620 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Genotyping Techniques/methods MH - *Genome, Human/genetics MH - DNA, Ancient MH - Genotype MH - Genome-Wide Association Study/methods MH - Polymorphism, Single Nucleotide PMC - PMC10282092 COIS- The authors declare no competing interests. EDAT- 2023/06/21 01:07 MHDA- 2023/06/22 06:41 PMCR- 2023/06/20 CRDT- 2023/06/20 23:17 PHST- 2022/10/12 00:00 [received] PHST- 2023/06/02 00:00 [accepted] PHST- 2023/06/22 06:41 [medline] PHST- 2023/06/21 01:07 [pubmed] PHST- 2023/06/20 23:17 [entrez] PHST- 2023/06/20 00:00 [pmc-release] AID - 10.1038/s41467-023-39202-0 [pii] AID - 39202 [pii] AID - 10.1038/s41467-023-39202-0 [doi] PST - epublish SO - Nat Commun. 2023 Jun 20;14(1):3660. doi: 10.1038/s41467-023-39202-0. PMID- 37372418 OWN - NLM STAT- MEDLINE DCOM- 20230629 LR - 20230701 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 14 IP - 6 DP - 2023 Jun 9 TI - Estimation of DNA Degradation in Archaeological Human Remains. LID - 10.3390/genes14061238 [doi] LID - 1238 AB - The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained. FAU - Bonfigli, Antonella AU - Bonfigli A AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy. FAU - Cesare, Patrizia AU - Cesare P AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy. FAU - Volpe, Anna Rita AU - Volpe AR AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy. FAU - Colafarina, Sabrina AU - Colafarina S AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy. FAU - Forgione, Alfonso AU - Forgione A AD - Department of Human Studies, University of L'Aquila, 67100 L'Aquila, Italy. FAU - Aloisi, Massimo AU - Aloisi M AUID- ORCID: 0000-0002-3978-2850 AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy. FAU - Zarivi, Osvaldo AU - Zarivi O AUID- ORCID: 0000-0002-8312-9955 AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy. FAU - Poma, Anna Maria Giuseppina AU - Poma AMG AUID- ORCID: 0000-0001-8627-6646 AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230609 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - *DNA, Ancient MH - Italy MH - *Body Remains MH - Bone and Bones MH - DNA, Mitochondrial/genetics PMC - PMC10298407 OTO - NOTNLM OT - DNA degradation OT - ancient DNA OT - bone remains OT - mitochondrial DNA OT - nuclear DNA OT - real-time qPCR COIS- The authors declare no conflict of interest. EDAT- 2023/06/28 06:43 MHDA- 2023/06/29 06:43 PMCR- 2023/06/09 CRDT- 2023/06/28 01:12 PHST- 2023/04/19 00:00 [received] PHST- 2023/06/01 00:00 [revised] PHST- 2023/06/07 00:00 [accepted] PHST- 2023/06/29 06:43 [medline] PHST- 2023/06/28 06:43 [pubmed] PHST- 2023/06/28 01:12 [entrez] PHST- 2023/06/09 00:00 [pmc-release] AID - genes14061238 [pii] AID - genes-14-01238 [pii] AID - 10.3390/genes14061238 [doi] PST - epublish SO - Genes (Basel). 2023 Jun 9;14(6):1238. doi: 10.3390/genes14061238. PMID- 37207647 OWN - NLM STAT- MEDLINE DCOM- 20230608 LR - 20240712 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 33 IP - 11 DP - 2023 Jun 5 TI - Historical genomes elucidate European settlement and the African diaspora in Delaware. PG - 2350-2358.e7 LID - S0960-9822(23)00551-1 [pii] LID - 10.1016/j.cub.2023.04.069 [doi] AB - The 17(th)-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.(1) The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.(2) European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.(3)(,)(4) To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.(5) Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17(th) and early 18(th) century North America. CI - Copyright © 2023 Elsevier Inc. All rights reserved. FAU - Fleskes, Raquel E AU - Fleskes RE AD - Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA; Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: raquel.fleskes@uconn.edu. FAU - Owsley, Douglas W AU - Owsley DW AD - Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA. Electronic address: owsleyd@si.edu. FAU - Bruwelheide, Karin S AU - Bruwelheide KS AD - Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA. FAU - Barca, Kathryn G AU - Barca KG AD - Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA. FAU - Griffith, Daniel R AU - Griffith DR AD - Archaeological Society of Delaware, Inc, Dover, DE 19903, USA. FAU - Cabana, Graciela S AU - Cabana GS AD - Department of Anthropology, University of Tennessee, Knoxville, TN 37996, USA; Molecular Anthropology Laboratories, University of Tennessee, Knoxville, TN 37996, USA. FAU - Schurr, Theodore G AU - Schurr TG AD - Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: tgschurr@sas.upenn.edu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20230518 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Child MH - Humans MH - *Black People/genetics MH - Delaware MH - DNA, Mitochondrial/genetics MH - Genetics, Population MH - Haplotypes MH - *Human Migration MH - White MH - Black or African American OTO - NOTNLM OT - North America OT - Y chromosome OT - ancient DNA OT - colonial OT - kinship OT - mitochondrial DNA OT - paleogenomics OT - trans-Atlantic slave trade COIS- Declaration of interests The authors declare no competing interests. EDAT- 2023/05/20 09:42 MHDA- 2023/06/08 06:42 CRDT- 2023/05/19 18:41 PHST- 2022/09/16 00:00 [received] PHST- 2023/02/01 00:00 [revised] PHST- 2023/04/24 00:00 [accepted] PHST- 2023/06/08 06:42 [medline] PHST- 2023/05/20 09:42 [pubmed] PHST- 2023/05/19 18:41 [entrez] AID - S0960-9822(23)00551-1 [pii] AID - 10.1016/j.cub.2023.04.069 [doi] PST - ppublish SO - Curr Biol. 2023 Jun 5;33(11):2350-2358.e7. doi: 10.1016/j.cub.2023.04.069. Epub 2023 May 18. PMID- 37433640 OWN - NLM STAT- MEDLINE DCOM- 20230927 LR - 20231002 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 33 IP - 6 DP - 2023 Jun TI - Accurate sequencing of DNA motifs able to form alternative (non-B) structures. PG - 907-922 LID - 10.1101/gr.277490.122 [doi] AB - Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA. CI - © 2023 Weissensteiner et al.; Published by Cold Spring Harbor Laboratory Press. FAU - Weissensteiner, Matthias H AU - Weissensteiner MH AD - Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. FAU - Cremona, Marzia A AU - Cremona MA AUID- ORCID: 0000-0001-8899-7316 AD - Department of Operations and Decision Systems, Université Laval, Quebec, Quebec G1V0A6, Canada. AD - Population Health and Optimal Health Practices, CHU de Québec-Université Laval Research Center, Québec, Quebec G1V4G2, Canada. AD - Center for Medical Genomics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. FAU - Guiblet, Wilfried M AU - Guiblet WM AD - Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. AD - Laboratory of Cell Biology, NCI-CCR, National Institutes of Health, Bethesda, Maryland 20892, USA. FAU - Stoler, Nicholas AU - Stoler N AD - Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. FAU - Harris, Robert S AU - Harris RS AD - Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. FAU - Cechova, Monika AU - Cechova M AD - Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. AD - Faculty of Informatics, Masaryk University, 60200 Brno, Czech Republic. FAU - Eckert, Kristin A AU - Eckert KA AD - Center for Medical Genomics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. AD - Department of Pathology, The Pennsylvania State University, College of Medicine, Hershey, Pennsylvania 17033, USA. FAU - Chiaromonte, Francesca AU - Chiaromonte F AD - Center for Medical Genomics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. AD - Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. AD - Institute of Economics and L'EMbeDS, Sant'Anna School of Advanced Studies, Pisa 56127, Italy. FAU - Huang, Yi-Fei AU - Huang YF AD - Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. AD - Center for Medical Genomics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. FAU - Makova, Kateryna D AU - Makova KD AD - Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; kdm16@psu.edu. AD - Center for Medical Genomics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. LA - eng GR - R01 GM136684/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20230711 PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (DNA, Z-Form) RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - Nucleotide Motifs MH - *DNA, Z-Form MH - Sequence Analysis, DNA MH - DNA/genetics MH - Base Composition MH - High-Throughput Nucleotide Sequencing MH - *Nanopores PMC - PMC10519405 EDAT- 2023/07/12 01:07 MHDA- 2023/09/27 06:43 PMCR- 2023/06/01 CRDT- 2023/07/11 21:03 PHST- 2022/11/09 00:00 [received] PHST- 2023/05/04 00:00 [accepted] PHST- 2023/09/27 06:43 [medline] PHST- 2023/07/12 01:07 [pubmed] PHST- 2023/07/11 21:03 [entrez] PHST- 2023/06/01 00:00 [pmc-release] AID - gr.277490.122 [pii] AID - 10.1101/gr.277490.122 [doi] PST - ppublish SO - Genome Res. 2023 Jun;33(6):907-922. doi: 10.1101/gr.277490.122. Epub 2023 Jul 11. PMID- 37138083 OWN - NLM STAT- MEDLINE DCOM- 20230613 LR - 20230613 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 618 IP - 7964 DP - 2023 Jun TI - Ancient human DNA recovered from a Palaeolithic pendant. PG - 328-332 LID - 10.1038/s41586-023-06035-2 [doi] AB - Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals(1) who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited(2-5). Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology. CI - © 2023. The Author(s). FAU - Essel, Elena AU - Essel E AUID- ORCID: 0000-0002-2642-8043 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. elena_essel@eva.mpg.de. FAU - Zavala, Elena I AU - Zavala EI AUID- ORCID: 0000-0001-7687-5370 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Biology, San Francisco State University, San Francisco, CA, USA. AD - Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. FAU - Schulz-Kornas, Ellen AU - Schulz-Kornas E AUID- ORCID: 0000-0003-1657-8256 AD - Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany. FAU - Kozlikin, Maxim B AU - Kozlikin MB AUID- ORCID: 0000-0001-5082-3345 AD - Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. FAU - Fewlass, Helen AU - Fewlass H AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Vernot, Benjamin AU - Vernot B AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Shunkov, Michael V AU - Shunkov MV AD - Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. FAU - Derevianko, Anatoly P AU - Derevianko AP AUID- ORCID: 0000-0003-1156-8331 AD - Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. FAU - Douka, Katerina AU - Douka K AUID- ORCID: 0000-0002-0558-0011 AD - Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences (HEAS) Research Network, University of Vienna, Vienna, Austria. FAU - Barnes, Ian AU - Barnes I AUID- ORCID: 0000-0001-8322-6918 AD - Earth Sciences Department, Natural History Museum, London, UK. FAU - Soulier, Marie-Cécile AU - Soulier MC AUID- ORCID: 0000-0003-2439-7308 AD - Maison de la Recherche, Université de Toulouse-Jean Jaurès, CNRS UMR 5608 TRACES, Toulouse, France. FAU - Schmidt, Anna AU - Schmidt A AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Szymanski, Merlin AU - Szymanski M AUID- ORCID: 0000-0001-8501-2497 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Tsanova, Tsenka AU - Tsanova T AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum, University of Bologna, Bologna, Italy. FAU - Sirakov, Nikolay AU - Sirakov N AD - National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria. FAU - Endarova, Elena AU - Endarova E AUID- ORCID: 0000-0002-5212-7498 AD - National Museum of History, Sofia, Bulgaria. FAU - McPherron, Shannon P AU - McPherron SP AUID- ORCID: 0000-0002-2063-468X AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Hublin, Jean-Jacques AU - Hublin JJ AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Chaire de Paléoanthropologie, Collège de France, Paris, France. FAU - Kelso, Janet AU - Kelso J AUID- ORCID: 0000-0002-3618-322X AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Pääbo, Svante AU - Pääbo S AUID- ORCID: 0000-0002-4670-6311 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Hajdinjak, Mateja AU - Hajdinjak M AUID- ORCID: 0000-0002-4064-0331 AD - Ancient Genomics Laboratory, The Francis Crick Institute, London, UK. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Soressi, Marie AU - Soressi M AUID- ORCID: 0000-0003-1733-7745 AD - Faculty of Archaeology, Leiden University, Leiden, The Netherlands. m.a.soressi@arch.leidenuniv.nl. FAU - Meyer, Matthias AU - Meyer M AUID- ORCID: 0000-0002-4760-558X AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. mmeyer@eva.mpg.de. LA - eng PT - Historical Article PT - Journal Article DEP - 20230503 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Female MH - Humans MH - Archaeology/methods MH - *Bone and Bones/chemistry MH - Deer/genetics MH - *DNA, Ancient/analysis/isolation & purification MH - DNA, Mitochondrial/analysis/isolation & purification MH - History, Ancient MH - Siberia MH - *Tooth/chemistry MH - Caves MH - Russia PMC - PMC10247382 COIS- The authors declare no competing interests. EDAT- 2023/05/04 00:42 MHDA- 2023/06/09 06:42 PMCR- 2023/05/03 CRDT- 2023/05/03 23:26 PHST- 2022/11/28 00:00 [received] PHST- 2023/03/30 00:00 [accepted] PHST- 2023/06/09 06:42 [medline] PHST- 2023/05/04 00:42 [pubmed] PHST- 2023/05/03 23:26 [entrez] PHST- 2023/05/03 00:00 [pmc-release] AID - 10.1038/s41586-023-06035-2 [pii] AID - 6035 [pii] AID - 10.1038/s41586-023-06035-2 [doi] PST - ppublish SO - Nature. 2023 Jun;618(7964):328-332. doi: 10.1038/s41586-023-06035-2. Epub 2023 May 3. PMID- 36930997 OWN - NLM STAT- MEDLINE DCOM- 20230612 LR - 20231116 IS - 1879-9825 (Electronic) IS - 1879-9817 (Linking) VI - 41 DP - 2023 Jun TI - Developing an archaeology of malaria. A critical review of current approaches and a discussion on ways forward. PG - 32-42 LID - S1879-9817(23)00017-7 [pii] LID - 10.1016/j.ijpp.2023.03.002 [doi] AB - OBJECTIVE: This paper presents the current state of the art in the investigation of past malaria by providing an extensive review of previous studies and identifying research possibilities for the future. MATERIALS: All previous research on the detection of malaria in human skeletal material using macroscopic and biomolecular approaches is considered. METHODS: The approaches and methods used by scholars and the results they obtained are evaluated and the limitations discussed. RESULTS: There is a link between malaria and porous lesions with significantly higher prevalence in malaria-endemic areas, however, they are not pathognomonic or specific for malaria. Malaria can be identified using biomolecular techniques, yet, to date there is no completely satisfactory method that is able to consistently diagnose the disease. CONCLUSIONS: Using macroscopic and biomolecular techniques, malaria can be investigated in past populations and the impact of the disease studied. Yet, this is not a straightforward process and the use of multiple lines of evidence is necessary to obtain the best results. SIGNIFICANCE: The extensive discussion on ways malaria can and cannot be identified in past populations and the suggestions for new approaches provide a steppingstone for future research into this debilitating, global disease. LIMITATIONS: Malaria is a difficult disease to study archaeologically and successful identification depends on many intrinsic and extrinsic factors. SUGGESTIONS FOR FURTHER RESEARCH: More large-scale spatial analyses of porous lesions as well as targeting different tissues or molecules for biomolecular identification may improve the archaeological understanding of malaria. CI - Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Schats, Rachel AU - Schats R AD - Leiden University, Faculty of Archaeology, Laboratory for Human Osteoarchaeology, Einsteinweg 2, 2333CC Leiden, the Netherlands. Electronic address: r.schats@arch.leidenuniv.nl. LA - eng PT - Journal Article PT - Review DEP - 20230315 PL - Netherlands TA - Int J Paleopathol JT - International journal of paleopathology JID - 101562474 SB - IM MH - Humans MH - *Archaeology MH - *Malaria/diagnosis/epidemiology MH - Forecasting MH - Prevalence OTO - NOTNLM OT - Ancient DNA OT - Anemia OT - Hemozoin OT - Immunological techniques OT - Plasmodium infection OT - Porotic skeletal lesions COIS- Declaration of interest None. EDAT- 2023/03/18 06:00 MHDA- 2023/06/12 06:42 CRDT- 2023/03/17 19:00 PHST- 2022/10/07 00:00 [received] PHST- 2023/02/17 00:00 [revised] PHST- 2023/03/04 00:00 [accepted] PHST- 2023/06/12 06:42 [medline] PHST- 2023/03/18 06:00 [pubmed] PHST- 2023/03/17 19:00 [entrez] AID - S1879-9817(23)00017-7 [pii] AID - 10.1016/j.ijpp.2023.03.002 [doi] PST - ppublish SO - Int J Paleopathol. 2023 Jun;41:32-42. doi: 10.1016/j.ijpp.2023.03.002. Epub 2023 Mar 15. PMID- 36919783 OWN - NLM STAT- MEDLINE DCOM- 20230519 LR - 20230525 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 181 IP - 2 DP - 2023 Jun TI - Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization. PG - 216-230 LID - 10.1002/ajpa.24727 [doi] AB - OBJECTIVE: This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes. MATERIALS AND METHODS: We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis. RESULTS: We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP. DISCUSSION: The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas. CI - © 2023 Wiley Periodicals LLC. FAU - Motti, Josefina M B AU - Motti JMB AUID- ORCID: 0000-0002-6624-1822 AD - Laboratorio de Ecología Evolutiva Humana, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Quequén, Buenos Aires, Argentina. FAU - Pauro, Maia AU - Pauro M AUID- ORCID: 0000-0003-3069-507X AD - Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina. FAU - Scabuzzo, Clara AU - Scabuzzo C AUID- ORCID: 0000-0002-7598-154X AD - Centro de Investigación Científica y de Transferencia a la Producción (CICyTTP)-CONICET, Provincia de Entre Ríos-Universidad Autónoma de Entre Ríos (UADER)-División Arqueología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Diamante, Entre Ríos, Argentina. FAU - García, Angelina AU - García A AUID- ORCID: 0000-0001-8137-9398 AD - Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina. AD - Facultad de Filosofía y Humanidades, Museo de Antropología, Universidad Nacional de Córdoba, Córdoba, Argentina. FAU - Aldazábal, Verónica AU - Aldazábal V AUID- ORCID: 0000-0003-1507-4259 AD - Instituto Multidisciplinario de Historia y Ciencias Humanas, CONICET, Buenos Aires, Argentina. FAU - Vecchi, Rodrigo AU - Vecchi R AUID- ORCID: 0000-0003-3974-8297 AD - Departamento de Humanidades, Universidad Nacional del Sur, CONICET, Bahía Blanca, Buenos Aires, Argentina. FAU - Bayón, Cristina AU - Bayón C AUID- ORCID: 0000-0003-4797-6978 AD - Departamento de Humanidades, Universidad Nacional del Sur, CONICET, Bahía Blanca, Buenos Aires, Argentina. FAU - Pastor, Nicolás AU - Pastor N AUID- ORCID: 0000-0001-8971-7910 AD - Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina. FAU - Demarchi, Darío A AU - Demarchi DA AUID- ORCID: 0000-0003-3782-8269 AD - Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina. AD - Facultad de Filosofía y Humanidades, Museo de Antropología, Universidad Nacional de Córdoba, Córdoba, Argentina. FAU - Bravi, Claudio M AU - Bravi CM AUID- ORCID: 0000-0002-2499-4471 AD - Instituto Multidisciplinario de Biología Celular, Centro Científico Tecnológica (CCT) La Plata CONICET, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA. AD - Broad Institute, Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA. FAU - Cabana, Graciela S AU - Cabana GS AUID- ORCID: 0000-0002-5399-1173 AD - Molecular Anthropology Laboratories, Department of Anthropology, University of Tennessee, Knoxville, Tennessee, USA. FAU - Nores, Rodrigo AU - Nores R AUID- ORCID: 0000-0002-9153-0626 AD - Instituto de Antropología de Córdoba, CONICET, Córdoba, Argentina. AD - Facultad de Filosofía y Humanidades, Museo de Antropología, Universidad Nacional de Córdoba, Córdoba, Argentina. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230315 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 SB - IM MH - Humans MH - Argentina MH - Phylogeny MH - *Genome, Mitochondrial/genetics MH - Bayes Theorem MH - South America OTO - NOTNLM OT - Pampas region OT - Southern Cone OT - ancient DNA OT - mitochondrial DNA OT - native Americans EDAT- 2023/03/16 06:00 MHDA- 2023/05/19 06:42 CRDT- 2023/03/15 06:32 PHST- 2023/02/13 00:00 [revised] PHST- 2022/11/04 00:00 [received] PHST- 2023/02/22 00:00 [accepted] PHST- 2023/05/19 06:42 [medline] PHST- 2023/03/16 06:00 [pubmed] PHST- 2023/03/15 06:32 [entrez] AID - 10.1002/ajpa.24727 [doi] PST - ppublish SO - Am J Biol Anthropol. 2023 Jun;181(2):216-230. doi: 10.1002/ajpa.24727. Epub 2023 Mar 15. PMID- 36812666 OWN - NLM STAT- MEDLINE DCOM- 20230612 LR - 20231116 IS - 1879-9825 (Electronic) IS - 1879-9817 (Linking) VI - 41 DP - 2023 Jun TI - Pilot study of correlation of selected genetic factors with cribra orbitalia in individuals from a medieval population from Slovakia. PG - 1-7 LID - S1879-9817(23)00005-0 [pii] LID - 10.1016/j.ijpp.2023.02.001 [doi] AB - OBJECTIVE: The aim of this study is to investigate the potential genetic etiology of cribra orbitalia noted on human skeletal remains. MATERIALS: We obtained and analyzed ancient DNA of 43 individuals with cribra orbitalia. The analyzed set represented medieval individuals from two cemeteries in western Slovakia, Castle Devín (11th-12th century AD) and Cífer-Pác (8th-9th century AD). METHODS: We performed a sequence analysis of 5 variants in 3 genes associated with anemia (HBB, G6PD, PKLR), which are the most common pathogenic variants in present day of European populations, and one variant MCM6:c.1917 + 326 C>T (rs4988235) associated with lactose intolerance. RESULTS: DNA variants associated with anemia were not found in the samples. The allele frequency of MCM6:c.1917 + 326 C was 0.875. This frequency is higher but not statistically significant in individuals displaying cribra orbitalia compared to individuals without the lesion. SIGNIFICANCE: This study seeks to expand our knowledge of the etiology of cribra orbitalia by exploring the potential association between the lesion and the presence of alleles linked to hereditary anemias and lactose intolerance. LIMITATIONS: A relatively small set of individuals were analyzed, so an unequivocal conclusion cannot be drawn. Hence, although it is unlikely, a genetic form of anemia caused by rare variants cannot be ruled out. SUGGESTIONS FOR FURTHER RESEARCH: Genetic research based on larger sample sizes and in more diverse geographical regions. CI - Copyright © 2023 Elsevier Inc. All rights reserved. FAU - Bľandová, Gabriela AU - Bľandová G AD - Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia. FAU - Patlevičová, Andrea AU - Patlevičová A AD - Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 917 01 Trnava, Slovakia. FAU - Palkovičová, Jana AU - Palkovičová J AD - Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia. FAU - Pavlíková, Štefánia AU - Pavlíková Š AD - Department of Anthropology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia. FAU - Beňuš, Radoslav AU - Beňuš R AD - Department of Anthropology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia. FAU - Repiská, Vanda AU - Repiská V AD - Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia. FAU - Baldovič, Marian AU - Baldovič M AD - Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia; Laboratory of Genomic Medicine, GHC GENETICS SK, Science Park Comenius University, Ilkovičova 8, 841 04 Bratislava, Slovakia. Electronic address: marian.baldovic@uniba.sk. LA - eng PT - Journal Article DEP - 20230220 PL - Netherlands TA - Int J Paleopathol JT - International journal of paleopathology JID - 101562474 SB - IM MH - Humans MH - Pilot Projects MH - Slovakia MH - *Lactose Intolerance/genetics MH - *Anemia MH - Cemeteries OTO - NOTNLM OT - Anemia OT - Lactose intolerance EDAT- 2023/02/23 06:00 MHDA- 2023/06/12 06:42 CRDT- 2023/02/22 18:03 PHST- 2022/08/10 00:00 [received] PHST- 2023/01/30 00:00 [revised] PHST- 2023/02/06 00:00 [accepted] PHST- 2023/06/12 06:42 [medline] PHST- 2023/02/23 06:00 [pubmed] PHST- 2023/02/22 18:03 [entrez] AID - S1879-9817(23)00005-0 [pii] AID - 10.1016/j.ijpp.2023.02.001 [doi] PST - ppublish SO - Int J Paleopathol. 2023 Jun;41:1-7. doi: 10.1016/j.ijpp.2023.02.001. Epub 2023 Feb 20. PMID- 37220274 OWN - NLM STAT- MEDLINE DCOM- 20230525 LR - 20231124 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 120 IP - 22 DP - 2023 May 30 TI - The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa. PG - e2213061120 LID - 10.1073/pnas.2213061120 [doi] LID - e2213061120 AB - The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine. FAU - Tobler, Raymond AU - Tobler R AUID- ORCID: 0000-0002-4603-1473 AD - Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA 5005, Australia. FAU - Souilmi, Yassine AU - Souilmi Y AUID- ORCID: 0000-0001-7543-4864 AD - Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA 5005, Australia. AD - Environment Institute, The University of Adelaide, Adelaide, SA 5005, Australia. FAU - Huber, Christian D AU - Huber CD AUID- ORCID: 0000-0002-2267-2604 AD - Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA 5005, Australia. FAU - Bean, Nigel AU - Bean N AUID- ORCID: 0000-0002-5351-3104 AD - Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA 5005, Australia. AD - School of Mathematical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia. FAU - Turney, Chris S M AU - Turney CSM AD - Division of Research, University of Technology Sydney, Ultimo, NSW 2007, Australia. FAU - Grey, Shane T AU - Grey ST AUID- ORCID: 0000-0003-2160-1625 AD - School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia. AD - Transplantation Immunology Group, Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA 5005, Australia. AD - Blue Sky Genetics, Ashton, SA 5137, Australia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230523 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Humans MH - Animals MH - Africa MH - *Neanderthals MH - Acclimatization MH - Arabia MH - Selection, Genetic PMC - PMC10235988 OTO - NOTNLM OT - adaptation OT - ancient DNA OT - hard sweeps OT - human migrations COIS- The authors declare no competing interest. EDAT- 2023/05/23 19:09 MHDA- 2023/05/25 06:42 PMCR- 2023/11/23 CRDT- 2023/05/23 15:13 PHST- 2023/05/25 06:42 [medline] PHST- 2023/05/23 19:09 [pubmed] PHST- 2023/05/23 15:13 [entrez] PHST- 2023/11/23 00:00 [pmc-release] AID - 202213061 [pii] AID - 10.1073/pnas.2213061120 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2023 May 30;120(22):e2213061120. doi: 10.1073/pnas.2213061120. Epub 2023 May 23. PMID- 37224187 OWN - NLM STAT- MEDLINE DCOM- 20230526 LR - 20230605 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 18 IP - 5 DP - 2023 TI - Confronting historical legacies of biological anthropology in South Africa-Restitution, redress and community-centered science: The Sutherland Nine. PG - e0284785 LID - 10.1371/journal.pone.0284785 [doi] LID - e0284785 AB - We describe a process of restitution of nine unethically acquired human skeletons to their families, together with attempts at redress. Between 1925-1927 C.E., the skeletonised remains of nine San or Khoekhoe people, eight of them known-in-life, were removed from their graves on the farm Kruisrivier, near Sutherland in the Northern Cape Province of South Africa. They were donated to the Anatomy Department at the University of Cape Town. This was done without the knowledge or permission of their families. The donor was a medical student who removed the remains from the labourers' cemetery on his family farm. Nearly 100 years later, the remains are being returned to their community, accompanied by a range of community-driven interdisciplinary historical, archaeological and analytical (osteobiographic, craniofacial, ancient DNA, stable isotope) studies to document, as far as possible, their lives and deaths. The restitution process began by contacting families living in the same area with the same surnames as the deceased. The restitution and redress process prioritises the descendant families' memories, wishes and desire to understand the situation, and learn more about their ancestors. The descendant families have described the process as helping them to reconnect with their ancestors. A richer appreciation of their ancestors' lives, gained in part from scientific analyses, culminating with reburial, is hoped to aid the descendant families and wider community in [re-]connecting with their heritage and culture, and contribute to restorative justice, reconciliation and healing while confronting a traumatic historical moment. While these nine individuals were exhumed as specimens, they will be reburied as people. CI - Copyright: © 2023 Gibbon et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. FAU - Gibbon, Victoria E AU - Gibbon VE AUID- ORCID: 0000-0001-7875-3297 AD - Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - Feris, Loretta AU - Feris L AD - Department of Public Law, University of Cape Town, Cape Town, South Africa. FAU - Gretzinger, Joscha AU - Gretzinger J AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Smith, Kathryn AU - Smith K AUID- ORCID: 0000-0002-7918-6367 AD - Face Lab, Liverpool John Moores University, Liverpool, United Kingdom. AD - VIZ.Lab, Department of Visual Arts, Stellenbosch University, Stellenbosch South Africa. FAU - Hall, Simon AU - Hall S AD - Department of Archaeology, University of Cape Town, Cape Town, South Africa. FAU - Penn, Nigel AU - Penn N AD - Department of History, University of Cape Town, Cape Town, South Africa. FAU - Mutsvangwa, Tinashe E M AU - Mutsvangwa TEM AD - Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - Heale, Michaela AU - Heale M AD - Department of Archaeology, University of Cape Town, Cape Town, South Africa. FAU - Finaughty, Devin A AU - Finaughty DA AD - Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa. AD - School of Chemistry and Forensic Science, Division of Natural Sciences, University of Kent, Canterbury, United Kingdom. FAU - Karanja, Yvonne W AU - Karanja YW AD - Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - Esterhuyse, Jan AU - Esterhuyse J AD - University of Cape Town, Cape Town, South Africa. FAU - Kotze, Daniël AU - Kotze D AUID- ORCID: 0000-0001-7495-7137 AD - Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - Barnes, Nina AU - Barnes N AD - Office for Inclusivity & Change, Office of the Deputy Vice Chancellor for Transformation: University of Cape Town, Cape Town, South Africa. FAU - Gunston, Geney AU - Gunston G AD - Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - May, Je'nine AU - May J AD - Office for Inclusivity & Change, Office of the Deputy Vice Chancellor for Transformation: University of Cape Town, Cape Town, South Africa. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Wilkinson, Caroline M AU - Wilkinson CM AD - Face Lab, Liverpool John Moores University, Liverpool, United Kingdom. FAU - Schiffels, Stephan AU - Schiffels S AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Februarie, Doreen AU - Februarie D AD - Social Work Private Practice, Cape Town, South Africa. FAU - Alves, Sianne AU - Alves S AD - Office for Inclusivity & Change, Office of the Deputy Vice Chancellor for Transformation: University of Cape Town, Cape Town, South Africa. FAU - Sealy, Judith C AU - Sealy JC AUID- ORCID: 0000-0001-5071-8211 AD - Department of Archaeology, University of Cape Town, Cape Town, South Africa. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230524 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - South Africa MH - *Anthropology MH - *Archaeology MH - Cemeteries MH - DNA, Ancient PMC - PMC10208512 COIS- The authors declare no competing interest. EDAT- 2023/05/24 19:13 MHDA- 2023/05/26 06:42 PMCR- 2023/05/24 CRDT- 2023/05/24 13:43 PHST- 2022/08/07 00:00 [received] PHST- 2023/04/05 00:00 [accepted] PHST- 2023/05/26 06:42 [medline] PHST- 2023/05/24 19:13 [pubmed] PHST- 2023/05/24 13:43 [entrez] PHST- 2023/05/24 00:00 [pmc-release] AID - PONE-D-22-22096 [pii] AID - 10.1371/journal.pone.0284785 [doi] PST - epublish SO - PLoS One. 2023 May 24;18(5):e0284785. doi: 10.1371/journal.pone.0284785. eCollection 2023. PMID- 37167404 OWN - NLM STAT- MEDLINE DCOM- 20230525 LR - 20230525 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 380 IP - 6645 DP - 2023 May 12 TI - Paleogenomic study of the Mexican past. PG - 578-579 LID - 10.1126/science.adh7902 [doi] AB - Ancient DNA analysis of ancestral Mexicans reveals a complex demographic history. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. FAU - Roca-Rada, Xavier AU - Roca-Rada X AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. LA - eng PT - Journal Article DEP - 20230511 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) RN - Mexican people SB - IM MH - Humans MH - *DNA, Ancient MH - Mexico MH - *North American People/genetics/history MH - Anthropology MH - Genomics MH - Demography EDAT- 2023/05/11 19:13 MHDA- 2023/05/15 06:42 CRDT- 2023/05/11 14:04 PHST- 2023/05/15 06:42 [medline] PHST- 2023/05/11 19:13 [pubmed] PHST- 2023/05/11 14:04 [entrez] AID - 10.1126/science.adh7902 [doi] PST - ppublish SO - Science. 2023 May 12;380(6645):578-579. doi: 10.1126/science.adh7902. Epub 2023 May 11. PMID- 37141315 OWN - NLM STAT- MEDLINE DCOM- 20230525 LR - 20230525 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 380 IP - 6645 DP - 2023 May 12 TI - Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. PG - 619-624 LID - 10.1126/science.adf5300 [doi] AB - Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. We investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans ranging from 100,000 years ago to the present and reconstructed 459 bacterial metagenome-assembled genomes. We identified a biosynthetic gene cluster shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites that we name "paleofurans." This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration. FAU - Klapper, Martin AU - Klapper M AUID- ORCID: 0000-0002-4977-2541 AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Hübner, Alexander AU - Hübner A AUID- ORCID: 0000-0003-3572-9996 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Ibrahim, Anan AU - Ibrahim A AUID- ORCID: 0000-0003-3719-901X AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Wasmuth, Ina AU - Wasmuth I AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Borry, Maxime AU - Borry M AUID- ORCID: 0000-0001-9140-7559 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Haensch, Veit G AU - Haensch VG AUID- ORCID: 0000-0003-0102-2124 AD - Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Zhang, Shuaibing AU - Zhang S AUID- ORCID: 0000-0003-4455-0971 AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Al-Jammal, Walid K AU - Al-Jammal WK AUID- ORCID: 0000-0003-4355-6431 AD - Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany. FAU - Suma, Harikumar AU - Suma H AUID- ORCID: 0000-0002-6670-2764 AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Fellows Yates, James A AU - Fellows Yates JA AUID- ORCID: 0000-0001-5585-6277 AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Frangenberg, Jasmin AU - Frangenberg J AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Velsko, Irina M AU - Velsko IM AUID- ORCID: 0000-0001-9810-9917 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Chowdhury, Somak AU - Chowdhury S AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Herbst, Rosa AU - Herbst R AUID- ORCID: 0000-0002-2379-7433 AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Bratovanov, Evgeni V AU - Bratovanov EV AD - Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Dahse, Hans-Martin AU - Dahse HM AD - Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Horch, Therese AU - Horch T AUID- ORCID: 0000-0002-3705-9423 AD - Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. FAU - Hertweck, Christian AU - Hertweck C AUID- ORCID: 0000-0002-0367-337X AD - Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. AD - Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany. FAU - González Morales, Manuel Ramon AU - González Morales MR AUID- ORCID: 0000-0001-7277-7837 AD - Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, 39071 Santander, Spain. FAU - Straus, Lawrence Guy AU - Straus LG AUID- ORCID: 0000-0003-0348-3338 AD - Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA. AD - Grupo I+D+i EvoAdapta, Departmento de Ciencias Históricas, Universidad de Cantabria, 39005 Santander, Spain. FAU - Vilotijevic, Ivan AU - Vilotijevic I AUID- ORCID: 0000-0001-6199-0632 AD - Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany. FAU - Warinner, Christina AU - Warinner C AUID- ORCID: 0000-0002-4528-5877 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. AD - Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany. AD - Department of Anthropology, Harvard University, Cambridge, MA 02138, USA. FAU - Stallforth, Pierre AU - Stallforth P AUID- ORCID: 0000-0001-7260-9921 AD - Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany. AD - Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany. LA - eng PT - Journal Article DEP - 20230504 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Biological Products) RN - 0 (Furans) RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Humans MH - *Biological Products/metabolism MH - *Genome, Bacterial MH - *Hominidae/genetics MH - Metagenome MH - *Neanderthals/genetics MH - *Furans/metabolism MH - DNA, Ancient EDAT- 2023/05/04 18:41 MHDA- 2023/05/15 06:42 CRDT- 2023/05/04 14:03 PHST- 2023/05/15 06:42 [medline] PHST- 2023/05/04 18:41 [pubmed] PHST- 2023/05/04 14:03 [entrez] AID - 10.1126/science.adf5300 [doi] PST - ppublish SO - Science. 2023 May 12;380(6645):619-624. doi: 10.1126/science.adf5300. Epub 2023 May 4. PMID- 36951219 OWN - NLM STAT- MEDLINE DCOM- 20230517 LR - 20230627 IS - 1474-9726 (Electronic) IS - 1474-9718 (Print) IS - 1474-9718 (Linking) VI - 22 IP - 5 DP - 2023 May TI - Current allele distribution of the human longevity gene APOE in Europe can mainly be explained by ancient admixture. PG - e13819 LID - 10.1111/acel.13819 [doi] LID - e13819 AB - Variation in apolipoprotein E (APOE) has been shown to have the strongest genetic effect on human longevity. The aim of this study was to unravel the evolutionary history of the three major APOE alleles in Europe by analysing ancient samples up to 12,000 years old. We detected significant allele frequency shifts between populations and over time. Our analyses indicated that selection led to large frequency differences between the earliest European populations (i.e., hunter-gatherers vs. first farmers), possibly due to changes in diet/lifestyle. In contrast, the allele distributions in populations from ~4000 BCE onward can mainly be explained by admixture, suggesting that it also played an important role in shaping current APOE variation. In any case, the resulting allele frequencies strongly influence the predisposition for longevity today, likely as a consequence of past adaptations and demographic processes. CI - © 2023 The Authors. Aging Cell published by Anatomical Society and John Wiley & Sons Ltd. FAU - Kolbe, Daniel AU - Kolbe D AUID- ORCID: 0000-0002-6607-7591 AD - Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, 24105, Germany. FAU - da Silva, Nicolas A AU - da Silva NA AD - Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, 24105, Germany. FAU - Dose, Janina AU - Dose J AD - Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, 24105, Germany. FAU - Torres, Guillermo G AU - Torres GG AD - Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, 24105, Germany. FAU - Caliebe, Amke AU - Caliebe A AD - Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, 24105, Germany. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AD - Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, 24105, Germany. FAU - Nebel, Almut AU - Nebel A AD - Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, 24105, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230323 PL - England TA - Aging Cell JT - Aging cell JID - 101130839 RN - 0 (Apolipoproteins E) SB - IM MH - Humans MH - Infant, Newborn MH - Alleles MH - Gene Frequency/genetics MH - *Longevity/genetics MH - *Apolipoproteins E/genetics MH - Europe PMC - PMC10186601 OTO - NOTNLM OT - Alzheimer's disease OT - age-related disease OT - aging OT - ancient DNA OT - ancient population genomics OT - evolution OT - longevity COIS- The authors declare no competing interests. EDAT- 2023/03/24 06:00 MHDA- 2023/05/17 06:42 PMCR- 2023/03/23 CRDT- 2023/03/23 06:33 PHST- 2023/02/21 00:00 [revised] PHST- 2022/10/26 00:00 [received] PHST- 2023/02/22 00:00 [accepted] PHST- 2023/05/17 06:42 [medline] PHST- 2023/03/24 06:00 [pubmed] PHST- 2023/03/23 06:33 [entrez] PHST- 2023/03/23 00:00 [pmc-release] AID - ACEL13819 [pii] AID - 10.1111/acel.13819 [doi] PST - ppublish SO - Aging Cell. 2023 May;22(5):e13819. doi: 10.1111/acel.13819. Epub 2023 Mar 23. PMID- 37117261 OWN - NLM STAT- MEDLINE DCOM- 20230501 LR - 20230510 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 13 IP - 1 DP - 2023 Apr 28 TI - Ancient DNA suggests anaemia and low bone mineral density as the cause for porotic hyperostosis in ancient individuals. PG - 6968 LID - 10.1038/s41598-023-33405-7 [doi] LID - 6968 AB - Porotic hyperostosis (PH) is a disease that had high prevalence during the Neolithic. Several hypotheses have been suggested to explain the origin of the disease, such as an iron deficiency diet, low B12 intake, malaria caused by Plasmodium spp., low haemoglobin levels or low vitamin D levels. None of these hypotheses have been tested genetically. Here, I calculated different genetic scores to test each hypothesis. Additionally, I calculated a genetic score of bone mineral density as it is a phenotype that seems to be selected in ancient Europeans. I apply these genetic scores on 80 ancient samples, 33 with diagnosed PH. The results seem to suggest anaemia and low bone mineral density as the main cause for this disease. Additionally, Neolithic individuals show the lowest genetic risk score for bone mineral density of all other periods tested here, which may explain the highest prevalence of the porotic hyperostosis during this age. CI - © 2023. The Author(s). FAU - Ferrando-Bernal, Manuel AU - Ferrando-Bernal M AD - Unaffiliated, Barcelona, Spain. manu.ferrandobernal@gmail.com. LA - eng SI - Dryad/10.5061/dryad.b5mkkwhfp PT - Journal Article DEP - 20230428 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Skull MH - DNA, Ancient MH - Paleopathology MH - *Anemia/complications MH - *Hyperostosis/genetics MH - *Bone Diseases, Metabolic/complications PMC - PMC10147686 COIS- The author declares no competing interests. EDAT- 2023/04/29 06:04 MHDA- 2023/05/01 06:42 PMCR- 2023/04/28 CRDT- 2023/04/28 23:20 PHST- 2023/01/12 00:00 [received] PHST- 2023/04/12 00:00 [accepted] PHST- 2023/05/01 06:42 [medline] PHST- 2023/04/29 06:04 [pubmed] PHST- 2023/04/28 23:20 [entrez] PHST- 2023/04/28 00:00 [pmc-release] AID - 10.1038/s41598-023-33405-7 [pii] AID - 33405 [pii] AID - 10.1038/s41598-023-33405-7 [doi] PST - epublish SO - Sci Rep. 2023 Apr 28;13(1):6968. doi: 10.1038/s41598-023-33405-7. PMID- 37239354 OWN - NLM STAT- MEDLINE DCOM- 20230529 LR - 20230531 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 14 IP - 5 DP - 2023 Apr 27 TI - Evaluating the Usefulness of Human DNA Quantification to Predict DNA Profiling Success of Historical Bone Samples. LID - 10.3390/genes14050994 [doi] LID - 994 AB - This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55-125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling. FAU - Thomas, Jacqueline Tyler AU - Thomas JT AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA. FAU - Cavagnino, Courtney AU - Cavagnino C AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA. FAU - Kjelland, Katelyn AU - Kjelland K AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - Amentum Services Inc. (Contractor Supporting the AFMES-AFDIL), Germantown, MD 20876, USA. FAU - Anderson, Elise AU - Anderson E AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - Amentum Services Inc. (Contractor Supporting the AFMES-AFDIL), Germantown, MD 20876, USA. FAU - Sturk-Andreaggi, Kimberly AU - Sturk-Andreaggi K AUID- ORCID: 0000-0001-6857-923X AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA. FAU - Daniels-Higginbotham, Jennifer AU - Daniels-Higginbotham J AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA. FAU - Amory, Christina AU - Amory C AD - Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria. FAU - Spatola, Brian AU - Spatola B AD - National Museum of Health and Medicine, Anatomical Division, Defense Health Agency, Silver Spring, MD 20910, USA. FAU - Moran, Kimberlee AU - Moran K AUID- ORCID: 0000-0002-8507-1646 AD - Forensic Science Program, Department of Chemistry, Rutgers University-Camden, Camden, NJ 08102, USA. FAU - Parson, Walther AU - Parson W AUID- ORCID: 0000-0002-5692-2392 AD - Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria. AD - Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16802, USA. FAU - Marshall, Charla AU - Marshall C AUID- ORCID: 0000-0002-8495-1748 AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA. AD - Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16802, USA. LA - eng PT - Journal Article DEP - 20230427 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - *DNA Fingerprinting/methods MH - *Microsatellite Repeats/genetics MH - Bone and Bones MH - DNA, Mitochondrial/genetics MH - Polymorphism, Single Nucleotide/genetics PMC - PMC10218391 OTO - NOTNLM OT - SNP OT - STR typing OT - ancient DNA OT - forensic DNA OT - massively parallel sequencing OT - mtDNA OT - next generation sequencing OT - qPCR COIS- The authors declare no conflict of interest. EDAT- 2023/05/27 09:42 MHDA- 2023/05/29 06:42 PMCR- 2023/04/27 CRDT- 2023/05/27 01:10 PHST- 2023/02/24 00:00 [received] PHST- 2023/04/14 00:00 [revised] PHST- 2023/04/22 00:00 [accepted] PHST- 2023/05/29 06:42 [medline] PHST- 2023/05/27 09:42 [pubmed] PHST- 2023/05/27 01:10 [entrez] PHST- 2023/04/27 00:00 [pmc-release] AID - genes14050994 [pii] AID - genes-14-00994 [pii] AID - 10.3390/genes14050994 [doi] PST - epublish SO - Genes (Basel). 2023 Apr 27;14(5):994. doi: 10.3390/genes14050994. PMID- 36958333 OWN - NLM STAT- MEDLINE DCOM- 20230427 LR - 20230724 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 33 IP - 8 DP - 2023 Apr 24 TI - Genomic analyses of hair from Ludwig van Beethoven. PG - 1431-1447.e22 LID - S0960-9822(23)00181-1 [pii] LID - 10.1016/j.cub.2023.02.041 [doi] AB - Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry. CI - Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Begg, Tristan James Alexander AU - Begg TJA AD - Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. Electronic address: tristanj.a.begg@gmail.com. FAU - Schmidt, Axel AU - Schmidt A AD - Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany. FAU - Kocher, Arthur AU - Kocher A AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. FAU - Larmuseau, Maarten H D AU - Larmuseau MHD AD - Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Laboratory of Human Genetic Genealogy, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; ARCHES - Antwerp Cultural Heritage Sciences, Faculty of Design Sciences, University of Antwerp, 2000 Antwerp, Belgium; Histories vzw, 9000 Gent, Belgium. FAU - Runfeldt, Göran AU - Runfeldt G AD - FamilyTreeDNA, Gene by Gene, Houston, TX 77008, USA. FAU - Maier, Paul Andrew AU - Maier PA AD - FamilyTreeDNA, Gene by Gene, Houston, TX 77008, USA. FAU - Wilson, John D AU - Wilson JD AD - Austrian Academy of Sciences, 1030 Vienna, Austria; University of Vienna, 1010 Vienna, Austria. FAU - Barquera, Rodrigo AU - Barquera R AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Maj, Carlo AU - Maj C AD - Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany; Center for Human Genetics, University Hospital of Marburg, Marburg, Germany. FAU - Szolek, András AU - Szolek A AD - Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany. FAU - Sager, Michael AU - Sager M AD - FamilyTreeDNA, Gene by Gene, Houston, TX 77008, USA. FAU - Clayton, Stephen AU - Clayton S AD - Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. FAU - Peltzer, Alexander AU - Peltzer A AD - Quantitative Biology Center (QBiC) University of Tübingen, Tübingen, Germany. FAU - Hui, Ruoyun AU - Hui R AD - MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; Alan Turing Institute, 2QR, John Dodson House, London NW1 2DB, UK. FAU - Ronge, Julia AU - Ronge J AD - Beethoven-Haus Bonn, 53111 Bonn, Germany. FAU - Reiter, Ella AU - Reiter E AD - Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany. FAU - Freund, Cäcilia AU - Freund C AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. FAU - Burri, Marta AU - Burri M AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. FAU - Aron, Franziska AU - Aron F AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. FAU - Tiliakou, Anthi AU - Tiliakou A AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. FAU - Osborn, Joanna AU - Osborn J AD - Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK. FAU - Behar, Doron M AU - Behar DM AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Boecker, Malte AU - Boecker M AD - Beethoven-Haus Bonn, 53111 Bonn, Germany. FAU - Brandt, Guido AU - Brandt G AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. FAU - Cleynen, Isabelle AU - Cleynen I AD - Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium. FAU - Strassburg, Christian AU - Strassburg C AD - Department of Internal Medicine I, University Hospital Bonn, 53127 Bonn, Germany. FAU - Prüfer, Kay AU - Prüfer K AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Kühnert, Denise AU - Kühnert D AD - Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. FAU - Meredith, William Rhea AU - Meredith WR AD - American Beethoven Society, San Jose State University, San Jose, CA 95192, USA; Ira F. Brilliant Center for Beethoven Studies, San Jose State University, San Jose, CA 95192, USA; School of Music and Dance, San Jose State University, San Jose, CA 95192, USA. FAU - Nöthen, Markus M AU - Nöthen MM AD - Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany. FAU - Attenborough, Robert David AU - Attenborough RD AD - MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; School of Archaeology & Anthropology, Australian National University, Canberra, ACT 0200, Australia. FAU - Kivisild, Toomas AU - Kivisild T AD - Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. Electronic address: toomas.kivisild@kuleuven.be. FAU - Krause, Johannes AU - Krause J AD - Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. Electronic address: krause@eva.mpg.de. LA - eng SI - Dryad/10.5061/dryad.k0p2ngfc4 PT - Journal Article DEP - 20230322 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM CIN - Gastroenterology. 2023 Aug;165(2):514. doi: 10.1053/j.gastro.2023.04.020. PMID: 37127096 MH - Male MH - Humans MH - Genetic Predisposition to Disease MH - *Famous Persons MH - *Deafness MH - Genomics MH - *Music MH - Hair OTO - NOTNLM OT - Ludwig van Beethoven OT - ancient DNA OT - extra-pair paternity OT - genetic genealogy OT - genobiography OT - geo-genetic triangulation OT - hair OT - hepatitis B virus OT - medical genetics OT - the Beethoven genome project COIS- Declaration of interests T.J.A.B. has received scholarships from the American Beethoven Society in support of his graduate studies. G.R., M.S., and P.A.M. are employees of GeneByGene. G.R. and M.S. hold stock options in MyDNA, Inc. M.M.N. has received fees for membership in an advisory board from HMG Systems Engineering GmbH (Fürth, Germany), for membership in the Medical-Scientific Editorial Office of the Deutsches Ärzteblatt, and for serving as a consultant for EVERIS Belgique SPRL in a project of the European Commission (REFORM/SC2020/029). M.M.N. receives salary payments from Life & Brain GmbH and holds shares in Life & Brain GmbH. EDAT- 2023/03/24 06:00 MHDA- 2023/04/27 06:42 CRDT- 2023/03/23 19:42 PHST- 2022/05/29 00:00 [received] PHST- 2022/10/11 00:00 [revised] PHST- 2023/02/13 00:00 [accepted] PHST- 2023/04/27 06:42 [medline] PHST- 2023/03/24 06:00 [pubmed] PHST- 2023/03/23 19:42 [entrez] AID - S0960-9822(23)00181-1 [pii] AID - 10.1016/j.cub.2023.02.041 [doi] PST - ppublish SO - Curr Biol. 2023 Apr 24;33(8):1431-1447.e22. doi: 10.1016/j.cub.2023.02.041. Epub 2023 Mar 22. PMID- 37101579 OWN - NLM STAT- MEDLINE DCOM- 20230501 LR - 20230501 IS - 2666-2477 (Electronic) IS - 2666-2477 (Linking) VI - 4 IP - 2 DP - 2023 Apr 13 TI - Community partnerships are fundamental to ethical ancient DNA research. PG - 100161 LID - 10.1016/j.xhgg.2022.100161 [doi] LID - 100161 AB - The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article "Ethics of DNA research on human remains: five globally applicable guidelines" published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of "scientific" and "community" concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines' authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on "ethical" grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research. CI - © 2022 The Authors. FAU - Kowal, Emma AU - Kowal E AD - Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Burwood, VIC, Australia. FAU - Weyrich, Laura S AU - Weyrich LS AD - Department of Anthropology, Pennsylvania State University, University Park, PA, USA. FAU - Argüelles, Juan Manuel AU - Argüelles JM AD - Dirección de Antropología Física, Instituto Nacional de Antropología Física, México City, Mexico. FAU - Bader, Alyssa C AU - Bader AC AD - Department of Anthropology, McGill University, Montréal, QC, Canada. AD - Sealaska Heritage Institute, Juneau, AK, USA. FAU - Colwell, Chip AU - Colwell C AD - SAPIENS, New York, NY, USA. AD - Department of Anthropology, University of Colorado, Denver, CO, USA. FAU - Cortez, Amanda Daniela AU - Cortez AD AD - Department of Anthropology, University of Connecticut, Storrs, CT, USA. FAU - Davis, Jenny L AU - Davis JL AD - American Indian Studies, University of Illinois, Urbana-Champaign, Urbana, IL, USA. AD - Department of Anthropology, University of Illinois, Urbana-Champaign, Urbana, IL, USA. FAU - Figueiro, Gonzalo AU - Figueiro G AD - Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay. FAU - Fox, Keolu AU - Fox K AD - Indigenous Futures Institute, University of California, San Diego, La Jolla, CA, USA. FAU - Malhi, Ripan S AU - Malhi RS AD - Department of Anthropology, University of Illinois, Urbana-Champaign, Urbana, IL, USA. AD - Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA. FAU - Matisoo-Smith, Elizabeth AU - Matisoo-Smith E AD - Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand. FAU - Nayak, Ayushi AU - Nayak A AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Nelson, Elizabeth A AU - Nelson EA AD - Microbial Paleogenomics Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France. FAU - Nicholas, George AU - Nicholas G AD - Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada. FAU - Nieves-Colón, Maria A AU - Nieves-Colón MA AD - Department of Anthropology, University of Minnesota Twin Cities, Minneapolis and Saint Paul, MN, USA. FAU - Russell, Lynette AU - Russell L AD - Monash Indigenous Studies Centre, Monash University, Melbourne, VIC, Australia. AD - Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Monash University, Victoria, Australia. FAU - Ulm, Sean AU - Ulm S AD - Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society and Education, James Cook University, Cairns, QLD, Australia. FAU - Vergara-Silva, Francisco AU - Vergara-Silva F AD - Laboratorio de Teoría Evolutiva e Historia de la Ciencia (Jardín Botánico), Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico. FAU - Villanea, Fernando A AU - Villanea FA AD - Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA. FAU - Wagner, Jennifer K AU - Wagner JK AD - School of Engineering Design, Technology, and Professional Programs, Pennsylvania State University, University Park, PA, USA. FAU - Yracheta, Joseph M AU - Yracheta JM AD - Native BioData Consortium, Cheyenne River Sioux Nation, SD, USA. FAU - Tsosie, Krystal S AU - Tsosie KS AD - Native BioData Consortium, Cheyenne River Sioux Nation, SD, USA. AD - School of Life Sciences, Arizona State University, Tempe, AZ, USA. LA - eng PT - Comment PT - Journal Article PT - Review DEP - 20230111 PL - United States TA - HGG Adv JT - HGG advances JID - 101772885 RN - 0 (DNA, Ancient) SB - IM CON - Nature. 2021 Nov;599(7883):41-46. doi: 10.1038/s41586-021-04008-x. PMID: 34671160 MH - Humans MH - *DNA, Ancient MH - *Ethics, Research MH - Family MH - Population Groups MH - Research Personnel MH - *Human Genetics/ethics MH - Guidelines as Topic MH - Stakeholder Participation MH - Community-Institutional Relations PMC - PMC10123407 COIS- J.W. is an associate editor of HGGA. EDAT- 2023/04/27 06:42 MHDA- 2023/04/28 06:42 PMCR- 2023/01/11 CRDT- 2023/04/27 02:06 PHST- 2023/04/28 06:42 [medline] PHST- 2023/04/27 06:42 [pubmed] PHST- 2023/04/27 02:06 [entrez] PHST- 2023/01/11 00:00 [pmc-release] AID - S2666-2477(22)00078-1 [pii] AID - 100161 [pii] AID - 10.1016/j.xhgg.2022.100161 [doi] PST - epublish SO - HGG Adv. 2023 Jan 11;4(2):100161. doi: 10.1016/j.xhgg.2022.100161. eCollection 2023 Apr 13. PMID- 37040705 OWN - NLM STAT- MEDLINE DCOM- 20230414 LR - 20230415 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 33 IP - 7 DP - 2023 Apr 10 TI - Human evolution: When admixture met selection. PG - R259-R261 LID - S0960-9822(23)00267-1 [pii] LID - 10.1016/j.cub.2023.02.077 [doi] AB - Admixture has been a major force during human evolution. Two new studies using ancient DNA now show how two key admixture events in the evolutionary history of Europeans altered their adaptive trajectories and facilitated rapid evolution. CI - Copyright © 2023 Elsevier Inc. All rights reserved. FAU - Wegmann, Daniel AU - Wegmann D AD - Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland. Electronic address: daniel.wegmann@unifr.ch. FAU - Eckel, Raphael AU - Eckel R AD - Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland. LA - eng PT - Comment PT - Journal Article PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM CON - Curr Biol. 2023 Apr 10;33(7):1365-1371.e3. doi: 10.1016/j.cub.2023.02.049. PMID: 36963383 MH - Humans MH - *DNA, Ancient MH - *Biological Evolution COIS- Declaration of interests The authors declare no competing interests. EDAT- 2023/04/12 06:00 MHDA- 2023/04/13 06:43 CRDT- 2023/04/11 18:17 PHST- 2023/04/13 06:43 [medline] PHST- 2023/04/11 18:17 [entrez] PHST- 2023/04/12 06:00 [pubmed] AID - S0960-9822(23)00267-1 [pii] AID - 10.1016/j.cub.2023.02.077 [doi] PST - ppublish SO - Curr Biol. 2023 Apr 10;33(7):R259-R261. doi: 10.1016/j.cub.2023.02.077. PMID- 36963383 OWN - NLM STAT- MEDLINE DCOM- 20230413 LR - 20240917 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 33 IP - 7 DP - 2023 Apr 10 TI - Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers. PG - 1365-1371.e3 LID - S0960-9822(23)00189-6 [pii] LID - 10.1016/j.cub.2023.02.049 [doi] AB - Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.(1)(,)(2)(,)(3)(,)(4) Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10(-56)). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age. CI - Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Davy, Tom AU - Davy T AD - Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK. Electronic address: tom.davy@crick.ac.uk. FAU - Ju, Dan AU - Ju D AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA. FAU - Skoglund, Pontus AU - Skoglund P AD - Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK. Electronic address: pontus.skoglund@crick.ac.uk. LA - eng GR - 852558/ERC_/European Research Council/International GR - 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom GR - R35 GM133708/GM/NIGMS NIH HHS/United States GR - WT_/Wellcome Trust/United Kingdom GR - FC001595/ARC_/Arthritis Research UK/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20230323 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 9007-49-2 (DNA) SB - IM CIN - Curr Biol. 2023 Apr 10;33(7):R259-R261. doi: 10.1016/j.cub.2023.02.077. PMID: 37040705 MH - Humans MH - *Farmers MH - Europe MH - *DNA MH - Alleles MH - Selection, Genetic PMC - PMC10153476 MID - NIHMS1882585 OTO - NOTNLM OT - Europe OT - MHC OT - Mesolithic OT - Neolithic OT - adaptation OT - admixture OT - ancient DNA OT - immunity OT - paleogenomics OT - pigmentation OT - selection COIS- Declaration of interests The authors declare no competing interests. EDAT- 2023/03/25 06:00 MHDA- 2023/04/13 06:42 PMCR- 2023/05/02 CRDT- 2023/03/24 19:41 PHST- 2022/09/02 00:00 [received] PHST- 2022/11/17 00:00 [revised] PHST- 2023/02/15 00:00 [accepted] PHST- 2023/04/13 06:42 [medline] PHST- 2023/03/25 06:00 [pubmed] PHST- 2023/03/24 19:41 [entrez] PHST- 2023/05/02 00:00 [pmc-release] AID - S0960-9822(23)00189-6 [pii] AID - 10.1016/j.cub.2023.02.049 [doi] PST - ppublish SO - Curr Biol. 2023 Apr 10;33(7):1365-1371.e3. doi: 10.1016/j.cub.2023.02.049. Epub 2023 Mar 23. PMID- 37072186 OWN - NLM STAT- MEDLINE DCOM- 20230517 LR - 20250104 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 33 IP - 4 DP - 2023 Apr TI - Density separation of petrous bone powders for optimized ancient DNA yields. PG - 622-631 LID - 10.1101/gr.277714.123 [doi] AB - Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders before DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using nontoxic heavy liquid solutions, we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into eight density intervals (2.15 to 2.45 g/cm(3), in 0.05 increments). We found that the 2.30 to 2.35 g/cm(3) and 2.35 to 2.40 g/cm(3) intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and not reducing library complexity. Although small 0.05 g/cm(3) intervals may maximally optimize yields, a single separation to remove materials with a density above 2.40 g/cm(3) yielded up to 2.57-fold more endogenous DNA on average, which enables the simultaneous separation of samples that vary in preservation or in the type of material analyzed. While requiring no new ancient DNA laboratory equipment and fewer than 30 min of extra laboratory work, the implementation of density separation before DNA extraction can substantially boost endogenous DNA yields without decreasing library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments. CI - © 2023 Fernandes et al.; Published by Cold Spring Harbor Laboratory Press. FAU - Fernandes, Daniel M AU - Fernandes DM AUID- ORCID: 0000-0002-7434-6552 AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria; ron.pinhasi@univie.ac.at daniel.fernandes@univie.ac.at. AD - CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal. AD - Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria. FAU - Sirak, Kendra A AU - Sirak KA AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. FAU - Cheronet, Olivia AU - Cheronet O AUID- ORCID: 0000-0001-6760-1204 AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. AD - Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria. FAU - Novak, Mario AU - Novak M AUID- ORCID: 0000-0002-4567-8742 AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia. FAU - Brück, Florian AU - Brück F AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Zelger, Evelyn AU - Zelger E AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Llanos-Lizcano, Alejandro AU - Llanos-Lizcano A AUID- ORCID: 0000-0002-7579-3573 AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Wagner, Anna AU - Wagner A AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Zettl, Anna AU - Zettl A AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Mandl, Kirsten AU - Mandl K AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Duffet Carlson, Kellie Sara AU - Duffet Carlson KS AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. AD - Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria. FAU - Oberreiter, Victoria AU - Oberreiter V AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. AD - Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria. FAU - Özdoğan, Kadir T AU - Özdoğan KT AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. AD - Department of History and Art History, Utrecht University, 3512 BS Utrecht, The Netherlands. FAU - Sawyer, Susanna AU - Sawyer S AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - La Pastina, Francesco AU - La Pastina F AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, United Kingdom. FAU - Borgia, Emanuela AU - Borgia E AD - Dipartimento di Scienze dell'Antichità, Sapienza Università di Roma, Rome 00185, Italy. FAU - Coppa, Alfredo AU - Coppa A AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. AD - Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria. AD - Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy. FAU - Dobeš, Miroslav AU - Dobeš M AUID- ORCID: 0000-0001-5327-5030 AD - Institute of Archaeology of the Czech Academy of Sciences, Prague 118 00, Czech Republic. FAU - Velemínský, Petr AU - Velemínský P AD - Department of Anthropology, National Museum, Prague 115 79, Czech Republic. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. FAU - Bell, Lynne S AU - Bell LS AD - Centre for Forensic Research, School of Criminology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria; ron.pinhasi@univie.ac.at daniel.fernandes@univie.ac.at. AD - Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria. LA - eng GR - M 3108/FWF_/Austrian Science Fund FWF/Austria PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230418 PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (DNA, Ancient) RN - 0 (Powders) RN - 0 (Plastics) RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - *DNA, Ancient MH - *Petrous Bone MH - Powders MH - Plastics MH - DNA/genetics PMC - PMC10234301 EDAT- 2023/04/19 06:00 MHDA- 2023/05/17 06:42 PMCR- 2023/10/01 CRDT- 2023/04/18 06:00 PHST- 2023/01/18 00:00 [received] PHST- 2023/04/11 00:00 [accepted] PHST- 2023/05/17 06:42 [medline] PHST- 2023/04/19 06:00 [pubmed] PHST- 2023/04/18 06:00 [entrez] PHST- 2023/10/01 00:00 [pmc-release] AID - gr.277714.123 [pii] AID - 10.1101/gr.277714.123 [doi] PST - ppublish SO - Genome Res. 2023 Apr;33(4):622-631. doi: 10.1101/gr.277714.123. Epub 2023 Apr 18. PMID- 36796758 OWN - NLM STAT- MEDLINE DCOM- 20230616 LR - 20230620 IS - 2320-2890 (Electronic) IS - 2319-4170 (Print) IS - 2319-4170 (Linking) VI - 46 IP - 2 DP - 2023 Apr TI - The 2022 nobel prize in physiology or medicine awarded for the decoding of the complete ancient human genome. PG - 100584 LID - S2319-4170(23)00008-2 [pii] LID - 10.1016/j.bj.2023.02.004 [doi] LID - 100584 AB - Since the publication of the first ancient DNA sequence in 1984, experimental methods used to recover ancient DNA have advanced greatly, illuminating previously unknown branches of the human family tree and opening up several promising new avenues for future studies of human evolution. The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for his work on ancient DNA and human evolution. On his first day back at work, he was thrown in the pond as part of his institute's tradition of celebrating award winners. CI - Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved. FAU - Min-Shan Ko, Albert AU - Min-Shan Ko A AD - Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Cardiovascular Department, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Healthy Aging Research Center, Chang Gung University, Taoyuan, Taiwan. Electronic address: koalbert@mail.cgu.edu.tw. LA - eng PT - Journal Article DEP - 20230214 PL - United States TA - Biomed J JT - Biomedical journal JID - 101599820 RN - 0 (DNA, Ancient) SB - IM MH - Male MH - Humans MH - *Nobel Prize MH - DNA, Ancient MH - Genome, Human/genetics MH - *Medicine MH - Germany PMC - PMC10267955 OTO - NOTNLM OT - 2022 nobel prize in physiology or medicine OT - Ancient DNA OT - Archaic humans OT - Svante pääbo EDAT- 2023/02/17 06:00 MHDA- 2023/06/16 06:42 PMCR- 2023/02/14 CRDT- 2023/02/16 19:29 PHST- 2022/12/02 00:00 [received] PHST- 2023/01/25 00:00 [revised] PHST- 2023/02/08 00:00 [accepted] PHST- 2023/06/16 06:42 [medline] PHST- 2023/02/17 06:00 [pubmed] PHST- 2023/02/16 19:29 [entrez] PHST- 2023/02/14 00:00 [pmc-release] AID - S2319-4170(23)00008-2 [pii] AID - 100584 [pii] AID - 10.1016/j.bj.2023.02.004 [doi] PST - ppublish SO - Biomed J. 2023 Apr;46(2):100584. doi: 10.1016/j.bj.2023.02.004. Epub 2023 Feb 14. PMID- 36841239 OWN - NLM STAT- MEDLINE DCOM- 20230330 LR - 20230415 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 33 IP - 6 DP - 2023 Mar 27 TI - Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark. PG - 1147-1152.e5 LID - S0960-9822(23)00133-1 [pii] LID - 10.1016/j.cub.2023.01.064 [doi] AB - The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.(1)(,)(2) A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.(3) Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.(4)(,)(5) To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research. CI - Copyright © 2023 Elsevier Inc. All rights reserved. FAU - Eaton, Katherine AU - Eaton K AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada. FAU - Sidhu, Ravneet K AU - Sidhu RK AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON L8S 4E8, Canada. FAU - Klunk, Jennifer AU - Klunk J AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Daicel Arbor Biosciences, Ann Arbor, MI 48103, USA. FAU - Gamble, Julia A AU - Gamble JA AD - Department of Anthropology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada. FAU - Boldsen, Jesper L AU - Boldsen JL AD - Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, 5260 Odense, Denmark. FAU - Carmichael, Ann G AU - Carmichael AG AD - Department of History, Indiana University Bloomington, Bloomington, IN 47405, USA. FAU - Varlık, Nükhet AU - Varlık N AD - Department of History, Rutgers University - Newark, Newark, NJ 07102, USA. FAU - Duchene, Sebastian AU - Duchene S AD - The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3004, Australia. FAU - Featherstone, Leo AU - Featherstone L AD - The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3004, Australia. FAU - Grimes, Vaughan AU - Grimes V AD - Department of Archaeology, Memorial University of Newfoundland, St. Johns, SC A1C 5S7, Canada. FAU - Golding, G Brian AU - Golding GB AD - Department of Biology, McMaster University, Hamilton, ON L8S 4E8, Canada. FAU - DeWitte, Sharon N AU - DeWitte SN AD - Department of Anthropology, University of South Carolina, Columbia, SC 29208, USA. FAU - Holmes, Edward C AU - Holmes EC AD - Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney 2006, Australia. FAU - Poinar, Hendrik N AU - Poinar HN AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Biochemistry, McMaster University, Hamilton, ON L82 4K1, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada. Electronic address: poinarh@mcmaster.ca. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230224 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Humans MH - *Yersinia pestis/genetics MH - *Plague/epidemiology/microbiology MH - Phylogeny MH - Genome, Bacterial MH - Denmark OTO - NOTNLM OT - Black Death OT - Scandinavia OT - Yersinia pestis OT - ancient DNA OT - phylogeography OT - plague OT - re-emerging infectious disease COIS- Declaration of interests J.K. declares financial interest in Daicel Arbor Biosciences, which provided the myBaits probes for targeted capture. EDAT- 2023/02/26 06:00 MHDA- 2023/03/30 06:11 CRDT- 2023/02/25 19:00 PHST- 2022/09/02 00:00 [received] PHST- 2022/12/08 00:00 [revised] PHST- 2023/01/30 00:00 [accepted] PHST- 2023/03/30 06:11 [medline] PHST- 2023/02/26 06:00 [pubmed] PHST- 2023/02/25 19:00 [entrez] AID - S0960-9822(23)00133-1 [pii] AID - 10.1016/j.cub.2023.01.064 [doi] PST - ppublish SO - Curr Biol. 2023 Mar 27;33(6):1147-1152.e5. doi: 10.1016/j.cub.2023.01.064. Epub 2023 Feb 24. PMID- 36980999 OWN - NLM STAT- MEDLINE DCOM- 20230330 LR - 20230424 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 14 IP - 3 DP - 2023 Mar 16 TI - Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data. LID - 10.3390/genes14030727 [doi] LID - 727 AB - Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans. FAU - Toncheva, Draga AU - Toncheva D AUID- ORCID: 0000-0002-2027-6122 AD - Medical Faculty, Department of Medical Genetics, Medical University of Sofia, Sofia 1000, Bulgaria. AD - Bulgarian Academy of Sciences, Sofia 1000, Bulgaria. FAU - Marinova, Maria AU - Marinova M AD - Department of Computer Systems and Technologies, Faculty of Electronics and Automation, Technical University of Sofia, Branch Plovdiv, Plovdiv 4000, Bulgaria. FAU - Chobanov, Todor AU - Chobanov T AD - Institute of Balkan Studies, Centre of Tracology at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria. FAU - Serbezov, Dimitar AU - Serbezov D AD - Medical Faculty, Department of Medical Genetics, Medical University of Sofia, Sofia 1000, Bulgaria. LA - eng PT - Journal Article DEP - 20230316 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Humans MH - Infant, Newborn MH - *Neanderthals/genetics MH - Rare Diseases/genetics MH - *Hominidae/genetics MH - Genome, Human MH - DNA PMC - PMC10048696 OTO - NOTNLM OT - ancient DNA OT - genome-wide data OT - monogenic diseases COIS- The authors declare no conflict of interest. EDAT- 2023/03/30 06:00 MHDA- 2023/03/30 06:11 PMCR- 2023/03/16 CRDT- 2023/03/29 01:27 PHST- 2023/02/15 00:00 [received] PHST- 2023/03/08 00:00 [revised] PHST- 2023/03/13 00:00 [accepted] PHST- 2023/03/30 06:11 [medline] PHST- 2023/03/29 01:27 [entrez] PHST- 2023/03/30 06:00 [pubmed] PHST- 2023/03/16 00:00 [pmc-release] AID - genes14030727 [pii] AID - genes-14-00727 [pii] AID - 10.3390/genes14030727 [doi] PST - epublish SO - Genes (Basel). 2023 Mar 16;14(3):727. doi: 10.3390/genes14030727. PMID- 36918761 OWN - NLM STAT- MEDLINE DCOM- 20230316 LR - 20230317 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 24 IP - 1 DP - 2023 Mar 14 TI - Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data. PG - 111 LID - 10.1186/s12864-023-09198-4 [doi] LID - 111 AB - BACKGROUND: The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and yet the identification and interpretation of kin relationships in prehistoric human groups is difficult. In recent years, the advent of archaeogenetic techniques have offered a fresh approach, and when combined with more traditional osteological and interpretive archaeological methods, allows for improved interpretation of the burial practices, cultural behaviours, and societal stratification in ancient societies. Although archaeogenetic techniques are developing at pace, questions remain as to their accuracy, particularly when applied to the low coverage datasets that results from the sequencing of DNA derived from highly degraded ancient material. RESULTS: The performance of six of the most commonly used kinship identifcation software methods was explored at a range of low and ultra low genome coverages. An asymmetrical response was observed across packages, with decreased genome coverage resulting in differences in both direction and degree of change of calculated kinship scores and thus pairwise relatedness estimates are dependant on both package used and genome coverage. Methods reliant upon genotype likelihoods methods (lcMLkin, NGSrelate and NGSremix) show a decreased level of prediction at coverage below 1x, although were consistent in the particular relationships identified at these coverages when compared to the pseudohaploid reliant methods tested (READ, the Kennett 2017 method and TKGWV2.0). The three pseudohaploid methods show predictive potential at coverages as low as 0.05x, although the accuracy of the relationships identified is questionable given the increase in the number of relationships identifIed at the low coverage (type I errors). CONCLUSION: Two pseudohaploid methods (READ and Kennett 2017) show relatively consistent inference of kin relationships at low coverage (0.5x), with READ only showing a significant performance drop off at ultralow coverages (< 0.2x). More generally, our results reveal asymmetrical kinship classifications in some software packages even at high coverages, highlighting the importance of applying multiple methods to authenticate kin relationships in ancient material, along with the continuing need to develop laboratory methods that maximise data output for downstream analyses. CI - © 2023. The Author(s). FAU - Marsh, William A AU - Marsh WA AD - Natural History Museum, Cromwell Road, SW7 5BD, London, England. w.marsh@nhm.ac.uk. AD - BioArCh, University of York, YO10 5NG, York, England. w.marsh@nhm.ac.uk. FAU - Brace, Selina AU - Brace S AD - Natural History Museum, Cromwell Road, SW7 5BD, London, England. FAU - Barnes, Ian AU - Barnes I AD - Natural History Museum, Cromwell Road, SW7 5BD, London, England. LA - eng PT - Journal Article DEP - 20230314 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - *Software MH - Genotype MH - Genome PMC - PMC10015695 OTO - NOTNLM OT - Ancient DNA OT - Biological kinship OT - Genotype likelihood OT - Low coverage OT - Pseudohaploid OT - Relatedness COIS- Authors declare no competing interests. EDAT- 2023/03/16 06:00 MHDA- 2023/03/17 06:00 PMCR- 2023/03/14 CRDT- 2023/03/15 01:32 PHST- 2022/08/18 00:00 [received] PHST- 2023/02/20 00:00 [accepted] PHST- 2023/03/15 01:32 [entrez] PHST- 2023/03/16 06:00 [pubmed] PHST- 2023/03/17 06:00 [medline] PHST- 2023/03/14 00:00 [pmc-release] AID - 10.1186/s12864-023-09198-4 [pii] AID - 9198 [pii] AID - 10.1186/s12864-023-09198-4 [doi] PST - epublish SO - BMC Genomics. 2023 Mar 14;24(1):111. doi: 10.1186/s12864-023-09198-4. PMID- 36930529 OWN - NLM STAT- MEDLINE DCOM- 20230403 LR - 20231101 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 15 IP - 3 DP - 2023 Mar 3 TI - An Adagio for Viruses, Played Out on Ancient DNA. LID - 10.1093/gbe/evad047 [doi] LID - evad047 AB - Studies of ancient DNA have transformed our understanding of human evolution. Paleogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic, and pandemic pathogens. Viruses-and in particular those with single- or double-stranded DNA genomes-are an important part of the paleogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly evolving viruses which cause disease. In this review, we revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We look at how paleogenomics works for viral pathogens, such as the need for careful precautions against modern contamination and robust computational pipelines to identify and analyze authenticated viral sequences. We discuss the insights into virus evolution which have been gained through paleogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical. CI - © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - de-Dios, Toni AU - de-Dios T AUID- ORCID: 0000-0001-9260-8846 AD - Institute of Genomics, University of Tartu, Estonia. FAU - Scheib, Christiana L AU - Scheib CL AD - Institute of Genomics, University of Tartu, Estonia. AD - St. John's College, University of Cambridge, United Kingdom. FAU - Houldcroft, Charlotte J AU - Houldcroft CJ AUID- ORCID: 0000-0002-1833-5285 AD - Department of Genetics, University of Cambridge, United Kingdom. LA - eng PT - Journal Article PT - Review PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - *Genomics/methods MH - DNA, Ancient MH - Paleontology MH - DNA MH - *Viruses/genetics PMC - PMC10063219 OTO - NOTNLM OT - aDNA OT - ancient biomolecules OT - evolution OT - paleogenomics OT - population genomics OT - virology EDAT- 2023/03/18 06:00 MHDA- 2023/04/03 06:42 PMCR- 2023/03/17 CRDT- 2023/03/17 12:43 PHST- 2023/03/09 00:00 [accepted] PHST- 2023/04/03 06:42 [medline] PHST- 2023/03/18 06:00 [pubmed] PHST- 2023/03/17 12:43 [entrez] PHST- 2023/03/17 00:00 [pmc-release] AID - 7079967 [pii] AID - evad047 [pii] AID - 10.1093/gbe/evad047 [doi] PST - ppublish SO - Genome Biol Evol. 2023 Mar 3;15(3):evad047. doi: 10.1093/gbe/evad047. PMID- 36869137 OWN - NLM STAT- MEDLINE DCOM- 20230307 LR - 20230322 IS - 2399-3642 (Electronic) IS - 2399-3642 (Linking) VI - 6 IP - 1 DP - 2023 Mar 3 TI - Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago. PG - 240 LID - 10.1038/s42003-023-04582-y [doi] LID - 240 AB - The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome. CI - © 2023. The Author(s). FAU - Rifkin, Riaan F AU - Rifkin RF AUID- ORCID: 0000-0003-1791-3706 AD - Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. riaanrifkin@gmail.com. AD - Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK. riaanrifkin@gmail.com. FAU - Vikram, Surendra AU - Vikram S AUID- ORCID: 0000-0002-4721-2890 AD - Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. FAU - Alcorta, Jaime AU - Alcorta J AD - Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile. FAU - Ramond, Jean-Baptiste AU - Ramond JB AUID- ORCID: 0000-0003-4790-6232 AD - Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. AD - Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK. AD - Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile. FAU - Cowan, Don A AU - Cowan DA AUID- ORCID: 0000-0001-8059-861X AD - Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. FAU - Jakobsson, Mattias AU - Jakobsson M AUID- ORCID: 0000-0001-7840-7853 AD - Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden. AD - Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa. AD - SciLifeLab, Uppsala, Sweden. FAU - Schlebusch, Carina M AU - Schlebusch CM AUID- ORCID: 0000-0002-8160-9621 AD - Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden. AD - Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa. AD - SciLifeLab, Uppsala, Sweden. FAU - Lombard, Marlize AU - Lombard M AUID- ORCID: 0000-0002-0675-0414 AD - Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa. mlombard@uj.ac.za. LA - eng GR - NGS-371R-18/National Geographic Society/ PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230303 PL - England TA - Commun Biol JT - Communications biology JID - 101719179 RN - 9007-49-2 (DNA) RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Child MH - *Rickettsia felis MH - Africa, Southern MH - DNA MH - South Africa MH - DNA, Ancient PMC - PMC9984395 COIS- The authors declare no competing interests. The funding sponsors had no role in the design of the study, the collection, analyses, and interpretation of data, in the writing of the manuscript or in the decision to distribute the results. EDAT- 2023/03/04 06:00 MHDA- 2023/03/08 06:00 PMCR- 2023/03/03 CRDT- 2023/03/03 23:19 PHST- 2020/07/31 00:00 [received] PHST- 2023/02/13 00:00 [accepted] PHST- 2023/03/03 23:19 [entrez] PHST- 2023/03/04 06:00 [pubmed] PHST- 2023/03/08 06:00 [medline] PHST- 2023/03/03 00:00 [pmc-release] AID - 10.1038/s42003-023-04582-y [pii] AID - 4582 [pii] AID - 10.1038/s42003-023-04582-y [doi] PST - epublish SO - Commun Biol. 2023 Mar 3;6(1):240. doi: 10.1038/s42003-023-04582-y. PMID- 36862777 OWN - NLM STAT- MEDLINE DCOM- 20230403 LR - 20230403 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 379 IP - 6635 DP - 2023 Mar 3 TI - Ancient DNA upends European prehistory. PG - 865-866 LID - 10.1126/science.adh3912 [doi] AB - Genes reveal striking diversity within similar ice age cultures. FAU - Curry, Andrew AU - Curry A LA - eng PT - News DEP - 20230302 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - *Cultural Diversity MH - *DNA, Ancient MH - Europe MH - Humans EDAT- 2023/03/03 06:00 MHDA- 2023/03/07 06:00 CRDT- 2023/03/02 14:03 PHST- 2023/03/02 14:03 [entrez] PHST- 2023/03/03 06:00 [pubmed] PHST- 2023/03/07 06:00 [medline] AID - 10.1126/science.adh3912 [doi] PST - ppublish SO - Science. 2023 Mar 3;379(6635):865-866. doi: 10.1126/science.adh3912. Epub 2023 Mar 2. PMID- 36991187 OWN - NLM STAT- MEDLINE DCOM- 20230406 LR - 20240216 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 615 IP - 7954 DP - 2023 Mar TI - Entwined African and Asian genetic roots of medieval peoples of the Swahili coast. PG - 866-873 LID - 10.1038/s41586-023-05754-w [doi] AB - The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people(1,2). The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast(3). After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia(4). Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced. CI - © 2023. The Author(s). FAU - Brielle, Esther S AU - Brielle ES AUID- ORCID: 0000-0002-6114-0301 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. ebrielle@fas.harvard.edu. FAU - Fleisher, Jeffrey AU - Fleisher J AUID- ORCID: 0000-0002-6505-9666 AD - Department of Anthropology, Rice University, Houston, TX, USA. jfleisher@rice.edu. FAU - Wynne-Jones, Stephanie AU - Wynne-Jones S AUID- ORCID: 0000-0002-3005-8647 AD - Department of Archaeology, University of York, York, UK. stephanie.wynne-jones@york.ac.uk. AD - University of South Africa, Pretoria, South Africa. stephanie.wynne-jones@york.ac.uk. FAU - Sirak, Kendra AU - Sirak K AUID- ORCID: 0000-0003-2347-3479 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AUID- ORCID: 0000-0001-5350-1608 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Callan, Kim AU - Callan K AUID- ORCID: 0000-0003-3170-8514 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Curtis, Elizabeth AU - Curtis E AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Iliev, Lora AU - Iliev L AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Lawson, Ann Marie AU - Lawson AM AUID- ORCID: 0000-0003-0990-2329 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Qiu, Lijun AU - Qiu L AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Workman, J Noah AU - Workman JN AUID- ORCID: 0000-0002-0921-1803 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Zalzala, Fatma AU - Zalzala F AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Ayodo, George AU - Ayodo G AD - Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya. FAU - Gidna, Agness O AU - Gidna AO AD - National Museums of Tanzania, Dar es Salaam, Tanzania. FAU - Kabiru, Angela AU - Kabiru A AUID- ORCID: 0000-0001-5115-5414 AD - Department of Archaeology, National Museums of Kenya, Nairobi, Kenya. AD - British Institute of Eastern Africa, Nairobi, Kenya. FAU - Kwekason, Amandus AU - Kwekason A AD - National Museums of Tanzania, Dar es Salaam, Tanzania. FAU - Mabulla, Audax Z P AU - Mabulla AZP AD - Department of Archaeology and Heritage Studies, University of Dar es Salaam, Dar es Salaam, Tanzania. FAU - Manthi, Fredrick K AU - Manthi FK AD - Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya. FAU - Ndiema, Emmanuel AU - Ndiema E AD - Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya. FAU - Ogola, Christine AU - Ogola C AD - Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya. FAU - Sawchuk, Elizabeth AU - Sawchuk E AUID- ORCID: 0000-0003-4398-2174 AD - Cleveland Museum of Natural History, Cleveland, OH, USA. AD - Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada. AD - Department of Anthropology, Stony Brook University, Stony Brook, NY, USA. FAU - Al-Gazali, Lihadh AU - Al-Gazali L AD - Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates. FAU - Ali, Bassam R AU - Ali BR AUID- ORCID: 0000-0003-1306-6618 AD - Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates. FAU - Ben-Salem, Salma AU - Ben-Salem S AD - Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates. FAU - Letellier, Thierry AU - Letellier T AD - Laboratoire Evolution et Santé Orale, Faculté de Chirurgie Dentaire, Université Toulouse III-Paul Sabatier, Toulouse, France. FAU - Pierron, Denis AU - Pierron D AD - Laboratoire Evolution et Santé Orale, Faculté de Chirurgie Dentaire, Université Toulouse III-Paul Sabatier, Toulouse, France. FAU - Radimilahy, Chantal AU - Radimilahy C AD - Institut de Civilisations/Musée d'Art et d'Archéologie, Université d'Antananarivo, Antananarivo, Madagascar. FAU - Rakotoarisoa, Jean-Aimé AU - Rakotoarisoa JA AD - Institut de Civilisations/Musée d'Art et d'Archéologie, Université d'Antananarivo, Antananarivo, Madagascar. FAU - Raaum, Ryan L AU - Raaum RL AD - Department of Anthropology, Lehman College and The Graduate Center, The City University of New York, New York, NY, USA. AD - The New York Consortium in Evolutionary Primatology, New York, NY, USA. FAU - Culleton, Brendan J AU - Culleton BJ AD - Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Patterson, Nick AU - Patterson N AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAU - Mwenje, Mohammed Ali AU - Mwenje MA AUID- ORCID: 0000-0003-1364-0536 AD - National Museums of Kenya, Lamu Museums, Lamu, Kenya. FAU - Ahmed, Khalfan Bini AU - Ahmed KB AD - Coastal Archaeology, Gede National Monument, Gede, Kenya. FAU - Mohamed, Mohamed Mchulla AU - Mohamed MM AD - Coastal Archaeology, Fort Jesus Museum, Mombasa, Kenya. FAU - Williams, Sloan R AU - Williams SR AD - Department of Anthropology, University of Illinois at Chicago, Chicago, IL, USA. FAU - Monge, Janet AU - Monge J AD - University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA, USA. FAU - Kusimba, Sibel AU - Kusimba S AD - Department of Anthropology, University of South Florida, Tampa, FL, USA. FAU - Prendergast, Mary E AU - Prendergast ME AUID- ORCID: 0000-0003-0275-6795 AD - Department of Anthropology, Rice University, Houston, TX, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. reich@genetics.med.harvard.edu. FAU - Kusimba, Chapurukha M AU - Kusimba CM AUID- ORCID: 0000-0002-4374-3475 AD - Department of Archaeology, National Museums of Kenya, Nairobi, Kenya. ckusimba@usf.edu. AD - Department of Anthropology, University of South Florida, Tampa, FL, USA. ckusimba@usf.edu. AD - Institute of African Studies, University of Nairobi, Museum Hill, Nairobi, Kenya. ckusimba@usf.edu. LA - eng GR - R01 HG012287/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20230329 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) RN - Persian people RN - Arabian people SB - IM MH - DNA, Ancient/analysis MH - Male MH - *Genetics, Population MH - History, 16th Century MH - Arabs MH - India/ethnology MH - Mozambique MH - Middle Eastern People MH - *Asian/genetics MH - History, Medieval MH - Comoros MH - Female MH - History, 17th Century MH - History, 15th Century MH - Kenya MH - Indian Ocean MH - Arabia/ethnology MH - Humans MH - *African People/genetics MH - Tanzania MH - Persia/ethnology PMC - PMC10060156 COIS- The authors declare no competing interests. EDAT- 2023/03/30 06:00 MHDA- 2023/03/31 06:41 PMCR- 2023/03/29 CRDT- 2023/03/29 23:24 PHST- 2022/07/07 00:00 [received] PHST- 2023/01/24 00:00 [accepted] PHST- 2023/03/31 06:41 [medline] PHST- 2023/03/29 23:24 [entrez] PHST- 2023/03/30 06:00 [pubmed] PHST- 2023/03/29 00:00 [pmc-release] AID - 10.1038/s41586-023-05754-w [pii] AID - 5754 [pii] AID - 10.1038/s41586-023-05754-w [doi] PST - ppublish SO - Nature. 2023 Mar;615(7954):866-873. doi: 10.1038/s41586-023-05754-w. Epub 2023 Mar 29. PMID- 36669262 OWN - NLM STAT- MEDLINE DCOM- 20230209 LR - 20230209 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 63 DP - 2023 Mar TI - Kinship analysis of skeletal remains from the Middle Ages. PG - 102829 LID - S1872-4973(23)00004-2 [pii] LID - 10.1016/j.fsigen.2023.102829 [doi] AB - Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry. CI - Copyright © 2023 Elsevier B.V. All rights reserved. FAU - Dzehverovic, Mirela AU - Dzehverovic M AD - University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, Sarajevo, Bosnia and Herzegovina. FAU - Jusic, Belma AU - Jusic B AD - University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, Sarajevo, Bosnia and Herzegovina. Electronic address: belma.jusic@hotmail.com. FAU - Pilav, Amela AU - Pilav A AD - University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, Sarajevo, Bosnia and Herzegovina. FAU - Lukic, Tamara AU - Lukic T AD - Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, Sarajevo, Bosnia and Herzegovina. FAU - Cakar, Jasmina AU - Cakar J AD - University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, Sarajevo, Bosnia and Herzegovina. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230116 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (Genetic Markers) SB - IM MH - Humans MH - Male MH - *Body Remains MH - Chromosomes, Human, Y MH - *DNA Fingerprinting/methods MH - Family MH - Genetic Markers MH - Haplotypes MH - Microsatellite Repeats MH - History, Medieval OTO - NOTNLM OT - Ancient DNA OT - Archaeology OT - Medieval Bosnia OT - STR markers OT - Skeletal remains COIS- Conflict of Interest No potential conflict of interest was reported by authors. EDAT- 2023/01/21 06:00 MHDA- 2023/02/08 06:00 CRDT- 2023/01/20 18:05 PHST- 2022/06/30 00:00 [received] PHST- 2023/01/13 00:00 [revised] PHST- 2023/01/15 00:00 [accepted] PHST- 2023/01/21 06:00 [pubmed] PHST- 2023/02/08 06:00 [medline] PHST- 2023/01/20 18:05 [entrez] AID - S1872-4973(23)00004-2 [pii] AID - 10.1016/j.fsigen.2023.102829 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2023 Mar;63:102829. doi: 10.1016/j.fsigen.2023.102829. Epub 2023 Jan 16. PMID- 36348137 OWN - NLM STAT- MEDLINE DCOM- 20230316 LR - 20230519 IS - 1556-2891 (Electronic) IS - 1547-769X (Linking) VI - 19 IP - 1 DP - 2023 Mar TI - Application of natural sciences methodology in archaeological study of Iron Age burials in Latvia: pilot study. PG - 8-15 LID - 10.1007/s12024-022-00553-7 [doi] AB - Natural sciences provide several modern methodologies that could be successfully applied in archaeological studies. In this pilot study, archaeological human remains from two Iron Age cemeteries (7th-twelfth centuries AD), Lejasbitēni and Čunkāni-Dreņģeri, which are located in different regions of Latvia, were studied. We applied ancient DNA (aDNA) and tooth enamel peptide analysis to determine the biological sex of the individuals. In addition, aDNA analysis was used to perform mtDNA haplogroup analysis. In most cases, the results of aDNA analysis regarding the biological sex of individuals coincided with the gender assigned based on grave orientation and grave goods. The results of sex determination using peptide analysis in all four individuals for whom data were available matched the possible gender. Of the 17 samples that had sufficient DNA for sequencing, seven samples had enough reads to perform mtDNA haplogroup analysis. The H2a2a, I4a1, H2a2a1, and H16c mtDNA haplogroups were identified in the individuals from the Lejasbitēni cemetery, while the T2b and K1a + 150 mtDNA haplogroups were identified in the individuals from the Čunkāni-Dreņģeri cemetery. Overall, the obtained results demonstrated the feasibility of applying aDNA and tooth enamel peptide analysis for biological sex determination within archaeological studies. The availability of human aDNA data will be highly useful for investigating the demographic history and social structures in Iron Age Latvia. CI - © 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature. FAU - Kimsis, Janis AU - Kimsis J AD - Latvian Biomedical Research and Study Centre, Riga, Latvia. FAU - Petersone-Gordina, Elina AU - Petersone-Gordina E AD - Institute of Latvian History, University of Latvia, Riga, Latvia. FAU - Poksane, Alise AU - Poksane A AD - Latvian Biomedical Research and Study Centre, Riga, Latvia. FAU - Vilcāne, Antonija AU - Vilcāne A AD - Institute of Latvian History, University of Latvia, Riga, Latvia. FAU - Moore, Joanna AU - Moore J AD - Department of Archaeology, Durham University, Durham, UK. FAU - Gerhards, Guntis AU - Gerhards G AD - Institute of Latvian History, University of Latvia, Riga, Latvia. FAU - Ranka, Renate AU - Ranka R AUID- ORCID: 0000-0002-3716-7950 AD - Latvian Biomedical Research and Study Centre, Riga, Latvia. renate_r@biomed.lu.lv. LA - eng GR - lzp-2018/1-0395./Latvijas Zinātnes Padome/ PT - Journal Article DEP - 20221108 PL - United States TA - Forensic Sci Med Pathol JT - Forensic science, medicine, and pathology JID - 101236111 RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - Pilot Projects MH - Latvia MH - *Burial MH - *DNA, Mitochondrial/genetics MH - Cemeteries/history OTO - NOTNLM OT - Ancient DNA OT - Bioarcheology OT - Iron Age OT - Latvia OT - Mitochondrial DNA OT - Sex identification EDAT- 2022/11/09 06:00 MHDA- 2023/03/17 06:00 CRDT- 2022/11/08 23:41 PHST- 2022/10/26 00:00 [accepted] PHST- 2022/11/09 06:00 [pubmed] PHST- 2023/03/17 06:00 [medline] PHST- 2022/11/08 23:41 [entrez] AID - 10.1007/s12024-022-00553-7 [pii] AID - 10.1007/s12024-022-00553-7 [doi] PST - ppublish SO - Forensic Sci Med Pathol. 2023 Mar;19(1):8-15. doi: 10.1007/s12024-022-00553-7. Epub 2022 Nov 8. PMID- 36855115 OWN - NLM STAT- MEDLINE DCOM- 20230302 LR - 20240913 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 24 IP - 1 DP - 2023 Feb 28 TI - correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes. PG - 38 LID - 10.1186/s13059-023-02882-4 [doi] LID - 38 AB - Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×-11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data. CI - © 2023. The Author(s). FAU - Nyerki, Emil AU - Nyerki E AD - Department of Pediatrics, University of Szeged Albert Szent-Györgyi Medical Center Faculty of Medicine, Szeged, Hungary. AD - Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary. FAU - Kalmár, Tibor AU - Kalmár T AD - Department of Pediatrics, University of Szeged Albert Szent-Györgyi Medical Center Faculty of Medicine, Szeged, Hungary. FAU - Schütz, Oszkár AU - Schütz O AD - Department of Genetics, University of Szeged, Szeged, Hungary. FAU - Lima, Rui M AU - Lima RM AD - Institute of Plant Biology, Biological Research Centre, Szeged, Hungary. FAU - Neparáczki, Endre AU - Neparáczki E AD - Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary. AD - Department of Genetics, University of Szeged, Szeged, Hungary. FAU - Török, Tibor AU - Török T AD - Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary. AD - Department of Genetics, University of Szeged, Szeged, Hungary. FAU - Maróti, Zoltán AU - Maróti Z AUID- ORCID: 0000-0002-0515-117X AD - Department of Pediatrics, University of Szeged Albert Szent-Györgyi Medical Center Faculty of Medicine, Szeged, Hungary. maroti.zoltan@med.u-szeged.hu. AD - Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary. maroti.zoltan@med.u-szeged.hu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230228 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 SB - IM MH - Humans MH - *Genome, Human MH - *Forensic Medicine MH - Whole Genome Sequencing PMC - PMC9972692 OTO - NOTNLM OT - Ancient DNA OT - Forensic OT - Genomics OT - Kinship OT - Low coverage COIS- The authors declare that they have no competing interests. EDAT- 2023/03/02 06:00 MHDA- 2023/03/03 06:00 PMCR- 2023/02/28 CRDT- 2023/03/01 00:37 PHST- 2022/04/20 00:00 [received] PHST- 2023/02/17 00:00 [accepted] PHST- 2023/03/01 00:37 [entrez] PHST- 2023/03/02 06:00 [pubmed] PHST- 2023/03/03 06:00 [medline] PHST- 2023/02/28 00:00 [pmc-release] AID - 10.1186/s13059-023-02882-4 [pii] AID - 2882 [pii] AID - 10.1186/s13059-023-02882-4 [doi] PST - epublish SO - Genome Biol. 2023 Feb 28;24(1):38. doi: 10.1186/s13059-023-02882-4. PMID- 36821583 OWN - NLM STAT- MEDLINE DCOM- 20230227 LR - 20230330 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 120 IP - 9 DP - 2023 Feb 28 TI - Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data. PG - e2218375120 LID - 10.1073/pnas.2218375120 [doi] LID - e2218375120 AB - The recent increase in openly available ancient human DNA samples allows for large-scale meta-analysis applications. Trans-generational past human mobility is one of the key aspects that ancient genomics can contribute to since changes in genetic ancestry-unlike cultural changes seen in the archaeological record-necessarily reflect movements of people. Here, we present an algorithm for spatiotemporal mapping of genetic profiles, which allow for direct estimates of past human mobility from large ancient genomic datasets. The key idea of the method is to derive a spatial probability surface of genetic similarity for each individual in its respective past. This is achieved by first creating an interpolated ancestry field through space and time based on multivariate statistics and Gaussian process regression and then using this field to map the ancient individuals into space according to their genetic profile. We apply this algorithm to a dataset of 3138 aDNA samples with genome-wide data from Western Eurasia in the last 10,000 y. Finally, we condense this sample-wise record with a simple summary statistic into a diachronic measure of mobility for subregions in Western, Central, and Southern Europe. For regions and periods with sufficient data coverage, our similarity surfaces and mobility estimates show general concordance with previous results and provide a meta-perspective of genetic changes and human mobility. FAU - Schmid, Clemens AU - Schmid C AUID- ORCID: 0000-0003-3448-5715 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. AD - International Max Planck Research School for the Science of Human History, Max Planck Institute for Geoanthropology (formerly known as Max Planck Institute for the Science of Human History), Jena 07745, Germany. FAU - Schiffels, Stephan AU - Schiffels S AUID- ORCID: 0000-0002-1017-9150 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. LA - eng GR - 851511/EC | H2020 | PRIORITY 'Excellent science' | H2020 European Research Council (ERC)/ PT - Historical Article PT - Journal Article PT - Meta-Analysis PT - Research Support, Non-U.S. Gov't DEP - 20230223 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - History, Ancient MH - *Genomics MH - *DNA, Ancient/analysis MH - Europe PMC - PMC9992830 OTO - NOTNLM OT - Gaussian process regression OT - aDNA OT - mobility estimation OT - prehistory COIS- The authors declare no competing interest. EDAT- 2023/02/24 06:00 MHDA- 2023/03/03 06:00 PMCR- 2023/02/23 CRDT- 2023/02/23 13:43 PHST- 2023/02/23 13:43 [entrez] PHST- 2023/02/24 06:00 [pubmed] PHST- 2023/03/03 06:00 [medline] PHST- 2023/02/23 00:00 [pmc-release] AID - 202218375 [pii] AID - 10.1073/pnas.2218375120 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2023 Feb 28;120(9):e2218375120. doi: 10.1073/pnas.2218375120. Epub 2023 Feb 23. PMID- 36812179 OWN - NLM STAT- MEDLINE DCOM- 20230224 LR - 20230324 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 18 IP - 2 DP - 2023 TI - Cranial trephination and infectious disease in the Eastern Mediterranean: The evidence from two elite brothers from Late Bronze Megiddo, Israel. PG - e0281020 LID - 10.1371/journal.pone.0281020 [doi] LID - e0281020 AB - Here we present the paleopathological profiles of two young adult males, identified as brothers through ancient DNA analysis, who were buried together beneath the floor of an elite early Late Bronze Age I (ca. 1550-1450 BC) domestic structure at the urban center of Megiddo (modern Israel). Both individuals displayed uncommon morphological variants related to developmental conditions, and each exhibited extensive bone remodeling consistent with chronic infectious disease. Additionally, one brother had a healed fracture of the nose, as well as a large square piece of bone cut from the frontal bone (cranial trephination). We consider the potential etiologies for the appearance of the skeletal anomalies and lesions. Based on the bioarchaeological context, we propose that a shared epigenetic landscape predisposed the brothers to acquiring an infectious disease and their elite status privileged them enough to endure it. We then contextualize these potential illnesses and disorders with the trephination procedure. The infrequency of trephination in the region indicates that only selected individuals could access such a procedure, and the severity of the pathological lesions suggests the procedure was possibly intended as curative to deteriorating health. Ultimately, both brothers were buried with the same rites as others in their community, thus demonstrating their continued integration in society even after death. CI - Copyright: © 2023 Kalisher et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. FAU - Kalisher, Rachel AU - Kalisher R AUID- ORCID: 0000-0002-7765-2352 AD - Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, Rhode Island, United States of America. FAU - Cradic, Melissa S AU - Cradic MS AD - Department of History, University at Albany, State University of New York, Albany, New York, United States of America. FAU - Adams, Matthew J AU - Adams MJ AUID- ORCID: 0000-0001-9447-6277 AD - W.F. Albright Institute for Archaeological Research, Jerusalem, Israel. FAU - Martin, Mario A S AU - Martin MAS AD - Leon Recanati Institute for Maritime Studies, University of Haifa, Haifa, Israel. AD - Institute of Ancient History and Ancient Near Eastern Studies, University of Innsbruck, Vienna, Austria. FAU - Finkelstein, Israel AU - Finkelstein I AD - School of Archaeology and Maritime Cultures, University of Haifa, Haifa, Israel. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230222 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) SB - IM MH - Male MH - Young Adult MH - Humans MH - History, Ancient MH - Israel MH - *Trephining MH - Siblings MH - DNA, Ancient MH - *Communicable Diseases PMC - PMC9946252 COIS- The authors have declared that no competing interests exist. EDAT- 2023/02/23 06:00 MHDA- 2023/02/25 06:00 PMCR- 2023/02/22 CRDT- 2023/02/22 16:20 PHST- 2022/06/12 00:00 [received] PHST- 2023/01/12 00:00 [accepted] PHST- 2023/02/22 16:20 [entrez] PHST- 2023/02/23 06:00 [pubmed] PHST- 2023/02/25 06:00 [medline] PHST- 2023/02/22 00:00 [pmc-release] AID - PONE-D-22-16903 [pii] AID - 10.1371/journal.pone.0281020 [doi] PST - epublish SO - PLoS One. 2023 Feb 22;18(2):e0281020. doi: 10.1371/journal.pone.0281020. eCollection 2023. PMID- 36833406 OWN - NLM STAT- MEDLINE DCOM- 20230301 LR - 20231117 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 14 IP - 2 DP - 2023 Feb 14 TI - Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. LID - 10.3390/genes14020479 [doi] LID - 479 AB - Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field. FAU - Dalal, Vasundhra AU - Dalal V AUID- ORCID: 0000-0002-8980-7497 AD - Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India. FAU - Pasupuleti, Nagarjuna AU - Pasupuleti N AUID- ORCID: 0000-0002-1886-4400 AD - Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India. FAU - Chaubey, Gyaneshwer AU - Chaubey G AUID- ORCID: 0000-0003-2899-3852 AD - Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India. FAU - Rai, Niraj AU - Rai N AUID- ORCID: 0000-0002-1251-9390 AD - Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India. FAU - Shinde, Vasant AU - Shinde V AUID- ORCID: 0000-0001-7070-9830 AD - Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20230214 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - *Evolution, Molecular MH - *Human Migration PMC - PMC9956214 OTO - NOTNLM OT - adaptation OT - ancient DNA OT - archaeogenetics OT - evolution OT - migration COIS- The authors declare no conflict of interest. EDAT- 2023/02/26 06:00 MHDA- 2023/03/03 06:00 PMCR- 2023/02/14 CRDT- 2023/02/25 02:16 PHST- 2023/01/11 00:00 [received] PHST- 2023/02/02 00:00 [revised] PHST- 2023/02/08 00:00 [accepted] PHST- 2023/02/25 02:16 [entrez] PHST- 2023/02/26 06:00 [pubmed] PHST- 2023/03/03 06:00 [medline] PHST- 2023/02/14 00:00 [pmc-release] AID - genes14020479 [pii] AID - genes-14-00479 [pii] AID - 10.3390/genes14020479 [doi] PST - epublish SO - Genes (Basel). 2023 Feb 14;14(2):479. doi: 10.3390/genes14020479. PMID- 36747166 OWN - NLM STAT- MEDLINE DCOM- 20230208 LR - 20231102 IS - 1741-7007 (Electronic) IS - 1741-7007 (Linking) VI - 21 IP - 1 DP - 2023 Feb 7 TI - A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland. PG - 9 LID - 10.1186/s12915-022-01509-7 [doi] LID - 9 AB - BACKGROUND: In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case. RESULTS: Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations. CONCLUSIONS: The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly. CI - © 2023. The Author(s). FAU - Sarhan, Mohamed S AU - Sarhan MS AUID- ORCID: 0000-0003-0904-976X AD - Eurac Research - Institute for Mummy Studies, 39100, Bolzano, Italy. mohamed.sarhan@eurac.edu. FAU - Wurst, Christina AU - Wurst C AD - Eurac Research - Institute for Mummy Studies, 39100, Bolzano, Italy. FAU - Tzankov, Alexandar AU - Tzankov A AD - Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031, Basel, Switzerland. FAU - Bircher, Andreas J AU - Bircher AJ AD - Department of Allergology, University Hospital Basel, 4031, Basel, Switzerland. AD - Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland. FAU - Wittig, Holger AU - Wittig H AD - Department of Biomedical Engineering, Institute of Forensic Medicine, University of Basel, 4056, Basel, Switzerland. FAU - Briellmann, Thomas AU - Briellmann T AD - Citizen Science Basel; formerly Institute of Forensic Medicine, Forensic Chemistry and Toxicology, University of Basel, 4056, Basel, Switzerland. FAU - Augsburger, Marc AU - Augsburger M AD - University Center of Legal Medicine, Lausanne, Geneva, Switzerland. FAU - Hotz, Gerhard AU - Hotz G AD - Natural History Museum Basel, 4051, Basel, Switzerland. AD - Integrative Prehistory and Archaeological Science, University of Basel, 4056, Basel, Switzerland. FAU - Zink, Albert AU - Zink A AD - Eurac Research - Institute for Mummy Studies, 39100, Bolzano, Italy. FAU - Maixner, Frank AU - Maixner F AD - Eurac Research - Institute for Mummy Studies, 39100, Bolzano, Italy. frank.maixner@eurac.edu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230207 PL - England TA - BMC Biol JT - BMC biology JID - 101190720 SB - IM MH - Humans MH - Female MH - Aged MH - Nontuberculous Mycobacteria/genetics MH - *Mycobacterium Infections, Nontuberculous/diagnosis/epidemiology/microbiology MH - Switzerland MH - *Syphilis MH - Virulence PMC - PMC9903526 OTO - NOTNLM OT - Ancient DNA (aDNA) OT - Anna Catharina Bischoff (ACB) OT - Bacteriophage OT - Brain infections OT - De novo assembly OT - Franciscan church mummy OT - Mycobacteriosis OT - Nontuberculous mycobacteria (NTM) OT - Syphilis COIS- The authors declare no competing interests. EDAT- 2023/02/08 06:00 MHDA- 2023/02/09 06:00 PMCR- 2023/02/07 CRDT- 2023/02/07 00:11 PHST- 2022/03/07 00:00 [received] PHST- 2022/12/15 00:00 [accepted] PHST- 2023/02/07 00:11 [entrez] PHST- 2023/02/08 06:00 [pubmed] PHST- 2023/02/09 06:00 [medline] PHST- 2023/02/07 00:00 [pmc-release] AID - 10.1186/s12915-022-01509-7 [pii] AID - 1509 [pii] AID - 10.1186/s12915-022-01509-7 [doi] PST - epublish SO - BMC Biol. 2023 Feb 7;21(1):9. doi: 10.1186/s12915-022-01509-7. PMID- 36638796 OWN - NLM STAT- MEDLINE DCOM- 20230209 LR - 20230319 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 33 IP - 3 DP - 2023 Feb 6 TI - Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia. PG - 423-433.e5 LID - S0960-9822(22)01892-9 [pii] LID - 10.1016/j.cub.2022.11.062 [doi] AB - The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward. CI - Copyright © 2022 Elsevier Inc. All rights reserved. FAU - Wang, Ke AU - Wang K AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany; Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Songhu Rd. 2005, Shanghai 200433, China. Electronic address: ke_wang@fudan.edu.cn. FAU - Yu, He AU - Yu H AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Yiheyuan Rd. 5, Beijing 100871, China. FAU - Radzevičiūtė, Rita AU - Radzevičiūtė R AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany. FAU - Kiryushin, Yuriy F AU - Kiryushin YF AD - Department of Archaeology, Ethnography and Museology, Altai State University, pr. Lenina 61, Barnaul 656049, Russia. FAU - Tishkin, Alexey A AU - Tishkin AA AD - Department of Archaeology, Ethnography and Museology, Altai State University, pr. Lenina 61, Barnaul 656049, Russia. FAU - Frolov, Yaroslav V AU - Frolov YV AD - Department of Archaeology, Ethnography and Museology, Altai State University, pr. Lenina 61, Barnaul 656049, Russia. FAU - Stepanova, Nadezhda F AU - Stepanova NF AD - Laboratory of Archaeology and Ethnography of South Siberia, Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Acad. Lavrentiev Avenue 17, Novosibirsk 630090, Russia. FAU - Kiryushin, Kirill Yu AU - Kiryushin KY AD - Department of Recreational Geography, Service, Tourism and Hospitality, Institute of Geography, Altai State University, pr. Lenina 61, Barnaul 656049, Russia. FAU - Kungurov, Artur L AU - Kungurov AL AD - Altai State Museum of Regional Studies, ul. Polzunova 46, Barnaul 656049, Russia. FAU - Shnaider, Svetlana V AU - Shnaider SV AD - Archaeozoology in Siberia and Central Asia - ZooSCAn, CNRS - IAET SB RAS International Research Laboratory, IRL 2013, Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Acad. Lavrentiev Avenue 17, Novosibirsk 630090, Russia. FAU - Tur, Svetlana S AU - Tur SS AD - Department of Archaeology, Ethnography and Museology, Altai State University, pr. Lenina 61, Barnaul 656049, Russia. FAU - Tiunov, Mikhail P AU - Tiunov MP AD - Federal Science Center of East Asian Terrestrial Biodiversity, Far East Branch, Russian Academy of Sciences, Pr-t 100-let Vladivostoka 159, Vladivostok 690022, Russia. FAU - Zubova, Alisa V AU - Zubova AV AD - Department of Anthropology, Peter the Great Museum of Anthropology and Ethnography (the Kunstkamera), Russian Acxademy of Sciences, Universitetskaya Naberezhnaya 3, St. Petersburg 199034, Russia; North-East Interdisciplinary Scientific Research Institute of Far East Branch of the Russian Academy of Sciences, Portovaya Street 16, Magadan 685000, Russia. FAU - Pevzner, Maria AU - Pevzner M AD - Laboratory for Isotope Geochemistry and Geochronology, Geological Institute of RAS, Pyzhevsky Iane 7, Moscow 119017, Russia. FAU - Karimov, Timur AU - Karimov T AD - D-REAMS Laboratory, Weizmann Institute of Science, Herzl Street 234, Rehovot 7610001, Israel. FAU - Buzhilova, Alexandra AU - Buzhilova A AD - Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Mokhovaya 11, Moscow 125009, Russia. FAU - Slon, Viviane AU - Slon V AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany; Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, P.O.B 39040 Ramat Aviv, Tel Aviv 6997801, Israel; The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, 12 Klausner St., Tel Aviv 6997801, Israel. FAU - Jeong, Choongwon AU - Jeong C AD - School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany. Electronic address: krause@eva.mpg.de. FAU - Posth, Cosimo AU - Posth C AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany; Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Hölderlinstr. 12, Tübingen 72074, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Hölderlinstr. 12, Tübingen 72074, Germany. Electronic address: cosimo.posth@uni-tuebingen.de. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230112 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Humans MH - History, Ancient MH - Infant, Newborn MH - *Gene Pool MH - *Genome, Human MH - Asia MH - Russia MH - Siberia MH - Human Migration MH - Genetics, Population OTO - NOTNLM OT - Altai OT - Kamchatka peninsula OT - Middle Holocene OT - Neolithic OT - North Asia OT - Russian Far East OT - ancient DNA OT - genomic history OT - hunter-gatherers OT - population genetics COIS- Declaration of interests The authors declare no competing interests. EDAT- 2023/01/14 06:00 MHDA- 2023/02/10 06:00 CRDT- 2023/01/13 18:42 PHST- 2022/09/07 00:00 [received] PHST- 2022/11/15 00:00 [revised] PHST- 2022/11/28 00:00 [accepted] PHST- 2023/01/14 06:00 [pubmed] PHST- 2023/02/10 06:00 [medline] PHST- 2023/01/13 18:42 [entrez] AID - S0960-9822(22)01892-9 [pii] AID - 10.1016/j.cub.2022.11.062 [doi] PST - ppublish SO - Curr Biol. 2023 Feb 6;33(3):423-433.e5. doi: 10.1016/j.cub.2022.11.062. Epub 2023 Jan 12. PMID- 37431939 OWN - NLM STAT- MEDLINE DCOM- 20230712 LR - 20230718 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 50 IP - 1 DP - 2023 Feb TI - Diversity in matrilineages among the Jomon individuals of Japan. PG - 324-331 LID - 10.1080/03014460.2023.2224060 [doi] AB - BACKGROUND: The Jomon period of Japan is characterised by a unique combination of sedentary and hunting/gathering lifestyles, spanning for more than 10,000 years from the final Pleistocene to the Holocene. The transition from the preceding Palaeolithic period to the Jomon period is known to have begun with the appearance of pottery usage. However, knowledge of the genetic background of the Jomon people is still limited. AIM: We aimed to determine the population-scale complete mitogenome sequences of the Initial Jomon human remains and compare the occurrence of mitochondrial haplogroups in the Jomon period from temporal and regional perspectives. SUBJECTS AND METHODS: For human remains dated to 8200-8600 cal BP, we determined their complete mitogenome sequences using target enrichment-coupled next-generation sequencing. RESULTS: We successfully obtained the complete mitogenome sequences with high depth of coverage and high concordance on consensus sequences. These sequences differed by more than three bases each, except for two individuals having completely identical sequences. Co-existence of individuals with haplogroups N9b and M7a was first observed at the same archaeological site from the Initial Jomon period. CONCLUSION: The genetic diversity within the population was not found to be low even in the Initial Jomon period. FAU - Mizuno, Fuzuki AU - Mizuno F AD - Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan. FAU - Taniguchi, Yasuhiro AU - Taniguchi Y AD - Department of Archaeology, Faculty of Letters, Kokugakuin University, Tokyo, Japan. FAU - Kondo, Osamu AU - Kondo O AD - Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. FAU - Hayashi, Michiko AU - Hayashi M AD - Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan. FAU - Kurosaki, Kunihiko AU - Kurosaki K AD - Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan. FAU - Ueda, Shintaroh AU - Ueda S AD - Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan. AD - Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. LA - eng PT - Journal Article PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 SB - IM MH - Humans MH - Japan MH - *Body Remains MH - *Archaeology MH - High-Throughput Nucleotide Sequencing MH - Knowledge OTO - NOTNLM OT - Jomon period OT - ancient DNA OT - haplogroup M7a OT - haplogroup N9b; OT - mitochondrial genome EDAT- 2023/07/11 13:10 MHDA- 2023/07/12 06:42 CRDT- 2023/07/11 08:04 PHST- 2023/07/12 06:42 [medline] PHST- 2023/07/11 13:10 [pubmed] PHST- 2023/07/11 08:04 [entrez] AID - 10.1080/03014460.2023.2224060 [doi] PST - ppublish SO - Ann Hum Biol. 2023 Feb;50(1):324-331. doi: 10.1080/03014460.2023.2224060. PMID- 36646948 OWN - NLM STAT- MEDLINE DCOM- 20230213 LR - 20240820 IS - 2397-334X (Electronic) IS - 2397-334X (Linking) VI - 7 IP - 2 DP - 2023 Feb TI - Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean. PG - 290-303 LID - 10.1038/s41559-022-01952-3 [doi] AB - The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe's prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by 'eastern' gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries BC, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices. CI - © 2023. The Author(s). FAU - Skourtanioti, Eirini AU - Skourtanioti E AUID- ORCID: 0000-0003-2975-3869 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. eirini_skourtanioti@eva.mpg.de. AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. eirini_skourtanioti@eva.mpg.de. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. eirini_skourtanioti@eva.mpg.de. FAU - Ringbauer, Harald AU - Ringbauer H AUID- ORCID: 0000-0002-4884-9682 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. FAU - Gnecchi Ruscone, Guido Alberto AU - Gnecchi Ruscone GA AUID- ORCID: 0000-0002-6490-8101 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Bianco, Raffaela Angelina AU - Bianco RA AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Burri, Marta AU - Burri M AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Freund, Cäcilia AU - Freund C AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Furtwängler, Anja AU - Furtwängler A AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Gomes Martins, Nuno Filipe AU - Gomes Martins NF AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Knolle, Florian AU - Knolle F AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Neumann, Gunnar U AU - Neumann GU AUID- ORCID: 0000-0003-3825-8536 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Tiliakou, Anthi AU - Tiliakou A AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Agelarakis, Anagnostis AU - Agelarakis A AD - Department of History, Adelphi University, New York, NY, USA. FAU - Andreadaki-Vlazaki, Maria AU - Andreadaki-Vlazaki M AD - Ephorate of Antiquities of Chania, Hellenic Ministry of Culture and Sports, Chania, Greece. FAU - Betancourt, Philip AU - Betancourt P AD - Institute for Aegean Prehistory, Temple University, Philadelphia, PA, USA. FAU - Hallager, Birgitta P AU - Hallager BP AD - Danish Institute at Athens, Athens, Greece. FAU - Jones, Olivia A AU - Jones OA AUID- ORCID: 0000-0002-7191-5449 AD - Department of Sociology and Anthropology, West Virginia University, Morgantown, WV, USA. FAU - Kakavogianni, Olga AU - Kakavogianni O AD - Ephorate of Antiquities of East Attica, Hellenic Ministry of Culture and Sports, Athens, Greece. FAU - Kanta, Athanasia AU - Kanta A AD - Antiquities for the Heraklion Prefecture (Director Emerita), Hellenic Ministry of Culture and Sports, Heraklion, Greece. FAU - Karkanas, Panagiotis AU - Karkanas P AD - Malcolm H. Wiener Laboratory for Archaeological Science, American School of Classical Studies at Athens, Athens, Greece. FAU - Kataki, Efthymia AU - Kataki E AD - Ephorate of Antiquities of Chania, Hellenic Ministry of Culture and Sports, Chania, Greece. FAU - Kissas, Konstantinos AU - Kissas K AD - Ephorate of Antiquities of Arcadia, Hellenic Ministry of Culture and Sports, Tripoli, Greece. FAU - Koehl, Robert AU - Koehl R AD - Classical and Oriental Studies, Hunter College, New York, NY, USA. FAU - Kvapil, Lynne AU - Kvapil L AD - Department of History, Anthropology, and Classics, Butler University, Indianapolis, IN, USA. FAU - Maran, Joseph AU - Maran J AD - Institute for Prehistory, Protohistory and Near Eastern Archaeology, University of Heidelberg, Heidelberg, Germany. FAU - McGeorge, Photini J P AU - McGeorge PJP AD - British School at Athens, Athens, Greece. FAU - Papadimitriou, Alkestis AU - Papadimitriou A AD - Ephorate of Antiquities of Argolida, Hellenic Ministry of Culture and Sports, Nafplio, Greece. FAU - Papathanasiou, Anastasia AU - Papathanasiou A AD - Ephorate of Palaeoanthropology and Speleology, Hellenic Ministry of Culture and Sports, Athens, Greece. FAU - Papazoglou-Manioudaki, Lena AU - Papazoglou-Manioudaki L AD - National Archaeological Museum, Athens, Greece. FAU - Paschalidis, Kostas AU - Paschalidis K AD - National Archaeological Museum, Athens, Greece. FAU - Polychronakou-Sgouritsa, Naya AU - Polychronakou-Sgouritsa N AD - Department of Archaeology and History of Art, University of Athens, Athens, Greece. FAU - Preve, Sofia AU - Preve S AD - Ephorate of Antiquities of Chania, Hellenic Ministry of Culture and Sports, Chania, Greece. FAU - Prevedorou, Eleni-Anna AU - Prevedorou EA AD - Malcolm H. Wiener Laboratory for Archaeological Science, American School of Classical Studies at Athens, Athens, Greece. AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. FAU - Price, Gypsy AU - Price G AD - SEARCH, Inc., Cornelius, NC, USA. FAU - Protopapadaki, Eftychia AU - Protopapadaki E AD - Ephorate of Antiquities of Chania, Hellenic Ministry of Culture and Sports, Chania, Greece. FAU - Schmidt-Schultz, Tyede AU - Schmidt-Schultz T AD - Center of Anatomy, University of Göttingen, Göttingen, Germany. FAU - Schultz, Michael AU - Schultz M AD - Center of Anatomy, University of Göttingen, Göttingen, Germany. AD - Department of Biology, University of Hildesheim, Hildesheim, Germany. FAU - Shelton, Kim AU - Shelton K AD - Department of Ancient Greek and Roman Studies, University of California, Berkeley, CA, USA. FAU - Wiener, Malcolm H AU - Wiener MH AD - Institute for Aegean Prehistory, Greenwich, CT, USA. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. krause@eva.mpg.de. AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. krause@eva.mpg.de. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. krause@eva.mpg.de. FAU - Jeong, Choongwon AU - Jeong C AUID- ORCID: 0000-0003-3049-2352 AD - School of Biological Sciences, Seoul National University, Seoul, Republic of Korea. pajuccw@gmail.com. FAU - Stockhammer, Philipp W AU - Stockhammer PW AUID- ORCID: 0000-0003-4702-9372 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. philipp.stockhammer@lmu.de. AD - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Leipzig, Germany. philipp.stockhammer@lmu.de. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. philipp.stockhammer@lmu.de. AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Germany. philipp.stockhammer@lmu.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230116 PL - England TA - Nat Ecol Evol JT - Nature ecology & evolution JID - 101698577 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - *Human Migration/history MH - Europe MH - Greece MH - Genome PMC - PMC9911347 COIS- The authors declare no competing interests. EDAT- 2023/01/17 06:00 MHDA- 2023/02/14 06:00 PMCR- 2023/01/16 CRDT- 2023/01/16 23:25 PHST- 2022/05/15 00:00 [received] PHST- 2022/11/11 00:00 [accepted] PHST- 2023/01/17 06:00 [pubmed] PHST- 2023/02/14 06:00 [medline] PHST- 2023/01/16 23:25 [entrez] PHST- 2023/01/16 00:00 [pmc-release] AID - 10.1038/s41559-022-01952-3 [pii] AID - 1952 [pii] AID - 10.1038/s41559-022-01952-3 [doi] PST - ppublish SO - Nat Ecol Evol. 2023 Feb;7(2):290-303. doi: 10.1038/s41559-022-01952-3. Epub 2023 Jan 16. PMID- 36721228 OWN - NLM STAT- MEDLINE DCOM- 20230202 LR - 20230330 IS - 1479-7364 (Electronic) IS - 1473-9542 (Print) IS - 1473-9542 (Linking) VI - 17 IP - 1 DP - 2023 Jan 31 TI - Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China. PG - 3 LID - 10.1186/s40246-023-00452-0 [doi] LID - 3 AB - BACKGROUND: Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized. OBJECTIVES: To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling. RESULTS: The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways. CONCLUSIONS: Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people. CI - © 2023. The Author(s). FAU - He, Guanglin AU - He G AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China. guanglinhescu@163.com. FAU - Wang, Jiawen AU - Wang J AD - College of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China. FAU - Yang, Lin AU - Yang L AD - College of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China. FAU - Duan, Shuhan AU - Duan S AD - School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China. FAU - Sun, Qiuxia AU - Sun Q AD - Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China. FAU - Li, Youjing AU - Li Y AD - Congjiang People's Hospital, Congjiang, 557499, China. FAU - Wu, Jun AU - Wu J AD - College of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China. FAU - Wu, Wenxin AU - Wu W AD - College of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China. FAU - Wang, Zheng AU - Wang Z AD - Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610000, China. FAU - Liu, Yan AU - Liu Y AD - Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China. AD - School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China. FAU - Tang, Renkuan AU - Tang R AD - Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China. FAU - Yang, Junbao AU - Yang J AD - School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China. FAU - Liu, Chao AU - Liu C AD - Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China. FAU - Yuan, Buhong AU - Yuan B AD - Longli People's Hospital, Longli, 551299, China. FAU - Wang, Daoyong AU - Wang D AD - Nayong Guohua Yixin Hospital, Nayong, 553306, China. FAU - Xu, Jianwei AU - Xu J AD - Department of Pharmacology, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China. 363912577@qq.com. FAU - Wang, Mengge AU - Wang M AD - Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China. menggewang2021@163.com. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230131 PL - England TA - Hum Genomics JT - Human genomics JID - 101202210 SB - IM EIN - Hum Genomics. 2023 Mar 30;17(1):32. doi: 10.1186/s40246-023-00477-5. PMID: 36998088 MH - Humans MH - Haplotypes/genetics MH - Alleles MH - China MH - *Asian People/genetics MH - *Adaptation, Biological PMC - PMC9887792 OTO - NOTNLM OT - Admixture model OT - Biological adaptation OT - Evolutionary history OT - Genetic structure OT - Miao COIS- The authors declare that they have no competing interests. EDAT- 2023/02/02 06:00 MHDA- 2023/02/03 06:00 PMCR- 2023/01/31 CRDT- 2023/02/01 00:10 PHST- 2022/10/18 00:00 [received] PHST- 2023/01/22 00:00 [accepted] PHST- 2023/02/01 00:10 [entrez] PHST- 2023/02/02 06:00 [pubmed] PHST- 2023/02/03 06:00 [medline] PHST- 2023/01/31 00:00 [pmc-release] AID - 10.1186/s40246-023-00452-0 [pii] AID - 452 [pii] AID - 10.1186/s40246-023-00452-0 [doi] PST - epublish SO - Hum Genomics. 2023 Jan 31;17(1):3. doi: 10.1186/s40246-023-00452-0. PMID- 37065506 OWN - NLM STAT- MEDLINE DCOM- 20230419 LR - 20230421 IS - 2046-1402 (Electronic) IS - 2046-1402 (Linking) VI - 12 DP - 2023 TI - Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases. PG - 109 LID - 10.12688/f1000research.129036.2 [doi] LID - 109 AB - Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research. CI - Copyright: © 2023 Gancz AS and Weyrich LS. FAU - Gancz, Abigail S AU - Gancz AS AUID- ORCID: 0000-0003-3865-4563 AD - Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA. FAU - Weyrich, Laura S AU - Weyrich LS AD - Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA. AD - School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia. AD - Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA. LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review DEP - 20230130 PL - England TA - F1000Res JT - F1000Research JID - 101594320 SB - IM MH - Humans MH - *Noncommunicable Diseases/epidemiology MH - *Microbiota/genetics MH - *Diabetes Mellitus/epidemiology MH - Diet MH - Prevalence PMC - PMC10090864 OTO - NOTNLM OT - NCDs OT - ancient health OT - dental calculus OT - frailty OT - oral microbiomes COIS- No competing interests were disclosed. EDAT- 2023/04/19 06:00 MHDA- 2023/04/19 06:41 PMCR- 2023/04/06 CRDT- 2023/04/18 01:43 PHST- 2023/04/05 00:00 [accepted] PHST- 2023/04/19 06:41 [medline] PHST- 2023/04/18 01:43 [entrez] PHST- 2023/04/19 06:00 [pubmed] PHST- 2023/04/06 00:00 [pmc-release] AID - 10.12688/f1000research.129036.2 [doi] PST - epublish SO - F1000Res. 2023 Jan 30;12:109. doi: 10.12688/f1000research.129036.2. eCollection 2023. PMID- 36833230 OWN - NLM STAT- MEDLINE DCOM- 20230228 LR - 20230306 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 14 IP - 2 DP - 2023 Jan 24 TI - Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review. LID - 10.3390/genes14020303 [doi] LID - 303 AB - Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed. FAU - Wiscovitch-Russo, Rosana A AU - Wiscovitch-Russo RA AD - J. Craig Venter Institute, Rockville, MD 20850, USA. FAU - Santiago-Rodriguez, Tasha M AU - Santiago-Rodriguez TM AD - Diversigen, Inc., New Brighton, MN 55112, USA. FAU - Toranzos, Gary A AU - Toranzos GA AD - Environmental Microbiology Laboratory, Department of Biology, University of Puerto Rico, San Juan, PR 00925, USA. LA - eng PT - Journal Article PT - Review DEP - 20230124 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 SB - IM MH - Animals MH - Humans MH - *Parasites MH - *Parasitic Diseases/parasitology MH - Paleopathology/methods MH - Diet MH - Life Style PMC - PMC9957072 OTO - NOTNLM OT - ancient DNA OT - paleoparasitology OT - paleopathology OT - parasites COIS- R.A.W.-R. and G.A.T. declare no conflict of interest. T.M.S.-R. is a current Diversigen employee, a microbiome services company. EDAT- 2023/02/26 06:00 MHDA- 2023/03/03 06:00 PMCR- 2023/01/24 CRDT- 2023/02/25 02:12 PHST- 2022/12/07 00:00 [received] PHST- 2023/01/18 00:00 [revised] PHST- 2023/01/21 00:00 [accepted] PHST- 2023/02/25 02:12 [entrez] PHST- 2023/02/26 06:00 [pubmed] PHST- 2023/03/03 06:00 [medline] PHST- 2023/01/24 00:00 [pmc-release] AID - genes14020303 [pii] AID - genes-14-00303 [pii] AID - 10.3390/genes14020303 [doi] PST - epublish SO - Genes (Basel). 2023 Jan 24;14(2):303. doi: 10.3390/genes14020303. PMID- 36649412 OWN - NLM STAT- MEDLINE DCOM- 20230119 LR - 20230718 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 120 IP - 4 DP - 2023 Jan 24 TI - Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant. PG - e2210611120 LID - 10.1073/pnas.2210611120 [doi] LID - e2210611120 AB - Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a "revolutionary" social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevalı Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevalı Çori together with newly generated radiocarbon dates. Our results are based on strontium ((87)Sr/(86)Sr), carbon, and oxygen (δ(18)O and δ(13)C(carb)) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevalı Çori. (87)Sr/(86)Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevalı Çori and Ba'ja demonstrate a diverse gene pool at Nevalı Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevalı Çori. FAU - Wang, Xiaoran AU - Wang X AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, 80799 Munich, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Skourtanioti, Eirini AU - Skourtanioti E AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Benz, Marion AU - Benz M AUID- ORCID: 0000-0002-7810-1165 AD - Institute of Near Eastern Archaeology, and ex oriente at Free University Berlin, 14195 Berlin, Germany. FAU - Gresky, Julia AU - Gresky J AUID- ORCID: 0000-0003-3493-2757 AD - German Archaeological Institute, Division of Natural Sciences/Central, 14195 Berlin, Germany. FAU - Ilgner, Jana AU - Ilgner J AUID- ORCID: 0000-0001-7210-8625 AD - Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany. FAU - Lucas, Mary AU - Lucas M AUID- ORCID: 0000-0002-6394-0345 AD - Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany. FAU - Morsch, Michael AU - Morsch M AUID- ORCID: 0000-0001-9715-2825 AD - Institute for Prehistory, Protohistory and Near Eastern Archaeology, University of Heidelberg, 69117 Heidelberg, Germany. FAU - Peters, Joris AU - Peters J AUID- ORCID: 0000-0003-0894-2628 AD - ArchaeoBioCenter, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig Maximilian University, 80539 Munich, Germany. AD - Bavarian State Collection for Palaeoanatomy, 80333 Munich, Germany. FAU - Pöllath, Nadja AU - Pöllath N AD - Bavarian State Collection for Palaeoanatomy, 80333 Munich, Germany. FAU - Ringbauer, Harald AU - Ringbauer H AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - le Roux, Petrus AU - le Roux P AUID- ORCID: 0000-0002-5930-4995 AD - Department of Geological Sciences, University of Cape Town, 7701 Rondebosch, South Africa. FAU - Schultz, Michael AU - Schultz M AUID- ORCID: 0000-0001-5028-2497 AD - Department of Anatomy, University of Göttingen, 37073 Göttingen, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Roberts, Patrick AU - Roberts P AUID- ORCID: 0000-0002-4403-7548 AD - Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany. AD - isoTROPIC Research Group, Max Planck Institute for Geoanthropology, 07745 Jena, Germany. FAU - Stockhammer, Philipp W AU - Stockhammer PW AUID- ORCID: 0000-0003-4702-9372 AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, 80799 Munich, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230117 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 7440-44-0 (Carbon) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Humans MH - History, Ancient MH - Turkey MH - Jordan MH - *Domestication MH - *Carbon MH - Archaeology MH - DNA PMC - PMC9942848 OTO - NOTNLM OT - 87Sr/86Sr OT - Near East OT - Neolithization OT - ancient DNA OT - δ18O and δ13C isotopes COIS- The authors declare no competing interest. EDAT- 2023/01/18 06:00 MHDA- 2023/01/20 06:00 PMCR- 2023/07/17 CRDT- 2023/01/17 14:03 PHST- 2023/01/17 14:03 [entrez] PHST- 2023/01/18 06:00 [pubmed] PHST- 2023/01/20 06:00 [medline] PHST- 2023/07/17 00:00 [pmc-release] AID - 202210611 [pii] AID - 10.1073/pnas.2210611120 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2023 Jan 24;120(4):e2210611120. doi: 10.1073/pnas.2210611120. Epub 2023 Jan 17. PMID- 36649410 OWN - NLM STAT- MEDLINE DCOM- 20230119 LR - 20230305 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 120 IP - 4 DP - 2023 Jan 24 TI - Ancient pathogens provide a window into health and well-being. PG - e2209476119 LID - 10.1073/pnas.2209476119 [doi] LID - e2209476119 AB - This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens. FAU - Lewis, Cecil M Jr AU - Lewis CM Jr AUID- ORCID: 0000-0002-2198-3427 AD - Department of Anthropology, University of Oklahoma, Norman, OK 73019. AD - Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019. FAU - Akinyi, Mercy Y AU - Akinyi MY AUID- ORCID: 0000-0002-3835-5793 AD - One Health Centre, Institute of Primate Research, Nairobi, 00502, Kenya. FAU - DeWitte, Sharon N AU - DeWitte SN AUID- ORCID: 0000-0003-0754-8485 AD - Department of Anthropology, University of South Carolina, Columbia, SC 29208. FAU - Stone, Anne C AU - Stone AC AUID- ORCID: 0000-0001-8021-8314 AD - Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287. AD - Center for Evolution and Medicine, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287. AD - Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287. LA - eng PT - Historical Article PT - Journal Article DEP - 20230117 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - History, Ancient MH - *Communicable Diseases MH - Genome MH - DNA, Ancient PMC - PMC9942913 OTO - NOTNLM OT - ancient DNA OT - disease OT - health OT - pathogens COIS- C.L. is an editor of an upcoming book for which A.C.S. has written a chapter. They are also coauthors on a review published in 2022. EDAT- 2023/01/18 06:00 MHDA- 2023/01/20 06:00 PMCR- 2023/01/17 CRDT- 2023/01/17 14:03 PHST- 2023/01/17 14:03 [entrez] PHST- 2023/01/18 06:00 [pubmed] PHST- 2023/01/20 06:00 [medline] PHST- 2023/01/17 00:00 [pmc-release] AID - 202209476 [pii] AID - 10.1073/pnas.2209476119 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2023 Jan 24;120(4):e2209476119. doi: 10.1073/pnas.2209476119. Epub 2023 Jan 17. PMID- 36650598 OWN - NLM STAT- MEDLINE DCOM- 20230119 LR - 20240911 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 24 IP - 1 DP - 2023 Jan 17 TI - KIN: a method to infer relatedness from low-coverage ancient DNA. PG - 10 LID - 10.1186/s13059-023-02847-7 [doi] LID - 10 AB - Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness of a pair of individuals from the identical-by-descent segments they share. KIN accurately classifies up to 3rd-degree relatives using at least 0.05x sequence coverage and differentiates siblings from parent-child pairs. It incorporates additional models to adjust for contamination and detect inbreeding, which improves classification accuracy. CI - © 2023. The Author(s). FAU - Popli, Divyaratan AU - Popli D AUID- ORCID: 0000-0002-0305-6427 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. divyaratan_popli@eva.mpg.de. FAU - Peyrégne, Stéphane AU - Peyrégne S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Peter, Benjamin M AU - Peter BM AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. benjamin_peter@eva.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230117 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - *Inbreeding PMC - PMC9843908 COIS- The authors declare that they have no competing interests. EDAT- 2023/01/18 06:00 MHDA- 2023/01/20 06:00 PMCR- 2023/01/17 CRDT- 2023/01/17 23:35 PHST- 2022/05/18 00:00 [received] PHST- 2023/01/04 00:00 [accepted] PHST- 2023/01/17 23:35 [entrez] PHST- 2023/01/18 06:00 [pubmed] PHST- 2023/01/20 06:00 [medline] PHST- 2023/01/17 00:00 [pmc-release] AID - 10.1186/s13059-023-02847-7 [pii] AID - 2847 [pii] AID - 10.1186/s13059-023-02847-7 [doi] PST - epublish SO - Genome Biol. 2023 Jan 17;24(1):10. doi: 10.1186/s13059-023-02847-7. PMID- 36623185 OWN - NLM STAT- MEDLINE DCOM- 20230216 LR - 20240712 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 120 IP - 3 DP - 2023 Jan 17 TI - Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina. PG - e2201620120 LID - 10.1073/pnas.2201620120 [doi] LID - e2201620120 AB - In this study, we present the results of community-engaged ancient DNA research initiated after the remains of 36 African-descended individuals dating to the late 18th century were unearthed in the port city of Charleston, South Carolina. The Gullah Society of Charleston, along with other Charleston community members, initiated a collaborative genomic study of these ancestors of presumed enslaved status, in an effort to visibilize their histories. We generated 18 low-coverage genomes and 31 uniparental haplotypes to assess their genetic origins and interrelatedness. Our results indicate that they have predominantly West and West-Central African genomic ancestry, with one individual exhibiting some genomic affiliation with populations in the Americas. Most were assessed as genetic males, and no autosomal kin were identified among them. Overall, this study expands our understanding of the colonial histories of African descendant populations in the US South. FAU - Fleskes, Raquel E AU - Fleskes RE AUID- ORCID: 0000-0002-2875-6286 AD - Department of Anthropology, University of Connecticut, Storrs, CT 06269. AD - The Anson Street African Burial Ground Project, Mount Pleasant, SC 29492. FAU - Cabana, Graciela S AU - Cabana GS AUID- ORCID: 0000-0002-5399-1173 AD - Department of Anthropology, University of Tennessee, Knoxville, TN 37996. FAU - Gilmore, Joanna K AU - Gilmore JK AUID- ORCID: 0000-0001-5597-2630 AD - The Anson Street African Burial Ground Project, Mount Pleasant, SC 29492. AD - Department of Sociology and Anthropology, The College of Charleston, Charleston, SC 29424. FAU - Juarez, Chelsey AU - Juarez C AUID- ORCID: 0000-0002-9097-1585 AD - Department of Anthropology, California State University, Fresno, CA 93740. FAU - Karcher, Emilee AU - Karcher E AUID- ORCID: 0000-0003-1682-5915 AD - Department of Anthropology, University of California, Davis, CA 95616. FAU - Oubré, La'Sheia AU - Oubré L AD - The Anson Street African Burial Ground Project, Mount Pleasant, SC 29492. FAU - Mishoe, Grant AU - Mishoe G AD - The Anson Street African Burial Ground Project, Mount Pleasant, SC 29492. FAU - Ofunniyin, Ade A AU - Ofunniyin AA AD - The Anson Street African Burial Ground Project, Mount Pleasant, SC 29492. AD - Department of Sociology and Anthropology, The College of Charleston, Charleston, SC 29424. FAU - Schurr, Theodore G AU - Schurr TG AUID- ORCID: 0000-0001-9323-9237 AD - The Anson Street African Burial Ground Project, Mount Pleasant, SC 29492. AD - Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104. LA - eng GR - P2C HD044964/HD/NICHD NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230109 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - Male MH - *Black People/genetics MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Genomics MH - Haplotypes/genetics MH - South Carolina/ethnology MH - Black or African American PMC - PMC9934026 OTO - NOTNLM OT - Colonial North America OT - ancestry OT - haplotype OT - paleogenomics OT - trans-Atlantic slave trade COIS- The authors declare no competing interest. EDAT- 2023/01/10 06:00 MHDA- 2023/01/12 06:00 PMCR- 2023/07/09 CRDT- 2023/01/09 15:32 PHST- 2023/01/09 15:32 [entrez] PHST- 2023/01/10 06:00 [pubmed] PHST- 2023/01/12 06:00 [medline] PHST- 2023/07/09 00:00 [pmc-release] AID - 202201620 [pii] AID - 10.1073/pnas.2201620120 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2023 Jan 17;120(3):e2201620120. doi: 10.1073/pnas.2201620120. Epub 2023 Jan 9. PMID- 36513080 OWN - NLM STAT- MEDLINE DCOM- 20230112 LR - 20230209 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 33 IP - 1 DP - 2023 Jan 9 TI - Genetic admixture and language shift in the medieval Volga-Oka interfluve. PG - 174-182.e10 LID - S0960-9822(22)01826-7 [pii] LID - 10.1016/j.cub.2022.11.036 [doi] AB - The Volga-Oka interfluve in northwestern Russia has an intriguing history of population influx and language shift during the Common Era. Today, most inhabitants of the region speak Russian, but until medieval times, northwestern Russia was inhabited by Uralic-speaking peoples.(1)(,)(2)(,)(3) A gradual shift to Slavic languages started in the second half of the first millennium with the expansion of Slavic tribes, which led to the foundation of the Kievan Rus' state in the late 9(th) century CE. The medieval Rus' was multicultural and multilingual-historical records suggest that its northern regions comprised Slavic and Uralic peoples ruled by Scandinavian settlers.(4)(,)(5)(,)(6) In the 10(th)-11(th) centuries, the introduction of Christianity and Cyrillic literature raised the prestige status of Slavic, driving a language shift from Uralic to Slavic.(3) This eventually led to the disappearance of the Uralic languages from northwestern Russia. Here, we study a 1,500-year time transect of 30 ancient genomes and stable isotope values from the Suzdal region in the Volga-Oka interfluve. We describe a previously unsampled local Iron Age population and a gradual genetic turnover in the following centuries. Our time transect captures the population shift associated with the spread of Slavic languages and illustrates the ethnically mixed state of medieval Suzdal principality, eventually leading to the formation of the admixed but fully Slavic-speaking population that inhabits the area today. We also observe genetic outliers that highlight the importance of the Suzdal region in medieval times as a hub of long-reaching contacts via trade and warfare. CI - Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Peltola, Sanni AU - Peltola S AD - Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. Electronic address: sanni.peltola@helsinki.fi. FAU - Majander, Kerttu AU - Majander K AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Makarov, Nikolaj AU - Makarov N AD - Institute of Archaeology, Russian Academy of Sciences, 117292 Moscow, Russia. FAU - Dobrovolskaya, Maria AU - Dobrovolskaya M AD - Institute of Archaeology, Russian Academy of Sciences, 117292 Moscow, Russia. FAU - Nordqvist, Kerkko AU - Nordqvist K AD - Department of Cultures, Archaeology, University of Helsinki, 00014 Helsinki, Finland. FAU - Salmela, Elina AU - Salmela E AD - Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Department of Biology, University of Turku, 20014 Turku, Finland. FAU - Onkamo, Päivi AU - Onkamo P AD - Department of Biology, University of Turku, 20014 Turku, Finland. Electronic address: paivi.onkamo@utu.fi. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221212 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Humans MH - *White People MH - Russia MH - Language MH - *Multilingualism OTO - NOTNLM OT - Iron Age OT - Uralic languages OT - Volga-Oka interfluve OT - ancient DNA OT - language shift OT - medieval times COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/12/14 06:00 MHDA- 2023/01/13 06:00 CRDT- 2022/12/13 18:43 PHST- 2022/07/01 00:00 [received] PHST- 2022/09/23 00:00 [revised] PHST- 2022/11/17 00:00 [accepted] PHST- 2022/12/14 06:00 [pubmed] PHST- 2023/01/13 06:00 [medline] PHST- 2022/12/13 18:43 [entrez] AID - S0960-9822(22)01826-7 [pii] AID - 10.1016/j.cub.2022.11.036 [doi] PST - ppublish SO - Curr Biol. 2023 Jan 9;33(1):174-182.e10. doi: 10.1016/j.cub.2022.11.036. Epub 2022 Dec 12. PMID- 36493775 OWN - NLM STAT- MEDLINE DCOM- 20230112 LR - 20230205 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 33 IP - 1 DP - 2023 Jan 9 TI - Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean. PG - 41-57.e15 LID - S0960-9822(22)01824-3 [pii] LID - 10.1016/j.cub.2022.11.034 [doi] AB - We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f(3)-based genetic distances, but not by the commonly used F(ST) statistic, due to the sensitivity of F(ST), but not outgroup-f(3), to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene. CI - Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Koptekin, Dilek AU - Koptekin D AD - Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey; Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. Electronic address: dilek.koptekin@metu.edu.tr. FAU - Yüncü, Eren AU - Yüncü E AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Rodríguez-Varela, Ricardo AU - Rodríguez-Varela R AD - Centre for Palaeogenetics, Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. FAU - Altınışık, N Ezgi AU - Altınışık NE AD - Human-G Laboratory, Department of Anthropology, Hacettepe University, Beytepe 06800, Ankara, Turkey. FAU - Psonis, Nikolaos AU - Psonis N AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece. FAU - Kashuba, Natalia AU - Kashuba N AD - Department of Archaeology and Ancient History, Archaeology, Uppsala University, Uppsala, Sweden. FAU - Yorulmaz, Sevgi AU - Yorulmaz S AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - George, Robert AU - George R AD - Centre for Palaeogenetics, Stockholm, Sweden; School of Medicine, University of Notre Dame, Sydney, Australia. FAU - Kazancı, Duygu Deniz AU - Kazancı DD AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey; Human-G Laboratory, Department of Anthropology, Hacettepe University, Beytepe 06800, Ankara, Turkey. FAU - Kaptan, Damla AU - Kaptan D AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Gürün, Kanat AU - Gürün K AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Vural, Kıvılcım Başak AU - Vural KB AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Gemici, Hasan Can AU - Gemici HC AD - Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey. FAU - Vassou, Despoina AU - Vassou D AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece. FAU - Daskalaki, Evangelia AU - Daskalaki E AD - Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. FAU - Karamurat, Cansu AU - Karamurat C AD - Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey. FAU - Lagerholm, Vendela K AU - Lagerholm VK AD - Centre for Palaeogenetics, Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. FAU - Erdal, Ömür Dilek AU - Erdal ÖD AD - Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey. FAU - Kırdök, Emrah AU - Kırdök E AD - Department of Biotechnology, Mersin University, 33343 Yenişehir, Mersin, Turkey. FAU - Marangoni, Aurelio AU - Marangoni A AD - Centre for Palaeogenetics, Stockholm, Sweden. FAU - Schachner, Andreas AU - Schachner A AD - Deutsches Archäologisches Institut, Inönü Cad. 10, Gümüşsuyu, 34437 İstanbul, Turkey. FAU - Üstündağ, Handan AU - Üstündağ H AD - Department of Archaeology, Anadolu University, 26470 Eskişehir, Turkey. FAU - Shengelia, Ramaz AU - Shengelia R AD - Department of the History of Medicine and Bioethics, Tbilisi State Medical University, Tbilisi 0162, Georgia. FAU - Bitadze, Liana AU - Bitadze L AD - Institute of History and Ethnology, Tbilisi State University, Tbilisi, Georgia. FAU - Elashvili, Mikheil AU - Elashvili M AD - Cultural Heritage and Environment Research Center, School of Natural Sciences and Medicine, Ilia State University, Tbilisi, Georgia. FAU - Stravopodi, Eleni AU - Stravopodi E AD - Ephorate of Palaeoanthropology and Speleology, Ministry of Culture and Sports, 11636 Athens, Greece. FAU - Özbaşaran, Mihriban AU - Özbaşaran M AD - Department of Prehistory, Istanbul University, 34134 Istanbul, Turkey. FAU - Duru, Güneş AU - Duru G AD - Mimar Sinan Fine Arts University, 34134 Istanbul, Turkey. FAU - Nafplioti, Argyro AU - Nafplioti A AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece. FAU - Rose, C Brian AU - Rose CB AD - Department of Classical Studies, University of Pennsylvania, Philadelphia, PA, USA. FAU - Gencer, Tuğba AU - Gencer T AD - Department of History of Medicine and Ethics, Cerrahpasa Faculty of Medicine, Istanbul University, Istanbul, Turkey. FAU - Darbyshire, Gareth AU - Darbyshire G AD - Penn Museum, Philadelphia, PA, USA. FAU - Gavashelishvili, Alexander AU - Gavashelishvili A AD - Center of Biodiversity Studies, Institute of Ecology, Ilia State University, Cholokashvili Str. 5, Tbilisi 0162, Georgia. FAU - Pitskhelauri, Konstantine AU - Pitskhelauri K AD - Ilia State University, Cholokashvili Str. 5, Tbilisi 0162, Georgia. FAU - Çevik, Özlem AU - Çevik Ö AD - Department of Archaeology, Trakya University, Edirne, Turkey. FAU - Vuruşkan, Osman AU - Vuruşkan O AD - Department of Archaeology, Trakya University, Edirne, Turkey. FAU - Kyparissi-Apostolika, Nina AU - Kyparissi-Apostolika N AD - Ephorate of Palaeoanthropology and Speleology, Ministry of Culture and Sports, 11636 Athens, Greece. FAU - Büyükkarakaya, Ali Metin AU - Büyükkarakaya AM AD - Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey; Human Behavioral Ecology and Archaeometry Laboratory (IDEA Lab), Hacettepe University, Ankara, Turkey. FAU - Oğuzhanoğlu, Umay AU - Oğuzhanoğlu U AD - Department of Archaeology, Pamukkale University, Denizli, Turkey. FAU - Günel, Sevinç AU - Günel S AD - Department of Archaeology, Hacettepe University, 06800 Beytepe, Ankara, Turkey. FAU - Tabakaki, Eugenia AU - Tabakaki E AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece. FAU - Aliev, Akper AU - Aliev A AD - Azerbaijan DNA Project, Family Tree DNA, Houston, TX, USA. FAU - Ibrahimov, Anar AU - Ibrahimov A AD - Khazar University, Baku, Azerbaijan. FAU - Shadlinski, Vaqif AU - Shadlinski V AD - Azerbaijan Medical University, Baku, Azerbaijan. FAU - Sampson, Adamantios AU - Sampson A AD - Department of Mediterranean Studies, University of Aegean, Dimokratias st., 85100 Rhodes, Greece. FAU - Kılınç, Gülşah Merve AU - Kılınç GM AD - Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey. FAU - Atakuman, Çiğdem AU - Atakuman Ç AD - Institute of Social Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Stamatakis, Alexandros AU - Stamatakis A AD - Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany. FAU - Poulakakis, Nikos AU - Poulakakis N AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece; Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, 71409 Irakleio, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, 70013 Irakleio, Greece. FAU - Erdal, Yılmaz Selim AU - Erdal YS AD - Human-G Laboratory, Department of Anthropology, Hacettepe University, Beytepe 06800, Ankara, Turkey; Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey. FAU - Pavlidis, Pavlos AU - Pavlidis P AD - Institute of Computer Science, Foundation for Research and Technology-Hellas (FORTH), 70013 Heraklion, Greece. FAU - Storå, Jan AU - Storå J AD - Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. FAU - Özer, Füsun AU - Özer F AD - Human-G Laboratory, Department of Anthropology, Hacettepe University, Beytepe 06800, Ankara, Turkey. FAU - Götherström, Anders AU - Götherström A AD - Centre for Palaeogenetics, Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. Electronic address: anders.gotherstrom@arklab.su.se. FAU - Somel, Mehmet AU - Somel M AD - Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey; Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. Electronic address: msomel@metu.edu.tr. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221208 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Humans MH - Male MH - History, Ancient MH - *Racial Groups MH - Iran MH - *Genome, Human MH - Gene Flow MH - Human Migration MH - Genetics, Population PMC - PMC9839366 OTO - NOTNLM OT - East Mediterranean OT - Southwest Asia OT - admixture OT - ancient DNA OT - human mobility OT - sex bias COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/12/10 06:00 MHDA- 2023/01/13 06:00 PMCR- 2023/01/09 CRDT- 2022/12/09 18:43 PHST- 2022/04/29 00:00 [received] PHST- 2022/08/13 00:00 [revised] PHST- 2022/11/15 00:00 [accepted] PHST- 2022/12/10 06:00 [pubmed] PHST- 2023/01/13 06:00 [medline] PHST- 2022/12/09 18:43 [entrez] PHST- 2023/01/09 00:00 [pmc-release] AID - S0960-9822(22)01824-3 [pii] AID - 10.1016/j.cub.2022.11.034 [doi] PST - ppublish SO - Curr Biol. 2023 Jan 9;33(1):41-57.e15. doi: 10.1016/j.cub.2022.11.034. Epub 2022 Dec 8. PMID- 36672874 OWN - NLM STAT- MEDLINE DCOM- 20230124 LR - 20240911 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 14 IP - 1 DP - 2023 Jan 3 TI - High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania. LID - 10.3390/genes14010133 [doi] LID - 133 AB - Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations. FAU - Borbély, Noémi AU - Borbély N AUID- ORCID: 0000-0002-1488-5298 AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary. AD - Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary. FAU - Székely, Orsolya AU - Székely O AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary. FAU - Szeifert, Bea AU - Szeifert B AUID- ORCID: 0000-0003-0786-1690 AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary. AD - Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary. FAU - Gerber, Dániel AU - Gerber D AUID- ORCID: 0000-0001-6463-6014 AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary. AD - Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary. FAU - Máthé, István AU - Máthé I AD - Department of Bioengineering, Socio-Human Sciences and Engineering, Faculty of Economics, Sapientia Hungarian University of Transylvania (Cluj-Napoca), Piața Libertății 1, 530104 Miercurea-Ciuc, Romania. FAU - Benkő, Elek AU - Benkő E AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary. FAU - Mende, Balázs Gusztáv AU - Mende BG AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary. FAU - Egyed, Balázs AU - Egyed B AUID- ORCID: 0000-0003-3960-2052 AD - Department of Genetics, Faculty of Natural Sciences, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary. FAU - Pamjav, Horolma AU - Pamjav H AUID- ORCID: 0000-0002-1719-9154 AD - Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institutes for Forensic Sciences, Mosonyi Street 9, 1087 Budapest, Hungary. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AUID- ORCID: 0000-0003-2095-738X AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20230103 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 SB - IM MH - Humans MH - Romania MH - *Genetics, Population MH - Phylogeny MH - *Genome, Mitochondrial/genetics MH - Chromosomes, Human, Y/genetics PMC - PMC9858685 OTO - NOTNLM OT - Hungarians OT - Székelys OT - Transylvania OT - Y-chromosome OT - genetic diversity OT - mitogenome OT - phylogenetics OT - phylogeography COIS- The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, and interpretation of data; in the writing of the manuscript, and in the decision to publish the results. EDAT- 2023/01/22 06:00 MHDA- 2023/01/25 06:00 PMCR- 2023/01/03 CRDT- 2023/01/21 01:15 PHST- 2022/11/04 00:00 [received] PHST- 2022/12/22 00:00 [revised] PHST- 2022/12/27 00:00 [accepted] PHST- 2023/01/21 01:15 [entrez] PHST- 2023/01/22 06:00 [pubmed] PHST- 2023/01/25 06:00 [medline] PHST- 2023/01/03 00:00 [pmc-release] AID - genes14010133 [pii] AID - genes-14-00133 [pii] AID - 10.3390/genes14010133 [doi] PST - epublish SO - Genes (Basel). 2023 Jan 3;14(1):133. doi: 10.3390/genes14010133. PMID- 36790637 OWN - NLM STAT- MEDLINE DCOM- 20230217 LR - 20230804 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 180 IP - 1 DP - 2023 Jan TI - Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y-chromosomal DNA. PG - 144-161 LID - 10.1002/ajpa.24638 [doi] AB - OBJECTIVES: This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H(0): All individuals were drawn from the same panmictic population; H(1): Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H(2): Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region. METHODS: Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed. RESULTS: Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, F(ST) comparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y-chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout. DISCUSSION: These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego-Patagonia. CI - © 2022 Wiley Periodicals LLC. FAU - Balentine, Christina M AU - Balentine CM AUID- ORCID: 0000-0001-7548-8790 AD - Department of Integrative Biology, University of Texas, Austin, Texas, USA. AD - Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA. FAU - Alfonso-Durruty, Marta AU - Alfonso-Durruty M AUID- ORCID: 0000-0002-5619-9245 AD - Department of Sociology, Anthropology, and Social Work, Kansas State University, Manhattan, Kansas, USA. FAU - Reynolds, Austin W AU - Reynolds AW AUID- ORCID: 0000-0002-7154-1379 AD - Department of Anthropology, Baylor University, Waco, Texas, USA. FAU - Vilar, Miguel AU - Vilar M AUID- ORCID: 0000-0002-8164-4064 AD - Department of Anthropology, University of Maryland, College Park, Maryland, USA. AD - National Geographic Society, Washington, DC, USA. FAU - Morello, Flavia AU - Morello F AUID- ORCID: 0000-0001-6379-7342 AD - Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas, Chile. AD - Cape Horn International Center, Puerto Williams, Chile. FAU - Román, Manuel San AU - Román MS AUID- ORCID: 0000-0002-6845-6616 AD - Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas, Chile. AD - Cape Horn International Center, Puerto Williams, Chile. FAU - Springs, Lauren C AU - Springs LC AD - Department of Anthropology, University of Texas at Austin, Austin, Texas, USA. FAU - Smith, Rick W A AU - Smith RWA AUID- ORCID: 0000-0002-3207-0519 AD - Department of Sociology and Anthropology, George Mason University, Fairfax, Virginia, USA. AD - Women and Gender Studies, George Mason University, Fairfax, Virginia, USA. FAU - Archer, Samantha M AU - Archer SM AD - Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA. FAU - Mata-Míguez, Jaime AU - Mata-Míguez J AD - Department of Anthropology, University of Texas at Austin, Austin, Texas, USA. FAU - Wing, Natalie AU - Wing N AD - Harvard College, Cambridge, Massachusetts, USA. FAU - Bolnick, Deborah A AU - Bolnick DA AUID- ORCID: 0000-0001-8444-5127 AD - Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA. AD - Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20221102 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM EIN - Am J Biol Anthropol. 2023 Oct;182(2):332. doi: 10.1002/ajpa.24808. PMID: 37539641 MH - Humans MH - Chile MH - *Mitochondria/genetics MH - *Archaeology MH - Y Chromosome MH - DNA, Ancient MH - DNA, Mitochondrial/genetics OTO - NOTNLM OT - Fuego‐Patagonia OT - Y‐chromosome DNA OT - ancient DNA OT - mtDNA OT - population history EDAT- 2023/02/16 06:00 MHDA- 2023/02/18 06:00 CRDT- 2023/02/15 11:23 PHST- 2022/09/26 00:00 [revised] PHST- 2021/12/15 00:00 [received] PHST- 2022/09/28 00:00 [accepted] PHST- 2023/02/15 11:23 [entrez] PHST- 2023/02/16 06:00 [pubmed] PHST- 2023/02/18 06:00 [medline] AID - 10.1002/ajpa.24638 [doi] PST - ppublish SO - Am J Biol Anthropol. 2023 Jan;180(1):144-161. doi: 10.1002/ajpa.24638. Epub 2022 Nov 2. PMID- 36625391 OWN - NLM STAT- MEDLINE DCOM- 20230130 LR - 20230322 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 74 IP - 1 DP - 2023 Jan TI - Ancient DNA sequencing: telling the tale of human history and evolution. PG - 5-7 LID - 10.2144/btn-2022-0121 [doi] AB - Standfirst: In the last decade, ancient DNA research has provided invaluable insights into the lives of ancient populations, adding detail and enriching the story of human evolution and development. [Formula: see text]. FAU - Straiton, Jenny AU - Straiton J AD - Contributing Editor. LA - eng PT - News DEP - 20230110 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - Sequence Analysis, DNA MH - Base Sequence EDAT- 2023/01/11 06:00 MHDA- 2023/01/31 06:00 CRDT- 2023/01/10 06:43 PHST- 2023/01/11 06:00 [pubmed] PHST- 2023/01/31 06:00 [medline] PHST- 2023/01/10 06:43 [entrez] AID - 10.2144/btn-2022-0121 [doi] PST - ppublish SO - Biotechniques. 2023 Jan;74(1):5-7. doi: 10.2144/btn-2022-0121. Epub 2023 Jan 10. PMID- 36520391 OWN - NLM STAT- MEDLINE DCOM- 20221219 LR - 20230304 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 2605 DP - 2023 TI - Analysis of Ancient Microbial DNA. PG - 103-131 LID - 10.1007/978-1-0716-2871-3_6 [doi] AB - The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota. CI - © 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature. FAU - Gorgé, Olivier AU - Gorgé O AD - Université Paris Cité, CNRS, Institut Jacques Monod, UMR 7592, Paris, France. FAU - Bennett, E Andrew AU - Bennett EA AD - Université Paris Cité, CNRS, Institut Jacques Monod, UMR 7592, Paris, France. FAU - Massilani, Diyendo AU - Massilani D AD - Université Paris Cité, CNRS, Institut Jacques Monod, UMR 7592, Paris, France. FAU - Daligault, Julien AU - Daligault J AD - Université Paris Cité, CNRS, Institut Jacques Monod, UMR 7592, Paris, France. FAU - Geigl, Eva-Maria AU - Geigl EM AD - Université Paris Cité, CNRS, Institut Jacques Monod, UMR 7592, Paris, France. eva-maria.geigl@ijm.fr. FAU - Grange, Thierry AU - Grange T AD - Université Paris Cité, CNRS, Institut Jacques Monod, UMR 7592, Paris, France. thierry.grange@ijm.fr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Humans MH - DNA, Ancient MH - Body Remains MH - *Hominidae/genetics MH - DNA/genetics MH - Genome, Microbial MH - *Neanderthals/genetics MH - Sequence Analysis, DNA/methods OTO - NOTNLM OT - Ancient DNA OT - Double-stranded library OT - Illumina, contamination OT - Ion Torrent OT - NGS OT - Single-stranded library EDAT- 2022/12/16 06:00 MHDA- 2022/12/20 06:00 CRDT- 2022/12/15 11:21 PHST- 2022/12/15 11:21 [entrez] PHST- 2022/12/16 06:00 [pubmed] PHST- 2022/12/20 06:00 [medline] AID - 10.1007/978-1-0716-2871-3_6 [doi] PST - ppublish SO - Methods Mol Biol. 2023;2605:103-131. doi: 10.1007/978-1-0716-2871-3_6. PMID- 36377787 OWN - NLM STAT- MEDLINE DCOM- 20230103 LR - 20230223 IS - 1367-4811 (Electronic) IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 39 IP - 1 DP - 2023 Jan 1 TI - Achieving improved accuracy for imputation of ancient DNA. LID - 10.1093/bioinformatics/btac738 [doi] LID - btac738 AB - MOTIVATION: Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data. RESULTS: We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU. AVAILABILITY AND IMPLEMENTATION: The C++ code for prophaser is available in the GitHub repository https://github.com/scicompuu/prophaser. SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online. CI - © The Author(s) 2022. Published by Oxford University Press. FAU - Ausmees, Kristiina AU - Ausmees K AUID- ORCID: 0000-0002-6212-539X AD - Department of Information Technology, Uppsala University, Uppsala 751 05, Sweden. FAU - Nettelblad, Carl AU - Nettelblad C AUID- ORCID: 0000-0003-0458-6902 AD - Department of Information Technology, Uppsala University, Uppsala 751 05, Sweden. LA - eng GR - 2017-00453/Formas/ PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Dogs MH - Humans MH - *DNA, Ancient MH - Genotype MH - Haplotypes MH - *Software MH - Ethnicity PMC - PMC9805568 EDAT- 2022/11/16 06:00 MHDA- 2023/01/04 06:00 PMCR- 2022/11/15 CRDT- 2022/11/15 07:52 PHST- 2022/06/02 00:00 [received] PHST- 2022/11/07 00:00 [revised] PHST- 2022/11/14 00:00 [accepted] PHST- 2022/11/16 06:00 [pubmed] PHST- 2023/01/04 06:00 [medline] PHST- 2022/11/15 07:52 [entrez] PHST- 2022/11/15 00:00 [pmc-release] AID - 6827812 [pii] AID - btac738 [pii] AID - 10.1093/bioinformatics/btac738 [doi] PST - ppublish SO - Bioinformatics. 2023 Jan 1;39(1):btac738. doi: 10.1093/bioinformatics/btac738. PMID- 36048238 OWN - NLM STAT- MEDLINE DCOM- 20230117 LR - 20230117 IS - 1432-1203 (Electronic) IS - 0340-6717 (Linking) VI - 142 IP - 1 DP - 2023 Jan TI - Comprehensive analysis of microsatellite polymorphisms in human populations. PG - 45-57 LID - 10.1007/s00439-022-02484-3 [doi] AB - Microsatellites (MS) are tandem repeats of short units, and have been used for population genetics, individual identification, and medical genetics. However, studies of MS on a whole-genome level are limited, and genotyping methods for MS have yet to be established. Here, we analyzed approximately 8.5 million MS regions using a previously developed MS caller for short reads (MIVcall method) for three large publicly available human genome sequencing data sets: the Korean Personal Genome Project, Simons Genome Diversity Project, and Human Genome Diversity Project. Our analysis identified 253,114 polymorphic MS. A comparison among different populations suggests that MS in the coding region evolved by random genetic drift and natural selection. In an analysis of genetic structures, MS clearly revealed population structures as SNPs and detected clusters that were not found by SNPs in African and Oceanian populations. Based on the MS polymorphisms, we selected MS marker candidates for individual identification. Finally, we applied our method to a deep sequenced ancient DNA sample. This study provides a comprehensive picture of MS polymorphisms and application to human population studies. CI - © 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. FAU - Gochi, Leo AU - Gochi L AD - Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0003, Japan. FAU - Kawai, Yosuke AU - Kawai Y AD - Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan. FAU - Fujimoto, Akihiro AU - Fujimoto A AUID- ORCID: 0000-0002-0075-0800 AD - Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0003, Japan. afujimoto@m.u-tokyo.ac.jp. LA - eng GR - 18H02680/Japan Society for the Promotion of Science London/ GR - 18H05511/MEXT KAKENHI/ GR - JP21km0908001/Japan Agency for Medical Research and Development/ PT - Journal Article DEP - 20220901 PL - Germany TA - Hum Genet JT - Human genetics JID - 7613873 SB - IM MH - Humans MH - *Genetics, Population MH - *Genome MH - Chromosome Mapping MH - Polymorphism, Single Nucleotide MH - Microsatellite Repeats/genetics EDAT- 2022/09/02 06:00 MHDA- 2023/01/18 06:00 CRDT- 2022/09/01 11:14 PHST- 2022/06/16 00:00 [received] PHST- 2022/08/24 00:00 [accepted] PHST- 2022/09/02 06:00 [pubmed] PHST- 2023/01/18 06:00 [medline] PHST- 2022/09/01 11:14 [entrez] AID - 10.1007/s00439-022-02484-3 [pii] AID - 10.1007/s00439-022-02484-3 [doi] PST - ppublish SO - Hum Genet. 2023 Jan;142(1):45-57. doi: 10.1007/s00439-022-02484-3. Epub 2022 Sep 1. PMID- 35922549 OWN - NLM STAT- MEDLINE DCOM- 20221129 LR - 20240102 IS - 1740-634X (Electronic) IS - 0893-133X (Print) IS - 0893-133X (Linking) VI - 48 IP - 1 DP - 2023 Jan TI - Echoes of ancient DNA in living modern humans affect risk for neuropsychiatric disease and brain structure and function of networks subserving higher-order cognition. PG - 236-237 LID - 10.1038/s41386-022-01396-0 [doi] FAU - Gregory, Michael D AU - Gregory MD AUID- ORCID: 0000-0003-3749-8343 AD - Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA. gregorymd@mail.nih.gov. FAU - Berman, Karen F AU - Berman KF AD - Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA. bermank@mail.nih.gov. LA - eng GR - ZIA MH002942/ImNIH/Intramural NIH HHS/United States GR - ZIA MH002652/ImNIH/Intramural NIH HHS/United States GR - ZIA MH002717/ImNIH/Intramural NIH HHS/United States PT - News PT - Research Support, N.I.H., Intramural PL - England TA - Neuropsychopharmacology JT - Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology JID - 8904907 RN - 0 (DNA, Ancient) SB - IM EIN - Neuropsychopharmacology. 2022 Nov;47(12):2173. doi: 10.1038/s41386-022-01439-6. PMID: 36050453 MH - Humans MH - *DNA, Ancient MH - *Cognition MH - Brain PMC - PMC9700764 COIS- The authors declare no competing interests. EDAT- 2022/08/04 06:00 MHDA- 2022/11/30 06:00 PMCR- 2024/01/01 CRDT- 2022/08/03 23:26 PHST- 2022/08/04 06:00 [pubmed] PHST- 2022/11/30 06:00 [medline] PHST- 2022/08/03 23:26 [entrez] PHST- 2024/01/01 00:00 [pmc-release] AID - 10.1038/s41386-022-01396-0 [pii] AID - 1396 [pii] AID - 10.1038/s41386-022-01396-0 [doi] PST - ppublish SO - Neuropsychopharmacology. 2023 Jan;48(1):236-237. doi: 10.1038/s41386-022-01396-0. PMID- 36576953 OWN - NLM STAT- MEDLINE DCOM- 20230105 LR - 20230111 IS - 2037-0644 (Electronic) IS - 1827-4765 (Linking) VI - 100 DP - 2022 Dec 30 TI - Ancient genomic research - From broad strokes to nuanced reconstructions of the past. PG - 193-230 LID - 10.4436/JASS.10017 [doi] AB - Ancient DNA (aDNA) studies have deployed genetic material from archaeological contexts to investigate human dispersals and interactions, corroborating some longstanding hypotheses and revealing new aspects of human history. After drawing the broad genomic strokes of human history, geneticists have discovered the exciting possibilities of applying this method to answer questions on a smaller scale. This review provides an overview of the commonly used methods, both in the laboratory and the analyses, and summarizes the current state of genomic research. It reviews human dispersals across the continents and additionally highlights some studies that integrated genomics to answer questions beyond biology to understand the cultural and societal traits of past societies. By shining a light from multiple angles, we gain a much better understanding of the real shape of the human past. FAU - Nägele, Kathrin AU - Nägele K AD - Max Planck Institute for Evolutionary Anthropology, Germany, kathrin_naegele@eva.mpg.de. FAU - Rivollat, Maite AU - Rivollat M AD - Max Planck Institute for Evolutionary Anthropology, Germany; Ghent University, Department of Archaeology, Belgium; Durham University, Department of Archaeology, UK; Bordeaux University, PACEA, France. FAU - Yu, He AU - Yu H AD - Max Planck Institute for Evolutionary Anthropology, Germany; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Yiheyuan Rd. 5, Haidian District, Beijing 100871, China. FAU - Wang, Ke AU - Wang K AD - Max Planck Institute for Evolutionary Anthropology, Germany; Department of Anthropology and Human Genetics, School of Life Science, Fudan University, China. LA - eng PT - Historical Article PT - Journal Article PT - Review PL - Italy TA - J Anthropol Sci JT - Journal of anthropological sciences = Rivista di antropologia : JASS JID - 101491368 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - History, Ancient MH - *Genomics MH - *Archaeology MH - DNA, Ancient OTO - NOTNLM OT - Ancient DNA OT - Archaeogenomics OT - Dispersals OT - Human history OT - Migrations EDAT- 2022/12/29 06:00 MHDA- 2023/01/06 06:00 CRDT- 2022/12/28 14:02 PHST- 2022/12/28 14:02 [entrez] PHST- 2022/12/29 06:00 [pubmed] PHST- 2023/01/06 06:00 [medline] AID - 10.4436/JASS.10017 [doi] PST - ppublish SO - J Anthropol Sci. 2022 Dec 30;100:193-230. doi: 10.4436/JASS.10017. PMID- 36565457 OWN - NLM STAT- MEDLINE DCOM- 20230106 LR - 20230111 IS - 2037-0644 (Electronic) IS - 1827-4765 (Linking) VI - 100 DP - 2022 Dec 30 TI - The future of the Eurasian past: highlighting plotholes and pillars of human population movements in the Late Pleistocene. PG - 231-241 LID - 10.4436/JASS.10013 [doi] AB - The major genetic divergences among non-Africans took place within a relatively short period of time, between 50 and 40 thousand years ago. These events shaped human diversity worldwide and set the basis for our current understanding of demographic history, patterns of adaptation and genetic burden across human populations. While the global picture appears already set, with the main human expansion Out of Africa inferred to have occurred between 60 and 70 thousand years ago and the main separation between contemporary East and West Eurasian to have taken place at around 40 thousand years ago, several finer details remain unresolved, including the whereabouts of such expansions and the dynamics of their interactions with archaic hominins and the interplay between environmental, cultural and demographic effectors. Here we review the major events that characterize human movements across and beyond Eurasia until the last glacial maximum and, at the end of each paragraph, spell out in italics the major questions that remain unsolved and that may provide major breakthroughs in the field in the upcoming years. FAU - Vallini, Leonardo AU - Vallini L AD - Department of Biology, University of Padova, Italy. FAU - Pagani, Luca AU - Pagani L AD - Department of Biology, University of Padova, Italy; Institute of Genomics, University of Tartu, Estonia, lp.lucapagani@gmail.com. LA - eng PT - Journal Article PT - Review PL - Italy TA - J Anthropol Sci JT - Journal of anthropological sciences = Rivista di antropologia : JASS JID - 101491368 SB - IM MH - Humans MH - Africa MH - Italy MH - *Population Dynamics OTO - NOTNLM OT - Ancient DNA OT - Open questions OT - Palaeolithic Eurasia EDAT- 2022/12/25 06:00 MHDA- 2023/01/06 06:00 CRDT- 2022/12/24 13:12 PHST- 2022/12/24 13:12 [entrez] PHST- 2022/12/25 06:00 [pubmed] PHST- 2023/01/06 06:00 [medline] AID - 10.4436/JASS.10013 [doi] PST - ppublish SO - J Anthropol Sci. 2022 Dec 30;100:231-241. doi: 10.4436/JASS.10013. PMID- 36581666 OWN - NLM STAT- MEDLINE DCOM- 20230102 LR - 20240910 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 12 IP - 1 DP - 2022 Dec 29 TI - Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st-3rd centuries CE. PG - 22507 LID - 10.1038/s41598-022-26799-3 [doi] LID - 22507 AB - Indian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40-50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78-234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations. CI - © 2022. The Author(s). FAU - Changmai, Piya AU - Changmai P AD - Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic. piya.changmai@osu.cz. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Pietrusewsky, Michael AU - Pietrusewsky M AD - Department of Anthropology, University of Hawai'i-Mānoa, Honolulu, HI, USA. FAU - Stark, Miriam T AU - Stark MT AD - Department of Anthropology, University of Hawai'i-Mānoa, Honolulu, HI, USA. FAU - Ikehara-Quebral, Rona Michi AU - Ikehara-Quebral RM AD - Department of Anthropology, University of Hawai'i-Mānoa, Honolulu, HI, USA. AD - International Archaeological Research Institute, Inc., Honolulu, HI, USA. FAU - Reich, David AU - Reich D AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. FAU - Flegontov, Pavel AU - Flegontov P AD - Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic. pavel.flegontov@osu.cz. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. pavel.flegontov@osu.cz. AD - Kalmyk Research Center of the Russian Academy of Sciences, Elista, Kalmykia, Russia. pavel.flegontov@osu.cz. AD - Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic. pavel.flegontov@osu.cz. LA - eng GR - R01 HG012287/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221229 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Genetics, Population MH - *DNA, Ancient MH - Cambodia MH - South Asian People MH - Asian People PMC - PMC9800559 COIS- The authors declare no competing interests. EDAT- 2022/12/30 06:00 MHDA- 2023/01/03 06:00 PMCR- 2022/12/29 CRDT- 2022/12/29 23:22 PHST- 2022/06/30 00:00 [received] PHST- 2022/12/20 00:00 [accepted] PHST- 2022/12/29 23:22 [entrez] PHST- 2022/12/30 06:00 [pubmed] PHST- 2023/01/03 06:00 [medline] PHST- 2022/12/29 00:00 [pmc-release] AID - 10.1038/s41598-022-26799-3 [pii] AID - 26799 [pii] AID - 10.1038/s41598-022-26799-3 [doi] PST - epublish SO - Sci Rep. 2022 Dec 29;12(1):22507. doi: 10.1038/s41598-022-26799-3. PMID- 36537881 OWN - NLM STAT- MEDLINE DCOM- 20221222 LR - 20241001 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 11 DP - 2022 Dec 20 TI - Modeling the spatiotemporal spread of beneficial alleles using ancient genomes. LID - 10.7554/eLife.73767 [doi] LID - e73767 AB - Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios. CI - © 2022, Muktupavela et al. FAU - Muktupavela, Rasa A AU - Muktupavela RA AUID- ORCID: 0000-0001-5590-5948 AD - Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of Health, Copenhagen, Denmark. FAU - Petr, Martin AU - Petr M AUID- ORCID: 0000-0003-4879-8421 AD - Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of Health, Copenhagen, Denmark. FAU - Ségurel, Laure AU - Ségurel L AUID- ORCID: 0000-0001-7339-0976 AD - UMR5558 Biométrie et Biologie Evolutive, CNRS - Université Lyon 1, Villeurbanne, France. FAU - Korneliussen, Thorfinn AU - Korneliussen T AD - Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of Health, Copenhagen, Denmark. FAU - Novembre, John AU - Novembre J AUID- ORCID: 0000-0001-5345-0214 AD - Department of Human Genetics, University of Chicago, Chicago, United States. FAU - Racimo, Fernando AU - Racimo F AUID- ORCID: 0000-0002-5025-2607 AD - Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of Health, Copenhagen, Denmark. LA - eng GR - R01 GM132383/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20221220 PL - England TA - Elife JT - eLife JID - 101579614 SB - IM MH - Humans MH - Alleles MH - Gene Frequency MH - *Selection, Genetic PMC - PMC9767474 OAB - Analyzing the genomes of our ancient ancestors can reveal how certain traits spread through the human population over the course of evolution. Mutations that make individuals better equipped to survive their environment are more likely to be passed on to the next generation and become more common. For example, a genetic variant that enables adult people to digest sugars in dairy products has become more common in humans over time. Yet evolution does not only happen across time: it transverses space as well. Modeling the geographic spread of such genetic mutations is challenging using existing methods. To overcome this, Muktupavela et al. developed a new computational method that uses modern and ancient human genomes to study the evolution of specific genetic variants across space and time. The tool can determine where certain variants first emerged, how quickly they spread across geographic areas, and how rapidly they became prevalent in human populations. Muktupavela et al. applied their new method, which was based on a previously published framework, to track the spread of two common genetic variations that have previously been reported to be subject to natural selection: one that allows adult humans to digest dairy products, and another associated with skin pigmentation. They found that the mutation that enabled dairy consumption originated around what is now southwestern Russia or eastern Ukraine. The variation then spread westward, becoming increasingly more common over the course of the Holocene. The mutation related to skin pigmentation emerged further south than the dairy-related variation, and then also spread westward. Massive human migrations during the Neolithic and Bronze Age eras may have helped disperse both variants. The model developed by Muktupavela et al. could help scientists track the geographic spread of other genetic variants in human populations, as well as provide new insights into how humans adapt to changing environmental conditions. Incorporating major events into the model, like mass migrations or glacial retreats, may lead to even more insights. OABL- eng OTO - NOTNLM OT - ancient DNA OT - diffusion OT - evolution OT - evolutionary biology OT - human OT - lactase persistence OT - natural selection OT - spatiotemporal inference COIS- RM, MP, LS, TK, JN, FR No competing interests declared EDAT- 2022/12/21 06:00 MHDA- 2022/12/23 06:00 PMCR- 2022/12/20 CRDT- 2022/12/20 09:53 PHST- 2021/09/09 00:00 [received] PHST- 2022/11/21 00:00 [accepted] PHST- 2022/12/20 09:53 [entrez] PHST- 2022/12/21 06:00 [pubmed] PHST- 2022/12/23 06:00 [medline] PHST- 2022/12/20 00:00 [pmc-release] AID - 73767 [pii] AID - 10.7554/eLife.73767 [doi] PST - epublish SO - Elife. 2022 Dec 20;11:e73767. doi: 10.7554/eLife.73767. PMID- 36553640 OWN - NLM STAT- MEDLINE DCOM- 20221226 LR - 20230109 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 13 IP - 12 DP - 2022 Dec 16 TI - Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects. LID - 10.3390/genes13122373 [doi] LID - 2373 AB - Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution. FAU - Taufik, Leonard AU - Taufik L AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia. AD - Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia. FAU - Teixeira, João C AU - Teixeira JC AUID- ORCID: 0000-0001-6417-4702 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia. AD - Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia. AD - Centre for Interdisciplinary Studies, University of Coimbra, 3004-531 Coimbra, Portugal. FAU - Llamas, Bastien AU - Llamas B AUID- ORCID: 0000-0002-5550-9176 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia. AD - Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia. AD - National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2601, Australia. AD - Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, SA 5001, Australia. FAU - Sudoyo, Herawati AU - Sudoyo H AD - Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia. FAU - Tobler, Raymond AU - Tobler R AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia. AD - Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia. FAU - Purnomo, Gludhug A AU - Purnomo GA AUID- ORCID: 0000-0001-7616-5977 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20221216 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 SB - IM MH - Animals MH - Humans MH - *Hominidae/genetics MH - Human Migration MH - New Guinea MH - Australia MH - Phylogeography MH - *Coleoptera PMC - PMC9778601 OTO - NOTNLM OT - Sahul OT - Wallacea OT - ancient DNA OT - human migrations OT - phylogeography COIS- The authors declare no conflict of interest. EDAT- 2022/12/24 06:00 MHDA- 2022/12/27 06:00 PMCR- 2022/12/16 CRDT- 2022/12/23 01:22 PHST- 2022/11/11 00:00 [received] PHST- 2022/12/08 00:00 [revised] PHST- 2022/12/13 00:00 [accepted] PHST- 2022/12/23 01:22 [entrez] PHST- 2022/12/24 06:00 [pubmed] PHST- 2022/12/27 06:00 [medline] PHST- 2022/12/16 00:00 [pmc-release] AID - genes13122373 [pii] AID - genes-13-02373 [pii] AID - 10.3390/genes13122373 [doi] PST - epublish SO - Genes (Basel). 2022 Dec 16;13(12):2373. doi: 10.3390/genes13122373. PMID- 36516232 OWN - NLM STAT- MEDLINE DCOM- 20230126 LR - 20230208 IS - 1553-7358 (Electronic) IS - 1553-734X (Print) IS - 1553-734X (Linking) VI - 18 IP - 12 DP - 2022 Dec TI - CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data. PG - e1010788 LID - 10.1371/journal.pcbi.1010788 [doi] LID - e1010788 AB - To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage. CI - Copyright: © 2022 Söylev et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. FAU - Söylev, Arda AU - Söylev A AUID- ORCID: 0000-0003-2198-1920 AD - Department of Computer Engineering, Konya Food and Agriculture University, Konya, Turkey. AD - Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany. FAU - Çokoglu, Sevim Seda AU - Çokoglu SS AD - Department of Biology, Middle East Technical University, Ankara, Turkey. FAU - Koptekin, Dilek AU - Koptekin D AD - Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey. FAU - Alkan, Can AU - Alkan C AD - Department of Computer Engineering, Bilkent University, Ankara, Turkey. FAU - Somel, Mehmet AU - Somel M AD - Department of Biology, Middle East Technical University, Ankara, Turkey. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221214 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 SB - IM MH - Humans MH - *DNA Copy Number Variations/genetics MH - Genotype MH - *Genomics/methods MH - Genome, Human/genetics MH - Genetics, Population MH - Polymorphism, Single Nucleotide/genetics PMC - PMC9873172 COIS- The authors have declared that no competing interests exist. EDAT- 2022/12/15 06:00 MHDA- 2023/01/27 06:00 PMCR- 2022/12/14 CRDT- 2022/12/14 13:53 PHST- 2022/08/07 00:00 [received] PHST- 2022/12/03 00:00 [accepted] PHST- 2023/01/24 00:00 [revised] PHST- 2022/12/15 06:00 [pubmed] PHST- 2023/01/27 06:00 [medline] PHST- 2022/12/14 13:53 [entrez] PHST- 2022/12/14 00:00 [pmc-release] AID - PCOMPBIOL-D-22-01205 [pii] AID - 10.1371/journal.pcbi.1010788 [doi] PST - epublish SO - PLoS Comput Biol. 2022 Dec 14;18(12):e1010788. doi: 10.1371/journal.pcbi.1010788. eCollection 2022 Dec. PMID- 36510283 OWN - NLM STAT- MEDLINE DCOM- 20221214 LR - 20240908 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 23 IP - 1 DP - 2022 Dec 13 TI - Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections. PG - 250 LID - 10.1186/s13059-022-02806-8 [doi] LID - 250 AB - BACKGROUND: The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim "Mittelhofen," in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically. RESULTS: Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK. CONCLUSIONS: The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later. CI - © 2022. The Author(s). FAU - Bonczarowska, Joanna H AU - Bonczarowska JH AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Susat, Julian AU - Susat J AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Mühlemann, Barbara AU - Mühlemann B AD - Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany. AD - German Centre for Infection Research (DZIF), partner site Charité, 10117, Berlin, Germany. FAU - Jasch-Boley, Isabelle AU - Jasch-Boley I AD - Institute for Archaeological Sciences, Palaeoanthropology Working Group, University of Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany. FAU - Brather, Sebastian AU - Brather S AD - Institute of Archaeology, Freiburg University, Belfortstraße 22, 79085, Freiburg, Germany. FAU - Höke, Benjamin AU - Höke B AD - Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Berliner Straße 12, 73728, Esslingen, Germany. FAU - Brather-Walter, Susanne AU - Brather-Walter S AD - Institute of Archaeology, Freiburg University, Belfortstraße 22, 79085, Freiburg, Germany. FAU - Schoenenberg, Valerie AU - Schoenenberg V AD - Museum im Ritterhaus, Ritterstraße 10, 77652, Offenburg, Germany. FAU - Scheschkewitz, Jonathan AU - Scheschkewitz J AD - Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Berliner Straße 12, 73728, Esslingen, Germany. FAU - Graenert, Gabriele AU - Graenert G AD - Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Berliner Straße 12, 73728, Esslingen, Germany. FAU - Krausse, Dirk AU - Krausse D AD - Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Berliner Straße 12, 73728, Esslingen, Germany. FAU - Francken, Michael AU - Francken M AD - Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Konstanz, Germany. FAU - Jones, Terry C AU - Jones TC AD - Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany. AD - Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK. FAU - Wahl, Joachim AU - Wahl J AD - Institute for Archaeological Sciences, Palaeoanthropology Working Group, University of Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany. FAU - Nebel, Almut AU - Nebel A AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AUID- ORCID: 0000-0001-9435-2872 AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. b.krause-kyora@ikmb.uni-kiel.de. LA - eng GR - HHSN272201400008C/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20221213 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (DNA, Ancient) SB - IM MH - Middle Aged MH - Humans MH - Phylogeny MH - *Coinfection MH - Mycobacterium leprae/genetics MH - *Leprosy/epidemiology/history/microbiology MH - DNA, Ancient PMC - PMC9746117 OTO - NOTNLM OT - Ancient DNA OT - Ancient genomics OT - Hepatitis B virus OT - Infectious diseases OT - Leprosy OT - Parvovirus B19 OT - Pathogen evolution OT - Pathogen genomics OT - Smallpox OT - Variola virus COIS- The authors declare no competing interests. EDAT- 2022/12/13 06:00 MHDA- 2022/12/15 06:00 PMCR- 2022/12/13 CRDT- 2022/12/12 23:53 PHST- 2022/01/27 00:00 [received] PHST- 2022/10/27 00:00 [accepted] PHST- 2022/12/12 23:53 [entrez] PHST- 2022/12/13 06:00 [pubmed] PHST- 2022/12/15 06:00 [medline] PHST- 2022/12/13 00:00 [pmc-release] AID - 10.1186/s13059-022-02806-8 [pii] AID - 2806 [pii] AID - 10.1186/s13059-022-02806-8 [doi] PST - epublish SO - Genome Biol. 2022 Dec 13;23(1):250. doi: 10.1186/s13059-022-02806-8. PMID- 36455558 OWN - NLM STAT- MEDLINE DCOM- 20221219 LR - 20221229 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 185 IP - 25 DP - 2022 Dec 8 TI - Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14(th) century. PG - 4703-4716.e16 LID - S0092-8674(22)01378-2 [pii] LID - 10.1016/j.cell.2022.11.002 [doi] AB - We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14(th) century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14(th) century and highlight late medieval genetic heterogeneity no longer present in modern AJ. CI - Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Waldman, Shamam AU - Waldman S AD - Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel. FAU - Backenroth, Daniel AU - Backenroth D AD - Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel. FAU - Harney, Éadaoin AU - Harney É AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Flohr, Stefan AU - Flohr S AD - Department of Biology, University of Hildesheim, 31141 Hildesheim, Germany. FAU - Neff, Nadia C AU - Neff NC AD - Department Anthropology, University of New Mexico, Albuquerque, NM 87131, USA; Center for Stable Isotopes, University of New Mexico, Albuquerque, NM 87106, USA. FAU - Buckley, Gina M AU - Buckley GM AD - Research Reactor Center, University of Missouri, Columbia, MO 65211, USA. FAU - Fridman, Hila AU - Fridman H AD - Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel; Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel. FAU - Akbari, Ali AU - Akbari A AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Olalde, Iñigo AU - Olalde I AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; Ikerbasque-Basque Foundation of Science, 48009 Bilbao, Spain. FAU - Cooper, Leo AU - Cooper L AD - Independent Scholar, Kalamazoo, MI 49008, USA. FAU - Lomes, Ariel AU - Lomes A AD - Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel. FAU - Lipson, Joshua AU - Lipson J AD - Independent Scholar, New York, NY 10027, USA. FAU - Cano Nistal, Jorge AU - Cano Nistal J AD - Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel. FAU - Yu, Jin AU - Yu J AD - Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA. FAU - Barzilai, Nir AU - Barzilai N AD - Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA. FAU - Peter, Inga AU - Peter I AD - Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. FAU - Atzmon, Gil AU - Atzmon G AD - Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel. FAU - Ostrer, Harry AU - Ostrer H AD - Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. FAU - Lencz, Todd AU - Lencz T AD - Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA. FAU - Maruvka, Yosef E AU - Maruvka YE AD - Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel. FAU - Lämmerhirt, Maike AU - Lämmerhirt M AD - Department of Medieval History, University of Erfurt, 99089 Erfurt, Germany. FAU - Beider, Alexander AU - Beider A AD - Independent Scholar, 92370 Chaville, France. FAU - Rutgers, Leonard V AU - Rutgers LV AD - Department of History and Art History, Utrecht University, Utrecht 3512 BS, the Netherlands. FAU - Renson, Virginie AU - Renson V AD - Research Reactor Center, University of Missouri, Columbia, MO 65211, USA. FAU - Prufer, Keith M AU - Prufer KM AD - Department Anthropology, University of New Mexico, Albuquerque, NM 87131, USA; Center for Stable Isotopes, University of New Mexico, Albuquerque, NM 87106, USA. FAU - Schiffels, Stephan AU - Schiffels S AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Ringbauer, Harald AU - Ringbauer H AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Sczech, Karin AU - Sczech K AD - World Heritage Coordinator, City of Erfurt, 99084 Erfurt, Germany. FAU - Carmi, Shai AU - Carmi S AD - Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel. Electronic address: shai.carmi@huji.ac.il. FAU - Reich, David AU - Reich D AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R01 HG012287/HG/NHGRI NIH HHS/United States PT - Journal Article DEP - 20221130 PL - United States TA - Cell JT - Cell JID - 0413066 SB - IM MH - Humans MH - *Jews/genetics MH - *White People MH - Genetics, Population MH - Genome, Human PMC - PMC9793425 MID - NIHMS1852590 OTO - NOTNLM OT - Ashkenazi Jews OT - IBD sharing OT - admixture OT - ancient DNA OT - demographic inference OT - founder event OT - mitochondrial DNA OT - pathogenic variants OT - population structure OT - runs of homozygosity COIS- Declaration of interests S.C. is a paid consultant and holds stock options at MyHeritage. D.B. is an employee and shareholder at The Janssen Pharmaceutical Companies of Johnson & Johnson. É.H. is an employee of 23andMe. EDAT- 2022/12/02 06:00 MHDA- 2022/12/15 06:00 PMCR- 2022/12/27 CRDT- 2022/12/01 18:42 PHST- 2022/05/08 00:00 [received] PHST- 2022/08/26 00:00 [revised] PHST- 2022/11/01 00:00 [accepted] PHST- 2022/12/02 06:00 [pubmed] PHST- 2022/12/15 06:00 [medline] PHST- 2022/12/01 18:42 [entrez] PHST- 2022/12/27 00:00 [pmc-release] AID - S0092-8674(22)01378-2 [pii] AID - 10.1016/j.cell.2022.11.002 [doi] PST - ppublish SO - Cell. 2022 Dec 8;185(25):4703-4716.e16. doi: 10.1016/j.cell.2022.11.002. Epub 2022 Nov 30. PMID- 36463384 OWN - NLM STAT- MEDLINE DCOM- 20221206 LR - 20230117 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 12 IP - 1 DP - 2022 Dec 3 TI - 4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists. PG - 20939 LID - 10.1038/s41598-022-25384-y [doi] LID - 20939 AB - Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation. CI - © 2022. The Author(s). FAU - Wang, Ke AU - Wang K AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. ke_wang@eva.mpg.de. AD - School of Life Sciences, Fudan University, Shanghai, China. ke_wang@eva.mpg.de. FAU - Bleasdale, Madeleine AU - Bleasdale M AD - Department of Archaeology, University of York, York, UK. AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Le Moyne, Charles AU - Le Moyne C AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - School of Social Science, The University of Queensland, Brisbane, Australia. FAU - Freund, Cacilia AU - Freund C AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Boivin, Nicole AU - Boivin N AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - School of Social Science, The University of Queensland, Brisbane, Australia. FAU - Schiffels, Stephan AU - Schiffels S AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. stephan_schiffels@eva.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221203 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - Africa, Eastern MH - *Hair MH - Sudan MH - Body Remains PMC - PMC9719486 COIS- The authors declare no competing interests. EDAT- 2022/12/04 06:00 MHDA- 2022/12/07 06:00 PMCR- 2022/12/03 CRDT- 2022/12/03 23:45 PHST- 2022/06/15 00:00 [received] PHST- 2022/11/29 00:00 [accepted] PHST- 2022/12/03 23:45 [entrez] PHST- 2022/12/04 06:00 [pubmed] PHST- 2022/12/07 06:00 [medline] PHST- 2022/12/03 00:00 [pmc-release] AID - 10.1038/s41598-022-25384-y [pii] AID - 25384 [pii] AID - 10.1038/s41598-022-25384-y [doi] PST - epublish SO - Sci Rep. 2022 Dec 3;12(1):20939. doi: 10.1038/s41598-022-25384-y. PMID- 36494546 OWN - NLM STAT- MEDLINE DCOM- 20221216 LR - 20230119 IS - 1476-5373 (Electronic) IS - 0007-0610 (Print) IS - 0007-0610 (Linking) VI - 233 IP - 11 DP - 2022 Dec TI - Dental calculus - oral health, forensic studies and archaeology: a review. PG - 961-967 LID - 10.1038/s41415-022-5266-7 [doi] AB - Dental calculus is recognised as a secondary aetiological factor in periodontal disease, and being a prominent plaque retentive factor, it is routinely removed by the dental team to maintain oral health. Conversely, dental calculus can potentially be useful in forensic studies by supplying data that may be helpful in the identification of human remains and assist in determining the cause of death. During the last few decades, dental calculus has been increasingly recognised as an informative tool to understand ancient diet and health. As an archaeological deposit, it may contain non-dietary debris which permits the exploration of human behaviour and activities. While optical and scanning electron microscopy were the original analytical methods utilised to study microparticles entrapped within the calcified matrix, more recently, molecular approaches, including ancient DNA (aDNA) and protein analyses, have been applied. Oral bacteria, a major component of calculus, is the primary target of these aDNA studies. Such analyses can detect changes in the oral microbiota, including those that have reflected the shift from agriculture to industrialisation, as well as identifying markers for various systemic diseases. CI - © 2022. The Author(s), under exclusive licence to the British Dental Association. FAU - Forshaw, Roger AU - Forshaw R AD - KNH Centre for Biomedical Egyptology, Faculty of Biology, Medicine and Health, Manchester University, Stopford Building, Oxford Road, Manchester, M13 9PL, UK. Roger.Forshaw@manchester.ac.uk. LA - eng PT - Journal Article PT - Review DEP - 20221209 PL - England TA - Br Dent J JT - British dental journal JID - 7513219 SB - IM MH - Humans MH - Dental Calculus MH - Oral Health MH - Archaeology MH - *Dental Plaque MH - *Microbiota PMC - PMC9734501 COIS- The author declares no conflicts of interest. EDAT- 2022/12/10 06:00 MHDA- 2022/12/15 06:00 PMCR- 2022/12/10 CRDT- 2022/12/09 23:41 PHST- 2022/01/28 00:00 [received] PHST- 2022/05/09 00:00 [accepted] PHST- 2022/12/09 23:41 [entrez] PHST- 2022/12/10 06:00 [pubmed] PHST- 2022/12/15 06:00 [medline] PHST- 2022/12/10 00:00 [pmc-release] AID - 10.1038/s41415-022-5266-7 [pii] AID - 5266 [pii] AID - 10.1038/s41415-022-5266-7 [doi] PST - ppublish SO - Br Dent J. 2022 Dec;233(11):961-967. doi: 10.1038/s41415-022-5266-7. Epub 2022 Dec 9. PMID- 36174312 OWN - NLM STAT- MEDLINE DCOM- 20221122 LR - 20221220 IS - 1879-9825 (Electronic) IS - 1879-9817 (Linking) VI - 39 DP - 2022 Dec TI - Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis. PG - 20-34 LID - S1879-9817(22)00042-0 [pii] LID - 10.1016/j.ijpp.2022.08.002 [doi] AB - OBJECTIVE: To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 (th) century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis. METHODS: Shotgun sequencing data from was examined to determine the presence of Brucella DNA. RESULTS: Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7-169), but for many the data quality was insufficient to withstand our identification and authentication criteria. CONCLUSIONS: We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification. SIGNIFICANCE: Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease. LIMITATIONS: Study focuses on pathogen recovery in a single individual. SUGGESTIONS FOR FURTHER RESEARCH: Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples. CI - Copyright © 2022 Elsevier Inc. All rights reserved. FAU - Hider, Jessica AU - Hider J AD - McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada. Electronic address: hiderj@mcmaster.ca. FAU - Duggan, Ana T AU - Duggan AT AD - McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada. FAU - Klunk, Jennifer AU - Klunk J AD - McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Daicel Arbor Biosciences, 5840 Interface Drive, Suite 101, Ann Arbor, MI 48103, USA. FAU - Eaton, Katherine AU - Eaton K AD - McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada. FAU - Long, George S AU - Long GS AD - Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada. FAU - Karpinski, Emil AU - Karpinski E AD - McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada. FAU - Giuffra, Valentina AU - Giuffra V AD - Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, Medical School, via Roma 57, 56126 Pisa, PI, Italy. FAU - Ventura, Luca AU - Ventura L AD - Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy; Division of Pathology, San Salvatore Hospital, University of L'Aquila, Coppito, 67100 L'Aquila, AQ, Italy. FAU - Fornaciari, Antonio AU - Fornaciari A AD - Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, Medical School, via Roma 57, 56126 Pisa, PI, Italy. FAU - Fornaciari, Gino AU - Fornaciari G AD - Maria Luisa di Borbone Academy, Villa Borbone, viale dei Tigli 32, 55049 Viareggio, LU, Italy. FAU - Golding, G Brian AU - Golding GB AD - Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada. FAU - Prowse, Tracy L AU - Prowse TL AD - Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada. FAU - Poinar, Hendrik N AU - Poinar HN AD - McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L9, Canada. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220926 PL - Netherlands TA - Int J Paleopathol JT - International journal of paleopathology JID - 101562474 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *Brucella melitensis/genetics MH - DNA, Ancient MH - *Monks MH - *Brucellosis MH - Italy OTO - NOTNLM OT - Ancient DNA OT - Bioinformatics OT - Brucellosis OT - Sample selection OT - Shotgun sequencing COIS- Declaration of Competing Interest The authors report no declarations of interest. EDAT- 2022/09/30 06:00 MHDA- 2022/11/23 06:00 CRDT- 2022/09/29 18:18 PHST- 2022/03/12 00:00 [received] PHST- 2022/08/05 00:00 [revised] PHST- 2022/08/13 00:00 [accepted] PHST- 2022/09/30 06:00 [pubmed] PHST- 2022/11/23 06:00 [medline] PHST- 2022/09/29 18:18 [entrez] AID - S1879-9817(22)00042-0 [pii] AID - 10.1016/j.ijpp.2022.08.002 [doi] PST - ppublish SO - Int J Paleopathol. 2022 Dec;39:20-34. doi: 10.1016/j.ijpp.2022.08.002. Epub 2022 Sep 26. PMID- 35210171 OWN - NLM STAT- MEDLINE DCOM- 20221128 LR - 20230123 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 137 DP - 2022 Dec TI - Metagenomic analysis reveals mixed Mycobacterium tuberculosis infection in a 18th century Hungarian midwife. PG - 102181 LID - S1472-9792(22)00018-X [pii] LID - 10.1016/j.tube.2022.102181 [doi] AB - The Vác Mummy Collection comprises 265 well documented mummified individuals from the late 16th to the early 18th century that were discovered in 1994 inside a crypt in Vác, Hungary. This collection offers a unique opportunity to study the relationship between humans and pathogens in the pre-antibiotic era, as previous studies have shown a high proportion of tuberculosis (TB) infections among the individuals. In this study, we recovered ancient DNA with shotgun sequencing from a rib bone sample of a 18th century midwife. This individual is part of the collection and shows clear skeletal changes that are associated with tuberculosis and syphilis. To provide molecular proof, we applied a metagenomic approach to screen for ancient pathogen DNA. While we were unsuccessful to recover any ancient Treponema pallidum DNA, we retrieved high coverage ancient TB DNA and identified a mixed infection with two distinct TB strains by detailed single-nucleotide polymorphism and phylogenetic analysis. Thereby, we have obtained comprehensive results demonstrating the long-time prevalence of mixed infections with the sublineages L4.1.2.1/Haarlem and L4.10/PGG3 within the local community in preindustrial Hungary and put them in context of sociohistorical factors. CI - Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Jäger, Heidi Y AU - Jäger HY AD - Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy. Electronic address: heidi.jaeger@eurac.edu. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy. Electronic address: frank.maixner@eurac.edu. FAU - Pap, Ildikó AU - Pap I AD - Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary; Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter sétány 1/c, Hungary. Electronic address: ildiko.pap.2@hotmail.com. FAU - Szikossy, Ildikó AU - Szikossy I AD - Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary; Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika tér 2-6, Hungary. Electronic address: szikossy@gmail.com. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary. Electronic address: palfigy@bio.u-szeged.hu. FAU - Zink, Albert R AU - Zink AR AD - Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy. Electronic address: albert.zink@eurac.edu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220221 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 0 (DNA, Bacterial) SB - IM MH - Female MH - Humans MH - *Coinfection/microbiology MH - DNA, Bacterial/genetics/analysis MH - Hungary MH - *Midwifery MH - *Mycobacterium tuberculosis/genetics MH - Phylogeny MH - *Tuberculosis/diagnosis/history MH - History, 18th Century MH - Metagenome OTO - NOTNLM OT - Ancient DNA OT - Metagenomics OT - Mixed infection OT - Phylogeny OT - Single nucleotide polymorphisms COIS- Declaration of competing interest We declare we have no competing interests. EDAT- 2022/02/26 06:00 MHDA- 2022/11/26 06:00 CRDT- 2022/02/25 05:33 PHST- 2021/12/07 00:00 [received] PHST- 2022/01/12 00:00 [revised] PHST- 2022/02/03 00:00 [accepted] PHST- 2022/02/26 06:00 [pubmed] PHST- 2022/11/26 06:00 [medline] PHST- 2022/02/25 05:33 [entrez] AID - S1472-9792(22)00018-X [pii] AID - 10.1016/j.tube.2022.102181 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2022 Dec;137:102181. doi: 10.1016/j.tube.2022.102181. Epub 2022 Feb 21. PMID- 36300941 OWN - NLM STAT- MEDLINE DCOM- 20221128 LR - 20221208 IS - 1098-5514 (Electronic) IS - 0022-538X (Print) IS - 0022-538X (Linking) VI - 96 IP - 22 DP - 2022 Nov 23 TI - Evolutionary Analysis of Placental Orthologues Reveals Two Ancient DNA Virus Integrations. PG - e0093322 LID - 10.1128/jvi.00933-22 [doi] LID - e00933-22 AB - The genomes of eukaryotes preserve a vast diversity of ancient viruses in the form of endogenous viral elements (EVEs). Study of this genomic fossil record provides insights into the diversity, origin, and evolution of viruses across geological timescales. In particular, Mavericks have emerged as one of the oldest groups of endogenous viruses infecting vertebrates (≥419 million years [My]). They have been found in the genomes of fish, amphibians, birds, and nonavian reptiles but had been overlooked in mammals. Thus, their evolutionary history and the causes of their demise in mammals remain puzzling questions. Here, we conducted a detailed evolutionary study of two Maverick integrations found on human chromosomes 7 and 8. We performed a comparative analysis of the integrations and determined their orthology across placental mammals (Eutheria) via the syntenic arrangement of neighboring genes. The integrations were absent at the orthologous sites in the genomes of marsupials and monotremes. These observations allowed us to reconstruct a time-calibrated phylogeny and infer the age of their most recent common ancestor at 127 to 262 My. In addition, we estimate the age of the individual integrations at ~102 My, which represents the oldest nonretroviral EVEs found in the human genome. Our findings suggest that active Mavericks still existed in the ancestors of modern mammals ~172 My ago (Jurassic Period) and potentially to the end of the Early Cretaceous. We hypothesize that Mavericks could have gone extinct in mammals from the evolution of an antiviral defense system or from reduced opportunities for transmission in terrestrial hosts. IMPORTANCE The genomes of vertebrates preserve a large diversity of endogenous viral elements (remnants of ancient viruses that accumulate in host genomes over evolutionary time). Although retroviruses account for the vast majority of these elements, diverse DNA viruses have also been found and novel lineages are being described. Here, we analyzed two elements found in the human genome belonging to an ancient group of DNA viruses called Mavericks. We studied their evolutionary history, finding that the elements are shared between humans and many different species of placental mammals. These observations suggest that the elements inserted at least ~102 million years ago (Mya) in the most recent common ancestor of placentals. We further estimated the age of the viral ancestor at around 127 to 262 My. Our results provide evidence for some of the oldest viral integrations in the human genome and insights into the ancient interactions of viruses with the ancestors of modern-day mammals. FAU - Nino Barreat, Jose Gabriel AU - Nino Barreat JG AUID- ORCID: 0000-0002-4589-9473 AD - Department of Biology, University of Oxfordgrid.4991.5, Oxford, United Kingdom. FAU - Katzourakis, Aris AU - Katzourakis A AUID- ORCID: 0000-0003-3328-6204 AD - Department of Biology, University of Oxfordgrid.4991.5, Oxford, United Kingdom. LA - eng SI - figshare/10.6084/m9.figshare.17819708 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221027 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Female MH - Humans MH - Pregnancy MH - *DNA, Ancient MH - Eutheria MH - *Evolution, Molecular MH - Genome, Human MH - *Mammals/genetics/virology MH - Marsupialia MH - Phylogeny MH - Virus Integration MH - *DNA Viruses/genetics PMC - PMC9683012 OTO - NOTNLM OT - EVEs OT - Homo sapiens OT - comparative genomics OT - endogenous viral elements OT - paleovirology COIS- The authors declare no conflict of interest. EDAT- 2022/10/28 06:00 MHDA- 2022/11/26 06:00 PMCR- 2022/10/27 CRDT- 2022/10/27 09:04 PHST- 2022/10/28 06:00 [pubmed] PHST- 2022/11/26 06:00 [medline] PHST- 2022/10/27 09:04 [entrez] PHST- 2022/10/27 00:00 [pmc-release] AID - 00933-22 [pii] AID - jvi.00933-22 [pii] AID - 10.1128/jvi.00933-22 [doi] PST - ppublish SO - J Virol. 2022 Nov 23;96(22):e0093322. doi: 10.1128/jvi.00933-22. Epub 2022 Oct 27. PMID- 36399550 OWN - NLM STAT- MEDLINE DCOM- 20221122 LR - 20221218 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 119 IP - 47 DP - 2022 Nov 22 TI - Earliest evidence of primate captivity and translocation supports gift diplomacy between Teotihuacan and the Maya. PG - e2212431119 LID - 10.1073/pnas.2212431119 [doi] LID - e2212431119 AB - A multimethod archaeometry study (zooarchaeological, isotopic, ancient DNA, paleobotanical, and radiocarbon dating) of a spider monkey sacrificed in the ceremonial center of Teotihuacan, Mexico (1 to 550 CE) is interpreted as a diplomatic gift exchange with neighboring Maya. Not only does this spider monkey provide the earliest known instance of primate translocation and captivity in Mesoamerica, it helps date incipient modes of interregional diplomacy between two major powers during Early Classic Mesoamerica: Teotihuacan and the Maya. Details of human-primate interaction include age at capture and transport (before ∼3 y of age), captive duration (over 2 y), anthropogenic diet (staple was maize, though secondary resources unique to anthropogenic diet including arrowroot and chili pepper were also found), context of sacrifice (tethered and associated with complete golden eagle and an array of other statecrafts), and general site context (including presence of Maya vessels and Maya-style murals). The timing of the spider monkey's sacrifice (250 to 300 CE) and its life history suggest a reconsideration of epigraphically attested militaristic involvement of Teotihuacan at certain Maya sites. We propose that a period of more multilateral and fluid ritual exchange with Maya dignitaries preceded the Teotihuacan state's eventual ascent to prominence. FAU - Sugiyama, Nawa AU - Sugiyama N AUID- ORCID: 0000-0002-5734-6462 AD - Department of Anthropology, University of California, Riverside, CA 92521. FAU - Sugiyama, Saburo AU - Sugiyama S AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287. AD - Research Institute for the Dynamics of Civilizations, Okayama University, Okayama 700-8530, Japan. FAU - Cagnato, Clarissa AU - Cagnato C AD - UMR 8096 Archéologie des Amériques, Paris 75004, France. FAU - France, Christine A M AU - France CAM AUID- ORCID: 0000-0001-9133-9058 AD - Smithsonian Museum Conservation Institute, Suitland, MD 20746. FAU - Iriki, Atsushi AU - Iriki A AUID- ORCID: 0000-0002-5262-163X AD - Laboratory for Symbolic Cognitive Development, Center for Biosystems Dynamics Research, RIKEN Institute, Kobe 650-0047, Japan. FAU - Hughes, Karissa S AU - Hughes KS AUID- ORCID: 0000-0002-8224-7431 AD - Department of Anthropology and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019. FAU - Singleton, Robin R AU - Singleton RR AUID- ORCID: 0000-0001-8564-5753 AD - Department of Anthropology and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019. FAU - Thornton, Erin AU - Thornton E AUID- ORCID: 0000-0003-0522-1294 AD - Department of Anthropology, Washington State University, Pullman, WA 99164. FAU - Hofman, Courtney A AU - Hofman CA AUID- ORCID: 0000-0002-6808-3370 AD - Department of Anthropology and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20221121 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Animals MH - *Diplomacy MH - Ceremonial Behavior MH - DNA, Ancient MH - *Atelinae MH - Mexico PMC - PMC9704712 OTO - NOTNLM OT - Mesoamerica OT - animal translocation OT - archaeometry OT - gift exchange OT - primate captivity COIS- The authors declare no competing interest. EDAT- 2022/11/19 06:00 MHDA- 2022/11/23 06:00 PMCR- 2022/11/21 CRDT- 2022/11/18 14:04 PHST- 2022/11/18 14:04 [entrez] PHST- 2022/11/19 06:00 [pubmed] PHST- 2022/11/23 06:00 [medline] PHST- 2022/11/21 00:00 [pmc-release] AID - 202212431 [pii] AID - 10.1073/pnas.2212431119 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2022 Nov 22;119(47):e2212431119. doi: 10.1073/pnas.2212431119. Epub 2022 Nov 21. PMID- 36400919 OWN - NLM STAT- MEDLINE DCOM- 20221122 LR - 20221220 IS - 2399-3642 (Electronic) IS - 2399-3642 (Linking) VI - 5 IP - 1 DP - 2022 Nov 18 TI - Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave. PG - 1262 LID - 10.1038/s42003-022-04190-2 [doi] LID - 1262 AB - Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology. CI - © 2022. The Author(s). FAU - Scorrano, Gabriele AU - Scorrano G AUID- ORCID: 0000-0002-0887-4023 AD - Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. g.scorrano@sund.ku.dk. AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. g.scorrano@sund.ku.dk. FAU - Nielsen, Sofie Holtsmark AU - Nielsen SH AUID- ORCID: 0000-0001-7463-360X AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Vetro, Domenico Lo AU - Vetro DL AUID- ORCID: 0000-0002-0663-6443 AD - Dipartimento di Storia, Archeologia, Geografia, Arte e Spettacolo (SAGAS), University of Florence, Florence, Italy. AD - Museo e Istituto Fiorentino di Preistoria, Florence, Italy. FAU - Sawafuji, Rikai AU - Sawafuji R AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Mackie, Meaghan AU - Mackie M AD - Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Margaryan, Ashot AU - Margaryan A AD - Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark. FAU - Fotakis, Anna K AU - Fotakis AK AD - Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Martínez-Labarga, Cristina AU - Martínez-Labarga C AD - Centro di Antropologia Molecolare per lo studio del DNA antico, Dipartimento di Biologia, University of Rome Tor Vergata, Rome, Italy. FAU - Fabbri, Pier Francesco AU - Fabbri PF AUID- ORCID: 0000-0003-3633-0178 AD - Dipartimento di Beni Culturali, University of Salento, Lecce, Italy. FAU - Allentoft, Morten E AU - Allentoft ME AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia. FAU - Carra, Marialetizia AU - Carra M AUID- ORCID: 0000-0001-5656-9157 AD - DANTE: Diet and Ancient Technology Laboratory, Sapienza University of Rome, Rome, Italy. FAU - Martini, Fabio AU - Martini F AD - Dipartimento di Storia, Archeologia, Geografia, Arte e Spettacolo (SAGAS), University of Florence, Florence, Italy. AD - Museo e Istituto Fiorentino di Preistoria, Florence, Italy. FAU - Rickards, Olga AU - Rickards O AUID- ORCID: 0000-0003-2880-7466 AD - Centro di Antropologia Molecolare per lo studio del DNA antico, Dipartimento di Biologia, University of Rome Tor Vergata, Rome, Italy. FAU - Olsen, Jesper V AU - Olsen JV AUID- ORCID: 0000-0002-4747-4938 AD - Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Pedersen, Mikkel Winther AU - Pedersen MW AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Cappellini, Enrico AU - Cappellini E AUID- ORCID: 0000-0001-7885-7811 AD - Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. ecappellini@sund.ku.dk. FAU - Sikora, Martin AU - Sikora M AUID- ORCID: 0000-0003-2818-8319 AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. martin.sikora@sund.ku.dk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221118 PL - England TA - Commun Biol JT - Communications biology JID - 101719179 SB - IM MH - Humans MH - Animals MH - *Proteomics MH - Dental Calculus MH - Diet MH - Genomics MH - *Microbiota/genetics PMC - PMC9674856 COIS- The authors declare no competing interests. EDAT- 2022/11/19 06:00 MHDA- 2022/11/23 06:00 PMCR- 2022/11/18 CRDT- 2022/11/18 23:47 PHST- 2021/12/21 00:00 [received] PHST- 2022/10/31 00:00 [accepted] PHST- 2022/11/19 06:00 [pubmed] PHST- 2022/11/23 06:00 [medline] PHST- 2022/11/18 23:47 [entrez] PHST- 2022/11/18 00:00 [pmc-release] AID - 10.1038/s42003-022-04190-2 [pii] AID - 4190 [pii] AID - 10.1038/s42003-022-04190-2 [doi] PST - epublish SO - Commun Biol. 2022 Nov 18;5(1):1262. doi: 10.1038/s42003-022-04190-2. PMID- 36322514 OWN - NLM STAT- MEDLINE DCOM- 20221104 LR - 20230418 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 289 IP - 1986 DP - 2022 Nov 9 TI - Genomic evidence for ancient human migration routes along South America's Atlantic coast. PG - 20221078 LID - 10.1098/rspb.2022.1078 [doi] LID - 20221078 AB - An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level. FAU - Campelo Dos Santos, Andre Luiz AU - Campelo Dos Santos AL AD - Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA. AD - Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco 50670-901, Brazil. FAU - Owings, Amanda AU - Owings A AD - Department of Anthropology, Emory University, Atlanta, GA 30322, USA. FAU - Sullasi, Henry Socrates Lavalle AU - Sullasi HSL AD - Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco 50670-901, Brazil. FAU - Gokcumen, Omer AU - Gokcumen O AD - Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA. FAU - DeGiorgio, Michael AU - DeGiorgio M AD - Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA. FAU - Lindo, John AU - Lindo J AUID- ORCID: 0000-0002-2533-8505 AD - Department of Anthropology, Emory University, Atlanta, GA 30322, USA. LA - eng GR - R35 GM128590/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20221102 PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 SB - IM MH - Humans MH - History, Ancient MH - Animals MH - *Human Migration MH - Genomics MH - Genome, Human MH - *Neanderthals MH - Brazil PMC - PMC9629774 OTO - NOTNLM OT - Northeast Brazil OT - ancient migrations OT - archaeogenomics OT - settlement of the Americas COIS- We declare we have no competing interests. EDAT- 2022/11/03 06:00 MHDA- 2022/11/05 06:00 PMCR- 2022/11/02 CRDT- 2022/11/02 13:32 PHST- 2022/11/02 13:32 [entrez] PHST- 2022/11/03 06:00 [pubmed] PHST- 2022/11/05 06:00 [medline] PHST- 2022/11/02 00:00 [pmc-release] AID - rspb20221078 [pii] AID - 10.1098/rspb.2022.1078 [doi] PST - ppublish SO - Proc Biol Sci. 2022 Nov 9;289(1986):20221078. doi: 10.1098/rspb.2022.1078. Epub 2022 Nov 2. PMID- 36426357 OWN - NLM STAT- MEDLINE DCOM- 20221128 LR - 20231101 IS - 1664-3224 (Electronic) IS - 1664-3224 (Linking) VI - 13 DP - 2022 TI - Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions. PG - 987655 LID - 10.3389/fimmu.2022.987655 [doi] LID - 987655 AB - Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype's typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools' robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA's typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype's typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high. CI - Copyright © 2022 Thuesen, Klausen, Gopalakrishnan, Trolle and Renaud. FAU - Thuesen, Nikolas Hallberg AU - Thuesen NH AD - Evaxion Biotech, Copenhagen, Denmark. AD - Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark. FAU - Klausen, Michael Schantz AU - Klausen MS AD - Evaxion Biotech, Copenhagen, Denmark. FAU - Gopalakrishnan, Shyam AU - Gopalakrishnan S AD - Section for Hologenomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark. FAU - Trolle, Thomas AU - Trolle T AD - Evaxion Biotech, Copenhagen, Denmark. FAU - Renaud, Gabriel AU - Renaud G AD - Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221108 PL - Switzerland TA - Front Immunol JT - Frontiers in immunology JID - 101560960 RN - 0 (HLA-A Antigens) SB - IM MH - Humans MH - Sequence Analysis, DNA/methods MH - Histocompatibility Testing/methods MH - *High-Throughput Nucleotide Sequencing/methods MH - *HLA-A Antigens/genetics MH - Algorithms PMC - PMC9679531 OTO - NOTNLM OT - algorithm OT - benchmark OT - depth of coverage OT - human leukycote antigen OT - next-generation sequencing (NGS) OT - typing resolution OT - whole exome sequencing COIS- NT, MK and TT are employed by Evaxion Biotech and have a financial stake in the company. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. EDAT- 2022/11/26 06:00 MHDA- 2022/11/29 06:00 PMCR- 2022/01/01 CRDT- 2022/11/25 03:03 PHST- 2022/07/06 00:00 [received] PHST- 2022/10/10 00:00 [accepted] PHST- 2022/11/25 03:03 [entrez] PHST- 2022/11/26 06:00 [pubmed] PHST- 2022/11/29 06:00 [medline] PHST- 2022/01/01 00:00 [pmc-release] AID - 10.3389/fimmu.2022.987655 [doi] PST - epublish SO - Front Immunol. 2022 Nov 8;13:987655. doi: 10.3389/fimmu.2022.987655. eCollection 2022. PMID- 36282902 OWN - NLM STAT- MEDLINE DCOM- 20221027 LR - 20221116 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 119 IP - 45 DP - 2022 Nov 8 TI - Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics. PG - e2208703119 LID - 10.1073/pnas.2208703119 [doi] LID - e2208703119 AB - The world's oceans are currently facing major stressors in the form of overexploitation and anthropogenic climate change. The Baltic Sea was home to the first "industrial" fishery ∼800 y ago targeting the Baltic herring, a species that is still economically and culturally important today. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. Here, we study long-term population dynamics of Baltic herring to evaluate the past impacts of humans on the marine environment. We combine modern whole-genome data with ancient DNA (aDNA) to identify the earliest-known long-distance herring trade in the region, illustrating that extensive fish trade began during the Viking Age. We further resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Øresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Øresund fishery had a negative impact on the western Baltic herring stock, the demographic shift to spring-spawning dominance did not occur until the 20th century. Instead, demographic reconstructions reveal population trajectories consistent with expected impacts of environmental change and historical reports on shifting fishing targets over time. This study illustrates the joint impact of climate change and human exploitation on marine species as well as the role historical ecology can play in conservation and management policies. FAU - Atmore, Lane M AU - Atmore LM AUID- ORCID: 0000-0002-8903-8149 AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway. FAU - Martínez-García, Lourdes AU - Martínez-García L AUID- ORCID: 0000-0002-1582-3611 AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway. FAU - Makowiecki, Daniel AU - Makowiecki D AUID- ORCID: 0000-0002-1821-4627 AD - Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, 87-100 Toruń, Poland. FAU - André, Carl AU - André C AUID- ORCID: 0000-0003-4404-7292 AD - Department of Marine Sciences-Tjärnö, University of Gothenburg, 452 96 Strömstad, Sweden. FAU - Lõugas, Lembi AU - Lõugas L AUID- ORCID: 0000-0003-2011-2141 AD - Archaeological Research Collection, Tallinn University, 10120 Tallinn, Estonia. FAU - Barrett, James H AU - Barrett JH AUID- ORCID: 0000-0002-6683-9891 AD - Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7012 Trondheim, Norway. FAU - Star, Bastiaan AU - Star B AUID- ORCID: 0000-0003-0235-9810 AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221025 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Humans MH - *Fisheries MH - *DNA, Ancient MH - Conservation of Natural Resources MH - Population Dynamics MH - Fishes/genetics MH - Genomics MH - Baltic States PMC - PMC9659336 OTO - NOTNLM OT - ancient DNA OT - ecology OT - fisheries OT - history OT - sustainability COIS- The authors declare no competing interest. EDAT- 2022/10/26 06:00 MHDA- 2022/10/28 06:00 PMCR- 2022/10/25 CRDT- 2022/10/25 14:17 PHST- 2022/10/25 14:17 [entrez] PHST- 2022/10/26 06:00 [pubmed] PHST- 2022/10/28 06:00 [medline] PHST- 2022/10/25 00:00 [pmc-release] AID - 202208703 [pii] AID - 10.1073/pnas.2208703119 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2022 Nov 8;119(45):e2208703119. doi: 10.1073/pnas.2208703119. Epub 2022 Oct 25. PMID- 36344562 OWN - NLM STAT- MEDLINE DCOM- 20221109 LR - 20230105 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 12 IP - 1 DP - 2022 Nov 7 TI - Female bone physiology resilience in a past Polynesian Outlier community. PG - 18857 LID - 10.1038/s41598-022-23171-3 [doi] LID - 18857 AB - Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in 69 individuals from ca. 440-150 BP Taumako in Solomon Islands, a remote 'Polynesian Outlier' island in Melanesia. We tested whether bone remodelling indicators differed between age groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-osteon (~ 8%) did not differ between the sexes. Our results indicate that, compared to males, localised femoral bone tissue of the Taumako females did not drastically decline with age, contrary to what is often observed in modern populations. However, our results match findings in other archaeological samples-a testament to past female bone physiology resilience, also now observed in the Pacific region. CI - © 2022. The Author(s). FAU - Miszkiewicz, Justyna J AU - Miszkiewicz JJ AUID- ORCID: 0000-0002-9769-2706 AD - School of Archaeology and Anthropology, Australian National University, Canberra, Australia. j.miszkiewicz@uq.edu.au. AD - School of Social Science, University of Queensland, St Lucia, Australia. j.miszkiewicz@uq.edu.au. FAU - Buckley, Hallie R AU - Buckley HR AD - Department of Anatomy, Otago School of Biomedical Sciences, University of Otago, Dunedin, New Zealand. FAU - Feldman, Michal AU - Feldman M AD - Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Kiko, Lawrence AU - Kiko L AD - The Solomon Islands National Museum, Honiara, Solomon Islands. FAU - Carlhoff, Selina AU - Carlhoff S AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Naegele, Kathrin AU - Naegele K AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Bertolini, Emilie AU - Bertolini E AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Guimarães, Nathalia R Dias AU - Guimarães NRD AD - School of Archaeology and Anthropology, Australian National University, Canberra, Australia. FAU - Walker, Meg M AU - Walker MM AD - School of Archaeology and Anthropology, Australian National University, Canberra, Australia. FAU - Powell, Adam AU - Powell A AD - Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Posth, Cosimo AU - Posth C AD - Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Kinaston, Rebecca L AU - Kinaston RL AD - Department of Anatomy, Otago School of Biomedical Sciences, University of Otago, Dunedin, New Zealand. AD - Centre for Social and Cultural Research, Griffith University, Southport, QLD, Australia. AD - BioArch South, Waitati, New Zealand. LA - eng SI - figshare/10.6084/m9.figshare.16815295 GR - DE190100068/Australian Research Council/ GR - ERC758967/European Research Council Starting Grant 'Waves'/ PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221107 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Male MH - Humans MH - Female MH - *Haversian System MH - *Femur MH - Bone and Bones MH - Bone Remodeling MH - Melanesia PMC - PMC9640697 COIS- The authors declare no competing interests. EDAT- 2022/11/08 06:00 MHDA- 2022/11/10 06:00 PMCR- 2022/11/07 CRDT- 2022/11/07 23:22 PHST- 2022/02/17 00:00 [received] PHST- 2022/10/26 00:00 [accepted] PHST- 2022/11/07 23:22 [entrez] PHST- 2022/11/08 06:00 [pubmed] PHST- 2022/11/10 06:00 [medline] PHST- 2022/11/07 00:00 [pmc-release] AID - 10.1038/s41598-022-23171-3 [pii] AID - 23171 [pii] AID - 10.1038/s41598-022-23171-3 [doi] PST - epublish SO - Sci Rep. 2022 Nov 7;12(1):18857. doi: 10.1038/s41598-022-23171-3. PMID- 36182700 OWN - NLM STAT- MEDLINE DCOM- 20221110 LR - 20221214 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 32 IP - 21 DP - 2022 Nov 7 TI - The population genomic legacy of the second plague pandemic. PG - 4743-4751.e6 LID - S0960-9822(22)01467-1 [pii] LID - 10.1016/j.cub.2022.09.023 [doi] AB - Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.(1) It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).(2) Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17(th)-19(th) century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large F(ST) values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics. CI - Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Gopalakrishnan, Shyam AU - Gopalakrishnan S AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark. Electronic address: shyam.gopalakrishnan@sund.ku.dk. FAU - Ebenesersdóttir, S Sunna AU - Ebenesersdóttir SS AD - deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland. FAU - Lundstrøm, Inge K C AU - Lundstrøm IKC AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark. FAU - Turner-Walker, Gordon AU - Turner-Walker G AD - National Yunlin University of Science & Technology, 123 University Road, Section 3, 64002 Douliu, Yun-Lin County, Taiwan; Department of Archaeology and Anthropology, National Museum of Natural Science, 1 Guanqian Road, North District Taichung City 404023, Taiwan. FAU - Moore, Kristjan H S AU - Moore KHS AD - deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland. FAU - Luisi, Pierre AU - Luisi P AD - Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina; Microbial Paleogenomics Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France. FAU - Margaryan, Ashot AU - Margaryan A AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark. FAU - Martin, Michael D AU - Martin MD AD - NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway. FAU - Ellegaard, Martin Rene AU - Ellegaard MR AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway. FAU - Magnússon, Ólafur Þ AU - Magnússon ÓÞ AD - deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland. FAU - Sigurðsson, Ásgeir AU - Sigurðsson Á AD - deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland. FAU - Snorradóttir, Steinunn AU - Snorradóttir S AD - deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland. FAU - Magnúsdóttir, Droplaug N AU - Magnúsdóttir DN AD - deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland. FAU - Laffoon, Jason E AU - Laffoon JE AD - Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, Leiden, the Netherlands. FAU - van Dorp, Lucy AU - van Dorp L AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK. FAU - Liu, Xiaodong AU - Liu X AD - Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. FAU - Moltke, Ida AU - Moltke I AD - Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AD - International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), Universidad Nacional Autónoma de México (UNAM), 3001 Boulevard Juriquilla, 76230 Querétaro, Mexico. FAU - Schraiber, Joshua G AU - Schraiber JG AD - Illumina Artificial Intelligence Laboratory, Illumina Inc., San Diego, CA, USA. FAU - Rasmussen, Simon AU - Rasmussen S AD - Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark. FAU - Juan, David AU - Juan D AD - Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain. FAU - Gelabert, Pere AU - Gelabert P AD - Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - de-Dios, Toni AU - de-Dios T AD - Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain. FAU - Fotakis, Anna K AU - Fotakis AK AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark. FAU - Iraeta-Orbegozo, Miren AU - Iraeta-Orbegozo M AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark. FAU - Vågene, Åshild J AU - Vågene ÅJ AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Denham, Sean Dexter AU - Denham SD AD - Museum of Archaeology, University of Stavanger, Stavanger, Norway. FAU - Christophersen, Axel AU - Christophersen A AD - NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway. FAU - Stenøien, Hans K AU - Stenøien HK AD - NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway. FAU - Vieira, Filipe G AU - Vieira FG AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark. FAU - Liu, Shanlin AU - Liu S AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. FAU - Günther, Torsten AU - Günther T AD - Evolutionsbiologisk Centrum EBC, Norbyv. 18A, 752 36 Uppsala, Sweden. FAU - Kivisild, Toomas AU - Kivisild T AD - KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia. FAU - Moseng, Ole Georg AU - Moseng OG AD - Department of Business, History and Social Sciences, University of South-Eastern Norway, Notodden, Norway. FAU - Skar, Birgitte AU - Skar B AD - NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway. FAU - Cheung, Christina AU - Cheung C AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; EA - Eco-anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France. FAU - Sandoval-Velasco, Marcela AU - Sandoval-Velasco M AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark. FAU - Wales, Nathan AU - Wales N AD - Department of Archaeology, Kings Manor and Principals House, University of York, Exhibition Square, York YO1 7EP, UK. FAU - Schroeder, Hannes AU - Schroeder H AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark. FAU - Campos, Paula F AU - Campos PF AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal. FAU - Guðmundsdóttir, Valdís B AU - Guðmundsdóttir VB AD - deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland. FAU - Sicheritz-Ponten, Thomas AU - Sicheritz-Ponten T AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia. FAU - Petersen, Bent AU - Petersen B AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia. FAU - Halgunset, Jostein AU - Halgunset J AD - Biobank1, St. Olavs Hospital HF, Trondheim, Norway. FAU - Gilbert, Edmund AU - Gilbert E AD - School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, Dublin, Ireland. FAU - Cavalleri, Gianpiero L AU - Cavalleri GL AD - School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, Dublin, Ireland. FAU - Hovig, Eivind AU - Hovig E AD - Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway. FAU - Kockum, Ingrid AU - Kockum I AD - Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden. FAU - Olsson, Tomas AU - Olsson T AD - Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden. FAU - Alfredsson, Lars AU - Alfredsson L AD - Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden. FAU - Hansen, Thomas F AU - Hansen TF AD - Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark. FAU - Werge, Thomas AU - Werge T AD - Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark; The Globe Institute, Lundbeck Foundation Center for Geogenetics, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. FAU - Balloux, Francois AU - Balloux F AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK. FAU - Marques-Bonet, Tomas AU - Marques-Bonet T AD - Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Museu de Ciències Naturals de Barcelona, 08019 Barcelona, Spain. FAU - Nielsen, Rasmus AU - Nielsen R AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720-3140, USA. FAU - Stefánsson, Kári AU - Stefánsson K AD - deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Faculty of Medicine, University of Iceland, Reykjavík, Iceland. FAU - Helgason, Agnar AU - Helgason A AD - deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland. FAU - Gilbert, M Thomas P AU - Gilbert MTP AD - The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221001 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Humans MH - *Plague/epidemiology/genetics MH - Pandemics/history MH - Metagenomics MH - Genome, Bacterial MH - Phylogeny PMC - PMC9671091 OTO - NOTNLM OT - Trondheim OT - Yersinia pestis OT - pandemic genomics OT - plague OT - population genomics OT - population replacement OT - second plague pandemic OT - selection COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/10/02 06:00 MHDA- 2022/11/11 06:00 PMCR- 2022/11/07 CRDT- 2022/10/01 23:04 PHST- 2022/06/07 00:00 [received] PHST- 2022/06/15 00:00 [revised] PHST- 2022/09/09 00:00 [accepted] PHST- 2022/10/02 06:00 [pubmed] PHST- 2022/11/11 06:00 [medline] PHST- 2022/10/01 23:04 [entrez] PHST- 2022/11/07 00:00 [pmc-release] AID - S0960-9822(22)01467-1 [pii] AID - 10.1016/j.cub.2022.09.023 [doi] PST - ppublish SO - Curr Biol. 2022 Nov 7;32(21):4743-4751.e6. doi: 10.1016/j.cub.2022.09.023. Epub 2022 Oct 1. PMID- 36517229 OWN - NLM STAT- MEDLINE DCOM- 20230111 LR - 20230123 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 32 IP - 11-12 DP - 2022 Nov-Dec TI - Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs. PG - 2068-2078 LID - 10.1101/gr.276728.122 [doi] AB - The strategy of in-solution enrichment for hundreds of thousands of single-nucleotide polymorphisms (SNPs) has been used to analyze >70% of individuals with genome-scale ancient DNA published to date. This approach makes it economical to study ancient samples with low proportions of human DNA and increases the rate of conversion of sampled remains into interpretable data. So far, nearly all such data have been generated using a set of bait sequences targeting about 1.24 million SNPs (the "1240k reagent"), but synthesis of the reagent has been cost-effective for only a few laboratories. In 2021, two companies, Daicel Arbor Biosciences and Twist Bioscience, made available assays that target the same core set of SNPs along with supplementary content. We test all three assays on a common set of 27 ancient DNA libraries and show that all three are effective at enriching many hundreds of thousands of SNPs. For all assays, one round of enrichment produces data that are as useful as two. In our testing, the "Twist Ancient DNA" assay produces the highest coverages, greatest uniformity on targeted positions, and almost no bias toward enriching one allele more than another relative to shotgun sequencing. We also identify hundreds of thousands of targeted SNPs for which there is minimal allelic bias when comparing 1240k data to either shotgun or Twist data. This facilitates coanalysis of the large data sets that have been generated using 1240k and Twist capture, as well as shotgun sequencing approaches. CI - © 2022 Rohland et al.; Published by Cold Spring Harbor Laboratory Press. FAU - Rohland, Nadin AU - Rohland N AUID- ORCID: 0000-0002-8112-9601 AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. FAU - Mallick, Swapan AU - Mallick S AUID- ORCID: 0000-0002-8442-9757 AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA. FAU - Mah, Matthew AU - Mah M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA. FAU - Maier, Robert AU - Maier R AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. FAU - Patterson, Nick AU - Patterson N AUID- ORCID: 0000-0002-2220-3648 AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20221214 PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - *DNA, Ancient/analysis MH - Sequence Analysis, DNA MH - *Polymorphism, Single Nucleotide MH - DNA/genetics MH - Gene Library PMC - PMC9808625 EDAT- 2022/12/15 06:00 MHDA- 2023/01/12 06:00 PMCR- 2022/11/01 CRDT- 2022/12/14 21:51 PHST- 2022/03/05 00:00 [received] PHST- 2022/11/16 00:00 [accepted] PHST- 2022/12/15 06:00 [pubmed] PHST- 2023/01/12 06:00 [medline] PHST- 2022/12/14 21:51 [entrez] PHST- 2022/11/01 00:00 [pmc-release] AID - gr.276728.122 [pii] AID - 10.1101/gr.276728.122 [doi] PST - ppublish SO - Genome Res. 2022 Nov-Dec;32(11-12):2068-2078. doi: 10.1101/gr.276728.122. Epub 2022 Dec 14. PMID- 36316157 OWN - NLM STAT- MEDLINE DCOM- 20230111 LR - 20230506 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 32 IP - 11-12 DP - 2022 Nov-Dec TI - Direct detection of natural selection in Bronze Age Britain. PG - 2057-2067 LID - 10.1101/gr.276862.122 [doi] AB - We developed a novel method for efficiently estimating time-varying selection coefficients from genome-wide ancient DNA data. In simulations, our method accurately recovers selective trajectories and is robust to misspecification of population size. We applied it to a large data set of ancient and present-day human genomes from Britain and identified seven loci with genome-wide significant evidence of selection in the past 4500 yr. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength of selection on individual loci varied substantially over time, suggesting that cultural or environmental factors moderated the genetic response. Of 28 complex anthropometric and metabolic traits, skin pigmentation was the only one with significant evidence of polygenic selection, further underscoring the importance of phenotypes related to vitamin D. Our approach illustrates the power of ancient DNA to characterize selection in human populations and illuminates the recent evolutionary history of Britain. CI - © 2022 Mathieson and Terhorst; Published by Cold Spring Harbor Laboratory Press. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. FAU - Terhorst, Jonathan AU - Terhorst J AUID- ORCID: 0000-0001-7765-2101 AD - Department of Statistics, University of Michigan, Ann Arbor, Michigan 48109, USA. LA - eng GR - R35 GM133708/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20221031 PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - United Kingdom MH - *Selection, Genetic MH - Skin Pigmentation MH - Genome, Human PMC - PMC9808619 EDAT- 2022/11/01 06:00 MHDA- 2023/01/12 06:00 PMCR- 2023/05/01 CRDT- 2022/10/31 21:42 PHST- 2022/04/24 00:00 [received] PHST- 2022/08/29 00:00 [accepted] PHST- 2022/11/01 06:00 [pubmed] PHST- 2023/01/12 06:00 [medline] PHST- 2022/10/31 21:42 [entrez] PHST- 2023/05/01 00:00 [pmc-release] AID - gr.276862.122 [pii] AID - 10.1101/gr.276862.122 [doi] PST - ppublish SO - Genome Res. 2022 Nov-Dec;32(11-12):2057-2067. doi: 10.1101/gr.276862.122. Epub 2022 Oct 31. PMID- 36261712 OWN - NLM STAT- MEDLINE DCOM- 20221109 LR - 20221114 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 611 IP - 7935 DP - 2022 Nov TI - Ancient DNA reveals rapid natural selection during the Black Death. PG - 237-238 LID - 10.1038/d41586-022-03160-2 [doi] FAU - Enard, David AU - Enard D LA - eng PT - Comment PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM CON - Nature. 2022 Nov;611(7935):312-319. doi: 10.1038/s41586-022-05349-x. PMID: 36261521 MH - Humans MH - *DNA, Ancient MH - *Plague MH - Selection, Genetic MH - Evolution, Molecular OTO - NOTNLM OT - Evolution OT - Genetics OT - Immunology EDAT- 2022/10/20 06:00 MHDA- 2022/11/10 06:00 CRDT- 2022/10/19 23:41 PHST- 2022/10/20 06:00 [pubmed] PHST- 2022/11/10 06:00 [medline] PHST- 2022/10/19 23:41 [entrez] AID - 10.1038/d41586-022-03160-2 [pii] AID - 10.1038/d41586-022-03160-2 [doi] PST - ppublish SO - Nature. 2022 Nov;611(7935):237-238. doi: 10.1038/d41586-022-03160-2. PMID- 36261521 OWN - NLM STAT- MEDLINE DCOM- 20221118 LR - 20250115 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 611 IP - 7935 DP - 2022 Nov TI - Evolution of immune genes is associated with the Black Death. PG - 312-319 LID - 10.1038/s41586-022-05349-x [doi] AB - Infectious diseases are among the strongest selective pressures driving human evolution(1,2). This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis(3). This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population(4). To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease. CI - © 2022. The Author(s), under exclusive licence to Springer Nature Limited. FAU - Klunk, Jennifer AU - Klunk J AUID- ORCID: 0000-0002-6521-8516 AD - McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada. AD - Daicel Arbor Biosciences, Ann Arbor, MI, USA. FAU - Vilgalys, Tauras P AU - Vilgalys TP AUID- ORCID: 0000-0002-0615-6888 AD - Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA. FAU - Demeure, Christian E AU - Demeure CE AUID- ORCID: 0000-0001-7195-1645 AD - Yersinia Research Unit, Institut Pasteur, Paris, France. FAU - Cheng, Xiaoheng AU - Cheng X AD - Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA. FAU - Shiratori, Mari AU - Shiratori M AD - Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA. FAU - Madej, Julien AU - Madej J AD - Yersinia Research Unit, Institut Pasteur, Paris, France. FAU - Beau, Rémi AU - Beau R AD - Yersinia Research Unit, Institut Pasteur, Paris, France. FAU - Elli, Derek AU - Elli D AD - Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA. FAU - Patino, Maria I AU - Patino MI AD - Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA. FAU - Redfern, Rebecca AU - Redfern R AD - Centre for Human Bioarchaeology, Museum of London, London, UK. FAU - DeWitte, Sharon N AU - DeWitte SN AUID- ORCID: 0000-0003-0754-8485 AD - Department of Anthropology, University of South Carolina, Columbia, SC, USA. FAU - Gamble, Julia A AU - Gamble JA AUID- ORCID: 0000-0001-7486-757X AD - Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, Canada. FAU - Boldsen, Jesper L AU - Boldsen JL AD - Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, Denmark. FAU - Carmichael, Ann AU - Carmichael A AUID- ORCID: 0000-0001-7516-7460 AD - History Department, Indiana University, Bloomington, IN, USA. FAU - Varlik, Nükhet AU - Varlik N AD - Department of History, Rutgers University, Newark, NJ, USA. FAU - Eaton, Katherine AU - Eaton K AD - McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada. FAU - Grenier, Jean-Christophe AU - Grenier JC AUID- ORCID: 0000-0001-7937-5160 AD - Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada. FAU - Golding, G Brian AU - Golding GB AD - McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada. FAU - Devault, Alison AU - Devault A AD - Daicel Arbor Biosciences, Ann Arbor, MI, USA. FAU - Rouillard, Jean-Marie AU - Rouillard JM AD - Daicel Arbor Biosciences, Ann Arbor, MI, USA. AD - Department of Chemical Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, USA. FAU - Yotova, Vania AU - Yotova V AUID- ORCID: 0000-0002-6730-2404 AD - Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada. FAU - Sindeaux, Renata AU - Sindeaux R AUID- ORCID: 0000-0002-5527-5015 AD - Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada. FAU - Ye, Chun Jimmie AU - Ye CJ AUID- ORCID: 0000-0001-6560-3783 AD - Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA. AD - Institute for Human Genetics, University of California, San Francisco, CA, USA. FAU - Bikaran, Matin AU - Bikaran M AD - Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA. AD - Institute for Human Genetics, University of California, San Francisco, CA, USA. FAU - Dumaine, Anne AU - Dumaine A AD - Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA. FAU - Brinkworth, Jessica F AU - Brinkworth JF AD - Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA. AD - Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. FAU - Missiakas, Dominique AU - Missiakas D AUID- ORCID: 0000-0001-6482-9633 AD - Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA. FAU - Rouleau, Guy A AU - Rouleau GA AUID- ORCID: 0000-0001-8403-1418 AD - Montreal Neurological Institute-Hospital, McGill University, Montréal, Quebec, Canada. FAU - Steinrücken, Matthias AU - Steinrücken M AD - Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA. AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. FAU - Pizarro-Cerdá, Javier AU - Pizarro-Cerdá J AD - Yersinia Research Unit, Institut Pasteur, Paris, France. FAU - Poinar, Hendrik N AU - Poinar HN AUID- ORCID: 0000-0002-0314-4160 AD - McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada. poinarh@mcmaster.ca. AD - Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada. poinarh@mcmaster.ca. AD - Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada. poinarh@mcmaster.ca. FAU - Barreiro, Luis B AU - Barreiro LB AUID- ORCID: 0000-0001-9456-367X AD - Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA. lbarreiro@uchicago.edu. AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. lbarreiro@uchicago.edu. AD - Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA. lbarreiro@uchicago.edu. AD - Committee on Immunology, University of Chicago, Chicago, IL, USA. lbarreiro@uchicago.edu. LA - eng GR - P30 DK042086/DK/NIDDK NIH HHS/United States GR - F32 GM140568/GM/NIGMS NIH HHS/United States GR - R01 GM146051/GM/NIGMS NIH HHS/United States GR - R56 AI146556/AI/NIAID NIH HHS/United States GR - R01 GM134376/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20221019 PL - England TA - Nature JT - Nature JID - 0410462 RN - EC 3.4.11.- (Aminopeptidases) RN - 0 (DNA, Ancient) RN - EC 3.4.11.- (ERAP2 protein, human) SB - IM CIN - Nature. 2022 Nov;611(7935):237-238. doi: 10.1038/d41586-022-03160-2. PMID: 36261712 CIN - Trends Immunol. 2023 Feb;44(2):90-92. doi: 10.1016/j.it.2022.12.001. PMID: 36526581 CIN - Gastroenterology. 2023 Apr;164(4):696. doi: 10.1053/j.gastro.2022.12.038. PMID: 36608717 EIN - Nature. 2025 Jan;637(8048):E30. doi: 10.1038/s41586-024-08522-6. PMID: 39814901 MH - Humans MH - Aminopeptidases/genetics/immunology MH - *DNA, Ancient MH - *Plague/genetics/immunology/microbiology/mortality MH - *Yersinia pestis/immunology/pathogenicity MH - *Selection, Genetic/immunology MH - Europe/epidemiology/ethnology MH - *Immunity/genetics MH - Datasets as Topic MH - *Genetic Predisposition to Disease MH - London/epidemiology MH - Denmark/epidemiology PMC - PMC9580435 COIS- J.K., A. Devault and J.-M.R. declare financial interest in Daicel Arbor Biosciences, which provided the myBaits hybridization capture kits for this work. All other authors declare no competing interests. EDAT- 2022/10/20 06:00 MHDA- 2022/11/15 06:00 PMCR- 2022/10/19 CRDT- 2022/10/19 23:29 PHST- 2022/01/12 00:00 [received] PHST- 2022/09/14 00:00 [accepted] PHST- 2022/10/20 06:00 [pubmed] PHST- 2022/11/15 06:00 [medline] PHST- 2022/10/19 23:29 [entrez] PHST- 2022/10/19 00:00 [pmc-release] AID - 10.1038/s41586-022-05349-x [pii] AID - 5349 [pii] AID - 10.1038/s41586-022-05349-x [doi] PST - ppublish SO - Nature. 2022 Nov;611(7935):312-319. doi: 10.1038/s41586-022-05349-x. Epub 2022 Oct 19. PMID- 36206720 OWN - NLM STAT- MEDLINE DCOM- 20221026 LR - 20221125 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 172 DP - 2022 Nov TI - Sedimentary ancient DNA metabarcoding as a tool for assessing prehistoric plant use at the Upper Paleolithic cave site Aghitu-3, Armenia. PG - 103258 LID - S0047-2484(22)00118-X [pii] LID - 10.1016/j.jhevol.2022.103258 [doi] AB - Current knowledge about Paleolithic human plant use is limited by the rare survival of identifiable plant remains as well as the availability of methods for plant detection and identification. By analyzing DNA preserved in cave sediments, we can identify organisms in the absence of any visible remains, opening up new ways to study details of past human behavior, including plant use. Aghitu-3 Cave contains a 15,000-yearlong record (from ∼39,000 to 24,000 cal BP) of Upper Paleolithic human settlement and environmental variability in the Armenian Highlands. Finds from this cave include stone artifacts, faunal remains, bone tools, shell beads, charcoal, and pollen, among others. We applied sedimentary ancient DNA (sedaDNA) metabarcoding to the Aghitu-3 sedimentary sequence and combined this with pollen data to obtain a temporal reconstruction of plant assemblages. Our results reveal a stratification of plant abundance and diversity where sedaDNA reflects periods of human occupation, showing higher diversity in layers with increased human activity. Low pollen concentrations combined with high sedaDNA abundance indicate plant remains may have been brought into the cave by animals or humans during the deposition of the lower two archaeological horizons. Most of the recovered plants are reported to be useful for food, flavor, medicine, and/or technical purposes, demonstrating the potential of the environment around Aghitu-3 Cave to support humans during the Upper Paleolithic. Moreover, we identified several specific plant taxa that strengthen previous findings about Upper Paleolithic plant use in this region (i.e., for medicine and the manufacturing and dyeing of textiles). This study represents the first application of plant sedaDNA analysis of cave sediments for the investigation of potential plant use by prehistoric humans. CI - Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved. FAU - Ter Schure, Anneke T M AU - Ter Schure ATM AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway. Electronic address: anneke.terschure@gmail.com. FAU - Bruch, Angela A AU - Bruch AA AD - The Role of Culture in Early Expansions of Humans, Heidelberg Academy of Sciences and Humanities, Senckenberg Research Institute, Frankfurt, Germany. FAU - Kandel, Andrew W AU - Kandel AW AD - The Role of Culture in Early Expansions of Humans, Heidelberg Academy of Sciences and Humanities, University of Tübingen, Tübingen, Germany. FAU - Gasparyan, Boris AU - Gasparyan B AD - Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia. FAU - Bussmann, Rainer W AU - Bussmann RW AD - Department of Ethnobotany, Institute of Botany, Ilia State University, Tbilisi, Georgia. FAU - Brysting, Anne K AU - Brysting AK AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway. FAU - de Boer, Hugo J AU - de Boer HJ AD - Natural History Museum, University of Oslo, Oslo, Norway. FAU - Boessenkool, Sanne AU - Boessenkool S AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway. Electronic address: sanne.boessenkool@ibv.uio.no. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221004 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 0 (DNA, Ancient) RN - 16291-96-6 (Charcoal) SB - IM MH - Humans MH - Animals MH - *DNA, Ancient MH - Armenia MH - DNA Barcoding, Taxonomic MH - Charcoal MH - Caves MH - *Hominidae/genetics MH - Archaeology/methods MH - Plants/genetics OTO - NOTNLM OT - Armenian Highlands OT - Cave sediments OT - Metabarcoding OT - Palynological analysis OT - SedaDNA COIS- Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. EDAT- 2022/10/08 06:00 MHDA- 2022/10/27 06:00 CRDT- 2022/10/07 18:26 PHST- 2022/03/12 00:00 [received] PHST- 2022/08/26 00:00 [revised] PHST- 2022/08/27 00:00 [accepted] PHST- 2022/10/08 06:00 [pubmed] PHST- 2022/10/27 06:00 [medline] PHST- 2022/10/07 18:26 [entrez] AID - S0047-2484(22)00118-X [pii] AID - 10.1016/j.jhevol.2022.103258 [doi] PST - ppublish SO - J Hum Evol. 2022 Nov;172:103258. doi: 10.1016/j.jhevol.2022.103258. Epub 2022 Oct 4. PMID- 36152077 OWN - NLM STAT- MEDLINE DCOM- 20221027 LR - 20221207 IS - 1617-4623 (Electronic) IS - 1617-4623 (Linking) VI - 297 IP - 6 DP - 2022 Nov TI - Ancient DNA from Tubo Kingdom-related tombs in northeastern Tibetan Plateau revealed their genetic affinity to both Tibeto-Burman and Altaic populations. PG - 1755-1765 LID - 10.1007/s00438-022-01955-6 [doi] AB - The rise of the Tubo Kingdom is considered as the key period for the formation of modern groups on the Tibetan Plateau. The ethnic origin of the residents of the Tubo Kingdom is quite complex, and their genetic structure remains unclear. The tombs of the Tubo Kingdom period in Dulan County, Qinghai Province, dating back to the seventh century, are considered to be the remains left by Tubo conquerors or the Tuyuhun people dominated by the Tubo Kingdom. The human remains of these tombs are ideal materials for studying the population dynamics in the Tubo Kingdom. In this paper, we analyzed the genome-wide data of eight remains from these tombs by shotgun sequencing and multiplex PCR panels and compared the results with data of available ancient and modern populations across East Asia. Genetic continuity between ancient Dulan people with ancient Xianbei tribes in Northeast Asia, ancient settlers on the Tibetan Plateau, and modern Tibeto-Burman populations was found. Surprisingly, one out of eight individuals showed typical genetic features of populations from Central Asia. In summary, the genetic diversity of ancient Dulan people and their affiliations with other populations provide an example of the complex origin of the residents in the Tubo Kingdom and their long-distance connection with populations in a vast geographic region across ancient Asia. CI - © 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. FAU - Yu, Xue-Er AU - Yu XE AD - MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China. FAU - Sun, Chang AU - Sun C AD - State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China. FAU - Zou, Ye-Tao AU - Zou YT AD - MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China. FAU - Li, Ji-Yuan AU - Li JY AD - Qinghai Provincial Institute of Cultural Relics and Archaeology, Xining, 810007, China. FAU - Ren, Xiaoyan AU - Ren X AD - Qinghai Provincial Institute of Cultural Relics and Archaeology, Xining, 810007, China. FAU - Li, Hui AU - Li H AUID- ORCID: 0000-0002-7642-215X AD - MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China. LHCA@Fudan.edu.cn. AD - Fudan-Datong Institute of Chinese Origin, Shanxi Academy of Advanced Research and Innovation, Datong, 037006, China. LHCA@Fudan.edu.cn. LA - eng GR - 2020YFE0201600/National Key Research and Development Program/ GR - 18490750300/B&R Joint Laboratory of Eurasian Anthropology/ GR - 91731303/National Natural Science Foundation of China/ GR - 31671297/National Natural Science Foundation of China/ PT - Journal Article DEP - 20220924 PL - Germany TA - Mol Genet Genomics JT - Molecular genetics and genomics : MGG JID - 101093320 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - *DNA, Ancient MH - *Genetics, Population MH - Tibet MH - Asian People/genetics MH - Ethnicity MH - Genetic Variation/genetics OTO - NOTNLM OT - Ancient DNA OT - Dulan County OT - Modern Tibetan populations OT - Tubo Kingdom EDAT- 2022/09/25 06:00 MHDA- 2022/10/28 06:00 CRDT- 2022/09/24 11:24 PHST- 2021/12/09 00:00 [received] PHST- 2022/08/27 00:00 [accepted] PHST- 2022/09/25 06:00 [pubmed] PHST- 2022/10/28 06:00 [medline] PHST- 2022/09/24 11:24 [entrez] AID - 10.1007/s00438-022-01955-6 [pii] AID - 10.1007/s00438-022-01955-6 [doi] PST - ppublish SO - Mol Genet Genomics. 2022 Nov;297(6):1755-1765. doi: 10.1007/s00438-022-01955-6. Epub 2022 Sep 24. PMID- 36114431 OWN - NLM STAT- MEDLINE DCOM- 20221014 LR - 20221014 IS - 1435-4373 (Electronic) IS - 0934-9723 (Linking) VI - 41 IP - 11 DP - 2022 Nov TI - Ancient DNA confirmation of lepromatous leprosy in a skeleton with concurrent osteosarcoma, excavated from the leprosarium of St. Mary Magdalen in Winchester, Hants., UK. PG - 1295-1304 LID - 10.1007/s10096-022-04494-5 [doi] AB - To establish a biological profile and disease aetiologies for one of four burials recovered during a Time Team dig at the St. Mary Magdalen leprosarium, Winchester, UK in AD 2000. Osteological techniques were applied to estimate age at death, biological sex, stature and pathology. Visual assessment of the material was supplemented by radiographic examination. Evidence for leprosy DNA was sought using ancient DNA (aDNA) analysis. The remains are those of a male individual excavated from a west-east aligned grave. The skeleton shows signs of two pathologies. Remodelling of the rhino-maxillary area and degenerative changes to small bones of the feet and reactive bone on the distal lower limbs suggest a multibacillary form of leprosy, whereas the right tibia and fibula show the presence of a primary neoplasm identified as an osteosarcoma. The aDNA study confirmed presence of Mycobacterium leprae in several skeletal elements, and the strain was genotyped to the 3I lineage, one of two main SNP types present in mediaeval Britain and ancestral to extant strains in America. This is a rare documentation of leprosy in association with a primary neoplasm. CI - © 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. FAU - Cole, G AU - Cole G AD - UCL Institute of Archaeology, 31-34 Gordon Square, London, WC1H 0PY, UK. FAU - Taylor, G M AU - Taylor GM AUID- ORCID: 0000-0002-4215-3916 AD - Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill Campus, Guildford, GU2 7XH, Surrey, UK. gm.taylor@surrey.ac.uk. FAU - Stewart, G R AU - Stewart GR AD - Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill Campus, Guildford, GU2 7XH, Surrey, UK. FAU - Dawson-Hobbis, H AU - Dawson-Hobbis H AD - Department of Archaeology, Anthropology and Geography, University of Winchester, Sparkford Road, Winchester, SO22 4NR, Hampshire, UK. LA - eng PT - Journal Article DEP - 20220917 PL - Germany TA - Eur J Clin Microbiol Infect Dis JT - European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology JID - 8804297 RN - 0 (DNA, Ancient) SB - IM MH - Bone and Bones MH - DNA, Ancient MH - Humans MH - *Leprosy/diagnosis MH - *Leprosy, Lepromatous/microbiology MH - Male MH - Mycobacterium leprae/genetics MH - *Osteosarcoma/genetics MH - United Kingdom OTO - NOTNLM OT - Genotyping OT - Hansen’s disease OT - Leprosy OT - M. leprae OT - Mediaeval OT - Osteosarcoma OT - PCR EDAT- 2022/09/17 06:00 MHDA- 2022/10/15 06:00 CRDT- 2022/09/16 23:37 PHST- 2022/07/12 00:00 [received] PHST- 2022/09/07 00:00 [accepted] PHST- 2022/09/17 06:00 [pubmed] PHST- 2022/10/15 06:00 [medline] PHST- 2022/09/16 23:37 [entrez] AID - 10.1007/s10096-022-04494-5 [pii] AID - 10.1007/s10096-022-04494-5 [doi] PST - ppublish SO - Eur J Clin Microbiol Infect Dis. 2022 Nov;41(11):1295-1304. doi: 10.1007/s10096-022-04494-5. Epub 2022 Sep 17. PMID- 36048257 OWN - NLM STAT- MEDLINE DCOM- 20221019 LR - 20221019 IS - 1437-1596 (Electronic) IS - 0937-9827 (Linking) VI - 136 IP - 6 DP - 2022 Nov TI - Comparison of DNA preservation between adult and non-adult ancient skeletons. PG - 1521-1539 LID - 10.1007/s00414-022-02881-3 [doi] AB - Studies evaluating DNA preservation in non-adults, or comparing preservation in adults and non-adults, are very rare. This study compares the preservation of DNA in the skeletal remains of adults and non-adults. It compares the quality and quantity of DNA recovered from different skeletal elements of adults and non-adults, and from non-adults of different age classes. In addition, the preservation of DNA in males and females is compared. Bone DNA preservation was estimated by measuring nuclear DNA concentration and its degradation, and through STR typing success. The study analyzed 29 adult skeletons and 23 non-adult skeletons from the Ljubljana-Polje archeological site, dating from the seventeenth to nineteenth century, and up to four skeletal elements (petrous bone, femur, calcaneus, and talus) were included. After full demineralization extraction, the PowerQuant System and the PowerPlex ESI 17 Fast System (Promega) were used for qPCR and STR typing, respectively. The results showed that, among the four bone types analyzed, only the petrous bone proved to be a suitable source of DNA for STR typing of non-adult skeletal remains, and DNA yield is even higher than in the adult petrous bone, which can be attributed to the higher DNA degradation observed in the adult petrous bone. In adult skeletons, petrous bones and tali produced high STR amplification success and low DNA yield was observed in adult femurs. The results of this study are applicable for the sampling strategy in routine forensic genetics cases for solving identification cases, including badly preserved non-adult and also adult skeletons. CI - © 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. FAU - Šuligoj, Ariana AU - Šuligoj A AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia. FAU - Mesesnel, Sara AU - Mesesnel S AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia. FAU - Leskovar, Tamara AU - Leskovar T AD - Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia. FAU - Podovšovnik, Eva AU - Podovšovnik E AD - Orthopedic Hospital of Valdoltra, Ankaran, Slovenia. FAU - Zupanič Pajnič, Irena AU - Zupanič Pajnič I AUID- ORCID: 0000-0002-6704-015X AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia. irena.zupanic@mf.uni-lj.si. LA - eng GR - J3-3080/Javna Agencija za Raziskovalno Dejavnost RS/ PT - Journal Article DEP - 20220901 PL - Germany TA - Int J Legal Med JT - International journal of legal medicine JID - 9101456 RN - 9007-49-2 (DNA) SB - IM MH - *Body Remains MH - Bone and Bones MH - DNA MH - *DNA Fingerprinting MH - Female MH - Humans MH - Male MH - Microsatellite Repeats OTO - NOTNLM OT - Ancient DNA OT - Bone sampling OT - Missing person identification OT - Non-adult skeletons OT - STR typing EDAT- 2022/09/02 06:00 MHDA- 2022/10/20 06:00 CRDT- 2022/09/01 11:15 PHST- 2022/06/01 00:00 [received] PHST- 2022/08/17 00:00 [accepted] PHST- 2022/09/02 06:00 [pubmed] PHST- 2022/10/20 06:00 [medline] PHST- 2022/09/01 11:15 [entrez] AID - 10.1007/s00414-022-02881-3 [pii] AID - 10.1007/s00414-022-02881-3 [doi] PST - ppublish SO - Int J Legal Med. 2022 Nov;136(6):1521-1539. doi: 10.1007/s00414-022-02881-3. Epub 2022 Sep 1. PMID- 36282813 OWN - NLM STAT- MEDLINE DCOM- 20221027 LR - 20221028 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 17 IP - 10 DP - 2022 TI - The petrous bone contains high concentrations of osteocytes: One possible reason why ancient DNA is better preserved in this bone. PG - e0269348 LID - 10.1371/journal.pone.0269348 [doi] LID - e0269348 AB - The characterization of ancient DNA in fossil bones is providing invaluable information on the genetics of past human and other animal populations. These studies have been aided enormously by the discovery that ancient DNA is relatively well preserved in the petrous bone compared to most other bones. The reasons for this better preservation are however not well understood. Here we examine the hypothesis that one reason for better DNA preservation in the petrous bone is that fresh petrous bone contains more DNA than other bones. We therefore determined the concentrations of osteocyte cells occluded inside lacunae within the petrous bone and compared these concentrations to other bones from the domestic pig using high resolution microCT. We show that the concentrations of osteocyte lacunae in the inner layer of the pig petrous bone adjacent to the otic chamber are about three times higher (around 95,000 lacunae per mm3) than in the mastoid of the temporal bone (around 28,000 lacunae per mm3), as well as the cortical bone of the femur (around 27,000 lacunae per mm3). The sizes and shapes of the lacuna in the inner layer of the petrous bone are similar to those in the femur. We also show that the pig petrous bone lacunae do contain osteocytes using a histological stain for DNA. We therefore confirm and significantly expand upon previous observations of osteocytic lacuna concentrations in the petrous bone, supporting the notion that one possible reason for better preservation of ancient DNA in the petrous bone is that this bone initially contains at least three times more DNA than other bones. Thus during diagenesis more DNA is likely to be preserved in the petrous bone compared to other bones. FAU - Ibrahim, Jamal AU - Ibrahim J AUID- ORCID: 0000-0002-8694-738X AD - Scientific Archaeology Unit, Weizmann Institute of Science, Rehovot, Israel. FAU - Brumfeld, Vlad AU - Brumfeld V AD - Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel. FAU - Addadi, Yoseph AU - Addadi Y AD - Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel. FAU - Rubin, Sarah AU - Rubin S AUID- ORCID: 0000-0002-1584-6602 AD - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. FAU - Weiner, Steve AU - Weiner S AD - Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel. FAU - Boaretto, Elisabetta AU - Boaretto E AD - Scientific Archaeology Unit, Weizmann Institute of Science, Rehovot, Israel. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20221025 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Humans MH - Swine MH - Animals MH - *Osteocytes/pathology MH - *DNA, Ancient MH - Petrous Bone/diagnostic imaging MH - Bone and Bones MH - DNA/genetics PMC - PMC9595551 COIS- The authors have declared that no competing interests exist. EDAT- 2022/10/26 06:00 MHDA- 2022/10/28 06:00 PMCR- 2022/10/25 CRDT- 2022/10/25 13:33 PHST- 2022/05/17 00:00 [received] PHST- 2022/09/22 00:00 [accepted] PHST- 2022/10/25 13:33 [entrez] PHST- 2022/10/26 06:00 [pubmed] PHST- 2022/10/28 06:00 [medline] PHST- 2022/10/25 00:00 [pmc-release] AID - PONE-D-22-14142 [pii] AID - 10.1371/journal.pone.0269348 [doi] PST - epublish SO - PLoS One. 2022 Oct 25;17(10):e0269348. doi: 10.1371/journal.pone.0269348. eCollection 2022. PMID- 36044903 OWN - NLM STAT- MEDLINE DCOM- 20221027 LR - 20230916 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 32 IP - 20 DP - 2022 Oct 24 TI - Genomes from a medieval mass burial show Ashkenazi-associated hereditary diseases pre-date the 12th century. PG - 4350-4359.e6 LID - S0960-9822(22)01355-0 [pii] LID - 10.1016/j.cub.2022.08.036 [doi] AB - We report genome sequence data from six individuals excavated from the base of a medieval well at a site in Norwich, UK. A revised radiocarbon analysis of the assemblage is consistent with these individuals being part of a historically attested episode of antisemitic violence on 6 February 1190 CE. We find that four of these individuals were closely related and all six have strong genetic affinities with modern Ashkenazi Jews. We identify four alleles associated with genetic disease in Ashkenazi Jewish populations and infer variation in pigmentation traits, including the presence of red hair. Simulations indicate that Ashkenazi-associated genetic disease alleles were already at appreciable frequencies, centuries earlier than previously hypothesized. These findings provide new insights into a significant historical crime, into Ashkenazi population history, and into the origins of genetic diseases associated with modern Jewish populations. CI - Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Brace, Selina AU - Brace S AD - Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK. FAU - Diekmann, Yoan AU - Diekmann Y AD - Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany. FAU - Booth, Thomas AU - Booth T AD - Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Francis Crick Institute, London NW1 1AT, UK; UCL Genetics Institute, University College London, London, UK. FAU - Macleod, Ruairidh AU - Macleod R AD - Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK. FAU - Timpson, Adrian AU - Timpson A AD - Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK. FAU - Stephen, Will AU - Stephen W AD - Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK. FAU - Emery, Giles AU - Emery G AD - Norvic Archaeology, 7 Foxburrow Road, Norwich NR7 8QU, UK. FAU - Cabot, Sophie AU - Cabot S AD - Norfolk Record Office, The Archive Centre, Martineau Lane, Norwich, Norfolk NR1 2DQ, UK. FAU - Thomas, Mark G AU - Thomas MG AD - Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK. Electronic address: m.thomas@ucl.ac.uk. FAU - Barnes, Ian AU - Barnes I AD - Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK. Electronic address: i.barnes@nhm.ac.uk. LA - eng GR - 100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220830 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Humans MH - Gene Frequency MH - *Jews/genetics/history MH - Alleles MH - *Burial PMC - PMC10499757 OTO - NOTNLM OT - Ashkenazi OT - Britain OT - Jewish OT - Medieval OT - ancient DNA OT - genetic disease COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/09/01 06:00 MHDA- 2022/10/28 06:00 PMCR- 2022/10/24 CRDT- 2022/08/31 18:43 PHST- 2022/06/21 00:00 [received] PHST- 2022/07/26 00:00 [revised] PHST- 2022/08/12 00:00 [accepted] PHST- 2022/09/01 06:00 [pubmed] PHST- 2022/10/28 06:00 [medline] PHST- 2022/08/31 18:43 [entrez] PHST- 2022/10/24 00:00 [pmc-release] AID - S0960-9822(22)01355-0 [pii] AID - 10.1016/j.cub.2022.08.036 [doi] PST - ppublish SO - Curr Biol. 2022 Oct 24;32(20):4350-4359.e6. doi: 10.1016/j.cub.2022.08.036. Epub 2022 Aug 30. PMID- 36191217 OWN - NLM STAT- MEDLINE DCOM- 20221005 LR - 20240905 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 119 IP - 41 DP - 2022 Oct 11 TI - The diverse genetic origins of a Classical period Greek army. PG - e2205272119 LID - 10.1073/pnas.2205272119 [doi] LID - e2205272119 AB - Trade and colonization caused an unprecedented increase in Mediterranean human mobility in the first millennium BCE. Often seen as a dividing force, warfare is in fact another catalyst of culture contact. We provide insight into the demographic dynamics of ancient warfare by reporting genome-wide data from fifth-century soldiers who fought for the army of the Greek Sicilian colony of Himera, along with representatives of the civilian population, nearby indigenous settlements, and 96 present-day individuals from Italy and Greece. Unlike the rest of the sample, many soldiers had ancestral origins in northern Europe, the Steppe, and the Caucasus. Integrating genetic, archaeological, isotopic, and historical data, these results illustrate the significant role mercenaries played in ancient Greek armies and highlight how participation in war contributed to continental-scale human mobility in the Classical world. FAU - Reitsema, Laurie J AU - Reitsema LJ AUID- ORCID: 0000-0003-1127-3496 AD - Department of Anthropology, University of Georgia, Athens, GA 30602. FAU - Mittnik, Alissa AU - Mittnik A AUID- ORCID: 0000-0002-6963-4824 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 04103 Leipzig, Germany. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Kyle, Britney AU - Kyle B AD - Department of Anthropology, University of Northern Colorado, Greeley, CO 80639. FAU - Catalano, Giulio AU - Catalano G AUID- ORCID: 0000-0002-2564-5775 AD - Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, 90123 Italy. FAU - Fabbri, Pier Francesco AU - Fabbri PF AUID- ORCID: 0000-0003-3633-0178 AD - Department of Cultural Heritage, Università del Salento, 73100 Lecce, Italy. FAU - Kazmi, Adam C S AU - Kazmi ACS AD - Department of Anthropology, University of Georgia, Athens, GA 30602. FAU - Reinberger, Katherine L AU - Reinberger KL AUID- ORCID: 0000-0001-9978-8421 AD - Department of Anthropology, University of Georgia, Athens, GA 30602. FAU - Sineo, Luca AU - Sineo L AUID- ORCID: 0000-0001-8634-2295 AD - Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, 90123 Italy. FAU - Vassallo, Stefano AU - Vassallo S AD - Soprintendenza per i Beni Culturali e Ambientali di Palermo, 90143 Palermo, Italy. FAU - Bernardos, Rebecca AU - Bernardos R AUID- ORCID: 0000-0003-4625-3727 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AUID- ORCID: 0000-0001-5350-1608 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. FAU - Callan, Kim AU - Callan K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Soprintendenza per i Beni Culturali e Ambientali di Palermo, 90143 Palermo, Italy. FAU - Candilio, Francesca AU - Candilio F AUID- ORCID: 0000-0002-4668-1361 AD - Servizio di Bioarcheologia, Museo delle Civiltà, 00144 Rome, Italy. FAU - Cheronet, Olivia AU - Cheronet O AUID- ORCID: 0000-0001-6760-1204 AD - Department of Evolutionary Anthropology, Universität Wien, 1090 Vienna, Austria. FAU - Curtis, Elizabeth AU - Curtis E AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. FAU - Fernandes, Daniel AU - Fernandes D AUID- ORCID: 0000-0002-7434-6552 AD - Department of Evolutionary Anthropology, Universität Wien, 1090 Vienna, Austria. AD - CIAS, Department of Life Sciences, Universidade de Coimbra, 3000-456 Coimbra, Portugal. FAU - Lari, Martina AU - Lari M AUID- ORCID: 0000-0002-7832-8212 AD - Dipartimento di Biologia, Università degli Studi di Firenze, Florence, 50122 Italy. FAU - Lawson, Ann Marie AU - Lawson AM AUID- ORCID: 0000-0003-0990-2329 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. FAU - Mah, Matthew AU - Mah M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. AD - Broad Institute of MIT and Harvard, Cambridge, MA 02142. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. AD - Broad Institute of MIT and Harvard, Cambridge, MA 02142. FAU - Mandl, Kirsten AU - Mandl K AUID- ORCID: 0000-0002-2078-0775 AD - Department of Evolutionary Anthropology, Universität Wien, 1090 Vienna, Austria. FAU - Micco, Adam AU - Micco A AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. AD - Broad Institute of MIT and Harvard, Cambridge, MA 02142. FAU - Modi, Alessandra AU - Modi A AD - Dipartimento di Biologia, Università degli Studi di Firenze, Florence, 50122 Italy. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. FAU - Özdogan, Kadir Toykan AU - Özdogan KT AD - Department of Evolutionary Anthropology, Universität Wien, 1090 Vienna, Austria. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. FAU - Vai, Stefania AU - Vai S AUID- ORCID: 0000-0003-3844-5147 AD - Dipartimento di Biologia, Università degli Studi di Firenze, Florence, 50122 Italy. FAU - Vergata, Chiara AU - Vergata C AUID- ORCID: 0000-0003-2727-7977 AD - Dipartimento di Biologia, Università degli Studi di Firenze, Florence, 50122 Italy. FAU - Workman, J Noah AU - Workman JN AUID- ORCID: 0000-0002-0921-1803 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. FAU - Zalzala, Fatma AU - Zalzala F AUID- ORCID: 0000-0002-8981-1277 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. FAU - Zaro, Valentina AU - Zaro V AUID- ORCID: 0000-0002-2902-225X AD - Dipartimento di Biologia, Università degli Studi di Firenze, Florence, 50122 Italy. FAU - Achilli, Alessandro AU - Achilli A AUID- ORCID: 0000-0001-6871-3451 AD - Department of Biology and Biotechnology "L. Spallanzani," Università di Pavia, Pavia 27100, Italy. FAU - Anagnostopoulos, Achilles AU - Anagnostopoulos A AUID- ORCID: 0000-0003-4384-9031 AD - Gene and Cell Therapy Center, Hematology-HCT Unit, General Hospital of Thessaloniki "George Papanikolaou", 55710 Thessaloniki, Greece. FAU - Capelli, Cristian AU - Capelli C AD - Department of Zoology, University of Oxford, Oxford OX1 3SZ, United Kingdom. AD - Department of Chemistry, Life Sciences and Environmental Sustainability, Università di Parma, 43124 Parma, Italy. FAU - Constantinou, Varnavas AU - Constantinou V AUID- ORCID: 0000-0002-5479-5529 AD - Gene and Cell Therapy Center, Hematology-HCT Unit, General Hospital of Thessaloniki "George Papanikolaou", 55710 Thessaloniki, Greece. FAU - Lancioni, Hovirag AU - Lancioni H AUID- ORCID: 0000-0001-5514-1853 AD - Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy. FAU - Olivieri, Anna AU - Olivieri A AD - Department of Biology and Biotechnology "L. Spallanzani," Università di Pavia, Pavia 27100, Italy. FAU - Papadopoulou, Anastasia AU - Papadopoulou A AUID- ORCID: 0000-0001-5385-8738 AD - Gene and Cell Therapy Center, Hematology-HCT Unit, General Hospital of Thessaloniki "George Papanikolaou", 55710 Thessaloniki, Greece. FAU - Psatha, Nikoleta AU - Psatha N AD - Gene and Cell Therapy Center, Hematology-HCT Unit, General Hospital of Thessaloniki "George Papanikolaou", 55710 Thessaloniki, Greece. FAU - Semino, Ornella AU - Semino O AUID- ORCID: 0000-0002-9675-9403 AD - Department of Biology and Biotechnology "L. Spallanzani," Università di Pavia, Pavia 27100, Italy. FAU - Stamatoyannopoulos, John AU - Stamatoyannopoulos J AD - Department of Medicine, University of Washington, Seattle, WA 98195. AD - Department of Genome Sciences, University of Washington, Seattle, WA 98195. FAU - Valliannou, Ioanna AU - Valliannou I AD - Gene and Cell Therapy Center, Hematology-HCT Unit, General Hospital of Thessaloniki "George Papanikolaou", 55710 Thessaloniki, Greece. FAU - Yannaki, Evangelia AU - Yannaki E AD - Gene and Cell Therapy Center, Hematology-HCT Unit, General Hospital of Thessaloniki "George Papanikolaou", 55710 Thessaloniki, Greece. FAU - Lazaridis, Iosif AU - Lazaridis I AUID- ORCID: 0000-0002-4094-9347 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. FAU - Patterson, Nick AU - Patterson N AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. AD - Broad Institute of MIT and Harvard, Cambridge, MA 02142. FAU - Ringbauer, Harald AU - Ringbauer H AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 04103 Leipzig, Germany. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Caramelli, David AU - Caramelli D AUID- ORCID: 0000-0001-6468-1675 AD - Dipartimento di Biologia, Università degli Studi di Firenze, Florence, 50122 Italy. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Dipartimento di Biologia, Università degli Studi di Firenze, Florence, 50122 Italy. AD - Human Evolution and Archaeological Sciences, Universität Wien, A-1030 Vienna, Austria. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 04103 Leipzig, Germany. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138. AD - Howard Hughes Medical Institute (HHMI), Harvard Medical School, Boston, MA 02115. AD - Broad Institute of MIT and Harvard, Cambridge, MA 02142. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R01 HG012287/HG/NHGRI NIH HHS/United States GR - n/a/Howard Hughes Medical Institute (HHMI)/ PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20221003 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - *Archaeology/methods MH - Europe MH - Greece MH - History, Ancient MH - Humans MH - *Military Personnel MH - Warfare PMC - PMC9564095 OTO - NOTNLM OT - Classical world OT - ancient DNA OT - ancient warfare OT - archaeology OT - history COIS- The authors declare no competing interest. EDAT- 2022/10/04 06:00 MHDA- 2022/10/06 06:00 PMCR- 2022/10/03 CRDT- 2022/10/03 15:23 PHST- 2022/10/03 15:23 [entrez] PHST- 2022/10/04 06:00 [pubmed] PHST- 2022/10/06 06:00 [medline] PHST- 2022/10/03 00:00 [pmc-release] AID - 202205272 [pii] AID - 10.1073/pnas.2205272119 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2022 Oct 11;119(41):e2205272119. doi: 10.1073/pnas.2205272119. Epub 2022 Oct 3. PMID- 36201580 OWN - NLM STAT- MEDLINE DCOM- 20221010 LR - 20221012 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 378 IP - 6615 DP - 2022 Oct 7 TI - Ancient DNA pioneer Svante Pääbo wins Nobel. PG - 12 LID - 10.1126/science.adf1845 [doi] AB - By sequencing ancient hominins' DNA, Pääbo explored "what makes us uniquely human". FAU - Curry, Andrew AU - Curry A LA - eng PT - News DEP - 20221006 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *DNA, Ancient MH - *Hominidae/genetics MH - Humans MH - Nobel Prize EDAT- 2022/10/07 06:00 MHDA- 2022/10/12 06:00 CRDT- 2022/10/06 14:02 PHST- 2022/10/06 14:02 [entrez] PHST- 2022/10/07 06:00 [pubmed] PHST- 2022/10/12 06:00 [medline] AID - 10.1126/science.adf1845 [doi] PST - ppublish SO - Science. 2022 Oct 7;378(6615):12. doi: 10.1126/science.adf1845. Epub 2022 Oct 6. PMID- 36161899 OWN - NLM STAT- MEDLINE DCOM- 20220928 LR - 20240905 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 119 IP - 40 DP - 2022 Oct 4 TI - Using neuroimaging genomics to investigate the evolution of human brain structure. PG - e2200638119 LID - 10.1073/pnas.2200638119 [doi] LID - e2200638119 AB - Alterations in brain size and organization represent some of the most distinctive changes in the emergence of our species. Yet, there is limited understanding of how genetic factors contributed to altered neuroanatomy during human evolution. Here, we analyze neuroimaging and genetic data from up to 30,000 people in the UK Biobank and integrate with genomic annotations for different aspects of human evolution, including those based on ancient DNA and comparative genomics. We show that previously reported signals of recent polygenic selection for cortical anatomy are not replicable in a more ancestrally homogeneous sample. We then investigate relationships between evolutionary annotations and common genetic variants shaping cortical surface area and white-matter connectivity for each hemisphere. Our analyses identify single-nucleotide polymorphism heritability enrichment in human-gained regulatory elements that are active in early brain development, affecting surface areas of several parts of the cortex, including left-hemispheric speech-associated regions. We also detect heritability depletion in genomic regions with Neanderthal ancestry for connectivity of the uncinate fasciculus; this is a white-matter tract involved in memory, language, and socioemotional processing with relevance to neuropsychiatric disorders. Finally, we show that common genetic loci associated with left-hemispheric pars triangularis surface area overlap with a human-gained enhancer and affect regulation of ZIC4, a gene implicated in neurogenesis. This work demonstrates how genomic investigations of present-day neuroanatomical variation can help shed light on the complexities of our evolutionary past. FAU - Alagöz, Gökberk AU - Alagöz G AUID- ORCID: 0000-0003-0530-2780 AD - Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands. FAU - Molz, Barbara AU - Molz B AUID- ORCID: 0000-0002-9300-761X AD - Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands. FAU - Eising, Else AU - Eising E AUID- ORCID: 0000-0001-9819-1260 AD - Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands. FAU - Schijven, Dick AU - Schijven D AUID- ORCID: 0000-0001-5190-7241 AD - Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands. FAU - Francks, Clyde AU - Francks C AUID- ORCID: 0000-0002-9098-890X AD - Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands. AD - Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HB Nijmegen, The Netherlands. AD - Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands. FAU - Stein, Jason L AU - Stein JL AUID- ORCID: 0000-0003-4829-0513 AD - Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. AD - UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. FAU - Fisher, Simon E AU - Fisher SE AUID- ORCID: 0000-0002-3132-1996 AD - Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands. AD - Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HB Nijmegen, The Netherlands. LA - eng GR - MC_PC_17228/MRC_/Medical Research Council/United Kingdom GR - MC_QA137853/MRC_/Medical Research Council/United Kingdom GR - R01 DC016977/DC/NIDCD NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20220926 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - *Biological Evolution MH - *Brain/growth & development/ultrastructure MH - DNA, Ancient MH - *Genomics/methods MH - Humans MH - *Neuroimaging/methods MH - *Polymorphism, Single Nucleotide PMC - PMC9546597 OTO - NOTNLM OT - evolution OT - genetics OT - neuroimaging COIS- The authors declare no competing interest. EDAT- 2022/09/27 06:00 MHDA- 2022/09/28 06:00 PMCR- 2022/09/26 CRDT- 2022/09/26 18:36 PHST- 2022/09/26 18:36 [entrez] PHST- 2022/09/27 06:00 [pubmed] PHST- 2022/09/28 06:00 [medline] PHST- 2022/09/26 00:00 [pmc-release] AID - 202200638 [pii] AID - 10.1073/pnas.2200638119 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2022 Oct 4;119(40):e2200638119. doi: 10.1073/pnas.2200638119. Epub 2022 Sep 26. PMID- 36790695 OWN - NLM STAT- MEDLINE DCOM- 20230217 LR - 20240910 IS - 2692-7691 (Electronic) IS - 2692-7691 (Linking) VI - 179 IP - 2 DP - 2022 Oct TI - Metagenomic analysis of Ancient Egyptian canopic jars. PG - 307-313 LID - 10.1002/ajpa.24600 [doi] AB - Ancient Egyptian remains have been of interest for anthropological research for decades. Despite many investigations, the ritual vessels for the internal organs removed during body preparation-liver, lungs, stomach, and intestines, of Egyptian mummies are rarely used for palaeopathological or medical investigations. These artifacts, commonly referred to as canopic jars, are the perfect combination of cultural and biological material and present an untapped resource for both Egyptological and medical fields. Nevertheless, technical challenges associated with this archeological material have prevented the application of current ancient DNA techniques for both the characterization of human and pathogenic DNA. We present shotgun-sequenced metagenomic profiles and ancient DNA degradation patterns from multiple canopic jars sampled from several European museum collections and enumerate current limitations and possible solutions for the future analysis of similar material. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars and the first associated metagenomic description of bacterial taxa in these funerary artifacts. OBJECTIVES: In this study, our objectives were to characterize the metagenomic profile of the Ancient Egyptian funerary vessels known as canopic jars to retrieve endogenous ancient human DNA, reconstruct ancient microbial communities, and identify possible pathogens that could shed light on disease states of individuals from the past. METHODS: We applied ancient DNA techniques on 140 canopic jars to extract DNA and generate whole-genome sequencing libraries for the analysis of both human and bacterial DNA. The samples were obtained from museum collections in Berlin (DE), Burgdorf (DE), Leiden (NE), Manchester (UK), Munich (DE), St. Gallen (CH), Turin (IT), and Zagreb (HR). RESULTS: Here we describe the first isolated DNA from the Egyptian artifacts that hold human viscera. No previous work was ever conducted on such material, which led to the first characterization of human DNA from Ancient Egyptian canopic jars and the profiling of the complex bacterial composition of this highly degraded, challenging, organic material. However, the DNA recovered was not of enough quality to confidently characterize bacterial taxa associated with infectious diseases, nor exclusive bacterial members of the human microbiome. DISCUSSION: In summary, we present the first genomic survey of the visceral content of Ancient Egyptian funerary artifacts and demonstrate the limitations of current molecular methods to analyze canopic jars, such as the incomplete history of the objects or the presence of uncharacterized compounds that can hamper the recovery of DNA. Our work highlights the main challenges and caveats when working with such complicated archeological material - and offers sampling recommendations for similarly complex future studies, such as incrementing the amount of starting material and sampling from the less exposed parts of the jar content. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars, and our results open new avenues in the study of neglected archeological artifacts. CI - © 2022 The Authors. American Journal of Biological Anthropology published by Wiley Periodicals LLC. FAU - Rayo, Enrique AU - Rayo E AUID- ORCID: 0000-0002-4497-4339 AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Neukamm, Judith AU - Neukamm J AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Tomoum, Nadja AU - Tomoum N AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Eppenberger, Patrick AU - Eppenberger P AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Breidenstein, Abagail AU - Breidenstein A AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Bouwman, Abigail S AU - Bouwman AS AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Rühli, Frank J AU - Rühli FJ AUID- ORCID: 0000-0001-7937-001X AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220805 PL - United States TA - Am J Biol Anthropol JT - American journal of biological anthropology JID - 101770171 RN - 0 (DNA, Ancient) SB - IM MH - Humans MH - Egypt MH - *DNA, Ancient MH - *Mummies/pathology MH - Lung MH - Base Sequence PMC - PMC9804471 OTO - NOTNLM OT - Ancient Egypt OT - ancient DNA OT - canopic jars OT - metagenomics COIS- The authors declare that we have no conflict of interest. EDAT- 2023/02/16 06:00 MHDA- 2023/02/18 06:00 PMCR- 2022/12/31 CRDT- 2023/02/15 11:26 PHST- 2022/07/13 00:00 [revised] PHST- 2021/05/20 00:00 [received] PHST- 2022/07/19 00:00 [accepted] PHST- 2023/02/15 11:26 [entrez] PHST- 2023/02/16 06:00 [pubmed] PHST- 2023/02/18 06:00 [medline] PHST- 2022/12/31 00:00 [pmc-release] AID - AJPA24600 [pii] AID - 10.1002/ajpa.24600 [doi] PST - ppublish SO - Am J Biol Anthropol. 2022 Oct;179(2):307-313. doi: 10.1002/ajpa.24600. Epub 2022 Aug 5. PMID- 36131019 OWN - NLM STAT- MEDLINE DCOM- 20221007 LR - 20240923 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 610 IP - 7930 DP - 2022 Oct TI - The Anglo-Saxon migration and the formation of the early English gene pool. PG - 112-119 LID - 10.1038/s41586-022-05247-2 [doi] AB - The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture(1). The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate(2-4). Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France(5,6). CI - © 2022. The Author(s). FAU - Gretzinger, Joscha AU - Gretzinger J AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Sayer, Duncan AU - Sayer D AUID- ORCID: 0000-0002-2769-1281 AD - University of Central Lancashire, Preston, UK. dsayer@uclan.ac.uk. FAU - Justeau, Pierre AU - Justeau P AD - University of Huddersfield, Huddersfield, UK. FAU - Altena, Eveline AU - Altena E AUID- ORCID: 0000-0001-8911-7771 AD - Leiden University, Leiden, Netherlands. FAU - Pala, Maria AU - Pala M AUID- ORCID: 0000-0001-9202-8331 AD - University of Huddersfield, Huddersfield, UK. FAU - Dulias, Katharina AU - Dulias K AD - University of Huddersfield, Huddersfield, UK. AD - Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Braunschweig, Germany. FAU - Edwards, Ceiridwen J AU - Edwards CJ AUID- ORCID: 0000-0001-9126-1377 AD - University of Huddersfield, Huddersfield, UK. AD - University of Oxford, Oxford, UK. FAU - Jodoin, Susanne AU - Jodoin S AD - University of Tübingen, Tübingen, Germany. FAU - Lacher, Laura AU - Lacher L AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Sabin, Susanna AU - Sabin S AD - Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA. FAU - Vågene, Åshild J AU - Vågene ÅJ AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Ebenesersdóttir, S Sunna AU - Ebenesersdóttir SS AUID- ORCID: 0000-0001-5912-4401 AD - deCODE Genetics/AMGEN Inc., Reykjavík, Iceland. AD - Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland. FAU - Moore, Kristjan H S AU - Moore KHS AUID- ORCID: 0000-0002-9579-4362 AD - deCODE Genetics/AMGEN Inc., Reykjavík, Iceland. FAU - Radzeviciute, Rita AU - Radzeviciute R AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Schmidt, Kara AU - Schmidt K AUID- ORCID: 0000-0003-1651-6119 AD - University of Münster, Münster, Germany. FAU - Brace, Selina AU - Brace S AUID- ORCID: 0000-0003-2126-6732 AD - Department of Earth Sciences, Natural History Museum, London, UK. FAU - Bager, Martina Abenhus AU - Bager MA AUID- ORCID: 0000-0002-6772-3831 AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Patterson, Nick AU - Patterson N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAU - Papac, Luka AU - Papac L AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AUID- ORCID: 0000-0001-5350-1608 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Callan, Kimberly AU - Callan K AUID- ORCID: 0000-0003-3170-8514 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Harney, Éadaoin AU - Harney É AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Iliev, Lora AU - Iliev L AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Lawson, Ann Marie AU - Lawson AM AUID- ORCID: 0000-0003-0990-2329 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Michel, Megan AU - Michel M AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Zalzala, Fatma AU - Zalzala F AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAU - Kappelhoff-Beckmann, Stefanie AU - Kappelhoff-Beckmann S AD - Landesmuseum Natur und Mensch, Oldenburg, Germany. FAU - Both, Frank AU - Both F AD - Landesmuseum Natur und Mensch, Oldenburg, Germany. FAU - Winger, Daniel AU - Winger D AD - University of Rostock, Rostock, Germany. FAU - Neumann, Daniel AU - Neumann D AUID- ORCID: 0000-0002-3533-7987 AD - Lower Saxony State Museum, Hanover, Germany. FAU - Saalow, Lars AU - Saalow L AD - Landesamt für Kultur und Denkmalpflege Mecklenburg-Vorpommern, Schwerin, Germany. FAU - Krabath, Stefan AU - Krabath S AD - Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany. FAU - Beckett, Sophie AU - Beckett S AUID- ORCID: 0000-0002-5997-8631 AD - Sedgeford Historical and Archaeological Research Project, Sedgeford, UK. AD - Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, Cranfield, UK. AD - Melbourne Dental School, University of Melbourne, Melbourne, Victoria, Australia. FAU - Van Twest, Melanie AU - Van Twest M AD - Sedgeford Historical and Archaeological Research Project, Sedgeford, UK. FAU - Faulkner, Neil AU - Faulkner N AD - Sedgeford Historical and Archaeological Research Project, Sedgeford, UK. FAU - Read, Chris AU - Read C AD - The Atlantic Technological University, Sligo, Ireland. FAU - Barton, Tabatha AU - Barton T AD - Milton Keynes Museum, Milton Keyes, UK. FAU - Caruth, Joanna AU - Caruth J AD - Cotswold Archaeology, Needham Market, UK. FAU - Hines, John AU - Hines J AD - Cardiff University, Cardiff, UK. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AUID- ORCID: 0000-0001-9435-2872 AD - University of Kiel, Kiel, Germany. FAU - Warnke, Ursula AU - Warnke U AD - Landesmuseum Natur und Mensch, Oldenburg, Germany. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - University of Zurich, Zurich, Switzerland. AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Barnes, Ian AU - Barnes I AUID- ORCID: 0000-0001-8322-6918 AD - Department of Earth Sciences, Natural History Museum, London, UK. FAU - Dahlström, Hanna AU - Dahlström H AUID- ORCID: 0000-0002-7979-6798 AD - Museum of Copenhagen, Copenhagen, Denmark. FAU - Clausen, Jane Jark AU - Clausen JJ AD - Museum of Copenhagen, Copenhagen, Denmark. FAU - Richardson, Andrew AU - Richardson A AD - Canterbury Archaeological Trust, Canterbury, UK. AD - Isle Heritage CIC, Sandgate, UK. FAU - Popescu, Elizabeth AU - Popescu E AD - Oxford Archaeology East, Cambridge, UK. FAU - Dodwell, Natasha AU - Dodwell N AD - Oxford Archaeology East, Cambridge, UK. FAU - Ladd, Stuart AU - Ladd S AD - Oxford Archaeology East, Cambridge, UK. FAU - Phillips, Tom AU - Phillips T AD - Oxford Archaeology East, Cambridge, UK. FAU - Mortimer, Richard AU - Mortimer R AD - Oxford Archaeology East, Cambridge, UK. AD - Cotswold Archaeology, Needham Market, UK. FAU - Sayer, Faye AU - Sayer F AD - University of Birmingham, Birmingham, UK. FAU - Swales, Diana AU - Swales D AD - Centre for Anatomy and Human Identification (CAHID), University of Dundee, Dundee, UK. FAU - Stewart, Allison AU - Stewart A AD - University of Central Lancashire, Preston, UK. FAU - Powlesland, Dominic AU - Powlesland D AUID- ORCID: 0000-0003-0935-0739 AD - The Landscape Research Centre Ltd, Yedingham, UK. FAU - Kenyon, Robert AU - Kenyon R AD - East Dorset Antiquarian Society (EDAS), West Bexington, UK. FAU - Ladle, Lilian AU - Ladle L AD - Department of Archaeology and Anthropology, Bournemouth University, Poole, UK. FAU - Peek, Christina AU - Peek C AD - Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany. FAU - Grefen-Peters, Silke AU - Grefen-Peters S AD - Ossatura-Wilhelm-Börker, Braunschweig, Germany. FAU - Ponce, Paola AU - Ponce P AD - University of York, York, UK. FAU - Daniels, Robin AU - Daniels R AUID- ORCID: 0000-0002-1706-3396 AD - Tees Archaeology, Hartlepool, UK. FAU - Spall, Cecily AU - Spall C AD - FAS Heritage, York, UK. FAU - Woolcock, Jennifer AU - Woolcock J AD - Royal Cornwall Museum, Truro, UK. FAU - Jones, Andy M AU - Jones AM AUID- ORCID: 0000-0001-9349-7818 AD - Cornwall Archaeological Unit, Truro, UK. FAU - Roberts, Amy V AU - Roberts AV AD - The Novium Museum, Chichester, UK. FAU - Symmons, Robert AU - Symmons R AD - Fishbourne Roman Palace, Fishbourne, UK. FAU - Rawden, Anooshka C AU - Rawden AC AD - Fishbourne Roman Palace, Fishbourne, UK. AD - South Downs Centre, Midhurst, UK. FAU - Cooper, Alan AU - Cooper A AD - BlueSkyGenetics, Adelaide, South Australia, Australia. FAU - Bos, Kirsten I AU - Bos KI AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Booth, Tom AU - Booth T AD - Natural History Museum, London, UK. FAU - Schroeder, Hannes AU - Schroeder H AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Thomas, Mark G AU - Thomas MG AUID- ORCID: 0000-0002-2452-981X AD - University College London, London, UK. FAU - Helgason, Agnar AU - Helgason A AD - deCODE Genetics/AMGEN Inc., Reykjavík, Iceland. AD - Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland. FAU - Richards, Martin B AU - Richards MB AUID- ORCID: 0000-0003-3118-0967 AD - University of Huddersfield, Huddersfield, UK. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Schiffels, Stephan AU - Schiffels S AUID- ORCID: 0000-0002-1017-9150 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. stephan_schiffels@eva.mpg.de. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - 851511/ERC_/European Research Council/International GR - R01 HG012287/HG/NHGRI NIH HHS/United States GR - WT_/Wellcome Trust/United Kingdom GR - 100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20220921 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM EIN - Nature. 2022 Nov;611(7934):E3. doi: 10.1038/s41586-022-05429-y. PMID: 36253469 MH - Archaeology MH - DNA, Ancient/analysis MH - Denmark MH - England MH - Female MH - France MH - *Gene Pool MH - Genetics, Population MH - Genome, Human/genetics MH - Germany MH - History, Medieval MH - *Human Migration/history MH - Humans MH - Language MH - Male MH - Population Dynamics MH - Weapons/history PMC - PMC9534755 COIS- The authors declare no competing interests. EDAT- 2022/09/22 06:00 MHDA- 2022/10/12 06:00 PMCR- 2022/09/21 CRDT- 2022/09/21 23:23 PHST- 2021/12/12 00:00 [received] PHST- 2022/08/17 00:00 [accepted] PHST- 2022/09/22 06:00 [pubmed] PHST- 2022/10/12 06:00 [medline] PHST- 2022/09/21 23:23 [entrez] PHST- 2022/09/21 00:00 [pmc-release] AID - 10.1038/s41586-022-05247-2 [pii] AID - 5247 [pii] AID - 10.1038/s41586-022-05247-2 [doi] PST - ppublish SO - Nature. 2022 Oct;610(7930):112-119. doi: 10.1038/s41586-022-05247-2. Epub 2022 Sep 21. PMID- 36064759 OWN - NLM STAT- MEDLINE DCOM- 20221004 LR - 20240214 IS - 2397-334X (Electronic) IS - 2397-334X (Linking) VI - 6 IP - 10 DP - 2022 Oct TI - Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins. PG - 1573-1585 LID - 10.1038/s41559-022-01875-z [doi] AB - Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA. CI - © 2022. The Author(s), under exclusive licence to Springer Nature Limited. FAU - Harvati, K AU - Harvati K AUID- ORCID: 0000-0001-5998-4794 AD - Paleoanthropology section, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany. katerina.harvati@ifu.uni-tuebingen.de. AD - DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany. katerina.harvati@ifu.uni-tuebingen.de. FAU - Ackermann, R R AU - Ackermann RR AUID- ORCID: 0000-0001-8757-6878 AD - Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa. becky.ackermann@uct.ac.za. AD - Department of Archaeology, University of Cape Town, Cape Town, South Africa. becky.ackermann@uct.ac.za. AD - DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany. becky.ackermann@uct.ac.za. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220905 PL - England TA - Nat Ecol Evol JT - Nature ecology & evolution JID - 101698577 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA, Ancient MH - Fossils MH - *Hominidae/anatomy & histology/genetics MH - Humans MH - Hybridization, Genetic MH - Mammals/genetics MH - *Neanderthals/genetics EDAT- 2022/09/07 06:00 MHDA- 2022/10/05 06:00 CRDT- 2022/09/06 00:05 PHST- 2019/04/24 00:00 [received] PHST- 2022/08/08 00:00 [accepted] PHST- 2022/09/07 06:00 [pubmed] PHST- 2022/10/05 06:00 [medline] PHST- 2022/09/06 00:05 [entrez] AID - 10.1038/s41559-022-01875-z [pii] AID - 10.1038/s41559-022-01875-z [doi] PST - ppublish SO - Nat Ecol Evol. 2022 Oct;6(10):1573-1585. doi: 10.1038/s41559-022-01875-z. Epub 2022 Sep 5. PMID- 36224018 OWN - NLM STAT- MEDLINE DCOM- 20221014 LR - 20221028 IS - 2768-6698 (Electronic) IS - 2768-6698 (Linking) VI - 27 IP - 9 DP - 2022 Sep 29 TI - Identifying Human Remains from 20th Century Warfare: A State of the Field Essay. PG - 271 LID - 10.31083/j.fbl2709271 [doi] AB - As we continually reflect on the wars of the 20th century, identification of the remains of victims takes an increasingly prominent position in ongoing research. Existing work on the identification of human remains from 20th century wars primarily covers the determination of phenotypic characteristics, kinship and geographic origins, supporting the establishment of genetic information databases. Compared with standard forensic methods, DNA analyses have revealed greater effectiveness. The process of DNA analysis includes DNA extraction, genetic marker testing and data analysis. Protocols from ancient DNA research can be applied to degraded remains, and next-generation sequencing (NGS) techniques can compensate for shortcomings in the most commonly-used PCR-capillary electrophoresis typing. As it stands, wide-ranging inter-governmental and inter-institutional collaboration is necessary in order to set up NGS-based public databases, and thereby promote the identification of human remains and archaeological forensics. CI - © 2022 The Author(s). Published by IMR Press. FAU - Xu, Yiran AU - Xu Y AD - Institute of Archaeological Science, Fudan University, 200433 Shanghai, China. FAU - Allen, Edward AU - Allen E AD - Institute of Archaeological Science, Fudan University, 200433 Shanghai, China. FAU - Wang, Lingxiang AU - Wang L AD - Institute of Archaeological Science, Fudan University, 200433 Shanghai, China. AD - MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, 200433 Shanghai, China. FAU - Wen, Shaoqing AU - Wen S AD - Institute of Archaeological Science, Fudan University, 200433 Shanghai, China. AD - MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, 200433 Shanghai, China. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Singapore TA - Front Biosci (Landmark Ed) JT - Frontiers in bioscience (Landmark edition) JID - 101612996 RN - 0 (DNA, Ancient) RN - 0 (Genetic Markers) SB - IM MH - Body Remains MH - *DNA Fingerprinting/methods MH - DNA, Ancient MH - Genetic Markers MH - High-Throughput Nucleotide Sequencing MH - Humans MH - *Microsatellite Repeats OTO - NOTNLM OT - STR typing OT - degraded samples OT - forensic science OT - next-generation sequencing OT - physical anthropology COIS- The authors declare no conflict of interest. EDAT- 2022/10/13 06:00 MHDA- 2022/10/15 06:00 CRDT- 2022/10/12 21:30 PHST- 2022/07/18 00:00 [received] PHST- 2022/08/17 00:00 [revised] PHST- 2022/08/31 00:00 [accepted] PHST- 2022/10/12 21:30 [entrez] PHST- 2022/10/13 06:00 [pubmed] PHST- 2022/10/15 06:00 [medline] AID - S2768-6701(22)00631-1 [pii] AID - 10.31083/j.fbl2709271 [doi] PST - ppublish SO - Front Biosci (Landmark Ed). 2022 Sep 29;27(9):271. doi: 10.31083/j.fbl2709271. PMID- 36066013 OWN - NLM STAT- MEDLINE DCOM- 20220919 LR - 20220919 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 73 IP - 3 DP - 2022 Sep TI - Ancient DNA analysis from epoxy resin Biodur(®)-embedded bones. PG - 113-122 LID - 10.2144/btn-2022-0056 [doi] AB - For microscopic investigation, archaeological bone samples are often embedded in Biodur(®) epoxy resin. This study wants to test whether it is possible to extract DNA suitable for PCR amplification from this sample type. For eight individuals a set of samples - each consisting of a Biodur-embedded femur sample, a native femur sample and a control sample of different anatomical origin - were submitted to organic DNA extraction. The extraction success was tested by autosomal short tandem repeat amplification. Seven out of eight Biodur-embedded femur samples revealed successful amplification results. If Biodur-embedded bone material exists from earlier microscopic investigations, our results encourage the use of this sample type as a source for genetic research. FAU - Flux, Anna Lena AU - Flux AL AD - University of Göttingen, Department of Historical Anthropology & Human Ecology, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Göttingen, 37073, Germany. FAU - Schultz, Michael AU - Schultz M AD - University Medical School Göttingen, Institute of Anatomy & Embryology, Göttingen, 37073, Germany. FAU - Hummel, Susanne AU - Hummel S AUID- ORCID: 0000-0002-3647-8968 AD - University of Göttingen, Department of Historical Anthropology & Human Ecology, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Göttingen, 37073, Germany. LA - eng PT - Journal Article DEP - 20220906 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Ancient) RN - 0 (Epoxy Resins) RN - 9007-49-2 (DNA) SB - IM MH - DNA/analysis/genetics MH - *DNA Fingerprinting/methods MH - *DNA, Ancient MH - Epoxy Resins MH - Humans MH - Microsatellite Repeats OTO - NOTNLM OT - Biodur®-embedded bones OT - DNA quantification OT - PCR OT - STR typing OT - ancient DNA EDAT- 2022/09/07 06:00 MHDA- 2022/09/20 06:00 CRDT- 2022/09/06 07:12 PHST- 2022/09/07 06:00 [pubmed] PHST- 2022/09/20 06:00 [medline] PHST- 2022/09/06 07:12 [entrez] AID - 10.2144/btn-2022-0056 [doi] PST - ppublish SO - Biotechniques. 2022 Sep;73(3):113-122. doi: 10.2144/btn-2022-0056. Epub 2022 Sep 6. PMID- 36006373 OWN - NLM STAT- MEDLINE DCOM- 20220915 LR - 20221207 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 39 IP - 9 DP - 2022 Sep 1 TI - The Genetic Echo of the Tarim Mummies in Modern Central Asians. LID - 10.1093/molbev/msac179 [doi] LID - msac179 AB - The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians. We found that the major ancestry of present-day Tajik populations can be traced back to the admixture of the Bronze Age Bactria-Margiana Archaeological Complex and Andronovo-related populations. Highland Tajik populations further received additional gene flow from the Tarim mummies, an isolated ancient North Eurasian-related population. The West Eurasian ancestry of Kyrgyz is mainly derived from Historical Era populations in Xinjiang of China. Furthermore, the recent admixture signals detected in both Tajik and Kyrgyz are ascribed to the expansions of Eastern Steppe nomadic pastoralists during the Historical Era. CI - © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Dai, Shan-Shan AU - Dai SS AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. AD - Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. FAU - Sulaiman, Xierzhatijiang AU - Sulaiman X AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. AD - Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, China. FAU - Isakova, Jainagul AU - Isakova J AD - Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan. FAU - Xu, Wei-Fang AU - Xu WF AD - Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen, China. FAU - Abdulloevich, Najmudinov Tojiddin AU - Abdulloevich NT AD - E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan. FAU - Afanasevna, Manilova Elena AU - Afanasevna ME AD - E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan. FAU - Ibrohimovich, Khudoidodov Behruz AU - Ibrohimovich KB AD - E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan. FAU - Chen, Xi AU - Chen X AD - Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China. AD - State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China. FAU - Yang, Wei-Kang AU - Yang WK AD - State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China. FAU - Wang, Ming-Shan AU - Wang MS AD - Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA. FAU - Shen, Quan-Kuan AU - Shen QK AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. AD - Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. FAU - Yang, Xing-Yan AU - Yang XY AD - Key Laboratory of Chemistry in Ethnic Medicinal Resource, Yunnan Minzu University, Kunming, China. AD - School of Chemistry and Environment, Yunnan Minzu University, Kunming, China. FAU - Yao, Yong-Gang AU - Yao YG AUID- ORCID: 0000-0002-2955-0693 AD - Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. AD - KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. AD - Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. FAU - Aldashev, Almaz A AU - Aldashev AA AD - Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan. FAU - Saidov, Abdusattor AU - Saidov A AD - E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan. FAU - Chen, Wei AU - Chen W AD - College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China. AD - State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China. FAU - Cheng, Lu-Feng AU - Cheng LF AD - Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, China. FAU - Peng, Min-Sheng AU - Peng MS AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. AD - KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. AD - Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. FAU - Zhang, Ya-Ping AU - Zhang YP AUID- ORCID: 0000-0002-5401-1114 AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. AD - KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. AD - Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. AD - State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) SB - IM MH - Asian People/genetics MH - *DNA, Ancient MH - Ethnicity MH - Gene Flow MH - Genetics, Population MH - Humans MH - *Mummies PMC - PMC9469894 OTO - NOTNLM OT - Central Asia OT - Kyrgyz OT - Steppe OT - Tajik OT - Tarim OT - admixture OT - genome EDAT- 2022/08/26 06:00 MHDA- 2022/09/16 06:00 PMCR- 2022/08/25 CRDT- 2022/08/25 10:43 PHST- 2022/08/26 06:00 [pubmed] PHST- 2022/09/16 06:00 [medline] PHST- 2022/08/25 10:43 [entrez] PHST- 2022/08/25 00:00 [pmc-release] AID - 6675590 [pii] AID - msac179 [pii] AID - 10.1093/molbev/msac179 [doi] PST - ppublish SO - Mol Biol Evol. 2022 Sep 1;39(9):msac179. doi: 10.1093/molbev/msac179. PMID- 35914369 OWN - NLM STAT- MEDLINE DCOM- 20220817 LR - 20220906 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 60 DP - 2022 Sep TI - Assessing the utility of quantitative and qualitative metrics in the DNA quantification process of skeletal remains for autosomal and Y-chromosome STR amplification purposes. PG - 102751 LID - S1872-4973(22)00092-8 [pii] LID - 10.1016/j.fsigen.2022.102751 [doi] AB - In historical cases, ancient DNA investigations and missing persons identification, teeth or bone samples are often the only and almost always the best biological material available for DNA typing. On the other hand, DNA obtained from bone material may be characterized by a high degradation index (DI) or its low content, or DNA tests cannot be repeated due to bone piece size limitation. That is often the effect of the environment in which the material was placed and the time during which exposure to unfavorable environmental factors took place. Therefore, it is very important to use appropriate procedures related to STR analysis. For our study, we selected 80 challenging bone samples. The amount of DNA was compared in qPCR using Quantifiler™ Trio DNA Quantification Kit and Investigator® Quantiplex® Pro RGQ. All qPCR results were confirmed by PCR-CE. The results of DNA concentrations and the assigned degradation index (DI) differed significantly within analyzed samples (~10%). Additionally, the Y-chromosome DI also differed from the autosomal DI in the samples. The difference in degradation indexes could explain the lower Y-chromosome amplification success rate compared to autosomal e.g. during human identification process. The results indicate that performing two DNA quantifications with the use of two different kits (primers sets) allows for a much more precise evaluation of the DNA quality and quantity in the isolate. We suggest that at least one of two suggested DNA concentration measurements should be based on an additional determination of the Y chromosome degradation index. Altogether, it allows for rational isolate management, especially when the volume is limited and the sample is unique. CI - Copyright © 2022. Published by Elsevier B.V. FAU - Doniec, Andrzej AU - Doniec A AD - Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland; Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland. Electronic address: adoniec@ies.gov.pl. FAU - Januła, Miłosz AU - Januła M AD - Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland. FAU - Grzmil, Paweł AU - Grzmil P AD - Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland. FAU - Kupiec, Tomasz AU - Kupiec T AD - Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland. Electronic address: tkupiec@ies.gov.pl. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220726 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 9007-49-2 (DNA) SB - IM MH - *Body Remains MH - DNA/analysis/genetics MH - DNA Fingerprinting MH - Humans MH - *Microsatellite Repeats MH - Real-Time Polymerase Chain Reaction MH - Y Chromosome/chemistry OTO - NOTNLM OT - Bone samples OT - DNA OT - Degradation OT - Y-chromosome EDAT- 2022/08/02 06:00 MHDA- 2022/08/18 06:00 CRDT- 2022/08/01 18:16 PHST- 2022/02/15 00:00 [received] PHST- 2022/06/30 00:00 [revised] PHST- 2022/07/25 00:00 [accepted] PHST- 2022/08/02 06:00 [pubmed] PHST- 2022/08/18 06:00 [medline] PHST- 2022/08/01 18:16 [entrez] AID - S1872-4973(22)00092-8 [pii] AID - 10.1016/j.fsigen.2022.102751 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2022 Sep;60:102751. doi: 10.1016/j.fsigen.2022.102751. Epub 2022 Jul 26. PMID- 35537469 OWN - NLM STAT- MEDLINE DCOM- 20220908 LR - 20250104 IS - 1545-293X (Electronic) IS - 1527-8204 (Print) IS - 1527-8204 (Linking) VI - 23 DP - 2022 Aug 31 TI - Ethical Guidance in Human Paleogenomics: New and Ongoing Perspectives. PG - 627-652 LID - 10.1146/annurev-genom-120621-090239 [doi] AB - Over the past two decades, the study of ancient genomes from Ancestral humans, or human paleogenomic research, has expanded rapidly in both scale and scope. Ethical discourse has subsequently emerged to address issues of social responsibility and scientific robusticity in conducting research. Here, we highlight and contextualize the primary sources of professional ethical guidance aimed at paleogenomic researchers. We describe the tension among existing guidelines, while addressing core issues such as consent, destructive research methods, and data access and management. Currently, there is a dissonance between guidelines that focus on scientific outcomes and those that hold scientists accountable to stakeholder communities,such as descendants. Thus, we provide additional tools to navigate the complexities of ancient DNA research while centering engagement with stakeholder communities in the scientific process. FAU - Fleskes, Raquel E AU - Fleskes RE AD - Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA; email: raquel.fleskes@uconn.edu. FAU - Bader, Alyssa C AU - Bader AC AD - Department of Anthropology, University of Colorado Boulder, Boulder, Colorado, USA; email: alyssa.bader@colorado.edu. AD - Sealaska Heritage Institute, Juneau, Alaska, USA. FAU - Tsosie, Krystal S AU - Tsosie KS AD - Native BioData Consortium, Eagle Butte, South Dakota, USA; email: krystal@nativebio.org. AD - College of Arts and Sciences, Vanderbilt University, Nashville, Tennessee, USA. FAU - Wagner, Jennifer K AU - Wagner JK AD - School of Engineering Design, Technology, and Professional Programs; Institute for Computational and Data Sciences; Department of Biomedical Engineering; and Rock Ethics Institute, Pennsylvania State University, University Park, Pennsylvania, USA; email: jkw131@psu.edu. FAU - Claw, Katrina G AU - Claw KG AD - Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; email: katrina.claw@cuanschutz.edu. FAU - Garrison, Nanibaa' A AU - Garrison NA AD - Institute for Society and Genetics, Institute for Precision Health, and Division of General Internal Medicine and Health Services Research, University of California, Los Angeles, California, USA; email: nanibaa@socgen.ucla.edu. LA - eng GR - R35 HG011319/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20220510 PL - United States TA - Annu Rev Genomics Hum Genet JT - Annual review of genomics and human genetics JID - 100911346 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient MH - *Genomics MH - Humans MH - Informed Consent MH - *Paleontology MH - Research Personnel PMC - PMC11657320 MID - NIHMS2027408 OTO - NOTNLM OT - Indigenous OT - ancient DNA OT - consent OT - ethics OT - paleogenomics OT - stakeholders COIS- DISCLOSURE STATEMENT K.S.T. serves as a noncompensated board member of the Native BioData Consortium, a nonprofit 501(c)(3) Indigenous biobank initiative in the United States. A.C.B. and K.G.C. are co–principal investigators and J.K.W., K.S.T., and N.A.G. are consultants on National Science Foundation grant 1922419. J.K.W. and N.A.G. are former members of the American Society of Human Genetics Social Issues committee. J.K.W. was a member and A.C.B. was a fellow of the American Association of Biological Anthropologists Ethics Committee. EDAT- 2022/05/11 06:00 MHDA- 2022/09/09 06:00 PMCR- 2024/12/19 CRDT- 2022/05/10 19:02 PHST- 2022/05/11 06:00 [pubmed] PHST- 2022/09/09 06:00 [medline] PHST- 2022/05/10 19:02 [entrez] PHST- 2024/12/19 00:00 [pmc-release] AID - 10.1146/annurev-genom-120621-090239 [doi] PST - ppublish SO - Annu Rev Genomics Hum Genet. 2022 Aug 31;23:627-652. doi: 10.1146/annurev-genom-120621-090239. Epub 2022 May 10. PMID- 35440148 OWN - NLM STAT- MEDLINE DCOM- 20220908 LR - 20230610 IS - 1545-293X (Electronic) IS - 1527-8204 (Print) IS - 1527-8204 (Linking) VI - 23 DP - 2022 Aug 31 TI - Predicting Archaic Hominin Phenotypes from Genomic Data. PG - 591-612 LID - 10.1146/annurev-genom-111521-121903 [doi] AB - Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. FAU - Brand, Colin M AU - Brand CM AD - Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; email: colin.brand@ucsf.edu, tony@capralab.org. AD - Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA. FAU - Colbran, Laura L AU - Colbran LL AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA. FAU - Capra, John A AU - Capra JA AD - Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; email: colin.brand@ucsf.edu, tony@capralab.org. AD - Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA. LA - eng GR - R35 GM127087/GM/NIGMS NIH HHS/United States GR - T32 HG009495/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20220419 PL - United States TA - Annu Rev Genomics Hum Genet JT - Annual review of genomics and human genetics JID - 100911346 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA, Ancient MH - Genome, Human MH - Genomics MH - *Hominidae/genetics MH - Humans MH - *Neanderthals/genetics MH - Phenotype PMC - PMC10250142 MID - NIHMS1899886 OTO - NOTNLM OT - Denisovan OT - Neanderthal OT - ancient DNA OT - archaic hominin OT - phenotype prediction EDAT- 2022/04/21 06:00 MHDA- 2022/09/09 06:00 PMCR- 2023/06/09 CRDT- 2022/04/20 05:21 PHST- 2022/04/21 06:00 [pubmed] PHST- 2022/09/09 06:00 [medline] PHST- 2022/04/20 05:21 [entrez] PHST- 2023/06/09 00:00 [pmc-release] AID - 10.1146/annurev-genom-111521-121903 [doi] PST - ppublish SO - Annu Rev Genomics Hum Genet. 2022 Aug 31;23:591-612. doi: 10.1146/annurev-genom-111521-121903. Epub 2022 Apr 19. PMID- 36007048 OWN - NLM STAT- MEDLINE DCOM- 20220829 LR - 20220901 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 377 IP - 6609 DP - 2022 Aug 26 TI - Ancient DNA from the Near East probes a cradle of civilization. PG - 908-909 LID - 10.1126/science.ade5539 [doi] AB - Studies seek clues to origins of farming, early languages. FAU - Curry, Andrew AU - Curry A LA - eng PT - Historical Article PT - News DEP - 20220825 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - *Civilization/history MH - *DNA, Ancient MH - *Farms/history MH - History, Ancient MH - Humans MH - *Language/history MH - Middle East EDAT- 2022/08/26 06:00 MHDA- 2022/08/30 06:00 CRDT- 2022/08/25 14:04 PHST- 2022/08/25 14:04 [entrez] PHST- 2022/08/26 06:00 [pubmed] PHST- 2022/08/30 06:00 [medline] AID - 10.1126/science.ade5539 [doi] PST - ppublish SO - Science. 2022 Aug 26;377(6609):908-909. doi: 10.1126/science.ade5539. Epub 2022 Aug 25. PMID- 36007032 OWN - NLM STAT- MEDLINE DCOM- 20220829 LR - 20220902 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 377 IP - 6609 DP - 2022 Aug 26 TI - Ancient genomes and West Eurasian history. PG - 922-923 LID - 10.1126/science.add9059 [doi] AB - Storytelling with ancient DNA reveals challenges and potential for writing new histories. FAU - Arbuckle, Benjamin S AU - Arbuckle BS AD - Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. FAU - Schwandt, Zoe AU - Schwandt Z AD - Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. LA - eng PT - Comment PT - Historical Article PT - Journal Article DEP - 20220825 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM CON - Science. 2022 Aug 26;377(6609):940-951. doi: 10.1126/science.abq0755. PMID: 36007020 CON - Science. 2022 Aug 26;377(6609):982-987. doi: 10.1126/science.abq0762. PMID: 36007054 CON - Science. 2022 Aug 26;377(6609):eabm4247. doi: 10.1126/science.abm4247. PMID: 36007055 MH - Asia MH - DNA, Ancient MH - Europe MH - *Genome, Human MH - History, Ancient MH - Humans MH - *Sequence Analysis, DNA EDAT- 2022/08/26 06:00 MHDA- 2022/08/30 06:00 CRDT- 2022/08/25 14:04 PHST- 2022/08/25 14:04 [entrez] PHST- 2022/08/26 06:00 [pubmed] PHST- 2022/08/30 06:00 [medline] AID - 10.1126/science.add9059 [doi] PST - ppublish SO - Science. 2022 Aug 26;377(6609):922-923. doi: 10.1126/science.add9059. Epub 2022 Aug 25. PMID- 36008437 OWN - NLM STAT- MEDLINE DCOM- 20220829 LR - 20221118 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 12 IP - 1 DP - 2022 Aug 25 TI - Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel. PG - 14528 LID - 10.1038/s41598-022-17399-2 [doi] LID - 14528 AB - Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA-information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts. CI - © 2022. The Author(s). FAU - Slon, Viviane AU - Slon V AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. viviane@tauex.tau.ac.il. AD - Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel. viviane@tauex.tau.ac.il. AD - The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, 6997801, Tel Aviv, Israel. viviane@tauex.tau.ac.il. FAU - Clark, Jamie L AU - Clark JL AD - Department of Sociology and Anthropology, George Mason University, MSN 3G5, Fairfax, VA, 22030, USA. AD - Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Hölderlinstr. 12, 72074, Tübingen, Germany. AD - The Role of Culture in Early Expansions of Humans, Heidelberg Academy of Sciences and Humanities at the University of Tübingen, Hölderlinstr. 12, 72074, Tübingen, Germany. FAU - Friesem, David E AU - Friesem DE AD - The Leon Recanati Institute for Maritime Studies, Department of Maritime Civilizations, School of Archaeology and Maritime Cultures, University of Haifa, Mount Carmel, 3498838, Haifa, Israel. AD - The Haifa Center for Mediterranean History, University of Haifa, Mount Carmel, 3498838, Haifa, Israel. FAU - Orbach, Meir AU - Orbach M AD - Zinman Institute of Archaeology, School of Archaeology and Maritime Cultures, University of Haifa, Mount Carmel, 3498838, Haifa, Israel. FAU - Porat, Naomi AU - Porat N AD - Geological Survey of Israel, 32 Yeshayahu Leibowitz Street, 9691200, Jerusalem, Israel. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. FAU - Kandel, Andrew W AU - Kandel AW AD - The Role of Culture in Early Expansions of Humans, Heidelberg Academy of Sciences and Humanities at the University of Tübingen, Hölderlinstr. 12, 72074, Tübingen, Germany. FAU - Shimelmitz, Ron AU - Shimelmitz R AD - Zinman Institute of Archaeology, School of Archaeology and Maritime Cultures, University of Haifa, Mount Carmel, 3498838, Haifa, Israel. LA - eng GR - 694707/ERC_/European Research Council/International PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220825 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Archaeology MH - Biological Evolution MH - Caves MH - *DNA, Ancient MH - Fossils MH - Humans MH - *Hyaenidae MH - Infant, Newborn MH - Israel PMC - PMC9411205 COIS- The authors declare no competing interests. EDAT- 2022/08/26 06:00 MHDA- 2022/08/30 06:00 PMCR- 2022/08/25 CRDT- 2022/08/25 23:19 PHST- 2021/07/09 00:00 [received] PHST- 2022/07/25 00:00 [accepted] PHST- 2022/08/25 23:19 [entrez] PHST- 2022/08/26 06:00 [pubmed] PHST- 2022/08/30 06:00 [medline] PHST- 2022/08/25 00:00 [pmc-release] AID - 10.1038/s41598-022-17399-2 [pii] AID - 17399 [pii] AID - 10.1038/s41598-022-17399-2 [doi] PST - epublish SO - Sci Rep. 2022 Aug 25;12(1):14528. doi: 10.1038/s41598-022-17399-2. PMID- 35734848 OWN - NLM STAT- MEDLINE DCOM- 20220729 LR - 20220729 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 79 IP - 4 DP - 2022 Aug 25 TI - Multidisciplinary analysis of a mummy from the War of the Pacific. PG - 451-465 LID - 10.1127/anthranz/2022/1543 [doi] AB - The War of the Pacific (1879-1884) was a big scale war between Chile against the alliance of Peru and Bolivia. One of the most important battles, the "Batalla del Campo de la Alianza" was situated in the desert near Tacna, Peru. The conditions of this environment favored the conservation of the dead soldiers after many years. Decades ago, the Natural History Museum of Concepción in Chile, received a naturally mummified individual of a probably Chilean soldier as a donation; its uncertain context was never studied nor confirmed. Considering this, our investigation analyzed this body under exploratory methods, ballistic analysis, archaeological contrast, (14)C radiocarbon dating, ancient DNA, and isotopic analysis to reconstruct the biological profile of this mummy. The results indicated that the mummy belongs to an adult man between 33-39 years of age (> 1.50 m) and has a perimortem wound in the left flank of the abdomen. CT scan and X-rays revealed the presence of a bullet (Comblain II or Gras) hosted near the L2 vertebra. It is possible that the individual died of bleeding from a gunshot wound done by a long-distance firearm projectile from an inferior level, whose trajectory was from left to right, with slight inclination towards the top, and without a projectile exit. Other analyses confirmed the historical context and suggests the Chilean origin of the mummy. Despite the passage of time and other factors, it was possible to reconstruct the death of this individual thanks to technology and approaches from different disciplines. FAU - Saldías, Eduardo AU - Saldías E AD - Departamento de Antropología. Universidad de Chile. Ignacio Carrera Pinto 1045, 6850331, Ñuñoa, Chile. AD - Museo de Historia Natural de Concepción. 4030000, Concepción, Chile. FAU - Valdebenito, Gabriela AU - Valdebenito G AD - Laboratorio de Criminalística de Carabineros de Chile. 8320000. Santiago, Chile. FAU - Zamora, Luis AU - Zamora L AD - Laboratorio de Criminalística de Carabineros de Chile. 8320000. Santiago, Chile. FAU - Bastías, Bruno AU - Bastías B AD - Laboratorio de Criminalística de Carabineros de Chile. 8320000. Santiago, Chile. FAU - Flores, Cristian AU - Flores C AD - Laboratorio de Criminalística de Carabineros de Chile. 8320000. Santiago, Chile. FAU - Vila, Bernardo AU - Vila B AD - Sanisera Archaeology Institute. Sharjah, United Arab Emirates. FAU - Vinueza, Diana AU - Vinueza D AD - Unitat d'Antropologia, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain. FAU - Tornero, Carlos AU - Tornero C AD - Departament de Prehistòria. Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain. FAU - Malgosa, Assumpció AU - Malgosa A AD - Unitat d'Antropologia, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain. FAU - Becker, Eduardo AU - Becker E AD - Museo de Historia Natural de Concepción. 4030000, Concepción, Chile. AD - Facultad de Ciencias para el Cuidado de la Salud. Universidad San Sebastian. 4080871. Concepción, Chile. LA - eng PT - Journal Article PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 SB - IM MH - Adult MH - Archaeology MH - Humans MH - Male MH - *Mummies MH - Peru MH - Tomography, X-Ray Computed MH - *Wounds, Gunshot EDAT- 2022/06/24 06:00 MHDA- 2022/07/30 06:00 CRDT- 2022/06/23 03:03 PHST- 2021/07/07 00:00 [received] PHST- 2022/04/01 00:00 [revised] PHST- 2022/04/08 00:00 [accepted] PHST- 2022/06/24 06:00 [pubmed] PHST- 2022/07/30 06:00 [medline] PHST- 2022/06/23 03:03 [entrez] AID - 10.1127/anthranz/2022/1543 [doi] PST - ppublish SO - Anthropol Anz. 2022 Aug 25;79(4):451-465. doi: 10.1127/anthranz/2022/1543. PMID- 35998599 OWN - NLM STAT- MEDLINE DCOM- 20220825 LR - 20220929 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 32 IP - 16 DP - 2022 Aug 22 TI - Ancient DNA: Pathogens caught in the Minoan labyrinth. PG - R886-R889 LID - S0960-9822(22)01133-2 [pii] LID - 10.1016/j.cub.2022.07.032 [doi] AB - Ancient DNA methodologies enable research on past prevalence and evolutionary history of pathogens. A new study found plague and typhoid fever-causing bacteria in Minoan Crete, showcasing both the potential and the limitations of the growing field of ancient pathogen genomics. CI - Copyright © 2022 Elsevier Inc. All rights reserved. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria; Institute of Evolutionary Medicine, University of Zurich, 8057 Zurich, Switzerland; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria. Electronic address: verena.schuenemann@iem.uzh.ch. LA - eng PT - Comment PT - Historical Article PT - Journal Article PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM CON - Curr Biol. 2022 Aug 22;32(16):3641-3649.e8. doi: 10.1016/j.cub.2022.06.094. PMID: 35882233 MH - Biological Evolution MH - DNA, Ancient MH - Genomics MH - History, Ancient MH - Humans MH - *Plague MH - *Typhoid Fever COIS- Declaration of interests The author declares no competing interests. EDAT- 2022/08/24 06:00 MHDA- 2022/08/26 06:00 CRDT- 2022/08/23 18:26 PHST- 2022/08/23 18:26 [entrez] PHST- 2022/08/24 06:00 [pubmed] PHST- 2022/08/26 06:00 [medline] AID - S0960-9822(22)01133-2 [pii] AID - 10.1016/j.cub.2022.07.032 [doi] PST - ppublish SO - Curr Biol. 2022 Aug 22;32(16):R886-R889. doi: 10.1016/j.cub.2022.07.032. PMID- 35882233 OWN - NLM STAT- MEDLINE DCOM- 20220825 LR - 20220929 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 32 IP - 16 DP - 2022 Aug 22 TI - Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete. PG - 3641-3649.e8 LID - S0960-9822(22)01101-0 [pii] LID - 10.1016/j.cub.2022.06.094 [doi] AB - During the late 3(rd) millennium BCE, the Eastern Mediterranean and Near East witnessed societal changes in many regions, which are usually explained with a combination of social and climatic factors.(1-4) However, recent archaeogenetic research forces us to rethink models regarding the role of infectious diseases in past societal trajectories.(5) The plague bacterium Yersinia pestis, which was involved in some of the most destructive historical pandemics,(5-8) circulated across Eurasia at least from the onset of the 3(rd) millennium BCE,(9-13) but the challenging preservation of ancient DNA in warmer climates has restricted the identification of Y. pestis from this period to temperate climatic regions. As such, evidence from culturally prominent regions such as the Eastern Mediterranean is currently lacking. Here, we present genetic evidence for the presence of Y. pestis and Salmonella enterica, the causative agent of typhoid/enteric fever, from this period of transformation in Crete, detected at the cave site Hagios Charalambos. We reconstructed one Y. pestis genome that forms part of a now-extinct lineage of Y. pestis strains from the Late Neolithic and Bronze Age that were likely not yet adapted for transmission via fleas. Furthermore, we reconstructed two ancient S. enterica genomes from the Para C lineage, which cluster with contemporary strains that were likely not yet fully host adapted to humans. The occurrence of these two virulent pathogens at the end of the Early Minoan period in Crete emphasizes the necessity to re-introduce infectious diseases as an additional factor possibly contributing to the transformation of early complex societies in the Aegean and beyond. CI - Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Neumann, Gunnar U AU - Neumann GU AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Skourtanioti, Eirini AU - Skourtanioti E AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Burri, Marta AU - Burri M AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Swiss Ornithological Institute, Seerose 1, 6204 Sempach, Switzerland. FAU - Nelson, Elizabeth A AU - Nelson EA AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Department of Anthropology, University of Connecticut, 354 Mansfield Road, Storrs, CT 06269, USA. FAU - Michel, Megan AU - Michel M AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Human Evolutionary Biology, Harvard University, 10 Divinity Avenue, Cambridge, MA 02138, USA. FAU - Hiss, Alina N AU - Hiss AN AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany. FAU - McGeorge, Photini J P AU - McGeorge PJP AD - The British School at Athens, Souidias 52, Athens 106 76, Greece. FAU - Betancourt, Philip P AU - Betancourt PP AD - Department of Art History and Archaeology, Temple University, 2001 N. 13(th) St., Philadelphia, PA 19122, USA. FAU - Spyrou, Maria A AU - Spyrou MA AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Hölderlinstr. 12, 72074 Tübingen, Germany. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. Electronic address: krause@eva.mpg.de. FAU - Stockhammer, Philipp W AU - Stockhammer PW AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80799 München, Germany. Electronic address: philipp.stockhammer@lmu.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220725 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM CIN - Curr Biol. 2022 Aug 22;32(16):R886-R889. doi: 10.1016/j.cub.2022.07.032. PMID: 35998599 MH - Genome, Bacterial MH - Greece MH - Humans MH - Phylogeny MH - *Salmonella enterica/genetics MH - *Yersinia pestis/genetics OTO - NOTNLM OT - Bronze Age OT - Crete OT - Salmonella enterica OT - Yersinia pestis OT - ancient DNA OT - ancient pathogens OT - enteric fever OT - paratyphoid fever OT - plague COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/07/27 06:00 MHDA- 2022/08/26 06:00 CRDT- 2022/07/26 18:43 PHST- 2022/01/28 00:00 [received] PHST- 2022/04/25 00:00 [revised] PHST- 2022/06/30 00:00 [accepted] PHST- 2022/07/27 06:00 [pubmed] PHST- 2022/08/26 06:00 [medline] PHST- 2022/07/26 18:43 [entrez] AID - S0960-9822(22)01101-0 [pii] AID - 10.1016/j.cub.2022.06.094 [doi] PST - ppublish SO - Curr Biol. 2022 Aug 22;32(16):3641-3649.e8. doi: 10.1016/j.cub.2022.06.094. Epub 2022 Jul 25. PMID- 36012483 OWN - NLM STAT- MEDLINE DCOM- 20220829 LR - 20220830 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 23 IP - 16 DP - 2022 Aug 16 TI - Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade. LID - 10.3390/ijms23169219 [doi] LID - 9219 AB - Despite the importance of ancient DNA for understanding human prehistoric dispersals, poor survival means that data remain sparse for many areas in the tropics, including in Africa. In such instances, analysis of contemporary genomes remains invaluable. One promising approach is founder analysis, which identifies and dates migration events in non-recombining systems. However, it has yet to be fully exploited as its application remains controversial. Here, we test the approach by evaluating the age of sub-Saharan mitogenome lineages sampled outside Africa. The analysis confirms that such lineages in the Americas date to recent centuries-the time of the Atlantic slave trade-thereby validating the approach. By contrast, in North Africa, Southwestern Asia and Europe, roughly half of the dispersal signal dates to the early Holocene, during the "greening" of the Sahara. We elaborate these results by showing that the main source regions for the two main dispersal episodes are distinct. For the recent dispersal, the major source was West Africa, but with two exceptions: South America, where the fraction from Southern Africa was greater, and Southwest Asia, where Eastern Africa was the primary source. These observations show the potential of founder analysis as both a supplement and complement to ancient DNA studies. FAU - Sá, Luísa AU - Sá L AUID- ORCID: 0000-0002-9770-1203 AD - CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal. AD - Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal. FAU - Almeida, Mafalda AU - Almeida M AD - CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal. AD - Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal. FAU - Azonbakin, Simon AU - Azonbakin S AD - Laboratory of Histology, Reproductive Biology, Cytogenetic and Medical Genetics, Faculty of Health Sciences, University of Abomey-Calavi, Cotonou 00229, Benin. FAU - Matos, Erica AU - Matos E AD - CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal. AD - Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal. FAU - Franco-Duarte, Ricardo AU - Franco-Duarte R AUID- ORCID: 0000-0002-2333-6127 AD - CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal. AD - Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal. FAU - Gómez-Carballa, Alberto AU - Gómez-Carballa A AUID- ORCID: 0000-0003-0927-1272 AD - Grupo de Investigacion en Genetica, Vacunas, Infecciones y Pediatria (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain. AD - GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Spain. AD - Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain. FAU - Salas, Antonio AU - Salas A AUID- ORCID: 0000-0002-2336-702X AD - Grupo de Investigacion en Genetica, Vacunas, Infecciones y Pediatria (GENVIP), Hospital Clínico Universitario, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain. AD - GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Santiago de Compostela, Spain. AD - Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain. FAU - Laleye, Anatóle AU - Laleye A AD - Laboratory of Histology, Reproductive Biology, Cytogenetic and Medical Genetics, Faculty of Health Sciences, University of Abomey-Calavi, Cotonou 00229, Benin. FAU - Rosa, Alexandra AU - Rosa A AD - Human Genetics Laboratory, Campus da Penteada, University of Madeira, 9020-105 Funchal, Portugal. AD - Faculty of Life Sciences, Campus da Penteada, University of Madeira, 9020-105 Funchal, Portugal. FAU - Brehm, António AU - Brehm A AD - Human Genetics Laboratory, Campus da Penteada, University of Madeira, 9020-105 Funchal, Portugal. FAU - Richards, Martin B AU - Richards MB AUID- ORCID: 0000-0003-3118-0967 AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK. FAU - Soares, Pedro AU - Soares P AD - CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal. AD - Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal. FAU - Rito, Teresa AU - Rito T AUID- ORCID: 0000-0002-8374-6347 AD - CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal. AD - Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal. LA - eng GR - PTDC/SOC-ANT/30316/2017/Fundação para a Ciência e Tecnologia/ GR - UIDB/04050/2020/Fundação para a Ciência e Tecnologia/ PT - Journal Article DEP - 20220816 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Africa South of the Sahara MH - Climate Change MH - DNA, Ancient MH - *DNA, Mitochondrial/genetics MH - *Enslaved Persons MH - Humans MH - Phylogeny MH - Phylogeography PMC - PMC9408831 OTO - NOTNLM OT - Holocene OT - computational approach OT - founder analysis OT - mitochondrial DNA OT - phylogeography OT - slave trade influence COIS- The authors declare no conflict of interest. EDAT- 2022/08/27 06:00 MHDA- 2022/08/30 06:00 PMCR- 2022/08/16 CRDT- 2022/08/26 01:24 PHST- 2022/07/28 00:00 [received] PHST- 2022/08/14 00:00 [revised] PHST- 2022/08/15 00:00 [accepted] PHST- 2022/08/26 01:24 [entrez] PHST- 2022/08/27 06:00 [pubmed] PHST- 2022/08/30 06:00 [medline] PHST- 2022/08/16 00:00 [pmc-release] AID - ijms23169219 [pii] AID - ijms-23-09219 [pii] AID - 10.3390/ijms23169219 [doi] PST - epublish SO - Int J Mol Sci. 2022 Aug 16;23(16):9219. doi: 10.3390/ijms23169219. PMID- 36011343 OWN - NLM STAT- MEDLINE DCOM- 20220829 LR - 20220915 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 13 IP - 8 DP - 2022 Aug 12 TI - Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach. LID - 10.3390/genes13081432 [doi] LID - 1432 AB - To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools. FAU - Zupanič Pajnič, Irena AU - Zupanič Pajnič I AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia. FAU - Zupanc, Tomaž AU - Zupanc T AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia. FAU - Leskovar, Tamara AU - Leskovar T AUID- ORCID: 0000-0002-4585-4726 AD - Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000 Ljubljana, Slovenia. FAU - Črešnar, Matija AU - Črešnar M AD - Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000 Ljubljana, Slovenia. FAU - Fattorini, Paolo AU - Fattorini P AUID- ORCID: 0000-0002-3416-1684 AD - Department of Medicine, Surgery and Health, University of Trieste, Strada per Fiume 447, 34149 Trieste, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220812 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Aged MH - *Body Remains MH - DNA/genetics MH - DNA, Ancient MH - *Eye Color/genetics MH - *Hair Color/genetics MH - Humans MH - Polymerase Chain Reaction MH - World War II PMC - PMC9407562 OTO - NOTNLM OT - DNA degradation OT - PCR artifact OT - PCR-MPS OT - phenotyping COIS- The authors declare no conflict of interest. EDAT- 2022/08/27 06:00 MHDA- 2022/08/30 06:00 PMCR- 2022/08/12 CRDT- 2022/08/26 01:16 PHST- 2022/06/20 00:00 [received] PHST- 2022/08/01 00:00 [revised] PHST- 2022/08/08 00:00 [accepted] PHST- 2022/08/26 01:16 [entrez] PHST- 2022/08/27 06:00 [pubmed] PHST- 2022/08/30 06:00 [medline] PHST- 2022/08/12 00:00 [pmc-release] AID - genes13081432 [pii] AID - genes-13-01432 [pii] AID - 10.3390/genes13081432 [doi] PST - epublish SO - Genes (Basel). 2022 Aug 12;13(8):1432. doi: 10.3390/genes13081432. PMID- 35960716 OWN - NLM STAT- MEDLINE DCOM- 20220816 LR - 20220824 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 17 IP - 8 DP - 2022 TI - Testing the existence of an unadmixed ancestor from a specific population t generations ago. PG - e0271097 LID - 10.1371/journal.pone.0271097 [doi] LID - e0271097 AB - The ancestry of each locus of the genome can be estimated (local ancestry) based on sequencing or genotyping information together with reference panels of ancestral source populations. The length of those ancestry-specific genomic segments are commonly used to understand migration waves and admixture events. In short time scales, it is often of interest to determine the existence of the most recent unadmixed ancestor from a specific population t generations ago. We built a hypothesis test to determine if an individual has an ancestor belonging to a target ancestral population t generations ago based on these lengths of the ancestry-specific segments at an individual level. We applied this test on a data set that includes 20 Uruguayan admixed individuals to estimate for each one how many generations ago the most recent indigenous ancestor lived. As this method tests each individual separately, it is particularly suited to small sample sizes, such as our study or ancient genome samples. FAU - Illanes, Gabriel AU - Illanes G AUID- ORCID: 0000-0003-4790-0412 AD - Centro de Matemática, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay. FAU - Fariello, María Inés AU - Fariello MI AD - Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay. AD - Facultad de Ingeniería, Universidad de la República, Uruguay. FAU - Spangenberg, Lucía AU - Spangenberg L AD - Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay. AD - Departamento de Informática, Universidad Católica del Uruguay, Montevideo, Uruguay. FAU - Mordecki, Ernesto AU - Mordecki E AD - Centro de Matemática, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay. FAU - Naya, Hugo AU - Naya H AD - Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay. AD - Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220812 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - *Genetics, Population MH - Genome, Human MH - Humans MH - *Polymorphism, Single Nucleotide MH - Uruguay PMC - PMC9374268 COIS- The authors have declared that no competing interests exist. EDAT- 2022/08/13 06:00 MHDA- 2022/08/17 06:00 PMCR- 2022/08/12 CRDT- 2022/08/12 13:42 PHST- 2021/12/06 00:00 [received] PHST- 2022/06/23 00:00 [accepted] PHST- 2022/08/12 13:42 [entrez] PHST- 2022/08/13 06:00 [pubmed] PHST- 2022/08/17 06:00 [medline] PHST- 2022/08/12 00:00 [pmc-release] AID - PONE-D-21-38583 [pii] AID - 10.1371/journal.pone.0271097 [doi] PST - epublish SO - PLoS One. 2022 Aug 12;17(8):e0271097. doi: 10.1371/journal.pone.0271097. eCollection 2022. PMID- 35944486 OWN - NLM STAT- MEDLINE DCOM- 20220811 LR - 20221207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 32 IP - 15 DP - 2022 Aug 8 TI - Human genetics: The dual origin of Three Kingdoms period Koreans. PG - R844-R847 LID - S0960-9822(22)01006-5 [pii] LID - 10.1016/j.cub.2022.06.044 [doi] AB - The genetic history of Koreans remains poorly understood due to a lack of ancient DNA. A new paleo-genomic study shows that population stratification in 4(th)-5(th) century South Korean populations was linked to a varied proportion of indigenous Jomon-related ancestry, which does not survive in present-day Koreans. CI - Copyright © 2022 Elsevier Inc. All rights reserved. FAU - Wang, Rui AU - Wang R AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China. FAU - Wang, Chuan-Chao AU - Wang CC AD - State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China. Electronic address: wang@xmu.edu.cn. LA - eng PT - Comment PT - Historical Article PT - Journal Article PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM CON - Curr Biol. 2022 Aug 8;32(15):3232-3244.e6. doi: 10.1016/j.cub.2022.06.004. PMID: 35732180 MH - *Asian People/genetics MH - *DNA, Ancient MH - Genetics, Population MH - Genome MH - History, Ancient MH - Humans MH - Republic of Korea COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/08/10 06:00 MHDA- 2022/08/12 06:00 CRDT- 2022/08/09 18:29 PHST- 2022/08/09 18:29 [entrez] PHST- 2022/08/10 06:00 [pubmed] PHST- 2022/08/12 06:00 [medline] AID - S0960-9822(22)01006-5 [pii] AID - 10.1016/j.cub.2022.06.044 [doi] PST - ppublish SO - Curr Biol. 2022 Aug 8;32(15):R844-R847. doi: 10.1016/j.cub.2022.06.044. PMID- 35732180 OWN - NLM STAT- MEDLINE DCOM- 20220811 LR - 20221207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 32 IP - 15 DP - 2022 Aug 8 TI - Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea. PG - 3232-3244.e6 LID - S0960-9822(22)00916-2 [pii] LID - 10.1016/j.cub.2022.06.004 [doi] AB - The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small number of ancient genomes are available. Here, we report the first paleogenomic data from the Korean Three Kingdoms period, a crucial point in the cultural and historic formation of Korea. These data comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th century CE and are best modeled as an admixture between a northern China Bronze Age genetic source and a source of Jomon-related ancestry that shares similarities with the present-day genomes from Japan. The observed substructure and proportion of Jomon-related ancestry suggest the presence of two genetic groups within the population and diversity among the Gaya population. We could not correlate the genomic differences between these two groups with either social status or sex. All the ancient individuals' genomic profiles, including phenotypically relevant SNPs associated with hair and eye color, facial morphology, and myopia, imply strong genetic and phenotypic continuity with modern Koreans for the last 1,700 years. CI - Copyright © 2022 Elsevier Inc. All rights reserved. FAU - Gelabert, Pere AU - Gelabert P AD - Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. Electronic address: pere.gelabert@univie.ac.at. FAU - Blazyte, Asta AU - Blazyte A AD - Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea. FAU - Chang, Yongjoon AU - Chang Y AD - Daegu National Museum, 321 Cheongho-ro, Suseong-gu, Daegu 42111, Republic of Korea. FAU - Fernandes, Daniel M AU - Fernandes DM AD - Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal. FAU - Jeon, Sungwon AU - Jeon S AD - Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Clinomics Inc., UNIST-gil 50, Ulsan 44919, Republic of Korea. FAU - Hong, Jin Geun AU - Hong JG AD - Jeonju National Museum, 249 Ssukgogae-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 55070, Republic of Korea. FAU - Yoon, Jiyeon AU - Yoon J AD - Gongju National Museum, 34 Gwangwangdanji-gil, Gongju-si, Chungcheongnam-do 32535, Republic of Korea. FAU - Ko, Youngmin AU - Ko Y AD - National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea. FAU - Oberreiter, Victoria AU - Oberreiter V AD - Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. FAU - Özdoğan, Kadir T AU - Özdoğan KT AD - Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. FAU - Sawyer, Susanna AU - Sawyer S AD - Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. FAU - Yang, Songhyok AU - Yang S AD - National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea. FAU - Greytak, Ellen McRae AU - Greytak EM AD - Parabon NanoLabs, Inc., 11260 Roger Bacon, Reston, VA 20170, USA. FAU - Choi, Hansol AU - Choi H AD - Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea. FAU - Kim, Jungeun AU - Kim J AD - Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28160, Republic of Korea. FAU - Kim, Jong-Il AU - Kim JI AD - Department of Archaeology and Art History, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea. FAU - Jeong, Choongwon AU - Jeong C AD - Seoul National University, School of Biological Sciences, 599 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea. FAU - Bae, Kidong AU - Bae K AD - National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea. Electronic address: bkd5374@korea.kr. FAU - Bhak, Jong AU - Bhak J AD - Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Clinomics Inc., UNIST-gil 50, Ulsan 44919, Republic of Korea. Electronic address: jongbhak@UNIST.AC.KR. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. Electronic address: bkd5374@korea.kr. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220621 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM CIN - Curr Biol. 2022 Aug 8;32(15):R844-R847. doi: 10.1016/j.cub.2022.06.044. PMID: 35944486 MH - Archaeology MH - *Asian People/genetics MH - *Ethnicity MH - Genome MH - History, Ancient MH - Humans MH - Polymorphism, Single Nucleotide OTO - NOTNLM OT - Korea Three Kingdoms period genomes OT - Korean ancient genomes OT - ancient DNA OT - ancient diploid genomes OT - phenotypic analyses OT - population continuity OT - population genetics COIS- Declaration of interests Clinomics paid for the eight TK period sample’s face prediction to the Parabon NanoLabs. EDAT- 2022/06/23 06:00 MHDA- 2022/08/12 06:00 CRDT- 2022/06/22 18:43 PHST- 2021/12/19 00:00 [received] PHST- 2022/04/05 00:00 [revised] PHST- 2022/06/01 00:00 [accepted] PHST- 2022/06/23 06:00 [pubmed] PHST- 2022/08/12 06:00 [medline] PHST- 2022/06/22 18:43 [entrez] AID - S0960-9822(22)00916-2 [pii] AID - 10.1016/j.cub.2022.06.004 [doi] PST - ppublish SO - Curr Biol. 2022 Aug 8;32(15):3232-3244.e6. doi: 10.1016/j.cub.2022.06.004. Epub 2022 Jun 21. PMID- 35695771 OWN - NLM STAT- MEDLINE DCOM- 20221114 LR - 20230417 IS - 1367-4811 (Electronic) IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 38 IP - 15 DP - 2022 Aug 2 TI - hapCon: estimating contamination of ancient genomes by copying from reference haplotypes. PG - 3768-3777 LID - 10.1093/bioinformatics/btac390 [doi] AB - MOTIVATION: Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1× average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1× and below) remains a challenging task for existing approaches. RESULTS: We present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&Stephens haplotype copying model for haploid X chromosomes, with mismatches modeled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1× for SNP capture data (1240k) and 0.02× for whole genome sequencing data, substantially extending the coverage limit of previous male X chromosome-based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25-30% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as ∼45 000 and various global ancestries. AVAILABILITY AND IMPLEMENTATION: We make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CI - © The Author(s) 2022. Published by Oxford University Press. FAU - Huang, Yilei AU - Huang Y AUID- ORCID: 0000-0002-2860-2543 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Ringbauer, Harald AU - Ringbauer H AUID- ORCID: 0000-0002-4884-9682 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. LA - eng GR - Max Planck Society/ PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (DNA, Ancient) SB - IM MH - Male MH - Humans MH - Haplotypes MH - Sequence Analysis, DNA/methods MH - *Genome MH - *Software MH - DNA, Ancient PMC - PMC9344841 EDAT- 2022/06/14 06:00 MHDA- 2022/11/15 06:00 PMCR- 2022/06/13 CRDT- 2022/06/13 10:17 PHST- 2021/12/22 00:00 [received] PHST- 2022/06/03 00:00 [revised] PHST- 2022/06/09 00:00 [accepted] PHST- 2022/06/14 06:00 [pubmed] PHST- 2022/11/15 06:00 [medline] PHST- 2022/06/13 10:17 [entrez] PHST- 2022/06/13 00:00 [pmc-release] AID - 6607584 [pii] AID - btac390 [pii] AID - 10.1093/bioinformatics/btac390 [doi] PST - ppublish SO - Bioinformatics. 2022 Aug 2;38(15):3768-3777. doi: 10.1093/bioinformatics/btac390. PMID- 35839766 OWN - NLM STAT- MEDLINE DCOM- 20220728 LR - 20220822 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 32 IP - 14 DP - 2022 Jul 25 TI - A Late Pleistocene human genome from Southwest China. PG - 3095-3109.e5 LID - S0960-9822(22)00928-9 [pii] LID - 10.1016/j.cub.2022.06.016 [doi] AB - Southern East Asia is the dispersal center regarding the prehistoric settlement and migrations of modern humans in Asia-Pacific regions. However, the settlement pattern and population structure of paleolithic humans in this region remain elusive, and ancient DNA can provide direct information. Here, we sequenced the genome of a Late Pleistocene hominin (MZR), dated ∼14.0 thousand years ago from Red Deer Cave located in Southwest China, which was previously reported possessing mosaic features of modern and archaic hominins. MZR is the first Late Pleistocene genome from southern East Asia. Our results indicate that MZR is a modern human who represents an early diversified lineage in East Asia. The mtDNA of MZR belongs to an extinct basal lineage of the M9 haplogroup, reflecting a rich matrilineal diversity in southern East Asia during the Late Pleistocene. Combined with the published data, we detected clear genetic stratification in ancient southern populations of East/Southeast Asia and some degree of south-versus-north divergency during the Late Pleistocene, and MZR was identified as a southern East Asian who exhibits genetic continuity to present day populations. Markedly, MZR is linked deeply to the East Asian ancestry that contributed to First Americans. CI - Copyright © 2022 Elsevier Inc. All rights reserved. FAU - Zhang, Xiaoming AU - Zhang X AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China. FAU - Ji, Xueping AU - Ji X AD - Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China. Electronic address: jxpchina@foxmail.com. FAU - Li, Chunmei AU - Li C AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China. FAU - Yang, Tingyu AU - Yang T AD - Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China. FAU - Huang, Jiahui AU - Huang J AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Zhao, Yinhui AU - Zhao Y AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Wu, Yun AU - Wu Y AD - Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; School of History, Wuhan University, Wuhan 430072, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China. FAU - Ma, Shiwu AU - Ma S AD - Mengzi Institute of Cultural Relics, Mengzi, Yunnan Province 661100, China. FAU - Pang, Yuhong AU - Pang Y AD - Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China. FAU - Huang, Yanyi AU - Huang Y AD - Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China. FAU - He, Yaoxi AU - He Y AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China. Electronic address: heyaoxi@mail.kiz.ac.cn. FAU - Su, Bing AU - Su B AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China. Electronic address: sub@mail.kiz.ac.cn. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220714 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Animals MH - China MH - *Deer MH - Fossils MH - Genome, Human MH - *Hominidae MH - Humans OTO - NOTNLM OT - First Americans OT - Late Pleistocene OT - Maludong OT - Red Deer Cave OT - Southwest China OT - ancient genome OT - diverse lineage OT - hominin cranium COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/07/16 06:00 MHDA- 2022/07/29 06:00 CRDT- 2022/07/15 18:42 PHST- 2021/12/24 00:00 [received] PHST- 2022/05/27 00:00 [revised] PHST- 2022/06/08 00:00 [accepted] PHST- 2022/07/16 06:00 [pubmed] PHST- 2022/07/29 06:00 [medline] PHST- 2022/07/15 18:42 [entrez] AID - S0960-9822(22)00928-9 [pii] AID - 10.1016/j.cub.2022.06.016 [doi] PST - ppublish SO - Curr Biol. 2022 Jul 25;32(14):3095-3109.e5. doi: 10.1016/j.cub.2022.06.016. Epub 2022 Jul 14. PMID- 35868268 OWN - NLM STAT- MEDLINE DCOM- 20220726 LR - 20220823 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 185 IP - 15 DP - 2022 Jul 21 TI - Evolving ancient DNA techniques and the future of human history. PG - 2632-2635 LID - S0092-8674(22)00714-0 [pii] LID - 10.1016/j.cell.2022.06.009 [doi] AB - Ancient DNA (aDNA) techniques applied to human genomics have significantly advanced in the past decade, enabling large-scale aDNA research, sometimes independent of human remains. This commentary reviews the major milestones of aDNA techniques and explores future directions to expand the scope of aDNA research and insights into present-day human health. CI - Copyright © 2022 Elsevier Inc. All rights reserved. FAU - Liu, Yichen AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China. FAU - Bennett, E Andrew AU - Bennett EA AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - *Genome, Human MH - History, Ancient MH - Humans OTO - NOTNLM OT - aDNA techniques OT - ancient DNA OT - human population history OT - paleogenomics COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/07/23 06:00 MHDA- 2022/07/27 06:00 CRDT- 2022/07/22 18:33 PHST- 2022/03/21 00:00 [received] PHST- 2022/05/31 00:00 [revised] PHST- 2022/06/06 00:00 [accepted] PHST- 2022/07/22 18:33 [entrez] PHST- 2022/07/23 06:00 [pubmed] PHST- 2022/07/27 06:00 [medline] AID - S0092-8674(22)00714-0 [pii] AID - 10.1016/j.cell.2022.06.009 [doi] PST - ppublish SO - Cell. 2022 Jul 21;185(15):2632-2635. doi: 10.1016/j.cell.2022.06.009. PMID- 35835776 OWN - NLM STAT- MEDLINE DCOM- 20220718 LR - 20220922 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 12 IP - 1 DP - 2022 Jul 14 TI - Genomic palaeoparasitology traced the occurrence of Taenia asiatica in ancient Iran (Sassanid Empire, 2th cent. CE-6th cent. CE). PG - 12045 LID - 10.1038/s41598-022-10690-2 [doi] LID - 12045 AB - Palaeoparasitology investigates parasitological infections in animals and humans of past distance by examining biological remains. Palaeofaeces (or coprolites) are biological remains that provide valuable information on the disease, diet, and population movements in ancient times. Today, advances in detecting ancient DNA have cast light on dark corners that microscopy could never reach. The archaeological site of the Chehrabad salt mine of Achaemenid (550-330 BC) and Sassanid (third-seventh century AD) provides remains of various biotic and abiotic samples, including animal coprolites, for multidisciplinary studies. In the present work, we investigated coprolites for helminth eggs and larvae by microscopy and traced their biological agents' DNA by Next Generation Sequencing. Our results revealed various helminths, including Taenia asiatica, the species introduced in the 1990s. Implementing advanced modern molecular techniques like NGS gives a paramount view of pathogenic agents in space and time. CI - © 2022. The Author(s). FAU - Askari, Zeynab AU - Askari Z AD - Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran. FAU - Ruehli, Frank AU - Ruehli F AD - Institute of Evolutionary Medicine, Zurich University, Zürich, Switzerland. FAU - Bouwman, Abigail AU - Bouwman A AD - Institute of Evolutionary Medicine, Zurich University, Zürich, Switzerland. FAU - Shariati, Vahid AU - Shariati V AD - NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran. FAU - Naddaf, Saied Reza AU - Naddaf SR AD - Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran. FAU - Otranto, Domenico AU - Otranto D AD - Department of Veterinary Medicine, University of Bari, Valenzano, Italy. AD - Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran. FAU - Mas-Coma, Santiago AU - Mas-Coma S AD - Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Burjassot, Valencia, Spain. FAU - Rezaeian, Mostafa AU - Rezaeian M AD - Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran. FAU - Boenke, Nicole AU - Boenke N AD - Institute for Archaeological Science, Ruhr-University Bochum, Bochum, Germany. AD - German Mining-Museum, Bochum, Germany. FAU - Stöllner, Thomas AU - Stöllner T AD - Institute for Archaeological Science, Ruhr-University Bochum, Bochum, Germany. AD - German Mining-Museum, Bochum, Germany. FAU - Aali, Abolfazl AU - Aali A AD - Archaeological Museum of Zanjan, Zanjan, Iran. FAU - Mobedi, Iraj AU - Mobedi I AD - Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran. FAU - Mowlavi, Gholamreza AU - Mowlavi G AD - Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran. molavig@yahoo.com. AD - Center for Research of Endemic Parasites of Iran (CREPI), Tehran University of Medical Sciences, Tehran, Iran. molavig@yahoo.com. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220714 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA, Ancient MH - Genomics MH - *Helminths/genetics MH - History, Ancient MH - Humans MH - Iran MH - *Taenia/genetics PMC - PMC9283436 COIS- The authors declare no competing interests. EDAT- 2022/07/15 06:00 MHDA- 2022/07/19 06:00 PMCR- 2022/07/14 CRDT- 2022/07/14 23:18 PHST- 2021/08/26 00:00 [received] PHST- 2022/04/11 00:00 [accepted] PHST- 2022/07/14 23:18 [entrez] PHST- 2022/07/15 06:00 [pubmed] PHST- 2022/07/19 06:00 [medline] PHST- 2022/07/14 00:00 [pmc-release] AID - 10.1038/s41598-022-10690-2 [pii] AID - 10690 [pii] AID - 10.1038/s41598-022-10690-2 [doi] PST - epublish SO - Sci Rep. 2022 Jul 14;12(1):12045. doi: 10.1038/s41598-022-10690-2. PMID- 35617951 OWN - NLM STAT- MEDLINE DCOM- 20220714 LR - 20221207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 32 IP - 13 DP - 2022 Jul 11 TI - The genetic origin of Huns, Avars, and conquering Hungarians. PG - 2858-2870.e7 LID - S0960-9822(22)00732-1 [pii] LID - 10.1016/j.cub.2022.04.093 [doi] AB - Huns, Avars, and conquering Hungarians were migration-period nomadic tribal confederations that arrived in three successive waves in the Carpathian Basin between the 5(th) and 9(th) centuries. Based on the historical data, each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations have been debated. Recently, hundreds of ancient genomes were analyzed from Central Asia, Mongolia, and China, from which we aimed to identify putative source populations for the above-mentioned groups. In this study, we have sequenced 9 Hun, 143 Avar, and 113 Hungarian conquest period samples and identified three core populations, representing immigrants from each period with no recent European ancestry. Our results reveal that this "immigrant core" of both Huns and Avars likely originated in present day Mongolia, and their origin can be traced back to Xiongnus (Asian Huns), as suggested by several historians. On the other hand, the "immigrant core" of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians, and descendants of late Xiongnus. We have also shown that a common "proto-Ugric" gene pool appeared in the Bronze Age from the admixture of Mezhovskaya and Nganasan people, supporting genetic and linguistic data. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period genetic outliers, indicating a genetic link between these successive nomadic groups. Aside from the immigrant core groups, we identified that the majority of the individuals from each period were local residents harboring "native European" ancestry. CI - Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Maróti, Zoltán AU - Maróti Z AD - Department of Archaeogenetics, Institute of Hungarian Research, 1041 Budapest, Hungary; Department of Pediatrics and Pediatric Health Center, University of Szeged, 6725 Szeged, Hungary. FAU - Neparáczki, Endre AU - Neparáczki E AD - Department of Archaeogenetics, Institute of Hungarian Research, 1041 Budapest, Hungary; Department of Genetics, University of Szeged, 6726 Szeged, Hungary. FAU - Schütz, Oszkár AU - Schütz O AD - Department of Genetics, University of Szeged, 6726 Szeged, Hungary. FAU - Maár, Kitti AU - Maár K AD - Department of Genetics, University of Szeged, 6726 Szeged, Hungary. FAU - Varga, Gergely I B AU - Varga GIB AD - Department of Archaeogenetics, Institute of Hungarian Research, 1041 Budapest, Hungary. FAU - Kovács, Bence AU - Kovács B AD - Department of Archaeogenetics, Institute of Hungarian Research, 1041 Budapest, Hungary; Department of Genetics, University of Szeged, 6726 Szeged, Hungary. FAU - Kalmár, Tibor AU - Kalmár T AD - Department of Pediatrics and Pediatric Health Center, University of Szeged, 6725 Szeged, Hungary. FAU - Nyerki, Emil AU - Nyerki E AD - Department of Archaeogenetics, Institute of Hungarian Research, 1041 Budapest, Hungary; Department of Pediatrics and Pediatric Health Center, University of Szeged, 6725 Szeged, Hungary. FAU - Nagy, István AU - Nagy I AD - SeqOmics Biotechnology Ltd., 6782 Mórahalom, Hungary; Institute of Biochemistry, Biological Research Centre, 6726 Szeged, Hungary. FAU - Latinovics, Dóra AU - Latinovics D AD - SeqOmics Biotechnology Ltd., 6782 Mórahalom, Hungary. FAU - Tihanyi, Balázs AU - Tihanyi B AD - Department of Archaeogenetics, Institute of Hungarian Research, 1041 Budapest, Hungary; Department of Biological Anthropology, University of Szeged, 6726 Szeged, Hungary. FAU - Marcsik, Antónia AU - Marcsik A AD - Department of Biological Anthropology, University of Szeged, 6726 Szeged, Hungary. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, University of Szeged, 6726 Szeged, Hungary. FAU - Bernert, Zsolt AU - Bernert Z AD - Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary. FAU - Gallina, Zsolt AU - Gallina Z AD - Ásatárs Ltd., 6000 Kecskemét, Hungary; Department of Archaeology, Institute of Hungarian Research, 1041 Budapest, Hungary. FAU - Horváth, Ciprián AU - Horváth C AD - Department of Archaeology, Institute of Hungarian Research, 1041 Budapest, Hungary. FAU - Varga, Sándor AU - Varga S AD - Móra Ferenc Museum, 6720 Szeged, Hungary. FAU - Költő, László AU - Költő L AD - Rippl-Rónai Municipal Museum with Country Scope, 7400 Kaposvár, Hungary. FAU - Raskó, István AU - Raskó I AD - Institute of Genetics, Biological Research Centre, 6726 Szeged, Hungary. FAU - Nagy, Péter L AU - Nagy PL AD - Praxis Genomics LLC, Atlanta, GA 30328, USA. FAU - Balogh, Csilla AU - Balogh C AD - Department of Art History, Istanbul Medeniyet University, 34720 Istanbul, Turkey. FAU - Zink, Albert AU - Zink A AD - Institute for Mummy Studies, EURAC Research, 39100 Bolzano, Italy. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, EURAC Research, 39100 Bolzano, Italy. FAU - Götherström, Anders AU - Götherström A AD - Department of Archaeology and Classical Studies, Stockholm University, 11418 Stockholm, Sweden. FAU - George, Robert AU - George R AD - Department of Archaeology and Classical Studies, Stockholm University, 11418 Stockholm, Sweden. FAU - Szalontai, Csaba AU - Szalontai C AD - Hungarian National Museum, Department of Archaeology, 1088 Budapest, Hungary. FAU - Szenthe, Gergely AU - Szenthe G AD - Hungarian National Museum, Department of Archaeology, 1088 Budapest, Hungary. FAU - Gáll, Erwin AU - Gáll E AD - "Vasile Pârvan" Institute of Archaeology, 010667 Bucharest, Romania. FAU - Kiss, Attila P AU - Kiss AP AD - Faculty of Humanities and Social Sciences, Institute of Archaeology, Pázmány Péter Catholic University, 1088 Budapest, Hungary. FAU - Gulyás, Bence AU - Gulyás B AD - Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Hungary. FAU - Kovacsóczy, Bernadett Ny AU - Kovacsóczy BN AD - Katona József Museum, 6000 Kecskemét, Hungary. FAU - Gál, Szilárd Sándor AU - Gál SS AD - Mureş County Museum, 540088 Târgu Mureș, Romania. FAU - Tomka, Péter AU - Tomka P AD - Department of Archaeology, Rómer Flóris Museum of Art and History, 9021 Győr, Hungary. FAU - Török, Tibor AU - Török T AD - Department of Archaeogenetics, Institute of Hungarian Research, 1041 Budapest, Hungary; Department of Genetics, University of Szeged, 6726 Szeged, Hungary. Electronic address: torokt@bio.u-szeged.hu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220525 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM CIN - Curr Biol. 2022 Jul 11;32(13):R738-R741. doi: 10.1016/j.cub.2022.05.058. PMID: 35820383 MH - Asian People MH - *Gene Pool MH - *Genetics, Population MH - Haplotypes MH - Humans MH - Hungary OTO - NOTNLM OT - Asian Hun OT - Carpathian Basin OT - Ugric OT - ancient DNA OT - f-statistics OT - migration period OT - qpAdm modeling COIS- Declaration of interests P.L.N. from Praxis Genomics LLC, I.N. and D.L. from SeqOmics Biotechnology Ltd., and Z.G. from Ásatárs Ltd. were not directly involved in the design of the experiments, data analysis, and evaluation. These affiliations do not alter our adherence to Current Biology’s policies on sharing data and materials. EDAT- 2022/05/27 06:00 MHDA- 2022/07/15 06:00 CRDT- 2022/05/26 18:42 PHST- 2022/01/28 00:00 [received] PHST- 2022/03/10 00:00 [revised] PHST- 2022/04/28 00:00 [accepted] PHST- 2022/05/27 06:00 [pubmed] PHST- 2022/07/15 06:00 [medline] PHST- 2022/05/26 18:42 [entrez] AID - S0960-9822(22)00732-1 [pii] AID - 10.1016/j.cub.2022.04.093 [doi] PST - ppublish SO - Curr Biol. 2022 Jul 11;32(13):2858-2870.e7. doi: 10.1016/j.cub.2022.04.093. Epub 2022 May 25. PMID- 35731946 OWN - NLM STAT- MEDLINE DCOM- 20220719 LR - 20220920 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 14 IP - 7 DP - 2022 Jul 2 TI - Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages. LID - 10.1093/gbe/evac097 [doi] LID - evac097 AB - Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age. CI - © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Översti, Sanni AU - Översti S AD - Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, Germany. AD - Organismal and Evolutionary Biology Research Programme, Faculty of Biological Sciences, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland. FAU - Palo, Jukka U AU - Palo JU AD - Department of Forensic Medicine, Faculty of Medicine, University of Helsinki, P.O. Box 40, FI-00014 Helsinki, Finland. AD - Forensic Chemistry Unit, Forensic Genetics Team, Finnish Institute for Health and Welfare, P.O. Box 30, FI-00271 Helsinki, Finland. LA - eng PT - Journal Article PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Bayes Theorem MH - *DNA, Ancient MH - *DNA, Mitochondrial/genetics MH - Evolution, Molecular MH - Fossils MH - Genetic Variation MH - Haplotypes MH - Humans MH - Phylogeny PMC - PMC9250076 OTO - NOTNLM OT - ancient DNA OT - demography OT - haplogroup U OT - mitochondrial DNA OT - substitution rate variation OT - time-dependence OT - tip-calibration EDAT- 2022/06/23 06:00 MHDA- 2022/07/20 06:00 PMCR- 2022/06/22 CRDT- 2022/06/22 14:53 PHST- 2022/06/16 00:00 [accepted] PHST- 2022/06/23 06:00 [pubmed] PHST- 2022/07/20 06:00 [medline] PHST- 2022/06/22 14:53 [entrez] PHST- 2022/06/22 00:00 [pmc-release] AID - 6613373 [pii] AID - evac097 [pii] AID - 10.1093/gbe/evac097 [doi] PST - ppublish SO - Genome Biol Evol. 2022 Jul 2;14(7):evac097. doi: 10.1093/gbe/evac097. PMID- 35771911 OWN - NLM STAT- MEDLINE DCOM- 20220704 LR - 20230306 IS - 1095-9203 (Electronic) IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 377 IP - 6601 DP - 2022 Jul TI - Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers. PG - 72-79 LID - 10.1126/science.abm6536 [doi] AB - Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain-related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up. FAU - Liu, Yue-Chen AU - Liu YC AUID- ORCID: 0000-0003-0448-8181 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Hunter-Anderson, Rosalind AU - Hunter-Anderson R AUID- ORCID: 0000-0002-9317-6130 AD - Independent Researcher, Albuquerque, NM 87106, USA. FAU - Cheronet, Olivia AU - Cheronet O AUID- ORCID: 0000-0001-6760-1204 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria. FAU - Eakin, Joanne AU - Eakin J AD - Independent Researcher, Albuquerque, NM 87107, USA. FAU - Camacho, Frank AU - Camacho F AUID- ORCID: 0000-0003-0080-727X AD - Department of Biology, University of Guam, Mangilao 96923, Guam. FAU - Pietrusewsky, Michael AU - Pietrusewsky M AD - Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. FAU - Ioannidis, Alexander AU - Ioannidis A AUID- ORCID: 0000-0002-4735-7803 AD - Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA. AD - Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA. FAU - Athens, J Stephen AU - Athens JS AUID- ORCID: 0000-0003-4502-4535 AD - International Archaeological Research Institute, Inc., Honolulu, HI 96826, USA. FAU - Douglas, Michele Toomay AU - Douglas MT AUID- ORCID: 0000-0002-4982-1761 AD - International Archaeological Research Institute, Inc., Honolulu, HI 96826, USA. FAU - Ikehara-Quebral, Rona Michi AU - Ikehara-Quebral RM AD - International Archaeological Research Institute, Inc., Honolulu, HI 96826, USA. FAU - Bernardos, Rebecca AU - Bernardos R AUID- ORCID: 0000-0003-4625-3727 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Culleton, Brendan J AU - Culleton BJ AUID- ORCID: 0000-0003-1200-9531 AD - Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Mah, Matthew AU - Mah M AUID- ORCID: 0000-0001-8987-6436 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Adamski, Nicole AU - Adamski N AUID- ORCID: 0000-0001-6486-9416 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AUID- ORCID: 0000-0001-5350-1608 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Callan, Kimberly AU - Callan K AUID- ORCID: 0000-0003-3170-8514 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Lawson, Ann Marie AU - Lawson AM AUID- ORCID: 0000-0003-0990-2329 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Mandl, Kirsten AU - Mandl K AUID- ORCID: 0000-0002-2078-0775 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria. FAU - Michel, Megan AU - Michel M AUID- ORCID: 0000-0002-5484-7974 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AUID- ORCID: 0000-0001-7973-6173 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Zalzala, Fatma AU - Zalzala F AUID- ORCID: 0000-0002-8981-1277 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Kidd, Kenneth AU - Kidd K AD - Department of Genetics, Yale Medical School, New Haven, CT 06520, USA. FAU - Kidd, Judith AU - Kidd J AD - Department of Genetics, Yale Medical School, New Haven, CT 06520, USA. FAU - Schurr, Theodore G AU - Schurr TG AUID- ORCID: 0000-0001-9323-9237 AD - Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Auckland, Kathryn AU - Auckland K AUID- ORCID: 0000-0002-7583-2886 AD - Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. FAU - Hill, Adrian V S AU - Hill AVS AUID- ORCID: 0000-0003-0900-9629 AD - Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. AD - The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK. FAU - Mentzer, Alexander J AU - Mentzer AJ AUID- ORCID: 0000-0002-4502-2209 AD - Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. AD - Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK. FAU - Quinto-Cortés, Consuelo D AU - Quinto-Cortés CD AUID- ORCID: 0000-0002-0338-3321 AD - National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico. FAU - Robson, Kathryn AU - Robson K AUID- ORCID: 0000-0003-4298-1874 AD - MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK. FAU - Kennett, Douglas J AU - Kennett DJ AUID- ORCID: 0000-0001-6144-7365 AD - Department of Anthropology, University of California, Santa Barbara, CA 93106, USA. FAU - Patterson, Nick AU - Patterson N AUID- ORCID: 0000-0003-0302-684X AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. AD - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. FAU - Bustamante, Carlos D AU - Bustamante CD AUID- ORCID: 0000-0002-4187-7920 AD - Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA. AD - Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA 94305, USA. FAU - Moreno-Estrada, Andrés AU - Moreno-Estrada A AUID- ORCID: 0000-0001-8329-8292 AD - National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico. FAU - Spriggs, Matthew AU - Spriggs M AUID- ORCID: 0000-0002-7293-6778 AD - School of Archaeology and Anthropology, The Australian National University, Canberra, ACT 2601, Australia. AD - Vanuatu National Museum, Vanuatu Culture Centre, PO Box 184, Port Vila, Vanuatu. FAU - Vilar, Miguel AU - Vilar M AUID- ORCID: 0000-0002-8164-4064 AD - Department of Anthropology, University of Maryland, College Park, MD 20742, USA. FAU - Lipson, Mark AU - Lipson M AUID- ORCID: 0000-0001-5346-9329 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, 1030 Vienna, Austria. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. AD - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R01 HG012287/HG/NHGRI NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article DEP - 20220630 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/genetics MH - Child MH - *DNA, Ancient MH - *DNA, Mitochondrial/genetics MH - Female MH - History, Ancient MH - *Human Migration/history MH - Humans MH - Male MH - Micronesia MH - Oceania PMC - PMC9983687 MID - NIHMS1873751 COIS- Competing Interests: C.D.B. is founder and CEO of Galatea Bio. The authors declare no other competing interests. EDAT- 2022/07/01 06:00 MHDA- 2022/07/06 06:00 PMCR- 2023/03/03 CRDT- 2022/06/30 14:02 PHST- 2022/06/30 14:02 [entrez] PHST- 2022/07/01 06:00 [pubmed] PHST- 2022/07/06 06:00 [medline] PHST- 2023/03/03 00:00 [pmc-release] AID - 10.1126/science.abm6536 [doi] PST - ppublish SO - Science. 2022 Jul;377(6601):72-79. doi: 10.1126/science.abm6536. Epub 2022 Jun 30. PMID- 35550934 OWN - NLM STAT- MEDLINE DCOM- 20220620 LR - 20221207 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 59 DP - 2022 Jul TI - Genetic and isotope analysis of a triple burial from medieval St. Peter's cemetery in Cölln/Berlin. PG - 102718 LID - S1872-4973(22)00059-X [pii] LID - 10.1016/j.fsigen.2022.102718 [doi] AB - The German capital Berlin originates from the two medieval settlements Berlin and Cölln on either side of the river Spree. Whereas Berlin is world famous, there is very little awareness of former Cölln. From 2007-2009, during excavations of the earliest cemetery of this forgotten medieval town; 3,126 graves were discovered containing the remains of 3,717 individuals. Amongst those graves was an unusual triple burial. This grave was exceptional due to the relative postures of the skeletons and their extensive facial injuries. Here we present genetic and isotope data for this grave. Genetic results confirmed all of them as biological male individuals and ruled out their biological kinship. Combining genetic ancestry information with strontium isotope data we furthermore determined that two of the men most likely originated from the Berlin-Brandenburg region, whereas a more distant origin of the third individual can be debated. CI - Copyright © 2022 Elsevier B.V. All rights reserved. FAU - Rath, Kristin AU - Rath K AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Germany. Electronic address: kristin.rath@charite.de. FAU - Käßner, Alexandra AU - Käßner A AD - Department of Isotopic Geochemistry & Geochronology, Institute of Mineralogy, TU Bergakademie Freiberg, Germany. FAU - Melisch, Claudia AU - Melisch C AD - Project Medieval Space and Population, Landesdenkmalamt Berlin, Germany. FAU - Powers, Natasha AU - Powers N AD - Project Medieval Space and Population, Landesdenkmalamt Berlin, Germany. FAU - Tichomirowa, Marion AU - Tichomirowa M AD - Department of Isotopic Geochemistry & Geochronology, Institute of Mineralogy, TU Bergakademie Freiberg, Germany. FAU - Nagy, Marion AU - Nagy M AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Germany. FAU - Friedrich, Ronny AU - Friedrich R AD - Curt-Engelhorn-Center Archaeometry, Mannheim, Germany. FAU - Riege, Johanna AU - Riege J AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Germany. FAU - Rothe, Jessica AU - Rothe J AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Germany. Electronic address: jessica.rothe@charite.de. LA - eng PT - Historical Article PT - Journal Article DEP - 20220504 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (Isotopes) SB - IM MH - Berlin MH - *Burial/history MH - *Cemeteries/history MH - History, Medieval MH - Humans MH - Isotopes MH - Male MH - White People OTO - NOTNLM OT - Ancient DNA OT - Medieval multiple burial OT - Medieval population of Berlin OT - MtDNA OT - St. Peters square (Petriplatz) OT - Strontium isotopes OT - Y-chromosome EDAT- 2022/05/14 06:00 MHDA- 2022/06/22 06:00 CRDT- 2022/05/13 13:02 PHST- 2022/02/01 00:00 [received] PHST- 2022/04/28 00:00 [revised] PHST- 2022/05/01 00:00 [accepted] PHST- 2022/05/14 06:00 [pubmed] PHST- 2022/06/22 06:00 [medline] PHST- 2022/05/13 13:02 [entrez] AID - S1872-4973(22)00059-X [pii] AID - 10.1016/j.fsigen.2022.102718 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2022 Jul;59:102718. doi: 10.1016/j.fsigen.2022.102718. Epub 2022 May 4. PMID- 35238427 OWN - NLM STAT- MEDLINE DCOM- 20220707 LR - 20220810 IS - 1520-6300 (Electronic) IS - 1042-0533 (Linking) VI - 34 IP - 7 DP - 2022 Jul TI - Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre-Hispanic populations from Central Argentina. PG - e23733 LID - 10.1002/ajhb.23733 [doi] AB - OBJECTIVES: The study of the ancient populations of Central Argentina has a crucial importance for our understanding of the evolutionary processes in the Southern Cone of South America, given its geographic position as a crossroads. Therefore, the aim of this study is to evaluate the temporal and geographical patterns of genetic variation among the groups that inhabited the current territory of Córdoba Province during the Middle and Late Holocene. METHODS: We analyzed the mitochondrial haplogroups of 74 individuals and 46 Hypervariable Region I (HVR-I) sequences, both novel and previously reported, from archeological populations of the eastern Plains and western Sierras regions of the province of Córdoba. The HVR-I sequences were also compared with other ancient groups from Argentina and with present-day populations from Central Argentina by pairwise distance analysis and identification of shared haplotypes. RESULTS: Significant differences in haplogroup and haplotype distributions between the two geographical regions were found. Sierras showed genetic affinities with certain ancient populations of Northwestern Argentina, while Plains resembled its neighbors from Santiago del Estero Province and the Pampas region. We did not observe genetic differences among the pre 1200 and post 1200 yBP temporal subsets of individuals defined by the emergence of horticulture, considering both geographical samples jointly. CONCLUSIONS: The observed patterns of geographical heterogeneity could indicate the existence of biologically distinct populations inhabiting the mountainous region and the eastern plains of Córdoba Province in pre-Hispanic times. Maternal lineages analyses support a scenario of local evolution with great temporal depth in Central Argentina, with continuity until the present. CI - © 2022 Wiley Periodicals LLC. FAU - Nores, Rodrigo AU - Nores R AD - Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología, Córdoba, Argentina. AD - CONICET, Instituto de Antropología de Córdoba (IDACOR), Córdoba, Argentina. FAU - Tavella, María Pía AU - Tavella MP AD - Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología, Córdoba, Argentina. AD - CONICET, Instituto de Antropología de Córdoba (IDACOR), Córdoba, Argentina. FAU - Fabra, Mariana AU - Fabra M AD - Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología, Córdoba, Argentina. AD - CONICET, Instituto de Antropología de Córdoba (IDACOR), Córdoba, Argentina. FAU - Demarchi, Darío A AU - Demarchi DA AD - Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología, Córdoba, Argentina. AD - CONICET, Instituto de Antropología de Córdoba (IDACOR), Córdoba, Argentina. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220303 PL - United States TA - Am J Hum Biol JT - American journal of human biology : the official journal of the Human Biology Council JID - 8915029 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Argentina MH - *DNA, Ancient MH - *DNA, Mitochondrial/genetics MH - Genetic Variation MH - *Genetics, Population MH - Haplotypes MH - Humans MH - *Indians, South American/genetics EDAT- 2022/03/04 06:00 MHDA- 2022/07/08 06:00 CRDT- 2022/03/03 08:55 PHST- 2022/02/03 00:00 [revised] PHST- 2021/10/25 00:00 [received] PHST- 2022/02/08 00:00 [accepted] PHST- 2022/03/04 06:00 [pubmed] PHST- 2022/07/08 06:00 [medline] PHST- 2022/03/03 08:55 [entrez] AID - 10.1002/ajhb.23733 [doi] PST - ppublish SO - Am J Hum Biol. 2022 Jul;34(7):e23733. doi: 10.1002/ajhb.23733. Epub 2022 Mar 3. PMID- 35749392 OWN - NLM STAT- MEDLINE DCOM- 20220628 LR - 20220716 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 17 IP - 6 DP - 2022 TI - Spatio-temporal dynamics of pathogenic variants associated with monogenic disorders reconstructed with ancient DNA. PG - e0269628 LID - 10.1371/journal.pone.0269628 [doi] LID - e0269628 AB - Genetic disease burden in ancient communities has barely been evaluated despite an ever expanding body of ancient genomes becoming available. In this study, we inspect 2729 publicly available ancient genomes (100 BP-52000 BP) for the presence of pathogenic variants in 32643 disease-associated loci. We base our subsequent analyses on 19 variants in seven genes-PAH, EDAR, F11, HBB, LRRK2, SLC12A6 and MAOA, associated with monogenic diseases and with well-established pathogenic impact in contemporary populations. We determine 230 homozygote genotypes of these variants in the screened 2729 ancient DNA samples. Eleven of these are in the PAH gene (126 ancient samples in total), a gene associated with the condition phenylketonuria in modern populations. The variants examined seem to show varying dynamics over the last 10000 years, some exhibiting a single upsurge in frequency and subsequently disappearing, while others maintain high frequency levels (compared to contemporary population frequencies) over long time periods. The geographic distribution and age of the ancient DNA samples with established pathogenic variants suggests multiple independent origin of these variants. Comparison of estimates of the geographic prevalence of these variants from ancient and contemporary data show discontinuity in their prevalence and supports their recurrent emergence. The oldest samples in which a variant is established might give an indication of their age and place origin, and an EDAR gene pathogenic variant was established in a sample estimated to be 33210-32480 calBCE. Knowledge about the historical prevalence of variants causing monogenic disorders provides insight on their emergence, dynamics and spread. FAU - Toncheva, Draga AU - Toncheva D AUID- ORCID: 0000-0002-2027-6122 AD - Department of Medical Genetics, Medical Faculty, Medical University-Sofia, Sofia, Bulgaria. AD - Bulgarian Academy of Sciences, Sofia, Bulgaria. FAU - Marinova, Maria AU - Marinova M AD - Department of Computer systems and Technologies, Faculty of Electronics and Automation, Technical University-Sofia, Branch Plovdiv, Bulgaria. FAU - Borovska, Plamenka AU - Borovska P AD - Department of Informatics, Faculty of Applied Mathematics and Informatics, Technical University of Sofia, Sofia, Bulgaria. FAU - Serbezov, Dimitar AU - Serbezov D AD - Department of Medical Genetics, Medical Faculty, Medical University-Sofia, Sofia, Bulgaria. LA - eng PT - Journal Article DEP - 20220624 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (SLC12A6 protein, human) RN - 0 (Symporters) SB - IM MH - DNA, Ancient MH - Gene Frequency MH - Genotype MH - Humans MH - *Phenylketonurias MH - *Symporters PMC - PMC9231702 COIS- The authors declare no competing interests. EDAT- 2022/06/25 06:00 MHDA- 2022/06/29 06:00 PMCR- 2022/06/24 CRDT- 2022/06/24 13:43 PHST- 2021/11/09 00:00 [received] PHST- 2022/05/24 00:00 [accepted] PHST- 2022/06/24 13:43 [entrez] PHST- 2022/06/25 06:00 [pubmed] PHST- 2022/06/29 06:00 [medline] PHST- 2022/06/24 00:00 [pmc-release] AID - PONE-D-21-35662 [pii] AID - 10.1371/journal.pone.0269628 [doi] PST - epublish SO - PLoS One. 2022 Jun 24;17(6):e0269628. doi: 10.1371/journal.pone.0269628. eCollection 2022. PMID- 35588742 OWN - NLM STAT- MEDLINE DCOM- 20220623 LR - 20240214 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 32 IP - 12 DP - 2022 Jun 20 TI - Ancient Maltese genomes and the genetic geography of Neolithic Europe. PG - 2668-2680.e6 LID - S0960-9822(22)00705-9 [pii] LID - 10.1016/j.cub.2022.04.069 [doi] AB - Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans. CI - Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Ariano, Bruno AU - Ariano B AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Mattiangeli, Valeria AU - Mattiangeli V AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Breslin, Emily M AU - Breslin EM AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Parkinson, Eóin W AU - Parkinson EW AD - Department of Classics and Archaeology, University of Malta, Msida 2080, Malta. FAU - McLaughlin, T Rowan AU - McLaughlin TR AD - Department of Scientific Research, The British Museum, Great Russell Street, London WC1B 3DG, UK. FAU - Thompson, Jess E AU - Thompson JE AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. FAU - Power, Ronika K AU - Power RK AD - Department of History and Archaeology, Macquarie University, 25B Wally's Walk, Sydney, NSW, Australia. FAU - Stock, Jay T AU - Stock JT AD - Department of Anthropology, Western University, 1151 Richmond St, London, ON N6G 2V4, Canada. FAU - Mercieca-Spiteri, Bernardette AU - Mercieca-Spiteri B AD - Superintendence of Cultural Heritage, St Christopher Street, Valletta 2000, Malta. FAU - Stoddart, Simon AU - Stoddart S AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. FAU - Malone, Caroline AU - Malone C AD - School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, UK. FAU - Gopalakrishnan, Shyam AU - Gopalakrishnan S AD - GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 København K, Denmark. Electronic address: fck245@ku.dk. FAU - Cassidy, Lara M AU - Cassidy LM AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. Electronic address: cassidsl1@tcd.ie. FAU - Bradley, Daniel G AU - Bradley DG AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. Electronic address: dbradley@tcd.ie. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 205072/WT_/Wellcome Trust/United Kingdom GR - 205072/Z/16/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220518 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture MH - *Archaeology MH - DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Europe MH - *Genome, Human MH - Geography MH - History, Ancient MH - Human Migration MH - Humans PMC - PMC9245899 OTO - NOTNLM OT - Neolithic OT - ancient DNA OT - island archaeology OT - migration OT - population genomics COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/05/20 06:00 MHDA- 2022/06/24 06:00 PMCR- 2022/06/20 CRDT- 2022/05/19 18:53 PHST- 2021/11/04 00:00 [received] PHST- 2022/02/07 00:00 [revised] PHST- 2022/04/22 00:00 [accepted] PHST- 2022/05/20 06:00 [pubmed] PHST- 2022/06/24 06:00 [medline] PHST- 2022/05/19 18:53 [entrez] PHST- 2022/06/20 00:00 [pmc-release] AID - S0960-9822(22)00705-9 [pii] AID - 10.1016/j.cub.2022.04.069 [doi] PST - ppublish SO - Curr Biol. 2022 Jun 20;32(12):2668-2680.e6. doi: 10.1016/j.cub.2022.04.069. Epub 2022 May 18. PMID- 35746807 OWN - NLM STAT- MEDLINE DCOM- 20220627 LR - 20220721 IS - 1999-4915 (Electronic) IS - 1999-4915 (Linking) VI - 14 IP - 6 DP - 2022 Jun 18 TI - Detection of Ancient Viruses and Long-Term Viral Evolution. LID - 10.3390/v14061336 [doi] LID - 1336 AB - The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution. FAU - Nishimura, Luca AU - Nishimura L AUID- ORCID: 0000-0003-2144-7867 AD - Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan. AD - Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan. FAU - Fujito, Naoko AU - Fujito N AD - Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan. AD - Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan. FAU - Sugimoto, Ryota AU - Sugimoto R AUID- ORCID: 0000-0003-4281-7871 AD - Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan. FAU - Inoue, Ituro AU - Inoue I AD - Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan. AD - Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20220618 PL - Switzerland TA - Viruses JT - Viruses JID - 101509722 RN - 0 (DNA, Ancient) SB - IM MH - *COVID-19 MH - DNA, Ancient MH - Evolution, Molecular MH - Genome, Viral MH - Humans MH - *Viruses/genetics PMC - PMC9230872 OTO - NOTNLM OT - NGS OT - PCR OT - TDRP OT - ancient DNA OT - ancient RNA OT - ancient virome OT - ancient virus OT - bioinformatics OT - viral evolution COIS- The authors declare no conflict of interest. EDAT- 2022/06/25 06:00 MHDA- 2022/06/28 06:00 PMCR- 2022/06/18 CRDT- 2022/06/24 01:44 PHST- 2022/04/30 00:00 [received] PHST- 2022/06/15 00:00 [revised] PHST- 2022/06/16 00:00 [accepted] PHST- 2022/06/24 01:44 [entrez] PHST- 2022/06/25 06:00 [pubmed] PHST- 2022/06/28 06:00 [medline] PHST- 2022/06/18 00:00 [pmc-release] AID - v14061336 [pii] AID - viruses-14-01336 [pii] AID - 10.3390/v14061336 [doi] PST - epublish SO - Viruses. 2022 Jun 18;14(6):1336. doi: 10.3390/v14061336. PMID- 35709264 OWN - NLM STAT- MEDLINE DCOM- 20220620 LR - 20220624 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 376 IP - 6599 DP - 2022 Jun 17 TI - Ancient DNA reveals Black Death source. PG - 1254-1255 LID - 10.1126/science.add4865 [doi] AB - Graves in Kyrgyzstan hold early victims of plague that swept medieval Europe. FAU - Gibbons, Ann AU - Gibbons A LA - eng PT - Historical Article PT - News DEP - 20220616 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Burial/history MH - DNA, Ancient MH - *Epidemics/history MH - History, Medieval MH - Humans MH - Kyrgyzstan/epidemiology MH - *Plague/epidemiology/history MH - *Yersinia pestis/isolation & purification EDAT- 2022/06/17 06:00 MHDA- 2022/06/22 06:00 CRDT- 2022/06/16 14:04 PHST- 2022/06/16 14:04 [entrez] PHST- 2022/06/17 06:00 [pubmed] PHST- 2022/06/22 06:00 [medline] AID - 10.1126/science.add4865 [doi] PST - ppublish SO - Science. 2022 Jun 17;376(6599):1254-1255. doi: 10.1126/science.add4865. Epub 2022 Jun 16. PMID- 35687599 OWN - NLM STAT- MEDLINE DCOM- 20220614 LR - 20220718 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 17 IP - 6 DP - 2022 TI - A qPCR-duplex assay for sex determination in ancient DNA. PG - e0269913 LID - 10.1371/journal.pone.0269913 [doi] LID - e0269913 AB - Molecular biology techniques are increasingly being used in sex identification of skeletal remains when traditional anthropometric analyzes are not successful in identifying sex of remains that are incomplete, fragmented and /or of immature individuals. In the present work, we investigated the possibility of determining sex by using the qPCR-duplex method for both ancient and modern DNA samples. This method involves the co-amplification of two genes in a single reaction system and the subsequent analysis of the fusion curves; the gene sequences used for the construction of suitable primers are those of steroid sulfatase (STS) and testis specific protein Y-linked 1 (TSPY) genes which turned out to be two sensitive markers as they have a detection limit of 60 pg and 20 pg respectively on modern DNA. The validity of the method was verified on modern DNA in which gender was identified in all the samples with 100% accuracy; thus, allowing for the same results as the classic method with amelogenin, but in a faster and more immediate way, as it allows for sex determination solely by analyzing the denaturation curves without having to perform an electrophoretic run. The proposed molecular technique proves to be sensitive and precise even on degraded DNA, in fact on 9 archaeological finds dating from the VII-XII century in which sex had been identified through anthropometric analysis, it confirmed the sex of 8 out of 9 finds correctly. FAU - Poma, Anna AU - Poma A AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy. FAU - Cesare, Patrizia AU - Cesare P AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy. FAU - Bonfigli, Antonella AU - Bonfigli A AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy. FAU - Volpe, Anna Rita AU - Volpe AR AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy. FAU - Colafarina, Sabrina AU - Colafarina S AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy. FAU - Vecchiotti, Giulia AU - Vecchiotti G AUID- ORCID: 0000-0001-6747-4225 AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy. FAU - Forgione, Alfonso AU - Forgione A AD - Department of Human Studies, University of L'Aquila, L'Aquila, Italy. FAU - Zarivi, Osvaldo AU - Zarivi O AUID- ORCID: 0000-0002-8312-9955 AD - Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220610 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Amelogenin) RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Amelogenin/genetics MH - DNA/analysis/genetics MH - *DNA, Ancient MH - Humans MH - Male MH - Real-Time Polymerase Chain Reaction MH - *Sex Determination Analysis/methods PMC - PMC9187067 COIS- The authors declare no conflict of interest. EDAT- 2022/06/11 06:00 MHDA- 2022/06/15 06:00 PMCR- 2022/06/10 CRDT- 2022/06/10 13:43 PHST- 2021/10/14 00:00 [received] PHST- 2022/05/30 00:00 [accepted] PHST- 2022/06/10 13:43 [entrez] PHST- 2022/06/11 06:00 [pubmed] PHST- 2022/06/15 06:00 [medline] PHST- 2022/06/10 00:00 [pmc-release] AID - PONE-D-21-32293 [pii] AID - 10.1371/journal.pone.0269913 [doi] PST - epublish SO - PLoS One. 2022 Jun 10;17(6):e0269913. doi: 10.1371/journal.pone.0269913. eCollection 2022. PMID- 35671731 OWN - NLM STAT- MEDLINE DCOM- 20220609 LR - 20220815 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 32 IP - 11 DP - 2022 Jun 6 TI - Paleogenomics: The demographic past of prehistoric Europeans. PG - R535-R538 LID - S0960-9822(22)00717-5 [pii] LID - 10.1016/j.cub.2022.04.081 [doi] AB - Ancient DNA provides answers to long-standing debates about past human history. New work using demographic modeling on ancient genomes documents the nature and timing of the demographic processes - population size changes, divergences and admixture - that took place in prehistoric Europe. CI - Copyright © 2022 Elsevier Inc. All rights reserved. FAU - Choin, Jeremy AU - Choin J AD - Institut Pasteur, Université Paris Cité, CNRS UMR2000, Unit of Human Evolutionary Genetics, F-75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, F-75005 Paris, France. FAU - Quintana-Murci, Lluis AU - Quintana-Murci L AD - Institut Pasteur, Université Paris Cité, CNRS UMR2000, Unit of Human Evolutionary Genetics, F-75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, F-75005 Paris, France. Electronic address: quintana@pasteur.fr. LA - eng PT - Comment PT - Historical Article PT - Journal Article PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM CON - Cell. 2022 May 26;185(11):1842-1859.e18. doi: 10.1016/j.cell.2022.04.008. PMID: 35561686 MH - DNA, Ancient MH - Demography MH - Europe MH - *Genome, Human MH - *Genomics MH - History, Ancient MH - Humans MH - Paleontology COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/06/08 06:00 MHDA- 2022/06/10 06:00 CRDT- 2022/06/07 18:27 PHST- 2022/06/07 18:27 [entrez] PHST- 2022/06/08 06:00 [pubmed] PHST- 2022/06/10 06:00 [medline] AID - S0960-9822(22)00717-5 [pii] AID - 10.1016/j.cub.2022.04.081 [doi] PST - ppublish SO - Curr Biol. 2022 Jun 6;32(11):R535-R538. doi: 10.1016/j.cub.2022.04.081. PMID- 35279516 OWN - NLM STAT- MEDLINE DCOM- 20220411 LR - 20220411 IS - 1873-3557 (Electronic) IS - 1386-1425 (Linking) VI - 274 DP - 2022 Jun 5 TI - Synchrotron Radiation Fourier Transform Infrared (SR-FTIR) spectroscopy in exploring ancient human hair from Roman period Juliopolis: Preservation status and alterations of organic compounds. PG - 121026 LID - S1386-1425(22)00174-3 [pii] LID - 10.1016/j.saa.2022.121026 [doi] AB - We explore the preservation status and alterations of organic compounds in Roman period human hairstrandsfrom a specific individual (M196) excavated at Juliopolis (JP). How do these organic compounds present in this c. 2000-year-old human hair compare to those present in modern hair? Alterations to organic compounds in archaeological human hair are caused by biological degradative processes dependent on multifactorial processes acting on the hair since the deposition of a body in a mortuary context. We investigate the type of organic compounds present using Synchrotron Radiation Fourier Transform Infrared (SR-FTIR). Juliopolis (Iuliopolis) is an ancient multiperiod city, located in the Çayırhan district of Nallıhan, northwest of Ankara. The Juliopolis necropolis from which M196 was recovered was in use throughout the Hellenistic, Roman, and Byzantine periods, and yielded over 700 tombs with numerous human remains. One tomb (M196) contained human remains of exceptional preservation status, including substantial amounts of hair. Human hair from archaeological contexts is not only extremely rare, but importantly, has high analytical value, with potential for analysis of diet, geographical origins, ancient DNA, metal exposure, and other aspects of life in a time-resolved manner. These data make significant contributions to the life history of the individual (osteobiography), as well as contribute towards key archaeological questions. As these analyses are in their majority destructive, prior evaluation of the preservation of sufficient amounts of the organic compounds on which many such analyses rely upon is crucial, to avoid unnecessary loss of precious ancient samples. The results of our SR-FTIR analyses at SESAME synchrotron show that keratin in the JP M196 is more degraded in comparison to the modern reference sample. However, the results also point to clear potential for further analyses with techniques relying on organic compound preservation, such as C and N isotopic analyses for diet, and aDNA. CI - Copyright © 2022 Elsevier B.V. All rights reserved. FAU - Lorentz, K O AU - Lorentz KO AD - Science and Technology in Archaeology and Culture Research Center (STARC), The Cyprus Institute (CyI), Nicosia, Cyprus. Electronic address: k.o.lorentz@cyi.ac.cy. FAU - Kamel, G AU - Kamel G AD - SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East), Allan, Jordan; Department of Physics, Faculty of Science, Helwan University, Cairo, Egypt. FAU - Lemmers, S A M AU - Lemmers SAM AD - Science and Technology in Archaeology and Culture Research Center (STARC), The Cyprus Institute (CyI), Nicosia, Cyprus. FAU - Miyauchi, Y AU - Miyauchi Y AD - Science and Technology in Archaeology and Culture Research Center (STARC), The Cyprus Institute (CyI), Nicosia, Cyprus; University of Tsukuba, Tsukuba, Japan. FAU - Çubukçu, E AU - Çubukçu E AD - Department of Geology, Hacettepe University, Ankara, Turkey. FAU - Alpagut, A AU - Alpagut A AD - The Museum of Anatolian Civilisations, Ankara, Turkey. FAU - Büyükkarakaya, A M AU - Büyükkarakaya AM AD - Department of Anthropology, Hacettepe University, Ankara, Turkey; Human Behavioral Ecology and Archaeometry Laboratory (IDEA Lab), Ankara, Turkey. LA - eng PT - Journal Article DEP - 20220212 PL - England TA - Spectrochim Acta A Mol Biomol Spectrosc JT - Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy JID - 9602533 RN - 0 (Organic Chemicals) SB - IM MH - Archaeology/methods MH - *Body Remains MH - Fourier Analysis MH - Hair/chemistry MH - Humans MH - Organic Chemicals MH - Spectroscopy, Fourier Transform Infrared/methods MH - *Synchrotrons OTO - NOTNLM OT - Ancient Anatolia OT - Ancient hair OT - Fourier transform infrared spectroscopy (FTIR) OT - Hair degradation, preservation and alteration OT - Juliopolis OT - Roman archaeology COIS- Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. EDAT- 2022/03/14 06:00 MHDA- 2022/04/12 06:00 CRDT- 2022/03/13 20:28 PHST- 2021/06/28 00:00 [received] PHST- 2022/02/07 00:00 [revised] PHST- 2022/02/09 00:00 [accepted] PHST- 2022/03/14 06:00 [pubmed] PHST- 2022/04/12 06:00 [medline] PHST- 2022/03/13 20:28 [entrez] AID - S1386-1425(22)00174-3 [pii] AID - 10.1016/j.saa.2022.121026 [doi] PST - ppublish SO - Spectrochim Acta A Mol Biomol Spectrosc. 2022 Jun 5;274:121026. doi: 10.1016/j.saa.2022.121026. Epub 2022 Feb 12. PMID- 35578825 OWN - NLM STAT- MEDLINE DCOM- 20220608 LR - 20220719 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 39 IP - 6 DP - 2022 Jun 2 TI - Population Genetics and Signatures of Selection in Early Neolithic European Farmers. LID - 10.1093/molbev/msac108 [doi] LID - msac108 AB - Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia. CI - © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Childebayeva, Ainash AU - Childebayeva A AD - Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany. AD - Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. FAU - Rohrlach, Adam Benjamin AU - Rohrlach AB AD - Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany. AD - Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. AD - ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia. FAU - Barquera, Rodrigo AU - Barquera R AD - Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany. AD - Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. FAU - Rivollat, Maïté AU - Rivollat M AD - Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany. AD - Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615 Pessac, France. FAU - Aron, Franziska AU - Aron F AD - Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany. FAU - Szolek, András AU - Szolek A AD - Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany. AD - Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany. FAU - Kohlbacher, Oliver AU - Kohlbacher O AUID- ORCID: 0000-0003-1739-4598 AD - Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany. AD - Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany. AD - Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany. AD - Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany. FAU - Nicklisch, Nicole AU - Nicklisch N AD - Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria. AD - State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany. FAU - Alt, Kurt W AU - Alt KW AD - Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria. AD - State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany. FAU - Gronenborn, Detlef AU - Gronenborn D AD - Römisch-Germanisches Zentralmuseum, Leibniz Research Institute for Archaeology, Ernst-Ludwig-Platz 2, 55116 Mainz, Germany. FAU - Meller, Harald AU - Meller H AD - State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany. FAU - Friederich, Susanne AU - Friederich S AD - State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany. FAU - Prüfer, Kay AU - Prüfer K AD - Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany. AD - Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615 Pessac, France. FAU - Krause, Johannes AU - Krause J AD - Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany. AD - Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0002-6467-5643 AD - Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany. AD - Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture MH - DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Europe MH - *Farmers MH - Genetics, Population MH - History, Ancient MH - *Human Migration MH - Humans PMC - PMC9171004 OTO - NOTNLM OT - Linear Pottery culture OT - ancient DNA OT - neolithization OT - selection EDAT- 2022/05/18 06:00 MHDA- 2022/06/09 06:00 PMCR- 2022/05/17 CRDT- 2022/05/17 03:43 PHST- 2022/05/18 06:00 [pubmed] PHST- 2022/06/09 06:00 [medline] PHST- 2022/05/17 03:43 [entrez] PHST- 2022/05/17 00:00 [pmc-release] AID - 6586604 [pii] AID - msac108 [pii] AID - 10.1093/molbev/msac108 [doi] PST - ppublish SO - Mol Biol Evol. 2022 Jun 2;39(6):msac108. doi: 10.1093/molbev/msac108. PMID- 35705867 OWN - NLM STAT- MEDLINE DCOM- 20220623 LR - 20220627 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 606 IP - 7915 DP - 2022 Jun TI - Ancient DNA traces origin of Black Death. PG - 635-636 LID - 10.1038/d41586-022-01673-4 [doi] FAU - Callaway, Ewen AU - Callaway E LA - eng PT - Comment PT - Historical Article PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM CON - Nature. 2022 Jun;606(7915):718-724. doi: 10.1038/s41586-022-04800-3. PMID: 35705810 MH - *DNA, Ancient MH - *DNA, Bacterial MH - History, Medieval MH - Humans MH - *Plague/epidemiology/genetics/history/microbiology OTO - NOTNLM OT - Diseases OT - History EDAT- 2022/06/16 06:00 MHDA- 2022/06/24 06:00 CRDT- 2022/06/15 23:35 PHST- 2022/06/16 06:00 [pubmed] PHST- 2022/06/24 06:00 [medline] PHST- 2022/06/15 23:35 [entrez] AID - 10.1038/d41586-022-01673-4 [pii] AID - 10.1038/d41586-022-01673-4 [doi] PST - ppublish SO - Nature. 2022 Jun;606(7915):635-636. doi: 10.1038/d41586-022-01673-4. PMID- 35705810 OWN - NLM STAT- MEDLINE DCOM- 20220624 LR - 20240831 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 606 IP - 7915 DP - 2022 Jun TI - The source of the Black Death in fourteenth-century central Eurasia. PG - 718-724 LID - 10.1038/s41586-022-04800-3 [doi] AB - The origin of the medieval Black Death pandemic (AD 1346-1353) has been a topic of continuous investigation because of the pandemic's extensive demographic impact and long-lasting consequences(1,2). Until now, the most debated archaeological evidence potentially associated with the pandemic's initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan(1,3-9). These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338-1339 state 'pestilence' as the cause of death for the buried individuals(9). Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic's emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia. CI - © 2022. The Author(s). FAU - Spyrou, Maria A AU - Spyrou MA AUID- ORCID: 0000-0002-3615-3936 AD - Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Tübingen, Germany. maria.spyrou@ifu.uni-tuebingen.de. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. maria.spyrou@ifu.uni-tuebingen.de. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. maria.spyrou@ifu.uni-tuebingen.de. FAU - Musralina, Lyazzat AU - Musralina L AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Laboratory of Population Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan. AD - Kazakh National University by al-Farabi, Almaty, Kazakhstan. FAU - Gnecchi Ruscone, Guido A AU - Gnecchi Ruscone GA AUID- ORCID: 0000-0002-6490-8101 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Kocher, Arthur AU - Kocher A AUID- ORCID: 0000-0002-9499-6472 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Borbone, Pier-Giorgio AU - Borbone PG AD - Department of Civilisations and Forms of Knowledge, University of Pisa, Pisa, Italy. FAU - Khartanovich, Valeri I AU - Khartanovich VI AUID- ORCID: 0000-0002-5533-0686 AD - Department of Physical Anthropology, Kunstkamera, Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russian Federation. FAU - Buzhilova, Alexandra AU - Buzhilova A AUID- ORCID: 0000-0001-6398-2177 AD - Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russian Federation. FAU - Djansugurova, Leyla AU - Djansugurova L AUID- ORCID: 0000-0002-6745-9903 AD - Laboratory of Population Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan. FAU - Bos, Kirsten I AU - Bos KI AUID- ORCID: 0000-0003-2937-3006 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Kühnert, Denise AU - Kühnert D AUID- ORCID: 0000-0002-5657-018X AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany. AD - European Virus Bioinformatics Center (EVBC), Jena, Germany. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Slavin, Philip AU - Slavin P AUID- ORCID: 0000-0002-6460-145X AD - Division of History, Heritage and Politics, University of Stirling, Stirling, UK. philip.slavin@stir.ac.uk. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. krause@eva.mpg.de. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. krause@eva.mpg.de. LA - eng GR - 771234/ERC_/European Research Council/International PT - Historical Article PT - Journal Article DEP - 20220615 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM CIN - Nature. 2022 Jun;606(7915):635-636. doi: 10.1038/d41586-022-01673-4. PMID: 35705867 CIN - Nat Rev Microbiol. 2022 Sep;20(9):509. doi: 10.1038/s41579-022-00769-y. PMID: 35778565 MH - Archaeology MH - Cemeteries MH - DNA, Ancient/analysis MH - DNA, Bacterial/analysis MH - History, Medieval MH - Humans MH - Kyrgyzstan/epidemiology MH - Pandemics/history MH - Phylogeny MH - *Plague/epidemiology/history/microbiology MH - *Yersinia pestis/classification/pathogenicity PMC - PMC9217749 COIS- The authors declare no competing interests. EDAT- 2022/06/16 06:00 MHDA- 2022/06/25 06:00 PMCR- 2022/06/15 CRDT- 2022/06/15 23:32 PHST- 2021/07/19 00:00 [received] PHST- 2022/04/25 00:00 [accepted] PHST- 2022/06/16 06:00 [pubmed] PHST- 2022/06/25 06:00 [medline] PHST- 2022/06/15 23:32 [entrez] PHST- 2022/06/15 00:00 [pmc-release] AID - 10.1038/s41586-022-04800-3 [pii] AID - 4800 [pii] AID - 10.1038/s41586-022-04800-3 [doi] PST - ppublish SO - Nature. 2022 Jun;606(7915):718-724. doi: 10.1038/s41586-022-04800-3. Epub 2022 Jun 15. PMID- 35635751 OWN - NLM STAT- MEDLINE DCOM- 20220720 LR - 20220912 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 11 DP - 2022 May 30 TI - The spatiotemporal patterns of major human admixture events during the European Holocene. LID - 10.7554/eLife.77625 [doi] LID - e77625 AB - Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES (Distribution of Ancestry Tracts of Evolutionary Signals) that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on~1100 ancient genomes from sixteen regions in Europe and west Asia, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry across Europe. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of Steppe pastoralism. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations. CI - © 2022, Chintalapati et al. FAU - Chintalapati, Manjusha AU - Chintalapati M AUID- ORCID: 0000-0002-9808-5991 AD - Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States. FAU - Patterson, Nick AU - Patterson N AUID- ORCID: 0000-0003-0302-684X AD - Broad Institute of Harvard and MIT, Cambridge, United States. AD - Human Evolutionary Biology, Harvard University, Boston, United States. FAU - Moorjani, Priya AU - Moorjani P AUID- ORCID: 0000-0002-0947-5673 AD - Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States. AD - Center for Computational Biology, University of California, Bekerley, Berkeley, United States. LA - eng GR - R35 GM142978/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20220530 PL - England TA - Elife JT - eLife JID - 101579614 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - DNA, Ancient MH - Europe MH - *Genome, Human MH - *Human Migration MH - Humans MH - Iran PMC - PMC9293011 OTO - NOTNLM OT - European Holocene OT - Neolithic OT - admixture OT - ancient DNA OT - evolutionary biology OT - genetics OT - genomic clocks OT - genomics OT - human OT - molecular clock COIS- MC, NP, PM No competing interests declared EDAT- 2022/06/01 06:00 MHDA- 2022/07/22 06:00 PMCR- 2022/05/30 CRDT- 2022/05/31 12:51 PHST- 2022/02/05 00:00 [received] PHST- 2022/05/29 00:00 [accepted] PHST- 2022/06/01 06:00 [pubmed] PHST- 2022/07/22 06:00 [medline] PHST- 2022/05/31 12:51 [entrez] PHST- 2022/05/30 00:00 [pmc-release] AID - 77625 [pii] AID - 10.7554/eLife.77625 [doi] PST - epublish SO - Elife. 2022 May 30;11:e77625. doi: 10.7554/eLife.77625. PMID- 35482488 OWN - NLM STAT- MEDLINE DCOM- 20220602 LR - 20221118 IS - 2160-1836 (Electronic) IS - 2160-1836 (Linking) VI - 12 IP - 6 DP - 2022 May 30 TI - An empirical evaluation of genotype imputation of ancient DNA. LID - 10.1093/g3journal/jkac089 [doi] LID - jkac089 AB - With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis. CI - © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. FAU - Ausmees, Kristiina AU - Ausmees K AUID- ORCID: 0000-0002-6212-539X AD - Department of Information Technology, Uppsala University, Uppsala 751 05, Sweden. FAU - Sanchez-Quinto, Federico AU - Sanchez-Quinto F AD - Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico. AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala 752 36, Sweden. FAU - Jakobsson, Mattias AU - Jakobsson M AUID- ORCID: 0000-0001-7840-7853 AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala 752 36, Sweden. FAU - Nettelblad, Carl AU - Nettelblad C AUID- ORCID: 0000-0003-0458-6902 AD - Department of Information Technology, Uppsala University, Uppsala 751 05, Sweden. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - G3 (Bethesda) JT - G3 (Bethesda, Md.) JID - 101566598 RN - 0 (DNA, Ancient) SB - IM MH - Alleles MH - *DNA, Ancient MH - Gene Frequency MH - *Genotype MH - Humans MH - Software PMC - PMC9157144 OTO - NOTNLM OT - ancient DNA OT - imputation OT - low coverage OT - phasing OT - reference bias EDAT- 2022/04/29 06:00 MHDA- 2022/06/03 06:00 PMCR- 2022/04/28 CRDT- 2022/04/28 12:52 PHST- 2022/02/28 00:00 [received] PHST- 2022/04/05 00:00 [accepted] PHST- 2022/04/29 06:00 [pubmed] PHST- 2022/06/03 06:00 [medline] PHST- 2022/04/28 12:52 [entrez] PHST- 2022/04/28 00:00 [pmc-release] AID - 6575448 [pii] AID - jkac089 [pii] AID - 10.1093/g3journal/jkac089 [doi] PST - ppublish SO - G3 (Bethesda). 2022 May 30;12(6):jkac089. doi: 10.1093/g3journal/jkac089. PMID- 35618734 OWN - NLM STAT- MEDLINE DCOM- 20220530 LR - 20221113 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 12 IP - 1 DP - 2022 May 26 TI - Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD. PG - 6468 LID - 10.1038/s41598-022-10899-1 [doi] LID - 6468 AB - The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius' eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian' genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site. CI - © 2022. The Author(s). FAU - Scorrano, Gabriele AU - Scorrano G AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome "Tor Vergata", 00133, Rome, Italy. gabrielescor@gmail.com. AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. gabrielescor@gmail.com. FAU - Viva, Serena AU - Viva S AD - Department of Cultural Heritage, University of Salento, 73100, Lecce, Italy. FAU - Pinotti, Thomaz AU - Pinotti T AD - Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. AD - Laboratório de Biodiversidade e Evolução Molecular (LBEM), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. FAU - Fabbri, Pier Francesco AU - Fabbri PF AD - Department of Cultural Heritage, University of Salento, 73100, Lecce, Italy. pierfrancesco.fabbri@unisalento.it. FAU - Rickards, Olga AU - Rickards O AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome "Tor Vergata", 00133, Rome, Italy. FAU - Macciardi, Fabio AU - Macciardi F AD - Laboratory of Molecular Psychiatry, Department of Psychiatry and Human Behavior, University of California, Irvine, CA, 92868, USA. fmacciar@uci.edu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220526 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Body Remains MH - *DNA, Ancient MH - *Exanthema MH - Humans MH - Italy PMC - PMC9135728 COIS- The authors declare no competing interests. EDAT- 2022/05/27 06:00 MHDA- 2022/05/31 06:00 PMCR- 2022/05/26 CRDT- 2022/05/26 23:17 PHST- 2021/12/17 00:00 [received] PHST- 2022/04/08 00:00 [accepted] PHST- 2022/05/26 23:17 [entrez] PHST- 2022/05/27 06:00 [pubmed] PHST- 2022/05/31 06:00 [medline] PHST- 2022/05/26 00:00 [pmc-release] AID - 10.1038/s41598-022-10899-1 [pii] AID - 10899 [pii] AID - 10.1038/s41598-022-10899-1 [doi] PST - epublish SO - Sci Rep. 2022 May 26;12(1):6468. doi: 10.1038/s41598-022-10899-1. PMID- 35729698 OWN - NLM STAT- MEDLINE DCOM- 20220623 LR - 20220623 IS - 0253-9772 (Print) IS - 0253-9772 (Linking) VI - 44 IP - 5 DP - 2022 May 20 TI - Exploration of adaptation, evolution and domestication of fermentation microorganisms by applying ancient DNA technology. PG - 414-423 LID - 10.16288/j.yczz.22-057 [doi] AB - Fermentation production is the most primitive application of microorganisms by humans, which is of great significance in human history. However, due to the lack of molecular evidence, the history of human fermentation production and the evolution and domestication of fermentation microorganisms remain to be further investigated. Taking wine and fermented dairy, the two most common types of fermented foods as examples, we introduce the archaeology evidence of fermented foods and the evolution and domestication of fermented microorganisms, introduce the research status of paleomicrobiology and fermented paleomicroorganisms, and explore the feasibility and challenges of the research of ancient fermented microorganisms applying microbial ancient DNA technology, as well as the application potential of ancient DNA capture technology in this field. FAU - Zheng, Ze-Quan AU - Zheng ZQ AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. AD - University of Chinese Academy of Sciences, Beijing 100049, China. AD - CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China. FAU - Fu, Qiao-Mei AU - Fu QM AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. AD - University of Chinese Academy of Sciences, Beijing 100049, China. AD - CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China. FAU - Liu, Yi-Chen AU - Liu YC AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. LA - eng PT - Journal Article PL - China TA - Yi Chuan JT - Yi chuan = Hereditas JID - 9436478 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - Domestication MH - Fermentation MH - *Fermented Foods MH - Humans MH - Technology OTO - NOTNLM OT - ancient DNA OT - evolution OT - fermentation OT - microorganism EDAT- 2022/06/22 06:00 MHDA- 2022/06/24 06:00 CRDT- 2022/06/21 23:48 PHST- 2022/06/21 23:48 [entrez] PHST- 2022/06/22 06:00 [pubmed] PHST- 2022/06/24 06:00 [medline] AID - 22-057 [pii] AID - 10.16288/j.yczz.22-057 [doi] PST - ppublish SO - Yi Chuan. 2022 May 20;44(5):414-423. doi: 10.16288/j.yczz.22-057. PMID- 35729694 OWN - NLM STAT- MEDLINE DCOM- 20220623 LR - 20220623 IS - 0253-9772 (Print) IS - 0253-9772 (Linking) VI - 44 IP - 5 DP - 2022 May 20 TI - Exploring the evolution of archaic humans through sedimentary ancient DNA. PG - 362-369 LID - 10.16288/j.yczz.22-032 [doi] AB - Recent success in the retrieval of nuclear DNA of ancient humans and animals from cave sediments paves the way for genome-wide studies of past populations directly from sediments. In three studies, nuclear genomes of different species were obtained from the sediments of multiple archeological caves and their genetic histories were revealed, including an unknown population replacement of Neanderthals from Estatuas cave in Spain, which was recovered using a new DNA capture approach. By extending sediments as a source of DNA beyond fossils, this breakthrough is of particular significance to the field of ancient human genomics, which brings about more possibilities for exploring the history of past population migration, evolution and adaptation within larger time-scales and geographical areas where no fossil remains exist. Here, we mainly review the significance of the technical advances in retrieving ancient nuclear DNA from sediments and present new insights into the genetic history of Neanderthals revealed by this technique. By combining ancient genomes retrieved from fossils and additional mitochondrial DNA extracted from sediments of archaeological sites, we may begin investigating diverse archaic populations and examine their genetic relationships, movements and replacements in detail. FAU - Ping, Wan-Jing AU - Ping WJ AD - Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Liu, Yi-Chen AU - Liu YC AD - Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Fu, Qiao-Mei AU - Fu QM AD - Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. LA - eng PT - Journal Article PL - China TA - Yi Chuan JT - Yi chuan = Hereditas JID - 9436478 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Genome, Human MH - *Hominidae/genetics MH - Humans MH - *Neanderthals/genetics OTO - NOTNLM OT - Denisovans OT - Neanderthals OT - archaic humans OT - hybridization capture OT - nuclear genomes OT - population replacement OT - probe-set OT - sedimentary ancient DNA EDAT- 2022/06/22 06:00 MHDA- 2022/06/24 06:00 CRDT- 2022/06/21 23:48 PHST- 2022/06/21 23:48 [entrez] PHST- 2022/06/22 06:00 [pubmed] PHST- 2022/06/24 06:00 [medline] AID - 22-032 [pii] AID - 10.16288/j.yczz.22-032 [doi] PST - ppublish SO - Yi Chuan. 2022 May 20;44(5):362-369. doi: 10.16288/j.yczz.22-032. PMID- 35294015 OWN - NLM STAT- MEDLINE DCOM- 20220509 LR - 20220716 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 221 IP - 1 DP - 2022 May 5 TI - Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples. LID - 10.1093/genetics/iyac038 [doi] LID - iyac038 AB - Archeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the nonrandom association of genetic variants at different loci (i.e. linkage disequilibrium). This may be in part because basic properties of linkage disequilibrium in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: (1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; (2) The product of the linkage disequilibrium coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and (3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples. CI - © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. FAU - Biddanda, Arjun AU - Biddanda A AUID- ORCID: 0000-0003-1861-1523 AD - Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. FAU - Steinrücken, Matthias AU - Steinrücken M AUID- ORCID: 0000-0001-6331-7900 AD - Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. AD - Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA. FAU - Novembre, John AU - Novembre J AUID- ORCID: 0000-0001-5345-0214 AD - Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. AD - Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA. LA - eng GR - R01 HG007089/HG/NHGRI NIH HHS/United States GR - T32 GM007197/GM/NIGMS NIH HHS/United States GR - T32 GM07197/GF/NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Genetics JT - Genetics JID - 0374636 SB - IM MH - Archaeology/*methods MH - Genetics, Population/*methods MH - Genotype MH - Haplotypes MH - Humans MH - Linkage Disequilibrium MH - Population Density PMC - PMC9245597 OTO - NOTNLM OT - ancient DNA OT - linkage disequilibrium OT - population genetics COIS- None declared. EDAT- 2022/03/17 06:00 MHDA- 2022/05/10 06:00 PMCR- 2022/03/16 CRDT- 2022/03/16 12:14 PHST- 2022/01/10 00:00 [received] PHST- 2022/02/06 00:00 [accepted] PHST- 2022/03/17 06:00 [pubmed] PHST- 2022/05/10 06:00 [medline] PHST- 2022/03/16 12:14 [entrez] PHST- 2022/03/16 00:00 [pmc-release] AID - 6549526 [pii] AID - iyac038 [pii] AID - 10.1093/genetics/iyac038 [doi] PST - ppublish SO - Genetics. 2022 May 5;221(1):iyac038. doi: 10.1093/genetics/iyac038. PMID- 35446690 OWN - NLM STAT- MEDLINE DCOM- 20220425 LR - 20221022 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 119 IP - 18 DP - 2022 May 3 TI - Ancient DNA gives new insights into a Norman Neolithic monumental cemetery dedicated to male elites. PG - e2120786119 LID - 10.1073/pnas.2120786119 [doi] LID - e2120786119 AB - The Middle Neolithic in western Europe is characterized by monumental funerary structures, known as megaliths, along the Atlantic façade. The first manifestations of this phenomenon occurred in modern-day France with the long mounds of the Cerny culture. Here, we present genome-wide data from the fifth-millennium BCE site of Fleury-sur-Orne in Normandy (France), famous for its impressively long monuments built for selected individuals. The site encompasses 32 monuments of variable sizes, containing the burials of 19 individuals from the Neolithic period. To address who was buried at the site, we generated genome-wide data for 14 individuals, of whom 13 are males, completing previously published data [M. Rivollat et al., Sci. Adv. 6, eaaz5344 (2020)]. Population genetic and Y chromosome analyses show that the Fleury-sur-Orne group fits within western European Neolithic genetic diversity and that the arrival of a new group is detected after 4,000 calibrated BCE. The results of analyzing uniparentally inherited markers and an overall low number of long runs of homozygosity suggest a patrilineal group practicing female exogamy. We find two pairs of individuals to be father and son, buried together in the same monument/grave. No other biological relationship can link monuments together, suggesting that each monument was dedicated to a genetically independent lineage. The combined data and documented father–son line of descent suggest a male-mediated transmission of sociopolitical authority. However, a single female buried with an arrowhead, otherwise considered a symbol of power of the male elite of the Cerny culture, questions a strictly biological sex bias in the burial rites of this otherwise “masculine” monumental cemetery. FAU - Rivollat, Maïté AU - Rivollat M AUID- ORCID: 0000-0002-4011-2862 AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie, Université de Bordeaux, CNRS, Pessac 33615, France. AD - Department of Archaeogenetics, Max Planck Institute for Science of Human History, Jena 07745, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Thomas, Aline AU - Thomas A AUID- ORCID: 0000-0003-4018-3123 AD - Eco-Anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris Musée de l'Homme, Paris 75116, France. FAU - Ghesquière, Emmanuel AU - Ghesquière E AUID- ORCID: 0000-0001-9418-1866 AD - Inrap Grand Ouest, Bourguébus 14540, France. AD - Centre de Recherche en Archéologie, Archéosciences, Histoire, Université de Rennes 1, CNRS, Rennes 35042, France. FAU - Rohrlach, Adam Benjamin AU - Rohrlach AB AUID- ORCID: 0000-0002-4204-5018 AD - Department of Archaeogenetics, Max Planck Institute for Science of Human History, Jena 07745, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. AD - Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia. FAU - Späth, Ellen AU - Späth E AUID- ORCID: 0000-0002-3851-3931 AD - Department of Archaeogenetics, Max Planck Institute for Science of Human History, Jena 07745, Germany. FAU - Pemonge, Marie-Hélène AU - Pemonge MH AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie, Université de Bordeaux, CNRS, Pessac 33615, France. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Department of Archaeogenetics, Max Planck Institute for Science of Human History, Jena 07745, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Chambon, Philippe AU - Chambon P AUID- ORCID: 0000-0003-1461-169X AD - Eco-Anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris Musée de l'Homme, Paris 75116, France. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie, Université de Bordeaux, CNRS, Pessac 33615, France. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220421 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - Burial/history MH - *Cemeteries MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Female MH - Genomics MH - History, Ancient MH - Humans MH - Male PMC - PMC9170172 OTO - NOTNLM OT - Middle Neolithic OT - Normandy OT - ancient DNA OT - monumental graves OT - patrilineality COIS- The authors declare no competing interest. EDAT- 2022/04/22 06:00 MHDA- 2022/04/26 06:00 PMCR- 2022/10/21 CRDT- 2022/04/21 17:11 PHST- 2022/04/21 17:11 [entrez] PHST- 2022/04/22 06:00 [pubmed] PHST- 2022/04/26 06:00 [medline] PHST- 2022/10/21 00:00 [pmc-release] AID - 202120786 [pii] AID - 10.1073/pnas.2120786119 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2022 May 3;119(18):e2120786119. doi: 10.1073/pnas.2120786119. Epub 2022 Apr 21. PMID- 35060661 OWN - NLM STAT- MEDLINE DCOM- 20220628 LR - 20220628 IS - 1520-6505 (Electronic) IS - 1060-1538 (Linking) VI - 31 IP - 3 DP - 2022 May TI - Anthropological genetic insights on Caribbean population history. PG - 118-137 LID - 10.1002/evan.21935 [doi] AB - As the last American region settled by humans, yet the first to experience European colonization, the Caribbean islands have a complex history characterized by continuous migration, admixture, and demographic change. In the last 20 years, genetics research has transformed our understanding of Caribbean population history and revisited major debates in Caribbean anthropology, such as those surrounding the first peopling of the Antilles and the relationship between ancient Indigenous communities and present-day islanders. Genetics studies have also contributed novel perspectives for understanding pivotal events in Caribbean post-contact history such as European colonization, the Atlantic Slave Trade, and the Asian Indenture system. Here, I discuss the last 20 years of Caribbean genetics research and emphasize the importance of integrating genetics with interdisciplinary historic, archaeological, and anthropological approaches. Such interdisciplinary research is essential for investigating the dynamic history of the Caribbean and characterizing its impact on the biocultural diversity of present-day Caribbean peoples. CI - © 2022 Wiley Periodicals LLC. FAU - Nieves-Colón, Maria A AU - Nieves-Colón MA AUID- ORCID: 0000-0001-9035-6091 AD - Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA. LA - eng PT - Journal Article PT - Review DEP - 20220121 PL - United States TA - Evol Anthropol JT - Evolutionary anthropology JID - 9306331 RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology MH - Caribbean Region MH - *DNA, Mitochondrial/genetics MH - Genetic Variation MH - *Genetics, Population MH - Humans MH - West Indies OTO - NOTNLM OT - Greater Antilles OT - Lesser Antilles OT - admixture OT - ancient DNA OT - genomics OT - migration EDAT- 2022/01/22 06:00 MHDA- 2022/06/29 06:00 CRDT- 2022/01/21 09:00 PHST- 2021/06/18 00:00 [revised] PHST- 2020/12/29 00:00 [received] PHST- 2021/12/15 00:00 [accepted] PHST- 2022/01/22 06:00 [pubmed] PHST- 2022/06/29 06:00 [medline] PHST- 2022/01/21 09:00 [entrez] AID - 10.1002/evan.21935 [doi] PST - ppublish SO - Evol Anthropol. 2022 May;31(3):118-137. doi: 10.1002/evan.21935. Epub 2022 Jan 21. PMID- 35412864 OWN - NLM STAT- MEDLINE DCOM- 20220414 LR - 20220716 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 119 IP - 17 DP - 2022 Apr 26 TI - Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague. PG - e2116722119 LID - 10.1073/pnas.2116722119 [doi] LID - e2116722119 AB - The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology. FAU - Andrades Valtueña, Aida AU - Andrades Valtueña A AUID- ORCID: 0000-0002-1737-2228 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Neumann, Gunnar U AU - Neumann GU AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Spyrou, Maria A AU - Spyrou MA AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, 72074 Tübingen, Germany. FAU - Musralina, Lyazzat AU - Musralina L AUID- ORCID: 0000-0001-8591-890X AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Biology and Biotechnology Faculty, Al-Farabi Kazakh National University, 050040 Almaty, Kazakhstan. AD - Institute of Genetics and Physiology, Al-Farabi Kazakh National University, Almaty, 050060 Kazakhstan. FAU - Aron, Franziska AU - Aron F AUID- ORCID: 0000-0003-4126-8612 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Faculty of Mathematics and Computer Science, Friedrich-Schiller University, 07743 Jena, Germany. FAU - Beisenov, Arman AU - Beisenov A AUID- ORCID: 0000-0003-2524-264X AD - Begazy-Tasmola Research Center of History and Archeology, 050008 Almaty, Kazakhstan. FAU - Belinskiy, Andrey B AU - Belinskiy AB AD - Nasledie Cultural Heritage Unit, 355006 Stavropol, Russian Federation. FAU - Bos, Kirsten I AU - Bos KI AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Buzhilova, Alexandra AU - Buzhilova A AUID- ORCID: 0000-0001-6398-2177 AD - Research Institute and Museum of Anthropology, Lomonosov Moscow State University, 125009 Moscow, Russian Federation. FAU - Conrad, Matthias AU - Conrad M AD - Department of Heritage Management, Archaeological Heritage Office Saxony, 01108 Dresden, Germany. FAU - Djansugurova, Leyla B AU - Djansugurova LB AUID- ORCID: 0000-0002-6745-9903 AD - Institute of Genetics and Physiology, Al-Farabi Kazakh National University, Almaty, 050060 Kazakhstan. FAU - Dobeš, Miroslav AU - Dobeš M AUID- ORCID: 0000-0001-5327-5030 AD - Department of Prehistoric Archaeology, Institute of Archaeology, Czech Academy of Sciences, 11801 Prague, Czech Republic. FAU - Ernée, Michal AU - Ernée M AUID- ORCID: 0000-0003-4847-8532 AD - Department of Prehistoric Archaeology, Institute of Archaeology, Czech Academy of Sciences, 11801 Prague, Czech Republic. FAU - Fernández-Eraso, Javier AU - Fernández-Eraso J AUID- ORCID: 0000-0002-9860-2610 AD - Department of Geography, Prehistory, and Archaeology, University of the Basque Country, Vitoria-Gasteiz, 01006 Spain. FAU - Frohlich, Bruno AU - Frohlich B AD - Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560. FAU - Furmanek, Mirosław AU - Furmanek M AUID- ORCID: 0000-0002-3558-3440 AD - Institute of Archaeology, University of Wrocław, 50139 Wrocław, Poland. FAU - Hałuszko, Agata AU - Hałuszko A AD - Institute of Archaeology, University of Wrocław, 50139 Wrocław, Poland. AD - Archeolodzy.org Foundation, 50316 Wrocław, Poland. FAU - Hansen, Svend AU - Hansen S AUID- ORCID: 0000-0002-6714-4629 AD - Eurasia-Department, German Archaeological Institute, 14195 Berlin, Germany. FAU - Harney, Éadaoin AU - Harney É AD - Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138. AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. FAU - Hiss, Alina N AU - Hiss AN AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Hübner, Alexander AU - Hübner A AUID- ORCID: 0000-0003-3572-9996 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Faculty of Biological Sciences, Friedrich-Schiller University, 07743 Jena, Germany. FAU - Key, Felix M AU - Key FM AUID- ORCID: 0000-0003-2812-6636 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Evolutionary Pathogenomics, Max Planck Institute for Infection Biology, 10117 Berlin, Germany. FAU - Khussainova, Elmira AU - Khussainova E AD - Institute of Genetics and Physiology, Al-Farabi Kazakh National University, Almaty, 050060 Kazakhstan. FAU - Kitov, Egor AU - Kitov E AUID- ORCID: 0000-0002-0159-3288 AD - Institute of Ethnology and Anthropology, Russian Academy of Science, 119991 Moscow, Russian Federation. AD - Research Laboratory of Paleoanthropological Study, Institute of Archaeology named after A.Kh Margulan, Almaty, 50010 Kazakhstan. AD - History Department, Al-Farabi Kazakh National University, 050040 Almaty, Kazakhstan. FAU - Kitova, Alexandra O AU - Kitova AO AD - Centre for Egyptological Studies of the Russian Academy of Sciences, Russian Academy of Sciences, 119991 Moscow, Russian Federation. FAU - Knipper, Corina AU - Knipper C AUID- ORCID: 0000-0002-4274-4636 AD - Curt Engelhorn Center Archaeometry, 68159 Mannheim, Germany. FAU - Kühnert, Denise AU - Kühnert D AD - Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology, Consejo Superior de Investigaciones Cientificas-Universitat Pompeu Fabra, 08003 Barcelona, Spain. FAU - Littleton, Judith AU - Littleton J AD - Department of Anthropology, University of Auckland, 01010 Auckland, New Zealand. FAU - Massy, Ken AU - Massy K AUID- ORCID: 0000-0002-7724-0702 AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80539 Munich, Germany. FAU - Mittnik, Alissa AU - Mittnik A AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. FAU - Mujika-Alustiza, José Antonio AU - Mujika-Alustiza JA AUID- ORCID: 0000-0002-2130-6338 AD - Department of Geography, Prehistory, and Archaeology, University of the Basque Country, Vitoria-Gasteiz, 01006 Spain. FAU - Olalde, Iñigo AU - Olalde I AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Institute of Evolutionary Biology, Consejo Superior de Investigaciones Cientificas-Universitat Pompeu Fabra, 08003 Barcelona, Spain. AD - BIOMICs Research Group, University of the Basque Country Universidad del Pais Vasco/Euskal Herriko Unibertsitatea, 01006 Vitoria-Gasteiz, Spain. FAU - Papac, Luka AU - Papac L AUID- ORCID: 0000-0003-2012-0782 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Penske, Sandra AU - Penske S AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Peška, Jaroslav AU - Peška J AD - Archaeological Centre, 779 00 Olomouc, Czech Republic. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. FAU - Reinhold, Sabine AU - Reinhold S AUID- ORCID: 0000-0002-8107-6300 AD - Eurasia-Department, German Archaeological Institute, 14195 Berlin, Germany. FAU - Stahl, Raphaela AU - Stahl R AUID- ORCID: 0000-0002-5915-9337 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Stäuble, Harald AU - Stäuble H AD - Department of Heritage Management, Archaeological Heritage Office Saxony, 01108 Dresden, Germany. FAU - Tukhbatova, Rezeda I AU - Tukhbatova RI AUID- ORCID: 0000-0002-1040-0951 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008 Russian Federation. AD - Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", 420111 Kazan, Russian Federation. FAU - Vasilyev, Sergey AU - Vasilyev S AUID- ORCID: 0000-0003-0128-6568 AD - Institute of Ethnology and Anthropology, Russian Academy of Science, 119991 Moscow, Russian Federation. FAU - Veselovskaya, Elizaveta AU - Veselovskaya E AD - Institute of Ethnology and Anthropology, Russian Academy of Science, 119991 Moscow, Russian Federation. FAU - Warinner, Christina AU - Warinner C AUID- ORCID: 0000-0002-4528-5877 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Faculty of Biological Sciences, Friedrich-Schiller University, 07743 Jena, Germany. AD - Department of Anthropology, Harvard University, Cambridge, MA 02138. FAU - Stockhammer, Philipp W AU - Stockhammer PW AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80539 Munich, Germany. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Herbig, Alexander AU - Herbig A AUID- ORCID: 0000-0003-1176-1166 AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. LA - eng PT - Historical Article PT - Journal Article DEP - 20220411 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM CIN - Proc Natl Acad Sci U S A. 2022 May 24;119(21):e2204044119. doi: 10.1073/pnas.2204044119. PMID: 35580179 MH - Animal Husbandry/history MH - Animals MH - DNA, Ancient MH - Genetic Variation MH - *Genome, Bacterial MH - History, Ancient MH - Human Migration/history MH - Humans MH - Phylogeny MH - *Plague/epidemiology/history/microbiology MH - *Yersinia pestis/classification/genetics/isolation & purification PMC - PMC9169917 OTO - NOTNLM OT - Yersinia pestis OT - ancient DNA OT - plague COIS- The authors declare no competing interest. EDAT- 2022/04/13 06:00 MHDA- 2022/04/15 06:00 PMCR- 2022/04/12 CRDT- 2022/04/12 17:11 PHST- 2022/04/12 17:11 [entrez] PHST- 2022/04/13 06:00 [pubmed] PHST- 2022/04/15 06:00 [medline] PHST- 2022/04/12 00:00 [pmc-release] AID - 202116722 [pii] AID - 10.1073/pnas.2116722119 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2022 Apr 26;119(17):e2116722119. doi: 10.1073/pnas.2116722119. Epub 2022 Apr 11. PMID- 35563041 OWN - NLM STAT- MEDLINE DCOM- 20220517 LR - 20231105 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 23 IP - 9 DP - 2022 Apr 22 TI - Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods. LID - 10.3390/ijms23094651 [doi] LID - 4651 AB - Retrieving high-quality endogenous ancient DNA (aDNA) poses several challenges, including low molecular copy number, high rates of fragmentation, damage at read termini, and potential presence of exogenous contaminant DNA. All these factors complicate a reliable reconstruction of consensus aDNA sequences in reads from high-throughput sequencing platforms. Here, we report findings from a thorough evaluation of two alternative tools (ANGSD and schmutzi) aimed at overcoming these issues and constructing high-quality ancient mitogenomes. Raw genomic data (BAM/FASTQ) from a total of 17 previously published whole ancient human genomes ranging from the 14th to the 7th millennium BCE were retrieved and mitochondrial consensus sequences were reconstructed using different quality filters, with their accuracy measured and compared. Moreover, the influence of different sequence parameters (number of reads, sequenced bases, mean coverage, and rate of deamination and contamination) as predictors of derived sequence quality was evaluated. Complete mitogenomes were successfully reconstructed for all ancient samples, and for the majority of them, filtering substantially improved mtDNA consensus calling and haplogroup prediction. Overall, the schmutzi pipeline, which estimates and takes into consideration exogenous contamination, appeared to have the edge over the much faster and user-friendly alternative method (ANGSD) in moderate to high coverage samples (>1,000,000 reads). ANGSD, however, through its read termini trimming filter, showed better capabilities in calling the consensus sequence from low-quality samples. Among all the predictors of overall sample quality examined, the strongest correlation was found for the available number of sequence reads and bases. In the process, we report a previously unassigned haplogroup (U3b) for an Early Chalcolithic individual from Southern Anatolia/Northern Levant. FAU - Heraclides, Alexandros AU - Heraclides A AUID- ORCID: 0000-0002-1304-3275 AD - Department of Health Sciences, European University Cyprus, Diogenis Str. 6, Nicosia 2404, Cyprus. FAU - Fernández-Domínguez, Eva AU - Fernández-Domínguez E AD - Department of Archaeology, Durham University, South Road, Durham DH1 3LE, UK. LA - eng PT - Journal Article DEP - 20220422 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Ancient MH - *DNA, Mitochondrial/genetics MH - *Genome, Mitochondrial MH - High-Throughput Nucleotide Sequencing/methods MH - Humans MH - Sequence Analysis, DNA/methods PMC - PMC9104972 OTO - NOTNLM OT - archaeogenetics OT - consensus sequence calling OT - mtDNA COIS- The authors declare no conflict of interest. EDAT- 2022/05/15 06:00 MHDA- 2022/05/18 06:00 PMCR- 2022/04/22 CRDT- 2022/05/14 01:03 PHST- 2022/04/01 00:00 [received] PHST- 2022/04/18 00:00 [revised] PHST- 2022/04/19 00:00 [accepted] PHST- 2022/05/14 01:03 [entrez] PHST- 2022/05/15 06:00 [pubmed] PHST- 2022/05/18 06:00 [medline] PHST- 2022/04/22 00:00 [pmc-release] AID - ijms23094651 [pii] AID - ijms-23-04651 [pii] AID - 10.3390/ijms23094651 [doi] PST - epublish SO - Int J Mol Sci. 2022 Apr 22;23(9):4651. doi: 10.3390/ijms23094651. PMID- 35366416 OWN - NLM STAT- MEDLINE DCOM- 20220419 LR - 20240913 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 185 IP - 8 DP - 2022 Apr 14 TI - Ancient genomes reveal origin and rapid trans-Eurasian migration of 7(th) century Avar elites. PG - 1402-1413.e21 LID - S0092-8674(22)00267-7 [pii] LID - 10.1016/j.cell.2022.03.007 [doi] AB - The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar's empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population. CI - Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Gnecchi-Ruscone, Guido Alberto AU - Gnecchi-Ruscone GA AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. Electronic address: guido_gnecchi@eva.mpg.de. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary. FAU - Koncz, István AU - Koncz I AD - Institute of Archaeological Sciences, ELTE Eötvös Loránd University, 1088 Budapest, Hungary. FAU - Csiky, Gergely AU - Csiky G AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary. FAU - Rácz, Zsófia AU - Rácz Z AD - Institute of Archaeological Sciences, ELTE Eötvös Loránd University, 1088 Budapest, Hungary. FAU - Rohrlach, A B AU - Rohrlach AB AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia. FAU - Brandt, Guido AU - Brandt G AD - Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. FAU - Csáky, Veronika AU - Csáky V AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Szeifert, Bea AU - Szeifert B AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary. FAU - Rácz, Tibor Ákos AU - Rácz TÁ AD - Ferenczy Museum Center, 2000 Szentendre, Hungary. FAU - Benedek, András AU - Benedek A AD - Móra Ferenc Museum, 6720 Szeged, Hungary. FAU - Bernert, Zsolt AU - Bernert Z AD - Hungarian National Museum, 1113 Budapest, Hungary. FAU - Berta, Norbert AU - Berta N AD - Salisbury Ltd., 1016 Budapest, Hungary. FAU - Czifra, Szabolcs AU - Czifra S AD - Hungarian National Museum, 1113 Budapest, Hungary. FAU - Dani, János AU - Dani J AD - Déri Museum, 4026 Debrecen, Hungary. FAU - Farkas, Zoltán AU - Farkas Z AD - Salisbury Ltd., 1016 Budapest, Hungary. FAU - Hága, Tamara AU - Hága T AD - Déri Museum, 4026 Debrecen, Hungary. FAU - Hajdu, Tamás AU - Hajdu T AD - Dept. of Biological Anthropology, Eötvös Loránd University (ELTE), 1117 Budapest, Hungary. FAU - Jászberényi, Mónika AU - Jászberényi M AD - Ferenczy Museum Center, 2000 Szentendre, Hungary. FAU - Kisjuhász, Viktória AU - Kisjuhász V AD - Aquincum Museum and Archaeological Park, 1031 Budapest, Hungary. FAU - Kolozsi, Barbara AU - Kolozsi B AD - Déri Museum, 4026 Debrecen, Hungary. FAU - Major, Péter AU - Major P AD - Salisbury Ltd., 1016 Budapest, Hungary. FAU - Marcsik, Antónia AU - Marcsik A AD - Dept. of Biological Anthropology, Szeged University, 6701 Szeged, Hungary. FAU - Kovacsóczy, Bernadett Ny AU - Kovacsóczy BN AD - Katona József Museum, 6000 Kecskemét, Hungary. FAU - Balogh, Csilla AU - Balogh C AD - Department of Art History, Istanbul Medeniyet University, 34720 Istanbul, Turkey. FAU - Lezsák, Gabriella M AU - Lezsák GM AD - Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary. FAU - Ódor, János Gábor AU - Ódor JG AD - Wosinsky Mór Museum, 7100 Szekszárd, Hungary. FAU - Szelekovszky, Márta AU - Szelekovszky M AD - Déri Museum, 4026 Debrecen, Hungary. FAU - Szeniczey, Tamás AU - Szeniczey T AD - Dept. of Biological Anthropology, Eötvös Loránd University (ELTE), 1117 Budapest, Hungary. FAU - Tárnoki, Judit AU - Tárnoki J AD - Damjanich Museum, 5000 Szolnok, Hungary. FAU - Tóth, Zoltán AU - Tóth Z AD - Dobó István Museum, 3300 Eger, Hungary. FAU - Tutkovics, Eszter K AU - Tutkovics EK AD - Rétközi Múzeum, 4600 Kisvárda, Hungary. FAU - Mende, Balázs G AU - Mende BG AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary. FAU - Geary, Patrick AU - Geary P AD - Institute for Advanced Study, Princeton, NJ 08540, USA. FAU - Pohl, Walter AU - Pohl W AD - Institute for Medieval Research, Austrian Academy of Sciences, 1020 Vienna, Austria; Institute of Austrian Historical Research, University of Vienna, 1010 Vienna, Austria. FAU - Vida, Tivadar AU - Vida T AD - Institute of Archaeological Sciences, ELTE Eötvös Loránd University, 1088 Budapest, Hungary. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Hofmanová, Zuzana AU - Hofmanová Z AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Department of Archaeology and Museology, Faculty of Arts, Masaryk University, 60200 Brno, Czech Republic. FAU - Jeong, Choongwon AU - Jeong C AD - School of Biological Sciences, Seoul National University, 08826 Seoul, Republic of Korea. Electronic address: cwjeong@snu.ac.kr. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. Electronic address: krause@eva.mpg.de. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220401 PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) RN - 70FD1KFU70 (Sulfur) SB - IM MH - *Asian People/genetics MH - *DNA, Ancient MH - *Genetics, Population MH - Genome MH - History, Ancient MH - Human Migration/history MH - Humans MH - Sulfur PMC - PMC9042794 OTO - NOTNLM OT - Avars OT - Carpathian Basin OT - Pannonia OT - ancient DNA OT - early medieval OT - human migration OT - migration period OT - population genomics OT - steppe nomads COIS- Declaration of interests The authors declare no competing interests. EDAT- 2022/04/03 06:00 MHDA- 2022/04/20 06:00 PMCR- 2022/04/14 CRDT- 2022/04/02 20:06 PHST- 2021/10/04 00:00 [received] PHST- 2022/01/28 00:00 [revised] PHST- 2022/03/04 00:00 [accepted] PHST- 2022/04/03 06:00 [pubmed] PHST- 2022/04/20 06:00 [medline] PHST- 2022/04/02 20:06 [entrez] PHST- 2022/04/14 00:00 [pmc-release] AID - S0092-8674(22)00267-7 [pii] AID - 10.1016/j.cell.2022.03.007 [doi] PST - ppublish SO - Cell. 2022 Apr 14;185(8):1402-1413.e21. doi: 10.1016/j.cell.2022.03.007. Epub 2022 Apr 1. PMID- 35389750 OWN - NLM STAT- MEDLINE DCOM- 20220415 LR - 20230928 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 119 IP - 15 DP - 2022 Apr 12 TI - An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers. PG - e2106743119 LID - 10.1073/pnas.2106743119 [doi] LID - e2106743119 AB - Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory. FAU - Marciniak, Stephanie AU - Marciniak S AUID- ORCID: 0000-0002-0052-8919 AD - Department of Anthropology, Pennsylvania State University, University Park, PA 16802. FAU - Bergey, Christina M AU - Bergey CM AUID- ORCID: 0000-0001-8336-8078 AD - Department of Anthropology, Pennsylvania State University, University Park, PA 16802. AD - Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854. FAU - Silva, Ana Maria AU - Silva AM AUID- ORCID: 0000-0002-1912-6581 AD - Research Centre for Anthropology and Health (Centro de Investigação em Antropologia e Saúde - CIAS), Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal. AD - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal. AD - Archeology Center of the University of Lisbon (UNIARQ), University of Lisbon, Lisbon 1600-214, Portugal. FAU - Hałuszko, Agata AU - Hałuszko A AUID- ORCID: 0000-0001-8312-3222 AD - Institute of Archaeology, University of Wrocław, Wrocław 50-139, Poland. AD - Archeolodzy.org Foundation, Wrocław 50-316, Poland. FAU - Furmanek, Mirosław AU - Furmanek M AUID- ORCID: 0000-0002-3558-3440 AD - Institute of Archaeology, University of Wrocław, Wrocław 50-139, Poland. FAU - Veselka, Barbara AU - Veselka B AUID- ORCID: 0000-0002-2692-9577 AD - Department of Chemistry, Analytical Environmental and Geo-Chemistry Research Unit, Vrije Univeristeit Brussels, Brussels 1050, Belgium. AD - Department of Art Studies and Archaeology, Maritime Cultures Research Institute, Vrije Univeristeit Brussels, Brussels 1050, Belgium. FAU - Velemínský, Petr AU - Velemínský P AUID- ORCID: 0000-0003-3691-7817 AD - Department of Anthropology, National Museum, Prague 115-79, Czech Republic. FAU - Vercellotti, Giuseppe AU - Vercellotti G AD - Department of Anthropology, Ohio State University, Columbus, OH 43210. AD - Institute for Research and Learning in Archaeology and Bioarchaeology, Columbus, OH 43215. FAU - Wahl, Joachim AU - Wahl J AD - Institute for Scientific Archaeology, Working Group Palaeoanthropology, University of Tübingen, Tübingen 72074, Germany. FAU - Zariņa, Gunita AU - Zariņa G AD - Institute of Latvian History, University of Latvia, Riga 1050, Latvia. FAU - Longhi, Cristina AU - Longhi C AD - Soprintendenza Archeologia, Belle Arti e Paesaggio, Rome 00186, Italy. FAU - Kolář, Jan AU - Kolář J AUID- ORCID: 0000-0001-8013-6992 AD - Department of Vegetation Ecology, Institute of Botany of the Czech Academy of Sciences, Průhonice 252-43, Czech Republic. AD - Institute of Archaeology and Museology, Masaryk University, Brno 602-00, Czech Republic. FAU - Garrido-Pena, Rafael AU - Garrido-Pena R AUID- ORCID: 0000-0001-8263-2949 AD - Department of Prehistory and Archaeology, Universidad Autónoma de Madrid, Madrid 28049, Spain. FAU - Flores-Fernández, Raúl AU - Flores-Fernández R AUID- ORCID: 0000-0003-3384-2055 AD - Professional archaeologist, Parla 28980, Spain. FAU - Herrero-Corral, Ana M AU - Herrero-Corral AM AUID- ORCID: 0000-0003-3536-1108 AD - Department of Prehistory, Universidad Complutense de Madrid, Madrid 28040, Spain. FAU - Simalcsik, Angela AU - Simalcsik A AUID- ORCID: 0000-0001-8639-3535 AD - Olga Necrasov Center for Anthropological Research, Romanian Academy - Iasi Branch, Iasi 700481, Romania. AD - Orheiul Vechi Cultural-Natural Reserve, Orhei 3506, Republic of Moldova. FAU - Müller, Werner AU - Müller W AUID- ORCID: 0000-0002-0319-984X AD - Laboratoire d'archéozoologie, Université de Neuchâtel, Neuchâtel 2000, Switzerland. FAU - Sheridan, Alison AU - Sheridan A AD - Department of Scottish History & Archaeology, National Museums Scotland, Edinburgh EH1 1JF, Scotland. FAU - Miliauskienė, Žydrūnė AU - Miliauskienė Ž AUID- ORCID: 0000-0003-2830-7154 AD - Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius 01513, Lithuania. FAU - Jankauskas, Rimantas AU - Jankauskas R AUID- ORCID: 0000-0001-7611-2576 AD - Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius 01513, Lithuania. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Department of Physical Anthropology, Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg 199034, Russia. FAU - Köhler, Kitti AU - Köhler K AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary. FAU - Király, Ágnes AU - Király Á AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary. FAU - Gamarra, Beatriz AU - Gamarra B AUID- ORCID: 0000-0003-3764-497X AD - Institut Català de Paleoecologia Humana i Evolució Social, Tarragona 43007, Spain. AD - Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Tarragona 43003, Spain. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna 1030, Austria. FAU - Szeverényi, Vajk AU - Szeverényi V AUID- ORCID: 0000-0002-0830-8566 AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary. AD - Department of Archaeology, Déri Múzeum, Debrecen 4026, Hungary. FAU - Kiss, Viktória AU - Kiss V AD - Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary. FAU - Szeniczey, Tamás AU - Szeniczey T AD - Department of Biological Anthropology, Eötvös Loránd University, Budapest 1053, Hungary. FAU - Kiss, Krisztián AU - Kiss K AUID- ORCID: 0000-0002-9371-3397 AD - Department of Biological Anthropology, Eötvös Loránd University, Budapest 1053, Hungary. AD - Department of Anthropology, Hungarian Natural History Museum, Budapest 1083, Hungary. FAU - Zoffmann, Zsuzsanna K AU - Zoffmann ZK AD - Department of Archaeology, Hungarian National Museum, Budapest 1088, Hungary. FAU - Koós, Judit AU - Koós J AD - Department of Archaeology, Herman Ottó Museum, Miskolc 3530, Hungary. FAU - Hellebrandt, Magdolna AU - Hellebrandt M AD - Department of Archaeology, Herman Ottó Museum, Miskolc 3530, Hungary. FAU - Maier, Robert M AU - Maier RM AUID- ORCID: 0000-0002-3044-090X AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. FAU - Domboróczki, László AU - Domboróczki L AD - Department of Archaeology, István Dobó Castle Museum, Eger 3300, Hungary. FAU - Virag, Cristian AU - Virag C AD - Department of Archaeology, Satu Mare County Museum, Satu Mare 440031, Romania. FAU - Novak, Mario AU - Novak M AUID- ORCID: 0000-0002-4567-8742 AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb 10000, Croatia. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Boston, MA 02115. AD - Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142. AD - HHMI, Harvard Medical School, Cambridge, MA 02138. FAU - Hajdu, Tamás AU - Hajdu T AD - Department of Biological Anthropology, Eötvös Loránd University, Budapest 1053, Hungary. FAU - von Cramon-Taubadel, Noreen AU - von Cramon-Taubadel N AUID- ORCID: 0000-0002-5263-3892 AD - Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, NY 14261-0026. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria. AD - Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna 1030, Austria. FAU - Perry, George H AU - Perry GH AUID- ORCID: 0000-0003-4527-3806 AD - Department of Anthropology, Pennsylvania State University, University Park, PA 16802. AD - Department of Biology, Pennsylvania State University, University Park, PA 16802. AD - Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802. AD - Deutsche Forschungsgemeinschaft (DFG) Center for Advanced Studies, University of Tübingen, Tübingen 72074, Germany. LA - eng GR - R01 GM115656/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article DEP - 20220406 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Adult MH - *Agriculture/history MH - *Body Height/genetics MH - Child MH - DNA, Ancient MH - Europe MH - *Farmers/history MH - Genetic Variation MH - Genomics MH - *Health/history MH - History, Ancient MH - Humans MH - Paleopathology MH - *Skeleton/anatomy & histology PMC - PMC9169634 OTO - NOTNLM OT - agriculture transition OT - health OT - paleogenomics OT - stature variation COIS- The authors declare no competing interest. EDAT- 2022/04/08 06:00 MHDA- 2022/04/16 06:00 PMCR- 2022/04/06 CRDT- 2022/04/07 17:12 PHST- 2022/04/07 17:12 [entrez] PHST- 2022/04/08 06:00 [pubmed] PHST- 2022/04/16 06:00 [medline] PHST- 2022/04/06 00:00 [pmc-release] AID - 202106743 [pii] AID - 10.1073/pnas.2106743119 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2022 Apr 12;119(15):e2106743119. doi: 10.1073/pnas.2106743119. Epub 2022 Apr 6. PMID- 35445261 OWN - NLM STAT- MEDLINE DCOM- 20220422 LR - 20240826 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 14 IP - 4 DP - 2022 Apr 10 TI - Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa. LID - 10.1093/gbe/evac045 [doi] LID - evac045 AB - The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub. CI - © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Vallini, Leonardo AU - Vallini L AUID- ORCID: 0000-0002-0590-6333 AD - Department of Biology, University of Padova, Italy. FAU - Marciani, Giulia AU - Marciani G AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. AD - Department of Physical Sciences, Earth and Environment, University of Siena, Italy. FAU - Aneli, Serena AU - Aneli S AUID- ORCID: 0000-0003-4303-2507 AD - Department of Biology, University of Padova, Italy. AD - Department of Public Health Sciences and Pediatrics, University of Turin, Italy. FAU - Bortolini, Eugenio AU - Bortolini E AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. FAU - Benazzi, Stefano AU - Benazzi S AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Pievani, Telmo AU - Pievani T AD - Department of Biology, University of Padova, Italy. FAU - Pagani, Luca AU - Pagani L AD - Department of Biology, University of Padova, Italy. AD - Institute of Genomics, University of Tartu, Estonia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 SB - IM MH - Africa MH - Animals MH - Anthropology, Cultural MH - Europe MH - Genetics, Population MH - Humans MH - *Neanderthals/genetics MH - Siberia PMC - PMC9021735 OTO - NOTNLM OT - ancient DNA OT - material culture OT - molecular anthropology OT - paleolithic Eurasia EDAT- 2022/04/22 06:00 MHDA- 2022/04/23 06:00 PMCR- 2022/04/07 CRDT- 2022/04/21 05:46 PHST- 2022/03/21 00:00 [accepted] PHST- 2022/04/21 05:46 [entrez] PHST- 2022/04/22 06:00 [pubmed] PHST- 2022/04/23 06:00 [medline] PHST- 2022/04/07 00:00 [pmc-release] AID - 6563828 [pii] AID - evac045 [pii] AID - 10.1093/gbe/evac045 [doi] PST - ppublish SO - Genome Biol Evol. 2022 Apr 10;14(4):evac045. doi: 10.1093/gbe/evac045. PMID- 35383854 OWN - NLM STAT- MEDLINE DCOM- 20220422 LR - 20220716 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 39 IP - 4 DP - 2022 Apr 10 TI - Challenging Ancient DNA Results About Putative HLA Protection or Susceptibility to Yersinia pestis. LID - 10.1093/molbev/msac073 [doi] LID - msac073 AB - In a recent article, Immel et al. (Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, et al. 2021. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol. 38:4059-4076) extracted DNA from 36 individuals dead from plague in Ellwangen, Southern Germany, during the 16th century. By comparing their human leukocyte antigen (HLA) genotypes with those of 50 present-day Ellwangen inhabitants, the authors reported a significant decrease of HLA-B*51:01 and HLA-C*06:02 and a significant increase of HLA-DRB1*13:01/13:02 frequencies from ancient to modern populations. After comparing these frequencies with a larger sample of 8,862 modern Germans and performing simulations of natural selection, they concluded that these changes had been driven by natural selection. In an attempt to provide more evidence on such stimulating results, we explored the HLA frequency patterns over all of Europe, we predicted binding affinities of HLA-B/C/DRB1 alleles to 106,515 Yersinia pestis-derived peptides, and we performed forward simulations of HLA genetic profiles under neutrality. Our analyses do not sustain the conclusions of HLA protection or susceptibility to plague based on ancient DNA. CI - © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. FAU - Di, Da AU - Di D AD - Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland. FAU - Simon Thomas, Jeanne AU - Simon Thomas J AD - Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland. FAU - Currat, Mathias AU - Currat M AUID- ORCID: 0000-0001-5211-8922 AD - Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland. AD - Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland. FAU - Nunes, José Manuel AU - Nunes JM AD - Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland. AD - Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland. FAU - Sanchez-Mazas, Alicia AU - Sanchez-Mazas A AUID- ORCID: 0000-0002-7714-2432 AD - Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland. AD - Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) RN - 0 (HLA Antigens) RN - 0 (Histocompatibility Antigens Class II) RN - 9007-49-2 (DNA) SB - IM MH - DNA MH - DNA, Ancient MH - Europe MH - *Genetic Predisposition to Disease MH - *HLA Antigens/genetics MH - Histocompatibility Antigens Class II MH - Humans MH - *Plague/genetics MH - Yersinia pestis PMC - PMC9021733 OTO - NOTNLM OT - Yersinia pestis OT - HLA OT - ancient DNA OT - computer simulations OT - pathogen-driven selection OT - peptide-binding predictions EDAT- 2022/04/07 06:00 MHDA- 2022/04/23 06:00 PMCR- 2022/04/06 CRDT- 2022/04/06 09:11 PHST- 2022/04/07 06:00 [pubmed] PHST- 2022/04/23 06:00 [medline] PHST- 2022/04/06 09:11 [entrez] PHST- 2022/04/06 00:00 [pmc-release] AID - 6564158 [pii] AID - msac073 [pii] AID - 10.1093/molbev/msac073 [doi] PST - ppublish SO - Mol Biol Evol. 2022 Apr 10;39(4):msac073. doi: 10.1093/molbev/msac073. PMID- 34533260 OWN - NLM STAT- MEDLINE DCOM- 20220405 LR - 20220527 IS - 1520-6300 (Electronic) IS - 1042-0533 (Linking) VI - 34 IP - 4 DP - 2022 Apr TI - Uniparental origins of the admixed Argentine Patagonia. PG - e23682 LID - 10.1002/ajhb.23682 [doi] AB - OBJECTIVES: We aimed to contribute to the understanding of the ancient geographic origins of the uniparentally inherited markers in modern admixed Argentinian populations from central Patagonia with new information provided for the city of Trelew. We attempted to highlight the importance of combining different genetic markers when studying population history. METHODS: The mtDNA control region sequence was typified in 89 individuals and 12 Y-STR and 15 Y-SNP loci were analyzed in 66 males. With these data, analysis of molecular variance and Network analyses were carried out. We exhaustively compared the modern data with ancient mtDNA information. Finally, we tested the differences in continental origins estimated by uniparental and previously published biparental markers. RESULTS: Native American mtDNAs (53.9%) increased when maternal ancestors were born in the northern (81.8%) and southern (58.5%) regions of Argentina or in Chile (77.8%). Population substructure was only observed for Y-chromosome haplotypes. Some mtDNA haplogroups have been present in the area for at least ca. 2762-2430 and ca. 500 (D1g and D1g4 haplogroups) and ca. 6736 and ca. 6620 (C1b and C1c haplogroups) years, respectively. In contrast, haplogroups B2i2 and C1b13, frequent in modern Patagonia populations, had not been found in previous ancient DNA studies of the region. CONCLUSIONS: The results suggest that Native American ancestry is well preserved in the region. Trelew samples had characteristic native mtDNA haplogroups previously described in Chilean and Argentine Patagonian populations, but not observed in ancient samples until now. These findings support the idea that these lineages have a recent regional origin. Finally, the estimated proportions of continental ancestry depend on the genetic marker analyzed. CI - © 2021 Wiley Periodicals LLC. FAU - Tamburrini, Camila AU - Tamburrini C AUID- ORCID: 0000-0001-8197-973X AD - Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina. FAU - de Saint Pierre, Michelle AU - de Saint Pierre M AUID- ORCID: 0000-0001-6516-5314 AD - Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago de Chile, Chile. FAU - Bravi, Claudio Marcelo AU - Bravi CM AD - Laboratorio de Genética Molecular Poblacional, IMBICE (CCT-CONICET, CIC-PBA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina. FAU - Bailliet, Graciela AU - Bailliet G AD - Laboratorio de Genética Molecular Poblacional, IMBICE (CCT-CONICET, CIC-PBA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina. FAU - Jurado Medina, Laura AU - Jurado Medina L AD - Laboratorio de Genética Molecular Poblacional, IMBICE (CCT-CONICET, CIC-PBA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina. FAU - Velázquez, Irina Florencia AU - Velázquez IF AD - Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina. FAU - Real, Luciano Esteban AU - Real LE AD - Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina. FAU - Holley, Alfredo AU - Holley A AD - Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina. FAU - Tedeschi, Claudia Marcela AU - Tedeschi CM AD - Servicio de Hemoterapia, Hospital Zonal de Trelew, Trelew, Chubut, Argentina. FAU - Basso, Néstor Guillermo AU - Basso NG AD - Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina. FAU - Parolin, María Laura AU - Parolin ML AD - Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210917 PL - United States TA - Am J Hum Biol JT - American journal of human biology : the official journal of the Human Biology Council JID - 8915029 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - *DNA, Mitochondrial/genetics MH - Genetic Markers MH - *Genetics, Population MH - Haplotypes MH - Humans MH - Male MH - Racial Groups EDAT- 2021/09/18 06:00 MHDA- 2022/04/06 06:00 CRDT- 2021/09/17 08:49 PHST- 2021/09/01 00:00 [revised] PHST- 2020/11/11 00:00 [received] PHST- 2021/09/06 00:00 [accepted] PHST- 2021/09/18 06:00 [pubmed] PHST- 2022/04/06 06:00 [medline] PHST- 2021/09/17 08:49 [entrez] AID - 10.1002/ajhb.23682 [doi] PST - ppublish SO - Am J Hum Biol. 2022 Apr;34(4):e23682. doi: 10.1002/ajhb.23682. Epub 2021 Sep 17. PMID- 35356467 OWN - NLM STAT- MEDLINE DCOM- 20230109 LR - 20230111 IS - 2167-8359 (Print) IS - 2167-8359 (Electronic) IS - 2167-8359 (Linking) VI - 10 DP - 2022 TI - Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study. PG - e12784 LID - 10.7717/peerj.12784 [doi] LID - e12784 AB - Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest. CI - ©2022 Arizmendi Cárdenas et al. FAU - Arizmendi Cárdenas, Yami Ommar AU - Arizmendi Cárdenas YO AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, Lausanne, Switzerland. FAU - Neuenschwander, Samuel AU - Neuenschwander S AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. AD - Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland. FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, Lausanne, Switzerland. LA - eng SI - Dryad/10.5061/dryad.mkkwh711w PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220324 PL - United States TA - PeerJ JT - PeerJ JID - 101603425 RN - 0 (DNA, Viral) RN - 0 (DNA, Ancient) MH - Humans MH - *DNA, Viral/genetics MH - DNA, Ancient MH - Sequence Analysis, DNA/methods MH - Metagenomics/methods MH - Benchmarking MH - High-Throughput Nucleotide Sequencing/methods MH - *Viruses/genetics PMC - PMC8958974 OTO - NOTNLM OT - Ancient DNA OT - Classifiers OT - Epidemiology OT - Genomics OT - Paleomicrobiology OT - Precision OT - Sensitivity OT - Simulations OT - Taxonomic binning OT - Virome COIS- The authors declare there are no competing interests. EDAT- 2022/04/01 06:00 MHDA- 2022/04/01 06:01 PMCR- 2022/03/24 CRDT- 2022/03/31 05:32 PHST- 2021/04/12 00:00 [received] PHST- 2021/12/21 00:00 [accepted] PHST- 2022/03/31 05:32 [entrez] PHST- 2022/04/01 06:00 [pubmed] PHST- 2022/04/01 06:01 [medline] PHST- 2022/03/24 00:00 [pmc-release] AID - 12784 [pii] AID - 10.7717/peerj.12784 [doi] PST - epublish SO - PeerJ. 2022 Mar 24;10:e12784. doi: 10.7717/peerj.12784. eCollection 2022. PMID- 35456371 OWN - NLM STAT- MEDLINE DCOM- 20220426 LR - 20221207 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 13 IP - 4 DP - 2022 Mar 23 TI - Maternal Lineages of Gepids from Transylvania. LID - 10.3390/genes13040563 [doi] LID - 563 AB - According to the written historical sources, the Gepids were a Germanic tribe that settled in the Carpathian Basin during the Migration Period. They were allies of the Huns, and an independent Gepid Kingdom arose after the collapse of the Hun Empire. In this period, the Carpathian Basin was characterized by so-called row-grave cemeteries. Due to the scarcity of historical and archaeological data, we have a poor knowledge of the origin and composition of these barbarian populations, and this is still a subject of debate. To better understand the genetic legacy of migration period societies, we obtained 46 full mitogenome sequences from three Gepid cemeteries located in Transylvania, Romania. The studied samples represent the Classical Gepidic period and illustrate the genetic make-up of this group from the late 5th and early 6th centuries AD, which is characterized by cultural markers associated with the Gepid culture in Transylvania. The genetic structure of the Gepid people is explored for the first time, providing new insights into the genetic makeup of this archaic group. The retrieved genetic data showed mainly the presence of Northwestern European mitochondrial ancient lineages in the Gepid group and all population genetic analyses reiterated the same genetic structure, showing that early ancient mitogenomes from Europe were the major contributors to the Gepid maternal genetic pool. FAU - Gînguță, Alexandra AU - Gînguță A AUID- ORCID: 0000-0001-8443-8015 AD - Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006 Cluj-Napoca, Romania. AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. FAU - Kovács, Bence AU - Kovács B AUID- ORCID: 0000-0002-4915-1462 AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. FAU - Tihanyi, Balázs AU - Tihanyi B AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. AD - Department of Biological Anthropology, University of Szeged, H-6726 Szeged, Hungary. FAU - Maár, Kitti AU - Maár K AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. FAU - Schütz, Oszkár AU - Schütz O AUID- ORCID: 0000-0001-5521-3044 AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. FAU - Maróti, Zoltán AU - Maróti Z AUID- ORCID: 0000-0002-0515-117X AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. AD - Department of Pediatrics and Pediatric Health Center, University of Szeged, H-6725 Szeged, Hungary. FAU - Varga, Gergely I B AU - Varga GIB AUID- ORCID: 0000-0001-9073-5788 AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. FAU - Kiss, Attila P AU - Kiss AP AD - Faculty of Humanities and Social Sciences, Institute of Archaeology, Pázmány Péter Catholic University, H-1088 Budapest, Hungary. FAU - Stanciu, Ioan AU - Stanciu I AD - Institute of Archaeology and Art History, Romanian Academy, Cluj-Napoca Branch, 400084 Cluj-Napoca, Romania. FAU - Török, Tibor AU - Török T AUID- ORCID: 0000-0002-2128-1126 AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. FAU - Neparáczki, Endre AU - Neparáczki E AUID- ORCID: 0000-0003-3466-0368 AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220323 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 SB - IM MH - Archaeology MH - Cemeteries MH - *Gene Pool MH - *Genetics, Population MH - Humans MH - White People PMC - PMC9032604 OTO - NOTNLM OT - Gepids OT - NGS OT - ancient DNA OT - migration period OT - mitogenome OT - population genetics COIS- The authors declare no conflict of interest. EDAT- 2022/04/24 06:00 MHDA- 2022/04/27 06:00 PMCR- 2022/03/23 CRDT- 2022/04/23 01:09 PHST- 2022/02/21 00:00 [received] PHST- 2022/03/16 00:00 [revised] PHST- 2022/03/21 00:00 [accepted] PHST- 2022/04/23 01:09 [entrez] PHST- 2022/04/24 06:00 [pubmed] PHST- 2022/04/27 06:00 [medline] PHST- 2022/03/23 00:00 [pmc-release] AID - genes13040563 [pii] AID - genes-13-00563 [pii] AID - 10.3390/genes13040563 [doi] PST - epublish SO - Genes (Basel). 2022 Mar 23;13(4):563. doi: 10.3390/genes13040563. PMID- 35318319 OWN - NLM STAT- MEDLINE DCOM- 20220412 LR - 20221022 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 13 IP - 1 DP - 2022 Mar 22 TI - South-to-north migration preceded the advent of intensive farming in the Maya region. PG - 1530 LID - 10.1038/s41467-022-29158-y [doi] LID - 1530 AB - The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region. CI - © 2022. The Author(s). FAU - Kennett, Douglas J AU - Kennett DJ AUID- ORCID: 0000-0001-6144-7365 AD - Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA. kennett@anth.ucsb.edu. FAU - Lipson, Mark AU - Lipson M AUID- ORCID: 0000-0001-5346-9329 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. mlipson@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. mlipson@genetics.med.harvard.edu. FAU - Prufer, Keith M AU - Prufer KM AUID- ORCID: 0000-0003-3173-1546 AD - Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA. kmp@unm.edu. AD - Center for Stable Isotopes, University of New Mexico, Albuquerque, NM, 87106, USA. kmp@unm.edu. FAU - Mora-Marín, David AU - Mora-Marín D AUID- ORCID: 0000-0001-9945-2389 AD - Department of Linguistics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA. FAU - George, Richard J AU - George RJ AD - Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - Robinson, Mark AU - Robinson M AD - Department of Archaeology, Exeter University, Exeter, UK. FAU - Trask, Willa R AU - Trask WR AD - Central Identification Laboratory, Defense POW/ MIA Accounting Agency, Joint Base Pearl Harbor-Hickam, Honolulu, HI, 96853, USA. FAU - Edgar, Heather H J AU - Edgar HHJ AUID- ORCID: 0000-0003-4093-8143 AD - Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA. FAU - Hill, Ethan C AU - Hill EC AD - Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA. FAU - Ray, Erin E AU - Ray EE AUID- ORCID: 0000-0002-1305-3780 AD - Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA. FAU - Lynch, Paige AU - Lynch P AD - Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA. FAU - Moes, Emily AU - Moes E AUID- ORCID: 0000-0002-0037-7604 AD - Department Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA. FAU - O'Donnell, Lexi AU - O'Donnell L AUID- ORCID: 0000-0003-4514-772X AD - Department of Sociology and Anthropology, University of Mississippi, University, Oxford, MS, 38677, USA. FAU - Harper, Thomas K AU - Harper TK AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA. FAU - Kate, Emily J AU - Kate EJ AUID- ORCID: 0000-0002-5490-4684 AD - Vienna Institute for Archaeological Science, University of Vienna, Vienna, Austria. FAU - Ramos, Josue AU - Ramos J AD - Belize Institute of Archaeology, Belmopan, Belize. FAU - Morris, John AU - Morris J AD - Belize Institute of Archaeology, Belmopan, Belize. FAU - Gutierrez, Said M AU - Gutierrez SM AUID- ORCID: 0000-0002-7343-5908 AD - Ya'axché Conservation Trust, Punta Gorda Town, Belize. FAU - Ryan, Timothy M AU - Ryan TM AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA. FAU - Culleton, Brendan J AU - Culleton BJ AD - Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, 16802, USA. FAU - Awe, Jaime J AU - Awe JJ AD - Belize Institute of Archaeology, Belmopan, Belize. AD - Department of Anthropology, Northern Arizona University, Flagstaff, AZ, 86001, USA. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R01 HG012287/HG/NHGRI NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20220322 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) SB - IM MH - *Agriculture MH - Central America MH - Colombia MH - *DNA, Ancient MH - Forests MH - Humans PMC - PMC8940966 COIS- The authors declare no competing interests. EDAT- 2022/03/24 06:00 MHDA- 2022/04/13 06:00 PMCR- 2022/03/22 CRDT- 2022/03/23 05:46 PHST- 2021/06/29 00:00 [received] PHST- 2022/02/25 00:00 [accepted] PHST- 2022/03/23 05:46 [entrez] PHST- 2022/03/24 06:00 [pubmed] PHST- 2022/04/13 06:00 [medline] PHST- 2022/03/22 00:00 [pmc-release] AID - 10.1038/s41467-022-29158-y [pii] AID - 29158 [pii] AID - 10.1038/s41467-022-29158-y [doi] PST - epublish SO - Nat Commun. 2022 Mar 22;13(1):1530. doi: 10.1038/s41467-022-29158-y. PMID- 35342764 OWN - NLM STAT- MEDLINE DCOM- 20220408 LR - 20220531 IS - 2314-6141 (Electronic) IS - 2314-6133 (Print) VI - 2022 DP - 2022 TI - Mitochondrial Haplogroup Classification of Ancient DNA Samples Using Haplotracker. PG - 5344418 LID - 10.1155/2022/5344418 [doi] LID - 5344418 AB - Mitochondrial DNA haplogroup classification is used to study maternal lineage of ancient human populations. The haplogrouping of ancient DNA is not easy because the DNA is usually found in small pieces in limited quantities. We have developed Haplotracker, a straightforward and efficient high-resolution haplogroup classification tool optimized specifically for ancient DNA samples. Haplotracker offers a user-friendly input interface for multiple mitochondrial DNA sequence fragments in a sample. It provides accurate haplogroup classification with full-length mitochondrial genome sequences and provides high-resolution haplogroup predictions for some fragmented control region sequences using a novel algorithm built on Phylotree mtDNA Build 17 (Phylotree) and our haplotype database (n = 118,869). Its performance for accuracy was demonstrated to be high through haplogroup classification using 8,216 Phylotree full-length and control region mitochondrial DNA sequences compared with HaploGrep 2, one of the most accurate current haplogroup classifiers. Haplotracker provides a novel haplogroup tracking solution for fragmented sequences to track subhaplogroups or verify the haplogroups efficiently. Using Haplotracker, we classified mitochondrial haplogroups to the final subhaplogroup level in nine ancient DNA samples extracted from human skeletal remains found in 2,000-year-old elite Xiongnu cemetery in Northeast Mongolia. Haplotracker can be freely accessed at https://haplotracker.cau.ac.kr. CI - Copyright © 2022 Kijeong Kim et al. FAU - Kim, Kijeong AU - Kim K AUID- ORCID: 0000-0002-5132-1774 AD - Institute of Gene and Genome Research, College of Medicine, Chung-Ang University, Seoul 06974, Republic of Korea. FAU - Kim, Dong-Han AU - Kim DH AD - Faculty of Science, University of Sydney, Sydney NSW 2016, Australia. FAU - Kim, Kyung-Yong AU - Kim KY AUID- ORCID: 0000-0002-1904-9061 AD - Institute of Gene and Genome Research, College of Medicine, Chung-Ang University, Seoul 06974, Republic of Korea. LA - eng PT - Journal Article DEP - 20220318 PL - United States TA - Biomed Res Int JT - BioMed research international JID - 101600173 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - *Genome, Mitochondrial/genetics MH - Haplotypes/genetics MH - Humans MH - Mitochondria/genetics PMC - PMC8956381 COIS- The authors have no conflict of interest to declare. EDAT- 2022/03/29 06:00 MHDA- 2022/04/09 06:00 PMCR- 2022/03/18 CRDT- 2022/03/28 05:31 PHST- 2021/09/10 00:00 [received] PHST- 2022/02/17 00:00 [revised] PHST- 2022/02/26 00:00 [accepted] PHST- 2022/03/28 05:31 [entrez] PHST- 2022/03/29 06:00 [pubmed] PHST- 2022/04/09 06:00 [medline] PHST- 2022/03/18 00:00 [pmc-release] AID - 10.1155/2022/5344418 [doi] PST - epublish SO - Biomed Res Int. 2022 Mar 18;2022:5344418. doi: 10.1155/2022/5344418. eCollection 2022. PMID- 35256608 OWN - NLM STAT- MEDLINE DCOM- 20220413 LR - 20240824 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 13 IP - 1 DP - 2022 Mar 7 TI - Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. PG - 1195 LID - 10.1038/s41467-022-28562-8 [doi] LID - 1195 AB - Previous ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal access to marine resources- a scenario incompatible with TB transmission directly from infected pinnipeds or their tissues. In this study, we investigate the causative agent of TB in ten pre-colonial, non-coastal individuals from South America. We reconstruct M. pinnipedii genomes (10- to 15-fold mean coverage) from three contemporaneous individuals from inland Peru and Colombia, demonstrating the widespread dissemination of M. pinnipedii beyond the coast, either through human-to-human and/or animal-mediated routes. Overall, our study suggests that TB transmission in the pre-colonial era Americas involved a more complex transmission pathway than simple pinniped-to-human transfer. CI - © 2022. The Author(s). FAU - Vågene, Åshild J AU - Vågene ÅJ AUID- ORCID: 0000-0002-7478-8297 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. ashild.vagene@sund.ku.dk. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. ashild.vagene@sund.ku.dk. AD - Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. ashild.vagene@sund.ku.dk. FAU - Honap, Tanvi P AU - Honap TP AUID- ORCID: 0000-0001-5271-9162 AD - School of Life Sciences, Arizona State University, Tempe, AZ, USA. thonap@asu.edu. AD - Department of Anthropology, University of Oklahoma, Norman, OK, USA. thonap@asu.edu. AD - Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA. thonap@asu.edu. FAU - Harkins, Kelly M AU - Harkins KM AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. FAU - Rosenberg, Michael S AU - Rosenberg MS AUID- ORCID: 0000-0001-7882-2467 AD - School of Life Sciences, Arizona State University, Tempe, AZ, USA. AD - Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA. FAU - Giffin, Karen AU - Giffin K AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Cárdenas-Arroyo, Felipe AU - Cárdenas-Arroyo F AD - Colombian Institute of Anthropology and History (ICANH), Bogotá, Colombia. FAU - Leguizamón, Laura Paloma AU - Leguizamón LP AUID- ORCID: 0000-0002-6101-5420 AD - Colombian Institute of Anthropology and History (ICANH), Bogotá, Colombia. FAU - Arnett, Judith AU - Arnett J AUID- ORCID: 0000-0002-1120-256X AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. AD - University of the Andes, School of Medicine, Bogotá, Colombia. FAU - Buikstra, Jane E AU - Buikstra JE AUID- ORCID: 0000-0003-0206-0165 AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. FAU - Herbig, Alexander AU - Herbig A AUID- ORCID: 0000-0003-1176-1166 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. krause@eva.mpg.de. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. krause@eva.mpg.de. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. krause@eva.mpg.de. FAU - Stone, Anne C AU - Stone AC AUID- ORCID: 0000-0001-8021-8314 AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. acstone@asu.edu. AD - Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA. acstone@asu.edu. AD - Institute of Human Origins, Arizona State University, Tempe, AZ, USA. acstone@asu.edu. FAU - Bos, Kirsten I AU - Bos KI AUID- ORCID: 0000-0003-2937-3006 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. kirsten_bos@eva.mpg.de. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. kirsten_bos@eva.mpg.de. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. kirsten_bos@eva.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20220307 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *Caniformia/genetics MH - DNA, Ancient MH - Humans MH - *Mycobacterium/genetics MH - *Mycobacterium tuberculosis/genetics MH - Racial Groups MH - South America/epidemiology MH - *Tuberculosis/epidemiology/microbiology PMC - PMC8901693 COIS- The authors declare no competing interests. EDAT- 2022/03/09 06:00 MHDA- 2022/04/14 06:00 PMCR- 2022/03/07 CRDT- 2022/03/08 05:37 PHST- 2019/06/10 00:00 [received] PHST- 2022/01/25 00:00 [accepted] PHST- 2022/03/08 05:37 [entrez] PHST- 2022/03/09 06:00 [pubmed] PHST- 2022/04/14 06:00 [medline] PHST- 2022/03/07 00:00 [pmc-release] AID - 10.1038/s41467-022-28562-8 [pii] AID - 28562 [pii] AID - 10.1038/s41467-022-28562-8 [doi] PST - epublish SO - Nat Commun. 2022 Mar 7;13(1):1195. doi: 10.1038/s41467-022-28562-8. PMID- 35526849 OWN - NLM STAT- MEDLINE DCOM- 20220510 LR - 20240825 IS - 1608-3040 (Electronic) IS - 0006-2979 (Print) IS - 0006-2979 (Linking) VI - 87 IP - 3 DP - 2022 Mar TI - Genomics of Ancient Pathogens: First Advances and Prospects. PG - 242-258 LID - 10.1134/S0006297922030051 [doi] AB - Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today's world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history. FAU - Malyarchuk, Alexandra B AU - Malyarchuk AB AD - Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. a_malyarchuk98@mail.ru. FAU - Andreeva, Tatiana V AU - Andreeva TV AD - Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. AD - Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. FAU - Kuznetsova, Irina L AU - Kuznetsova IL AD - Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. AD - Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia. FAU - Kunizheva, Svetlana S AU - Kunizheva SS AD - Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. AD - Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia. FAU - Protasova, Maria S AU - Protasova MS AD - Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. FAU - Uralsky, Lev I AU - Uralsky LI AD - Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. AD - Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia. FAU - Tyazhelova, Tatiana V AU - Tyazhelova TV AD - Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. FAU - Gusev, Fedor E AU - Gusev FE AD - Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. FAU - Manakhov, Andrey D AU - Manakhov AD AD - Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. AD - Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia. FAU - Rogaev, Evgeny I AU - Rogaev EI AD - Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. rogaev@vigg.ru. AD - Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia. AD - Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA. LA - eng PT - Historical Article PT - Journal Article PT - Review PL - United States TA - Biochemistry (Mosc) JT - Biochemistry. Biokhimiia JID - 0376536 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient MH - *Genomics/methods MH - History, Ancient MH - Humans MH - Mycobacterium leprae/genetics MH - Paleontology MH - *Yersinia pestis/genetics PMC - PMC8916790 OTO - NOTNLM OT - ancient DNA OT - cholera OT - human populations OT - leprosy OT - paleogenomics OT - paleopathology OT - pathogen OT - plague OT - smallpox OT - syphilis OT - tuberculosis COIS- Authors declare no conflicts of interests. This article does not contain description of studies with the involvement of humans or animal subjects. EDAT- 2022/05/09 06:00 MHDA- 2022/05/11 06:00 PMCR- 2022/03/11 CRDT- 2022/05/08 20:42 PHST- 2022/05/08 20:42 [entrez] PHST- 2022/05/09 06:00 [pubmed] PHST- 2022/05/11 06:00 [medline] PHST- 2022/03/11 00:00 [pmc-release] AID - BCM87030258 [pii] AID - 2302 [pii] AID - 10.1134/S0006297922030051 [doi] PST - ppublish SO - Biochemistry (Mosc). 2022 Mar;87(3):242-258. doi: 10.1134/S0006297922030051. PMID- 35197631 OWN - NLM STAT- MEDLINE DCOM- 20220415 LR - 20221207 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 603 IP - 7900 DP - 2022 Mar TI - Ancient DNA and deep population structure in sub-Saharan African foragers. PG - 290-296 LID - 10.1038/s41586-022-04430-9 [doi] AB - Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa(1-4). Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations(3,5). Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch. CI - © 2022. The Author(s). FAU - Lipson, Mark AU - Lipson M AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. mlipson@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. mlipson@genetics.med.harvard.edu. FAU - Sawchuk, Elizabeth A AU - Sawchuk EA AUID- ORCID: 0000-0003-4398-2174 AD - Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada. esawchuk@ualberta.ca. AD - Department of Anthropology, Stony Brook University, Stony Brook, NY, USA. esawchuk@ualberta.ca. FAU - Thompson, Jessica C AU - Thompson JC AUID- ORCID: 0000-0003-1627-4949 AD - Department of Anthropology and Peabody Museum of Natural History, Yale University, New Haven, CT, USA. jessica.thompson@yale.edu. AD - Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. jessica.thompson@yale.edu. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA. FAU - Tryon, Christian A AU - Tryon CA AUID- ORCID: 0000-0002-2354-3273 AD - Department of Anthropology, University of Connecticut, Storrs, CT, USA. AD - Department of Anthropology, Harvard University, Cambridge, MA, USA. AD - Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA. FAU - Ranhorn, Kathryn L AU - Ranhorn KL AUID- ORCID: 0000-0002-9048-5966 AD - Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. FAU - de Luna, Kathryn M AU - de Luna KM AUID- ORCID: 0000-0002-3496-2115 AD - Department of History, Georgetown University, Washington, DC, USA. FAU - Sirak, Kendra A AU - Sirak KA AUID- ORCID: 0000-0003-2347-3479 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. FAU - Olalde, Iñigo AU - Olalde I AUID- ORCID: 0000-0002-2660-6807 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain. FAU - Ambrose, Stanley H AU - Ambrose SH AUID- ORCID: 0000-0002-8785-0512 AD - Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA. FAU - Arthur, John W AU - Arthur JW AUID- ORCID: 0000-0002-4968-5843 AD - Department of Anthropology, University of South Florida,, St Petersburg, FL, USA. FAU - Arthur, Kathryn J W AU - Arthur KJW AD - Department of Anthropology, University of South Florida,, St Petersburg, FL, USA. FAU - Ayodo, George AU - Ayodo G AD - School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya. FAU - Bertacchi, Alex AU - Bertacchi A AUID- ORCID: 0000-0002-2269-2437 AD - Department of Anthropology and Peabody Museum of Natural History, Yale University, New Haven, CT, USA. FAU - Cerezo-Román, Jessica I AU - Cerezo-Román JI AUID- ORCID: 0000-0002-7752-8079 AD - Department of Anthropology, University of Oklahoma, Norman, OK, USA. FAU - Culleton, Brendan J AU - Culleton BJ AD - Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA. FAU - Curtis, Matthew C AU - Curtis MC AUID- ORCID: 0000-0003-4692-3241 AD - Anthropology Program, California State University-Channel Islands, Camarillo, CA, USA. FAU - Davis, Jacob AU - Davis J AD - Independent researcher, New Haven, CT, USA. FAU - Gidna, Agness O AU - Gidna AO AD - National Museums of Tanzania, Dar es Salaam, Tanzania. FAU - Hanson, Annalys AU - Hanson A AD - Sol Solutions LLC, Scottsdale, AZ, USA. FAU - Kaliba, Potiphar AU - Kaliba P AD - Malawi Department of Museums and Monuments, Lilongwe, Malawi. FAU - Katongo, Maggie AU - Katongo M AUID- ORCID: 0000-0002-5286-1350 AD - Department of Anthropology, Rice University, Houston, TX, USA. AD - Livingstone Museum, Livingstone, Zambia. FAU - Kwekason, Amandus AU - Kwekason A AD - National Museums of Tanzania, Dar es Salaam, Tanzania. FAU - Laird, Myra F AU - Laird MF AUID- ORCID: 0000-0002-8636-0407 AD - Department of Integrative Anatomical Sciences, University of Southern California, Los Angeles, CA, USA. FAU - Lewis, Jason AU - Lewis J AUID- ORCID: 0000-0001-8325-1128 AD - Department of Anthropology, Stony Brook University, Stony Brook, NY, USA. FAU - Mabulla, Audax Z P AU - Mabulla AZP AD - Department of Archaeology and Heritage Studies, University of Dar es Salaam, Dar es Salaam, Tanzania. FAU - Mapemba, Fredrick AU - Mapemba F AD - Malawi Department of Museums and Monuments, Lilongwe, Malawi. FAU - Morris, Alan AU - Morris A AD - Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - Mudenda, George AU - Mudenda G AD - Livingstone Museum, Livingstone, Zambia. FAU - Mwafulirwa, Raphael AU - Mwafulirwa R AD - Mzuzu University, Mzuzu, Malawi. FAU - Mwangomba, Daudi AU - Mwangomba D AD - University of Malawi, Zomba, Malawi. FAU - Ndiema, Emmanuel AU - Ndiema E AD - Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya. FAU - Ogola, Christine AU - Ogola C AD - Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya. FAU - Schilt, Flora AU - Schilt F AUID- ORCID: 0000-0002-2144-3017 AD - Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), FCHS, Universidade do Algarve, Faro, Portugal. FAU - Willoughby, Pamela R AU - Willoughby PR AD - Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada. FAU - Wright, David K AU - Wright DK AUID- ORCID: 0000-0003-1704-0423 AD - Department of Archaeology, Conservation and History, University of Oslo, Oslo, Norway. AD - State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xian, China. FAU - Zipkin, Andrew AU - Zipkin A AUID- ORCID: 0000-0002-3813-8051 AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences - HEAS, University of Vienna, Vienna, Austria. FAU - Kennett, Douglas J AU - Kennett DJ AUID- ORCID: 0000-0001-6144-7365 AD - Department of Anthropology, University of California, Santa Barbara, CA, USA. FAU - Manthi, Fredrick Kyalo AU - Manthi FK AD - Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Patterson, Nick AU - Patterson N AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. FAU - Prendergast, Mary E AU - Prendergast ME AUID- ORCID: 0000-0003-0275-6795 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. mary@rice.edu. AD - Department of Anthropology, Rice University, Houston, TX, USA. mary@rice.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R01 HG012287/HG/NHGRI NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20220223 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Africa South of the Sahara MH - Archaeology MH - *Black People/genetics/history MH - *DNA, Ancient/analysis MH - Gene Flow/genetics MH - *Genetics, Population MH - Genome, Human/genetics MH - History, Ancient MH - Humans PMC - PMC8907066 COIS- The authors declare no competing interests. EDAT- 2022/02/25 06:00 MHDA- 2022/04/16 06:00 PMCR- 2022/02/23 CRDT- 2022/02/24 05:40 PHST- 2021/06/22 00:00 [received] PHST- 2022/01/14 00:00 [accepted] PHST- 2022/02/25 06:00 [pubmed] PHST- 2022/04/16 06:00 [medline] PHST- 2022/02/24 05:40 [entrez] PHST- 2022/02/23 00:00 [pmc-release] AID - 10.1038/s41586-022-04430-9 [pii] AID - 4430 [pii] AID - 10.1038/s41586-022-04430-9 [doi] PST - ppublish SO - Nature. 2022 Mar;603(7900):290-296. doi: 10.1038/s41586-022-04430-9. Epub 2022 Feb 23. PMID- 34731404 OWN - NLM STAT- MEDLINE DCOM- 20220323 LR - 20220323 IS - 1896-1851 (Electronic) IS - 1230-2821 (Linking) VI - 67 IP - 1 DP - 2022 Mar TI - Ancient DNA of Metagonimus yokogawai Recovered from Joseon Period Human Remains Newly Discovered at Goryeong County in South Korea. PG - 539-545 LID - 10.1007/s11686-021-00487-0 [doi] AB - PURPOSE: Metagonimiasis, commonly seen in East Asian countries, is a parasitic disorder caused by definitive hosts' ingestion of undercooked freshwater fishes. Recently, genetic analysis has proved 28S rRNA and cytochrome c oxidase subunit I (COI) mtDNA gene to be a successful marker differentiating species of the genus Metagonimus. In the present study, using specimens from the newly discovered Joseon Dynasty human remains of Goryeong, we obtained updated genetic data on genus Metagonimus, which was also prevalent during the Joseon period. METHODS: The ancient DNA (aDNA) was retrieved from the coprolite sample of the seventeenth century, half-mummified individual discovered at Goryeong Country, South Korea. Cloning and sequencing were performed on PCR-amplified amplicons for M. yokogawai 28S rRNA and COI mtDNA gene. The consensus sequences were used for species identification and phylogenetic analysis using NCBI/BLAST and MEGA X software. RESULTS: Based on the COI mtDNA gene region, the Goryeong sequence was confirmed as belonging to M. yokogawai, as it was shown to form a separate cluster with other M. yokogawai taxa that are distinct also from M. takahashii and M. miyatai. CONCLUSION: In a series of our genetic analyses on genus Metagonimus using samples retrieved from Joseon-period cases, aDNA sequences of genus Metagonimus revealed in South Korea thus far are those of M. yokogawai, but not of M. miyatai or M. takahashii yet. CI - © 2021. The Author(s) under exclusive licence to Witold Stefański Institute of Parasitology, Polish Academy of Sciences. FAU - Oh, Chang Seok AU - Oh CS AD - Department of Mortuary Science, College of Bio-Convergence, Eulji University, 553, Sanseongdae-ro, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13135, South Korea. FAU - Hong, Jong Ha AU - Hong JH AD - Institute of Korean Archaeology and Ancient History, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, South Korea. FAU - Chai, Jong Yil AU - Chai JY AD - Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul, 07649, South Korea. AD - Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, 103, Daehak-ro, Chongno-gu, Seoul, 03080, South Korea. FAU - Song, Mi Kyung AU - Song MK AD - Department of Fashion Design and Marketing, Seoul Women's University, 621, Hwarang-ro, Nowon-gu, Seoul, 01797, South Korea. FAU - Jang, Ho-Jin AU - Jang HJ AD - Gaon Research Institute of Cultural Properties, 1311, Daegaya-ro, Daegaya-eup, Goryeong-gun, Gyeongsangbuk-do, 40141, South Korea. FAU - Seo, Min AU - Seo M AD - Department of Parasitology, Dankook University College of Medicine, 119, Dandae-ro, Dongnam-gu, Cheonan-si, Chungcheongnam-do, 31116, South Korea. bbbenji@naver.com. FAU - Shin, Dong Hoon AU - Shin DH AD - Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, 103, Daehak-ro, Chongno-gu, Seoul, 03080, South Korea. cuteminjae@gmail.com. LA - eng GR - 2019S1A5C2A01083578/ministry of education/ GR - 2020R1A2C1010708/ministry of science and ict (kr)/ PT - Journal Article DEP - 20211103 PL - Switzerland TA - Acta Parasitol JT - Acta parasitologica JID - 9301947 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Body Remains MH - DNA, Ancient MH - *Heterophyidae/genetics MH - Humans MH - Phylogeny MH - Republic of Korea MH - *Trematode Infections/parasitology OTO - NOTNLM OT - Ancient DNA OT - Cytochrome c oxidase subunit I OT - Goryeong OT - Metagonimus yokogawai OT - South Korea EDAT- 2021/11/04 06:00 MHDA- 2022/03/24 06:00 CRDT- 2021/11/03 17:29 PHST- 2021/06/18 00:00 [received] PHST- 2021/10/18 00:00 [accepted] PHST- 2021/11/04 06:00 [pubmed] PHST- 2022/03/24 06:00 [medline] PHST- 2021/11/03 17:29 [entrez] AID - 10.1007/s11686-021-00487-0 [pii] AID - 10.1007/s11686-021-00487-0 [doi] PST - ppublish SO - Acta Parasitol. 2022 Mar;67(1):539-545. doi: 10.1007/s11686-021-00487-0. Epub 2021 Nov 3. PMID- 35131896 OWN - NLM STAT- MEDLINE DCOM- 20220314 LR - 20221005 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 119 IP - 8 DP - 2022 Feb 22 TI - Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney. LID - 10.1073/pnas.2108001119 [doi] LID - e2108001119 AB - Orkney was a major cultural center during the Neolithic, 3800 to 2500 BC. Farming flourished, permanent stone settlements and chambered tombs were constructed, and long-range contacts were sustained. From ∼3200 BC, the number, density, and extravagance of settlements increased, and new ceremonial monuments and ceramic styles, possibly originating in Orkney, spread across Britain and Ireland. By ∼2800 BC, this phenomenon was waning, although Neolithic traditions persisted to at least 2500 BC. Unlike elsewhere in Britain, there is little material evidence to suggest a Beaker presence, suggesting that Orkney may have developed along an insular trajectory during the second millennium BC. We tested this by comparing new genomic evidence from 22 Bronze Age and 3 Iron Age burials in northwest Orkney with Neolithic burials from across the archipelago. We identified signals of inward migration on a scale unsuspected from the archaeological record: As elsewhere in Bronze Age Britain, much of the population displayed significant genome-wide ancestry deriving ultimately from the Pontic-Caspian Steppe. However, uniquely in northern and central Europe, most of the male lineages were inherited from the local Neolithic. This suggests that some male descendants of Neolithic Orkney may have remained distinct well into the Bronze Age, although there are signs that this had dwindled by the Iron Age. Furthermore, although the majority of mitochondrial DNA lineages evidently arrived afresh with the Bronze Age, we also find evidence for continuity in the female line of descent from Mesolithic Britain into the Bronze Age and even to the present day. CI - Copyright © 2022 the Author(s). Published by PNAS. FAU - Dulias, Katharina AU - Dulias K AUID- ORCID: 0000-0002-3938-6663 AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. AD - Department of Archaeology, University of York, York YO10 5DD, United Kingdom. AD - Institut für Geosysteme und Bioindikation, Technische Universität Braunschweig 38106 Braunschweig, Germany. FAU - Foody, M George B AU - Foody MGB AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. FAU - Justeau, Pierre AU - Justeau P AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. FAU - Silva, Marina AU - Silva M AUID- ORCID: 0000-0002-3756-0920 AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. FAU - Martiniano, Rui AU - Martiniano R AUID- ORCID: 0000-0003-0216-778X AD - School of Biological and Environmental Sciences, Faculty of Science, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom. FAU - Oteo-García, Gonzalo AU - Oteo-García G AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. FAU - Fichera, Alessandro AU - Fichera A AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. FAU - Rodrigues, Simão AU - Rodrigues S AUID- ORCID: 0000-0003-2323-2069 AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. FAU - Gandini, Francesca AU - Gandini F AUID- ORCID: 0000-0001-8930-8295 AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. FAU - Meynert, Alison AU - Meynert A AUID- ORCID: 0000-0001-5839-1751 AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom. FAU - Donnelly, Kevin AU - Donnelly K AUID- ORCID: 0000-0001-7633-9113 AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom. FAU - Aitman, Timothy J AU - Aitman TJ AUID- ORCID: 0000-0002-7875-4502 AD - Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom. CN - Scottish Genomes Partnership FAU - Chamberlain, Andrew AU - Chamberlain A AUID- ORCID: 0000-0003-1517-6538 AD - Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom. FAU - Lelong, Olivia AU - Lelong O AD - Department of Research, Business and Innovation, University of West England, Bristol, BS16 1QY, United Kingdom. FAU - Kozikowski, George AU - Kozikowski G AD - Private address, Broadford, Isle of Skye IV49 9BB, United Kingdom. FAU - Powlesland, Dominic AU - Powlesland D AUID- ORCID: 0000-0003-0935-0739 AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. AD - The Landscape Research Centre Ltd, Malton YO17 8SL, United Kingdom. FAU - Waddington, Clive AU - Waddington C AUID- ORCID: 0000-0002-6318-5650 AD - Archaeological Research Services Ltd, Bakewell DE45 1HB, United Kingdom. FAU - Mattiangeli, Valeria AU - Mattiangeli V AUID- ORCID: 0000-0001-9785-1714 AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 VF25, Ireland. FAU - Bradley, Daniel G AU - Bradley DG AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 VF25, Ireland. FAU - Bryk, Jaroslaw AU - Bryk J AUID- ORCID: 0000-0002-2791-9709 AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. FAU - Soares, Pedro AU - Soares P AUID- ORCID: 0000-0002-2807-690X AD - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho 4710-057 Braga, Portugal. FAU - Wilson, James F AU - Wilson JF AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom. AD - Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom. FAU - Wilson, Graeme AU - Wilson G AUID- ORCID: 0000-0002-7934-3692 AD - Environment and Archaeology Services, Midbea Schoolhouse, Westray, Orkney KW17 2DP, United Kingdom. FAU - Moore, Hazel AU - Moore H AUID- ORCID: 0000-0002-6645-7594 AD - Environment and Archaeology Services, Midbea Schoolhouse, Westray, Orkney KW17 2DP, United Kingdom. FAU - Pala, Maria AU - Pala M AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom. FAU - Edwards, Ceiridwen J AU - Edwards CJ AUID- ORCID: 0000-0001-9126-1377 AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom; c.j.edwards@hud.ac.uk m.b.richards@hud.ac.uk. FAU - Richards, Martin B AU - Richards MB AUID- ORCID: 0000-0003-3118-0967 AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom; c.j.edwards@hud.ac.uk m.b.richards@hud.ac.uk. LA - eng GR - MC_PC_15080/MRC_/Medical Research Council/United Kingdom GR - G0901467/MRC_/Medical Research Council/United Kingdom GR - MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom GR - WT_/Wellcome Trust/United Kingdom GR - G0802729/MRC_/Medical Research Council/United Kingdom GR - G0400116/MRC_/Medical Research Council/United Kingdom GR - 205072/Z/16/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/*genetics MH - England MH - Europe MH - Female MH - Fossils MH - Gene Pool MH - Genome, Human/genetics MH - Genomics MH - Haplotypes MH - History, Ancient MH - History, Medieval MH - Human Migration/*history MH - Humans MH - Ireland MH - Male MH - Paternal Inheritance/*genetics MH - Scotland PMC - PMC8872714 OTO - NOTNLM OT - Bronze Age OT - Neolithic OT - Orkney OT - ancient DNA OT - genome-wide COIS- The authors declare no competing interest. FIR - Aitman, Tim J IR - Aitman TJ FIR - Miedzybrodzka, Zosia IR - Miedzybrodzka Z FIR - Williams, Nicola IR - Williams N FIR - Meynert, Alison IR - Meynert A FIR - Biankin, Andrew V IR - Biankin AV FIR - Santoyo-Lopez, Javier IR - Santoyo-Lopez J EDAT- 2022/02/09 06:00 MHDA- 2022/03/15 06:00 PMCR- 2022/02/07 CRDT- 2022/02/08 05:49 PHST- 2021/12/14 00:00 [accepted] PHST- 2022/02/08 05:49 [entrez] PHST- 2022/02/09 06:00 [pubmed] PHST- 2022/03/15 06:00 [medline] PHST- 2022/02/07 00:00 [pmc-release] AID - 2108001119 [pii] AID - 202108001 [pii] AID - 10.1073/pnas.2108001119 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2022 Feb 22;119(8):e2108001119. doi: 10.1073/pnas.2108001119. PMID- 35109894 OWN - NLM STAT- MEDLINE DCOM- 20220404 LR - 20240822 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 23 IP - 1 DP - 2022 Feb 3 TI - An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim. PG - 22 LID - 10.1186/s13059-021-02580-z [doi] LID - 22 AB - BACKGROUND: The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen's evolutionary history, and no genomes dating prior to 1940 were available. RESULTS: We describe a Hib genome isolated from a 6-year-old Anglo-Saxon plague victim, from approximately 540 to 550 CE, Edix Hill, England, showing signs of invasive infection on its skeleton. We find that the genome clusters in phylogenetic division II with Hib strain NCTC8468, which also caused invasive disease. While the virulence profile of our genome was distinct, its genomic similarity to NCTC8468 points to mostly clonal evolution of the clade since the 6th century. We also reconstruct a partial Yersinia pestis genome, which is likely identical to a published first plague pandemic genome of Edix Hill. CONCLUSIONS: Our study presents the earliest genomic evidence for H. influenzae, points to the potential presence of larger genomic diversity in the phylogenetic division II serotype b clade in the past, and allows the first insights into the evolutionary history of this major human pathogen. The identification of both plague and Hib opens questions on the effect of plague in immunocompromised individuals already affected by infectious diseases. CI - © 2022. The Author(s). FAU - Guellil, Meriam AU - Guellil M AUID- ORCID: 0000-0002-7235-4604 AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. meriam.guellil@ut.ee. FAU - Keller, Marcel AU - Keller M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. marcel.keller@ut.ee. FAU - Dittmar, Jenna M AU - Dittmar JM AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK. AD - Department of Archaeology, University of Aberdeen, St. Mary's, Elphinstone Road, Aberdeen, Scotland, AB24 3UF, UK. FAU - Inskip, Sarah A AU - Inskip SA AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK. AD - School of Archaeology and Ancient History, University of Leicester, University Road, Leicester, LE1 7RH, UK. FAU - Cessford, Craig AU - Cessford C AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK. AD - Cambridge Archaeological Unit, University of Cambridge, 34 A&B Storey's Way, Cambridge, CB3 0DT, UK. FAU - Solnik, Anu AU - Solnik A AD - Core Facility, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. FAU - Kivisild, Toomas AU - Kivisild T AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. AD - Department of Human Genetics, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium. FAU - Metspalu, Mait AU - Metspalu M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. FAU - Robb, John E AU - Robb JE AD - Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK. FAU - Scheib, Christiana L AU - Scheib CL AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. cls83@ut.ee. AD - St John's College, University of Cambridge, St John's Street, Cambridge, CB2 1TP, UK. cls83@ut.ee. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom GR - 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220203 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (Haemophilus Vaccines) SB - IM MH - Child MH - *Haemophilus Vaccines MH - Haemophilus influenzae/genetics MH - Humans MH - Infant MH - Phylogeny MH - *Plague MH - Serogroup PMC - PMC8812261 OTO - NOTNLM OT - Ancient DNA OT - Haemophilus influenzae OT - Microbial genomics OT - Osteology OT - Paleogenomics OT - Pathogen genomics OT - Plague OT - Serotype b OT - Yersinia pestis OT - aDNA COIS- The authors declare that they have no competing interests. EDAT- 2022/02/04 06:00 MHDA- 2022/04/05 06:00 PMCR- 2022/02/03 CRDT- 2022/02/03 05:28 PHST- 2021/07/22 00:00 [received] PHST- 2021/12/13 00:00 [accepted] PHST- 2022/02/03 05:28 [entrez] PHST- 2022/02/04 06:00 [pubmed] PHST- 2022/04/05 06:00 [medline] PHST- 2022/02/03 00:00 [pmc-release] AID - 10.1186/s13059-021-02580-z [pii] AID - 2580 [pii] AID - 10.1186/s13059-021-02580-z [doi] PST - epublish SO - Genome Biol. 2022 Feb 3;23(1):22. doi: 10.1186/s13059-021-02580-z. PMID- 35084493 OWN - NLM STAT- MEDLINE DCOM- 20220331 LR - 20240214 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 39 IP - 2 DP - 2022 Feb 3 TI - Placing Ancient DNA Sequences into Reference Phylogenies. LID - 10.1093/molbev/msac017 [doi] LID - msac017 AB - Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree. CI - © The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Martiniano, Rui AU - Martiniano R AUID- ORCID: 0000-0003-0216-778X AD - Department of Genetics, University of Cambridge, Cambridge, United Kingdom. AD - School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom. FAU - De Sanctis, Bianca AU - De Sanctis B AUID- ORCID: 0000-0002-0648-4224 AD - Department of Genetics, University of Cambridge, Cambridge, United Kingdom. AD - Department of Zoology, University of Cambridge, Cambridge, United Kingdom. FAU - Hallast, Pille AU - Hallast P AUID- ORCID: 0000-0002-0588-3987 AD - Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia. AD - Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom. FAU - Durbin, Richard AU - Durbin R AUID- ORCID: 0000-0002-9130-1006 AD - Department of Genetics, University of Cambridge, Cambridge, United Kingdom. AD - Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom GR - WT207492/WT_/Wellcome Trust/United Kingdom GR - WT220023/WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - *Chromosomes, Human, Y MH - *DNA, Ancient/analysis MH - DNA, Mitochondrial/genetics MH - Haplotypes MH - Humans MH - Likelihood Functions MH - Male MH - *Phylogeny MH - Sequence Analysis, DNA/methods PMC - PMC8857924 OTO - NOTNLM OT - Y chromosome haplogroups OT - ancient DNA OT - phylogenetic placement EDAT- 2022/01/28 06:00 MHDA- 2022/04/01 06:00 PMCR- 2022/01/27 CRDT- 2022/01/27 12:15 PHST- 2022/01/28 06:00 [pubmed] PHST- 2022/04/01 06:00 [medline] PHST- 2022/01/27 12:15 [entrez] PHST- 2022/01/27 00:00 [pmc-release] AID - 6516020 [pii] AID - msac017 [pii] AID - 10.1093/molbev/msac017 [doi] PST - ppublish SO - Mol Biol Evol. 2022 Feb 3;39(2):msac017. doi: 10.1093/molbev/msac017. PMID- 34963129 OWN - NLM STAT- MEDLINE DCOM- 20220331 LR - 20220401 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 39 IP - 2 DP - 2022 Feb 3 TI - Ancient Human Genomes and Environmental DNA from the Cement Attaching 2,000-Year-Old Head Lice Nits. LID - 10.1093/molbev/msab351 [doi] LID - msab351 AB - Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500-2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Pedersen, Mikkel W AU - Pedersen MW AD - GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark. FAU - Antunes, Catia AU - Antunes C AD - Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom. FAU - De Cahsan, Binia AU - De Cahsan B AD - GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark. FAU - Moreno-Mayar, J Víctor AU - Moreno-Mayar JV AD - GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark. FAU - Sikora, Martin AU - Sikora M AD - GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark. FAU - Vinner, Lasse AU - Vinner L AD - GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark. FAU - Mann, Darren AU - Mann D AD - Oxford University Museum of Natural History, Oxford, United Kingdom. FAU - Klimov, Pavel B AU - Klimov PB AD - School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom. AD - Department of Ecology and Evolutionary Biology, University of Michigan, Museum of Zoology, Ann Arbor, MI, USA. FAU - Black, Stuart AU - Black S AD - Department of Geography and Environmental Science, Wager Building, University of Reading, Reading, United Kingdom. FAU - Michieli, Catalina Teresa AU - Michieli CT AD - Instituto de Investigaciones Arqueológicas y Museo "Prof. Mariano Gambier", Universidad Nacional de San Juan, San Juan, Argentina. FAU - Braig, Henk R AU - Braig HR AD - School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom. AD - Institute and Museum of Natural Sciences, Faculty of Exact, Physical and Natural Sciences, National University of San Juan, San Juan, Argentina. FAU - Perotti, M Alejandra AU - Perotti MA AUID- ORCID: 0000-0002-3769-7126 AD - Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom. LA - eng GR - BB/N001400/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/N001443/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Environmental) SB - IM MH - Animals MH - *DNA, Environmental MH - Genome, Human MH - Genome-Wide Association Study MH - Humans MH - Infant, Newborn MH - *Pediculus/genetics MH - Skull PMC - PMC8829908 OTO - NOTNLM OT - Merkel cell polyomavirus OT - aDNA OT - ancient head lice OT - ancient host genomes EDAT- 2021/12/29 06:00 MHDA- 2022/04/01 06:00 PMCR- 2021/12/28 CRDT- 2021/12/28 20:09 PHST- 2021/12/29 06:00 [pubmed] PHST- 2022/04/01 06:00 [medline] PHST- 2021/12/28 20:09 [entrez] PHST- 2021/12/28 00:00 [pmc-release] AID - 6481551 [pii] AID - msab351 [pii] AID - 10.1093/molbev/msab351 [doi] PST - ppublish SO - Mol Biol Evol. 2022 Feb 3;39(2):msab351. doi: 10.1093/molbev/msab351. PMID- 35037474 OWN - NLM STAT- MEDLINE DCOM- 20220502 LR - 20220502 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 72 IP - 2 DP - 2022 Feb TI - Non-destructive extraction of DNA from preserved tissues in medical collections. PG - 60-64 LID - 10.2144/btn-2021-0014 [doi] AB - Museum specimens and histologically fixed material are valuable samples for the study of historical soft tissues and represent a possible pathogen-specific source for retrospective molecular investigations. However, current methods for molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology, thus damaging the sample, and conserving the material for future investigations. Here the authors present the first tests of a non-destructive alternative that facilitates genetic analysis of fixed wet tissues while avoiding tissue damage. The authors extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. The results show that human historical DNA can be retrieved from the fixative material of medical specimens and provide new options for sampling valuable collections. FAU - Rayo, Enrique AU - Rayo E AUID- ORCID: 0000-0002-4497-4339 AD - Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland. AD - Plant Ecology Genomics Group, Institute of Integrative Biology (IBZ), ETH Zürich, CH-8092, Switzerland. FAU - Ferrari, Giada AU - Ferrari G AD - Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland. AD - Royal Botanical Garden Edinburgh, Edinburgh, EH3 5NZ, UK. FAU - Neukamm, Judith AU - Neukamm J AD - Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, DE-72074, Germany. FAU - Akgül, Gülfirde AU - Akgül G AD - Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland. FAU - Breidenstein, Abagail M AU - Breidenstein AM AD - Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland. FAU - Cooke, Martyn AU - Cooke M AD - Museums & Archives, The Royal College of Surgeons of England, London, WC2A 3PE, UK. FAU - Phillips, Carina AU - Phillips C AD - Museums & Archives, The Royal College of Surgeons of England, London, WC2A 3PE, UK. FAU - Bouwman, Abigail S AU - Bouwman AS AD - Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland. FAU - Rühli, Frank J AU - Rühli FJ AD - Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220117 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (Fixatives) RN - 9007-49-2 (DNA) SB - IM MH - *DNA/genetics MH - Fixatives MH - Humans MH - *Preservation, Biological/methods MH - Retrospective Studies MH - Sequence Analysis, DNA/methods OTO - NOTNLM OT - ancient DNA OT - historical DNA OT - metagenomics OT - museomics EDAT- 2022/01/18 06:00 MHDA- 2022/05/03 06:00 CRDT- 2022/01/17 08:50 PHST- 2022/01/18 06:00 [pubmed] PHST- 2022/05/03 06:00 [medline] PHST- 2022/01/17 08:50 [entrez] AID - 10.2144/btn-2021-0014 [doi] PST - ppublish SO - Biotechniques. 2022 Feb;72(2):60-64. doi: 10.2144/btn-2021-0014. Epub 2022 Jan 17. PMID- 34850636 OWN - NLM STAT- MEDLINE DCOM- 20220404 LR - 20220405 IS - 1750-192X (Electronic) IS - 1750-192X (Linking) VI - 14 IP - 4 DP - 2022 Feb TI - Assessing the achievements and uncertain future of paleoepigenomics. PG - 167-173 LID - 10.2217/epi-2021-0382 [doi] FAU - Smith, Rick Wa AU - Smith RW AUID- ORCID: 0000-0002-3207-0519 AD - Department of Sociology and Anthropology, George Mason University, Fairfax, VA 22030, USA. FAU - Non, Amy L AU - Non AL AUID- ORCID: 0000-0001-9781-2985 AD - Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20211201 PL - England TA - Epigenomics JT - Epigenomics JID - 101519720 SB - IM MH - *DNA Methylation MH - Epigenesis, Genetic MH - *Epigenomics MH - Humans OTO - NOTNLM OT - DNA methylation OT - ancient DNA OT - ancient epigenomics OT - paleoepigenomics EDAT- 2021/12/02 06:00 MHDA- 2022/04/05 06:00 CRDT- 2021/12/01 08:41 PHST- 2021/12/02 06:00 [pubmed] PHST- 2022/04/05 06:00 [medline] PHST- 2021/12/01 08:41 [entrez] AID - 10.2217/epi-2021-0382 [doi] PST - ppublish SO - Epigenomics. 2022 Feb;14(4):167-173. doi: 10.2217/epi-2021-0382. Epub 2021 Dec 1. PMID- 35205247 OWN - NLM STAT- MEDLINE DCOM- 20220425 LR - 20220722 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 13 IP - 2 DP - 2022 Jan 23 TI - Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family. LID - 10.3390/genes13020202 [doi] LID - 202 AB - This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome sequences of Tsar Nicholas II and his wife, Tsarina Alexandra, made these samples ideal to assess this DNA extraction protocol and evaluate the types of genetic information that can be recovered by sequencing ultrashort fragments. Using this method, the mtGenome of the Tsarina's lineage was identified in hairs that were concealed in a pendant made by Karl Fabergé for Alexandra Feodorovna Romanov. In addition, to determine if the lock originated from more than one individual, two hairs from the locket were extracted independently and converted into Illumina libraries for shotgun sequencing on a NextSeq 500 platform. From these data, autosomal SNPs were analyzed to assess relatedness. The results indicated that the two hairs came from a single individual. Genetic testing of hairs that were found in the second artifact, a framed photograph of Louise of Hesse-Kassel, Queen of Denmark and maternal grandmother of Tsar Nicholas II, revealed that the hair belonged to a woman who shared Tsar Nicholas' maternal lineage, including the well-known point heteroplasmy at position 16169. FAU - Loreille, Odile AU - Loreille O AUID- ORCID: 0000-0001-7437-7298 AD - Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA. FAU - Tillmar, Andreas AU - Tillmar A AD - Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, SE-587 58 Linkoping, Sweden. AD - Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, SE-582 25 Linkoping, Sweden. FAU - Brandhagen, Michael D AU - Brandhagen MD AD - Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA. FAU - Otterstatter, Linda AU - Otterstatter L AD - Federal Bureau of Investigation Laboratory, Trace Evidence Unit, Quantico, VA 22135, USA. FAU - Irwin, Jodi A AU - Irwin JA AD - Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA. LA - eng PT - Journal Article DEP - 20220123 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/analysis/genetics MH - Famous Persons MH - Female MH - *Genome, Mitochondrial MH - Hair/chemistry MH - Heteroplasmy MH - *High-Throughput Nucleotide Sequencing/methods MH - Humans MH - Polymorphism, Single Nucleotide MH - Russia PMC - PMC8872530 OTO - NOTNLM OT - Romanov family OT - ancient DNA OT - biological sexing OT - heteroplasmy OT - hybridization capture OT - kinship analyses OT - mitochondrial DNA OT - next generation sequencing (NGS) OT - single nucleotide polymorphism (SNP) COIS- Names of commercial manufacturers are provided for identification purposes only and inclusion does not imply endorsement of the manufacturer, or its products or services by the FBI. The views expressed are those of the authors and do not necessarily reflect the official policy or position of the FBI. This is FBI Laboratory publication #22–08. EDAT- 2022/02/26 06:00 MHDA- 2022/04/26 06:00 PMCR- 2022/01/23 CRDT- 2022/02/25 01:06 PHST- 2021/11/29 00:00 [received] PHST- 2022/01/18 00:00 [revised] PHST- 2022/01/20 00:00 [accepted] PHST- 2022/02/25 01:06 [entrez] PHST- 2022/02/26 06:00 [pubmed] PHST- 2022/04/26 06:00 [medline] PHST- 2022/01/23 00:00 [pmc-release] AID - genes13020202 [pii] AID - genes-13-00202 [pii] AID - 10.3390/genes13020202 [doi] PST - epublish SO - Genes (Basel). 2022 Jan 23;13(2):202. doi: 10.3390/genes13020202. PMID- 35052476 OWN - NLM STAT- MEDLINE DCOM- 20220222 LR - 20220222 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 13 IP - 1 DP - 2022 Jan 13 TI - First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First-Third Centuries AD). LID - 10.3390/genes13010136 [doi] LID - 136 AB - This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first-third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops. FAU - De Angelis, Flavio AU - De Angelis F AUID- ORCID: 0000-0002-4747-2385 AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy. FAU - Romboni, Marco AU - Romboni M AUID- ORCID: 0000-0003-2460-9382 AD - Department of Biology, University of Pisa, 56121 Pisa, Italy. FAU - Veltre, Virginia AU - Veltre V AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy. AD - PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome Tor Vergata, 00133 Roma, Italy. FAU - Catalano, Paola AU - Catalano P AD - Former Servizio di Antropologia, Soprintendenza Speciale Archeologia, Belle Arti e Paesaggio di Roma, 00185 Roma, Italy. FAU - Martínez-Labarga, Cristina AU - Martínez-Labarga C AUID- ORCID: 0000-0003-0439-0379 AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy. FAU - Gazzaniga, Valentina AU - Gazzaniga V AD - Unità di Storia della Medicina e Bioetica, Sapienza University of Rome, 00185 Roma, Italy. FAU - Rickards, Olga AU - Rickards O AUID- ORCID: 0000-0003-2880-7466 AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220113 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) SB - IM MH - Adolescent MH - Bacteria/*classification/genetics/isolation & purification MH - Bone and Bones/*metabolism/*microbiology MH - Child MH - Child, Preschool MH - DNA, Ancient/*analysis/isolation & purification MH - Female MH - Genome, Human MH - Genomics/*methods MH - Humans MH - Infant MH - Male MH - Paleopathology MH - Rome MH - Whole Genome Sequencing PMC - PMC8774527 OTO - NOTNLM OT - Roman fullers OT - ancient DNA OT - children OT - metagenomes OT - microbes COIS- The authors declare no conflict of interest. EDAT- 2022/01/22 06:00 MHDA- 2022/02/23 06:00 PMCR- 2022/01/13 CRDT- 2022/01/21 01:02 PHST- 2021/11/24 00:00 [received] PHST- 2022/01/04 00:00 [revised] PHST- 2022/01/08 00:00 [accepted] PHST- 2022/01/21 01:02 [entrez] PHST- 2022/01/22 06:00 [pubmed] PHST- 2022/02/23 06:00 [medline] PHST- 2022/01/13 00:00 [pmc-release] AID - genes13010136 [pii] AID - genes-13-00136 [pii] AID - 10.3390/genes13010136 [doi] PST - epublish SO - Genes (Basel). 2022 Jan 13;13(1):136. doi: 10.3390/genes13010136. PMID- 35052469 OWN - NLM STAT- MEDLINE DCOM- 20220222 LR - 20220222 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 13 IP - 1 DP - 2022 Jan 11 TI - Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns. LID - 10.3390/genes13010129 [doi] LID - 129 AB - The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains. FAU - Zavala, Elena I AU - Zavala EI AUID- ORCID: 0000-0001-7687-5370 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Thomas, Jacqueline Tyler AU - Thomas JT AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA. FAU - Sturk-Andreaggi, Kimberly AU - Sturk-Andreaggi K AUID- ORCID: 0000-0001-6857-923X AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA. AD - Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 08 Uppsala, Sweden. FAU - Daniels-Higginbotham, Jennifer AU - Daniels-Higginbotham J AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA. FAU - Meyers, Kerriann K AU - Meyers KK AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA. FAU - Barrit-Ross, Suzanne AU - Barrit-Ross S AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. FAU - Aximu-Petri, Ayinuer AU - Aximu-Petri A AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Richter, Julia AU - Richter J AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Nickel, Birgit AU - Nickel B AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Berg, Gregory E AU - Berg GE AUID- ORCID: 0000-0003-4225-1783 AD - Defense Personnel Accounting Agency, Central Identification Laboratory, Hickam Air Force Base, Oahu, HI 96853, USA. FAU - McMahon, Timothy P AU - McMahon TP AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Marshall, Charla AU - Marshall C AUID- ORCID: 0000-0002-8495-1748 AD - Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA. AD - SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA. AD - Forensic Science Program, Pennsylvania State University, State College, PA 16802, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220111 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) SB - IM MH - Body Remains/*metabolism MH - DNA Fingerprinting/*methods MH - DNA, Ancient/*analysis/isolation & purification MH - *Forensic Genetics MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Korean War MH - *Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA/*methods MH - World War II PMC - PMC8774965 OTO - NOTNLM OT - ancient DNA OT - degraded DNA OT - forensic DNA profiling OT - human identification OT - massively parallel sequencing (MPS) OT - mitochondrial DNA COIS- The authors declare no conflict of interest. EDAT- 2022/01/22 06:00 MHDA- 2022/02/23 06:00 PMCR- 2022/01/11 CRDT- 2022/01/21 01:02 PHST- 2021/12/15 00:00 [received] PHST- 2022/01/06 00:00 [revised] PHST- 2022/01/07 00:00 [accepted] PHST- 2022/01/21 01:02 [entrez] PHST- 2022/01/22 06:00 [pubmed] PHST- 2022/02/23 06:00 [medline] PHST- 2022/01/11 00:00 [pmc-release] AID - genes13010129 [pii] AID - genes-13-00129 [pii] AID - 10.3390/genes13010129 [doi] PST - epublish SO - Genes (Basel). 2022 Jan 11;13(1):129. doi: 10.3390/genes13010129. PMID- 34937939 OWN - NLM STAT- MEDLINE DCOM- 20220422 LR - 20220802 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 601 IP - 7894 DP - 2022 Jan TI - A high-resolution picture of kinship practices in an Early Neolithic tomb. PG - 584-587 LID - 10.1038/s41586-021-04241-4 [doi] AB - To explore kinship practices at chambered tombs in Early Neolithic Britain, here we combined archaeological and genetic analyses of 35 individuals who lived about 5,700 years ago and were entombed at Hazleton North long cairn(1). Twenty-seven individuals are part of the first extended pedigree reconstructed from ancient DNA, a five-generation family whose many interrelationships provide statistical power to document kinship practices that were invisible without direct genetic data. Patrilineal descent was key in determining who was buried in the tomb, as all 15 intergenerational transmissions were through men. The presence of women who had reproduced with lineage men and the absence of adult lineage daughters suggest virilocal burial and female exogamy. We demonstrate that one male progenitor reproduced with four women: the descendants of two of those women were buried in the same half of the tomb over all generations. This suggests that maternal sub-lineages were grouped into branches whose distinctiveness was recognized during the construction of the tomb. Four men descended from non-lineage fathers and mothers who also reproduced with lineage male individuals, suggesting that some men adopted the children of their reproductive partners by other men into their patriline. Eight individuals were not close biological relatives of the main lineage, raising the possibility that kinship also encompassed social bonds independent of biological relatedness. CI - © 2021. The Author(s), under exclusive licence to Springer Nature Limited. FAU - Fowler, Chris AU - Fowler C AUID- ORCID: 0000-0003-3794-9298 AD - School of History, Classics and Archaeology, Newcastle University, Newcastle upon Tyne, UK. chris.fowler@newcastle.ac.uk. FAU - Olalde, Iñigo AU - Olalde I AUID- ORCID: 0000-0002-2660-6807 AD - BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain. inigo.olalde@ehu.eus. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. inigo.olalde@ehu.eus. AD - Ikerbasque-Basque Foundation of Science, Bilbao, Spain. inigo.olalde@ehu.eus. FAU - Cummings, Vicki AU - Cummings V AUID- ORCID: 0000-0001-9460-1517 AD - School of Natural Sciences, University of Central Lancashire, Preston, Lancashire, UK. FAU - Armit, Ian AU - Armit I AD - Department of Archaeology, University of York, York, UK. FAU - Büster, Lindsey AU - Büster L AUID- ORCID: 0000-0003-4121-9431 AD - Department of Archaeology, University of York, York, UK. FAU - Cuthbert, Sarah AU - Cuthbert S AD - Department of Archaeology, University of Exeter, Exeter, UK. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Boston, MA, USA. reich@genetics.med.harvard.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R01 HG012287/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20211222 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM CIN - Nature. 2022 Jan;601(7894):510-512. doi: 10.1038/d41586-021-03799-3. PMID: 34949860 MH - Adult MH - Archaeology MH - *Burial MH - Child MH - *DNA, Ancient MH - Female MH - Humans MH - Male MH - Mothers MH - Pedigree PMC - PMC8896835 MID - NIHMS1779406 COIS- Competing interests The authors declare no competing interests. EDAT- 2021/12/24 06:00 MHDA- 2022/04/23 06:00 PMCR- 2022/07/01 CRDT- 2021/12/23 05:43 PHST- 2021/06/22 00:00 [received] PHST- 2021/11/15 00:00 [accepted] PHST- 2021/12/24 06:00 [pubmed] PHST- 2022/04/23 06:00 [medline] PHST- 2021/12/23 05:43 [entrez] PHST- 2022/07/01 00:00 [pmc-release] AID - 10.1038/s41586-021-04241-4 [pii] AID - 10.1038/s41586-021-04241-4 [doi] PST - ppublish SO - Nature. 2022 Jan;601(7894):584-587. doi: 10.1038/s41586-021-04241-4. Epub 2021 Dec 22. PMID- 34656830 OWN - NLM STAT- MEDLINE DCOM- 20220131 LR - 20220131 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 56 DP - 2022 Jan TI - The Lady from Basel's Barfüsserkirche - Molecular confirmation of the Mummy's identity through mitochondrial DNA of living relatives spanning 22 generations. PG - 102604 LID - S1872-4973(21)00141-1 [pii] LID - 10.1016/j.fsigen.2021.102604 [doi] AB - The identity of the mummified Lady from the Barfüsser Church in Basel, Switzerland has been unsolved for decades, despite the prominent location of the burial place in front of the choir screen. A recent multidisciplinary research approach came up with a possible candidate, Anna Catharina Bischoff who died in Basel in 1787 with an age of 69 years (1719-1787). To verify the identity of the mummy, genealogists of the Citizen Science Basel discovered three living individuals of the maternal lineage of two different family branches, separated from Anna Catharina Bischoff by up to 22 generations. In this study we compare the ancient mitochondrial DNA of the mummy recovered from a premolar to the mitochondrial DNA of these three candidates. Initially the mitochondrial hypervariable regions I and II of the living individuals were screened using the Sanger sequencing method. This was followed by a mitochondrial capture approach and next generation sequencing to enrich for the whole mitochondrial genome of the mummy and one living person. A full mitochondrial genome has been recovered of both individuals sharing an identical haplotype. The sequence was assigned to the mitochondrial haplogroup U5a1+!16192 including two private mutations 10006G and 16293C. Only by using an interdisciplinary approach combining ancient DNA analysis and genealogy a maternal lineage of a non-noble family spanning 22 generations could be confirmed. CI - Copyright © 2021 Elsevier B.V. All rights reserved. FAU - Wurst, Christina AU - Wurst C AD - Institute for Mummy Studies, Eurac Research, Drususallee/Viale Druso 1, 39100 Bozen, Bolzano, Italy; Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Saarstraße 21, 55122 Mainz, Germany. Electronic address: Christina.Wurst@eurac.edu. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, Eurac Research, Drususallee/Viale Druso 1, 39100 Bozen, Bolzano, Italy. FAU - Castella, Vincent AU - Castella V AD - Forensic Genetics Unit, University Center of Legal Medicine, Lausanne - Geneva, Lausanne University Hospital and University of Lausanne, Ch. de la Vulliette 4, 1000 Lausanne 25, Switzerland. FAU - Cipollini, Giovanna AU - Cipollini G AD - Institute for Mummy Studies, Eurac Research, Drususallee/Viale Druso 1, 39100 Bozen, Bolzano, Italy. FAU - Hotz, Gerhard AU - Hotz G AD - Natural History Museum Basel, Augustinergasse 2, 4051 Basel, Switzerland; Integrative Prehistory and Archaeological Science, University of Basel, Bernoullistrasse 32, 4056 Basel, Switzerland. FAU - Zink, Albert AU - Zink A AD - Institute for Mummy Studies, Eurac Research, Drususallee/Viale Druso 1, 39100 Bozen, Bolzano, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20211009 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/genetics MH - *Genome, Mitochondrial MH - Haplotypes MH - Humans MH - *Mummies MH - Sequence Analysis, DNA OTO - NOTNLM OT - Ancient DNA OT - Genealogy OT - Identity reconstruction OT - MtDNA capture OT - Mummy EDAT- 2021/10/18 06:00 MHDA- 2022/02/01 06:00 CRDT- 2021/10/17 20:43 PHST- 2021/08/02 00:00 [received] PHST- 2021/10/04 00:00 [revised] PHST- 2021/10/06 00:00 [accepted] PHST- 2021/10/18 06:00 [pubmed] PHST- 2022/02/01 06:00 [medline] PHST- 2021/10/17 20:43 [entrez] AID - S1872-4973(21)00141-1 [pii] AID - 10.1016/j.fsigen.2021.102604 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2022 Jan;56:102604. doi: 10.1016/j.fsigen.2021.102604. Epub 2021 Oct 9. PMID- 34937536 OWN - NLM STAT- MEDLINE DCOM- 20220124 LR - 20220124 IS - 1608-3040 (Electronic) IS - 0006-2979 (Linking) VI - 86 IP - 12 DP - 2021 Dec TI - Genetic Evidence of Authenticity of a Hair Shaft Relic from the Portrait of Tsesarevich Alexei, Son of the Last Russian Emperor. PG - 1572-1578 LID - 10.1134/S0006297921120063 [doi] AB - To determine the value of an art piece, authenticity of the artwork must be verified. We demonstrate here a genetic approach to determine origin of a historic relic in the museum piece. We tested two hair shafts of unknown origin framed into a watercolor portrait of Tsesarevich Alexei Romanov, son of the last Russian Tzar Nicholas II, which is a unique item kept in the State Historical Museum. Genetic identification of the hair shafts was performed by analysis of mitochondrial DNA (mtDNA) markers using both massive parallel genomic sequencing and multiplex targeted PCR, followed by Sanger sequencing. In previous works, we reconstructed the complete mtDNA sequence inherited to Alexei Romanov through the Queen Victoria lineage [Rogaev et al. (2009) Proc. Natl. Acad. Sci. USA, 106, 5258-5263]. DNA extracts were obtained from the two thin hair shafts and used for comparative genetic analysis. Despite the very low quantity and quality of the DNA templates retrieved from the historical single hair shaft specimen, informative mtDNA sequences were determined. The mtDNA haplotype in the hair shafts corresponds to the mtDNA haplotype of Tsarevich Alexei, his sisters, and his mother, Empress Alexandra Feodorovna. This haplotype remains unique in the currently available mtDNA databases. Our results reveal that the hair relic from the portrait is associated with the family of the last Russian Emperor Nicholas II. The study is an example of first application of the genetic methodology for verification of the value of museum artwork items. FAU - Andreeva, Tatiana AU - Andreeva T AD - Centre for Genetics and Genetic Technologies, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119192, Russia. andreeva@rogaevlab.ru. AD - Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. FAU - Manakhov, Andrey AU - Manakhov A AD - Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia. manakhov@rogaevlab.ru. FAU - Kunizheva, Svetlana AU - Kunizheva S AD - Centre for Genetics and Genetic Technologies, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119192, Russia. kunizheva@gmail.com. FAU - Rogaev, Evgeny AU - Rogaev E AD - Centre for Genetics and Genetic Technologies, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119192, Russia. rogaev@vigg.ru. AD - Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. AD - Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia. AD - Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA. LA - eng PT - Journal Article PL - United States TA - Biochemistry (Mosc) JT - Biochemistry. Biokhimiia JID - 0376536 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - *Forensic Anthropology MH - *Forensic Genetics MH - *Hair MH - *High-Throughput Nucleotide Sequencing MH - Humans MH - Russia OTO - NOTNLM OT - NGS OT - ancient DNA OT - hair shaft DNA OT - human identification OT - mtDNA OT - museum item EDAT- 2021/12/24 06:00 MHDA- 2022/01/27 06:00 CRDT- 2021/12/23 05:26 PHST- 2021/12/23 05:26 [entrez] PHST- 2021/12/24 06:00 [pubmed] PHST- 2022/01/27 06:00 [medline] AID - BCM86121818 [pii] AID - 10.1134/S0006297921120063 [doi] PST - ppublish SO - Biochemistry (Mosc). 2021 Dec;86(12):1572-1578. doi: 10.1134/S0006297921120063. PMID- 34937535 OWN - NLM STAT- MEDLINE DCOM- 20220124 LR - 20220124 IS - 1608-3040 (Electronic) IS - 0006-2979 (Linking) VI - 86 IP - 12 DP - 2021 Dec TI - Progress and Prospects in Epigenetic Studies of Ancient DNA. PG - 1563-1571 LID - 10.1134/S0006297921120051 [doi] AB - Development of technologies for high-throughput whole-genome sequencing and improvement of sample preparation techniques made it possible to study ancient DNA (aDNA) from archaeological samples over a million year old. The studies of aDNA have shed light on the history of human migration, replacement of populations, interbreeding of Cro-Magnons with Neanderthals and Denisovans, evolution of human pathogens, etc. Equally important is the possibility to investigate epigenetic modifications of ancient genomes, which has allowed to obtain previously inaccessible information on gene expression, nucleosome positioning, and DNA methylation. Analysis of methylation status of certain genomic sites can predict an individual's age at death and reconstruct some phenotypic features, as it was done for the Denisovan genome, and even to elucidate unfavorable environmental factors that had affected this archaic individual. In this review, we discuss current progress in epigenetic studies of aDNA, including methodological approaches and promising research directions in this field. FAU - Zhur, Kristina V AU - Zhur KV AD - Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia. FAU - Trifonov, Victor A AU - Trifonov VA AD - Institute for History of Material Culture, Russian Academy of Sciences, St.-Petersburg, 191186, Russia. FAU - Prokhortchouk, Egor B AU - Prokhortchouk EB AD - Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia. zhur_kv@mail.ru. LA - eng PT - Journal Article PT - Review PL - United States TA - Biochemistry (Mosc) JT - Biochemistry. Biokhimiia JID - 0376536 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *DNA Methylation MH - *DNA, Ancient MH - *Epigenesis, Genetic MH - Epigenomics/trends MH - *Evolution, Molecular MH - Human Migration MH - Humans MH - Neanderthals/*genetics OTO - NOTNLM OT - ancient DNA OT - epigenetic clock OT - epigenome editing OT - obesity OT - paleoepigenetics EDAT- 2021/12/24 06:00 MHDA- 2022/01/27 06:00 CRDT- 2021/12/23 05:26 PHST- 2021/12/23 05:26 [entrez] PHST- 2021/12/24 06:00 [pubmed] PHST- 2022/01/27 06:00 [medline] AID - BCM86121808 [pii] AID - 10.1134/S0006297921120051 [doi] PST - ppublish SO - Biochemistry (Mosc). 2021 Dec;86(12):1563-1571. doi: 10.1134/S0006297921120051. PMID- 34848867 OWN - NLM STAT- MEDLINE DCOM- 20220105 LR - 20220119 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 600 IP - 7887 DP - 2021 Dec TI - Ancient-DNA researchers write their own rules. PG - 37 LID - 10.1038/d41586-021-03542-y [doi] FAU - Tsosie, Krystal S AU - Tsosie KS AUID- ORCID: 0000-0002-7291-670X FAU - Bader, Alyssa C AU - Bader AC AUID- ORCID: 0000-0002-0077-9005 FAU - Fox, Keolu AU - Fox K AUID- ORCID: 0000-0003-4215-5273 FAU - Bolnick, Deborah A AU - Bolnick DA AUID- ORCID: 0000-0001-8444-5127 FAU - Garrison, Nanibaa' A AU - Garrison NA AUID- ORCID: 0000-0002-6228-3216 FAU - Smith, Rick W A AU - Smith RWA AUID- ORCID: 0000-0002-3207-0519 LA - eng PT - Comment PT - Letter PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM CON - Nature. 2021 Nov;599(7883):41-46. doi: 10.1038/s41586-021-04008-x. PMID: 34671160 MH - *DNA, Ancient MH - Ethics, Research MH - Humans MH - *Research Personnel MH - Writing OTO - NOTNLM OT - Ethics OT - Genetics OT - Research management EDAT- 2021/12/02 06:00 MHDA- 2022/01/06 06:00 CRDT- 2021/12/01 06:48 PHST- 2021/12/01 06:48 [entrez] PHST- 2021/12/02 06:00 [pubmed] PHST- 2022/01/06 06:00 [medline] AID - 10.1038/d41586-021-03542-y [pii] AID - 10.1038/d41586-021-03542-y [doi] PST - ppublish SO - Nature. 2021 Dec;600(7887):37. doi: 10.1038/d41586-021-03542-y. PMID- 34927609 OWN - NLM STAT- MEDLINE DCOM- 20220405 LR - 20220405 IS - 1940-087X (Electronic) IS - 1940-087X (Linking) IP - 177 DP - 2021 Nov 30 TI - Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains. LID - 10.3791/63250 [doi] AB - The methods presented here seek to maximize the chances for the recovery of human DNA from ancient archaeological remains while limiting input sample material. This was done by targeting anatomical sampling locations previously determined to yield the highest amounts of ancient DNA (aDNA) in a comparative analysis of DNA recovery across the skeleton. Prior research has suggested that these protocols maximize the chances for the successful recovery of ancient human and pathogen DNA from archaeological remains. DNA yields were previously assessed by Parker et al. 2020 in a broad survey of aDNA preservation across multiple skeletal elements from 11 individuals recovered from the medieval (radiocarbon dated to a period of circa (ca.) 1040-1400 CE, calibrated 2-sigma range) graveyard at Krakauer Berg, an abandoned medieval settlement near Peißen Germany. These eight sampling spots, which span five skeletal elements (pars petrosa, permanent molars, thoracic vertebra, distal phalanx, and talus) successfully yielded high-quality ancient human DNA, where yields were significantly greater than the overall average across all elements and individuals. Yields were adequate for use in most common downstream population genetic analyses. Our results support the preferential use of these anatomical sampling locations for most studies involving the analyses of ancient human DNA from archaeological remains. Implementation of these methods will help to minimize the destruction of precious archaeological specimens. FAU - Parker, Cody E AU - Parker CE AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History; School of Human Evolution and Social Change, Arizona State University; cody.parker@asu.edu. FAU - Bos, Kirsten I AU - Bos KI AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology. FAU - Haak, Wolfgang AU - Haak W AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Video-Audio Media DEP - 20211130 PL - United States TA - J Vis Exp JT - Journal of visualized experiments : JoVE JID - 101313252 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - *Archaeology/methods MH - Bone and Bones/chemistry MH - DNA/genetics MH - *DNA, Ancient/analysis MH - Humans MH - Sequence Analysis, DNA/methods EDAT- 2021/12/21 06:00 MHDA- 2022/04/06 06:00 CRDT- 2021/12/20 08:50 PHST- 2021/12/20 08:50 [entrez] PHST- 2021/12/21 06:00 [pubmed] PHST- 2022/04/06 06:00 [medline] AID - 10.3791/63250 [doi] PST - epublish SO - J Vis Exp. 2021 Nov 30;(177). doi: 10.3791/63250. PMID- 34718543 OWN - NLM STAT- MEDLINE DCOM- 20220331 LR - 20240404 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 13 IP - 11 DP - 2021 Nov 5 TI - Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment. LID - 10.1093/gbe/evab237 [doi] LID - evab237 AB - As humans populated the world, they adapted to many varying environmental factors, including climate, diet, and pathogens. Because many of these adaptations were mediated by multiple noncoding variants with small effects on gene regulation, it has been difficult to link genomic signals of selection to specific genes, and to describe the regulatory response to selection. To overcome this challenge, we adapted PrediXcan, a machine learning method for imputing gene regulation from genotype data, to analyze low-coverage ancient human DNA (aDNA). First, we used simulated genomes to benchmark strategies for adapting PrediXcan to increase robustness to incomplete data. Applying the resulting models to 490 ancient Eurasians, we found that genes with the strongest divergent regulation among ancient populations with hunter-gatherer, pastoralist, and agricultural lifestyles are enriched for metabolic and immune functions. Next, we explored the contribution of divergent gene regulation to two traits with strong evidence of recent adaptation: dietary metabolism and skin pigmentation. We found enrichment for divergent regulation among genes proposed to be involved in diet-related local adaptation, and the predicted effects on regulation often suggest explanations for known signals of selection, for example, at FADS1, GPX1, and LEPR. In contrast, skin pigmentation genes show little regulatory change over a 38,000-year time series of 2,999 ancient Europeans, suggesting that adaptation mainly involved large-effect coding variants. This work demonstrates that combining aDNA with present-day genomes is informative about the biological differences among ancient populations, the role of gene regulation in adaptation, and the relationship between genetic diversity and complex traits. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Colbran, Laura L AU - Colbran LL AUID- ORCID: 0000-0002-7752-6671 AD - Vanderbilt Genetics Institute, Vanderbilt University Medical Center, USA. AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, USA. FAU - Johnson, Maya R AU - Johnson MR AD - School for Science and Math at Vanderbilt, Vanderbilt University, USA. AD - Department of Computer Science, Bryn Mawr College, Pennsylvania, USA. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, USA. FAU - Capra, John A AU - Capra JA AUID- ORCID: 0000-0001-9743-1795 AD - Vanderbilt Genetics Institute, Vanderbilt University Medical Center, USA. AD - Department of Biological Sciences, Vanderbilt University, USA. AD - Department of Biomedical Informatics, Vanderbilt University, USA. AD - Bakar Computational Health Sciences Institute, University of California, San Francisco, USA. AD - Department of Epidemiology and Biostatistics, University of California, San Francisco, USA. LA - eng GR - T32 GM080178/GM/NIGMS NIH HHS/United States GR - R35 GM133708/GM/NIGMS NIH HHS/United States GR - R35 GM127087/GM/NIGMS NIH HHS/United States GR - T32 HG009495/HG/NHGRI NIH HHS/United States GR - R01 GM115836/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 RN - 0 (DNA, Ancient) SB - IM MH - *Adaptation, Biological/genetics MH - Adaptation, Physiological MH - Biological Evolution MH - DNA, Ancient MH - *Genome, Human MH - Humans MH - Multifactorial Inheritance MH - Selection, Genetic PMC - PMC8576593 OTO - NOTNLM OT - gene regulation OT - human evolution OT - machine learning EDAT- 2021/11/01 06:00 MHDA- 2022/04/01 06:00 PMCR- 2021/10/28 CRDT- 2021/10/31 21:04 PHST- 2021/10/16 00:00 [accepted] PHST- 2021/11/01 06:00 [pubmed] PHST- 2022/04/01 06:00 [medline] PHST- 2021/10/31 21:04 [entrez] PHST- 2021/10/28 00:00 [pmc-release] AID - 6413637 [pii] AID - evab237 [pii] AID - 10.1093/gbe/evab237 [doi] PST - ppublish SO - Genome Biol Evol. 2021 Nov 5;13(11):evab237. doi: 10.1093/gbe/evab237. PMID- 34671160 OWN - NLM STAT- MEDLINE DCOM- 20220128 LR - 20230428 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 599 IP - 7883 DP - 2021 Nov TI - Ethics of DNA research on human remains: five globally applicable guidelines. PG - 41-46 LID - 10.1038/s41586-021-04008-x [doi] AB - We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward. CI - © 2021. The Author(s), under exclusive licence to Springer Nature Limited. FAU - Alpaslan-Roodenberg, Songül AU - Alpaslan-Roodenberg S AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Anthony, David AU - Anthony D AD - Department of Anthropology, Hartwick College, Oneonta, NY, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. FAU - Babiker, Hiba AU - Babiker H AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Bánffy, Eszter AU - Bánffy E AUID- ORCID: 0000-0001-5156-826X AD - Romano-Germanic Commission of the German Archaeological Institute, Frankfurt am Main, Germany. FAU - Booth, Thomas AU - Booth T AD - Francis Crick Institute, London, UK. FAU - Capone, Patricia AU - Capone P AD - Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA, USA. FAU - Deshpande-Mukherjee, Arati AU - Deshpande-Mukherjee A AD - Department of Ancient Indian History Culture and Archaeology, Deccan College Post Graduate and Research Institute, Pune, India. FAU - Eisenmann, Stefanie AU - Eisenmann S AUID- ORCID: 0000-0002-6301-5889 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AUID- ORCID: 0000-0001-5510-1114 AD - Department of Anthropology, University of California, Santa Cruz, CA, USA. lfehrens@ucsc.edu. AD - UCSC Genomics Institute, University of California, Santa Cruz, CA, USA. lfehrens@ucsc.edu. FAU - Frachetti, Michael AU - Frachetti M AUID- ORCID: 0000-0001-6906-4334 AD - Department of Anthropology, Washington University in St Louis, St Louis, MO, USA. FAU - Fujita, Ricardo AU - Fujita R AD - Centro de Genética y Biología Molecular, Facultad de Medicina, Universidad de San Martín de Porres, Lima, Peru. FAU - Frieman, Catherine J AU - Frieman CJ AUID- ORCID: 0000-0002-9030-4483 AD - School of Archaeology and Anthropology, The Australian National University, Canberra, Australian Capital Territory, Australia. FAU - Fu, Qiaomei AU - Fu Q AUID- ORCID: 0000-0002-7141-0002 AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. FAU - Gibbon, Victoria AU - Gibbon V AUID- ORCID: 0000-0001-7875-3297 AD - Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Hajdinjak, Mateja AU - Hajdinjak M AUID- ORCID: 0000-0002-4064-0331 AD - Francis Crick Institute, London, UK. FAU - Hofmann, Kerstin P AU - Hofmann KP AUID- ORCID: 0000-0003-4405-5751 AD - Romano-Germanic Commission of the German Archaeological Institute, Frankfurt am Main, Germany. FAU - Holguin, Brian AU - Holguin B AD - Department of Anthropology, University of California, Santa Barbara, CA, USA. FAU - Inomata, Takeshi AU - Inomata T AD - School of Anthropology, University of Arizona, Tucson, AZ, USA. FAU - Kanzawa-Kiriyama, Hideaki AU - Kanzawa-Kiriyama H AD - National Museum of Nature and Science, Ibaraki, Japan. FAU - Keegan, William AU - Keegan W AD - Florida Museum of Natural History, Gainesville, FL, USA. FAU - Kelso, Janet AU - Kelso J AUID- ORCID: 0000-0002-3618-322X AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Kumaresan, Ganesan AU - Kumaresan G AUID- ORCID: 0000-0003-0533-3181 AD - Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India. FAU - Kusimba, Chapurukha AU - Kusimba C AD - Department of Anthropology, University of South Florida, Tampa, FL, USA. FAU - Kusimba, Sibel AU - Kusimba S AD - Department of Anthropology, University of South Florida, Tampa, FL, USA. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain. FAU - Llamas, Bastien AU - Llamas B AUID- ORCID: 0000-0002-5550-9176 AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. AD - ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia. FAU - MacEachern, Scott AU - MacEachern S AUID- ORCID: 0000-0002-4859-3998 AD - Office of the Chancellors, Duke Kunshan University, Jiangsu, China. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Boston, MA, USA. AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. FAU - Matsumura, Hirofumi AU - Matsumura H AUID- ORCID: 0000-0001-5453-7987 AD - School of Health Science, Sapporo Medical University, Sapporo, Japan. FAU - Morales-Arce, Ana Y AU - Morales-Arce AY AUID- ORCID: 0000-0002-2934-3141 AD - Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. FAU - Matuzeviciute, Giedre Motuzaite AU - Matuzeviciute GM AUID- ORCID: 0000-0001-9069-1551 AD - Lithuanian Institute of History and Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania. FAU - Mushrif-Tripathy, Veena AU - Mushrif-Tripathy V AUID- ORCID: 0000-0002-4749-1316 AD - Department of Ancient Indian History Culture and Archaeology, Deccan College Post Graduate and Research Institute, Pune, India. FAU - Nakatsuka, Nathan AU - Nakatsuka N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Nores, Rodrigo AU - Nores R AD - Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Instituto de Antropología de Córdoba (IDACOR), CONICET, Córdoba, Argentina. FAU - Ogola, Christine AU - Ogola C AD - Earth Sciences Department, National Museums of Kenya, Nairobi, Kenya. FAU - Okumura, Mercedes AU - Okumura M AD - Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil. FAU - Patterson, Nick AU - Patterson N AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria. FAU - Prasad, Samayamantri P R AU - Prasad SPR AD - DBT-Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India. FAU - Prendergast, Mary E AU - Prendergast ME AUID- ORCID: 0000-0003-0275-6795 AD - Department of Anthropology, Rice University, Houston, TX, USA. mary@rice.edu. FAU - Punzo, Jose Luis AU - Punzo JL AUID- ORCID: 0000-0002-1025-9169 AD - Instituto Nacional de Antropología e Historia, Michoacán, Mexico. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. reich@genetics.med.harvard.edu. FAU - Sawafuji, Rikai AU - Sawafuji R AUID- ORCID: 0000-0002-8174-2326 AD - School of Advanced Sciences, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, Japan. FAU - Sawchuk, Elizabeth AU - Sawchuk E AD - Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada. AD - Department of Anthropology, Stony Brook University, Stony Brook, NY, USA. FAU - Schiffels, Stephan AU - Schiffels S AUID- ORCID: 0000-0002-1017-9150 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Sedig, Jakob AU - Sedig J AUID- ORCID: 0000-0001-6642-7734 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. Jakob_Sedig@hms.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. Jakob_Sedig@hms.harvard.edu. FAU - Shnaider, Svetlana AU - Shnaider S AD - ArchaeoZOOlogy in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, Novosibirsk, Russia. FAU - Sirak, Kendra AU - Sirak K AUID- ORCID: 0000-0003-2347-3479 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. Kendra_Sirak@hms.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. Kendra_Sirak@hms.harvard.edu. FAU - Skoglund, Pontus AU - Skoglund P AUID- ORCID: 0000-0002-3021-5913 AD - Francis Crick Institute, London, UK. FAU - Slon, Viviane AU - Slon V AD - Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. AD - The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel. FAU - Snow, Meradeth AU - Snow M AD - Anthropology Department, University of Montana, Missoula, MO, USA. FAU - Soressi, Marie AU - Soressi M AUID- ORCID: 0000-0003-1733-7745 AD - Faculty of Archaeology, Leiden University, Leiden, Netherlands. FAU - Spriggs, Matthew AU - Spriggs M AUID- ORCID: 0000-0002-7293-6778 AD - School of Archaeology and Anthropology, The Australian National University, Canberra, Australian Capital Territory, Australia. AD - Vanuatu Cultural Centre, Port Vila, Vanuatu. FAU - Stockhammer, Philipp W AU - Stockhammer PW AUID- ORCID: 0000-0003-4702-9372 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. philipp.stockhammer@lmu.de. AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Germany. philipp.stockhammer@lmu.de. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AUID- ORCID: 0000-0003-2095-738X AD - Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary. FAU - Thangaraj, Kumarasamy AU - Thangaraj K AD - DBT-Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India. AD - CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India. FAU - Tiesler, Vera AU - Tiesler V AUID- ORCID: 0000-0003-0532-5819 AD - School of Anthropological Sciences, Universidad Autónoma de Yucatán, Mérida, Mexico. FAU - Tobler, Ray AU - Tobler R AD - Department of Anthropology, University of South Florida, Tampa, FL, USA. AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. FAU - Wang, Chuan-Chao AU - Wang CC AUID- ORCID: 0000-0001-9628-0307 AD - Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China. AD - School of Basic Medical Sciences, Zhejiang University School of Medicine, and Institute of Asian Civilizations, Zhejiang University, Hangzhou, China. FAU - Warinner, Christina AU - Warinner C AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Anthropology, Harvard University, Cambridge, MA, USA. FAU - Yasawardene, Surangi AU - Yasawardene S AUID- ORCID: 0000-0002-9193-4372 AD - Department of Anatomy, University of Sri Jayewardenepura, Nugegoda, Sri Lanka. FAU - Zahir, Muhammad AU - Zahir M AUID- ORCID: 0000-0002-1765-6319 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Department of Archaeology, Hazara University, Mansehra, Pakistan. LA - eng GR - T32 GM007753/GM/NIGMS NIH HHS/United States GR - FC001595/MRC_/Medical Research Council/United Kingdom GR - FC001595/WT_/Wellcome Trust/United Kingdom GR - WT_/Wellcome Trust/United Kingdom GR - FC001595/ARC_/Arthritis Research UK/United Kingdom GR - FC001595/CRUK_/Cancer Research UK/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20211020 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM CIN - Nature. 2021 Dec;600(7887):37. doi: 10.1038/d41586-021-03541-z. PMID: 34848866 CIN - Nature. 2021 Dec;600(7887):37. doi: 10.1038/d41586-021-03542-y. PMID: 34848867 CIN - HGG Adv. 2023 Jan 11;4(2):100161. doi: 10.1016/j.xhgg.2022.100161. PMID: 37101579 MH - American Indian or Alaska Native MH - Anthropology/ethics MH - Archaeology/ethics MH - *Cadaver MH - Community-Institutional Relations MH - DNA, Ancient/*analysis MH - *Guidelines as Topic MH - Human Genetics/*ethics MH - Humans MH - Indigenous Peoples MH - *Internationality MH - Molecular Biology/*ethics MH - Stakeholder Participation MH - Translations PMC - PMC7612683 MID - EMS144572 COIS- Competing interests The authors declare no competing interests. EDAT- 2021/10/22 06:00 MHDA- 2022/01/29 06:00 PMCR- 2022/05/02 CRDT- 2021/10/21 06:05 PHST- 2021/03/20 00:00 [received] PHST- 2021/09/08 00:00 [accepted] PHST- 2021/10/22 06:00 [pubmed] PHST- 2022/01/29 06:00 [medline] PHST- 2021/10/21 06:05 [entrez] PHST- 2022/05/02 00:00 [pmc-release] AID - 10.1038/s41586-021-04008-x [pii] AID - 10.1038/s41586-021-04008-x [doi] PST - ppublish SO - Nature. 2021 Nov;599(7883):41-46. doi: 10.1038/s41586-021-04008-x. Epub 2021 Oct 20. PMID- 34184252 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 176 IP - 3 DP - 2021 Nov TI - Uniparental genetic markers in Native Americans: A summary of all available data from ancient and contemporary populations. PG - 445-458 LID - 10.1002/ajpa.24357 [doi] AB - OBJECTIVES: The aim of this study was to create a comprehensive summary of available mtDNA and Y-chromosome data for Native Americans from North, Central, and South America, including both modern and ancient DNA. To illustrate the usefulness of this dataset we present a broad picture of the genetic variation for both markers across the Americas. METHODS: We searched PubMed, ResearchGate, Google Scholar for studies about mtDNA or Y-chromosome variation in Native American populations, including geographic, linguistic, ecological (ecoregion), archeological and chronological information. We used AMOVA to estimate the genetic structure associated with language and ecoregion grouping and Mantel tests to evaluate the correlation between genetic and geographic distances. RESULTS: Genetic data were obtained from 321 primary sources, including 22,569 individuals from 298 contemporary populations, and 3628 individuals from 202 archeological populations. MtDNA lineages of probable non-Amerindian origin were rare, in contrast with Y-chromosome lineages. Mantel tests showed a statistically significant correlation for the whole continent considering mtDNA but not the Y-chromosome. Genetic structure between groups was always stronger for mtDNA than for the Y-chromosome. CONCLUSIONS: This study summarizes decades of research conducted in Native American populations for both mtDNA and the Y-chromosome. Continental or sub-continental patterns of variation reveal that most of the genetic variation occurs within populations rather than among linguistic or ecoregional groups, and that isolation by distance is barely detectable in most population sets. The genetic structure among groups was always larger for mtDNA than for the Y-chromosome, suggesting between-sex differences in gene flow. CI - © 2021 Wiley Periodicals LLC. FAU - Bisso-Machado, Rafael AU - Bisso-Machado R AUID- ORCID: 0000-0003-1384-8054 AD - Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. FAU - Fagundes, Nelson J R AU - Fagundes NJR AUID- ORCID: 0000-0003-0456-0323 AD - Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. AD - Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. AD - Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210628 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - *Chromosomes, Human, Y/genetics MH - DNA, Mitochondrial/genetics MH - Female MH - Genetic Markers/genetics MH - Genetic Variation/genetics MH - Genetics, Population MH - Haplotypes MH - Humans MH - Male MH - *American Indian or Alaska Native OTO - NOTNLM OT - Y-chromosome OT - ancient DNA OT - genetics OT - language and geography OT - mitochondrial DNA OT - peopling of the Americas EDAT- 2021/06/30 06:00 MHDA- 2021/10/26 06:00 CRDT- 2021/06/29 06:41 PHST- 2021/05/26 00:00 [revised] PHST- 2020/12/24 00:00 [received] PHST- 2021/06/16 00:00 [accepted] PHST- 2021/06/30 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] PHST- 2021/06/29 06:41 [entrez] AID - 10.1002/ajpa.24357 [doi] PST - ppublish SO - Am J Phys Anthropol. 2021 Nov;176(3):445-458. doi: 10.1002/ajpa.24357. Epub 2021 Jun 28. PMID- 34711884 OWN - NLM STAT- MEDLINE DCOM- 20220127 LR - 20240403 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 11 IP - 1 DP - 2021 Oct 28 TI - TKGWV2: an ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data. PG - 21262 LID - 10.1038/s41598-021-00581-3 [doi] LID - 21262 AB - Estimation of genetically related individuals is playing an increasingly important role in the ancient DNA field. In recent years, the numbers of sequenced individuals from single sites have been increasing, reflecting a growing interest in understanding the familial and social organisation of ancient populations. Although a few different methods have been specifically developed for ancient DNA, namely to tackle issues such as low-coverage homozygous data, they require a 0.1-1× minimum average genomic coverage per analysed pair of individuals. Here we present an updated version of a method that enables estimates of 1st and 2nd-degrees of relatedness with as little as 0.026× average coverage, or around 18,000 SNPs from 1.3 million aligned reads per sample with average length of 62 bp-four times less data than 0.1× coverage at similar read lengths. By using simulated data to estimate false positive error rates, we further show that a threshold even as low as 0.012×, or around 4000 SNPs from 600,000 reads, will always show 1st-degree relationships as related. Lastly, by applying this method to published data, we are able to identify previously undocumented relationships using individuals that had been excluded from prior kinship analysis due to their very low coverage. This methodological improvement has the potential to enable relatedness estimation on ancient whole genome shotgun data during routine low-coverage screening, and therefore improve project management when decisions need to be made on which individuals are to be further sequenced. CI - © 2021. The Author(s). FAU - Fernandes, Daniel M AU - Fernandes DM AD - Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria. dani.mag.fernandes@gmail.com. AD - CIAS, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal. dani.mag.fernandes@gmail.com. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria. FAU - Gelabert, Pere AU - Gelabert P AD - Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria. LA - eng PT - Journal Article DEP - 20211028 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Algorithms MH - *Alleles MH - Computational Biology/methods MH - *DNA, Ancient MH - Databases, Genetic MH - Genetic Variation MH - *Genome, Human MH - *Genomics/methods MH - Humans MH - Models, Genetic MH - Polymorphism, Single Nucleotide PMC - PMC8553948 COIS- The authors declare no competing interests. EDAT- 2021/10/30 06:00 MHDA- 2022/01/28 06:00 PMCR- 2021/10/28 CRDT- 2021/10/29 06:07 PHST- 2021/06/22 00:00 [received] PHST- 2021/10/14 00:00 [accepted] PHST- 2021/10/29 06:07 [entrez] PHST- 2021/10/30 06:00 [pubmed] PHST- 2022/01/28 06:00 [medline] PHST- 2021/10/28 00:00 [pmc-release] AID - 10.1038/s41598-021-00581-3 [pii] AID - 581 [pii] AID - 10.1038/s41598-021-00581-3 [doi] PST - epublish SO - Sci Rep. 2021 Oct 28;11(1):21262. doi: 10.1038/s41598-021-00581-3. PMID- 34320653 OWN - NLM STAT- MEDLINE DCOM- 20220328 LR - 20220401 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 38 IP - 11 DP - 2021 Oct 27 TI - Genetic Continuity of Bronze Age Ancestry with Increased Steppe-Related Ancestry in Late Iron Age Uzbekistan. PG - 4908-4917 LID - 10.1093/molbev/msab216 [doi] AB - Although Uzbekistan and Central Asia are known for the well-studied Bronze Age civilization of the Bactria-Margiana Archaeological Complex (BMAC), the lesser-known Iron Age was also a dynamic period that resulted in increased interaction and admixture among different cultures from this region. To broaden our understanding of events that impacted the demography and population structure of this region, we generated 27 genome-wide single-nucleotide polymorphism capture data sets of Late Iron Age individuals around the Historical Kushan time period (∼2100-1500 BP) from three sites in South Uzbekistan. Overall, Bronze Age ancestry persists into the Iron Age in Uzbekistan, with no major replacements of populations with Steppe-related ancestry. However, these individuals suggest diverse ancestries related to Iranian farmers, Anatolian farmers, and Steppe herders, with a small amount of West European Hunter Gatherer, East Asian, and South Asian Hunter Gatherer ancestry as well. Genetic affinity toward the Late Bronze Age Steppe herders and a higher Steppe-related ancestry than that found in BMAC populations suggest an increased mobility and interaction of individuals from the Northern Steppe in a Southward direction. In addition, a decrease of Iranian and an increase of Anatolian farmer-like ancestry in Uzbekistan Iron Age individuals were observed compared with the BMAC populations from Uzbekistan. Thus, despite continuity from the Bronze Age, increased admixture played a major role in the shift from the Bronze to the Iron Age in southern Uzbekistan. This mixed ancestry is also observed in other parts of the Steppe and Central Asia, suggesting more widespread admixture among local populations. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Kumar, Vikas AU - Kumar V AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. AD - Shanghai Qi Zhi Institute, Shanghai 200232, China. FAU - Bennett, E Andrew AU - Bennett EA AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. FAU - Zhao, Dongyue AU - Zhao D AD - School of Cultural Heritage, Northwest University, Xi'an, China. FAU - Liang, Yun AU - Liang Y AD - School of Cultural Heritage, Northwest University, Xi'an, China. FAU - Tang, Yunpeng AU - Tang Y AD - School of Cultural Heritage, Northwest University, Xi'an, China. FAU - Ren, Meng AU - Ren M AD - School of Cultural Heritage, Northwest University, Xi'an, China. FAU - Dai, Qinyan AU - Dai Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. FAU - Yang, Ruowei AU - Yang R AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. FAU - Liu, Feng AU - Liu F AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. FAU - Ping, Wanjing AU - Ping W AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. FAU - Zhang, Ming AU - Zhang M AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. AD - University of Chinese Academy of Sciences, Beijing, China. FAU - Ding, Manyu AU - Ding M AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. AD - University of Chinese Academy of Sciences, Beijing, China. FAU - Yang, Melinda A AU - Yang MA AD - Department of Biology, University of Richmond, Richmond, VA, USA. FAU - Amridin, Berdimurodov AU - Amridin B AD - Institute of Archaeology, Academy of Sciences of Uzbekistan, Samarkand, Uzbekistan. FAU - Muttalib, Hasanov AU - Muttalib H AD - Institute of Archaeology, Academy of Sciences of Uzbekistan, Samarkand, Uzbekistan. FAU - Wang, Jianxin AU - Wang J AD - School of Cultural Heritage, Northwest University, Xi'an, China. FAU - Fu, Qiaomei AU - Fu Q AUID- ORCID: 0000-0002-7141-0002 AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China. AD - Shanghai Qi Zhi Institute, Shanghai 200232, China. AD - University of Chinese Academy of Sciences, Beijing, China. LA - eng GR - 55008731/HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) SB - IM MH - *Archaeology MH - DNA, Ancient MH - Farmers MH - Genome, Human MH - History, Ancient MH - *Human Migration MH - Humans MH - Iran MH - Uzbekistan PMC - PMC8557446 OTO - NOTNLM OT - ancient DNA OT - evolution OT - population genomics EDAT- 2021/07/29 06:00 MHDA- 2022/03/29 06:00 PMCR- 2021/07/28 CRDT- 2021/07/28 20:16 PHST- 2021/07/29 06:00 [pubmed] PHST- 2022/03/29 06:00 [medline] PHST- 2021/07/28 20:16 [entrez] PHST- 2021/07/28 00:00 [pmc-release] AID - 6329832 [pii] AID - msab216 [pii] AID - 10.1093/molbev/msab216 [doi] PST - ppublish SO - Mol Biol Evol. 2021 Oct 27;38(11):4908-4917. doi: 10.1093/molbev/msab216. PMID- 34702906 OWN - NLM STAT- MEDLINE DCOM- 20220131 LR - 20230207 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 11 IP - 1 DP - 2021 Oct 26 TI - Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291-1329 CE) indicates the first known case of late-onset Pompe disease. PG - 21070 LID - 10.1038/s41598-021-00559-1 [doi] LID - 21070 AB - Mummified remains of relevant historical figures are nowadays an important source of information to retrace data concerning their private life and health, especially when historical archives are not available. Next-generation-sequencing was proved to be a valuable tool to unravel the characteristics of these individuals through their genetic heritage. Using the strictest criteria currently available for the validation of ancient DNA sequences, whole-genome and whole-exome sequencing were generated from the mummy remains of an Italian nobleman died almost 700 years ago, Cangrande della Scala. While its genome sequencing could not yield sufficient coverage for in depth investigation, exome sequencing could overcome the limitations of this approach to achieve significantly high coverage on coding regions, thus allowing to perform the first extensive exome analysis of a mummy genome. Similar to a standard "clinical exome analysis" conducted on modern DNA, an in-depth variant annotation, high-quality filtering and interpretation was performed, leading to the identification of a genotype associated with late-onset Pompe disease (glycogen storage disease type II). This genetic diagnosis was concordant with the limited clinical history available for Cangrande della Scala, who likely represents the earliest known case of this autosomal recessive metabolic disorder. CI - © 2021. The Author(s). FAU - Iadarola, Barbara AU - Iadarola B AD - Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. FAU - Lavezzari, Denise AU - Lavezzari D AD - Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. FAU - Modi, Alessandra AU - Modi A AD - Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy. FAU - Degli Esposti, Chiara AU - Degli Esposti C AD - Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. FAU - Beltrami, Cristina AU - Beltrami C AD - Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. FAU - Rossato, Marzia AU - Rossato M AD - Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. FAU - Zaro, Valentina AU - Zaro V AD - Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy. FAU - Napione, Ettore AU - Napione E AD - UNESCO Office, Municipality of Verona, Piazza Bra 1, 37121, Verona, Italy. FAU - Latella, Leonardo AU - Latella L AD - Department of Zoology, Natural History Museum of Verona, Lungadige Porta Vittoria 9, 37129, Verona, Italy. FAU - Lari, Martina AU - Lari M AD - Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy. FAU - Caramelli, David AU - Caramelli D AD - Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy. david.caramelli@unifi.it. FAU - Salviati, Alessandro AU - Salviati A AD - Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. FAU - Delledonne, Massimo AU - Delledonne M AD - Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. massimo.delledonne@univr.it. LA - eng PT - Historical Article PT - Journal Article DEP - 20211026 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - Glycogen Storage Disease Type II/*genetics/history MH - History, Medieval MH - Humans MH - Male MH - *Mummies MH - *Exome Sequencing PMC - PMC8548527 COIS- The authors declare no competing interests. EDAT- 2021/10/28 06:00 MHDA- 2022/02/01 06:00 PMCR- 2021/10/26 CRDT- 2021/10/27 06:40 PHST- 2021/06/08 00:00 [received] PHST- 2021/10/14 00:00 [accepted] PHST- 2021/10/27 06:40 [entrez] PHST- 2021/10/28 06:00 [pubmed] PHST- 2022/02/01 06:00 [medline] PHST- 2021/10/26 00:00 [pmc-release] AID - 10.1038/s41598-021-00559-1 [pii] AID - 559 [pii] AID - 10.1038/s41598-021-00559-1 [doi] PST - epublish SO - Sci Rep. 2021 Oct 26;11(1):21070. doi: 10.1038/s41598-021-00559-1. PMID- 34437844 OWN - NLM STAT- MEDLINE DCOM- 20220408 LR - 20220408 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 31 IP - 20 DP - 2021 Oct 25 TI - The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans. PG - 4650-4658.e6 LID - S0960-9822(21)01112-X [pii] LID - 10.1016/j.cub.2021.08.010 [doi] AB - Following the advent of industrial-scale antibiotic production in the 1940s,(1) antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.(2)(,)(3) Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.(4) However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.(4)(,)(5) One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife. CI - Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Brealey, Jaelle C AU - Brealey JC AD - Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden. Electronic address: jaelle.brealey@ntnu.no. FAU - Leitão, Henrique G AU - Leitão HG AD - Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden. FAU - Hofstede, Thijs AU - Hofstede T AD - Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden. FAU - Kalthoff, Daniela C AU - Kalthoff DC AD - Department of Zoology, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden. FAU - Guschanski, Katerina AU - Guschanski K AD - Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden; Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK. Electronic address: katerina.guschanski@ebc.uu.se. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210825 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (Anti-Bacterial Agents) SB - IM CIN - Curr Biol. 2021 Oct 25;31(20):R1385-R1387. doi: 10.1016/j.cub.2021.08.037. PMID: 34699802 MH - Animals MH - Animals, Wild MH - Anti-Bacterial Agents/pharmacology MH - Drug Resistance, Bacterial/genetics MH - Humans MH - *Microbiota/genetics MH - Sweden MH - *Ursidae OTO - NOTNLM OT - ancient DNA OT - antibiotic resistance genes OT - antimicrobial resistance OT - brown bear OT - dental calculus OT - environmental contamination OT - metagenomics COIS- Declaration of interests The authors declare no competing interests. EDAT- 2021/08/27 06:00 MHDA- 2022/04/09 06:00 CRDT- 2021/08/26 20:12 PHST- 2021/06/17 00:00 [received] PHST- 2021/07/23 00:00 [revised] PHST- 2021/08/02 00:00 [accepted] PHST- 2021/08/27 06:00 [pubmed] PHST- 2022/04/09 06:00 [medline] PHST- 2021/08/26 20:12 [entrez] AID - S0960-9822(21)01112-X [pii] AID - 10.1016/j.cub.2021.08.010 [doi] PST - ppublish SO - Curr Biol. 2021 Oct 25;31(20):4650-4658.e6. doi: 10.1016/j.cub.2021.08.010. Epub 2021 Aug 25. PMID- 34419425 OWN - NLM STAT- MEDLINE DCOM- 20240724 LR - 20240725 IS - 1673-8527 (Print) IS - 1673-8527 (Linking) VI - 48 IP - 10 DP - 2021 Oct 20 TI - Maternal genetic history of southern East Asians over the past 12,000 years. PG - 899-907 LID - S1673-8527(21)00170-3 [pii] LID - 10.1016/j.jgg.2021.06.002 [doi] AB - Southern East Asia, including Guangxi and Fujian provinces in China, is home to diverse ethnic groups, languages, and cultures. Previous studies suggest a high complexity regarding population dynamics and the history of southern East Asians. However, large-scale genetic studies on ancient populations in this region are hindered by limited sample preservation. Here, using highly efficient DNA capture techniques, we obtain 48 complete mitochondrial genomes of individuals from Guangxi and Fujian in China and reconstruct their maternal genetic history over the past 12,000 years. We find a strong connection between southern East Asians dating to ~12,000-6000 years ago and present-day Southeast Asians. In addition, stronger genetic affinities to northern East Asians are observed in historical southern East Asians than Neolithic southern East Asians, suggesting increased interactions between northern and southern East Asians over time. Overall, we reveal dynamic connections between ancient southern East Asians and populations located in surrounding regions, as well as a shift in maternal genetic structure within the populations over time. CI - Copyright © 2021 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved. FAU - Liu, Yalin AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Sino-Danish Center, University of the Chinese Academy of Sciences, Beijing 100049, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Wang, Tianyi AU - Wang T AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Northwest University, Xi'an 710069, China. FAU - Wu, Xichao AU - Wu X AD - Fujian Longyan Museum, Longyan 364000, China. FAU - Fan, Xuechun AU - Fan X AD - International Research Center for Austronesian Archaeology, Pingtan 350000, China; Fujian Museum, Fuzhou 350001, China. FAU - Wang, Wei AU - Wang W AD - Institute of Cultural Heritage, Shandong University, Qingdao 266237, China. FAU - Xie, Guangmao AU - Xie G AD - Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China; College of History, Culture and Tourism, Guangxi Normal University, Guilin 541001, China. FAU - Li, Zhen AU - Li Z AD - Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China. FAU - Yang, Qingping AU - Yang Q AD - Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Yang, Ruowei AU - Yang R AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Liu, Feng AU - Liu F AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Dai, Qingyan AU - Dai Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Ping, Wanjing AU - Ping W AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Miao, Bo AU - Miao B AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Northwest University, Xi'an 710069, China. FAU - Wu, Yun AU - Wu Y AD - Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China. FAU - Liu, Yichen AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. Electronic address: yichen.liu@ivpp.ac.cn. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng GR - 55008731/HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article DEP - 20210621 PL - China TA - J Genet Genomics JT - Journal of genetics and genomics = Yi chuan xue bao JID - 101304616 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) MH - Female MH - Humans MH - Asia, Eastern MH - *Asian People/genetics MH - China MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/genetics MH - Genetics, Population MH - Genome, Mitochondrial/genetics MH - Haplotypes/genetics MH - History, Ancient MH - Maternal Inheritance/genetics OTO - NOTNLM OT - Ancient DNA OT - Maternal genetic structure OT - Population history OT - Southern East Asians EDAT- 2021/08/23 06:00 MHDA- 2022/02/25 06:00 CRDT- 2021/08/22 20:41 PHST- 2021/04/19 00:00 [received] PHST- 2021/06/04 00:00 [revised] PHST- 2021/06/05 00:00 [accepted] PHST- 2021/08/23 06:00 [pubmed] PHST- 2022/02/25 06:00 [medline] PHST- 2021/08/22 20:41 [entrez] AID - S1673-8527(21)00170-3 [pii] AID - 10.1016/j.jgg.2021.06.002 [doi] PST - ppublish SO - J Genet Genomics. 2021 Oct 20;48(10):899-907. doi: 10.1016/j.jgg.2021.06.002. Epub 2021 Jun 21. PMID- 34610848 OWN - NLM STAT- MEDLINE DCOM- 20220201 LR - 20231102 IS - 1741-7007 (Electronic) IS - 1741-7007 (Linking) VI - 19 IP - 1 DP - 2021 Oct 5 TI - Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes. PG - 220 LID - 10.1186/s12915-021-01120-2 [doi] LID - 220 AB - BACKGROUND: Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. RESULTS: Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. CONCLUSIONS: Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions. CI - © 2021. The Author(s). FAU - Pfrengle, Saskia AU - Pfrengle S AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. FAU - Neukamm, Judith AU - Neukamm J AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. AD - Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany. FAU - Guellil, Meriam AU - Guellil M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. FAU - Keller, Marcel AU - Keller M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. FAU - Molak, Martyna AU - Molak M AD - Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland. FAU - Avanzi, Charlotte AU - Avanzi C AD - Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, USA. AD - Swiss and Tropical Public Health Institute, Basel, Switzerland. FAU - Kushniarevich, Alena AU - Kushniarevich A AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. FAU - Montes, Núria AU - Montes N AD - Unitat d'Antropologia Biològica, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain. FAU - Neumann, Gunnar U AU - Neumann GU AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. FAU - Reiter, Ella AU - Reiter E AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. FAU - Tukhbatova, Rezeda I AU - Tukhbatova RI AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. AD - Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation, 420008. FAU - Berezina, Nataliya Y AU - Berezina NY AD - Research Institute and Museum of Anthropology, Moscow State University, 125009, Mokhovaya str. 11, Moscow, Russian Federation. FAU - Buzhilova, Alexandra P AU - Buzhilova AP AD - Research Institute and Museum of Anthropology, Moscow State University, 125009, Mokhovaya str. 11, Moscow, Russian Federation. FAU - Korobov, Dmitry S AU - Korobov DS AD - The Institute of Archaeology of the Russian Academy of Sciences, 117292, Dm. Uljanova str. 19, Moscow, Russian Federation. FAU - Suppersberger Hamre, Stian AU - Suppersberger Hamre S AD - Department of Archaeology, History, Cultural studies and religion, University of Bergen, 5020, Bergen, Norway. FAU - Matos, Vitor M J AU - Matos VMJ AD - Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. FAU - Ferreira, Maria T AU - Ferreira MT AD - Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Centre for Functional Ecology, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. AD - Área de Antropología Física, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana, 24071, León, Spain. FAU - González-Garrido, Laura AU - González-Garrido L AD - Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. AD - Área de Antropología Física, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana, 24071, León, Spain. AD - Institute of Biomedicine (IBIOMED), Universidad de León, Campus de Vegazana, 24071, León, Spain. FAU - Wasterlain, Sofia N AU - Wasterlain SN AD - Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. FAU - Lopes, Célia AU - Lopes C AD - Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. AD - Laboratory of Biological Anthropology, Department of Biology; School of Science and Technology, University of Évora, Évora, Portugal. FAU - Santos, Ana Luisa AU - Santos AL AD - Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. FAU - Antunes-Ferreira, Nathalie AU - Antunes-Ferreira N AD - Laboratório de Ciências Forenses e Psicológicas Egas Moniz (LCFPEM), Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Egas Moniz CRL, Monte de Caparica, Portugal. AD - Laboratory of Biological Anthropology and Human Osteology (LABOH), CRIA/FCSH, Universidade NOVA de Lisboa, Lisbon, Portugal. FAU - Duarte, Vitória AU - Duarte V AD - Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. FAU - Silva, Ana Maria AU - Silva AM AD - Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. AD - Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Centre for Functional Ecology, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. AD - UNIARQ - University of Lisbon, Lisbon, Portugal. FAU - Melo, Linda AU - Melo L AD - Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal. FAU - Sarkic, Natasa AU - Sarkic N AD - OSTEO Research, Camino de la Iglesia 1, Barrio de mata, Santiuste De Pedraza, 40171, Segovia, Spain. FAU - Saag, Lehti AU - Saag L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. FAU - Tambets, Kristiina AU - Tambets K AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. FAU - Busso, Philippe AU - Busso P AD - Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. FAU - Cole, Stewart T AU - Cole ST AD - Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. AD - Institut Pasteur, 25-28, rue du Docteur Roux, 75724, Paris Cedex 15, France. FAU - Avlasovich, Alexei AU - Avlasovich A AD - Department of Archeology, History of Belarus and Special Historical Disciplines, Mogilev State A. Kuleshov University, Str Kosmonavtov 1, Mogilev, 212022, Republic of Belarus. FAU - Roberts, Charlotte A AU - Roberts CA AD - Department of Archaeology, Durham University, South Road, Durham, DH1 3 LE, UK. FAU - Sheridan, Alison AU - Sheridan A AD - Department of Scottish History and Archaeology, National Museums Scotland, Chambers Street, Edinburgh, EH1 1JF, UK. FAU - Cessford, Craig AU - Cessford C AD - Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK. FAU - Robb, John AU - Robb J AD - Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK. FAU - Krause, Johannes AU - Krause J AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. AD - Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. FAU - Scheib, Christiana L AU - Scheib CL AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. cls83@ut.ee. AD - St John's College, University of Cambridge, Cambridge, CB2 1TP, UK. cls83@ut.ee. FAU - Inskip, Sarah A AU - Inskip SA AD - School of Archaeology and Ancient History, University of Leicester, Leicester, LE1 7RH, UK. si159@leicester.ac.uk. FAU - Schuenemann, Verena J AU - Schuenemann VJ AUID- ORCID: 0000-0002-8593-3672 AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. verena.schuenemann@iem.uzh.ch. AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. verena.schuenemann@iem.uzh.ch. AD - Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. verena.schuenemann@iem.uzh.ch. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom GR - 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20211005 PL - England TA - BMC Biol JT - BMC biology JID - 101190720 SB - IM MH - Europe MH - Genome, Bacterial/genetics MH - Humans MH - Leprosy/genetics MH - *Mycobacterium leprae/genetics MH - Population Dynamics PMC - PMC8493730 OTO - NOTNLM OT - Ancient DNA OT - Ancient pathogen genomics OT - Leprosaria OT - Mycobacterium leprae OT - Paleomicrobiology OT - Paleopathology OT - Pathogen diversity OT - Pathogen population dynamics COIS- The authors declare no competing interests. EDAT- 2021/10/07 06:00 MHDA- 2022/02/02 06:00 PMCR- 2021/10/05 CRDT- 2021/10/06 05:33 PHST- 2021/05/28 00:00 [received] PHST- 2021/08/07 00:00 [accepted] PHST- 2021/10/06 05:33 [entrez] PHST- 2021/10/07 06:00 [pubmed] PHST- 2022/02/02 06:00 [medline] PHST- 2021/10/05 00:00 [pmc-release] AID - 10.1186/s12915-021-01120-2 [pii] AID - 1120 [pii] AID - 10.1186/s12915-021-01120-2 [doi] PST - epublish SO - BMC Biol. 2021 Oct 5;19(1):220. doi: 10.1186/s12915-021-01120-2. PMID- 34424406 OWN - NLM STAT- MEDLINE DCOM- 20210930 LR - 20211204 IS - 1432-1203 (Electronic) IS - 0340-6717 (Linking) VI - 140 IP - 10 DP - 2021 Oct TI - Dissecting the genetic history of the Roman Catholic populations of West Coast India. PG - 1487-1498 LID - 10.1007/s00439-021-02346-4 [doi] AB - Migration and admixture history of populations have always been curious and an interesting theme. The West Coast of India harbours a rich diversity, bestowing various ethno-linguistic groups, with many of them having well-documented history of migrations. The Roman Catholic is one such distinct group, whose origin was much debated. While some historians and anthropologists relating them to ancient group of Gaud Saraswat Brahmins, others relating them for being members of the Jews Lost Tribes in the first Century migration to India. Historical records suggests that this community was later forcibly converted to Christianity by the Portuguese in Goa during the Sixteenth Century. Till date, no genetic study was done on this group to infer their origin and genetic affinity. Hence, we analysed 110 Roman Catholics from three different locations of West Coast of India including Goa, Kumta and Mangalore using both uniparental and autosomal markers to understand their genetic history. We found that the Roman Catholics have close affinity with the Indo-European linguistic groups, particularly Brahmins. Additionally, we detected genetic signal of Jews in the linkage disequilibrium-based admixture analysis, which was absent in other Indo-European populations, who are inhabited in the same geographical regions. Haplotype-based analysis suggests that the Roman Catholics consist of South Asian-specific ancestry and showed high drift. Ancestry-specific historical population size estimation points to a possible bottleneck around the time of Goan inquisition (fifteenth century). Analysis of the Roman Catholics data along with ancient DNA data of Neolithic and bronze age revealed that the Roman Catholics fits well in a basic model of ancient ancestral composition, typical of most of the Indo-European caste groups of India. Mitochondrial DNA (mtDNA) analysis suggests that most of the Roman Catholics have aboriginal Indian maternal genetic ancestry; while the Y chromosomal DNA analysis indicates high frequency of R1a lineage, which is predominant in groups with higher ancestral North Indian (ANI) component. Therefore, we conclude that the Roman Catholics of Goa, Kumta and Mangalore regions are the remnants of very early lineages of Brahmin community of India, having Indo-Europeans genetic affinity along with cryptic Jewish admixture, which needs to be explored further. CI - © 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. FAU - Kumar, Lomous AU - Kumar L AD - CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India. FAU - Farias, Kranti AU - Farias K AD - Canadian Institute for Jewish Research, Montreal, Canada. FAU - Prakash, Satya AU - Prakash S AD - CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India. FAU - Mishra, Anshuman AU - Mishra A AD - Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, 590 53, Ulrika, Sweden. FAU - Mustak, Mohammed S AU - Mustak MS AD - Department of Applied Zoology, Mangalore University, Mangalore, 574199, India. FAU - Rai, Niraj AU - Rai N AD - Birbal Sahni Institute of Palaeosciences, Uttar Pradesh, 53 University Road, Lucknow, 226007, India. nirajrai@bsip.res.in. FAU - Thangaraj, Kumarasamy AU - Thangaraj K AD - CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India. thangs@ccmb.res.in. AD - DBT-Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, 500007, India. thangs@ccmb.res.in. LA - eng PT - Journal Article DEP - 20210823 PL - Germany TA - Hum Genet JT - Human genetics JID - 7613873 SB - IM MH - *Catholicism MH - Ethnicity/*genetics/statistics & numerical data MH - Europe MH - *Evolution, Molecular MH - *Genetic Variation MH - Genetics, Population/*statistics & numerical data MH - *Geography MH - Humans MH - India MH - Jews/genetics MH - Phylogeny MH - *Population Dynamics EDAT- 2021/08/24 06:00 MHDA- 2021/10/01 06:00 CRDT- 2021/08/23 12:29 PHST- 2021/04/09 00:00 [received] PHST- 2021/08/12 00:00 [accepted] PHST- 2021/08/24 06:00 [pubmed] PHST- 2021/10/01 06:00 [medline] PHST- 2021/08/23 12:29 [entrez] AID - 10.1007/s00439-021-02346-4 [pii] AID - 10.1007/s00439-021-02346-4 [doi] PST - ppublish SO - Hum Genet. 2021 Oct;140(10):1487-1498. doi: 10.1007/s00439-021-02346-4. Epub 2021 Aug 23. PMID- 34308549 OWN - NLM STAT- MEDLINE DCOM- 20211011 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 176 IP - 2 DP - 2021 Oct TI - Maternal genetic origin of the late and final Neolithic human populations from present-day Poland. PG - 223-236 LID - 10.1002/ajpa.24372 [doi] AB - OBJECTIVE: We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS: We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS: The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION: The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances. CI - © 2021 Wiley Periodicals LLC. FAU - Juras, Anna AU - Juras A AUID- ORCID: 0000-0002-2585-127X AD - Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland. FAU - Ehler, Edvard AU - Ehler E AD - Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i, Prague, Czech Republic. FAU - Chyleński, Maciej AU - Chyleński M AD - Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland. FAU - Pospieszny, Łukasz AU - Pospieszny Ł AD - Department of Anthropology and Archaeology, University of Bristol, Bristol, UK. AD - Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland. FAU - Spinek, Anna Elżbieta AU - Spinek AE AUID- ORCID: 0000-0003-0304-081X AD - Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland. FAU - Malmström, Helena AU - Malmström H AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. AD - Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa. FAU - Krzewińska, Maja AU - Krzewińska M AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. AD - Centre for Palaeogenetics, Stockholm, Sweden. FAU - Szostek, Krzysztof AU - Szostek K AD - Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, Warszawa, Poland. FAU - Pasterkiewicz, Wojciech AU - Pasterkiewicz W AD - Institute of Archaeology, University of Rzeszów, Rzeszów, Poland. FAU - Florek, Marek AU - Florek M AD - Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland. FAU - Wilk, Stanisław AU - Wilk S AD - Institute of Archaeology, Jagiellonian University, Kraków, Poland. AD - The Karkonosze Museum in Jelenia Góra, Jelenia Góra, Poland. FAU - Mnich, Barbara AU - Mnich B AD - Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University in Kraków, Kraków, Poland. FAU - Kruk, Janusz AU - Kruk J AD - Polish Academy of Sciences, Institute of Archaeology and Ethnology, Kraków, Poland. FAU - Szmyt, Marzena AU - Szmyt M AD - Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland. AD - Archaeological Museum, Poznań, Poland. FAU - Kozieł, Sławomir AU - Kozieł S AD - Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland. FAU - Götherström, Anders AU - Götherström A AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. AD - Centre for Palaeogenetics, Stockholm, Sweden. FAU - Jakobsson, Mattias AU - Jakobsson M AUID- ORCID: 0000-0001-7840-7853 AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. AD - Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa. FAU - Dabert, Miroslawa AU - Dabert M AD - Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210726 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - *DNA, Ancient MH - DNA, Mitochondrial/*genetics MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Poland MH - White People/*genetics OTO - NOTNLM OT - Central Europe OT - Neolithic OT - ancient DNA OT - human population OT - mitochondrial haplogroups EDAT- 2021/07/27 06:00 MHDA- 2021/10/12 06:00 CRDT- 2021/07/26 06:58 PHST- 2021/06/22 00:00 [revised] PHST- 2021/01/18 00:00 [received] PHST- 2021/07/07 00:00 [accepted] PHST- 2021/07/27 06:00 [pubmed] PHST- 2021/10/12 06:00 [medline] PHST- 2021/07/26 06:58 [entrez] AID - 10.1002/ajpa.24372 [doi] PST - ppublish SO - Am J Phys Anthropol. 2021 Oct;176(2):223-236. doi: 10.1002/ajpa.24372. Epub 2021 Jul 26. PMID- 34210535 OWN - NLM STAT- MEDLINE DCOM- 20210927 LR - 20210927 IS - 1872-8383 (Electronic) IS - 0169-5347 (Linking) VI - 36 IP - 10 DP - 2021 Oct TI - Archaeology and agriculture: plants, people, and past land-use. PG - 943-954 LID - S0169-5347(21)00176-2 [pii] LID - 10.1016/j.tree.2021.06.003 [doi] AB - As a specialised branch of archaeology requiring specific field and laboratory methodologies, the contributions of archaeobotany have often been overlooked by the ecological research community. Developments in the fields of botany, chemistry, and ancient DNA analyses have greatly increased the potential for archaeobotany to contribute to topical questions relating to the Anthropocene and landscape transformations. We review the role of archaeobotany in identifying and describing past arable land use. Analytical techniques are illustrated with examples at both local and regional scales, demonstrating how archaeobotany can provide unique details of the wide array of past subsistence and land-use strategies. These data and their potential should be better recognised as important information that could underpin models seeking to evaluate or predict the effects of socioenvironmental interactions. CI - Copyright © 2021 Elsevier Ltd. All rights reserved. FAU - de Vareilles, Anne AU - de Vareilles A AD - Historic England, Fort Cumberland, Fort Cumberland Road, Portsmouth P04 9LD, UK. Electronic address: anne.devareilles@historicengland.org.uk. FAU - Pelling, Ruth AU - Pelling R AD - Historic England, Fort Cumberland, Fort Cumberland Road, Portsmouth P04 9LD, UK. FAU - Woodbridge, Jessie AU - Woodbridge J AD - School of Geography, Earth and Environmental Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK. FAU - Fyfe, Ralph AU - Fyfe R AD - School of Geography, Earth and Environmental Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20210628 PL - England TA - Trends Ecol Evol JT - Trends in ecology & evolution JID - 8805125 SB - IM MH - Agriculture MH - *Archaeology MH - *Botany MH - Humans MH - Plants OTO - NOTNLM OT - ancient agriculture OT - archaeobotany OT - land cover OT - land use OT - landscape transformations COIS- Declaration of interests The authors declare no conflicts of interest. EDAT- 2021/07/03 06:00 MHDA- 2021/09/28 06:00 CRDT- 2021/07/02 05:45 PHST- 2021/02/12 00:00 [received] PHST- 2021/05/27 00:00 [revised] PHST- 2021/06/03 00:00 [accepted] PHST- 2021/07/03 06:00 [pubmed] PHST- 2021/09/28 06:00 [medline] PHST- 2021/07/02 05:45 [entrez] AID - S0169-5347(21)00176-2 [pii] AID - 10.1016/j.tree.2021.06.003 [doi] PST - ppublish SO - Trends Ecol Evol. 2021 Oct;36(10):943-954. doi: 10.1016/j.tree.2021.06.003. Epub 2021 Jun 28. PMID- 33992907 OWN - NLM STAT- MEDLINE DCOM- 20211124 LR - 20221221 IS - 1879-0372 (Electronic) IS - 0952-7915 (Print) IS - 0952-7915 (Linking) VI - 72 DP - 2021 Oct TI - New insights into human immunity from ancient genomics. PG - 116-125 LID - S0952-7915(21)00045-5 [pii] LID - 10.1016/j.coi.2021.04.006 [doi] AB - Population genetic studies have clearly indicated that immunity and host defense are among the functions most frequently subject to natural selection, and increased our understanding of the biological relevance of the corresponding genes and their contribution to variable immune traits and diseases. Herein, we will focus on some recently studied forms of human adaptation to infectious agents, including hybridization with now-extinct hominins, such as Neanderthals and Denisovans, and admixture between modern human populations. These studies, which are partly enabled by the technological advances in the sequencing of DNA from ancient remains, provide new insight into the sources of immune response variation in contemporary humans, such as the recently reported link between Neanderthal heritage and susceptibility to severe COVID-19 disease. Furthermore, ancient DNA analyses, in both humans and pathogens, allow to measure the action of natural selection on immune genes across time and to reconstruct the impact of past epidemics on the evolution of human immunity. CI - Copyright © 2021 Elsevier Ltd. All rights reserved. FAU - Kerner, Gaspard AU - Kerner G AD - Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France. FAU - Patin, Etienne AU - Patin E AD - Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France. FAU - Quintana-Murci, Lluis AU - Quintana-Murci L AD - Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France; Chair Human Genomics and Evolution, Collège de France, Paris 75005, France. Electronic address: quintana@pasteur.fr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20210513 PL - England TA - Curr Opin Immunol JT - Current opinion in immunology JID - 8900118 SB - IM MH - Animals MH - COVID-19/epidemiology/genetics/*immunology MH - Evolution, Molecular MH - Genetic Predisposition to Disease MH - Genetics, Population MH - Genomics MH - Hominidae MH - Humans MH - Immunity/*genetics MH - SARS-CoV-2/*physiology PMC - PMC8452260 EDAT- 2021/05/17 06:00 MHDA- 2021/11/25 06:00 PMCR- 2021/05/13 CRDT- 2021/05/16 20:44 PHST- 2021/03/25 00:00 [received] PHST- 2021/04/13 00:00 [revised] PHST- 2021/04/14 00:00 [accepted] PHST- 2021/05/17 06:00 [pubmed] PHST- 2021/11/25 06:00 [medline] PHST- 2021/05/16 20:44 [entrez] PHST- 2021/05/13 00:00 [pmc-release] AID - S0952-7915(21)00045-5 [pii] AID - 10.1016/j.coi.2021.04.006 [doi] PST - ppublish SO - Curr Opin Immunol. 2021 Oct;72:116-125. doi: 10.1016/j.coi.2021.04.006. Epub 2021 May 13. PMID- 34593021 OWN - NLM STAT- MEDLINE DCOM- 20211022 LR - 20240403 IS - 2049-2618 (Electronic) IS - 2049-2618 (Linking) VI - 9 IP - 1 DP - 2021 Sep 30 TI - Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. PG - 197 LID - 10.1186/s40168-021-01132-8 [doi] LID - 197 AB - BACKGROUND: Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE). RESULTS: We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. CONCLUSIONS: We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract. CI - © 2021. The Author(s). FAU - Granehäll, Lena AU - Granehäll L AUID- ORCID: 0000-0001-9970-4080 AD - Institute for Mummy Studies, Eurac Research, 39100, Bolzano, Italy. lena.granehaell@eurac.edu. AD - Faculty of Biology, Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University of Munich, 82152, Planegg-Martinsried, Germany. lena.granehaell@eurac.edu. FAU - Huang, Kun D AU - Huang KD AD - CIBIO Department, University of Trento, 38123, Trento, Italy. kun.huang@unitn.it. AD - Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy. kun.huang@unitn.it. FAU - Tett, Adrian AU - Tett A AD - CIBIO Department, University of Trento, 38123, Trento, Italy. AD - CUBE - Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. FAU - Manghi, Paolo AU - Manghi P AD - CIBIO Department, University of Trento, 38123, Trento, Italy. FAU - Paladin, Alice AU - Paladin A AD - Institute for Mummy Studies, Eurac Research, 39100, Bolzano, Italy. FAU - O'Sullivan, Niall AU - O'Sullivan N AD - Institute for Mummy Studies, Eurac Research, 39100, Bolzano, Italy. FAU - Rota-Stabelli, Omar AU - Rota-Stabelli O AD - Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy. AD - Center Agriculture Food Environment, University of Trento, 38123, Trento, Italy. FAU - Segata, Nicola AU - Segata N AD - CIBIO Department, University of Trento, 38123, Trento, Italy. nicola.segata@unitn.it. FAU - Zink, Albert AU - Zink A AD - Institute for Mummy Studies, Eurac Research, 39100, Bolzano, Italy. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, Eurac Research, 39100, Bolzano, Italy. frank.maixner@eurac.edu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Video-Audio Media DEP - 20210930 PL - England TA - Microbiome JT - Microbiome JID - 101615147 SB - IM MH - *Archaea/genetics MH - Dental Calculus MH - Humans MH - *Metagenome MH - Methanobrevibacter/genetics MH - Middle Aged MH - Phylogeny PMC - PMC8485483 OTO - NOTNLM OT - Ancient DNA OT - Ancient dental calculus OT - De novo assembly OT - Metagenomics OT - Methanobrevibacter OT - Oral microbiome COIS- The authors declare that they have no competing interests. EDAT- 2021/10/02 06:00 MHDA- 2023/02/25 06:00 PMCR- 2021/09/30 CRDT- 2021/10/01 05:44 PHST- 2021/03/12 00:00 [received] PHST- 2021/07/01 00:00 [accepted] PHST- 2021/10/01 05:44 [entrez] PHST- 2021/10/02 06:00 [pubmed] PHST- 2023/02/25 06:00 [medline] PHST- 2021/09/30 00:00 [pmc-release] AID - 10.1186/s40168-021-01132-8 [pii] AID - 1132 [pii] AID - 10.1186/s40168-021-01132-8 [doi] PST - epublish SO - Microbiome. 2021 Sep 30;9(1):197. doi: 10.1186/s40168-021-01132-8. PMID- 34002224 OWN - NLM STAT- MEDLINE DCOM- 20220325 LR - 20241214 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 38 IP - 10 DP - 2021 Sep 27 TI - Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes. PG - 4059-4076 LID - 10.1093/molbev/msab147 [doi] AB - Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes, we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggest that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Immel, Alexander AU - Immel A AUID- ORCID: 0000-0002-8970-4383 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. AD - Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Key, Felix M AU - Key FM AUID- ORCID: 0000-0003-2812-6636 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Infection Biology, Berlin, Germany. FAU - Szolek, András AU - Szolek A AD - Applied Bioinformatics, Department for Computer Science, University of Tübingen, Tübingen, Germany. FAU - Barquera, Rodrigo AU - Barquera R AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Robinson, Madeline K AU - Robinson MK AD - Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, Boulder, CO, USA. FAU - Harrison, Genelle F AU - Harrison GF AD - Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, Boulder, CO, USA. FAU - Palmer, William H AU - Palmer WH AD - Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, Boulder, CO, USA. FAU - Spyrou, Maria A AU - Spyrou MA AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Susat, Julian AU - Susat J AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Bos, Kirsten I AU - Bos KI AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Forrest, Stephen AU - Forrest S AD - Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Hernández-Zaragoza, Diana I AU - Hernández-Zaragoza DI AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico. FAU - Sauter, Jürgen AU - Sauter J AD - DKMS, Tübingen, Germany. FAU - Solloch, Ute AU - Solloch U AD - DKMS, Tübingen, Germany. FAU - Schmidt, Alexander H AU - Schmidt AH AD - DKMS, Tübingen, Germany. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Reiter, Ella AU - Reiter E AD - Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Kairies, Madita S AU - Kairies MS AD - Institute for Archaeological Sciences, WG Palaeoanthropology, University of Tübingen, Tübingen, Germany. FAU - Weiß, Rainer AU - Weiß R AD - State Office for Cultural Heritage Management, Stuttgart Regional Council, Esslingen, Germany. FAU - Arnold, Susanne AU - Arnold S AD - State Office for Cultural Heritage Management, Stuttgart Regional Council, Esslingen, Germany. FAU - Wahl, Joachim AU - Wahl J AD - Institute for Archaeological Sciences, WG Palaeoanthropology, University of Tübingen, Tübingen, Germany. AD - State Office for Cultural Heritage Management, Stuttgart Regional Council, Esslingen, Germany. FAU - Hollenbach, Jill A AU - Hollenbach JA AD - UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA. FAU - Kohlbacher, Oliver AU - Kohlbacher O AD - Applied Bioinformatics, Department for Computer Science, University of Tübingen, Tübingen, Germany. AD - Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany. AD - Quantitative Biology Center, University of Tübingen, Tübingen, Germany. AD - Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany. AD - Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany. FAU - Herbig, Alexander AU - Herbig A AUID- ORCID: 0000-0003-1176-1166 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Norman, Paul J AU - Norman PJ AD - Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, Boulder, CO, USA. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. LA - eng GR - R01 AI158410/AI/NIAID NIH HHS/United States GR - R01 AI158861/AI/NIAID NIH HHS/United States GR - R56 AI151549/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 9007-49-2 (DNA) SB - IM MH - DNA MH - Genomics MH - Humans MH - Pandemics/history MH - *Plague/genetics MH - *Yersinia pestis/genetics PMC - PMC8476174 OTO - NOTNLM OT - HLA OT - Yersinia pestis OT - aDNA OT - ancient DNA OT - human immunity OT - natural selection OT - plague EDAT- 2021/05/19 06:00 MHDA- 2022/03/26 06:00 PMCR- 2021/05/18 CRDT- 2021/05/18 07:12 PHST- 2021/05/19 06:00 [pubmed] PHST- 2022/03/26 06:00 [medline] PHST- 2021/05/18 07:12 [entrez] PHST- 2021/05/18 00:00 [pmc-release] AID - 6277411 [pii] AID - msab147 [pii] AID - 10.1093/molbev/msab147 [doi] PST - ppublish SO - Mol Biol Evol. 2021 Sep 27;38(10):4059-4076. doi: 10.1093/molbev/msab147. PMID- 34554811 OWN - NLM STAT- MEDLINE DCOM- 20211001 LR - 20220302 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 373 IP - 6562 DP - 2021 Sep 24 TI - Insights into human history from the first decade of ancient human genomics. PG - 1479-1484 LID - 10.1126/science.abi8202 [doi] AB - Recent advancements in DNA sequencing technologies and laboratory preparation protocols have rapidly expanded the scope of ancient DNA research over the past decade, both temporally and geographically. Discoveries include interactions between archaic and modern humans as well as modern human population dynamics, including those coinciding with the Last Glacial Maximum and the settlement history of most world regions. This new type of data allows us to examine the deep past of human population dynamics and sharpen the current understanding of our present. The continued development in the ancient DNA field has transformed our understanding of human genetic history and will keep uncovering the further mysteries of our recent evolutionary past. FAU - Liu, Yichen AU - Liu Y AUID- ORCID: 0000-0002-7187-6232 AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China. FAU - Mao, Xiaowei AU - Mao X AUID- ORCID: 0000-0002-1758-6867 AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Fu, Qiaomei AU - Fu Q AUID- ORCID: 0000-0002-7141-0002 AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China. AD - University of the Chinese Academy of Sciences, Beijing, 100049, China. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20210923 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Africa MH - Americas MH - Animals MH - Asia MH - Biological Evolution MH - *DNA, Ancient MH - Europe MH - *Genome, Human MH - *Genomics MH - History, Ancient MH - Human Migration MH - Humans MH - Neanderthals/genetics MH - Oceania MH - *Population Dynamics MH - Siberia EDAT- 2021/09/24 06:00 MHDA- 2021/10/02 06:00 CRDT- 2021/09/23 17:14 PHST- 2021/09/23 17:14 [entrez] PHST- 2021/09/24 06:00 [pubmed] PHST- 2021/10/02 06:00 [medline] AID - 10.1126/science.abi8202 [doi] PST - ppublish SO - Science. 2021 Sep 24;373(6562):1479-1484. doi: 10.1126/science.abi8202. Epub 2021 Sep 23. PMID- 34547027 OWN - NLM STAT- MEDLINE DCOM- 20211126 LR - 20240403 IS - 1553-7374 (Electronic) IS - 1553-7366 (Print) IS - 1553-7366 (Linking) VI - 17 IP - 9 DP - 2021 Sep TI - A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road. PG - e1009886 LID - 10.1371/journal.ppat.1009886 [doi] LID - e1009886 AB - Salmonella enterica (S. enterica) has infected humans for a long time, but its evolutionary history and geographic spread across Eurasia is still poorly understood. Here, we screened for pathogen DNA in 14 ancient individuals from the Bronze Age Quanergou cemetery (XBQ), Xinjiang, China. In 6 individuals we detected S. enterica. We reconstructed S. enterica genomes from those individuals, which form a previously undetected phylogenetic branch basal to Paratyphi C, Typhisuis and Choleraesuis-the so-called Para C lineage. Based on pseudogene frequency, our analysis suggests that the ancient S. enterica strains were not host adapted. One genome, however, harbors the Salmonella pathogenicity island 7 (SPI-7), which is thought to be involved in (para)typhoid disease in humans. This offers first evidence that SPI-7 was acquired prior to the emergence of human-adapted Paratyphi C around 1,000 years ago. Altogether, our results show that Salmonella enterica infected humans in Eastern Eurasia at least 3,000 years ago, and provide the first ancient DNA evidence for the spread of a pathogen along the Proto-Silk Road. FAU - Wu, Xiyan AU - Wu X AUID- ORCID: 0000-0003-3061-9325 AD - School of Life Sciences, Jilin University, Changchun, China. AD - School of History and Culture, Henan University, Kaifeng, China. FAU - Ning, Chao AU - Ning C AUID- ORCID: 0000-0002-8848-3961 AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Key, Felix M AU - Key FM AUID- ORCID: 0000-0003-2812-6636 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Infection Biology, Berlin, Germany. FAU - Andrades Valtueña, Aida AU - Andrades Valtueña A AUID- ORCID: 0000-0002-1737-2228 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Lankapalli, Aditya Kumar AU - Lankapalli AK AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Gao, Shizhu AU - Gao S AD - College of Pharmacia Sciences, Jilin University, Changchun, China. FAU - Yang, Xuan AU - Yang X AD - School of Life Sciences, Jilin University, Changchun, China. FAU - Zhang, Fan AU - Zhang F AUID- ORCID: 0000-0001-9259-2223 AD - School of Life Sciences, Jilin University, Changchun, China. FAU - Liu, Linlin AU - Liu L AD - Department of Radiation Oncology, The Second Hospital of Jilin University, Changchun, China. FAU - Nie, Zhongzhi AU - Nie Z AD - Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China. FAU - Ma, Jian AU - Ma J AD - School of Cultural Heritage, Northwest University, Xi'an, China. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Herbig, Alexander AU - Herbig A AUID- ORCID: 0000-0003-1176-1166 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Cui, Yinqiu AU - Cui Y AD - School of Life Sciences, Jilin University, Changchun, China. AD - Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China. AD - Key Laboratory for Evolution of Past Life and Environment in Northeast Asia (Jilin University), Ministry of Education, Changchun, China. LA - eng GR - 646612/ERC_/European Research Council/International PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210921 PL - United States TA - PLoS Pathog JT - PLoS pathogens JID - 101238921 RN - 0 (DNA, Ancient) RN - 0 (Virulence Factors) SB - IM MH - China MH - DNA, Ancient MH - Evolution, Molecular MH - History, Ancient MH - Humans MH - Phylogeny MH - Salmonella Infections/*genetics/*history/*transmission MH - Salmonella enterica/*genetics MH - Virulence Factors/genetics PMC - PMC8486138 COIS- The authors have declared that no competing interests exist. EDAT- 2021/09/22 06:00 MHDA- 2021/11/27 06:00 PMCR- 2021/09/21 CRDT- 2021/09/21 17:22 PHST- 2021/02/21 00:00 [received] PHST- 2021/08/11 00:00 [accepted] PHST- 2021/10/01 00:00 [revised] PHST- 2021/09/22 06:00 [pubmed] PHST- 2021/11/27 06:00 [medline] PHST- 2021/09/21 17:22 [entrez] PHST- 2021/09/21 00:00 [pmc-release] AID - PPATHOGENS-D-21-00397 [pii] AID - 10.1371/journal.ppat.1009886 [doi] PST - epublish SO - PLoS Pathog. 2021 Sep 21;17(9):e1009886. doi: 10.1371/journal.ppat.1009886. eCollection 2021 Sep. PMID- 34616690 OWN - NLM STAT- MEDLINE DCOM- 20211019 LR - 20220716 IS - 2235-2988 (Electronic) IS - 2235-2988 (Linking) VI - 11 DP - 2021 TI - Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT. PG - 723821 LID - 10.3389/fcimb.2021.723821 [doi] LID - 723821 AB - Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603-1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history. CI - Copyright © 2021 Shiba, Komatsu, Sudo, Sawafuji, Saso, Ueda, Watanabe, Nemoto, Kano, Nagai, Ohsugi, Katagiri, Takeuchi, Kobayashi and Iwata. FAU - Shiba, Takahiko AU - Shiba T AD - Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Komatsu, Keiji AU - Komatsu K AD - Department of Lifetime Oral Health Care Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Sudo, Takeaki AU - Sudo T AD - Institute of Education, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Sawafuji, Rikai AU - Sawafuji R AD - Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, Japan. FAU - Saso, Aiko AU - Saso A AD - Department of Physical Therapy, Faculty of Rehabilitation, Niigata University of Health and Welfare, Niigata, Japan. FAU - Ueda, Shintaroh AU - Ueda S AD - Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. AD - Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan. FAU - Watanabe, Takayasu AU - Watanabe T AD - Department of Chemistry, Nihon University School of Dentistry, Tokyo, Japan. FAU - Nemoto, Takashi AU - Nemoto T AD - Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Kano, Chihiro AU - Kano C AD - Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Nagai, Takahiko AU - Nagai T AD - Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Ohsugi, Yujin AU - Ohsugi Y AD - Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Katagiri, Sayaka AU - Katagiri S AD - Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Takeuchi, Yasuo AU - Takeuchi Y AD - Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Kobayashi, Hiroaki AU - Kobayashi H AD - Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. FAU - Iwata, Takanori AU - Iwata T AD - Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210920 PL - Switzerland TA - Front Cell Infect Microbiol JT - Frontiers in cellular and infection microbiology JID - 101585359 RN - Actinomyces oricola RN - Eggerthella lenta RN - Fusobacterium nucleatum subsp. vincentii RN - Prevotella pleuritidis RN - Treponema socranskii SB - IM EIN - Front Cell Infect Microbiol. 2022 Apr 13;12:871340. doi: 10.3389/fcimb.2022.871340. PMID: 35493745 MH - Actinobacteria MH - Actinomyces MH - Bacteria/*classification MH - Fusobacterium MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Japan MH - *Periodontitis/diagnosis/history/microbiology MH - Porphyromonas gingivalis MH - Prevotella MH - Treponema MH - X-Ray Microtomography PMC - PMC8488429 OTO - NOTNLM OT - 16S rDNA sequencing OT - EDO OT - ancient skeletons OT - periodontal microbiome OT - periodontitis COIS- The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. EDAT- 2021/10/08 06:00 MHDA- 2021/10/21 06:00 PMCR- 2021/01/01 CRDT- 2021/10/07 06:59 PHST- 2021/06/11 00:00 [received] PHST- 2021/08/17 00:00 [accepted] PHST- 2021/10/07 06:59 [entrez] PHST- 2021/10/08 06:00 [pubmed] PHST- 2021/10/21 06:00 [medline] PHST- 2021/01/01 00:00 [pmc-release] AID - 10.3389/fcimb.2021.723821 [doi] PST - epublish SO - Front Cell Infect Microbiol. 2021 Sep 20;11:723821. doi: 10.3389/fcimb.2021.723821. eCollection 2021. PMID- 34521843 OWN - NLM STAT- MEDLINE DCOM- 20211012 LR - 20230206 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 12 IP - 1 DP - 2021 Sep 14 TI - Parental relatedness through time revealed by runs of homozygosity in ancient DNA. PG - 5425 LID - 10.1038/s41467-021-25289-w [doi] LID - 5425 AB - Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide. CI - © 2021. The Author(s). FAU - Ringbauer, Harald AU - Ringbauer H AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. harald_ringbauer@eva.mpg.de. AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. harald_ringbauer@eva.mpg.de. FAU - Novembre, John AU - Novembre J AUID- ORCID: 0000-0001-5345-0214 AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. AD - Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA. FAU - Steinrücken, Matthias AU - Steinrücken M AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. AD - Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA. LA - eng GR - R01 GM132383/GM/NIGMS NIH HHS/United States GR - R01 HG007089/HG/NHGRI NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20210914 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) SB - IM MH - Agriculture/history MH - DNA, Ancient/*analysis MH - Female MH - *Genome, Human MH - *Haplotypes MH - History, Ancient MH - *Homozygote MH - Humans MH - *Inheritance Patterns MH - Male MH - Population Dynamics/*history PMC - PMC8440622 COIS- The authors declare no competing interests. EDAT- 2021/09/16 06:00 MHDA- 2021/10/13 06:00 PMCR- 2021/09/14 CRDT- 2021/09/15 06:21 PHST- 2020/09/22 00:00 [received] PHST- 2021/07/21 00:00 [accepted] PHST- 2021/09/15 06:21 [entrez] PHST- 2021/09/16 06:00 [pubmed] PHST- 2021/10/13 06:00 [medline] PHST- 2021/09/14 00:00 [pmc-release] AID - 10.1038/s41467-021-25289-w [pii] AID - 25289 [pii] AID - 10.1038/s41467-021-25289-w [doi] PST - epublish SO - Nat Commun. 2021 Sep 14;12(1):5425. doi: 10.1038/s41467-021-25289-w. PMID- 34573393 OWN - NLM STAT- MEDLINE DCOM- 20220216 LR - 20220216 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 12 IP - 9 DP - 2021 Sep 13 TI - Ancient and Archaic Genomes. LID - 10.3390/genes12091411 [doi] LID - 1411 AB - The first data obtained from ancient DNA samples were published more than thirty years ago [...]. FAU - Vai, Stefania AU - Vai S AUID- ORCID: 0000-0003-3844-5147 AD - Department of Biology, University of Florence, 50122 Florence, Italy. FAU - Lari, Martina AU - Lari M AUID- ORCID: 0000-0002-7832-8212 AD - Department of Biology, University of Florence, 50122 Florence, Italy. FAU - Caramelli, David AU - Caramelli D AUID- ORCID: 0000-0001-6468-1675 AD - Department of Biology, University of Florence, 50122 Florence, Italy. LA - eng PT - Editorial PT - Historical Article DEP - 20210913 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *DNA, Ancient/analysis MH - Evolution, Molecular MH - Fossils/pathology MH - Genome/*genetics MH - Genome, Human MH - History, Ancient MH - Hominidae/genetics MH - Humans PMC - PMC8470403 COIS- The authors declare no conflict of interest. EDAT- 2021/09/29 06:00 MHDA- 2022/02/17 06:00 PMCR- 2021/09/13 CRDT- 2021/09/28 01:08 PHST- 2021/08/30 00:00 [received] PHST- 2021/09/08 00:00 [accepted] PHST- 2021/09/28 01:08 [entrez] PHST- 2021/09/29 06:00 [pubmed] PHST- 2022/02/17 06:00 [medline] PHST- 2021/09/13 00:00 [pmc-release] AID - genes12091411 [pii] AID - genes-12-01411 [pii] AID - 10.3390/genes12091411 [doi] PST - epublish SO - Genes (Basel). 2021 Sep 13;12(9):1411. doi: 10.3390/genes12091411. PMID- 34518562 OWN - NLM STAT- MEDLINE DCOM- 20211215 LR - 20240403 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 11 IP - 1 DP - 2021 Sep 13 TI - Biomolecular insights into North African-related ancestry, mobility and diet in eleventh-century Al-Andalus. PG - 18121 LID - 10.1038/s41598-021-95996-3 [doi] LID - 18121 AB - Historical records document medieval immigration from North Africa to Iberia to create Islamic al-Andalus. Here, we present a low-coverage genome of an eleventh century CE man buried in an Islamic necropolis in Segorbe, near Valencia, Spain. Uniparental lineages indicate North African ancestry, but at the autosomal level he displays a mosaic of North African and European-like ancestries, distinct from any present-day population. Altogether, the genome-wide evidence, stable isotope results and the age of the burial indicate that his ancestry was ultimately a result of admixture between recently arrived Amazigh people (Berbers) and the population inhabiting the Peninsula prior to the Islamic conquest. We detect differences between our sample and a previously published group of contemporary individuals from Valencia, exemplifying how detailed, small-scale aDNA studies can illuminate fine-grained regional and temporal differences. His genome demonstrates how ancient DNA studies can capture portraits of past genetic variation that have been erased by later demographic shifts-in this case, most likely the seventeenth century CE expulsion of formerly Islamic communities as tolerance dissipated following the Reconquista by the Catholic kingdoms of the north. CI - © 2021. The Author(s). FAU - Silva, Marina AU - Silva M AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. marina.silva@crick.ac.uk. AD - Ancient Genomics Laboratory, The Francis Crick Institute, London, UK. marina.silva@crick.ac.uk. FAU - Oteo-García, Gonzalo AU - Oteo-García G AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. gonzalo.oteo-garcia@hud.ac.uk. FAU - Martiniano, Rui AU - Martiniano R AD - Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. AD - School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK. FAU - Guimarães, João AU - Guimarães J AD - Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal. FAU - von Tersch, Matthew AU - von Tersch M AD - BioArCh, Department of Archaeology, University of York, York, UK. FAU - Madour, Ali AU - Madour A AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - Shoeib, Tarek AU - Shoeib T AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. AD - Department of Forensic Science, Faculty of Biomedical Science, University of Benghazi, P.O. Box: 1308, Benghazi, Libya. FAU - Fichera, Alessandro AU - Fichera A AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - Justeau, Pierre AU - Justeau P AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - Foody, M George B AU - Foody MGB AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - McGrath, Krista AU - McGrath K AD - BioArCh, Department of Archaeology, University of York, York, UK. AD - Department of Prehistory and Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. FAU - Barrachina, Amparo AU - Barrachina A AD - Servei d'Investigacions Arqueològiques i Prehistòriques - Museu Belles Arts de Castelló, Av. Germans Bou, 28, 12003, Castellón, Spain. FAU - Palomar, Vicente AU - Palomar V AD - Museo Municipal de Arqueología y Etnología de Segorbe, Calle Colón, 98, 12400, Segorbe, Castellón, Spain. FAU - Dulias, Katharina AU - Dulias K AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. AD - BioArCh, Department of Archaeology, University of York, York, UK. AD - Institut für Geosysteme und Bioindikation, Technische Universität Braunschweig, Langer Kamp 19c, 38106, Braunschweig, Germany. FAU - Yau, Bobby AU - Yau B AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - Gandini, Francesca AU - Gandini F AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - Clarke, Douglas J AU - Clarke DJ AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - Rosa, Alexandra AU - Rosa A AD - Faculty of Life Sciences, University of Madeira, Campus of Penteada, 9000-390, Funchal, Portugal. AD - Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9000-390, Funchal, Portugal. FAU - Brehm, António AU - Brehm A AD - Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9000-390, Funchal, Portugal. FAU - Flaquer, Antònia AU - Flaquer A AD - Institute for Medical Information Processing, Biometry and Epidemiology - IBE, LMU University, Munich, Germany. FAU - Rito, Teresa AU - Rito T AD - Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal. AD - Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal. AD - ICVS/3B's, PT Government Associate Laboratory, 4710-057, Braga, Portugal. FAU - Olivieri, Anna AU - Olivieri A AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani, Università di Pavia, 27100, Pavia, Italy. FAU - Achilli, Alessandro AU - Achilli A AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani, Università di Pavia, 27100, Pavia, Italy. FAU - Torroni, Antonio AU - Torroni A AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani, Università di Pavia, 27100, Pavia, Italy. FAU - Gómez-Carballa, Alberto AU - Gómez-Carballa A AD - Grupo de Investigacion en Genetica, Vacunas, Infecciones y Pediatria (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain. AD - GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain. FAU - Salas, Antonio AU - Salas A AD - Grupo de Investigacion en Genetica, Vacunas, Infecciones y Pediatria (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain. AD - GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain. AD - Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain. FAU - Bryk, Jaroslaw AU - Bryk J AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - Ditchfield, Peter W AU - Ditchfield PW AD - School of Archaeology, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK. FAU - Alexander, Michelle AU - Alexander M AD - BioArCh, Department of Archaeology, University of York, York, UK. FAU - Pala, Maria AU - Pala M AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - Soares, Pedro A AU - Soares PA AD - Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal. AD - Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal. FAU - Edwards, Ceiridwen J AU - Edwards CJ AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. FAU - Richards, Martin B AU - Richards MB AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. m.b.richards@hud.ac.uk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210913 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Africa, Northern MH - Anthropology MH - Archaeology MH - *Diet MH - Genetic Background MH - *Genetics, Population MH - Genome, Human MH - History, Medieval MH - *Human Migration MH - Humans MH - Phylogeny MH - Phylogeography MH - Spain PMC - PMC8438022 COIS- The authors declare no competing interests. EDAT- 2021/09/15 06:00 MHDA- 2021/12/16 06:00 PMCR- 2021/09/13 CRDT- 2021/09/14 06:19 PHST- 2021/05/03 00:00 [received] PHST- 2021/07/27 00:00 [accepted] PHST- 2021/09/14 06:19 [entrez] PHST- 2021/09/15 06:00 [pubmed] PHST- 2021/12/16 06:00 [medline] PHST- 2021/09/13 00:00 [pmc-release] AID - 10.1038/s41598-021-95996-3 [pii] AID - 95996 [pii] AID - 10.1038/s41598-021-95996-3 [doi] PST - epublish SO - Sci Rep. 2021 Sep 13;11(1):18121. doi: 10.1038/s41598-021-95996-3. PMID- 34465619 OWN - NLM STAT- MEDLINE DCOM- 20220104 LR - 20240403 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 118 IP - 36 DP - 2021 Sep 7 TI - Assessing the origins of the European Plagues following the Black Death: A synthesis of genomic, historical, and ecological information. LID - 10.1073/pnas.2101940118 [doi] LID - e2101940118 AB - The second plague pandemic started in Europe with the Black Death in 1346 and lasted until the 19th century. Based on ancient DNA studies, there is a scientific disagreement over whether the bacterium, Yersinia pestis, came into Europe once (Hypothesis 1) or repeatedly over the following four centuries (Hypothesis 2). Here, we synthesize the most updated phylogeny together with historical, archeological, evolutionary, and ecological information. On the basis of this holistic view, we conclude that Hypothesis 2 is the most plausible. We also suggest that Y. pestis lineages might have developed attenuated virulence during transmission, which can explain the convergent evolutionary signals, including pla decay, that appeared at the end of the pandemics. CI - Copyright © 2021 the Author(s). Published by PNAS. FAU - Bramanti, Barbara AU - Bramanti B AUID- ORCID: 0000-0002-5433-663X AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; barbara.bramanti@ibv.uio.no n.c.stenseth@mn.uio.no cuiyujun.new@gmail.com. AD - Department of Neuroscience and Rehabilitation, Faculty of Medicine, Pharmacy and Prevention, University of Ferrara, 44121 Ferrara, Italy. FAU - Wu, Yarong AU - Wu Y AUID- ORCID: 0000-0003-4900-315X AD - State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China. FAU - Yang, Ruifu AU - Yang R AUID- ORCID: 0000-0003-3219-7269 AD - State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China. FAU - Cui, Yujun AU - Cui Y AUID- ORCID: 0000-0001-7236-2412 AD - State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; barbara.bramanti@ibv.uio.no n.c.stenseth@mn.uio.no cuiyujun.new@gmail.com. FAU - Stenseth, Nils Chr AU - Stenseth NC AUID- ORCID: 0000-0002-1591-5399 AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; barbara.bramanti@ibv.uio.no n.c.stenseth@mn.uio.no cuiyujun.new@gmail.com. AD - Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Bacterial) SB - IM CIN - Proc Natl Acad Sci U S A. 2021 Sep 28;118(39):e2114241118. doi: 10.1073/pnas.2114241118. PMID: 34551981 MH - DNA, Bacterial/genetics MH - Europe MH - Genome, Bacterial/genetics MH - Genomics/methods MH - History, 19th Century MH - History, 20th Century MH - History, 21st Century MH - Humans MH - Pandemics/history MH - Phylogeny MH - Plague/*epidemiology/*etiology/*genetics MH - Virulence/genetics MH - Yersinia pestis/genetics/pathogenicity PMC - PMC8433512 OTO - NOTNLM OT - Black Death OT - European plague OT - Yersinia pestis OT - ecological epidemiology OT - molecular evolution COIS- The authors declare no competing interest. EDAT- 2021/09/02 06:00 MHDA- 2022/01/05 06:00 PMCR- 2021/08/31 CRDT- 2021/09/01 06:41 PHST- 2021/09/01 06:41 [entrez] PHST- 2021/09/02 06:00 [pubmed] PHST- 2022/01/05 06:00 [medline] PHST- 2021/08/31 00:00 [pmc-release] AID - 2101940118 [pii] AID - 202101940 [pii] AID - 10.1073/pnas.2101940118 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2021 Sep 7;118(36):e2101940118. doi: 10.1073/pnas.2101940118. PMID- 34411538 OWN - NLM STAT- MEDLINE DCOM- 20210915 LR - 20220323 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 108 IP - 9 DP - 2021 Sep 2 TI - Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population. PG - 1792-1806 LID - S0002-9297(21)00280-9 [pii] LID - 10.1016/j.ajhg.2021.07.012 [doi] AB - The Finnish population is a unique example of a genetic isolate affected by a recent founder event. Previous studies have suggested that the ancestors of Finnic-speaking Finns and Estonians reached the circum-Baltic region by the 1(st) millennium BC. However, high linguistic similarity points to a more recent split of their languages. To study genetic connectedness between Finns and Estonians directly, we first assessed the efficacy of imputation of low-coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23×) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1× coverage can be reliably used in principal-component analyses without projection. By searching for long shared allele intervals (LSAIs; similar to identity-by-descent segments) in unphased data for >143,000 present-day Estonians, 99 Finns, and 14 imputed ancient genomes from Estonia, we find unexpectedly high levels of individual connectedness between Estonians and Finns for the last eight centuries in contrast to their clear differentiation by allele frequencies. High levels of sharing of these segments between Estonians and Finns predate the demographic expansion and late settlement process of Finland. One plausible source of this extensive sharing is the 8(th)-10(th) centuries AD migration event from North Estonia to Finland that has been proposed to explain uniquely shared linguistic features between the Finnish language and the northern dialect of Estonian and shared Christianity-related loanwords from Slavic. These results suggest that LSAI detection provides a computationally tractable way to detect fine-scale structure in large cohorts. CI - Copyright © 2021 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. FAU - Kivisild, Toomas AU - Kivisild T AD - Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK. Electronic address: toomas.kivisild@kuleuven.be. FAU - Saag, Lehti AU - Saag L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Research Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK. FAU - Hui, Ruoyun AU - Hui R AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK. FAU - Biagini, Simone Andrea AU - Biagini SA AD - Department of Human Genetics, KU Leuven, Leuven 3000, Belgium. FAU - Pankratov, Vasili AU - Pankratov V AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - D'Atanasio, Eugenia AU - D'Atanasio E AD - Instituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy. FAU - Pagani, Luca AU - Pagani L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology, University of Padova, 35131 Padova, Italy. FAU - Saag, Lauri AU - Saag L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Rootsi, Siiri AU - Rootsi S AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Mägi, Reedik AU - Mägi R AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Metspalu, Ene AU - Metspalu E AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Valk, Heiki AU - Valk H AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia. FAU - Malve, Martin AU - Malve M AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia. FAU - Irdt, Kadri AU - Irdt K AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Reisberg, Tuuli AU - Reisberg T AD - Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Solnik, Anu AU - Solnik A AD - Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Scheib, Christiana L AU - Scheib CL AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; St John's College, University of Cambridge, Cambridge CB2 1TP, UK. FAU - Seidman, Daniel N AU - Seidman DN AD - Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA. FAU - Williams, Amy L AU - Williams AL AD - Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA. CN - Estonian Biobank Research Team AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Tambets, Kristiina AU - Tambets K AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Metspalu, Mait AU - Metspalu M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom GR - R35 GM133805/GM/NIGMS NIH HHS/United States GR - 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20210818 PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Ancient) SB - IM MH - *Alleles MH - DNA, Ancient/*analysis MH - Estonia MH - Female MH - Finland MH - Gene Frequency MH - Genealogy and Heraldry MH - *Genome, Human MH - High-Throughput Nucleotide Sequencing MH - History, 21st Century MH - History, Ancient MH - History, Medieval MH - Human Migration/*history MH - Humans MH - Language/history MH - Male MH - *Pedigree PMC - PMC8456179 OTO - NOTNLM OT - Estonian Biobank OT - Finnish bottleneck OT - ancient DNA OT - community structure OT - identity by descent OT - imputation OT - long shared allele intervals OT - medieval Estonian genomes OT - population structure COIS- Declaration of interests A.L.W. is a paid consultant for 23andMe and the owner of HAPI-DNA LLC. All other authors declare no competing interests. EDAT- 2021/08/20 06:00 MHDA- 2021/09/16 06:00 PMCR- 2022/03/02 CRDT- 2021/08/19 20:13 PHST- 2021/03/29 00:00 [received] PHST- 2021/07/23 00:00 [accepted] PHST- 2021/08/20 06:00 [pubmed] PHST- 2021/09/16 06:00 [medline] PHST- 2021/08/19 20:13 [entrez] PHST- 2022/03/02 00:00 [pmc-release] AID - S0002-9297(21)00280-9 [pii] AID - 10.1016/j.ajhg.2021.07.012 [doi] PST - ppublish SO - Am J Hum Genet. 2021 Sep 2;108(9):1792-1806. doi: 10.1016/j.ajhg.2021.07.012. Epub 2021 Aug 18. PMID- 33834210 OWN - NLM STAT- MEDLINE DCOM- 20211122 LR - 20211122 IS - 1477-4054 (Electronic) IS - 1467-5463 (Linking) VI - 22 IP - 5 DP - 2021 Sep 2 TI - Systematic benchmark of ancient DNA read mapping. LID - bbab076 [pii] LID - 10.1093/bib/bbab076 [doi] AB - The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA 'reads') against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30-80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software-BWA-aln, BWA-mem, NovoAlign and Bowtie2-and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations. CI - © The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. FAU - Oliva, Adrien AU - Oliva A AUID- ORCID: 0000-0001-9950-7220 AD - Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia. FAU - Tobler, Raymond AU - Tobler R AD - Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia. FAU - Cooper, Alan AU - Cooper A AD - South Australian Museum, Adelaide, SA 5005, Australia. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia. AD - The Environment Institute, The University of Adelaide, South Australia, 5005, Australia. FAU - Souilmi, Yassine AU - Souilmi Y AD - Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia. AD - The Environment Institute, The University of Adelaide, South Australia, 5005, Australia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Brief Bioinform JT - Briefings in bioinformatics JID - 100912837 RN - 0 (DNA, Ancient) SB - IM MH - Algorithms MH - Benchmarking/*methods MH - Computational Biology/*methods MH - DNA, Ancient/*analysis/chemistry MH - Genome, Human/*genetics MH - High-Throughput Nucleotide Sequencing/methods MH - Humans MH - Polymorphism, Single Nucleotide MH - Reproducibility of Results MH - Sequence Alignment/*methods MH - Sequence Analysis, DNA/*methods MH - Software OTO - NOTNLM OT - alignment OT - ancient DNA OT - benchmarking OT - reference bias EDAT- 2021/04/10 06:00 MHDA- 2021/11/23 06:00 CRDT- 2021/04/09 06:34 PHST- 2020/07/28 00:00 [received] PHST- 2021/01/05 00:00 [revised] PHST- 2021/02/16 00:00 [accepted] PHST- 2021/04/10 06:00 [pubmed] PHST- 2021/11/23 06:00 [medline] PHST- 2021/04/09 06:34 [entrez] AID - 6217726 [pii] AID - 10.1093/bib/bbab076 [doi] PST - ppublish SO - Brief Bioinform. 2021 Sep 2;22(5):bbab076. doi: 10.1093/bib/bbab076. PMID- 34480555 OWN - NLM STAT- MEDLINE DCOM- 20220331 LR - 20220401 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 13 IP - 9 DP - 2021 Sep 1 TI - Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations. LID - 10.1093/gbe/evab194 [doi] LID - evab194 AB - The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Ferreira, Joana C AU - Ferreira JC AD - i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal. AD - IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal. AD - ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal. FAU - Alshamali, Farida AU - Alshamali F AD - Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates. FAU - Montinaro, Francesco AU - Montinaro F AD - Department of Biology-Genetics, University of Bari, Italy. AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia. FAU - Cavadas, Bruno AU - Cavadas B AD - i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal. AD - IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal. FAU - Torroni, Antonio AU - Torroni A AD - Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy. FAU - Pereira, Luisa AU - Pereira L AD - i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal. AD - IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal. FAU - Raveane, Alessandro AU - Raveane A AUID- ORCID: 0000-0002-8322-5461 AD - Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy. AD - Laboratory of Haematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy. FAU - Fernandes, Veronica AU - Fernandes V AUID- ORCID: 0000-0002-3873-2034 AD - i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal. AD - IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA, Ancient MH - Genetics, Population MH - Genome, Human MH - Human Migration MH - Humans MH - Indian Ocean MH - Iran MH - *Neanderthals/genetics PMC - PMC8435661 OTO - NOTNLM OT - Arabian Peninsula OT - Iran OT - ancient and archaic ancestry OT - basal Eurasian lineage OT - main human population groups stratification OT - out of Africa migration EDAT- 2021/09/05 06:00 MHDA- 2022/04/01 06:00 PMCR- 2021/09/04 CRDT- 2021/09/04 12:06 PHST- 2021/08/17 00:00 [accepted] PHST- 2021/09/05 06:00 [pubmed] PHST- 2022/04/01 06:00 [medline] PHST- 2021/09/04 12:06 [entrez] PHST- 2021/09/04 00:00 [pmc-release] AID - 6364187 [pii] AID - evab194 [pii] AID - 10.1093/gbe/evab194 [doi] PST - ppublish SO - Genome Biol Evol. 2021 Sep 1;13(9):evab194. doi: 10.1093/gbe/evab194. PMID- 34265517 OWN - NLM STAT- MEDLINE DCOM- 20211125 LR - 20211125 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 54 DP - 2021 Sep TI - Progress in forensic bone DNA analysis: Lessons learned from ancient DNA. PG - 102538 LID - S1872-4973(21)00076-4 [pii] LID - 10.1016/j.fsigen.2021.102538 [doi] AB - Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable. CI - Copyright © 2021 Elsevier B.V. All rights reserved. FAU - Hofreiter, Michael AU - Hofreiter M AD - Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany. Electronic address: michi@palaeo.eu. FAU - Sneberger, Jiri AU - Sneberger J AD - Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Department of the History of the Middle Ages of Museum of West Bohemia, Kopeckeho sady 2, Pilsen 30100, Czech Republic; Nuclear Physics Institute of the CAS, Na Truhlarce 39/64, Prague 18086, Czech Republic. FAU - Pospisek, Martin AU - Pospisek M AD - Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Biologicals s.r.o., Sramkova 315, Ricany 25101, Czech Republic. FAU - Vanek, Daniel AU - Vanek D AD - Forensic DNA Service, Janovskeho 18, Prague 7 17000, Czech Republic; Institute of Legal Medicine, Bulovka Hospital, Prague, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, Prague, Czech Republic. Electronic address: daniel.vanek@fdnas.cz. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20210529 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Aged MH - *DNA/genetics MH - DNA Degradation, Necrotic MH - DNA Fingerprinting MH - *DNA, Ancient MH - Forensic Genetics MH - Humans OTO - NOTNLM OT - Ancient DNA OT - Degraded DNA OT - Forensic OT - Inhibitors EDAT- 2021/07/16 06:00 MHDA- 2021/11/26 06:00 CRDT- 2021/07/15 20:20 PHST- 2020/09/08 00:00 [received] PHST- 2021/03/07 00:00 [revised] PHST- 2021/05/25 00:00 [accepted] PHST- 2021/07/16 06:00 [pubmed] PHST- 2021/11/26 06:00 [medline] PHST- 2021/07/15 20:20 [entrez] AID - S1872-4973(21)00076-4 [pii] AID - 10.1016/j.fsigen.2021.102538 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2021 Sep;54:102538. doi: 10.1016/j.fsigen.2021.102538. Epub 2021 May 29. PMID- 33833423 OWN - NLM STAT- MEDLINE DCOM- 20211006 LR - 20230129 IS - 2397-3374 (Electronic) IS - 2397-3374 (Linking) VI - 5 IP - 9 DP - 2021 Sep TI - Evidence for early dispersal of domestic sheep into Central Asia. PG - 1169-1179 LID - 10.1038/s41562-021-01083-y [doi] AB - The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca. 6,000 BCE. Zooarchaeological and collagen peptide mass fingerprinting show exploitation of Ovis and Capra, while cementum analysis of intact teeth implicates possible pastoral slaughter during the fall season. Most significantly, ancient DNA reveals these directly dated specimens as the domestic O. aries, within the genetic diversity of domesticated sheep lineages. Together, these results provide the earliest evidence for the use of livestock in the mountains of the Ferghana Valley, predating previous evidence by 3,000 years and suggesting that domestic animal economies reached the mountains of interior Central Asia far earlier than previously recognized. CI - © 2021. The Author(s), under exclusive licence to Springer Nature Limited. FAU - Taylor, William T T AU - Taylor WTT AUID- ORCID: 0000-0002-0836-7814 AD - Museum of Natural History, University of Colorado-Boulder, Boulder, CO, USA. william.taylor@colorado.edu. AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. william.taylor@colorado.edu. FAU - Pruvost, Mélanie AU - Pruvost M AUID- ORCID: 0000-0001-7824-2155 AD - De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux, Pessac, France. FAU - Posth, Cosimo AU - Posth C AUID- ORCID: 0000-0002-8206-3907 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Rendu, William AU - Rendu W AUID- ORCID: 0000-0003-2137-1276 AD - De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux, Pessac, France. AD - ArchaeoZOOlogy in Siberia and Central Asia - ZooSCAn, CNRS - IAET SB RAS International Research Laboratory, IRL 2013, Institute of Archaeology SB RAS, Novosibirsk, Russia. FAU - Krajcarz, Maciej T AU - Krajcarz MT AD - Institute of Geological Sciences, Polish Academy of Sciences, Warszawa, Poland. FAU - Abdykanova, Aida AU - Abdykanova A AUID- ORCID: 0000-0002-7238-9065 AD - American University of Central Asia, Bishkek, Kyrgyzstan. FAU - Brancaleoni, Greta AU - Brancaleoni G AUID- ORCID: 0000-0002-5563-3724 AD - Institute of Geological Sciences, Polish Academy of Sciences, Warszawa, Poland. FAU - Spengler, Robert AU - Spengler R AUID- ORCID: 0000-0002-5648-6930 AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Hermes, Taylor AU - Hermes T AUID- ORCID: 0000-0002-8377-468X AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Schiavinato, Stéphanie AU - Schiavinato S AD - Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France. FAU - Hodgins, Gregory AU - Hodgins G AUID- ORCID: 0000-0002-6669-0396 AD - Accelerator Mass Spectrometry Laboratory, University of Arizona, Tucson, AZ, USA. FAU - Stahl, Raphaela AU - Stahl R AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Min, Jina AU - Min J AD - School of Biological Sciences, Seoul National University, Seoul, Republic of Korea. FAU - Alisher Kyzy, Saltanat AU - Alisher Kyzy S AUID- ORCID: 0000-0003-3138-0942 AD - Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia. AD - Novosibirsk State University, Novosibirsk, Russia. FAU - Fedorowicz, Stanisław AU - Fedorowicz S AD - Department of Geomorphology and Quaternary Geology, University of Gdańsk, Gdańsk, Poland. FAU - Orlando, Ludovic AU - Orlando L AD - American University of Central Asia, Bishkek, Kyrgyzstan. FAU - Douka, Katerina AU - Douka K AUID- ORCID: 0000-0002-0558-0011 AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Krivoshapkin, Andrey AU - Krivoshapkin A AD - Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia. AD - Novosibirsk State University, Novosibirsk, Russia. FAU - Jeong, Choongwon AU - Jeong C AUID- ORCID: 0000-0003-3049-2352 AD - School of Biological Sciences, Seoul National University, Seoul, Republic of Korea. FAU - Warinner, Christina AU - Warinner C AUID- ORCID: 0000-0002-4528-5877 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Department of Anthropology, Harvard University, Cambridge, MA, USA. FAU - Shnaider, Svetlana AU - Shnaider S AUID- ORCID: 0000-0003-2230-4286 AD - ArchaeoZOOlogy in Siberia and Central Asia - ZooSCAn, CNRS - IAET SB RAS International Research Laboratory, IRL 2013, Institute of Archaeology SB RAS, Novosibirsk, Russia. sveta.shnayder@gmail.com. AD - Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia. sveta.shnayder@gmail.com. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210408 PL - England TA - Nat Hum Behav JT - Nature human behaviour JID - 101697750 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animal Husbandry/*history MH - Animals MH - Asia MH - DNA, Mitochondrial/*history MH - History, Ancient MH - Humans MH - Kazakhstan MH - Kyrgyzstan MH - Sheep MH - *Sheep, Domestic MH - Tajikistan MH - Uzbekistan EDAT- 2021/04/10 06:00 MHDA- 2021/10/07 06:00 CRDT- 2021/04/09 06:19 PHST- 2020/09/07 00:00 [received] PHST- 2021/02/17 00:00 [accepted] PHST- 2021/04/10 06:00 [pubmed] PHST- 2021/10/07 06:00 [medline] PHST- 2021/04/09 06:19 [entrez] AID - 10.1038/s41562-021-01083-y [pii] AID - 10.1038/s41562-021-01083-y [doi] PST - ppublish SO - Nat Hum Behav. 2021 Sep;5(9):1169-1179. doi: 10.1038/s41562-021-01083-y. Epub 2021 Apr 8. PMID- 34429408 OWN - NLM STAT- MEDLINE DCOM- 20210907 LR - 20240403 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 12 IP - 1 DP - 2021 Aug 24 TI - Climatic windows for human migration out of Africa in the past 300,000 years. PG - 4889 LID - 10.1038/s41467-021-24779-1 [doi] LID - 4889 AB - Whilst an African origin of modern humans is well established, the timings and routes of their expansions into Eurasia are the subject of heated debate, due to the scarcity of fossils and the lack of suitably old ancient DNA. Here, we use high-resolution palaeoclimate reconstructions to estimate how difficult it would have been for humans in terms of rainfall availability to leave the African continent in the past 300k years. We then combine these results with an anthropologically and ecologically motivated estimate of the minimum level of rainfall required by hunter-gatherers to survive, allowing us to reconstruct when, and along which geographic paths, expansions out of Africa would have been climatically feasible. The estimated timings and routes of potential contact with Eurasia are compatible with archaeological and genetic evidence of human expansions out of Africa, highlighting the key role of palaeoclimate variability for modern human dispersals. CI - © 2021. The Author(s). FAU - Beyer, Robert M AU - Beyer RM AD - Department of Zoology, University of Cambridge, Cambridge, UK. robert.beyer@pik-potsdam.de. AD - Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany. robert.beyer@pik-potsdam.de. FAU - Krapp, Mario AU - Krapp M AUID- ORCID: 0000-0002-2599-0683 AD - Department of Zoology, University of Cambridge, Cambridge, UK. AD - GNS Science, Lower Hutt, New Zealand. FAU - Eriksson, Anders AU - Eriksson A AUID- ORCID: 0000-0003-3436-3726 AD - cGEM, cGEM, Institute of Genomics, University of Tartu, Tartu, Estonia. AD - Department of Medical and Molecular Genetics, King's College London, London, UK. FAU - Manica, Andrea AU - Manica A AUID- ORCID: 0000-0003-1895-450X AD - Department of Zoology, University of Cambridge, Cambridge, UK. am315@cam.ac.uk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210824 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) SB - IM MH - Africa MH - Animals MH - Biological Evolution MH - *DNA, Ancient MH - Emigration and Immigration MH - Fossils MH - Genetic Variation MH - Genome, Human MH - History, Ancient MH - Hominidae/*genetics MH - Human Migration/*history MH - Humans MH - Models, Genetic PMC - PMC8384873 COIS- The authors declare no competing interests. EDAT- 2021/08/26 06:00 MHDA- 2021/09/08 06:00 PMCR- 2021/08/24 CRDT- 2021/08/25 05:49 PHST- 2020/10/21 00:00 [received] PHST- 2021/07/02 00:00 [accepted] PHST- 2021/08/25 05:49 [entrez] PHST- 2021/08/26 06:00 [pubmed] PHST- 2021/09/08 06:00 [medline] PHST- 2021/08/24 00:00 [pmc-release] AID - 10.1038/s41467-021-24779-1 [pii] AID - 24779 [pii] AID - 10.1038/s41467-021-24779-1 [doi] PST - epublish SO - Nat Commun. 2021 Aug 24;12(1):4889. doi: 10.1038/s41467-021-24779-1. PMID- 34256019 OWN - NLM STAT- MEDLINE DCOM- 20220228 LR - 20220228 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 31 IP - 16 DP - 2021 Aug 23 TI - Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment. PG - 3564-3574.e9 LID - S0960-9822(21)00818-6 [pii] LID - 10.1016/j.cub.2021.06.023 [doi] AB - Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships. CI - Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Gelabert, Pere AU - Gelabert P AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. Electronic address: pere.gelabert@univie.ac.at. FAU - Sawyer, Susanna AU - Sawyer S AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Bergström, Anders AU - Bergström A AD - Ancient Genomics Laboratory, Francis Crick Institute, London, UK. Electronic address: anders.bergstrom@crick.ac.uk. FAU - Margaryan, Ashot AU - Margaryan A AD - Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark. FAU - Collin, Thomas C AU - Collin TC AD - School of Medicine, University College Dublin, Dublin, Ireland. FAU - Meshveliani, Tengiz AU - Meshveliani T AD - Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia. FAU - Belfer-Cohen, Anna AU - Belfer-Cohen A AD - Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Lordkipanidze, David AU - Lordkipanidze D AD - Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia. FAU - Jakeli, Nino AU - Jakeli N AD - Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia. FAU - Matskevich, Zinovi AU - Matskevich Z AD - Israel Antiquities Authority, Jerusalem, Israel. FAU - Bar-Oz, Guy AU - Bar-Oz G AD - Zinman Institute of Archaeology, University of Haifa, Haifa, Israel. FAU - Fernandes, Daniel M AU - Fernandes DM AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Özdoğan, Kadir T AU - Özdoğan KT AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Oberreiter, Victoria AU - Oberreiter V AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Feeney, Robin N M AU - Feeney RNM AD - School of Medicine, University College Dublin, Dublin, Ireland. FAU - Stahlschmidt, Mareike C AU - Stahlschmidt MC AD - Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Skoglund, Pontus AU - Skoglund P AD - Ancient Genomics Laboratory, Francis Crick Institute, London, UK. Electronic address: pontus.skoglund@crick.ac.uk. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. Electronic address: ron.pinhasi@univie.ac.at. LA - eng GR - 852558/ERC_/European Research Council/International GR - 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom GR - FC001595/MRC_/Medical Research Council/United Kingdom GR - FC001595/WT_/Wellcome Trust/United Kingdom GR - WT_/Wellcome Trust/United Kingdom GR - FC001595/ARC_/Arthritis Research UK/United Kingdom GR - FC001595/CRUK_/Cancer Research UK/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210712 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM CIN - Curr Biol. 2021 Aug 23;31(16):R993-R995. doi: 10.1016/j.cub.2021.06.074. PMID: 34428419 MH - Animals MH - *Bison/genetics MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - *Genome, Mitochondrial MH - Georgia (Republic) MH - Humans MH - Phylogeny MH - *Wolves/genetics PMC - PMC8409484 OTO - NOTNLM OT - Canis OT - Caucasus OT - Upper Paleolithic OT - bison OT - enviromental DNA OT - human OT - shotgun OT - soil sequencing COIS- Declaration of interests The authors declare no competing interests. EDAT- 2021/07/14 06:00 MHDA- 2022/03/01 06:00 PMCR- 2021/08/23 CRDT- 2021/07/13 20:08 PHST- 2021/01/06 00:00 [received] PHST- 2021/04/23 00:00 [revised] PHST- 2021/06/09 00:00 [accepted] PHST- 2021/07/14 06:00 [pubmed] PHST- 2022/03/01 06:00 [medline] PHST- 2021/07/13 20:08 [entrez] PHST- 2021/08/23 00:00 [pmc-release] AID - S0960-9822(21)00818-6 [pii] AID - 10.1016/j.cub.2021.06.023 [doi] PST - ppublish SO - Curr Biol. 2021 Aug 23;31(16):3564-3574.e9. doi: 10.1016/j.cub.2021.06.023. Epub 2021 Jul 12. PMID- 34408163 OWN - NLM STAT- MEDLINE DCOM- 20211112 LR - 20241005 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 11 IP - 1 DP - 2021 Aug 18 TI - Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia. PG - 16729 LID - 10.1038/s41598-021-94932-9 [doi] LID - 16729 AB - Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies. Present-day Croatia lies at the heart of ancient migration routes through Europe, yet our knowledge about social and genetic processes here remains sparse. To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE-400 CE from two sites in present-day eastern Croatia. In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple closely related males suggesting a patrilocal social organisation. We also find in that community an unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today. CI - © 2021. The Author(s). FAU - Freilich, Suzanne AU - Freilich S AD - Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria. freilich@shh.mpg.de. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. freilich@shh.mpg.de. FAU - Ringbauer, Harald AU - Ringbauer H AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. AD - Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA. FAU - Los, Dženi AU - Los D AD - Kaducej Ltd., 21000, Split, Croatia. FAU - Novak, Mario AU - Novak M AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000, Zagreb, Croatia. FAU - Pavičić, Dinko Tresić AU - Pavičić DT AD - Kaducej Ltd., 21000, Split, Croatia. FAU - Schiffels, Stephan AU - Schiffels S AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. schiffels@shh.mpg.de. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria. ron.pinhasi@univie.ac.at. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210818 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - *Archaeology MH - Croatia MH - *DNA, Ancient MH - *Genome, Human MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Male PMC - PMC8373892 COIS- The authors declare no competing interests. EDAT- 2021/08/20 06:00 MHDA- 2021/11/16 06:00 PMCR- 2021/08/18 CRDT- 2021/08/19 06:03 PHST- 2021/05/14 00:00 [received] PHST- 2021/07/13 00:00 [accepted] PHST- 2021/08/19 06:03 [entrez] PHST- 2021/08/20 06:00 [pubmed] PHST- 2021/11/16 06:00 [medline] PHST- 2021/08/18 00:00 [pmc-release] AID - 10.1038/s41598-021-94932-9 [pii] AID - 94932 [pii] AID - 10.1038/s41598-021-94932-9 [doi] PST - epublish SO - Sci Rep. 2021 Aug 18;11(1):16729. doi: 10.1038/s41598-021-94932-9. PMID- 34312252 OWN - NLM STAT- MEDLINE DCOM- 20211217 LR - 20240403 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 118 IP - 32 DP - 2021 Aug 10 TI - Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus. LID - 10.1073/pnas.2102116118 [doi] LID - e2102116118 AB - Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent. CI - Copyright © 2021 the Author(s). Published by PNAS. FAU - Ottoni, Claudio AU - Ottoni C AUID- ORCID: 0000-0001-8870-1589 AD - DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy; claudio.ottoni@uniroma2.it emanuela.cristiani@uniroma1.it. FAU - Borić, Dušan AU - Borić D AD - The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027. AD - Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria. FAU - Sparacello, Vitale AU - Sparacello V AUID- ORCID: 0000-0002-6357-7363 AD - Department of Environmental and Life Sciences, University of Cagliari, 09042 Monserrato, Italy. FAU - Dori, Irene AU - Dori I AD - Soprintendenza Archeologia, Belle Arti e Paesaggio per le province di Verona, Rovigo e Vicenza, 37121 Verona, Italy. FAU - Coppa, Alfredo AU - Coppa A AUID- ORCID: 0000-0002-7708-2484 AD - Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy. AD - Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria. AD - Department of Genetics, Harvard Medical School, Harvard University, Cambridge, MA 02138. FAU - Antonović, Dragana AU - Antonović D AUID- ORCID: 0000-0002-6534-1258 AD - Institute of Archaeology, 11000 Belgrade, Serbia. FAU - Vujević, Dario AU - Vujević D AUID- ORCID: 0000-0003-3526-9205 AD - Department of Archaeology, University of Zadar, 23000 Zadar, Croatia. FAU - Price, T Douglas AU - Price TD AUID- ORCID: 0000-0001-5951-5621 AD - Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria. FAU - Cristiani, Emanuela AU - Cristiani E AUID- ORCID: 0000-0002-2748-9171 AD - DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy; claudio.ottoni@uniroma2.it emanuela.cristiani@uniroma1.it. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Agriculture/*history MH - Bacteria/genetics MH - Balkan Peninsula MH - *DNA, Ancient MH - Dental Calculus/chemistry/*genetics/*microbiology MH - Drug Resistance, Microbial/genetics MH - Europe MH - History, Ancient MH - History, Medieval MH - Humans MH - Microbiota/*genetics MH - Phylogeny MH - Plants/chemistry PMC - PMC8364157 OTO - NOTNLM OT - Southern Europe OT - ancient DNA OT - dental calculus OT - metagenomics COIS- The authors declare no competing interest. EDAT- 2021/07/28 06:00 MHDA- 2021/12/18 06:00 PMCR- 2021/07/26 CRDT- 2021/07/27 06:31 PHST- 2021/07/27 06:31 [entrez] PHST- 2021/07/28 06:00 [pubmed] PHST- 2021/12/18 06:00 [medline] PHST- 2021/07/26 00:00 [pmc-release] AID - 2102116118 [pii] AID - 202102116 [pii] AID - 10.1073/pnas.2102116118 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2021 Aug 10;118(32):e2102116118. doi: 10.1073/pnas.2102116118. PMID- 34350829 OWN - NLM STAT- MEDLINE DCOM- 20211019 LR - 20240403 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 10 DP - 2021 Aug 5 TI - Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade. LID - 10.7554/eLife.68612 [doi] LID - e68612 AB - After the European colonization of the Americas, there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover the diversity of viral pathogens during this period, we designed an enrichment assay targeting ancient DNA (aDNA) from viruses of clinical importance and applied it to DNA extracts from individuals found in a Colonial hospital and a Colonial chapel (16th-18th century) where records suggest that victims of epidemics were buried during important outbreaks in Mexico City. This allowed us to reconstruct three ancient human parvovirus B19 genomes and one ancient human hepatitis B virus genome from distinct individuals. The viral genomes are similar to African strains, consistent with the inferred morphological and genetic African ancestry of the hosts as well as with the isotopic analysis of the human remains, suggesting an origin on the African continent. This study provides direct molecular evidence of ancient viruses being transported to the Americas during the transatlantic slave trade and their subsequent introduction to New Spain. Altogether, our observations enrich the discussion about the etiology of infectious diseases during the Colonial period in Mexico. CI - © 2021, Guzmán-Solís et al. FAU - Guzmán-Solís, Axel A AU - Guzmán-Solís AA AUID- ORCID: 0000-0001-6878-206X AD - Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, Mexico. FAU - Villa-Islas, Viridiana AU - Villa-Islas V AD - Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, Mexico. FAU - Bravo-López, Miriam J AU - Bravo-López MJ AD - Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, Mexico. FAU - Sandoval-Velasco, Marcela AU - Sandoval-Velasco M AD - Section for Evolutionary Genomics, The Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark. FAU - Wesp, Julie K AU - Wesp JK AD - Department of Sociology and Anthropology, North Carolina State University, Raleigh, United States. FAU - Gómez-Valdés, Jorge A AU - Gómez-Valdés JA AUID- ORCID: 0000-0001-6996-2732 AD - Escuela Nacional de Antropología e Historia, Mexico City, Mexico. FAU - Moreno-Cabrera, María de la Luz AU - Moreno-Cabrera ML AD - Instituto Nacional de Antropología e Historia, Mexico City, Mexico. FAU - Meraz, Alejandro AU - Meraz A AD - Instituto Nacional de Antropología e Historia, Mexico City, Mexico. FAU - Solís-Pichardo, Gabriela AU - Solís-Pichardo G AD - Laboratorio Universitario de Geoquímica Isotópica (LUGIS), Instituto de Geología, Universidad Nacional Autónoma de México, Mexico City, Mexico. FAU - Schaaf, Peter AU - Schaaf P AD - LUGIS, Instituto de Geofísica, Universidad Nacional Autónoma de México, Mexico City, Mexico. FAU - TenOever, Benjamin R AU - TenOever BR AUID- ORCID: 0000-0003-0324-3078 AD - Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States. FAU - Blanco-Melo, Daniel AU - Blanco-Melo D AUID- ORCID: 0000-0002-0256-5019 AD - Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States. AD - Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States. FAU - Ávila Arcos, María C AU - Ávila Arcos MC AUID- ORCID: 0000-0003-1691-1696 AD - Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, Mexico. LA - eng SI - Dryad/10.5061/dryad.5x69p8d2s GR - WT_/Wellcome Trust/United Kingdom GR - 208934/Z/17/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210805 PL - England TA - Elife JT - eLife JID - 101579614 RN - 0 (DNA, Ancient) SB - IM CIN - Elife. 2021 Sep 09;10:e72791. doi: 10.7554/eLife.72791. PMID: 34499030 MH - Black People/history MH - DNA, Ancient/*analysis MH - Enslaved Persons/*history MH - Genome, Viral/*genetics MH - Hepatitis B virus/*genetics/isolation & purification MH - High-Throughput Nucleotide Sequencing MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - Humans MH - Metagenomics MH - Parvovirus B19, Human/*genetics/isolation & purification PMC - PMC8423449 OAB - The arrival of European colonists to the Americas, beginning in the 15(th) century, contributed to the spread of new viruses amongst Indigenous people. This led to massive outbreaks of disease, and millions of deaths that caused an important Native population to collapse. The exact viruses that caused these outbreaks are unknown, but smallpox, measles, and mumps are all suspected. During these times, traders and colonists forcibly enslaved and displaced millions of people mainly from the West Coast of Africa to the Americas. The cruel, unsanitary, and overcrowded conditions on ships transporting these people across the Atlantic contributed to the spread of infectious diseases onboard. Once on land, infectious diseases spread quickly, partly due to the poor conditions that enslaved and ndigenous people were made to endure. Native people were also immunologically naïve to the newly introduced pathogens, making them susceptible to severe or fatal outcomes. The new field of paleovirology may help scientists identify the viruses that were circulating in the first years of colonization and trace how viruses arrived in the Americas. Using next-generation DNA sequencing and other cutting-edge techniques, Guzmán-Solís et al. extracted and enriched viral DNA from skeletal remains dating back to the 16(th) century. These remains were found in mass graves that were used to bury epidemic victims at a colonial hospital and chapel in what is now Mexico City. The experiments identified two viruses, human parvovirus B19 and a human hepatitis B virus. These viral genomes were recovered from human remains of first-generation African people in Mexico, as well as an individual who was an Indigenous person. Although the genetic material of these ancient viruses resembled pathogens that originated in Africa, the study did not determine if the victims died from these viruses or another cause. On the other hand, the results indicate that viruses frequently found in modern Africa were circulating in the Americas during the slave trade period of Mexico. Finally, the results provide evidence that colonists who forcibly brought African people to the Americas participated in the introduction of viruses to Mexico. This constant influx of viruses from the old world, led to dramatic declines in the populations of Indigenous people in the Americas. OABL- eng OTO - NOTNLM OT - Africa OT - B19V OT - HBV OT - aDNA OT - genetics OT - genomics OT - human OT - infectious disease OT - microbiology OT - paleogenomics OT - paleovirology OT - viruses COIS- AG, VV, MS, JW, JG, MM, AM, GS, PS, BT, DB, MÁ None, MB none EDAT- 2021/08/06 06:00 MHDA- 2021/10/21 06:00 PMCR- 2021/08/05 CRDT- 2021/08/05 08:42 PHST- 2021/03/21 00:00 [received] PHST- 2021/07/30 00:00 [accepted] PHST- 2021/08/06 06:00 [pubmed] PHST- 2021/10/21 06:00 [medline] PHST- 2021/08/05 08:42 [entrez] PHST- 2021/08/05 00:00 [pmc-release] AID - 68612 [pii] AID - 10.7554/eLife.68612 [doi] PST - epublish SO - Elife. 2021 Aug 5;10:e68612. doi: 10.7554/eLife.68612. PMID- 34433944 OWN - NLM STAT- MEDLINE DCOM- 20220211 LR - 20230206 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 596 IP - 7873 DP - 2021 Aug TI - Genome of a middle Holocene hunter-gatherer from Wallacea. PG - 543-547 LID - 10.1038/s41586-021-03823-6 [doi] AB - Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA(1). So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)(1). Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge(2) in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex(3,4), shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago(5). We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today. CI - © 2021. The Author(s). FAU - Carlhoff, Selina AU - Carlhoff S AUID- ORCID: 0000-0001-9118-2839 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Duli, Akin AU - Duli A AD - Departemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia. FAU - Nägele, Kathrin AU - Nägele K AUID- ORCID: 0000-0003-3861-8677 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Nur, Muhammad AU - Nur M AD - Departemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia. FAU - Skov, Laurits AU - Skov L AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Sumantri, Iwan AU - Sumantri I AD - Departemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia. FAU - Oktaviana, Adhi Agus AU - Oktaviana AA AD - Pusat Penelitian Arkeologi Nasional (ARKENAS), Jakarta, Indonesia. AD - Place, Evolution and Rock Art Heritage Unit, Griffith Centre for Social and Cultural Research, Griffith University, Gold Coast, Queensland, Australia. FAU - Hakim, Budianto AU - Hakim B AD - Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia. FAU - Burhan, Basran AU - Burhan B AUID- ORCID: 0000-0002-9172-5888 AD - Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland, Australia. FAU - Syahdar, Fardi Ali AU - Syahdar FA AD - Independent researcher, Makassar, Indonesia. FAU - McGahan, David P AU - McGahan DP AUID- ORCID: 0000-0002-3161-1512 AD - Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland, Australia. FAU - Bulbeck, David AU - Bulbeck D AD - Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, Australian Capital Territory, Australia. FAU - Perston, Yinika L AU - Perston YL AUID- ORCID: 0000-0002-8043-6466 AD - Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland, Australia. FAU - Newman, Kim AU - Newman K AUID- ORCID: 0000-0002-6840-1658 AD - Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland, Australia. FAU - Saiful, Andi Muhammad AU - Saiful AM AD - Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia. FAU - Ririmasse, Marlon AU - Ririmasse M AD - Pusat Penelitian Arkeologi Nasional (ARKENAS), Jakarta, Indonesia. FAU - Chia, Stephen AU - Chia S AD - Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia. FAU - Hasanuddin AU - Hasanuddin AD - Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia. FAU - Pulubuhu, Dwia Aries Tina AU - Pulubuhu DAT AD - Departemen Sosiologi, Fakultas Ilmu Sosial, Universitas Hasanuddin, Makassar, Indonesia. FAU - Suryatman AU - Suryatman AD - Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia. FAU - Supriadi AU - Supriadi AD - Departemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia. FAU - Jeong, Choongwon AU - Jeong C AUID- ORCID: 0000-0003-3049-2352 AD - School of Biological Sciences, Seoul National University, Seoul, Republic of Korea. FAU - Peter, Benjamin M AU - Peter BM AUID- ORCID: 0000-0003-2526-8081 AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Prüfer, Kay AU - Prüfer K AUID- ORCID: 0000-0001-6242-3058 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Powell, Adam AU - Powell A AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. krause@eva.mpg.de. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. krause@eva.mpg.de. FAU - Posth, Cosimo AU - Posth C AUID- ORCID: 0000-0002-8206-3907 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. cosimo.posth@uni-tuebingen.de. AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. cosimo.posth@uni-tuebingen.de. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. cosimo.posth@uni-tuebingen.de. FAU - Brumm, Adam AU - Brumm A AUID- ORCID: 0000-0002-2276-3258 AD - Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland, Australia. a.brumm@griffith.edu.au. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210825 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Asia, Southeastern MH - Australia MH - Bone and Bones/metabolism MH - Caves MH - DNA, Ancient/*analysis MH - Female MH - *Fossils MH - Genome, Human/*genetics MH - *Genomics MH - History, Ancient MH - Human Migration/history MH - Humans MH - Indonesia/ethnology MH - Islands/*ethnology MH - New Guinea MH - *Phylogeny PMC - PMC8387238 COIS- The authors declare no competing interests. EDAT- 2021/08/27 06:00 MHDA- 2022/02/12 06:00 PMCR- 2021/08/25 CRDT- 2021/08/26 06:06 PHST- 2020/11/27 00:00 [received] PHST- 2021/07/13 00:00 [accepted] PHST- 2021/08/26 06:06 [entrez] PHST- 2021/08/27 06:00 [pubmed] PHST- 2022/02/12 06:00 [medline] PHST- 2021/08/25 00:00 [pmc-release] AID - 10.1038/s41586-021-03823-6 [pii] AID - 3823 [pii] AID - 10.1038/s41586-021-03823-6 [doi] PST - ppublish SO - Nature. 2021 Aug;596(7873):543-547. doi: 10.1038/s41586-021-03823-6. Epub 2021 Aug 25. PMID- 34198074 OWN - NLM STAT- MEDLINE DCOM- 20210819 LR - 20210819 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 325 DP - 2021 Aug TI - Efficacy of a novel bone preprocessing method for better DNA yield. PG - 110887 LID - S0379-0738(21)00207-3 [pii] LID - 10.1016/j.forsciint.2021.110887 [doi] AB - In cases involving identification of missing persons, mass disasters and ancient DNA investigations, bone and teeth samples are often the only, and almost always the best, biological material available for DNA profiling. Standard methods for extraction of DNA from such samples involve grinding of the bone and teeth samples. Here, we present an extremely efficient protocol for recovery of DNA from bone samples by a method of scrapping. The study was carried out on 25 samples and it was found that the quantity of DNA isolated by the scrapping method was up to 1.131 ng/µl with a success rate of 93% as compared to a much lower yield of 0.359 ng/µl DNA isolated with a success rate of 28% through the grinding method. The scrapping method of DNA extraction has been proven to be extremely useful in forensic examination of challenging samples that had multiple failures using the traditional grinding method. CI - Copyright © 2021 Elsevier B.V. All rights reserved. FAU - Sahoo, Subhasish AU - Sahoo S AD - DNA Profiling Unit, State Forensic Science Laboratory, Rasulgarh, Bhubaneswar 751010, Odisha, India; ViStA Lab, Department of Biological Sciences, BITS, Pilani - K K Birla Goa Campus, Goa 403726, India. FAU - Samal, Rashmita AU - Samal R AD - DNA Profiling Unit, State Forensic Science Laboratory, Rasulgarh, Bhubaneswar 751010, Odisha, India. FAU - Biswas, Sumit AU - Biswas S AD - ViStA Lab, Department of Biological Sciences, BITS, Pilani - K K Birla Goa Campus, Goa 403726, India. Electronic address: sumit@goa.bits-pilani.ac.in. LA - eng PT - Journal Article DEP - 20210624 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 9007-49-2 (DNA) SB - IM EIN - Forensic Sci Int. 2021 Sep;326:110936. doi: 10.1016/j.forsciint.2021.110936. PMID: 34353672 MH - DNA/*analysis MH - *DNA Fingerprinting MH - Femur/*chemistry MH - Forensic Genetics/methods MH - Humans MH - *Microsatellite Repeats MH - Multiplex Polymerase Chain Reaction MH - Specimen Handling/*methods OTO - NOTNLM OT - Bone OT - Human identification OT - STR profiling OT - Scrapping method COIS- Conflict of interest The authors declare that there is no conflict of interest whatsoever and all the authors have read and approved the manuscript. EDAT- 2021/07/02 06:00 MHDA- 2021/08/20 06:00 CRDT- 2021/07/01 20:19 PHST- 2020/12/03 00:00 [received] PHST- 2021/06/06 00:00 [revised] PHST- 2021/06/18 00:00 [accepted] PHST- 2021/07/02 06:00 [pubmed] PHST- 2021/08/20 06:00 [medline] PHST- 2021/07/01 20:19 [entrez] AID - S0379-0738(21)00207-3 [pii] AID - 10.1016/j.forsciint.2021.110887 [doi] PST - ppublish SO - Forensic Sci Int. 2021 Aug;325:110887. doi: 10.1016/j.forsciint.2021.110887. Epub 2021 Jun 24. PMID- 34294811 OWN - NLM STAT- MEDLINE DCOM- 20211105 LR - 20211105 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 11 IP - 1 DP - 2021 Jul 22 TI - Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe. PG - 15005 LID - 10.1038/s41598-021-94491-z [doi] LID - 15005 AB - Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe. CI - © 2021. The Author(s). FAU - Rohrlach, Adam B AU - Rohrlach AB AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. rohrlach@shh.mpg.de. AD - ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia. rohrlach@shh.mpg.de. FAU - Papac, Luka AU - Papac L AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Childebayeva, Ainash AU - Childebayeva A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Rivollat, Maïté AU - Rivollat M AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. AD - Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France. FAU - Villalba-Mouco, Vanessa AU - Villalba-Mouco V AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. AD - Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain. FAU - Neumann, Gunnar U AU - Neumann GU AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Penske, Sandra AU - Penske S AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Skourtanioti, Eirini AU - Skourtanioti E AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - van de Loosdrecht, Marieke AU - van de Loosdrecht M AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Akar, Murat AU - Akar M AD - Department of Archaeology, Mustafa Kemal University, 31060, Alahan-Antakya, Hatay, Turkey. FAU - Boyadzhiev, Kamen AU - Boyadzhiev K AD - National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria. FAU - Boyadzhiev, Yavor AU - Boyadzhiev Y AD - National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France. FAU - Dobeš, Miroslav AU - Dobeš M AD - Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic. FAU - Erdal, Yilmaz S AU - Erdal YS AD - Department of Anthropology, Hacettepe University, 06800, Ankara, Turkey. FAU - Ernée, Michal AU - Ernée M AD - Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic. FAU - Frangipane, Marcella AU - Frangipane M AD - Department of Classics, Sapienza University of Rome, 00185, Rome, Italy. FAU - Furmanek, Mirosław AU - Furmanek M AD - Institute of Archaeology, University of Wrocław, Wrocław, Poland. FAU - Friederich, Susanne AU - Friederich S AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany. FAU - Ghesquière, Emmanuel AU - Ghesquière E AD - Inrap Grand Ouest, Bourguébus, France. AD - Université de Rennes 1, CNRS, CReAAH-UMR, 6566, Rennes, France. FAU - Hałuszko, Agata AU - Hałuszko A AD - Institute of Archaeology, University of Wrocław, Wrocław, Poland. AD - Archeolodzy.org Foundation, Wrocław, Poland. FAU - Hansen, Svend AU - Hansen S AD - Eurasia Department, German Archaeological Institute, Berlin, Germany. FAU - Küßner, Mario AU - Küßner M AD - Thuringian State Office for Heritage Management and Archeology, Weimar, Germany. FAU - Mannino, Marcello AU - Mannino M AD - Department of Archaeology, School of Culture and Society, Aarhus University, 8270, Højbjerg, Denmark. FAU - Özbal, Rana AU - Özbal R AD - Department of Archaeology and History of Art, Koç University, 34450, Istanbul, Turkey. FAU - Reinhold, Sabine AU - Reinhold S AD - Eurasia Department, German Archaeological Institute, Berlin, Germany. FAU - Rottier, Stéphane AU - Rottier S AD - Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France. FAU - Salazar-García, Domingo Carlos AU - Salazar-García DC AD - Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain. AD - Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, Spain. AD - Department of Geological Sciences, University of Cape Town, Cape Town, South Africa. FAU - Diaz, Jorge Soler AU - Diaz JS AD - MARQ Archaeological Museum of Alicante, Alicante, Spain. FAU - Stockhammer, Philipp W AU - Stockhammer PW AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. AD - Ludwig Maximilian University Munich, 80799, Munich, Germany. FAU - de Togores Muñoz, Consuelo Roca AU - de Togores Muñoz CR AD - MARQ Archaeological Museum of Alicante, Alicante, Spain. FAU - Yener, K Aslihan AU - Yener KA AD - Institute for the Study of the Ancient World (ISAW), New York University, New York, NY, 10028, USA. FAU - Posth, Cosimo AU - Posth C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. AD - Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences Eberhard Karls University Tübingen, 72070, Tübingen, Germany. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Herbig, Alexander AU - Herbig A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Haak, Wolfgang AU - Haak W AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. haak@shh.mpg.de. AD - School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia. haak@shh.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210722 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - *Alleles MH - *Chromosomes, Human, Y MH - DNA, Mitochondrial MH - Genetic Markers MH - Genetic Testing MH - *Genetics, Population/methods MH - *Haplotypes MH - Humans MH - Polymorphism, Single Nucleotide PMC - PMC8298398 COIS- The authors declare no competing interests. EDAT- 2021/07/24 06:00 MHDA- 2021/11/06 06:00 PMCR- 2021/07/22 CRDT- 2021/07/23 06:23 PHST- 2021/02/26 00:00 [received] PHST- 2021/07/09 00:00 [accepted] PHST- 2021/07/23 06:23 [entrez] PHST- 2021/07/24 06:00 [pubmed] PHST- 2021/11/06 06:00 [medline] PHST- 2021/07/22 00:00 [pmc-release] AID - 10.1038/s41598-021-94491-z [pii] AID - 94491 [pii] AID - 10.1038/s41598-021-94491-z [doi] PST - epublish SO - Sci Rep. 2021 Jul 22;11(1):15005. doi: 10.1038/s41598-021-94491-z. PMID- 34335597 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20221207 IS - 1664-3224 (Electronic) IS - 1664-3224 (Linking) VI - 12 DP - 2021 TI - Ancient DNA Study in Medieval Europeans Shows an Association Between HLA-DRB1*03 and Paratyphoid Fever. PG - 691475 LID - 10.3389/fimmu.2021.691475 [doi] LID - 691475 AB - Outbreaks of infectious diseases repeatedly affected medieval Europe, leaving behind a large number of dead often inhumed in mass graves. Human remains interred in two burial pits from 14(th) century CE Germany exhibited molecular evidence of Salmonella enterica Paratyphi C (S. Paratyphi C) infection. The pathogen is responsible for paratyphoid fever, which was likely the cause of death for the buried individuals. This finding presented the unique opportunity to conduct a paratyphoid fever association study in a European population. We focused on HLA-DRB1*03:01 that is a known risk allele for enteric fever in present-day South Asians. We generated HLA profiles for 29 medieval S. Paratyphi C cases and 24 contemporaneous controls and compared these to a modern German population. The frequency of the risk allele was higher in the medieval cases (29.6%) compared to the contemporaneous controls (13%; p = 0.189), albeit not significantly so, possibly because of small sample sizes. Indeed, in comparison with the modern controls (n = 39,689; 10.2%; p = 0.005) the frequency difference became statistically significant. This comparison also suggested a slight decrease in the allele's prevalence between the medieval and modern controls. Up to now, this is the first study on the genetic predisposition to Salmonella infection in Europeans and the only association analysis on paratyphoid fever C. Functional investigation using computational binding prediction between HLA variants and S. Paratyphi and S. Typhi peptides supported a reduced recognition capacity of bacterial proteins by DRB1*03:01 relative to other common DRB1 variants. This pattern could potentially explain the disease association. Our results suggest a slightly reduced predisposition to paratyphoid fever in modern Europeans. The causative allele, however, is still common today, which can be explained by a trade-off, as DRB1*03:01 is protective against infectious respiratory diseases such as severe respiratory syndrome (SARS). It is thus possible that the allele also provided resistance to corona-like viruses in the past. CI - Copyright © 2021 Haller, Bonczarowska, Rieger, Lenz, Nebel and Krause-Kyora. FAU - Haller, Magdalena AU - Haller M AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Bonczarowska, Joanna H AU - Bonczarowska JH AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Rieger, Dirk AU - Rieger D AD - Department of Archaeology, Hanseatic City of Lübeck Historic Monuments Protection Authority, Lübeck, Germany. FAU - Lenz, Tobias L AU - Lenz TL AD - Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany. AD - Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, Hamburg, Germany. FAU - Nebel, Almut AU - Nebel A AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210715 PL - Switzerland TA - Front Immunol JT - Frontiers in immunology JID - 101560960 RN - 0 (DNA, Ancient) RN - 0 (HLA-DRB1 Chains) SB - IM MH - DNA, Ancient MH - Genetic Predisposition to Disease MH - Germany MH - HLA-DRB1 Chains/*genetics MH - Humans MH - Paratyphoid Fever/*genetics MH - White People/*genetics PMC - PMC8320744 OTO - NOTNLM OT - Salmonella enterica Paratyphi C OT - antigen binding prediction OT - enteric fever OT - human leukocyte antigen OT - trade-off COIS- The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. EDAT- 2021/08/03 06:00 MHDA- 2021/10/26 06:00 PMCR- 2021/01/01 CRDT- 2021/08/02 05:55 PHST- 2021/04/06 00:00 [received] PHST- 2021/06/28 00:00 [accepted] PHST- 2021/08/02 05:55 [entrez] PHST- 2021/08/03 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] PHST- 2021/01/01 00:00 [pmc-release] AID - 10.3389/fimmu.2021.691475 [doi] PST - epublish SO - Front Immunol. 2021 Jul 15;12:691475. doi: 10.3389/fimmu.2021.691475. eCollection 2021. PMID- 34242562 OWN - NLM STAT- MEDLINE DCOM- 20211223 LR - 20211223 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 184 IP - 14 DP - 2021 Jul 8 TI - Before and after farming: The genetic structure of South China and Southeast Asia. PG - 3597-3598 LID - S0092-8674(21)00751-0 [pii] LID - 10.1016/j.cell.2021.06.016 [doi] AB - In this issue of Cell, Wang et al. harness ancient DNA methods to produce and analyze new genomic data from 31 individuals from South China, dated between 500 and 10,000-12,000 years ago. The study reveals a complex interplay between groups of three different genetic ancestries and provides a new perspective on interactions and agricultural dispersals in South China and Southeast Asia. CI - Copyright © 2021 Elsevier Inc. All rights reserved. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Althansgrasse 14, 1090, Vienna, Austria. Electronic address: ron.pinhasi@univie.ac.at. FAU - Douka, Katerina AU - Douka K AD - Department of Evolutionary Anthropology, University of Vienna, Althansgrasse 14, 1090, Vienna, Austria; Department of Archaeology, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. LA - eng PT - Comment PT - Journal Article PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) SB - IM CON - Cell. 2021 Jul 8;184(14):3812-3828.e30. doi: 10.1016/j.cell.2021.06.004. PMID: 34214472 MH - *Agriculture MH - Asia, Southeastern MH - China MH - *DNA, Ancient MH - Genetic Structures MH - Humans EDAT- 2021/07/10 06:00 MHDA- 2021/12/24 06:00 CRDT- 2021/07/09 20:12 PHST- 2021/07/09 20:12 [entrez] PHST- 2021/07/10 06:00 [pubmed] PHST- 2021/12/24 06:00 [medline] AID - S0092-8674(21)00751-0 [pii] AID - 10.1016/j.cell.2021.06.016 [doi] PST - ppublish SO - Cell. 2021 Jul 8;184(14):3597-3598. doi: 10.1016/j.cell.2021.06.016. PMID- 34171307 OWN - NLM STAT- MEDLINE DCOM- 20220103 LR - 20221207 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 184 IP - 14 DP - 2021 Jul 8 TI - Human population history at the crossroads of East and Southeast Asia since 11,000 years ago. PG - 3829-3841.e21 LID - S0092-8674(21)00635-8 [pii] LID - 10.1016/j.cell.2021.05.018 [doi] AB - Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest humans sequenced from southern China. We discovered a deeply diverged East Asian ancestry in the Guangxi region that persisted until at least 6,000 years ago. We found that ∼9,000- to 6,000-year-old Guangxi populations were a mixture of local ancestry, southern ancestry previously sampled in Fujian, and deep Asian ancestry related to Southeast Asian Hòabìnhian hunter-gatherers, showing broad admixture in the region predating the appearance of farming. Historical Guangxi populations dating to ∼1,500 to 500 years ago are closely related to Tai-Kadai and Hmong-Mien speakers. Our results show heavy interactions among three distinct ancestries at the crossroads of East and Southeast Asia. CI - Copyright © 2021 Elsevier Inc. All rights reserved. FAU - Wang, Tianyi AU - Wang T AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Northwest University, Xi'an 710069, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Wang, Wei AU - Wang W AD - Institute of Cultural Heritage, Shandong University, Qingdao 266237, China. FAU - Xie, Guangmao AU - Xie G AD - Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China; College of History, Culture and Tourism, Guangxi Normal University, Guilin 541001, China. FAU - Li, Zhen AU - Li Z AD - Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China. FAU - Fan, Xuechun AU - Fan X AD - International Research Center for Austronesian Archaeology, Pingtan 350000, China; Fujian Museum, Fuzhou 350001, China. FAU - Yang, Qingping AU - Yang Q AD - Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China. FAU - Wu, Xichao AU - Wu X AD - Fujian Longyan Museum, Longyan 364000, China. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Liu, Yichen AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China. FAU - Yang, Ruowei AU - Yang R AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Liu, Feng AU - Liu F AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Dai, Qingyan AU - Dai Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Wu, Xiaohong AU - Wu X AD - School of Archaeology and Museology, Peking University, Beijing 100871, China. FAU - Qin, Ling AU - Qin L AD - School of Archaeology and Museology, Peking University, Beijing 100871, China. FAU - Li, Fajun AU - Li F AD - Department of Anthropology, School of Sociology and Anthropology, Sun Yat-Sen University, Guangzhou 510275, China. FAU - Ping, Wanjing AU - Ping W AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Zhang, Lizhao AU - Zhang L AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Zhang, Ming AU - Zhang M AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Liu, Yalin AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Chen, Xiaoshan AU - Chen X AD - Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China. FAU - Zhang, Dongju AU - Zhang D AD - Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China. FAU - Zhou, Zhenyu AU - Zhou Z AD - Institute of Archaeology, Chinese Academy of Social Sciences, Beijing 100710, China. FAU - Wu, Yun AU - Wu Y AD - Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China. FAU - Shafiey, Hassan AU - Shafiey H AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Gao, Xing AU - Gao X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Curnoe, Darren AU - Curnoe D AD - Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia. FAU - Mao, Xiaowei AU - Mao X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China. FAU - Bennett, E Andrew AU - Bennett EA AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Ji, Xueping AU - Ji X AD - Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming 650500, China. Electronic address: jxpchina@foxmail.com. FAU - Yang, Melinda A AU - Yang MA AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Department of Biology, University of Richmond, Richmond, VA 23173, USA. Electronic address: myang@richmond.edu. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of the Chinese Academy of Sciences, Beijing 100049, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng GR - 55008731/HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210624 PL - United States TA - Cell JT - Cell JID - 0413066 SB - IM MH - Asia, Southeastern MH - Asia, Eastern MH - *Genetics, Population MH - Geography MH - Humans OTO - NOTNLM OT - 12,000-year-old humans OT - admixture OT - ancient DNA OT - cross-interactions OT - deeply diverged ancestry OT - pre-farming COIS- Declaration of interests The authors declare no competing interests. EDAT- 2021/06/26 06:00 MHDA- 2022/01/04 06:00 CRDT- 2021/06/25 20:11 PHST- 2020/12/21 00:00 [received] PHST- 2021/03/17 00:00 [revised] PHST- 2021/05/14 00:00 [accepted] PHST- 2021/06/26 06:00 [pubmed] PHST- 2022/01/04 06:00 [medline] PHST- 2021/06/25 20:11 [entrez] AID - S0092-8674(21)00635-8 [pii] AID - 10.1016/j.cell.2021.05.018 [doi] PST - ppublish SO - Cell. 2021 Jul 8;184(14):3829-3841.e21. doi: 10.1016/j.cell.2021.05.018. Epub 2021 Jun 24. PMID- 34213855 OWN - NLM STAT- MEDLINE DCOM- 20210706 LR - 20210706 IS - 1768-3238 (Electronic) IS - 1631-0691 (Linking) VI - 344 IP - 2 DP - 2021 Jul 2 TI - Reconstructing 50,000 years of human history from our DNA: lessons from modern genomics. PG - 177-187 LID - 10.5802/crbiol.55 [doi] AB - The advent of high throughput sequencing approaches and ancient DNA techniques have enabled reconstructing the history of human populations at an unprecedented level of resolution. The symposium from the French Academy of Sciences "50,000 ans d'épopée humaine dans notre ADN" has reviewed some of the latest contributions from the fields of genomics, archaeology, and linguistics to our understanding of  > 300,000 years of human history. DNA has revealed the richness of the human journey, from the deep divergences between human populations in Africa, to the first encounters of Homo Sapiens with other hominins on their way to Eurasia and the peopling of Remote Oceania. The symposium has also emphasized how migrations, cultural practices, and environmental pathogens have contributed to shape the genetic diversity of modern humans, through admixture, genetic drift or genetic adaptation. Finally, special attention was also given to how human behaviours have shaped the genome of other species, through the spreading of microbes and pathogens, as in the case of Yersinia Pestis, or through domestication, as elegantly demonstrated for dogs, horses, and apples. Altogether, this conference illustrated how the complex history of human populations is tightly linked with their contemporary genetic diversity that, in turn, has direct effects on their identity and health. FAU - Rotival, Maxime AU - Rotival M AUID- ORCID: 0000-0003-2519-8044 AD - Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France. FAU - Cossart, Pascale AU - Cossart P AD - Bacteria/Cell Interactions Unit, Institut Pasteur, U604, Inserm, Paris 75015, France. FAU - Quintana-Murci, Lluis AU - Quintana-Murci L AD - Chair of Human Genomics and Evolution, Collège de France, Paris, 75005, France. AD - Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France. LA - eng PT - Historical Article PT - Journal Article DEP - 20210702 PL - France TA - C R Biol JT - Comptes rendus biologies JID - 101140040 RN - 9007-49-2 (DNA) SB - IM MH - Africa MH - Animals MH - Archaeology MH - *DNA MH - Dogs MH - Genome MH - Genome, Human MH - *Genomics MH - History, Ancient MH - Horses MH - Humans OTO - NOTNLM OT - Ancient DNA OT - Anthropology OT - Domesticated species OT - Genomics OT - Human history OT - Population genetics EDAT- 2021/07/03 06:00 MHDA- 2021/07/07 06:00 CRDT- 2021/07/02 12:29 PHST- 2021/05/28 00:00 [received] PHST- 2021/06/03 00:00 [accepted] PHST- 2021/07/02 12:29 [entrez] PHST- 2021/07/03 06:00 [pubmed] PHST- 2021/07/07 06:00 [medline] AID - 10.5802/crbiol.55 [doi] PST - epublish SO - C R Biol. 2021 Jul 2;344(2):177-187. doi: 10.5802/crbiol.55. PMID- 34187204 OWN - NLM STAT- MEDLINE DCOM- 20211206 LR - 20211214 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 71 IP - 1 DP - 2021 Jul TI - The influence of sample quantity and lysis parameters on the success of ancient DNA extraction from skeletal remains. PG - 376-381 LID - 10.2144/btn-2020-0169 [doi] AB - DNA extraction is of utmost importance in archaeobiology, as it determines the success of further DNA analyses. This study concentrates on the success of ancient DNA extraction using silica spin columns and PCR-based analysis from archaeological skeletal material and investigates the influence of sample quantity, lysis time and lysis temperature during sample preparation. The results show that lysis times ranging from 2 to 48 h are suitable, and that lysis should be carried out at a constant temperature of 56°C. Concerning sample quantity, 10 mg for mitochondrial DNA and 50 mg for chromosomal DNA are sufficient for high quality analyses. Thus invaluable sample material can be saved, and time of sample preparation can be reduced considerably. FAU - Euskirchen, Alina AU - Euskirchen A AUID- ORCID: 0000-0002-8712-6655 AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. FAU - Hartmann, Larissa AU - Hartmann L AUID- ORCID: 0000-0002-6775-286X AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. FAU - Mazanec, Janine AU - Mazanec J AUID- ORCID: 0000-0002-8437-2084 AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. FAU - Wittmeier, Patrick AU - Wittmeier P AUID- ORCID: 0000-0001-6240-6338 AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. FAU - Hummel, Susanne AU - Hummel S AUID- ORCID: 0000-0002-3647-8968 AD - Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany. LA - eng PT - Journal Article DEP - 20210630 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Ancient) SB - IM MH - *Body Remains MH - DNA Fingerprinting MH - *DNA, Ancient/isolation & purification MH - Humans MH - Microsatellite Repeats OTO - NOTNLM OT - STR typing OT - ancient DNA extraction OT - archaeological skeletal remains OT - chromosomal DNA OT - lysis duration OT - lysis temperature OT - mitochondrial DNA OT - sample amount OT - sample preparation parameters OT - sequence analysis EDAT- 2021/07/01 06:00 MHDA- 2021/12/15 06:00 CRDT- 2021/06/30 05:27 PHST- 2021/07/01 06:00 [pubmed] PHST- 2021/12/15 06:00 [medline] PHST- 2021/06/30 05:27 [entrez] AID - 10.2144/btn-2020-0169 [doi] PST - ppublish SO - Biotechniques. 2021 Jul;71(1):376-381. doi: 10.2144/btn-2020-0169. Epub 2021 Jun 30. PMID- 34164993 OWN - NLM STAT- MEDLINE DCOM- 20211206 LR - 20211214 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 71 IP - 1 DP - 2021 Jul TI - A method for the temperature-controlled extraction of DNA from ancient bones. PG - 382-386 LID - 10.2144/btn-2021-0025 [doi] AB - Contamination with microbial and other exogenous DNA poses a significant challenge in the generation of genome-wide sequence data from ancient skeletal remains. Here we describe a method for separating ancient DNA into multiple fractions during DNA extraction by sequential temperature-controlled release of DNA into sodium phosphate buffer. An evaluation of the effectiveness of the method using a set of three ancient bones resulted in between 1.6- and 32-fold enrichment of endogenous DNA compared with regular DNA extraction. For two bones, the method outperformed previous methods of decontaminating ancient bones, including hypochlorite treatment, which resulted in near-complete destruction of DNA in the worst-preserved sample. This extraction method expands the spectrum of methods available for depleting contaminant DNA from ancient skeletal remains. FAU - Essel, Elena AU - Essel E AUID- ORCID: 0000-0002-2642-8043 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D-04103, Germany. FAU - Korlević, Petra AU - Korlević P AUID- ORCID: 0000-0002-5418-5587 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D-04103, Germany. AD - Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK. FAU - Meyer, Matthias AU - Meyer M AUID- ORCID: 0000-0002-4760-558X AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D-04103, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210624 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Ancient) SB - IM MH - *Body Remains MH - *Bone and Bones MH - *DNA, Ancient/isolation & purification MH - Humans MH - Temperature OTO - NOTNLM OT - ancient DNA OT - archaeological material OT - contamination removal OT - endogenous DNA OT - sequential DNA extraction EDAT- 2021/06/25 06:00 MHDA- 2021/12/15 06:00 CRDT- 2021/06/24 08:46 PHST- 2021/06/25 06:00 [pubmed] PHST- 2021/12/15 06:00 [medline] PHST- 2021/06/24 08:46 [entrez] AID - 10.2144/btn-2021-0025 [doi] PST - ppublish SO - Biotechniques. 2021 Jul;71(1):382-386. doi: 10.2144/btn-2021-0025. Epub 2021 Jun 24. PMID- 34039840 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20230914 IS - 1473-6519 (Electronic) IS - 1363-1950 (Linking) VI - 24 IP - 4 DP - 2021 Jul 1 TI - Recent advances in understanding the adaptive evolution of metabolic genes and traits. PG - 308-314 LID - 10.1097/MCO.0000000000000770 [doi] AB - PURPOSE OF REVIEW: This review summarizes the recent advances in understanding the adaptive evolution of metabolic genes and traits, providing insights into gene-diet interactions in human evolution and health. RECENT FINDINGS: The rapid accumulation of ancient DNA across time and geography illuminates unprecedented details of some well-established examples of genetic adaptation to diet, such as the LCT and FADS genes. Novel cases of thrifty genes were identified, especially a microRNA at the LCT locus that controls energy expenditure and glucose homeostasis, connecting the historical adaptation to present-day metabolic disorders. A new example of gene-diet-microbiota interactions was established among the AMY1 copy number, starchy diets, and resistant-starch-digesting Ruminococcus. The explosion of genome-wide association studies in large cohorts unravels the present-day health implications of historically adaptive genetic variants. It also enables studies into the polygenic adaptation of metabolic traits, revealing intriguing adaptive signals for increased bone mineral density, blood pressure, and risk of type 2 diabetes, but decreased body mass index and HbA1c. SUMMARY: The rapid accumulation of ancient and modern DNA has fueled the characterization of novel and existing cases of genetic adaptation. However, transferring these evolutionary insights into genome-informed precision nutrition requires extensive mechanistic studies and genotype-aware clinical trials. CI - Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved. FAU - Yang, Shuang AU - Yang S AD - Department of Genetics, Franklin College of Arts and Sciences. FAU - Ye, Kaixiong AU - Ye K AD - Department of Genetics, Franklin College of Arts and Sciences. AD - Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA. LA - eng PT - Journal Article PT - Review PL - England TA - Curr Opin Clin Nutr Metab Care JT - Current opinion in clinical nutrition and metabolic care JID - 9804399 RN - 0 (MicroRNAs) SB - IM MH - *Diabetes Mellitus, Type 2/genetics MH - Genome MH - Genome-Wide Association Study MH - Humans MH - *MicroRNAs MH - Phenotype EDAT- 2021/05/28 06:00 MHDA- 2021/10/26 06:00 CRDT- 2021/05/27 05:53 PHST- 2021/05/28 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] PHST- 2021/05/27 05:53 [entrez] AID - 00075197-202107000-00006 [pii] AID - 10.1097/MCO.0000000000000770 [doi] PST - ppublish SO - Curr Opin Clin Nutr Metab Care. 2021 Jul 1;24(4):308-314. doi: 10.1097/MCO.0000000000000770. PMID- 34037863 OWN - NLM STAT- MEDLINE DCOM- 20210625 LR - 20221207 IS - 1617-4623 (Electronic) IS - 1617-4623 (Linking) VI - 296 IP - 4 DP - 2021 Jul TI - Origin of ethnic groups, linguistic families, and civilizations in China viewed from the Y chromosome. PG - 783-797 LID - 10.1007/s00438-021-01794-x [doi] AB - East Asia, geographically extending to the Pamir Plateau in the west, to the Himalayan Mountains in the southwest, to Lake Baikal in the north and to the South China Sea in the south, harbors a variety of people, cultures, and languages. To reconstruct the natural history of East Asians is a mission of multiple disciplines, including genetics, archaeology, linguistics, and ethnology. Geneticists confirm the recent African origin of modern East Asians. Anatomically modern humans arose in Africa and immigrated into East Asia via a southern route approximately 50,000 years ago. Following the end of the Last Glacial Maximum approximately 12,000 years ago, rice and millet were domesticated in the south and north of East Asia, respectively, which allowed human populations to expand and linguistic families and ethnic groups to develop. These Neolithic populations produced a strong relation between the present genetic structures and linguistic families. The expansion of the Hongshan people from northeastern China relocated most of the ethnic populations on a large scale approximately 5300 years ago. Most of the ethnic groups migrated to remote regions, producing genetic structure differences between the edge and center of East Asia. In central China, pronounced population admixture occurred and accelerated over time, which subsequently formed the Han Chinese population and eventually the Chinese civilization. Population migration between the north and the south throughout history has left a smooth gradient in north-south changes in genetic structure. Observation of the process of shaping the genetic structure of East Asians may help in understanding the global natural history of modern humans. FAU - Yu, Xueer AU - Yu X AD - MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China. AD - Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, Datong, 037006, China. FAU - Li, Hui AU - Li H AUID- ORCID: 0000-0002-7642-215X AD - MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China. LHCA@Fudan.edu.cn. AD - Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, Datong, 037006, China. LHCA@Fudan.edu.cn. LA - eng GR - 2020YFE0201600/the National Key R&D Program of China/ GR - 91731303/National Natural Science Foundation of China/ GR - 31671297/National Natural Science Foundation of China/ GR - 18490750300/B&R Joint Laboratory of Eurasian Anthropology/ GR - ERC-2019-AdG-TRAM-883700/European Research Council project/ PT - Historical Article PT - Journal Article PT - Review DEP - 20210526 PL - Germany TA - Mol Genet Genomics JT - Molecular genetics and genomics : MGG JID - 101093320 SB - IM MH - Anthropology, Cultural MH - Asian People/classification/ethnology/genetics MH - China/ethnology MH - Chromosomes, Human, Y/*genetics MH - Civilization/*history MH - Ethnicity/classification/genetics/*history MH - Asia, Eastern/ethnology MH - Gene Flow MH - Genetics, Population/history MH - History, Ancient MH - Humans MH - Linguistics/classification/history MH - Phylogeny OTO - NOTNLM OT - Ancient DNA OT - Civilization OT - East Asia OT - Neolithic Age OT - Population Genetics OT - Y chromosome EDAT- 2021/05/27 06:00 MHDA- 2021/06/29 06:00 CRDT- 2021/05/26 12:38 PHST- 2020/09/30 00:00 [received] PHST- 2021/04/22 00:00 [accepted] PHST- 2021/05/27 06:00 [pubmed] PHST- 2021/06/29 06:00 [medline] PHST- 2021/05/26 12:38 [entrez] AID - 10.1007/s00438-021-01794-x [pii] AID - 10.1007/s00438-021-01794-x [doi] PST - ppublish SO - Mol Genet Genomics. 2021 Jul;296(4):783-797. doi: 10.1007/s00438-021-01794-x. Epub 2021 May 26. PMID- 33872864 OWN - NLM STAT- MEDLINE DCOM- 20210817 LR - 20210817 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 53 DP - 2021 Jul TI - Beyond simple kinship and identification: aDNA analyses from a 17th-19th century crypt in Germany. PG - 102498 LID - S1872-4973(21)00037-5 [pii] LID - 10.1016/j.fsigen.2021.102498 [doi] AB - Ancient DNA (aDNA) analysis is a powerful tool in multidisciplinary research on human remains, potentially leading to kinship scenarios and historical identifications. In this study, we present a genetic investigation of three noble families from the 17th to 19th centuries AD entombed in burial crypts at the cloister church of Riesa (Germany). Tests were aimed at identifying anticipated and incidental genetic relationships in our sample and the implications thereof for the assumed identity of the deceased. A total of 17 individuals were investigated via morphological, radiographic and aDNA analysis, yielding complete and partial autosomal and Y-STR profiles and reliable mtDNA sequences. Biostatistics and lineage markers revealed the presence of first to third degree relationships within the cohort. The pedigrees of the families Hanisch/von Odeleben and von Welck were thereby successfully reproduced, while four previously unknown individuals could be linked to the von Felgenhauer family. However, limitations of biostatistical kinship analysis became evident when the kinship scenario went beyond simple relationships. A combined analysis with archaeological data and historical records resulted in (almost) unambiguous identification of 14 of the 17 individuals. CI - Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved. FAU - Alterauge, Amelie AU - Alterauge A AD - Department of Prehistoric Archaeology, Institute of Archaeological Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland; Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland. FAU - Lösch, Sandra AU - Lösch S AD - Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland. FAU - Sulzer, Andrea AU - Sulzer A AD - Department of Forensic Genetics, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zürich, Switzerland. FAU - Gysi, Mario AU - Gysi M AD - Department of Forensic Genetics, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zürich, Switzerland. FAU - Haas, Cordula AU - Haas C AD - Department of Forensic Genetics, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zürich, Switzerland. Electronic address: cordula.haas@irm.uzh.ch. LA - eng PT - Historical Article PT - Journal Article DEP - 20210317 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Chromosomes, Human, Y MH - DNA Fingerprinting MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Famous Persons MH - Germany MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Microsatellite Repeats MH - *Pedigree OTO - NOTNLM OT - Autosomal STRs OT - Crypt burial OT - Identification OT - Kinship OT - Noble family OT - Y-chromosomal STRs OT - aDNA OT - mtDNA EDAT- 2021/04/20 06:00 MHDA- 2021/08/18 06:00 CRDT- 2021/04/19 20:17 PHST- 2020/10/05 00:00 [received] PHST- 2021/02/24 00:00 [revised] PHST- 2021/03/15 00:00 [accepted] PHST- 2021/04/20 06:00 [pubmed] PHST- 2021/08/18 06:00 [medline] PHST- 2021/04/19 20:17 [entrez] AID - S1872-4973(21)00037-5 [pii] AID - 10.1016/j.fsigen.2021.102498 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2021 Jul;53:102498. doi: 10.1016/j.fsigen.2021.102498. Epub 2021 Mar 17. PMID- 34191795 OWN - NLM STAT- MEDLINE DCOM- 20240724 LR - 20240724 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 16 IP - 6 DP - 2021 TI - Human mobility at Tell Atchana (Alalakh), Hatay, Turkey during the 2nd millennium BC: Integration of isotopic and genomic evidence. PG - e0241883 LID - 10.1371/journal.pone.0241883 [doi] LID - e0241883 AB - The Middle and Late Bronze Age, a period roughly spanning the 2nd millennium BC (ca. 2000-1200 BC) in the Near East, is frequently referred to as the first 'international age', characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh, located in Hatay, Turkey), we explored the role of mobility at the capital of a regional kingdom, named Mukish during the Late Bronze Age, which spanned the Amuq Valley and some areas beyond. We generated strontium and oxygen isotope data from dental enamel for 53 individuals and 77 individuals, respectively, and added ancient DNA data of 10 newly sequenced individuals to a dataset of 27 individuals published in 2020. Additionally, we improved the DNA coverage of one individual from this 2020 dataset. The DNA data revealed a very homogeneous gene pool. This picture of an overwhelmingly local ancestry was consistent with the evidence of local upbringing in most of the individuals indicated by the isotopic data, where only five were found to be non-local. High levels of contact, trade, and exchange of ideas and goods in the Middle and Late Bronze Ages, therefore, seem not to have translated into high levels of individual mobility detectable at Tell Atchana. FAU - Ingman, Tara AU - Ingman T AUID- ORCID: 0000-0002-0338-0489 AD - Koç University Research Center for Anatolian Civilizations (ANAMED), Koc University, Istanbul, Turkey. FAU - Eisenmann, Stefanie AU - Eisenmann S AUID- ORCID: 0000-0002-6301-5889 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Skourtanioti, Eirini AU - Skourtanioti E AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Akar, Murat AU - Akar M AD - Department of Archaeology, Mustafa Kemal University, Alahan-Antakya, Hatay, Turkey. FAU - Ilgner, Jana AU - Ilgner J AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Gnecchi Ruscone, Guido Alberto AU - Gnecchi Ruscone GA AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - le Roux, Petrus AU - le Roux P AUID- ORCID: 0000-0002-5930-4995 AD - Department of Geological Sciences, University of Cape Town, Rondebosch, South Africa. FAU - Shafiq, Rula AU - Shafiq R AD - Anthropology Department, Yeditepe University, Istanbul, Turkey. FAU - Neumann, Gunnar U AU - Neumann GU AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Keller, Marcel AU - Keller M AUID- ORCID: 0000-0001-9668-6817 AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Freund, Cäcilia AU - Freund C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Marzo, Sara AU - Marzo S AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Lucas, Mary AU - Lucas M AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Roberts, Patrick AU - Roberts P AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Yener, K Aslıhan AU - Yener KA AD - Institute for the Study of the Ancient World (ISAW), New York University, New York, NY, United States of America. FAU - Stockhammer, Philipp W AU - Stockhammer PW AUID- ORCID: 0000-0003-4702-9372 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Germany. LA - eng PT - Historical Article PT - Journal Article DEP - 20210630 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (Strontium Isotopes) RN - 0 (Oxygen Isotopes) MH - Humans MH - Turkey MH - *Human Migration/history MH - History, Ancient MH - *DNA, Ancient/analysis MH - *Strontium Isotopes/analysis MH - Oxygen Isotopes/analysis MH - Genomics/methods MH - Dental Enamel/chemistry MH - Archaeology MH - Male MH - Female PMC - PMC8244877 COIS- The authors have declared that no competing interests exist. EDAT- 2021/07/01 06:00 MHDA- 2023/02/25 06:00 PMCR- 2021/06/30 CRDT- 2021/06/30 17:22 PHST- 2020/10/21 00:00 [received] PHST- 2021/05/28 00:00 [accepted] PHST- 2021/06/30 17:22 [entrez] PHST- 2021/07/01 06:00 [pubmed] PHST- 2023/02/25 06:00 [medline] PHST- 2021/06/30 00:00 [pmc-release] AID - PONE-D-20-33062 [pii] AID - 10.1371/journal.pone.0241883 [doi] PST - epublish SO - PLoS One. 2021 Jun 30;16(6):e0241883. doi: 10.1371/journal.pone.0241883. eCollection 2021. PMID- 33974848 OWN - NLM STAT- MEDLINE DCOM- 20220224 LR - 20220224 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 31 IP - 12 DP - 2021 Jun 21 TI - Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula. PG - 2576-2591.e12 LID - S0960-9822(21)00535-2 [pii] LID - 10.1016/j.cub.2021.04.022 [doi] AB - Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition. CI - Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Saupe, Tina AU - Saupe T AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia. Electronic address: tina.saupe@ut.ee. FAU - Montinaro, Francesco AU - Montinaro F AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy. FAU - Scaggion, Cinzia AU - Scaggion C AD - Department of Geosciences, University of Padova, Via Gradenigo 6, Padova 35131, Italy. FAU - Carrara, Nicola AU - Carrara N AD - Museum of Anthropology, University of Padova, Palazzo Cavalli, via Giotto 1, Padova 35121, Italy. FAU - Kivisild, Toomas AU - Kivisild T AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven, Herestraat 49 3000, Belgium. FAU - D'Atanasio, Eugenia AU - D'Atanasio E AD - Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Rome 00185, Italy. FAU - Hui, Ruoyun AU - Hui R AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK. FAU - Solnik, Anu AU - Solnik A AD - Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia. FAU - Lebrasseur, Ophélie AU - Lebrasseur O AD - Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK; Palaeogenomics & Bio-Archaeology Research Network, School of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK. FAU - Larson, Greger AU - Larson G AD - Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy. FAU - Alessandri, Luca AU - Alessandri L AD - Groningen Institute of Archaeology, University of Groningen, Poststraat 6, Groningen 9712, the Netherlands. FAU - Arienzo, Ilenia AU - Arienzo I AD - Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy. FAU - De Angelis, Flavio AU - De Angelis F AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome "Tor Vergata," Via della Ricerca Scientifica 1, Rome 00133, Italy. FAU - Rolfo, Mario Federico AU - Rolfo MF AD - Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy. FAU - Skeates, Robin AU - Skeates R AD - Department of Archaeology, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK. FAU - Silvestri, Letizia AU - Silvestri L AD - Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy. FAU - Beckett, Jessica AU - Beckett J AD - Independent scholar, Cagliari, Italy. FAU - Talamo, Sahra AU - Talamo S AD - Department of Chemistry "Giacomo Ciamician," University of Bologna, Via Selmi 2, Bologna 40126, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany. FAU - Dolfini, Andrea AU - Dolfini A AD - School of History, Classics and Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK. FAU - Miari, Monica AU - Miari M AD - Superintendency of Archeology, Fine Arts and Landscape for the metropolitan city of Bologna and the provinces of Modena, Reggio Emilia and Ferrara, Comune di Bologna, Sede Via Belle Arti n. 52, Bologna 40126, Italy. FAU - Metspalu, Mait AU - Metspalu M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia. FAU - Benazzi, Stefano AU - Benazzi S AD - Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1, Ravenna 40126, Italy. FAU - Capelli, Cristian AU - Capelli C AD - Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma 43124, Italy. FAU - Pagani, Luca AU - Pagani L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi, 58/B, Padova 35122, Italy. FAU - Scheib, Christiana L AU - Scheib CL AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; St. John's College, University of Cambridge, St. John's Street, Cambridge CB2 1TP, UK. Electronic address: cls83@ut.ee. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210510 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - Datasets as Topic MH - Genetics, Population MH - Genome, Human/*genetics MH - Genomics MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Italy MH - Leprosy/genetics MH - Phenotype OTO - NOTNLM OT - ancient DNA OT - gene flow OT - genome-wide shotgun data OT - human population genetics OT - immunity OT - isotopes OT - kinship OT - later prehistory COIS- Declaration of interests The authors declare no competing interests. EDAT- 2021/05/12 06:00 MHDA- 2022/02/25 06:00 CRDT- 2021/05/11 20:10 PHST- 2020/04/10 00:00 [received] PHST- 2020/11/28 00:00 [revised] PHST- 2021/04/09 00:00 [accepted] PHST- 2021/05/12 06:00 [pubmed] PHST- 2022/02/25 06:00 [medline] PHST- 2021/05/11 20:10 [entrez] AID - S0960-9822(21)00535-2 [pii] AID - 10.1016/j.cub.2021.04.022 [doi] PST - ppublish SO - Curr Biol. 2021 Jun 21;31(12):2576-2591.e12. doi: 10.1016/j.cub.2021.04.022. Epub 2021 May 10. PMID- 33831350 OWN - NLM STAT- MEDLINE DCOM- 20210825 LR - 20210825 IS - 1096-0309 (Electronic) IS - 0003-2697 (Linking) VI - 623 DP - 2021 Jun 15 TI - Testing a series of modifications on genomic library preparation methods for ancient or degraded DNA. PG - 114193 LID - S0003-2697(21)00094-4 [pii] LID - 10.1016/j.ab.2021.114193 [doi] AB - Technological advancements have revolutionized ancient and degraded DNA analysis, moving the field to the Next Generation Sequencing era. One of the advancements, the ancient DNA-oriented high-throughput library preparation methods, enabled the sequencing of more endogenous molecules. Although fairly optimized, both single- and double-stranded library preparation methods hold the potential for further improvement. Here, we test a series of modifications made at different steps of both single- and double-stranded library preparation methods. Given all the modifications tested, we found that two of them provide further benefits, including the use of Endonuclease VIII as a pre-treatment step before preparing single-stranded libraries and the use of a modified second adapter of the single stranded-libraries as an alternative option to enable sequencing of single stranded-libraries with the standard Illumina sequencing primer instead of the custom designed as described in the single stranded library preparation method. Furthermore, we propose uracil-DNA-glycosylase (UDG) could also be considered for both single- and double-stranded library preparation methods, although additional parameters should be taken into account depending on the sequencing strategy and the sample characteristics. Further modifications were also tested and although they were not advantageous, they could be considered as equivalent to the published options. CI - Copyright © 2021 Elsevier Inc. All rights reserved. FAU - Psonis, Nikolaos AU - Psonis N AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), N. Plastira 100, Vassilika Vouton, Irakleio, GR70013, Greece. Electronic address: nikos.psonis@gmail.com. FAU - Vassou, Despoina AU - Vassou D AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), N. Plastira 100, Vassilika Vouton, Irakleio, GR70013, Greece. FAU - Kafetzopoulos, Dimitris AU - Kafetzopoulos D AD - Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), N. Plastira 100, Vassilika Vouton, Irakleio, GR70013, Greece. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210406 PL - United States TA - Anal Biochem JT - Analytical biochemistry JID - 0370535 RN - 0 (DNA Primers) RN - 0 (DNA, Ancient) RN - 0 (DNA, Single-Stranded) RN - 9007-49-2 (DNA) RN - EC 3.2.2.- (Uracil-DNA Glycosidase) SB - IM MH - DNA/*analysis/chemistry/metabolism MH - DNA Primers/chemistry MH - DNA, Ancient/*analysis/chemistry MH - DNA, Single-Stranded/analysis/chemistry MH - *Genomic Library MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Sequence Analysis, DNA/*methods MH - Uracil-DNA Glycosidase/chemistry/metabolism OTO - NOTNLM OT - Double-stranded library OT - Next generation sequencing OT - Single-stranded library EDAT- 2021/04/09 06:00 MHDA- 2021/08/26 06:00 CRDT- 2021/04/08 20:15 PHST- 2020/11/16 00:00 [received] PHST- 2021/03/18 00:00 [revised] PHST- 2021/03/27 00:00 [accepted] PHST- 2021/04/09 06:00 [pubmed] PHST- 2021/08/26 06:00 [medline] PHST- 2021/04/08 20:15 [entrez] AID - S0003-2697(21)00094-4 [pii] AID - 10.1016/j.ab.2021.114193 [doi] PST - ppublish SO - Anal Biochem. 2021 Jun 15;623:114193. doi: 10.1016/j.ab.2021.114193. Epub 2021 Apr 6. PMID- 34208224 OWN - NLM STAT- MEDLINE DCOM- 20210921 LR - 20210921 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 12 IP - 6 DP - 2021 Jun 11 TI - How a Paleogenomic Approach Can Provide Details on Bioarchaeological Reconstruction: A Case Study from the Globular Amphorae Culture. LID - 10.3390/genes12060910 [doi] LID - 910 AB - Ancient human remains have the potential to explain a great deal about the prehistory of humankind. Due to recent technological and bioinformatics advances, their study, at the palaeogenomic level, can provide important information about population dynamics, culture changes, and the lifestyles of our ancestors. In this study, mitochondrial and nuclear genome data obtained from human bone remains associated with the Neolithic Globular Amphorae culture, which were recovered in the Megalithic barrow of Kierzkowo (Poland), were reanalysed to gain insight into the social organisation and use of the archaeological site and to provide information at the individual level. We were able to successfully estimate the minimum number of individuals, sex, kin relationships, and phenotypic traits of the buried individuals, despite the low level of preservation of the bone samples and the intricate taphonomic conditions. In addition, the evaluation of damage patterns allowed us to highlight the presence of "intruders"-that is, of more recent skeletal remains that did not belong to the original burial. Due to its characteristics, the study of the Kierzkowo barrow represented a challenge for the reconstruction of the biological profile of the human community who exploited it and an excellent example of the contribution that ancient genomic analysis can provide to archaeological reconstruction. FAU - Vai, Stefania AU - Vai S AD - Department of Biology, University of Florence, 50122 Florence, Italy. FAU - Diroma, Maria Angela AU - Diroma MA AUID- ORCID: 0000-0003-1427-8946 AD - Department of Biology, University of Florence, 50122 Florence, Italy. FAU - Cannariato, Costanza AU - Cannariato C AUID- ORCID: 0000-0003-3669-1002 AD - Department of Biology, University of Florence, 50122 Florence, Italy. FAU - Budnik, Alicja AU - Budnik A AUID- ORCID: 0000-0002-9916-9775 AD - Department of Human Biology, Institute of Biological Sciences, Cardinal Stefan Wyszyński University, 01-938 Warsaw, Poland. FAU - Lari, Martina AU - Lari M AD - Department of Biology, University of Florence, 50122 Florence, Italy. FAU - Caramelli, David AU - Caramelli D AD - Department of Biology, University of Florence, 50122 Florence, Italy. FAU - Pilli, Elena AU - Pilli E AD - Department of Biology, University of Florence, 50122 Florence, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210611 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology/*methods MH - Biological Evolution MH - *DNA, Ancient MH - Genome, Human MH - Genomics/*methods MH - Humans MH - Pedigree MH - Social Evolution PMC - PMC8230892 OTO - NOTNLM OT - Neolithic OT - ancient DNA OT - kinship OT - multiple burial OT - palaeogenomics OT - phenotypic traits COIS- The authors declare no conflict of interest. EDAT- 2021/07/03 06:00 MHDA- 2021/09/22 06:00 PMCR- 2021/06/11 CRDT- 2021/07/02 01:34 PHST- 2021/04/28 00:00 [received] PHST- 2021/06/02 00:00 [revised] PHST- 2021/06/08 00:00 [accepted] PHST- 2021/07/02 01:34 [entrez] PHST- 2021/07/03 06:00 [pubmed] PHST- 2021/09/22 06:00 [medline] PHST- 2021/06/11 00:00 [pmc-release] AID - genes12060910 [pii] AID - genes-12-00910 [pii] AID - 10.3390/genes12060910 [doi] PST - epublish SO - Genes (Basel). 2021 Jun 11;12(6):910. doi: 10.3390/genes12060910. PMID- 34048699 OWN - NLM STAT- MEDLINE DCOM- 20220105 LR - 20221207 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 184 IP - 12 DP - 2021 Jun 10 TI - The deep population history of northern East Asia from the Late Pleistocene to the Holocene. PG - 3256-3266.e13 LID - S0092-8674(21)00575-4 [pii] LID - 10.1016/j.cell.2021.04.040 [doi] AB - Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6-3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). At the close of the LGM stadial, the earliest northern East Asian appeared in the Amur region, and this population is basal to ancient northern East Asians. Human populations in the Amur region have maintained genetic continuity from 14 ka, and these early inhabitants represent the closest East Asian source known for Ancient Paleo-Siberians. We also observed that EDAR V370A was likely to have been elevated to high frequency after the LGM, suggesting the possible timing for its selection. This study provides a deep look into the population dynamics of northern East Asia. CI - Copyright © 2021 Elsevier Inc. All rights reserved. FAU - Mao, Xiaowei AU - Mao X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Zhang, Hucai AU - Zhang H AD - Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences (CAS), Beijing 100101, China. Electronic address: zhanghc@ynu.edu.cn. FAU - Qiao, Shiyu AU - Qiao S AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of the Chinese Academy of Sciences, Beijing 100049, China. FAU - Liu, Yichen AU - Liu Y AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China. FAU - Chang, Fengqin AU - Chang F AD - Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China. FAU - Xie, Ping AU - Xie P AD - Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China. FAU - Zhang, Ming AU - Zhang M AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Wang, Tianyi AU - Wang T AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Northwest University, Xi'an 710069, China. FAU - Li, Mian AU - Li M AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Yang, Ruowei AU - Yang R AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Liu, Feng AU - Liu F AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Dai, Qingyan AU - Dai Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Ping, Wanjing AU - Ping W AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Lei, Chuzhao AU - Lei C AD - Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China. FAU - Olsen, John W AU - Olsen JW AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; School of Anthropology, University of Arizona, Tucson, AZ 85721-0030, USA. FAU - Bennett, E Andrew AU - Bennett EA AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of the Chinese Academy of Sciences, Beijing 100049, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210527 PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/analysis MH - Asia, Eastern MH - Female MH - Genetic Variation MH - Genetics, Population MH - Genome, Human MH - Geography MH - Humans MH - Ice Cover MH - Likelihood Functions MH - Male MH - Models, Genetic MH - Phylogeny MH - *Population Dynamics MH - Principal Component Analysis MH - Time Factors OTO - NOTNLM OT - Last Glacial Maximum OT - ancient DNA OT - northern East Asia OT - population dynamics COIS- Declaration of interests The authors declare no competing interests. EDAT- 2021/05/29 06:00 MHDA- 2022/01/06 06:00 CRDT- 2021/05/28 20:10 PHST- 2020/10/16 00:00 [received] PHST- 2021/01/20 00:00 [revised] PHST- 2021/04/23 00:00 [accepted] PHST- 2021/05/29 06:00 [pubmed] PHST- 2022/01/06 06:00 [medline] PHST- 2021/05/28 20:10 [entrez] AID - S0092-8674(21)00575-4 [pii] AID - 10.1016/j.cell.2021.04.040 [doi] PST - ppublish SO - Cell. 2021 Jun 10;184(12):3256-3266.e13. doi: 10.1016/j.cell.2021.04.040. Epub 2021 May 27. PMID- 34038549 OWN - NLM STAT- MEDLINE DCOM- 20220209 LR - 20220209 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 13 IP - 6 DP - 2021 Jun 8 TI - HuConTest: Testing Human Contamination in Great Ape Samples. LID - 10.1093/gbe/evab117 [doi] LID - evab117 AB - Modern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in noninvasive samples. Here, we present a simple method to detect human contamination in short-read sequencing data from different species: HuConTest. We demonstrate its feasibility using blood and tissue samples from these species. This test is particularly useful for more complex samples (such as museum and noninvasive samples) which have smaller amounts of endogenous DNA, as we show here. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Kuhlwilm, Martin AU - Kuhlwilm M AUID- ORCID: 0000-0002-0115-1797 AD - Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain. FAU - Fontsere, Claudia AU - Fontsere C AUID- ORCID: 0000-0003-2233-6026 AD - Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain. FAU - Han, Sojung AU - Han S AUID- ORCID: 0000-0002-6113-1042 AD - Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain. FAU - Alvarez-Estape, Marina AU - Alvarez-Estape M AUID- ORCID: 0000-0001-8242-1092 AD - Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain. FAU - Marques-Bonet, Tomas AU - Marques-Bonet T AUID- ORCID: 0000-0002-5597-3075 AD - Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain. AD - CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. AD - Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain. AD - Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Barcelona, Spain. LA - eng SI - figshare/10.6084/m9.figshare.14237834 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 SB - IM MH - Animals MH - *DNA Contamination MH - Hominidae/*genetics MH - Humans PMC - PMC8247554 OTO - NOTNLM OT - ancient DNA OT - contamination OT - fecal DNA OT - next-generation sequencing OT - nonhuman primates EDAT- 2021/05/27 06:00 MHDA- 2022/02/10 06:00 PMCR- 2021/05/26 CRDT- 2021/05/26 17:43 PHST- 2021/05/19 00:00 [accepted] PHST- 2021/05/27 06:00 [pubmed] PHST- 2022/02/10 06:00 [medline] PHST- 2021/05/26 17:43 [entrez] PHST- 2021/05/26 00:00 [pmc-release] AID - 6284962 [pii] AID - evab117 [pii] AID - 10.1093/gbe/evab117 [doi] PST - ppublish SO - Genome Biol Evol. 2021 Jun 8;13(6):evab117. doi: 10.1093/gbe/evab117. PMID- 34083588 OWN - NLM STAT- MEDLINE DCOM- 20211122 LR - 20211122 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 11 IP - 1 DP - 2021 Jun 3 TI - Ancient DNA, lipid biomarkers and palaeoecological evidence reveals construction and life on early medieval lake settlements. PG - 11807 LID - 10.1038/s41598-021-91057-x [doi] LID - 11807 AB - Direct evidence of ancient human occupation is typically established through archaeological excavation. Excavations are costly and destructive, and practically impossible in some lake and wetland environments. We present here an alternative approach, providing direct evidence from lake sediments using DNA metabarcoding, steroid lipid biomarkers (bile acids) and from traditional environmental analyses. Applied to an early Medieval Celtic settlement in Ireland (a crannog) this approach provides a site chronology and direct evidence of human occupation, crops, animal farming and on-site slaughtering. This is the first independently-dated, continuous molecular archive of human activity from an archeological site, demonstrating a link between animal husbandry, food resources, island use. These sites are under threat but are impossible to preserve in-situ so this approach can be used, with or without excavation, to produce a robust and full site chronology and provide direct evidence of occupation, the use of plants and animals, and activities such as butchery. FAU - Brown, A G AU - Brown AG AD - Tromsø Museum, Artic University of Norway, Tromsø, Norway. antony.g.brown@uit.no. AD - School of Geography and Environmental Science, University of Southampton, Southampton, UK. antony.g.brown@uit.no. FAU - Van Hardenbroek, M AU - Van Hardenbroek M AD - School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK. FAU - Fonville, T AU - Fonville T AD - School of Geography and Environmental Science, University of Southampton, Southampton, UK. FAU - Davies, K AU - Davies K AD - School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK. AD - IMSET, Bournemouth University, Poole, UK. FAU - Mackay, H AU - Mackay H AD - School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK. AD - Department of Geography, Durham University, Durham, UK. FAU - Murray, E AU - Murray E AD - Archaeology, Queens University, Belfast, Northern Ireland, UK. FAU - Head, K AU - Head K AD - School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK. FAU - Barratt, P AU - Barratt P AD - School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK. FAU - McCormick, F AU - McCormick F AD - Archaeology, Queens University, Belfast, Northern Ireland, UK. FAU - Ficetola, G F AU - Ficetola GF AD - Department of Environmental Science and Policy, University of Milan, Milan, Italy. AD - LECA, Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble, France. FAU - Gielly, L AU - Gielly L AD - LECA, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble, France. FAU - Henderson, A C G AU - Henderson ACG AD - School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK. FAU - Crone, A AU - Crone A AD - AOC Group Ltd., Edinburgh, Scotland, UK. FAU - Cavers, G AU - Cavers G AD - AOC Group Ltd., Edinburgh, Scotland, UK. FAU - Langdon, P G AU - Langdon PG AD - School of Geography and Environmental Science, University of Southampton, Southampton, UK. FAU - Whitehouse, N J AU - Whitehouse NJ AD - Department of Archaeology, School of Humanities, University of Glasgow, Glasgow, UK. FAU - Pirrie, D AU - Pirrie D AD - School of Applied Sciences, University of South Wales, Pontypridd, UK. FAU - Alsos, I G AU - Alsos IG AD - Tromsø Museum, Artic University of Norway, Tromsø, Norway. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210603 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (Biomarkers) RN - 0 (DNA, Ancient) RN - 0 (Lipids) RN - 0 (Minerals) SB - IM MH - Animals MH - *Archaeology/methods MH - *Biomarkers MH - *DNA, Ancient MH - History, Medieval MH - Humans MH - Ireland MH - *Lakes MH - *Lipids MH - Minerals/analysis MH - Radiometric Dating MH - United Kingdom PMC - PMC8175756 COIS- The authors declare no competing interests. EDAT- 2021/06/05 06:00 MHDA- 2021/11/23 06:00 PMCR- 2021/06/03 CRDT- 2021/06/04 06:25 PHST- 2020/11/20 00:00 [received] PHST- 2021/05/04 00:00 [accepted] PHST- 2021/06/04 06:25 [entrez] PHST- 2021/06/05 06:00 [pubmed] PHST- 2021/11/23 06:00 [medline] PHST- 2021/06/03 00:00 [pmc-release] AID - 10.1038/s41598-021-91057-x [pii] AID - 91057 [pii] AID - 10.1038/s41598-021-91057-x [doi] PST - epublish SO - Sci Rep. 2021 Jun 3;11(1):11807. doi: 10.1038/s41598-021-91057-x. PMID- 34128784 OWN - NLM STAT- MEDLINE DCOM- 20211228 LR - 20211228 IS - 2057-5858 (Electronic) IS - 2057-5858 (Linking) VI - 7 IP - 6 DP - 2021 Jun TI - Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection. LID - 10.1099/mgen.0.000580 [doi] LID - 000580 AB - Specific lineages of serogroup O1 Vibrio cholerae are notorious for causing cholera pandemics, of which there have been seven since the 1800s. Much is known about the sixth pandemic (1899–1923) and the ongoing seventh pandemic (1961–present), but we know very little about the bacteriology of pandemics 1 to 5. Moreover, although we are learning about the contribution of non-O1 non-pandemic V. cholerae to cholera dynamics during the current pandemic, we know almost nothing about their role in the past. A recent ancient DNA study has presented what may be the first molecular evidence of a V. cholerae infection from the fifth cholera pandemic period (1886–1887 AD) in Argentina. Here, we place the molecular evidence from that study into the genomic context of non-pandemic V. cholerae from Latin America and elsewhere, and show that a gene fragment amplified from ancient DNA is most similar to that of V. cholerae from the Americas, and from Argentina. Our results corroborate and reinforce the findings of the original study, and collectively suggest that even in the 1880s, non-pandemic V. cholerae local to the Americas may have caused sporadic infections in Argentina, just as we know this to have happened during the seventh pandemic in Latin America. FAU - Dorman, Matthew J AU - Dorman MJ AD - Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK. AD - Churchill College, Storey's Way, Cambridge, CB3 0DS, UK. FAU - Thomson, Nicholas R AU - Thomson NR AD - Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK. AD - London School of Hygiene and Tropical Medicine, Keppel St., Bloomsbury, London, WC1E 7HT, UK. FAU - Campos, Josefina AU - Campos J AD - Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina. LA - eng SI - figshare/10.6084/m9.figshare.14384225.v1 SI - figshare/10.6084/m9.figshare.13636577 SI - figshare/10.6084/m9.figshare.11310131 GR - WT_/Wellcome Trust/United Kingdom GR - 206194/WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Microb Genom JT - Microbial genomics JID - 101671820 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - Americas/epidemiology MH - Argentina/epidemiology MH - Cholera/*epidemiology/microbiology MH - *DNA, Ancient MH - DNA, Bacterial/genetics MH - *Genomics MH - Humans MH - *Pandemics MH - Vibrio cholerae/*genetics PMC - PMC8461468 OTO - NOTNLM OT - VCR OT - Vibrio cholerae OT - aDNA OT - ancient DNA OT - cholera OT - fifth pandemic COIS- The authors declare that there are no conflicts of interest. EDAT- 2021/06/16 06:00 MHDA- 2021/12/29 06:00 PMCR- 2021/06/15 CRDT- 2021/06/15 13:20 PHST- 2021/06/15 13:20 [entrez] PHST- 2021/06/16 06:00 [pubmed] PHST- 2021/12/29 06:00 [medline] PHST- 2021/06/15 00:00 [pmc-release] AID - 000580 [pii] AID - 10.1099/mgen.0.000580 [doi] PST - ppublish SO - Microb Genom. 2021 Jun;7(6):000580. doi: 10.1099/mgen.0.000580. PMID- 33971396 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20211025 IS - 1879-9825 (Electronic) IS - 1879-9817 (Linking) VI - 33 DP - 2021 Jun TI - Ancient DNA analysis of rare genetic bone disorders. PG - 182-187 LID - S1879-9817(21)00025-5 [pii] LID - 10.1016/j.ijpp.2021.04.009 [doi] AB - OBJECTIVE: Review of the current advancements in the field of paleogenetics that provide new opportunities in studying the evolution of rare genetic bone diseases. MATERIAL AND METHODS: Based on cases from the literature, the genetics of rare bone diseases will be introduced and the main methodological issues will be addressed, focusing on the opportunities presented by the application of aDNA analyses in the field of paleopathology. RESULTS: Medical literature provides large datasets on the genes responsible for rare bone disorders. These genes, subdivided in functional categories, display important future targets when analyzing rare genetic bone disorders in ancient human remains. CONCLUSIONS: Knowledge on both phenotype and genotype is required to study rare diseases in ancient human remains. SIGNIFICANCE: The proposed interdisciplinary research will provide new insight into the occurrence and spread of genetic risk factors in the past and will help in the diagnostics of these rare and often neglected diseases. LIMITATIONS: The current limitations in ancient DNA research and targeting the disease-causing specific mutations (e.g., somatic or germline). SUGGESTIONS FOR FURTHER RESEARCH: Methodological advancements and candidate gene lists provide the optimal basis for future interdisciplinary studies of rare genetic bone disorders in ancient human remains. CI - Copyright © 2021 Elsevier Inc. All rights reserved. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, Eurac Research, Bolzano, Italy. Electronic address: frank.maixner@eurac.edu. FAU - Gresky, Julia AU - Gresky J AD - German Archaeological Institute, Department of Natural Sciences, Berlin, Germany. FAU - Zink, Albert AU - Zink A AD - Institute for Mummy Studies, Eurac Research, Bolzano, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210507 PL - Netherlands TA - Int J Paleopathol JT - International journal of paleopathology JID - 101562474 RN - 0 (DNA, Ancient) SB - IM MH - *Bone Diseases/genetics MH - Bone and Bones MH - *DNA, Ancient MH - Humans MH - Paleopathology MH - Rare Diseases OTO - NOTNLM OT - Enrichment capture OT - Genetic risk factors OT - Germline OT - Next generation sequencing OT - Somatic EDAT- 2021/05/11 06:00 MHDA- 2021/10/26 06:00 CRDT- 2021/05/10 20:17 PHST- 2020/10/16 00:00 [received] PHST- 2021/04/22 00:00 [revised] PHST- 2021/04/24 00:00 [accepted] PHST- 2021/05/11 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] PHST- 2021/05/10 20:17 [entrez] AID - S1879-9817(21)00025-5 [pii] AID - 10.1016/j.ijpp.2021.04.009 [doi] PST - ppublish SO - Int J Paleopathol. 2021 Jun;33:182-187. doi: 10.1016/j.ijpp.2021.04.009. Epub 2021 May 7. PMID- 33911223 OWN - NLM STAT- MEDLINE DCOM- 20210823 LR - 20210823 IS - 1471-0064 (Electronic) IS - 1471-0056 (Linking) VI - 22 IP - 6 DP - 2021 Jun TI - Bone-free ancient DNA. PG - 342 LID - 10.1038/s41576-021-00368-2 [doi] FAU - Clyde, Dorothy AU - Clyde D AD - Nature Reviews Genetics, . nrg@nature.com. LA - eng PT - Comment PT - Journal Article PL - England TA - Nat Rev Genet JT - Nature reviews. Genetics JID - 100962779 RN - 0 (DNA, Ancient) SB - IM CON - Science. 2021 May 7;372(6542):eabf1667. doi: 10.1126/science.abf1667. PMID: 33858989 MH - *Bone and Bones MH - *DNA, Ancient MH - Fossils MH - Humans EDAT- 2021/04/30 06:00 MHDA- 2021/08/24 06:00 CRDT- 2021/04/29 06:16 PHST- 2021/04/30 06:00 [pubmed] PHST- 2021/08/24 06:00 [medline] PHST- 2021/04/29 06:16 [entrez] AID - 10.1038/s41576-021-00368-2 [pii] AID - 10.1038/s41576-021-00368-2 [doi] PST - ppublish SO - Nat Rev Genet. 2021 Jun;22(6):342. doi: 10.1038/s41576-021-00368-2. PMID- 33429070 OWN - NLM STAT- MEDLINE DCOM- 20220111 LR - 20220111 IS - 1567-7257 (Electronic) IS - 1567-1348 (Linking) VI - 90 DP - 2021 Jun TI - Gastrointestinal parasite burden in 4th-5th c. CE Florence highlighted by microscopy and paleogenetics. PG - 104713 LID - S1567-1348(21)00010-1 [pii] LID - 10.1016/j.meegid.2021.104713 [doi] AB - The study of ancient parasites, named paleoparasitology, traditionally focused on microscopic eggs disseminated in past environments and archaeological structures by humans and other animals infested by gastrointestinal parasites. Since the development of paleogenetics in the early 1980s, few paleoparasitological studies have been based on the ancient DNA (aDNA) of parasites, although such studies have clearly proven their utility and reliability. In this paper, we describe our integrative approach for the paleoparasitological study of an ancient population from Florence in Italy, dated to the 4th-5th c. CE. The first stage consisted in the study of sediment samples from the pelvic area of 18 individuals under light microscopy. This allowed us to detect Ascarid-type eggs belonging very probably to the human-infesting roundworm Ascaris lumbricoides. Ten subsamples were selected corresponding to five individuals, and we extracted their whole DNA following sediment aDNA protocols. A targeted approach allowed us to detect two nematodes and one trematode aDNA fragments, namely Ascaris sp., Trichuris trichiura, and Dicrocoelium dendriticum. Among the five individuals tested for microscopic eggs and aDNA, three of them showed the remains of eggs (only Ascarid-type), but all of them tested positive to the presence of at least one parasite aDNA. Microscopic diagnosis first guided our research for the selection of promising samples while the targeted aDNA approach significantly improved our knowledge in terms of parasitic diversity and frequency in this population subgroup. These results enabled us to discuss the possible impact of latent parasitism in this past population at the time of an epidemic, as suggested in Florence. In particular, the singular case of D. dendriticum detection is discussed in light of the present-day scarcity of genuine human infections. Nevertheless, actual infections are known in the paleoparasitological record, and food habits may have led to false parasitism in this historical context. aDNA leaching from overlying strata may also explain this detection. This study strongly pleads for a systematic integrative approach combining microscopy and aDNA in paleoparasitology. CI - Copyright © 2021. Published by Elsevier B.V. FAU - Kévin, Roche AU - Kévin R AD - Université Bordeaux Montaigne, CNRS UMR 5607 Ausonius, France; Université de Bourgogne Franche-Comté, CNRS UMR 6249 Chrono-Environnement, France. Electronic address: kevin.roche.paleo@gmail.com. FAU - Nicolas, Capelli AU - Nicolas C AD - Université de Bourgogne Franche-Comté, CNRS UMR 6249 Chrono-Environnement, France. FAU - Elsa, Pacciani AU - Elsa P AD - Soprintendenza Archeologia, Belle Arti e Paesaggio of Firenze, Pistoia and Prato, Italy. FAU - Paolo, Lelli AU - Paolo L AD - Cooperativa Archeologia, Firenze, Italy. FAU - Pasquino, Pallecchi AU - Pasquino P AD - Soprintendenza Archeologia, Belle Arti e Paesaggio of Firenze, Pistoia and Prato, Italy. FAU - Raffaella, Bianucci AU - Raffaella B AD - Legal Medicine Section, Department of Public Health and Paediatric Sciences, University of Turin, Italy; Warwick Medical School, Biomedical Sciences, University of Warwick, United Kingdom; ADES (UMR 7268), Laboratoire d'Anthropologie bio-culturelle, Droit, Ethique & Santé (Adés), Faculté de Médecine de Marseille, France. FAU - Matthieu, Le Bailly AU - Matthieu LB AD - Université de Bourgogne Franche-Comté, CNRS UMR 6249 Chrono-Environnement, France. Electronic address: matthieu.lebailly@univ-fcomte.fr. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210108 PL - Netherlands TA - Infect Genet Evol JT - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JID - 101084138 SB - IM MH - Animals MH - Ascariasis/*history/parasitology MH - Ascaris/*isolation & purification MH - Cities MH - Dicrocoeliasis/*history/parasitology MH - Dicrocoelium/*isolation & purification MH - History, Ancient MH - Humans MH - Intestinal Diseases, Parasitic/*history/parasitology MH - Italy MH - Trichuriasis/*history/parasitology MH - Trichuris/*isolation & purification OTO - NOTNLM OT - Bioarchaeology OT - Emergency burial site OT - Florence OT - Lancet liver fluke OT - Microscopy OT - Paleogenetics OT - Paleoparasitology OT - Roundworm OT - Whipworm EDAT- 2021/01/12 06:00 MHDA- 2022/01/12 06:00 CRDT- 2021/01/11 20:10 PHST- 2020/10/01 00:00 [received] PHST- 2020/11/25 00:00 [revised] PHST- 2021/01/06 00:00 [accepted] PHST- 2021/01/12 06:00 [pubmed] PHST- 2022/01/12 06:00 [medline] PHST- 2021/01/11 20:10 [entrez] AID - S1567-1348(21)00010-1 [pii] AID - 10.1016/j.meegid.2021.104713 [doi] PST - ppublish SO - Infect Genet Evol. 2021 Jun;90:104713. doi: 10.1016/j.meegid.2021.104713. Epub 2021 Jan 8. PMID- 33787889 OWN - NLM STAT- MEDLINE DCOM- 20220217 LR - 20231101 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 218 IP - 1 DP - 2021 May 17 TI - The timing of human adaptation from Neanderthal introgression. LID - 10.1093/genetics/iyab052 [doi] LID - iyab052 AB - Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long-term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of adaptive Neanderthal introgression. From these, we identify cases in which Neanderthal-introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. All rights reserved. For permissions, please email: journals.permissions@oup.com. FAU - Yair, Sivan AU - Yair S AD - Center for Population Biology, University of California, Davis, Davis, CA 95616, USA. AD - Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA. FAU - Lee, Kristin M AU - Lee KM AD - Department of Biological Sciences, Columbia University, New York, NY 10027, USA. FAU - Coop, Graham AU - Coop G AD - Center for Population Biology, University of California, Davis, Davis, CA 95616, USA. AD - Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA. LA - eng GR - R01 GM108779/GM/NIGMS NIH HHS/United States GR - R01 GM121372/GM/NIGMS NIH HHS/United States GR - R35 GM136290/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Genetics JT - Genetics JID - 0374636 SB - IM MH - Adaptation, Biological/genetics/physiology MH - Adaptation, Physiological/genetics MH - Alleles MH - Animals MH - Biological Evolution MH - Evolution, Molecular MH - Gene Frequency/genetics MH - Genetic Introgression/*genetics MH - Genome, Human/genetics MH - Haplotypes/genetics MH - Hominidae/*genetics MH - Humans MH - Neanderthals/*genetics MH - Phylogeny MH - Polymorphism, Single Nucleotide/genetics MH - Selection, Genetic/genetics PMC - PMC8128397 OTO - NOTNLM OT - adaptive introgression OT - ancient DNA OT - genetic hitchhiking EDAT- 2021/04/01 06:00 MHDA- 2022/02/19 06:00 PMCR- 2022/03/31 CRDT- 2021/03/31 13:22 PHST- 2020/10/20 00:00 [received] PHST- 2021/02/26 00:00 [accepted] PHST- 2021/04/01 06:00 [pubmed] PHST- 2022/02/19 06:00 [medline] PHST- 2021/03/31 13:22 [entrez] PHST- 2022/03/31 00:00 [pmc-release] AID - 6205711 [pii] AID - iyab052 [pii] AID - 10.1093/genetics/iyab052 [doi] PST - ppublish SO - Genetics. 2021 May 17;218(1):iyab052. doi: 10.1093/genetics/iyab052. PMID- 33986442 OWN - NLM STAT- MEDLINE DCOM- 20211108 LR - 20211108 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 11 IP - 1 DP - 2021 May 13 TI - Genomic selection signatures in autism spectrum disorder identifies cognitive genomic tradeoff and its relevance in paradoxical phenotypes of deficits versus potentialities. PG - 10245 LID - 10.1038/s41598-021-89798-w [doi] LID - 10245 AB - Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder characterized by paradoxical phenotypes of deficits as well as gain in brain function. To address this a genomic tradeoff hypothesis was tested and followed up with the biological interaction and evolutionary significance of positively selected ASD risk genes. SFARI database was used to retrieve the ASD risk genes while for population datasets 1000 genome data was used. Common risk SNPs were subjected to machine learning as well as independent tests for selection, followed by Bayesian analysis to identify the cumulative effect of selection on risk SNPs. Functional implication of these positively selected risk SNPs was assessed and subjected to ontology analysis, pertaining to their interaction and enrichment of biological and cellular functions. This was followed by comparative analysis with the ancient genomes to identify their evolutionary patterns. Our results identified significant positive selection signals in 18 ASD risk SNPs. Functional and ontology analysis indicate the role of biological and cellular processes associated with various brain functions. The core of the biological interaction network constitutes genes for cognition and learning while genes in the periphery of the network had direct or indirect impact on brain function. Ancient genome analysis identified de novo and conserved evolutionary selection clusters. The de-novo evolutionary cluster represented genes involved in cognitive function. Relative enrichment of the ASD risk SNPs from the respective evolutionary cluster or biological interaction networks may help in addressing the phenotypic diversity in ASD. This cognitive genomic tradeoff signatures impacting the biological networks can explain the paradoxical phenotypes in ASD. FAU - Prakash, Anil AU - Prakash A AD - Human Molecular Genetics Lab, Neurobiology and Genetics Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India. AD - Department of Biotechnology, University of Kerala, Kariavattom, Thiruvananthapuram, Kerala, India. FAU - Banerjee, Moinak AU - Banerjee M AD - Human Molecular Genetics Lab, Neurobiology and Genetics Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India. mbanerjee@rgcb.res.in. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210513 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Autism Spectrum Disorder/*genetics/metabolism MH - Bayes Theorem MH - Biological Evolution MH - Cognition/*physiology MH - Databases, Genetic MH - Gain of Function Mutation/physiology MH - Genetic Predisposition to Disease/genetics MH - Genome MH - Genome-Wide Association Study/methods MH - Genomics MH - Genotype MH - Humans MH - Phenotype MH - Polymorphism, Single Nucleotide/genetics MH - Risk Factors PMC - PMC8119484 COIS- The authors declare no competing interests. EDAT- 2021/05/15 06:00 MHDA- 2021/11/09 06:00 PMCR- 2021/05/13 CRDT- 2021/05/14 06:46 PHST- 2020/11/10 00:00 [received] PHST- 2021/04/26 00:00 [accepted] PHST- 2021/05/14 06:46 [entrez] PHST- 2021/05/15 06:00 [pubmed] PHST- 2021/11/09 06:00 [medline] PHST- 2021/05/13 00:00 [pmc-release] AID - 10.1038/s41598-021-89798-w [pii] AID - 89798 [pii] AID - 10.1038/s41598-021-89798-w [doi] PST - epublish SO - Sci Rep. 2021 May 13;11(1):10245. doi: 10.1038/s41598-021-89798-w. PMID- 33930288 OWN - NLM STAT- MEDLINE DCOM- 20211221 LR - 20240923 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 184 IP - 10 DP - 2021 May 13 TI - The genomic history of the Aegean palatial civilizations. PG - 2565-2586.e21 LID - S0092-8674(21)00370-6 [pii] LID - 10.1016/j.cell.2021.03.039 [doi] AB - The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes. CI - Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Clemente, Florian AU - Clemente F AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Unterländer, Martina AU - Unterländer M AD - Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece; Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany. FAU - Dolgova, Olga AU - Dolgova O AD - CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain. FAU - Amorim, Carlos Eduardo G AU - Amorim CEG AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Coroado-Santos, Francisco AU - Coroado-Santos F AD - CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal. FAU - Neuenschwander, Samuel AU - Neuenschwander S AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Ganiatsou, Elissavet AU - Ganiatsou E AD - Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece. FAU - Cruz Dávalos, Diana I AU - Cruz Dávalos DI AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Anchieri, Lucas AU - Anchieri L AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Michaud, Frédéric AU - Michaud F AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Winkelbach, Laura AU - Winkelbach L AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany. FAU - Blöcher, Jens AU - Blöcher J AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany. FAU - Arizmendi Cárdenas, Yami Ommar AU - Arizmendi Cárdenas YO AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Sousa da Mota, Bárbara AU - Sousa da Mota B AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Kalliga, Eleni AU - Kalliga E AD - Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece. FAU - Souleles, Angelos AU - Souleles A AD - Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece. FAU - Kontopoulos, Ioannis AU - Kontopoulos I AD - Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Karamitrou-Mentessidi, Georgia AU - Karamitrou-Mentessidi G AD - Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece. FAU - Philaniotou, Olga AU - Philaniotou O AD - Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece. FAU - Sampson, Adamantios AU - Sampson A AD - Department of Mediterranean Studies, University of the Aegean, 85132 Rhodes, Greece. FAU - Theodorou, Dimitra AU - Theodorou D AD - Ephorate of Antiquities of Kozani, Hellenic Ministry of Culture and Sports, 50004 Kozani, Greece. FAU - Tsipopoulou, Metaxia AU - Tsipopoulou M AD - Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece. FAU - Akamatis, Ioannis AU - Akamatis I AD - Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece. FAU - Halstead, Paul AU - Halstead P AD - Department of Archaeology, University of Sheffield, Minalloy House, 10-16 Regent St., Sheffield S1 3NJ, UK. FAU - Kotsakis, Kostas AU - Kotsakis K AD - Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece. FAU - Urem-Kotsou, Dushka AU - Urem-Kotsou D AD - Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece. FAU - Panagiotopoulos, Diamantis AU - Panagiotopoulos D AD - Institute of Classical Archaeology, University of Heidelberg, Marstallhof 4, 69117 Heidelberg, Germany. FAU - Ziota, Christina AU - Ziota C AD - Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100 Florina, Greece. FAU - Triantaphyllou, Sevasti AU - Triantaphyllou S AD - Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece. FAU - Delaneau, Olivier AU - Delaneau O AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Jensen, Jeffrey D AU - Jensen JD AD - School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA. FAU - Moreno-Mayar, J Víctor AU - Moreno-Mayar JV AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark; National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico. FAU - Burger, Joachim AU - Burger J AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany. FAU - Sousa, Vitor C AU - Sousa VC AD - CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal. FAU - Lao, Oscar AU - Lao O AD - CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain. FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. Electronic address: annasapfo.malaspinas@unil.ch. FAU - Papageorgopoulou, Christina AU - Papageorgopoulou C AD - Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece. Electronic address: cpapage@he.duth.gr. LA - eng GR - R01 GM135899/GM/NIGMS NIH HHS/United States GR - R35 GM139383/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20210429 PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) SB - IM MH - Civilization/*history MH - DNA, Ancient MH - *Genome, Human MH - *Genome, Mitochondrial MH - Greece, Ancient MH - History, Ancient MH - Human Migration/*history MH - Humans PMC - PMC8127963 OTO - NOTNLM OT - Anatolia OT - Bronze Age OT - Cycladic civilization OT - Greece OT - Helladic civilization OT - Minoan civilization OT - Mycenean civilization OT - ancient DNA OT - paleogenomics OT - population genetics COIS- Declaration of interests The authors declare no competing interests. EDAT- 2021/05/01 06:00 MHDA- 2021/12/22 06:00 PMCR- 2021/05/13 CRDT- 2021/04/30 20:17 PHST- 2020/04/17 00:00 [received] PHST- 2020/09/17 00:00 [revised] PHST- 2021/03/18 00:00 [accepted] PHST- 2021/05/01 06:00 [pubmed] PHST- 2021/12/22 06:00 [medline] PHST- 2021/04/30 20:17 [entrez] PHST- 2021/05/13 00:00 [pmc-release] AID - S0092-8674(21)00370-6 [pii] AID - 10.1016/j.cell.2021.03.039 [doi] PST - ppublish SO - Cell. 2021 May 13;184(10):2565-2586.e21. doi: 10.1016/j.cell.2021.03.039. Epub 2021 Apr 29. PMID- 34459345 OWN - NLM STAT- MEDLINE DCOM- 20211119 LR - 20220426 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 48 IP - 3 DP - 2021 May TI - Where Asia meets Europe - recent insights from ancient human genomics. PG - 191-202 LID - 10.1080/03014460.2021.1949039 [doi] AB - CONTEXT: The peopling of Europe by modern humans is a widely debated topic in the field of modern and ancient genomics. While several recent syntheses have focussed on this topic, little has been discussed about the genetic history of populations in the continent's surrounding regions. OBJECTIVE: We explore genetic transformations in three key areas that played an essential role in the formation of the European genetic landscape through time, focussing on the periods spanning from the Epipalaeolithic/Mesolithic and up until the Iron Age. METHODS: We review published ancient genomic studies and integrate the associated data to provide a quantification and visualisation of major trends in the population histories of the Near East, the western Eurasian Steppe and North East Europe. RESULTS: We describe cross-regional as well as localised prehistoric demographic shifts and discuss potential research directions while highlighting geo-temporal gaps in the data. CONCLUSION: In recent years, archaeogenetic studies have contributed to the understanding of human genetic diversity through time in regions located at the doorstep of Europe. Further studies focussing on these areas will allow for a better characterisation of genetic shifts and regionally-specific patterns of admixture across western Eurasia. FAU - Feldman, Michal AU - Feldman M AUID- ORCID: 0000-0003-4618-1460 AD - Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. AD - Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Gnecchi-Ruscone, Guido A AU - Gnecchi-Ruscone GA AUID- ORCID: 0000-0002-6490-8101 AD - Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Lamnidis, Thiseas C AU - Lamnidis TC AUID- ORCID: 0000-0003-4485-8570 AD - Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Posth, Cosimo AU - Posth C AUID- ORCID: 0000-0002-8206-3907 AD - Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. AD - Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany. LA - eng PT - Journal Article PT - Review PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Asia MH - DNA, Ancient/*analysis MH - Europe MH - *Gene Flow MH - *Genome, Human MH - Genomics MH - *Human Migration MH - Humans MH - Middle East OTO - NOTNLM OT - Ancient DNA; Near East; Eurasian Steppe; North East Europe; Human population genetics; Archaeogenetics; Epipalaeolithic; Mesolithic; Neolithic; Chalcolithic Bronze; Age Iron Age; Prehistoric EDAT- 2021/08/31 06:00 MHDA- 2021/11/20 06:00 CRDT- 2021/08/30 08:43 PHST- 2021/08/30 08:43 [entrez] PHST- 2021/08/31 06:00 [pubmed] PHST- 2021/11/20 06:00 [medline] AID - 10.1080/03014460.2021.1949039 [doi] PST - ppublish SO - Ann Hum Biol. 2021 May;48(3):191-202. doi: 10.1080/03014460.2021.1949039. PMID- 34459344 OWN - NLM STAT- MEDLINE DCOM- 20211119 LR - 20220426 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 48 IP - 3 DP - 2021 May TI - More data on ancient human mitogenome variability in Italy: new mitochondrial genome sequences from three Upper Palaeolithic burials. PG - 213-222 LID - 10.1080/03014460.2021.1942549 [doi] AB - BACKGROUND: Recently, the study of mitochondrial variability in ancient humans has allowed the definition of population dynamics that characterised Europe in the Late Pleistocene and Early Holocene. Despite the abundance of sites and skeletal remains few data are available for Italy. AIM: We reconstructed the mitochondrial genomes of three Upper Palaeolithic individuals for some of the most important Italian archaeological contexts: Paglicci (South-Eastern Italy), San Teodoro (South-Western Italy) and Arene Candide (North-Western Italy) caves. SUBJECTS AND METHODS: We explored the phylogenetic relationships of the three mitogenomes in the context of Western Eurasian ancient and modern variability. RESULTS: Paglicci 12 belongs to sub-haplogroup U8c, described in only two other Gravettian individuals; San Teodoro 2 harbours a U2'3'4'7'8'9 sequence, the only lineage found in Sicily during the Late Pleistocene and Early Holocene; Arene Candide 16 displays an ancestral U5b1 haplotype already detected in other Late Pleistocene hunter-gatherers from Central Europe. CONCLUSION: Regional genetic continuity is highlighted in the Gravettian groups that succeeded in Paglicci. Data from one of the oldest human remains from Sicily reinforce the hypothesis that Epigravettian groups carrying U2'3'4'7'8'9 could be the first inhabitants of the island. The first pre-Neolithic mitogenome from North-Western Italy, sequenced here, shows more affinity with continental Europe than with the Italian peninsula. FAU - Modi, Alessandra AU - Modi A AD - Dipartimento di Biologia, Università di Firenze, Firenze, Italy. FAU - Vai, Stefania AU - Vai S AD - Dipartimento di Biologia, Università di Firenze, Firenze, Italy. FAU - Posth, Cosimo AU - Posth C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Vergata, Chiara AU - Vergata C AD - Dipartimento di Biologia, Università di Firenze, Firenze, Italy. FAU - Zaro, Valentina AU - Zaro V AD - Dipartimento di Biologia, Università di Firenze, Firenze, Italy. FAU - Diroma, Maria Angela AU - Diroma MA AD - Dipartimento di Biologia, Università di Firenze, Firenze, Italy. FAU - Boschin, Francesco AU - Boschin F AD - Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università degli Studi di Siena, Siena, Italy. FAU - Capecchi, Giulia AU - Capecchi G AD - Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università degli Studi di Siena, Siena, Italy. FAU - Ricci, Stefano AU - Ricci S AD - Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università degli Studi di Siena, Siena, Italy. FAU - Ronchitelli, Annamaria AU - Ronchitelli A AD - Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università degli Studi di Siena, Siena, Italy. FAU - Catalano, Giulio AU - Catalano G AD - Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy. FAU - Lauria, Gabriele AU - Lauria G AD - Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy. AD - Departamento de Ciencia Animal, Universitat Politecnica de Valencia, Valencia, Spain. FAU - D'Amore, Giuseppe AU - D'Amore G AD - Istituto di Studi Archeo-antropologici - I.S.A, Scandicci, Italy. FAU - Sineo, Luca AU - Sineo L AD - Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy. FAU - Caramelli, David AU - Caramelli D AD - Dipartimento di Biologia, Università di Firenze, Firenze, Italy. FAU - Lari, Martina AU - Lari M AD - Dipartimento di Biologia, Università di Firenze, Firenze, Italy. LA - eng PT - Journal Article PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - DNA, Ancient/*analysis MH - *Genome, Human MH - *Genome, Mitochondrial MH - Humans MH - Italy OTO - NOTNLM OT - Italian hunter-gatherers OT - LGM OT - Mitochondrial DNA OT - Upper Palaeolithic OT - ancient DNA EDAT- 2021/08/31 06:00 MHDA- 2021/11/20 06:00 CRDT- 2021/08/30 08:43 PHST- 2021/08/30 08:43 [entrez] PHST- 2021/08/31 06:00 [pubmed] PHST- 2021/11/20 06:00 [medline] AID - 10.1080/03014460.2021.1942549 [doi] PST - ppublish SO - Ann Hum Biol. 2021 May;48(3):213-222. doi: 10.1080/03014460.2021.1942549. PMID- 34459342 OWN - NLM STAT- MEDLINE DCOM- 20211119 LR - 20211119 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 48 IP - 3 DP - 2021 May TI - Paleogenomics of the prehistory of Europe: human migrations, domestication and disease. PG - 179-190 LID - 10.1080/03014460.2021.1942205 [doi] AB - A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate. FAU - Serrano, Javier G AU - Serrano JG AD - Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain. FAU - Ordóñez, Alejandra C AU - Ordóñez AC AD - Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain. AD - Departamento Geografía e Historia, Facultad de Humanidades, Universidad de La Laguna, La Laguna, Spain. FAU - Fregel, Rosa AU - Fregel R AD - Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain. LA - eng PT - Journal Article PT - Review PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Communicable Diseases/*epidemiology/microbiology/parasitology/virology MH - DNA, Ancient/*analysis MH - *Domestication MH - Europe MH - *Genome, Human MH - Genomics MH - *Human Migration MH - Humans OTO - NOTNLM OT - European prehistory OT - Paleogenomics OT - domesticates OT - human migration OT - pathogens EDAT- 2021/08/31 06:00 MHDA- 2021/11/20 06:00 CRDT- 2021/08/30 08:43 PHST- 2021/08/30 08:43 [entrez] PHST- 2021/08/31 06:00 [pubmed] PHST- 2021/11/20 06:00 [medline] AID - 10.1080/03014460.2021.1942205 [doi] PST - ppublish SO - Ann Hum Biol. 2021 May;48(3):179-190. doi: 10.1080/03014460.2021.1942205. PMID- 34459340 OWN - NLM STAT- MEDLINE DCOM- 20211119 LR - 20220426 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 48 IP - 3 DP - 2021 May TI - Insights into Punic genetic signatures in the southern necropolis of Tharros (Sardinia). PG - 247-259 LID - 10.1080/03014460.2021.1937699 [doi] AB - BACKGROUND: Phoenician and Punic expansions have been protagonists of intense trade networks and settlements in the Mediterranean Sea. AIMS: The maternal genetic variability of ancient Punic samples from the Sardinian necropolis of Tharros was analysed, with the aim to explore genetic interactions and signatures of past population events. SUBJECTS AND METHODS: The mtDNA HVS-I and coding region SNPs were analysed in 14 Punic samples and 74 modern individuals from Cabras and Belvì (for which the HVS-II region was also analysed). The results were compared with 5,590 modern Euro-Mediterranean sequences and 127 ancient samples. RESULTS: While contemporary groups fall within the genetic variability of other modern Sardinians, our Punic samples reveal proximity to present-day North-African and Iberian populations. Furthermore, Cabras and Belvì cluster mainly with pre-Phoenician groups, while samples from Tharros project with other Punic Sardinian individuals. CONCLUSION: This study provides the first preliminary insights into the population dynamics of the Punic site of Tharros. While the number of currently available samples does not allow definitive investigation of the connection with indigenous Sardinian groups, our results seem to confirm internal migratory phenomena in the central-western Mediterranean and female participation in the Punic mobility. FAU - Sarno, Stefania AU - Sarno S AUID- ORCID: 0000-0001-9673-3281 AD - Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy. FAU - Cilli, Elisabetta AU - Cilli E AUID- ORCID: 0000-0003-0407-267X AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. FAU - Serventi, Patrizia AU - Serventi P AD - Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy. AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. FAU - De Fanti, Sara AU - De Fanti S AD - Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy. AD - Interdepartmental Centre "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)", University of Bologna, Bologna, Italy. FAU - Corona, Andrea AU - Corona A AD - Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy. AD - Dipartimento di Scienze del Sistema Nervoso e del Comportamento, Università di Pavia, Pavia, Italy. FAU - Fontani, Francesco AU - Fontani F AUID- ORCID: 0000-0002-7242-0659 AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. FAU - Traversari, Mirko AU - Traversari M AUID- ORCID: 0000-0002-6376-7626 AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. FAU - Ferri, Gianmarco AU - Ferri G AD - Department of Diagnostic and Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy. FAU - Fariselli, Anna Chiara AU - Fariselli AC AUID- ORCID: 0000-0003-2507-9344 AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. FAU - Luiselli, Donata AU - Luiselli D AUID- ORCID: 0000-0003-2105-2478 AD - Department of Cultural Heritage, University of Bologna, Ravenna, Italy. LA - eng PT - Journal Article PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Child MH - Child, Preschool MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*analysis MH - Female MH - *Genetic Variation MH - *Human Migration MH - Humans MH - Infant MH - Infant, Newborn MH - Italy MH - Male MH - Population Dynamics MH - Tunisia OTO - NOTNLM OT - Ancient DNA OT - Punic Sardinia OT - Tharros OT - archaeology OT - mtDNA EDAT- 2021/08/31 06:00 MHDA- 2021/11/20 06:00 CRDT- 2021/08/30 08:43 PHST- 2021/08/30 08:43 [entrez] PHST- 2021/08/31 06:00 [pubmed] PHST- 2021/11/20 06:00 [medline] AID - 10.1080/03014460.2021.1937699 [doi] PST - ppublish SO - Ann Hum Biol. 2021 May;48(3):247-259. doi: 10.1080/03014460.2021.1937699. PMID- 34459338 OWN - NLM STAT- MEDLINE DCOM- 20211119 LR - 20220426 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 48 IP - 3 DP - 2021 May TI - Ancient genomes from a rural site in Imperial Rome (1(st)-3(rd) cent. CE): a genetic junction in the Roman Empire. PG - 234-246 LID - 10.1080/03014460.2021.1944313 [doi] AB - BACKGROUND: Rome became the prosperous Capital of the Roman Empire through the political and military conquests of neighbouring areas. People were able to move Romeward modifying the Rome area's demographic structure. However, the genomic evidence for the population of one of the broadest Empires in antiquity has been sparse until recently. AIM: The genomic analysis of people buried in Quarto Cappello del Prete (QCP) necropolis was carried out to help elucidate the genomic structure of Imperial Rome inhabitants. SUBJECTS AND METHODS: We recruited twenty-five individuals from QCP for ancient DNA analysis through whole-genome sequencing. Multiple investigations were carried out to unveil the genetic components featuring in the studied samples and the community's putative demographic structure. RESULTS: We generated reliable whole-genome data for 7 samples surviving quality controls. The distribution of Imperial Romans from QCP partly overlaps with present-day Southern Mediterranean and Southern-Near Eastern populations. CONCLUSION: The genomic legacy with the south-eastern shores of the Mediterranean Sea and the Central and Western Northern-African coast funerary influence pave the way for considering people buried in QCP as resembling a Punic-derived human group. FAU - De Angelis, Flavio AU - De Angelis F AUID- ORCID: 0000-0002-4747-2385 AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy. FAU - Veltre, Virginia AU - Veltre V AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy. AD - PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome Tor Vergata, Rome, Italy. FAU - Romboni, Marco AU - Romboni M AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy. FAU - Di Corcia, Tullia AU - Di Corcia T AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy. FAU - Scano, Giuseppina AU - Scano G AUID- ORCID: 0000-0002-4302-7583 AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy. FAU - Martínez-Labarga, Cristina AU - Martínez-Labarga C AUID- ORCID: 0000-0003-0439-0379 AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy. FAU - Catalano, Paola AU - Catalano P AD - Former Soprintendenza Speciale Archeologia, Belle Arti e Paesaggio di Roma. Piazza dei Cinquecento, Rome, Italy. FAU - Rickards, Olga AU - Rickards O AUID- ORCID: 0000-0003-2880-7466 AD - Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy. LA - eng PT - Journal Article PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) SB - IM MH - Adolescent MH - Archaeology MH - Child MH - Child, Preschool MH - DNA, Ancient/*analysis MH - Female MH - *Genome, Human MH - *Human Migration MH - Humans MH - Infant MH - Infant, Newborn MH - Italy MH - Male MH - Roman World MH - *Rural Population MH - Whole Genome Sequencing OTO - NOTNLM OT - Ancient Romans OT - ancient DNA OT - genomics EDAT- 2021/08/31 06:00 MHDA- 2021/11/20 06:00 CRDT- 2021/08/30 08:43 PHST- 2021/08/30 08:43 [entrez] PHST- 2021/08/31 06:00 [pubmed] PHST- 2021/11/20 06:00 [medline] AID - 10.1080/03014460.2021.1944313 [doi] PST - ppublish SO - Ann Hum Biol. 2021 May;48(3):234-246. doi: 10.1080/03014460.2021.1944313. PMID- 33951239 OWN - NLM STAT- MEDLINE DCOM- 20210624 LR - 20220316 IS - 1520-6505 (Electronic) IS - 1060-1538 (Print) IS - 1060-1538 (Linking) VI - 30 IP - 3 DP - 2021 May TI - Inferring archaic introgression from hominin genetic data. PG - 199-220 LID - 10.1002/evan.21895 [doi] AB - Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus. CI - © 2021 The Authors. Evolutionary Anthropology published by Wiley Periodicals LLC. FAU - Gopalan, Shyamalika AU - Gopalan S AUID- ORCID: 0000-0002-2608-8472 AD - Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA. AD - Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA. FAU - Atkinson, Elizabeth G AU - Atkinson EG AD - Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA. AD - Analytic and Translational Genetics Unit, Massachusetts General Hospital and Stanley Center for Psychiatric Research, Broad Institute, Boston, Massachusetts, USA. FAU - Buck, Laura T AU - Buck LT AD - Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK. FAU - Weaver, Timothy D AU - Weaver TD AD - Department of Anthropology, University of California, Davis, California, USA. FAU - Henn, Brenna M AU - Henn BM AD - Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA. AD - Department of Anthropology, University of California, Davis, California, USA. AD - UC Davis Genome Center, University of California, Davis, California, USA. LA - eng GR - R35 GM133531/GM/NIGMS NIH HHS/United States GR - K12-GM102778/NH/NIH HHS/United States GR - K01-MH121659/NH/NIH HHS/United States GR - R35-GM133531/NH/NIH HHS/United States GR - K01 MH121659/MH/NIMH NIH HHS/United States GR - K12 GM102778/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Review DEP - 20210505 PL - United States TA - Evol Anthropol JT - Evolutionary anthropology JID - 9306331 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Anthropology, Physical MH - *Biological Evolution MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/genetics MH - Genetic Introgression/*genetics MH - Hominidae/classification/genetics MH - Humans MH - Neanderthals/classification/*genetics PMC - PMC8360192 MID - NIHMS1703574 OTO - NOTNLM OT - ancient DNA OT - archaic hominins OT - genetics OT - introgression EDAT- 2021/05/06 06:00 MHDA- 2021/06/25 06:00 PMCR- 2021/08/12 CRDT- 2021/05/05 17:56 PHST- 2020/08/03 00:00 [revised] PHST- 2019/09/11 00:00 [received] PHST- 2021/03/29 00:00 [accepted] PHST- 2021/05/06 06:00 [pubmed] PHST- 2021/06/25 06:00 [medline] PHST- 2021/05/05 17:56 [entrez] PHST- 2021/08/12 00:00 [pmc-release] AID - EVAN21895 [pii] AID - 10.1002/evan.21895 [doi] PST - ppublish SO - Evol Anthropol. 2021 May;30(3):199-220. doi: 10.1002/evan.21895. Epub 2021 May 5. PMID- 33650010 OWN - NLM STAT- MEDLINE DCOM- 20210528 LR - 20221207 IS - 1617-4623 (Electronic) IS - 1617-4623 (Linking) VI - 296 IP - 3 DP - 2021 May TI - New insights into the fine-scale history of western-eastern admixture of the northwestern Chinese population in the Hexi Corridor via genome-wide genetic legacy. PG - 631-651 LID - 10.1007/s00438-021-01767-0 [doi] AB - Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f(3)/f(4) statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population. FAU - Yao, Hongbin AU - Yao H AD - Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China. yaohongb@126.com. FAU - Wang, Mengge AU - Wang M AD - Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China. FAU - Zou, Xing AU - Zou X AD - Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China. FAU - Li, Yingxiang AU - Li Y AD - Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China. AD - AnLan AI, Shenzhen, China. FAU - Yang, Xiaomin AU - Yang X AD - Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China. FAU - Li, Ailin AU - Li A AD - Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China. FAU - Yeh, Hui-Yuan AU - Yeh HY AD - School of Humanities, Nanyang Technological University, Nanyang, Singapore, 639798, Singapore. FAU - Wang, Peixin AU - Wang P AD - College of Medical Information, Chongqing Medical University, Chongqing, 400331, China. FAU - Wang, Zheng AU - Wang Z AD - Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China. FAU - Bai, Jingya AU - Bai J AD - Department of Medicine, Northwest Minzu University, Lanzhou, 730000, Gansu, China. AD - Key Laboratory for Physique and Health of the Minorities, Northwest Minzu University, Lanzhou, 730000, Gansu, China. FAU - Guo, Jianxin AU - Guo J AD - Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China. FAU - Chen, Jinwen AU - Chen J AD - Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China. FAU - Ding, Xiao AU - Ding X AD - Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China. FAU - Zhang, Yan AU - Zhang Y AD - Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China. FAU - Lin, Baoquan AU - Lin B AD - Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China. FAU - Wang, Chuan-Chao AU - Wang CC AD - Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China. wang@xmu.edu.cn. FAU - He, Guanglin AU - He G AUID- ORCID: 0000-0002-6614-5267 AD - Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China. Guanglinhescu@163.com. AD - Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China. Guanglinhescu@163.com. LA - eng GR - X2123302/Nanqiang Outstanding Young Talents Program of Xiamen University/ GR - 31801040/National Natural Science Foundation of China/ PT - Journal Article DEP - 20210301 PL - Germany TA - Mol Genet Genomics JT - Molecular genetics and genomics : MGG JID - 101093320 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/*genetics MH - China MH - Chromosomes, Human, Y/genetics MH - DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Ethnicity/genetics MH - Genetics, Population/methods MH - Genome/*genetics MH - Genome-Wide Association Study/methods MH - Human Migration MH - Humans MH - Phylogeny MH - Polymorphism, Single Nucleotide/genetics OTO - NOTNLM OT - Admixture history OT - Genetic structure OT - Genome-wide data OT - Hexi Corridor OT - Short tandem repeat (STR) OT - Trans-Eurasian exchange EDAT- 2021/03/03 06:00 MHDA- 2021/05/29 06:00 CRDT- 2021/03/02 06:22 PHST- 2020/11/07 00:00 [received] PHST- 2021/02/08 00:00 [accepted] PHST- 2021/03/03 06:00 [pubmed] PHST- 2021/05/29 06:00 [medline] PHST- 2021/03/02 06:22 [entrez] AID - 10.1007/s00438-021-01767-0 [pii] AID - 10.1007/s00438-021-01767-0 [doi] PST - ppublish SO - Mol Genet Genomics. 2021 May;296(3):631-651. doi: 10.1007/s00438-021-01767-0. Epub 2021 Mar 1. PMID- 33022107 OWN - NLM STAT- MEDLINE DCOM- 20210521 LR - 20210521 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 175 IP - 1 DP - 2021 May TI - Ancestry, health, and lived experiences of enslaved Africans in 18th century Charleston: An osteobiographical analysis. PG - 3-24 LID - 10.1002/ajpa.24149 [doi] AB - OBJECTIVES: In 2013, the burials of 36 individuals of putative African ancestry were discovered during renovation of the Gaillard Center in downtown Charleston, South Carolina. The Charleston community facilitated a bioarchaeological and mitogenomic study to gain insights into the lives of these unknown persons, referred to as the Anson Street Ancestors, including their ancestry, health, and lived experiences in the 18th century. METHODS: Metric and morphological assessments of skeletal and dental characteristics were recorded, and enamel and cortical bone strontium stable isotope values generated. Whole mitochondrial genomes were sequenced and analyzed. RESULTS: Osteological analysis identified adults, both females and males, and subadults at the site, and estimated African ancestry for most individuals. Skeletal trauma and pathology were infrequent, but many individuals exhibited dental decay and abscesses. Strontium isotope data suggested these individuals mostly originated in Charleston or sub-Saharan Africa, with many being long-term residents of Charleston. Nearly all had mitochondrial lineages belonging to African haplogroups (L0-L3, H1cb1a), with two individuals sharing the same L3e2a haplotype, while one had a Native American A2 mtDNA. DISCUSSION: This study generated detailed osteobiographies of the Anson Street Ancestors, who were likely of enslaved status. Our results indicate that the Ancestors have diverse maternal African ancestries and are largely unrelated, with most being born locally. These details reveal the demographic impact of the trans-Atlantic slave trade. Our analysis further illuminates the lived experiences of individuals buried at Anson Street, and expands our understanding of 18th century African history in Charleston. CI - © 2020 Wiley Periodicals LLC. FAU - Fleskes, Raquel E AU - Fleskes RE AUID- ORCID: 0000-0002-2875-6286 AD - Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. FAU - Ofunniyin, Ade A AU - Ofunniyin AA AD - The Gullah Society, Inc., Mount Pleasant, South Carolina, USA. AD - Department of Sociology and Anthropology, The College of Charleston, Charleston, South Carolina, USA. FAU - Gilmore, Joanna K AU - Gilmore JK AD - The Gullah Society, Inc., Mount Pleasant, South Carolina, USA. AD - Department of Sociology and Anthropology, The College of Charleston, Charleston, South Carolina, USA. FAU - Poplin, Eric AU - Poplin E AD - Brockington and Associates, Inc., Mount Pleasant, South Carolina, USA. FAU - Abel, Suzanne M AU - Abel SM AD - Charleston County Coroner's Office, North Charleston, South Carolina, USA. FAU - Bueschgen, Wolf D AU - Bueschgen WD AD - Charleston County Coroner's Office, North Charleston, South Carolina, USA. FAU - Juarez, Chelsey AU - Juarez C AUID- ORCID: 0000-0002-9097-1585 AD - Department of Anthropology, California State University, Fresno, California, USA. FAU - Butler, Nic AU - Butler N AD - Charleston County Public Library, Charleston, South Carolina, USA. FAU - Mishoe, Grant AU - Mishoe G AD - The Gullah Society, Inc., Mount Pleasant, South Carolina, USA. FAU - Oubré, La'Sheia AU - Oubré L AD - The Gullah Society, Inc., Mount Pleasant, South Carolina, USA. FAU - Cabana, Graciela S AU - Cabana GS AUID- ORCID: 0000-0002-5399-1173 AD - Department of Anthropology, University of Tennessee, Knoxville, Tennessee, USA. FAU - Schurr, Theodore G AU - Schurr TG AUID- ORCID: 0000-0001-9323-9237 AD - Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20201006 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Strontium Isotopes) SB - IM MH - Adolescent MH - Adult MH - Anthropology, Physical MH - Bone and Bones/chemistry MH - Burial/history MH - Child MH - Child, Preschool MH - Enslaved Persons/*history/statistics & numerical data MH - Enslavement/*ethnology/*history MH - Family/ethnology/history MH - Female MH - Genome, Mitochondrial/genetics MH - Health Status MH - History, 18th Century MH - Humans MH - Infant MH - Infant, Newborn MH - Male MH - South Carolina/ethnology MH - Strontium Isotopes/analysis MH - Tooth/chemistry/pathology MH - Young Adult OTO - NOTNLM OT - ancient DNA OT - colonization OT - isotope OT - osteology OT - slavery EDAT- 2020/10/07 06:00 MHDA- 2021/05/22 06:00 CRDT- 2020/10/06 17:13 PHST- 2020/08/30 00:00 [revised] PHST- 2020/06/18 00:00 [received] PHST- 2020/09/13 00:00 [accepted] PHST- 2020/10/07 06:00 [pubmed] PHST- 2021/05/22 06:00 [medline] PHST- 2020/10/06 17:13 [entrez] AID - 10.1002/ajpa.24149 [doi] PST - ppublish SO - Am J Phys Anthropol. 2021 May;175(1):3-24. doi: 10.1002/ajpa.24149. Epub 2020 Oct 6. PMID- 33059357 OWN - NLM STAT- MEDLINE DCOM- 20220324 LR - 20220324 IS - 1460-2083 (Electronic) IS - 0964-6906 (Linking) VI - 30 IP - R1 DP - 2021 Apr 26 TI - Insights from ancient DNA analysis of Egyptian human mummies: clues to disease and kinship. PG - R24-R28 LID - 10.1093/hmg/ddaa223 [doi] AB - The molecular Egyptology field started in the mid-eighties with the first publication on the ancient DNA (aDNA) analysis of an Egyptian mummy. Egypt has been a major interest for historians, archeologists, laymen as well as scientists. The aDNA research on Egyptian biological remains has been fueled by their abundance and relatively well-preserved states through artificial mummification and by the advanced analytical techniques. Early doubts of aDNA integrity within the Egyptian mummies and data authenticity were later abated with studies proving successfully authenticated aDNA retrieval. The current review tries to recapitulate the published studies presenting paleogenomic evidence of disease diagnosis and kinship establishment for the Egyptian human remains. Regarding disease diagnosis, the prevailing literature was on paleogenomic evidence of infectious diseases in the human remains. A series of reports presented evidence for the presence of tuberculosis and/or malaria. In addition, there were solitary reports of the presence of leprosy, diphtheria, bacteremia, toxoplasmosis, schistosomiasis and leishmaniasis. On the contrary, paleogenomic evidence of the presence of rare diseases was quite scarce and mentioned only in two articles. On the other hand, kinship analysis of Egyptian human remains, including that of Tutankhamen, was done using both mitochondrial DNA sequences and nuclear DNA markers, to establish family relationships in four studies. It is clear that the field of molecular Egyptology is still a largely unexplored territory. Nevertheless, the paleogenomic investigation of Egyptian remains could make significant contributions to biomedical sciences (e.g. elucidation of coevolution of human host-microbe interrelationship) as well as to evidence-based archeology. CI - © The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. FAU - Gad, Yehia Z AU - Gad YZ AD - Ancient DNA Lab. AD - Department of Medical Molecular Genetics, Division of Human Genetics and Genome Research. FAU - Hassan, Naglaa Abu-Mandil AU - Hassan NA AD - Ancient DNA Lab. AD - Department of Biological Anthropology, Medical Research Division, National Research Centre, Giza 12622, Egypt. FAU - Mousa, Dalia M AU - Mousa DM AD - Ancient DNA Lab. FAU - Fouad, Fayrouz A AU - Fouad FA AD - Ancient DNA Lab. FAU - El-Sayed, Safaa G AU - El-Sayed SG AD - Human Remains Lab. FAU - Abdelazeem, Marwa A AU - Abdelazeem MA AD - Ancient DNA Lab, The Egyptian Museum, Cairo 11556, Egypt. FAU - Mahdy, Samah M AU - Mahdy SM AD - Biophysics Lab, National Museum of Egyptian Civilization (NMEC), Cairo 11654, Egypt. FAU - Othman, Hend Y AU - Othman HY AD - Ancient DNA Lab. FAU - Ibrahim, Dina W AU - Ibrahim DW AD - Ancient DNA Lab, The Egyptian Museum, Cairo 11556, Egypt. FAU - Khairat, Rabab AU - Khairat R AD - Department of Medical Molecular Genetics, Division of Human Genetics and Genome Research. AD - Ancient DNA Lab, The Egyptian Museum, Cairo 11556, Egypt. FAU - Ismail, Somaia AU - Ismail S AD - Department of Medical Molecular Genetics, Division of Human Genetics and Genome Research. LA - eng PT - Historical Article PT - Journal Article PT - Review PL - England TA - Hum Mol Genet JT - Human molecular genetics JID - 9208958 RN - 0 (DNA, Ancient) SB - IM MH - Communicable Diseases/*epidemiology/history MH - DNA, Ancient/*analysis MH - Egypt/epidemiology MH - Family/history MH - Genetics, Population MH - Genomics MH - History, Ancient MH - Humans MH - Mummies/*history MH - Paleography EDAT- 2020/10/16 06:00 MHDA- 2022/03/25 06:00 CRDT- 2020/10/15 20:18 PHST- 2020/08/23 00:00 [received] PHST- 2020/10/08 00:00 [revised] PHST- 2020/10/09 00:00 [accepted] PHST- 2020/10/16 06:00 [pubmed] PHST- 2022/03/25 06:00 [medline] PHST- 2020/10/15 20:18 [entrez] AID - 5924364 [pii] AID - 10.1093/hmg/ddaa223 [doi] PST - ppublish SO - Hum Mol Genet. 2021 Apr 26;30(R1):R24-R28. doi: 10.1093/hmg/ddaa223. PMID- 33922908 OWN - NLM STAT- MEDLINE DCOM- 20210823 LR - 20210823 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 12 IP - 5 DP - 2021 Apr 25 TI - First Bronze Age Human Mitogenomes from Calabria (Grotta Della Monaca, Southern Italy). LID - 10.3390/genes12050636 [doi] LID - 636 AB - The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA studies in Southern Italy are, at present, still limited to prehistoric and Roman Apulia. Here, we present the first mitogenomes from a Middle Bronze Age cave burial in Calabria to address this knowledge gap. We adopted a hybridization capture approach, which enabled the recovery of one complete and one partial mitochondrial genome. Phylogenetic analysis assigned these two individuals to the H1e and H5 subhaplogroups, respectively. This preliminary phylogenetic analysis supports affinities with coeval Sicilian populations, along with Linearbandkeramik and Bell Beaker cultures maternal lineages from Central Europe and Iberia. Our work represents a starting point which contributes to the comprehension of migrations and population dynamics in Southern Italy, and highlights this knowledge gap yet to be filled by genomic studies. FAU - Fontani, Francesco AU - Fontani F AUID- ORCID: 0000-0002-7242-0659 AD - Department of Cultural Heritage, University of Bologna, via Degli Ariani 1, 48121 Ravenna, Italy. FAU - Cilli, Elisabetta AU - Cilli E AUID- ORCID: 0000-0003-0407-267X AD - Department of Cultural Heritage, University of Bologna, via Degli Ariani 1, 48121 Ravenna, Italy. FAU - Arena, Fabiola AU - Arena F AUID- ORCID: 0000-0002-0705-9713 AD - Department of Neuroscience and Rehabilitation, University of Ferrara, Corso Ercole I D'Este 32, 44121 Ferrara, Italy. AD - Centro Regionale di Speleologia "Enzo dei Medici", via Lucania 3, 87070 Roseto Capo Spulico, Italy. FAU - Sarno, Stefania AU - Sarno S AD - Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy. FAU - Modi, Alessandra AU - Modi A AUID- ORCID: 0000-0001-9514-9868 AD - Department of Biology, Università degli Studi di Firenze, via del Proconsolo 12, 50125 Firenze, Italy. FAU - De Fanti, Sara AU - De Fanti S AD - Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy. AD - Interdepartmental Centre "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)", University of Bologna, via Petroni 26, 40126 Bologna, Italy. FAU - Andrews, Adam Jon AU - Andrews AJ AD - Department of Cultural Heritage, University of Bologna, via Degli Ariani 1, 48121 Ravenna, Italy. AD - Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy. FAU - Latorre, Adriana AU - Latorre A AD - Department of Cultural Heritage, University of Bologna, via Degli Ariani 1, 48121 Ravenna, Italy. FAU - Abondio, Paolo AU - Abondio P AD - Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy. FAU - Larocca, Felice AU - Larocca F AD - Centro Regionale di Speleologia "Enzo dei Medici", via Lucania 3, 87070 Roseto Capo Spulico, Italy. AD - Gruppo di Ricerca Speleo-Archeologica, Università degli Studi di Bari "Aldo Moro", Piazza Umberto I 1, 70121 Bari, Italy. FAU - Lari, Martina AU - Lari M AD - Department of Biology, Università degli Studi di Firenze, via del Proconsolo 12, 50125 Firenze, Italy. FAU - Caramelli, David AU - Caramelli D AD - Department of Biology, Università degli Studi di Firenze, via del Proconsolo 12, 50125 Firenze, Italy. FAU - Gualdi-Russo, Emanuela AU - Gualdi-Russo E AUID- ORCID: 0000-0002-7274-547X AD - Department of Neuroscience and Rehabilitation, University of Ferrara, Corso Ercole I D'Este 32, 44121 Ferrara, Italy. FAU - Luiselli, Donata AU - Luiselli D AUID- ORCID: 0000-0003-2105-2478 AD - Department of Cultural Heritage, University of Bologna, via Degli Ariani 1, 48121 Ravenna, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210425 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - Evolution, Molecular MH - *Genome, Human MH - *Genome, Mitochondrial MH - Humans MH - Italy PMC - PMC8146030 OTO - NOTNLM OT - Bronze Age OT - Italy OT - ancient DNA OT - archaeology OT - human OT - mitochondrial DNA OT - paleogenomics COIS- The authors declare no conflict of interest. EDAT- 2021/05/01 06:00 MHDA- 2021/08/24 06:00 PMCR- 2021/04/25 CRDT- 2021/04/30 01:23 PHST- 2021/02/26 00:00 [received] PHST- 2021/04/02 00:00 [revised] PHST- 2021/04/20 00:00 [accepted] PHST- 2021/04/30 01:23 [entrez] PHST- 2021/05/01 06:00 [pubmed] PHST- 2021/08/24 06:00 [medline] PHST- 2021/04/25 00:00 [pmc-release] AID - genes12050636 [pii] AID - genes-12-00636 [pii] AID - 10.3390/genes12050636 [doi] PST - epublish SO - Genes (Basel). 2021 Apr 25;12(5):636. doi: 10.3390/genes12050636. PMID- 33772284 OWN - NLM STAT- MEDLINE DCOM- 20210922 LR - 20210922 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 217 IP - 4 DP - 2021 Apr 15 TI - Assessing the performance of qpAdm: a statistical tool for studying population admixture. LID - 10.1093/genetics/iyaa045 [doi] LID - iyaa045 AB - qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and nonhuman) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. FAU - Harney, Éadaoin AU - Harney É AD - Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Patterson, Nick AU - Patterson N AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Wakeley, John AU - Wakeley J AD - Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Genetics JT - Genetics JID - 0374636 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA, Ancient MH - Evolution, Molecular MH - Genetics, Population/*methods MH - Humans MH - Pedigree MH - Population/*genetics MH - Practice Guidelines as Topic MH - Software/*standards PMC - PMC8049561 OTO - NOTNLM OT - AdmixTools OT - admixture OT - qpAdm OT - simulation EDAT- 2021/03/28 06:00 MHDA- 2021/09/23 06:00 PMCR- 2021/01/08 CRDT- 2021/03/27 06:22 PHST- 2020/10/14 00:00 [received] PHST- 2020/12/11 00:00 [accepted] PHST- 2021/03/28 06:00 [pubmed] PHST- 2021/09/23 06:00 [medline] PHST- 2021/03/27 06:22 [entrez] PHST- 2021/01/08 00:00 [pmc-release] AID - 6070149 [pii] AID - iyaa045 [pii] AID - 10.1093/genetics/iyaa045 [doi] PST - ppublish SO - Genetics. 2021 Apr 15;217(4):iyaa045. doi: 10.1093/genetics/iyaa045. PMID- 33638983 OWN - NLM STAT- MEDLINE DCOM- 20220125 LR - 20221207 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 13 IP - 4 DP - 2021 Apr 5 TI - Improving Selection Detection with Population Branch Statistic on Admixed Populations. LID - 10.1093/gbe/evab039 [doi] LID - evab039 AB - Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. (2019) for cross-population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared with the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Yelmen, Burak AU - Yelmen B AD - Institute of Genomics, University of Tartu, Estonia. AD - Institute of Molecular and Cell Biology, University of Tartu, Estonia. FAU - Marnetto, Davide AU - Marnetto D AD - Institute of Genomics, University of Tartu, Estonia. FAU - Molinaro, Ludovica AU - Molinaro L AD - Institute of Genomics, University of Tartu, Estonia. AD - Institute of Molecular and Cell Biology, University of Tartu, Estonia. FAU - Flores, Rodrigo AU - Flores R AD - Institute of Genomics, University of Tartu, Estonia. FAU - Mondal, Mayukh AU - Mondal M AD - Institute of Genomics, University of Tartu, Estonia. FAU - Pagani, Luca AU - Pagani L AD - Institute of Genomics, University of Tartu, Estonia. AD - Department of Biology, University of Padova, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 SB - IM MH - Asian People/genetics MH - Computer Simulation MH - Haplotypes MH - Humans MH - Polymorphism, Single Nucleotide MH - *Selection, Genetic PMC - PMC8046333 OTO - NOTNLM OT - PBS OT - South Asia OT - XP-EHH OT - admixed populations OT - local ancestry inference OT - natural selection EDAT- 2021/02/28 06:00 MHDA- 2022/01/27 06:00 PMCR- 2021/02/26 CRDT- 2021/02/27 17:04 PHST- 2021/02/22 00:00 [accepted] PHST- 2021/02/28 06:00 [pubmed] PHST- 2022/01/27 06:00 [medline] PHST- 2021/02/27 17:04 [entrez] PHST- 2021/02/26 00:00 [pmc-release] AID - 6151747 [pii] AID - evab039 [pii] AID - 10.1093/gbe/evab039 [doi] PST - ppublish SO - Genome Biol Evol. 2021 Apr 5;13(4):evab039. doi: 10.1093/gbe/evab039. PMID- 33811235 OWN - NLM STAT- MEDLINE DCOM- 20211029 LR - 20230130 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 11 IP - 1 DP - 2021 Apr 2 TI - Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus. PG - 7456 LID - 10.1038/s41598-021-86100-w [doi] LID - 7456 AB - Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA. FAU - Farrer, Andrew G AU - Farrer AG AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Wright, Sterling L AU - Wright SL AD - The Department of Anthropology, The Pennsylvania State University, University Park, PA, USA. FAU - Skelly, Emily AU - Skelly E AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Eisenhofer, Raphael AU - Eisenhofer R AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. AD - Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia. FAU - Dobney, Keith AU - Dobney K AD - Department of Archaeology, University of Sydney, Sydney, NSW, Australia. FAU - Weyrich, Laura S AU - Weyrich LS AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. laura.weyrich@adelaide.edu.au. AD - The Department of Anthropology, The Pennsylvania State University, University Park, PA, USA. laura.weyrich@adelaide.edu.au. AD - Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia. laura.weyrich@adelaide.edu.au. AD - The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA, USA. laura.weyrich@adelaide.edu.au. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210402 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (RNA, Ribosomal, 16S) SB - IM MH - Biodiversity MH - DNA, Ancient/*analysis MH - *Decontamination MH - Dental Calculus/*genetics/*microbiology MH - Environment MH - Humans MH - Metagenomics MH - Mouth/microbiology MH - Phylogeny MH - Principal Component Analysis MH - RNA, Ribosomal, 16S/genetics MH - Species Specificity PMC - PMC8018977 COIS- The authors declare no competing interests. EDAT- 2021/04/04 06:00 MHDA- 2021/10/30 06:00 PMCR- 2021/04/02 CRDT- 2021/04/03 05:47 PHST- 2020/12/27 00:00 [received] PHST- 2021/02/26 00:00 [accepted] PHST- 2021/04/03 05:47 [entrez] PHST- 2021/04/04 06:00 [pubmed] PHST- 2021/10/30 06:00 [medline] PHST- 2021/04/02 00:00 [pmc-release] AID - 10.1038/s41598-021-86100-w [pii] AID - 86100 [pii] AID - 10.1038/s41598-021-86100-w [doi] PST - epublish SO - Sci Rep. 2021 Apr 2;11(1):7456. doi: 10.1038/s41598-021-86100-w. PMID- 34042097 OWN - NLM STAT- MEDLINE DCOM- 20211028 LR - 20211028 IS - 1591-951X (Electronic) IS - 0031-2983 (Print) IS - 0031-2983 (Linking) VI - 113 IP - 2 DP - 2021 Apr TI - Ancient DNA and paleogenetics: risks and potentiality. PG - 141-146 LID - 10.32074/1591-951X-146 [doi] AB - Paleopathology, the science that studies the diseases of the past, has always been addressed to the future in the use of new diagnostic methods. One of its relatively recent branches is paleogenetics, which is the study of genetic material from the past. Nuclear and mitochondrial DNA recovered from archaeological and paleontological specimens is called ancient DNA (aDNA), which can be extracted from a large variety of biological materials, of different origin, state of preservation and age, such as bones, teeth, coprolites, mummified tissues and hairs. There are many applications for ancient DNA research in the field of archaeology and paleopathology: population demography, genealogy, disease studies, archaeological reconstruction of plant vegetation, calibration of the molecular clock, phylogenetic relationship between different mammals and interpretation of the paleoclimate. However, the study of ancient genetic material is extremely difficult due to its poor quality and quantity, as well possible contamination with modern DNA. New advanced methods will allow extracting DNA from a greater variety of materials, and improvements in sequencing techniques will unveil data that are currently concealed. The aim of this paper is to provide initial insights into paleogenetics and ancient DNA study and to illustrate the limits, risks and potentiality of the research on the genetic material of ancient specimens, whose results have a strong impact on the present and future medicine. CI - Copyright © 2021 Società Italiana di Anatomia Patologica e Citopatologia Diagnostica, Divisione Italiana della International Academy of Pathology. FAU - Gaeta, Raffaele AU - Gaeta R AD - Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, Italy. LA - eng PT - Journal Article PL - Italy TA - Pathologica JT - Pathologica JID - 0401123 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *DNA, Ancient MH - Humans MH - *Paleopathology MH - Phylogeny PMC - PMC8167392 OTO - NOTNLM OT - ancient DNA OT - metagenomics OT - mummies OT - paleogenetics OT - paleopathology COIS- Conflict of interest The Author declares no conflict of interest. EDAT- 2021/05/28 06:00 MHDA- 2021/10/29 06:00 PMCR- 2021/04/01 CRDT- 2021/05/27 08:48 PHST- 2020/06/03 00:00 [received] PHST- 2020/06/19 00:00 [accepted] PHST- 2021/05/27 08:48 [entrez] PHST- 2021/05/28 06:00 [pubmed] PHST- 2021/10/29 06:00 [medline] PHST- 2021/04/01 00:00 [pmc-release] AID - 10.32074/1591-951X-146 [doi] PST - ppublish SO - Pathologica. 2021 Apr;113(2):141-146. doi: 10.32074/1591-951X-146. PMID- 33781248 OWN - NLM STAT- MEDLINE DCOM- 20210924 LR - 20240331 IS - 1741-7007 (Electronic) IS - 1741-7007 (Linking) VI - 19 IP - 1 DP - 2021 Mar 29 TI - Insights into the demographic history of Asia from common ancestry and admixture in the genomic landscape of present-day Austroasiatic speakers. PG - 61 LID - 10.1186/s12915-021-00981-x [doi] LID - 61 AB - BACKGROUND: The demographic history of South and Southeast Asia (S&SEA) is complex and contentious, with multiple waves of human migration. Some of the earliest footfalls were of the ancestors of modern Austroasiatic (AA) language speakers. Understanding the history of the AA language family, comprising of over 150 languages and their speakers distributed across broad geographical region in isolated small populations of various sizes, can help shed light on the peopling of S&SEA. Here we investigated the genetic relatedness of two AA groups, their relationship with other ethno-linguistically distinct populations, and the relationship of these groups with ancient genomes of individuals living in S&SEA at different time periods, to infer about the demographic history of this region. RESULTS: We analyzed 1451 extant genomes, 189 AAs from India and Malaysia, and 43 ancient genomes from S&SEA. Population structure analysis reveals neither language nor geography appropriately correlates with genetic diversity. The inconsistency between "language and genetics" or "geography and genetics" can largely be attributed to ancient admixture with East Asian populations. We estimated a pre-Neolithic origin of AA language speakers, with shared ancestry between Indian and Malaysian populations until about 470 generations ago, contesting the existing model of Neolithic expansion of the AA culture. We observed a spatio-temporal transition in the genetic ancestry of SEA with genetic contribution from East Asia significantly increasing in the post-Neolithic period. CONCLUSION: Our study shows that contrary to assumptions in many previous studies and despite having linguistic commonality, Indian AAs have a distinct genomic structure compared to Malaysian AAs. This linguistic-genetic discordance is reflective of the complex history of population migration and admixture shaping the genomic landscape of S&SEA. We postulate that pre-Neolithic ancestors of today's AAs were widespread in S&SEA, and the fragmentation and dissipation of the population have largely been a resultant of multiple migrations of East Asian farmers during the Neolithic period. It also highlights the resilience of AAs in continuing to speak their language in spite of checkered population distribution and possible dominance from other linguistic groups. FAU - Tagore, Debashree AU - Tagore D AD - National Institute of Biomedical Genomics, Kalyani, 741251, India. FAU - Aghakhanian, Farhang AU - Aghakhanian F AD - Oklahoma Medical Research Foundation, Genes and Human Disease Program, 825 NE 13th Street, Oklahoma City, OK, 73104, USA. AD - Genomics Facility, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia. FAU - Naidu, Rakesh AU - Naidu R AD - Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. FAU - Phipps, Maude E AU - Phipps ME AD - Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. FAU - Basu, Analabha AU - Basu A AUID- ORCID: 0000-0002-1564-0284 AD - National Institute of Biomedical Genomics, Kalyani, 741251, India. ab1@nibmg.ac.in. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210329 PL - England TA - BMC Biol JT - BMC biology JID - 101190720 SB - IM EIN - BMC Biol. 2021 Nov 4;19(1):238. doi: 10.1186/s12915-021-01174-2. PMID: 34736468 MH - *Demography MH - *Genome, Human MH - Humans MH - India MH - Indigenous Peoples/*genetics MH - *Language MH - Malaysia PMC - PMC8008685 OTO - NOTNLM OT - Admixture OT - Ancient DNA OT - Austroasiatic OT - Genetic ancestry OT - Linguistic group OT - Migration COIS- The authors declare that they have no competing interests. EDAT- 2021/03/31 06:00 MHDA- 2021/09/25 06:00 PMCR- 2021/03/29 CRDT- 2021/03/30 05:54 PHST- 2020/07/24 00:00 [received] PHST- 2021/02/12 00:00 [accepted] PHST- 2021/03/30 05:54 [entrez] PHST- 2021/03/31 06:00 [pubmed] PHST- 2021/09/25 06:00 [medline] PHST- 2021/03/29 00:00 [pmc-release] AID - 10.1186/s12915-021-00981-x [pii] AID - 981 [pii] AID - 10.1186/s12915-021-00981-x [doi] PST - epublish SO - BMC Biol. 2021 Mar 29;19(1):61. doi: 10.1186/s12915-021-00981-x. PMID- 33807111 OWN - NLM STAT- MEDLINE DCOM- 20210730 LR - 20241119 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 12 IP - 3 DP - 2021 Mar 23 TI - Maternal Lineages from 10-11th Century Commoner Cemeteries of the Carpathian Basin. LID - 10.3390/genes12030460 [doi] LID - 460 AB - Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10-11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (Fst) and haplogroup-based population genetic methods. The haplogroup composition of the commoner population markedly differs from that of the elite, and, in contrast to the elite, commoners cluster with European populations. Alongside this, detectable sub-haplogroup sharing indicates admixture between the elite and the commoners. The majority of the 10-11th century commoners most likely represent local populations of the Carpathian Basin, which admixed with the eastern immigrant groups (which included conquering Hungarians). FAU - Maár, Kitti AU - Maár K AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. FAU - Varga, Gergely I B AU - Varga GIB AUID- ORCID: 0000-0001-9073-5788 AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. FAU - Kovács, Bence AU - Kovács B AUID- ORCID: 0000-0002-4915-1462 AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. FAU - Schütz, Oszkár AU - Schütz O AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. FAU - Maróti, Zoltán AU - Maróti Z AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. AD - Department of Pediatrics and Pediatric Health Center, University of Szeged, H-6725 Szeged, Hungary. FAU - Kalmár, Tibor AU - Kalmár T AUID- ORCID: 0000-0002-0419-2009 AD - Department of Pediatrics and Pediatric Health Center, University of Szeged, H-6725 Szeged, Hungary. FAU - Nyerki, Emil AU - Nyerki E AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. AD - Department of Pediatrics and Pediatric Health Center, University of Szeged, H-6725 Szeged, Hungary. FAU - Nagy, István AU - Nagy I AUID- ORCID: 0000-0003-2528-9173 AD - SeqOmics Biotechnology Ltd., H-6782 Mórahalom, Hungary. AD - Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary. FAU - Latinovics, Dóra AU - Latinovics D AD - SeqOmics Biotechnology Ltd., H-6782 Mórahalom, Hungary. FAU - Tihanyi, Balázs AU - Tihanyi B AUID- ORCID: 0000-0001-5124-4468 AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. AD - Department of Biological Anthropology, University of Szeged, H-6726 Szeged, Hungary. FAU - Marcsik, Antónia AU - Marcsik A AD - Department of Biological Anthropology, University of Szeged, H-6726 Szeged, Hungary. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, University of Szeged, H-6726 Szeged, Hungary. FAU - Bernert, Zsolt AU - Bernert Z AD - Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary. FAU - Gallina, Zsolt AU - Gallina Z AD - Ásatárs Ltd., H-6000 Kecskemét, Hungary. AD - Department of Archaeology, Institute of Hungarian Research, H-1014 Budapest, Hungary. FAU - Varga, Sándor AU - Varga S AD - Ferenc Móra Museum, H-6720 Szeged, Hungary. FAU - Költő, László AU - Költő L AD - Rippl-Rónai Municipal Museum with Country Scope, H-7400 Kaposvár, Hungary. FAU - Raskó, István AU - Raskó I AD - Institute of Genetics, Biological Research Centre, H-6726 Szeged, Hungary. FAU - Török, Tibor AU - Török T AUID- ORCID: 0000-0002-2128-1126 AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. FAU - Neparáczki, Endre AU - Neparáczki E AUID- ORCID: 0000-0003-3466-0368 AD - Department of Genetics, University of Szeged, H-6726 Szeged, Hungary. AD - Department of Archaeogenetics, Institute of Hungarian Research, H-1014 Budapest, Hungary. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210323 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Mitochondrial) SB - IM MH - Cemeteries MH - DNA, Mitochondrial/*genetics MH - Genetics, Population MH - Haplotypes MH - High-Throughput Nucleotide Sequencing MH - History, Medieval MH - Humans MH - Hungary/ethnology MH - Maternal Inheritance MH - Mitochondria/*genetics MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA/*methods MH - Transients and Migrants/*history PMC - PMC8005002 OTO - NOTNLM OT - Carpathian Basin OT - Hungarian commoners OT - ancient mitogenome COIS- I.N. and D.L. at SeqOmics Biotechnology Ltd. and Zs.G. at Ásatárs Ltd. had consulting positions during the time the study was conceived. SeqOmics Biotechnology Ltd. and Ásatárs Ltd. were not directly involved in the design and execution of the experiments or in the writing of the manuscript. This affiliation does not alter our adherence to Genes’ policies on sharing data and materials. EDAT- 2021/04/04 06:00 MHDA- 2021/07/31 06:00 PMCR- 2021/03/23 CRDT- 2021/04/03 01:25 PHST- 2021/01/26 00:00 [received] PHST- 2021/03/10 00:00 [revised] PHST- 2021/03/16 00:00 [accepted] PHST- 2021/04/03 01:25 [entrez] PHST- 2021/04/04 06:00 [pubmed] PHST- 2021/07/31 06:00 [medline] PHST- 2021/03/23 00:00 [pmc-release] AID - genes12030460 [pii] AID - genes-12-00460 [pii] AID - 10.3390/genes12030460 [doi] PST - epublish SO - Genes (Basel). 2021 Mar 23;12(3):460. doi: 10.3390/genes12030460. PMID- 33690651 OWN - NLM STAT- MEDLINE DCOM- 20210826 LR - 20210826 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 16 IP - 3 DP - 2021 TI - Genome-wide analysis of nearly all the victims of a 6200 year old massacre. PG - e0247332 LID - 10.1371/journal.pone.0247332 [doi] LID - e0247332 AB - Paleogenomic and bioanthropological studies of ancient massacres have highlighted sites where the victims were male and plausibly died all in battle, or were executed members of the same family as might be expected from a killing intentionally directed at subsets of a community, or where the massacred individuals were plausibly members of a migrant community in conflict with previously established groups, or where there was evidence that the killing was part of a religious ritual. Here we provide evidence of killing on a massive scale in prehistory that was not directed to a specific family, based on genome-wide ancient DNA for 38 of the 41 documented victims of a 6,200 year old massacre in Potočani, Croatia and combining our results with bioanthropological data. We highlight three results: (i) the majority of individuals were unrelated and instead were a sample of what was clearly a large farming population, (ii) the ancestry of the individuals was homogenous which makes it unlikely that the massacre was linked to the arrival of new genetic ancestry, and (iii) there were approximately equal numbers of males and females. Combined with the bioanthropological evidence that the victims were of a wide range of ages, these results show that large-scale indiscriminate killing is a horror that is not just a feature of the modern and historic periods, but was also a significant process in pre-state societies. FAU - Novak, Mario AU - Novak M AUID- ORCID: 0000-0002-4567-8742 AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. FAU - Olalde, Iñigo AU - Olalde I AD - Institute of Evolutionary Biology, CSIC - Universitat Pompeu Fabra, Barcelona, Spain. AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America. FAU - Ringbauer, Harald AU - Ringbauer H AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America. AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America. FAU - Ahern, James AU - Ahern J AD - Department of Anthropology, University of Wyoming, Laramie, Wyoming, United States of America. FAU - Balen, Jacqueline AU - Balen J AD - Archaeological Museum in Zagreb, Zagreb, Croatia. FAU - Janković, Ivor AU - Janković I AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. AD - Department of Anthropology, University of Wyoming, Laramie, Wyoming, United States of America. FAU - Potrebica, Hrvoje AU - Potrebica H AD - Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America. AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America. AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20210310 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - Croatia MH - Disaster Victims/*history MH - Female MH - Forensic Anthropology/*methods MH - History, Ancient MH - Humans MH - Male MH - Pedigree MH - Whole Genome Sequencing/*methods PMC - PMC7946188 COIS- I have read the journal’s policy and the authors of this manuscript have the following competing interests: Mario Novak and Ron Pinhasi serve as Academic Editors for PLOS ONE. EDAT- 2021/03/11 06:00 MHDA- 2021/08/27 06:00 PMCR- 2021/03/10 CRDT- 2021/03/10 18:11 PHST- 2020/11/09 00:00 [received] PHST- 2021/02/04 00:00 [accepted] PHST- 2021/03/10 18:11 [entrez] PHST- 2021/03/11 06:00 [pubmed] PHST- 2021/08/27 06:00 [medline] PHST- 2021/03/10 00:00 [pmc-release] AID - PONE-D-20-35229 [pii] AID - 10.1371/journal.pone.0247332 [doi] PST - epublish SO - PLoS One. 2021 Mar 10;16(3):e0247332. doi: 10.1371/journal.pone.0247332. eCollection 2021. PMID- 33434506 OWN - NLM STAT- MEDLINE DCOM- 20220203 LR - 20220203 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 31 IP - 5 DP - 2021 Mar 8 TI - Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France. PG - 1072-1083.e10 LID - S0960-9822(20)31835-2 [pii] LID - 10.1016/j.cub.2020.12.015 [doi] AB - The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.(1) These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes(2)(,)(3) into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.(4-8) This transition is documented through extensive ancient genomic data from present-day Britain,(9)(,)(10) Ireland,(11)(,)(12) Iberia,(13) Mediterranean islands,(14)(,)(15) and Germany.(8) It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),(8)(,)(9)(,)(16) with the exception of one Late Neolithic genome sequenced at 0.05× coverage.(16) This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Seguin-Orlando, Andaine AU - Seguin-Orlando A AD - Centre d'Anthropobiologie et de Génomique de Toulouse CAGT, CNRS UMR 5288, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France; Institute for Advanced Study in Toulouse IAST, Université Toulouse I Capitole, Esplanade de l'Université, 31080 Toulouse Cedex 06, France. Electronic address: andaine.seguin@univ-tlse3.fr. FAU - Donat, Richard AU - Donat R AD - Centre d'Anthropobiologie et de Génomique de Toulouse CAGT, CNRS UMR 5288, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France; Institut National de Recherches Archéologiques Préventives INRAP, 561 Rue Etienne Lenoir, 30900 Nîmes, France. FAU - Der Sarkissian, Clio AU - Der Sarkissian C AD - Centre d'Anthropobiologie et de Génomique de Toulouse CAGT, CNRS UMR 5288, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France. FAU - Southon, John AU - Southon J AD - Earth System Science Department, B321 Croul Hall, University of California, Irvine, Irvine, CA 92697-3100, USA. FAU - Thèves, Catherine AU - Thèves C AD - Centre d'Anthropobiologie et de Génomique de Toulouse CAGT, CNRS UMR 5288, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France. FAU - Manen, Claire AU - Manen C AD - Laboratoire Travaux et Recherches Archéologiques sur les Cultures, les Espaces et les Sociétés TRACES, CNRS UMR 5608, Université Toulouse II Jean Jaurès, Maison de la Recherche, 5 allées A. Machado, 31058 Toulouse Cedex 9, France. FAU - Tchérémissinoff, Yaramila AU - Tchérémissinoff Y AD - Institut National de Recherches Archéologiques Préventives INRAP, 561 Rue Etienne Lenoir, 30900 Nîmes, France; Laboratoire Méditerranéen de Préhistoire Europe Afrique LAMPEA, CNRS UMR 7269, Aix Marseille Université, 5 rue du Château de l'horloge, 13094 Aix-en-Provence, France. FAU - Crubézy, Eric AU - Crubézy E AD - Centre d'Anthropobiologie et de Génomique de Toulouse CAGT, CNRS UMR 5288, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France. FAU - Shapiro, Beth AU - Shapiro B AD - Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA. FAU - Deleuze, Jean-François AU - Deleuze JF AD - Centre National de Recherche en Génomique Humaine CNRGH, Institut de Biologie François Jacob, Université Paris Saclay, CEA, 2 rue Gaston Crémieux CP 5721, 91057 Evry, France. FAU - Dalén, Love AU - Dalén L AD - Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden. FAU - Guilaine, Jean AU - Guilaine J AD - Collège de France, 11, place Marcelin-Berthelot, 75005 Paris, France. FAU - Orlando, Ludovic AU - Orlando L AD - Centre d'Anthropobiologie et de Génomique de Toulouse CAGT, CNRS UMR 5288, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France. Electronic address: ludovic.orlando@univ-tlse3.fr. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - Europe MH - France MH - Genome, Human MH - Genomics MH - History, Ancient MH - *Human Migration MH - Humans OTO - NOTNLM OT - Bell Beaker OT - Late Neolithic OT - Mesolithic OT - Yamnaya OT - admixture OT - ancient DNA OT - collective burial OT - methylome OT - oral microbiome OT - paleogenomics COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2021/01/13 06:00 MHDA- 2022/02/04 06:00 CRDT- 2021/01/12 20:07 PHST- 2020/09/14 00:00 [received] PHST- 2020/12/11 00:00 [revised] PHST- 2020/12/11 00:00 [accepted] PHST- 2021/01/13 06:00 [pubmed] PHST- 2022/02/04 06:00 [medline] PHST- 2021/01/12 20:07 [entrez] AID - S0960-9822(20)31835-2 [pii] AID - 10.1016/j.cub.2020.12.015 [doi] PST - ppublish SO - Curr Biol. 2021 Mar 8;31(5):1072-1083.e10. doi: 10.1016/j.cub.2020.12.015. PMID- 33667394 OWN - NLM STAT- MEDLINE DCOM- 20210324 LR - 20210403 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 108 IP - 3 DP - 2021 Mar 4 TI - Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years. PG - 517-524 LID - S0002-9297(21)00051-3 [pii] LID - 10.1016/j.ajhg.2021.02.009 [doi] AB - Tuberculosis (TB), usually caused by Mycobacterium tuberculosis bacteria, is the first cause of death from an infectious disease at the worldwide scale, yet the mode and tempo of TB pressure on humans remain unknown. The recent discovery that homozygotes for the P1104A polymorphism of TYK2 are at higher risk to develop clinical forms of TB provided the first evidence of a common, monogenic predisposition to TB, offering a unique opportunity to inform on human co-evolution with a deadly pathogen. Here, we investigate the history of human exposure to TB by determining the evolutionary trajectory of the TYK2 P1104A variant in Europe, where TB is considered to be the deadliest documented infectious disease. Leveraging a large dataset of 1,013 ancient human genomes and using an approximate Bayesian computation approach, we find that the P1104A variant originated in the common ancestors of West Eurasians ∼30,000 years ago. Furthermore, we show that, following large-scale population movements of Anatolian Neolithic farmers and Eurasian steppe herders into Europe, P1104A has markedly fluctuated in frequency over the last 10,000 years of European history, with a dramatic decrease in frequency after the Bronze Age. Our analyses indicate that such a frequency drop is attributable to strong negative selection starting ∼2,000 years ago, with a relative fitness reduction on homozygotes of 20%, among the highest in the human genome. Together, our results provide genetic evidence that TB has imposed a heavy burden on European health over the last two millennia. CI - Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Kerner, Gaspard AU - Kerner G AD - Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris University, Imagine Institute, 75015 Paris, France. Electronic address: gakerner@pasteur.fr. FAU - Laval, Guillaume AU - Laval G AD - Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France. FAU - Patin, Etienne AU - Patin E AD - Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France. FAU - Boisson-Dupuis, Stéphanie AU - Boisson-Dupuis S AD - Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris University, Imagine Institute, 75015 Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA. FAU - Abel, Laurent AU - Abel L AD - Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris University, Imagine Institute, 75015 Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA. FAU - Casanova, Jean-Laurent AU - Casanova JL AD - Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris University, Imagine Institute, 75015 Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA. FAU - Quintana-Murci, Lluis AU - Quintana-Murci L AD - Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, 75005 Paris, France. Electronic address: quintana@pasteur.fr. LA - eng GR - R01 AI088364/AI/NIAID NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Ancient) RN - EC 2.7.10.2 (TYK2 Kinase) RN - EC 2.7.10.2 (TYK2 protein, human) SB - IM MH - Body Remains MH - DNA, Ancient/*analysis MH - Europe MH - Female MH - Genome, Human/genetics MH - History, Ancient MH - Humans MH - Male MH - Polymorphism, Genetic/*genetics MH - TYK2 Kinase/*genetics MH - Tuberculosis/*genetics/history/microbiology PMC - PMC8008489 OTO - NOTNLM OT - Approximate Bayesian Computation OT - Europeans OT - Mycobacterium tuberculosis OT - ancient DNA OT - disease OT - evolution OT - genetics OT - human OT - natural selection OT - tuberculosis COIS- The authors declare no competing interests. EDAT- 2021/03/06 06:00 MHDA- 2021/03/25 06:00 PMCR- 2021/03/04 CRDT- 2021/03/05 20:10 PHST- 2020/10/12 00:00 [received] PHST- 2021/02/05 00:00 [accepted] PHST- 2021/03/05 20:10 [entrez] PHST- 2021/03/06 06:00 [pubmed] PHST- 2021/03/25 06:00 [medline] PHST- 2021/03/04 00:00 [pmc-release] AID - S0002-9297(21)00051-3 [pii] AID - 10.1016/j.ajhg.2021.02.009 [doi] PST - ppublish SO - Am J Hum Genet. 2021 Mar 4;108(3):517-524. doi: 10.1016/j.ajhg.2021.02.009. PMID- 33801556 OWN - NLM STAT- MEDLINE DCOM- 20210803 LR - 20240331 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 12 IP - 3 DP - 2021 Mar 2 TI - Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics. LID - 10.3390/genes12030360 [doi] LID - 360 AB - The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas. FAU - Lindo, John AU - Lindo J AUID- ORCID: 0000-0002-2533-8505 AD - Department of Anthropology, Emory University, Atlanta, GA 30322, USA. FAU - DeGiorgio, Michael AU - DeGiorgio M AD - Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA. LA - eng GR - R35 GM128590/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review DEP - 20210302 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) SB - IM MH - *Adaptation, Biological MH - DNA, Ancient/*analysis MH - Evolution, Molecular MH - Gene Flow MH - Genetics, Population MH - Genomics/*methods MH - Humans MH - Selection, Genetic MH - South America/ethnology PMC - PMC8001801 OTO - NOTNLM OT - South America OT - ancient DNA OT - natural selection COIS- The authors declare no conflict of interest. EDAT- 2021/04/04 06:00 MHDA- 2021/08/04 06:00 PMCR- 2021/03/02 CRDT- 2021/04/03 01:08 PHST- 2021/01/28 00:00 [received] PHST- 2021/02/18 00:00 [revised] PHST- 2021/02/22 00:00 [accepted] PHST- 2021/04/03 01:08 [entrez] PHST- 2021/04/04 06:00 [pubmed] PHST- 2021/08/04 06:00 [medline] PHST- 2021/03/02 00:00 [pmc-release] AID - genes12030360 [pii] AID - genes-12-00360 [pii] AID - 10.3390/genes12030360 [doi] PST - epublish SO - Genes (Basel). 2021 Mar 2;12(3):360. doi: 10.3390/genes12030360. PMID- 33734062 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20240613 IS - 2324-6200 (Electronic) IS - 2324-6200 (Linking) VI - 9 IP - 2 DP - 2021 Mar TI - Ancient Antibiotics, Ancient Resistance. LID - 10.1128/ecosalplus.ESP-0027-2020 [doi] LID - eESP-0027-2020 AB - As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a preantibiotic era requires the discovery of new drugs. While therapeutic use of antibiotics followed by the inevitable selection of resistance is a modern phenomenon, these molecules and the genetic determinants of resistance were in use by environmental microbes long before humans discovered them. In this review, we discuss evidence that antibiotics and resistance were present in the environment before anthropogenic use, describing techniques including direct sampling of ancient DNA and phylogenetic analyses that are used to reconstruct the past. We also pay special attention to the ecological and evolutionary forces that have shaped the natural history of antibiotic biosynthesis, including a discussion of competitive versus signaling roles for antibiotics, proto-resistance, and substrate promiscuity of biosynthetic and resistance enzymes. Finally, by applying an evolutionary lens, we describe concepts governing the origins and evolution of biosynthetic gene clusters and cluster-associated resistance determinants. These insights into microbes' use of antibiotics in nature, a game they have been playing for millennia, can provide inspiration for discovery technologies and management strategies to combat the growing resistance crisis. FAU - Waglechner, Nicholas AU - Waglechner N AD - These authors contributed equally to this work. AD - M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada. FAU - Culp, Elizabeth J AU - Culp EJ AD - These authors contributed equally to this work. AD - M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada. FAU - Wright, Gerard D AU - Wright GD AD - M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada. LA - eng GR - FRN-148463/CIHR/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - EcoSal Plus JT - EcoSal Plus JID - 101631050 RN - 0 (Anti-Bacterial Agents) SB - IM MH - *Anti-Bacterial Agents/pharmacology/therapeutic use MH - Drug Resistance, Microbial/genetics MH - Humans MH - *Multigene Family MH - Phylogeny PMC - PMC11163840 EDAT- 2021/03/19 06:00 MHDA- 2021/10/26 06:00 PMCR- 2021/03/17 CRDT- 2021/03/18 12:33 PHST- 2021/03/18 12:33 [entrez] PHST- 2021/03/19 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] PHST- 2021/03/17 00:00 [pmc-release] AID - ESP-0027-2020 [pii] AID - ecosalplus.esp-0027-2020 [pii] AID - 10.1128/ecosalplus.ESP-0027-2020 [doi] PST - ppublish SO - EcoSal Plus. 2021 Mar;9(2):eESP-0027-2020. doi: 10.1128/ecosalplus.ESP-0027-2020. PMID- 33618348 OWN - NLM STAT- MEDLINE DCOM- 20210527 LR - 20240331 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 591 IP - 7850 DP - 2021 Mar TI - Genomic insights into the formation of human populations in East Asia. PG - 413-419 LID - 10.1038/s41586-021-03336-2 [doi] AB - The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people(1,2). Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan. FAU - Wang, Chuan-Chao AU - Wang CC AUID- ORCID: 0000-0001-9628-0307 AD - Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China. wang@xmu.edu.cn. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. wang@xmu.edu.cn. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. wang@xmu.edu.cn. AD - MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China. wang@xmu.edu.cn. FAU - Yeh, Hui-Yuan AU - Yeh HY AD - School of Humanities, Nanyang Technological University, Nanyang, Singapore. FAU - Popov, Alexander N AU - Popov AN AD - Scientific Museum, Far Eastern Federal University, Vladivostok, Russia. FAU - Zhang, Hu-Qin AU - Zhang HQ AD - Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China. FAU - Matsumura, Hirofumi AU - Matsumura H AUID- ORCID: 0000-0001-5453-7987 AD - School of Health Science, Sapporo Medical University, Sapporo, Japan. FAU - Sirak, Kendra AU - Sirak K AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. FAU - Cheronet, Olivia AU - Cheronet O AUID- ORCID: 0000-0001-6760-1204 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Kovalev, Alexey AU - Kovalev A AUID- ORCID: 0000-0003-2637-3131 AD - Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Kim, Alexander M AU - Kim AM AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Department of Anthropology, Harvard University, Cambridge, MA, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Bernardos, Rebecca AU - Bernardos R AUID- ORCID: 0000-0003-4625-3727 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Tumen, Dashtseveg AU - Tumen D AD - Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia. FAU - Zhao, Jing AU - Zhao J AD - Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China. FAU - Liu, Yi-Chang AU - Liu YC AD - Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan. FAU - Liu, Jiun-Yu AU - Liu JY AD - Department of Anthropology, University of Washington, Seattle, WA, USA. FAU - Mah, Matthew AU - Mah M AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Wang, Ke AU - Wang K AUID- ORCID: 0000-0003-3935-8344 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Zhang, Zhao AU - Zhang Z AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Adamski, Nicole AU - Adamski N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AUID- ORCID: 0000-0001-5350-1608 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Callan, Kimberly AU - Callan K AUID- ORCID: 0000-0003-3170-8514 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Candilio, Francesca AU - Candilio F AUID- ORCID: 0000-0002-4668-1361 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Carlson, Kellie Sara Duffett AU - Carlson KSD AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Culleton, Brendan J AU - Culleton BJ AD - Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA. FAU - Eccles, Laurie AU - Eccles L AD - Department of Anthropology, Pennsylvania State University, University Park, PA, USA. FAU - Freilich, Suzanne AU - Freilich S AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Keating, Denise AU - Keating D AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Lawson, Ann Marie AU - Lawson AM AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Mandl, Kirsten AU - Mandl K AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Özdoğan, Kadir Toykan AU - Özdoğan KT AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Wen, Shaoqing AU - Wen S AD - Institute of Archaeological Science, Fudan University, Shanghai, China. FAU - Yan, Shi AU - Yan S AUID- ORCID: 0000-0001-8304-8445 AD - School of Ethnology and Sociology, Minzu University of China, Beijing, China. FAU - Zalzala, Fatma AU - Zalzala F AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Chuang, Richard AU - Chuang R AD - Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan. FAU - Huang, Ching-Jung AU - Huang CJ AD - Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan. FAU - Looh, Hana AU - Looh H AD - Institute of History and Philology, Institute of History and Philology, Academia Sinica, Taipei, Taiwan. FAU - Shiung, Chung-Ching AU - Shiung CC AD - Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan. FAU - Nikitin, Yuri G AU - Nikitin YG AD - Museum of Archaeology and Ethnology, Institute of History, Archaeology and Ethnology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia. FAU - Tabarev, Andrei V AU - Tabarev AV AD - Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia. FAU - Tishkin, Alexey A AU - Tishkin AA AD - Department of Archeology, Ethnography and Museology, Altai State University, Barnaul, Russia. FAU - Lin, Song AU - Lin S AD - Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China. FAU - Sun, Zhou-Yong AU - Sun ZY AD - Shaanxi Provincial Institute of Archaeology, Xi'an, China. FAU - Wu, Xiao-Ming AU - Wu XM AUID- ORCID: 0000-0003-0908-0986 AD - Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China. FAU - Yang, Tie-Lin AU - Yang TL AD - Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China. FAU - Hu, Xi AU - Hu X AD - Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China. FAU - Chen, Liang AU - Chen L AD - School of Cultural Heritage, Northwest University, Xi'an, China. FAU - Du, Hua AU - Du H AD - Xi'an AMS Center, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China. FAU - Bayarsaikhan, Jamsranjav AU - Bayarsaikhan J AD - Research Center at the National Museum of Mongolia, Ulaanbaatar, Mongolia. FAU - Mijiddorj, Enkhbayar AU - Mijiddorj E AD - Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia. FAU - Erdenebaatar, Diimaajav AU - Erdenebaatar D AD - Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia. FAU - Iderkhangai, Tumur-Ochir AU - Iderkhangai TO AD - Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia. FAU - Myagmar, Erdene AU - Myagmar E AUID- ORCID: 0000-0003-0400-1177 AD - Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia. FAU - Kanzawa-Kiriyama, Hideaki AU - Kanzawa-Kiriyama H AD - Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan. FAU - Nishino, Masato AU - Nishino M AD - Archaeological Center of Chiba City, Chiba, Japan. FAU - Shinoda, Ken-Ichi AU - Shinoda KI AD - Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan. FAU - Shubina, Olga A AU - Shubina OA AD - Department of Archeology, Sakhalin Regional Museum, Yuzhno-Sakhalinsk, Russia. FAU - Guo, Jianxin AU - Guo J AD - Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China. FAU - Cai, Wangwei AU - Cai W AD - Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China. FAU - Deng, Qiongying AU - Deng Q AD - Department of Human Anatomy and Center for Genomics and Personalized Medicine, Guangxi Medical University, Nanning, China. FAU - Kang, Longli AU - Kang L AD - Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Ministry of Education, School of Medicine, Xizang Minzu University (Tibet University for Nationalities), Xianyang, China. FAU - Li, Dawei AU - Li D AD - Institute for History and Culture of Science & Technology, Guangxi University for Nationalities, Nanning, China. FAU - Li, Dongna AU - Li D AD - Department of Biology, Hainan Medical University, Haikou, China. FAU - Lin, Rong AU - Lin R AUID- ORCID: 0000-0001-9161-6844 AD - Department of Biology, Hainan Medical University, Haikou, China. FAU - Nini AU - Nini AD - Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Ministry of Education, School of Medicine, Xizang Minzu University (Tibet University for Nationalities), Xianyang, China. FAU - Shrestha, Rukesh AU - Shrestha R AD - MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China. FAU - Wang, Ling-Xiang AU - Wang LX AD - MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China. FAU - Wei, Lanhai AU - Wei L AUID- ORCID: 0000-0003-3119-7400 AD - Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China. FAU - Xie, Guangmao AU - Xie G AD - College of History, Culture and Tourism, Guangxi Normal University, Guilin, China. AD - Guangxi Institute of Cultural Relics Protection and Archaeology, Nanning, China. FAU - Yao, Hongbing AU - Yao H AD - Belt and Road Research Center for Forensic Molecular Anthropology, Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, China. FAU - Zhang, Manfei AU - Zhang M AD - MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China. FAU - He, Guanglin AU - He G AD - Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China. FAU - Yang, Xiaomin AU - Yang X AD - Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China. FAU - Hu, Rong AU - Hu R AD - Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China. FAU - Robbeets, Martine AU - Robbeets M AUID- ORCID: 0000-0002-2860-0230 AD - Eurasia3angle Research group, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Schiffels, Stephan AU - Schiffels S AUID- ORCID: 0000-0002-1017-9150 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Kennett, Douglas J AU - Kennett DJ AUID- ORCID: 0000-0001-6144-7365 AD - Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA. FAU - Jin, Li AU - Jin L AD - MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China. FAU - Li, Hui AU - Li H AD - MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. krause@shh.mpg.de. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - ERC_/European Research Council/International PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20210222 PL - England TA - Nature JT - Nature JID - 0410462 SB - IM MH - China MH - Crop Production/history MH - Female MH - Genome, Human/*genetics MH - *Genomics MH - Haplotypes/genetics MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Japan MH - Language/history MH - Male MH - Mongolia MH - Nepal MH - Oryza MH - Polymorphism, Single Nucleotide/genetics MH - Siberia MH - Taiwan PMC - PMC7993749 MID - NIHMS1671260 COIS- Competing interests The authors declare no competing interests. EDAT- 2021/02/23 06:00 MHDA- 2021/05/28 06:00 PMCR- 2021/08/22 CRDT- 2021/02/22 20:18 PHST- 2020/03/19 00:00 [received] PHST- 2021/02/05 00:00 [accepted] PHST- 2021/02/23 06:00 [pubmed] PHST- 2021/05/28 06:00 [medline] PHST- 2021/02/22 20:18 [entrez] PHST- 2021/08/22 00:00 [pmc-release] AID - 10.1038/s41586-021-03336-2 [pii] AID - 10.1038/s41586-021-03336-2 [doi] PST - ppublish SO - Nature. 2021 Mar;591(7850):413-419. doi: 10.1038/s41586-021-03336-2. Epub 2021 Feb 22. PMID- 33579752 OWN - NLM STAT- MEDLINE DCOM- 20220207 LR - 20240126 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 31 IP - 3 DP - 2021 Mar TI - A minimally destructive protocol for DNA extraction from ancient teeth. PG - 472-483 LID - 10.1101/gr.267534.120 [doi] AB - Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods. CI - © 2021 Harney et al.; Published by Cold Spring Harbor Laboratory Press. FAU - Harney, Éadaoin AU - Harney É AUID- ORCID: 0000-0001-9385-7297 AD - Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena D-07745, Germany. AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. FAU - Cheronet, Olivia AU - Cheronet O AUID- ORCID: 0000-0001-6760-1204 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria. FAU - Fernandes, Daniel M AU - Fernandes DM AD - Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria. AD - CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal. FAU - Sirak, Kendra AU - Sirak K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. FAU - Mah, Matthew AU - Mah M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Bernardos, Rebecca AU - Bernardos R AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Adamski, Nicole AU - Adamski N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Callan, Kimberly AU - Callan K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Lawson, Ann Marie AU - Lawson AM AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Zalzala, Fatma AU - Zalzala F AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Anders, Alexandra AU - Anders A AD - Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Hungary. FAU - Candilio, Francesca AU - Candilio F AD - Superintendency of Archaeology, Fine Arts and Landscape for the City of Cagliari and the Provinces of Oristano and South Sardinia, 09121 Cagliari, Italy. FAU - Constantinescu, Mihai AU - Constantinescu M AD - Fr. I. Rainer Institute of Anthropology, Bucharest 050711, Romania. FAU - Coppa, Alfredo AU - Coppa A AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria. AD - Department of Environmental Biology, Sapienza University, 00185 Rome, Italy. FAU - Ciobanu, Ion AU - Ciobanu I AD - Cultural-Natural Reserve "Orheiul Vechi", 3552 Orhei, Republic of Moldova. AD - Institute of Bioarchaeological and Ethnocultural Research, 2012 Chișinău, Republic of Moldova. FAU - Dani, János AU - Dani J AD - Déri Museum, 4026 Debrecen, Hungary. FAU - Gallina, Zsolt AU - Gallina Z AD - Ásatárs Kulturális, Régészeti Szolgáltató és Kereskedelmi Limited, 6000 Kecskemét, Hungary. FAU - Genchi, Francesco AU - Genchi F AD - Department of Environmental Biology, Sapienza University, 00185 Rome, Italy. FAU - Nagy, Emese Gyöngyvér AU - Nagy EG AD - Déri Museum, 4026 Debrecen, Hungary. FAU - Hajdu, Tamás AU - Hajdu T AD - Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary. AD - Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary. FAU - Hellebrandt, Magdolna AU - Hellebrandt M AD - Herman Ottó Museum, 3529 Miskolc, Hungary. FAU - Horváth, Antónia AU - Horváth A AD - Herman Ottó Museum, 3529 Miskolc, Hungary. FAU - Király, Ágnes AU - Király Á AD - Institute of Archaeology, Research Centre for the Humanities, 1097 Budapest, Hungary. FAU - Kiss, Krisztián AU - Kiss K AD - Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary. AD - Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary. FAU - Kolozsi, Barbara AU - Kolozsi B AD - Déri Museum, 4026 Debrecen, Hungary. FAU - Kovács, Péter AU - Kovács P AD - Damjanich János Museum, 5000 Szolnok, Hungary. FAU - Köhler, Kitti AU - Köhler K AD - Institute of Archaeology, Research Centre for the Humanities, 1097 Budapest, Hungary. FAU - Lucci, Michaela AU - Lucci M AD - Department of History, Anthropology, Religion, Arts and Performing Arts, Sapienza University, 00185 Rome, Italy. FAU - Pap, Ildikó AU - Pap I AD - Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary. FAU - Popovici, Sergiu AU - Popovici S AD - National Agency for Archaeology, 2012 Chișinău, Republic of Moldova. FAU - Raczky, Pál AU - Raczky P AD - Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Hungary. FAU - Simalcsik, Angela AU - Simalcsik A AD - Institute of Bioarchaeological and Ethnocultural Research, 2012 Chișinău, Republic of Moldova. AD - Olga Necrasov Center for Anthropological Research, Romanian Academy, 700481 Iasi, Romania. FAU - Szeniczey, Tamás AU - Szeniczey T AD - Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary. AD - Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary. FAU - Vasilyev, Sergey AU - Vasilyev S AD - Institute of Ethnology and Anthropology of the Russian Academy of Sciences, 119991 Moscow, Russia. AD - Center for Egyptological Studies of the Russian Academy of Sciences, 119071 Moscow, Russia. FAU - Virag, Cristian AU - Virag C AD - Satu Mare County Museum, 440031 Satu Mare, Romania. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. FAU - Reich, David AU - Reich D AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena D-07745, Germany. AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210212 PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/*isolation & purification MH - Dental Cementum/*chemistry MH - Humans MH - Male MH - Tooth/anatomy & histology/*chemistry PMC - PMC7919446 EDAT- 2021/02/14 06:00 MHDA- 2022/02/08 06:00 PMCR- 2021/09/01 CRDT- 2021/02/13 05:39 PHST- 2020/06/17 00:00 [received] PHST- 2020/12/14 00:00 [accepted] PHST- 2021/02/14 06:00 [pubmed] PHST- 2022/02/08 06:00 [medline] PHST- 2021/02/13 05:39 [entrez] PHST- 2021/09/01 00:00 [pmc-release] AID - gr.267534.120 [pii] AID - 10.1101/gr.267534.120 [doi] PST - ppublish SO - Genome Res. 2021 Mar;31(3):472-483. doi: 10.1101/gr.267534.120. Epub 2021 Feb 12. PMID- 33455740 OWN - NLM STAT- MEDLINE DCOM- 20210222 LR - 20220531 IS - 1872-8383 (Electronic) IS - 0169-5347 (Linking) VI - 36 IP - 3 DP - 2021 Mar TI - Examining Natural History through the Lens of Palaeogenomics. PG - 258-267 LID - S0169-5347(20)30282-2 [pii] LID - 10.1016/j.tree.2020.10.005 [doi] AB - The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer. CI - Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Mitchell, Kieren J AU - Mitchell KJ AD - Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. Electronic address: kieren.mitchell@adelaide.edu.au. FAU - Rawlence, Nicolas J AU - Rawlence NJ AD - Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20210114 PL - England TA - Trends Ecol Evol JT - Trends in ecology & evolution JID - 8805125 SB - IM MH - *Fossils MH - *Genomics MH - Humans MH - Paleontology OTO - NOTNLM OT - Holocene OT - Pleistocene OT - ancient DNA OT - extinction OT - megafauna EDAT- 2021/01/19 06:00 MHDA- 2021/02/23 06:00 CRDT- 2021/01/18 05:25 PHST- 2020/07/31 00:00 [received] PHST- 2020/10/05 00:00 [revised] PHST- 2020/10/07 00:00 [accepted] PHST- 2021/01/19 06:00 [pubmed] PHST- 2021/02/23 06:00 [medline] PHST- 2021/01/18 05:25 [entrez] AID - S0169-5347(20)30282-2 [pii] AID - 10.1016/j.tree.2020.10.005 [doi] PST - ppublish SO - Trends Ecol Evol. 2021 Mar;36(3):258-267. doi: 10.1016/j.tree.2020.10.005. Epub 2021 Jan 14. PMID- 33453495 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20211025 IS - 1879-9825 (Electronic) IS - 1879-9817 (Linking) VI - 32 DP - 2021 Mar TI - Detection of Vibrio cholerae aDNA in human burials from the fifth cholera pandemic in Argentina (1886-1887 AD). PG - 74-79 LID - S1879-9817(20)30071-1 [pii] LID - 10.1016/j.ijpp.2020.12.004 [doi] AB - OBJECTIVE: Detecting traces of ancient DNA of Vibrio cholerae to provide genetic information associated with the fifth cholera pandemic. MATERIALS: Sediment samples from the sacral foramina of four individuals were analyzed, recovered from a mass grave near an institution dedicated exclusively to the isolation and treatment of citizens infected with cholera in the late 19th century in the city of Cordoba, Argentina. METHODS: Paleogenetic techniques (ancient DNA extraction, PCR amplification, and Sanger sequencing) were applied. Specific primers for Vibrio cholerae (VCR, ctxA, ctxB, and tcpA) were designed. RESULTS: By amplifying and sequencing the Vibrio cholerae repeats fragment, the infection in at least one individual was confirmed. CONCLUSIONS: The synthesis of the paleogenetic results with the archaeological and historical evidence strongly supports that at least one individual from the mass grave in Cordoba, Argentina, was a victim of the fifth cholera pandemic. SIGNIFICANCE: Confirming the presence of the disease through multiple lines of evidence, including genetic, archaeological, and historical analyses, strengthens and affirms our understanding of the presence, effects, and potential evolutionary paths of the disease in the past. LIMITATIONS: Vibrio cholerae repeats were sequenced in one individual, while the remaining genes could not be amplified, which is likely related to gene copy number. SUGGESTIONS FOR FUTURE RESEARCH: Paleogenetic examination of ancient samples from different locations will broaden our understanding of the origin, evolution, and past dissemination of Vibrio cholerae epidemic strains. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Ramirez, Darío Alejandro AU - Ramirez DA AD - Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba (UNC), Córdoba, Argentina. Electronic address: darioramirez092@gmail.com. FAU - Saka, Héctor Alex AU - Saka HA AD - Centro de Investigación en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Córdoba, Argentina. Electronic address: alex.saka@unc.edu.ar. FAU - Nores, Rodrigo AU - Nores R AD - Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba (UNC), Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba (UNC), Córdoba, Argentina. Electronic address: rodrigonores@ffyh.unc.edu.ar. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210113 PL - Netherlands TA - Int J Paleopathol JT - International journal of paleopathology JID - 101562474 SB - IM MH - Argentina/epidemiology MH - Burial MH - *Cholera/epidemiology MH - Humans MH - Pandemics MH - *Vibrio cholerae/genetics OTO - NOTNLM OT - Ancient bacteria OT - Cholera OT - Infectious diseases OT - Paleogenetics OT - Paleomicrobiology OT - Sediments EDAT- 2021/01/17 06:00 MHDA- 2021/10/26 06:00 CRDT- 2021/01/16 20:10 PHST- 2020/09/08 00:00 [received] PHST- 2020/12/28 00:00 [revised] PHST- 2020/12/28 00:00 [accepted] PHST- 2021/01/17 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] PHST- 2021/01/16 20:10 [entrez] AID - S1879-9817(20)30071-1 [pii] AID - 10.1016/j.ijpp.2020.12.004 [doi] PST - ppublish SO - Int J Paleopathol. 2021 Mar;32:74-79. doi: 10.1016/j.ijpp.2020.12.004. Epub 2021 Jan 13. PMID- 33139852 OWN - NLM STAT- MEDLINE DCOM- 20220114 LR - 20220129 IS - 1476-5438 (Electronic) IS - 1018-4813 (Print) IS - 1018-4813 (Linking) VI - 29 IP - 3 DP - 2021 Mar TI - Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain. PG - 512-523 LID - 10.1038/s41431-020-00747-z [doi] AB - The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia. FAU - Lall, Gurdeep Matharu AU - Lall GM AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. FAU - Larmuseau, Maarten H D AU - Larmuseau MHD AD - Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium. AD - Laboratory of Socioecology and Social Evolution, KU Leuven-University of Leuven, Leuven, Belgium. AD - Histories vzw, Zoutwerf 5, 2800, Mechelen, Belgium. FAU - Wetton, Jon H AU - Wetton JH AUID- ORCID: 0000-0001-8337-4654 AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - School of History, Politics and International Relations, University of Leicester, Leicester, UK. FAU - Batini, Chiara AU - Batini C AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK. FAU - Hallast, Pille AU - Hallast P AUID- ORCID: 0000-0002-0588-3987 AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - Wellcome Sanger Institute, Hinxton, Cambridge, UK. AD - Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, 50411, Estonia. FAU - Huszar, Tunde I AU - Huszar TI AUID- ORCID: 0000-0002-1469-6876 AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. FAU - Zadik, Daniel AU - Zadik D AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, UK. FAU - Aase, Sigurd AU - Aase S AD - Postboks 420, 5501, Haugesund, Norway. FAU - Baker, Tina AU - Baker T AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK. FAU - Balaresque, Patricia AU - Balaresque P AD - UMR5288, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Université Paul Sabatier, Toulouse, France. FAU - Bodmer, Walter AU - Bodmer W AD - Department of Oncology, University of Oxford, Oxford, UK. FAU - Børglum, Anders D AU - Børglum AD AUID- ORCID: 0000-0001-8627-7219 AD - Department of Biomedicine & Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark. FAU - de Knijff, Peter AU - de Knijff P AD - Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands. FAU - Dunn, Hayley AU - Dunn H AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - School of Archaeology and Ancient History, University of Leicester, Leicester, UK. FAU - Harding, Stephen E AU - Harding SE AD - National Centre for Macromolecular Hydrodynamics, University of Nottingham, Sutton Bonington Campus, Loughborough, UK. AD - Museum of Cultural History, University of Oslo, Oslo, Norway. FAU - Løvvik, Harald AU - Løvvik H AD - Lille Borgenveien 2B, 0370, Oslo, Norway. FAU - Dupuy, Berit Myhre AU - Dupuy BM AD - Division of Forensic Sciences, Norwegian Institute of Public Health, Oslo, Norway. FAU - Pamjav, Horolma AU - Pamjav H AD - Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, Budapest, Hungary. FAU - Tillmar, Andreas O AU - Tillmar AO AD - Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden. FAU - Tomaszewski, Maciej AU - Tomaszewski M AUID- ORCID: 0000-0001-8215-6567 AD - Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK. AD - Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester, UK. FAU - Tyler-Smith, Chris AU - Tyler-Smith C AD - Wellcome Sanger Institute, Hinxton, Cambridge, UK. FAU - Verdugo, Marta Pereira AU - Verdugo MP AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland. FAU - Winney, Bruce AU - Winney B AD - Department of Oncology, University of Oxford, Oxford, UK. FAU - Vohra, Pragya AU - Vohra P AD - School of History, Politics and International Relations, University of Leicester, Leicester, UK. AD - Department of History, University of York, Heslington, York, UK. FAU - Story, Joanna AU - Story J AUID- ORCID: 0000-0002-1022-9381 AD - School of History, Politics and International Relations, University of Leicester, Leicester, UK. FAU - King, Turi E AU - King TE AUID- ORCID: 0000-0003-3025-3829 AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. tek2@le.ac.uk. FAU - Jobling, Mark A AU - Jobling MA AUID- ORCID: 0000-0002-8061-1308 AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. maj4@le.ac.uk. LA - eng GR - 084060/Wellcome Trust/United Kingdom GR - 072974/Wellcome Trust/United Kingdom GR - BB/M016706/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom GR - 087576/Wellcome Trust/United Kingdom GR - 057559/Wellcome Trust/United Kingdom GR - 088262/Wellcome Trust/United Kingdom GR - Wellcome Trust/United Kingdom GR - PG/16/49/32176/BHF_/British Heart Foundation/United Kingdom GR - 098051/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201102 PL - England TA - Eur J Hum Genet JT - European journal of human genetics : EJHG JID - 9302235 SB - IM MH - Chromosomes, Human, Y/*genetics MH - Evolution, Molecular MH - *Haplotypes MH - *Human Migration MH - Humans MH - Male MH - Minisatellite Repeats MH - Pedigree MH - Polymorphism, Single Nucleotide MH - Scandinavian and Nordic Countries MH - United Kingdom PMC - PMC7940619 COIS- The authors declare that they have no conflict of interest. EDAT- 2020/11/04 06:00 MHDA- 2022/01/15 06:00 PMCR- 2020/11/02 CRDT- 2020/11/03 05:44 PHST- 2019/08/23 00:00 [received] PHST- 2020/10/07 00:00 [accepted] PHST- 2020/09/08 00:00 [revised] PHST- 2020/11/04 06:00 [pubmed] PHST- 2022/01/15 06:00 [medline] PHST- 2020/11/03 05:44 [entrez] PHST- 2020/11/02 00:00 [pmc-release] AID - 10.1038/s41431-020-00747-z [pii] AID - 747 [pii] AID - 10.1038/s41431-020-00747-z [doi] PST - ppublish SO - Eur J Hum Genet. 2021 Mar;29(3):512-523. doi: 10.1038/s41431-020-00747-z. Epub 2020 Nov 2. PMID- 32994538 OWN - NLM STAT- MEDLINE DCOM- 20210713 LR - 20221207 IS - 1435-232X (Electronic) IS - 1434-5161 (Linking) VI - 66 IP - 3 DP - 2021 Mar TI - Identification of ancient viruses from metagenomic data of the Jomon people. PG - 287-296 LID - 10.1038/s10038-020-00841-6 [doi] AB - Ancient DNA studies provide genomic information about the origins, population structures, and physical characteristics of ancient humans that cannot be solely examined by archeological studies. The DNAs extracted from ancient human bones, teeth, or tissues are often contaminated with coexisting bacterial and viral genomes that contain DNA from ancient microbes infecting those of ancient humans. Information on ancient viral genomes is useful in making inferences about the viral evolution. Here, we have utilized metagenomic sequencing data from the dental pulp of five Jomon individuals, who lived on the Japanese archipelago more than 3000 years ago; this is to detect ancient viral genomes. We conducted de novo assembly of the non-human reads where we have obtained 277,387 contigs that were longer than 1000 bp. These contigs were subjected to homology searches against a collection of modern viral genome sequences. We were able to detect eleven putative ancient viral genomes. Among them, we reconstructed the complete sequence of the Siphovirus contig89 (CT89) viral genome. The Jomon CT89-like sequence was determined to contain 59 open reading frames, among which five genes known to encode phage proteins were under strong purifying selection. The host of CT89 was predicted to be Schaalia meyeri, a bacterium residing in the human oral cavity. Finally, the CT89 phylogenetic tree showed two clusters, from both of which the Jomon sequence was separated. Our results suggest that metagenomic information from the dental pulp of the Jomon people is essential in retrieving ancient viral genomes used to examine their evolution. FAU - Nishimura, Luca AU - Nishimura L AUID- ORCID: 0000-0003-2144-7867 AD - Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan. AD - Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan. FAU - Sugimoto, Ryota AU - Sugimoto R AD - Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan. FAU - Inoue, Jun AU - Inoue J AD - Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan. AD - Genetic Research Section, Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Japan. FAU - Nakaoka, Hirofumi AU - Nakaoka H AUID- ORCID: 0000-0002-8454-1159 AD - Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan. AD - Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan. AD - Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan. FAU - Kanzawa-Kiriyama, Hideaki AU - Kanzawa-Kiriyama H AD - Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan. FAU - Shinoda, Ken-Ichi AU - Shinoda KI AD - Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan. FAU - Inoue, Ituro AU - Inoue I AD - Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan. itinoue@nig.ac.jp. AD - Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan. itinoue@nig.ac.jp. LA - eng PT - Comparative Study PT - Historical Article PT - Journal Article DEP - 20200930 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (DNA, Viral) RN - Schaalia meyeri SB - IM MH - Actinomycetaceae/virology MH - *Asian People/history MH - Clustered Regularly Interspaced Short Palindromic Repeats MH - Contig Mapping MH - DNA, Viral/*isolation & purification MH - Dental Pulp/chemistry/*virology MH - *Ethnicity/history MH - Female MH - Fossils/history/microbiology/*virology MH - *Genome, Viral MH - History, Ancient MH - Humans MH - Japan MH - Likelihood Functions MH - Male MH - *Metagenome MH - Molecular Sequence Annotation MH - Mouth/microbiology/virology MH - Open Reading Frames/genetics MH - Phylogeny MH - Sequence Alignment MH - Sequence Homology, Nucleic Acid MH - Siphoviridae/genetics/*isolation & purification MH - Whole Genome Sequencing EDAT- 2020/10/01 06:00 MHDA- 2021/07/14 06:00 CRDT- 2020/09/30 06:10 PHST- 2020/06/23 00:00 [received] PHST- 2020/09/05 00:00 [accepted] PHST- 2020/08/20 00:00 [revised] PHST- 2020/10/01 06:00 [pubmed] PHST- 2021/07/14 06:00 [medline] PHST- 2020/09/30 06:10 [entrez] AID - 10.1038/s10038-020-00841-6 [pii] AID - 10.1038/s10038-020-00841-6 [doi] PST - ppublish SO - J Hum Genet. 2021 Mar;66(3):287-296. doi: 10.1038/s10038-020-00841-6. Epub 2020 Sep 30. PMID- 33558418 OWN - NLM STAT- MEDLINE DCOM- 20210802 LR - 20211121 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 118 IP - 8 DP - 2021 Feb 23 TI - Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China. LID - 10.1073/pnas.2019158118 [doi] LID - e2019158118 AB - The expansion of anatomically modern humans (AMHs) from Africa around 65,000 to 45,000 y ago (ca. 65 to 45 ka) led to the establishment of present-day non-African populations. Some paleoanthropologists have argued that fossil discoveries from Huanglong, Zhiren, Luna, and Fuyan caves in southern China indicate one or more prior dispersals, perhaps as early as ca. 120 ka. We investigated the age of the human remains from three of these localities and two additional early AMH sites (Yangjiapo and Sanyou caves, Hubei) by combining ancient DNA (aDNA) analysis with a multimethod geological dating strategy. Although U-Th dating of capping flowstones suggested they lie within the range ca. 168 to 70 ka, analyses of aDNA and direct AMS (14)C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS (14)C analysis of mammal teeth and charcoal also demonstrated major discrepancies from the flowstone ages; the difference between them being an order of magnitude or more at most of these localities. Our work highlights the surprisingly complex depositional history recorded at these subtropical caves which involved one or more episodes of erosion and redeposition or intrusion as recently as the late Holocene. In light of our findings, the first appearance datum for AMHs in southern China should probably lie within the timeframe set by molecular data of ca. 50 to 45 ka. FAU - Sun, Xue-Feng AU - Sun XF AUID- ORCID: 0000-0002-2688-4663 AD - School of Geography and Ocean Science, Nanjing University, 210023 Nanjing, China; xuefeng@nju.edu.cn darrencurnoe@icloud.com lhca@fudan.edu.cn. FAU - Wen, Shao-Qing AU - Wen SQ AUID- ORCID: 0000-0003-1223-4720 AD - School of Life Sciences & Institute of Archaeological Science, Fudan University, Shanghai 200438, China. FAU - Lu, Cheng-Qiu AU - Lu CQ AD - Hubei Provincial Institute of Cultural Relics and Archeology, 430077 Wuhan, China. FAU - Zhou, Bo-Yan AU - Zhou BY AD - School of Life Sciences & Institute of Archaeological Science, Fudan University, Shanghai 200438, China. FAU - Curnoe, Darren AU - Curnoe D AUID- ORCID: 0000-0001-8622-4141 AD - Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia; xuefeng@nju.edu.cn darrencurnoe@icloud.com lhca@fudan.edu.cn. FAU - Lu, Hua-Yu AU - Lu HY AUID- ORCID: 0000-0002-6306-6985 AD - School of Geography and Ocean Science, Nanjing University, 210023 Nanjing, China. FAU - Li, Hong-Chun AU - Li HC AUID- ORCID: 0000-0001-9614-7119 AD - Department of Geosciences, National Taiwan University, 106 Taipei, Taiwan. FAU - Wang, Wei AU - Wang W AD - Institute of Cultural Heritage, Shandong University, 266237 Qingdao, China. FAU - Cheng, Hai AU - Cheng H AUID- ORCID: 0000-0002-5305-9458 AD - Institute of Global Environmental Change, Xi'an Jiaotong University, 710049 Xi'an, China. FAU - Yi, Shuang-Wen AU - Yi SW AD - School of Geography and Ocean Science, Nanjing University, 210023 Nanjing, China. FAU - Jia, Xin AU - Jia X AUID- ORCID: 0000-0003-4690-0621 AD - School of Geography Science, Nanjing Normal University, 210023 Nanjing, China. FAU - Du, Pan-Xin AU - Du PX AD - School of Life Sciences & Institute of Archaeological Science, Fudan University, Shanghai 200438, China. FAU - Xu, Xing-Hua AU - Xu XH AUID- ORCID: 0000-0002-5804-8563 AD - School of Geography and Ocean Science, Nanjing University, 210023 Nanjing, China. FAU - Lu, Yi-Ming AU - Lu YM AD - School of Geography and Ocean Science, Nanjing University, 210023 Nanjing, China. FAU - Lu, Ying AU - Lu Y AD - School of Geography and Ocean Science, Nanjing University, 210023 Nanjing, China. FAU - Zheng, Hong-Xiang AU - Zheng HX AD - School of Life Sciences & Institute of Archaeological Science, Fudan University, Shanghai 200438, China. FAU - Zhang, Hong AU - Zhang H AD - School of Life Sciences & Institute of Archaeological Science, Fudan University, Shanghai 200438, China. FAU - Sun, Chang AU - Sun C AD - School of Life Sciences & Institute of Archaeological Science, Fudan University, Shanghai 200438, China. FAU - Wei, Lan-Hai AU - Wei LH AD - School of Life Sciences & Institute of Archaeological Science, Fudan University, Shanghai 200438, China. FAU - Han, Fei AU - Han F AD - Research Centre for Earth System Science, Yunnan University, 650500 Kunming, China. FAU - Huang, Juan AU - Huang J AD - Cultural Relics Administration of Daoxian County, Daoxian 425300, China. FAU - Edwards, R Lawrence AU - Edwards RL AD - Department of Geology and Geophysics, University of Minnesota, Minneapolis, MN 55455. FAU - Jin, Li AU - Jin L AD - School of Life Sciences & Institute of Archaeological Science, Fudan University, Shanghai 200438, China. FAU - Li, Hui AU - Li H AD - School of Life Sciences & Institute of Archaeological Science, Fudan University, Shanghai 200438, China; xuefeng@nju.edu.cn darrencurnoe@icloud.com lhca@fudan.edu.cn. AD - Fudan-Datong Institute of Chinese Origin, Shanxi Academy of Advanced Research and Innovation, 037006 Datong, China. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM CIN - Proc Natl Acad Sci U S A. 2021 Mar 9;118(10):e2101173118. doi: 10.1073/pnas.2101173118. PMID: 33602727 CIN - Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):e2102961118. doi: 10.1073/pnas.2102961118. PMID: 34031253 CIN - Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):e2103798118. doi: 10.1073/pnas.2103798118. PMID: 34031254 CIN - Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):e2104818118. doi: 10.1073/pnas.2104818118. PMID: 34031256 MH - *Archaeology MH - Caves/*chemistry MH - China MH - DNA, Ancient/*analysis MH - *Fossils MH - Geologic Sediments/*analysis MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Radiometric Dating/*methods PMC - PMC7923607 OTO - NOTNLM OT - East Asia OT - Late Pleistocene OT - anatomically modern humans OT - ancient DNA OT - dating COIS- The authors declare no competing interest. EDAT- 2021/02/10 06:00 MHDA- 2021/08/03 06:00 PMCR- 2021/08/08 CRDT- 2021/02/09 06:09 PHST- 2021/02/09 06:09 [entrez] PHST- 2021/02/10 06:00 [pubmed] PHST- 2021/08/03 06:00 [medline] PHST- 2021/08/08 00:00 [pmc-release] AID - 2019158118 [pii] AID - 202019158 [pii] AID - 10.1073/pnas.2019158118 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2021 Feb 23;118(8):e2019158118. doi: 10.1073/pnas.2019158118. PMID- 33671794 OWN - NLM STAT- MEDLINE DCOM- 20210720 LR - 20210720 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 12 IP - 2 DP - 2021 Feb 22 TI - The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles. LID - 10.3390/genes12020309 [doi] LID - 309 AB - Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16-17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment. FAU - Kazarina, Alisa AU - Kazarina A AD - Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia. FAU - Petersone-Gordina, Elina AU - Petersone-Gordina E AD - Institute of Latvian History, University of Latvia, Kalpaka Bulvaris 4, LV-1050 Riga, Latvia. FAU - Kimsis, Janis AU - Kimsis J AD - Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia. FAU - Kuzmicka, Jevgenija AU - Kuzmicka J AD - Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia. FAU - Zayakin, Pawel AU - Zayakin P AUID- ORCID: 0000-0002-5336-3484 AD - Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia. FAU - Griškjans, Žans AU - Griškjans Ž AD - Institute of Stomatology, Riga Stradins University, Dzirciema Str. 20, LV-1007 Riga, Latvia. FAU - Gerhards, Guntis AU - Gerhards G AD - Institute of Latvian History, University of Latvia, Kalpaka Bulvaris 4, LV-1050 Riga, Latvia. FAU - Ranka, Renate AU - Ranka R AD - Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210222 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - Adolescent MH - Adult MH - Archaeology MH - Body Remains MH - Burial MH - Child MH - DNA, Ancient/analysis MH - DNA, Bacterial/*genetics MH - Dental Calculus/genetics/*microbiology MH - Dental Plaque/genetics/*microbiology MH - Female MH - Humans MH - Latvia/epidemiology MH - Male MH - Metagenome/genetics MH - Microbiota/*genetics MH - Middle Aged MH - Soil Microbiology MH - Young Adult PMC - PMC7927102 OTO - NOTNLM OT - ancient DNA OT - dental calculus OT - dental plaque OT - metagenomics OT - oral microbiome COIS- The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. EDAT- 2021/03/07 06:00 MHDA- 2021/07/21 06:00 PMCR- 2021/02/22 CRDT- 2021/03/06 01:11 PHST- 2021/01/24 00:00 [received] PHST- 2021/02/17 00:00 [revised] PHST- 2021/02/19 00:00 [accepted] PHST- 2021/03/06 01:11 [entrez] PHST- 2021/03/07 06:00 [pubmed] PHST- 2021/07/21 06:00 [medline] PHST- 2021/02/22 00:00 [pmc-release] AID - genes12020309 [pii] AID - genes-12-00309 [pii] AID - 10.3390/genes12020309 [doi] PST - epublish SO - Genes (Basel). 2021 Feb 22;12(2):309. doi: 10.3390/genes12020309. PMID- 33417716 OWN - NLM STAT- MEDLINE DCOM- 20210528 LR - 20220111 IS - 1460-2350 (Electronic) IS - 0268-1161 (Linking) VI - 36 IP - 3 DP - 2021 Feb 18 TI - Deleterious variants in genes regulating mammalian reproduction in Neanderthals, Denisovans and extant humans. PG - 734-755 LID - 10.1093/humrep/deaa347 [doi] AB - STUDY QUESTION: Were Neanderthals and Denisovans (referred here also as extinct hominidae) carrying deleterious variants in genes regulating reproduction? SUMMARY ANSWER: The majority of extinct hominidae analyzed here, presented a considerable number of deleterious variants per individual in proteins regulating different aspects of reproduction, including gonad and uterine function, and gametogenesis. WHAT IS KNOWN ALREADY: Neanderthals, Denisovans and extant humans were interfertile and hybridized while occupying geographically overlapping areas in Europe and Asia. This is evidenced by the small archaic genome component (average ∼2%) present in non-African extant humans. STUDY DESIGN, SIZE, DURATION: The genome of eight extinct hominidae, together with five human genome databases, plus 44 mothers and 48 fathers (fertile controls), were screened to look for deleterious variants in 1734 protein-coding genes regulating reproduction. PARTICIPANTS/MATERIALS, SETTING, METHODS: Ancient DNA from six Neanderthals and two Denisovans dated between ∼82 000 and 43 000 calibrated years was retrieved from the public European Nucleotide Archive. The hominins analyzed include Altai, Vindija 33.15, 33.19, 33.25 and 33.26, El Sidron 1253, Denisova 3 and 11. Their DNA was analyzed using the CLC Genomics Workbench 12, by mapping overlapping paired-end reads (Illumina, FASTQ files) to the human genome assembly GRCh37 (hg19) (Vindija 33.19, 33.25, 33.26, Denisova 3 and Denisova 11) or by analyzing BAM files (Altai, El Sidron 1253 and Vindija 33.15) (human genome reference, GRCh37 (hg19)). Non-synonymous reproductive variants were classified as deleterious or tolerated (PolyPhen-2 and SIFT analyses) and were compared to deleterious variants obtained from extant human genome databases (Genome Aggregation Database (GnomAD), 1000 Genomes, the Haplotype Map (HapMap), Single Nucleotide Polymorphism Database (dbSNPs)) across different populations. A genetic intersection between extant or extinct DNA variants and other genetic disorders was evaluated by annotating the obtained variants with the Clinical Variant (ClinVar) database. MAIN RESULTS AND THE ROLE OF CHANCE: Among the eight extinct hominidae analyzed, a total of 9650 non-synonymous variants (only coverage ≥20 reads included; frameshift mutations were excluded) in 1734 reproductive protein-coding genes were found, 24% of which were classified as deleterious. The majority (73%) of the deleterious alleles present in extant humans that are shared between extant humans and extinct hominidae were found to be rare (<1%) in extant human populations. A set of 8044 variants were found uniquely in extinct hominidae. At the single-gene level, no extinct individual was found to be homozygous for deleterious variants in genes necessary for gamete recognition and fusion, and no higher chance of embryo-lethality (calculated by Mendelian Genetics) was found upon simulated mating between extant human and extinct hominidae compared to extant human-extant human. However, three of the eight extinct hominidae were found to be homozygous for 48-69 deleterious variants in 55 genes controlling ovarian and uterine functions, or oogenesis (AKAP1, BUB1B, CCDC141, CDC73, DUSP6, ESR1, ESR2, PATL2, PSMC3IP, SEMA3A, WT1 and WNT4). Moreover, we report the distribution of nine Neanderthal variants in genes associated with a human fertility phenotype found in extant human populations, one of which has been associated with polycystic ovarian syndrome and primary congenital glaucoma. LIMITATIONS, REASONS FOR CAUTION: While analyzing archaic DNA, stringent filtering criteria were adopted to screen for deleterious variants in Neanderthals and Denisovans, which could result in missing a number of variants. Such restraints preserve the potential for detection of additional deleterious variants in reproductive proteins in extinct hominidae. WIDER IMPLICATIONS OF THE FINDINGS: This study provides a comprehensive overview of putatively deleterious variants in extant human populations and extinct individuals occurring in 1734 protein-coding genes controlling reproduction and provides the fundaments for future functional studies of extinct variants in human reproduction. STUDY FUNDING/COMPETING INTEREST(S): This study was supported by the Department of Biological Science and by the Office of Research and Sponsored Programs at the University of Tulsa (Faculty Research Grant and Faculty Research Summer Fellowship) to M.A. and the University of Tulsa, Tulsa Undergraduate Research Challenge (TURC) program to E.L.; no conflict of interest to declare. TRIAL REGISTRATION NUMBER: N/A. CI - © The Author(s) 2021. Published by Oxford University Press on behalf of European Society of Human Reproduction and Embryology. All rights reserved. For permissions, please email: journals.permissions@oup.com. FAU - Greer, Cory AU - Greer C AD - Department of Biological Science, College of Engineering and Natural Sciences, University of Tulsa, Tulsa, OK 74104, USA. FAU - Bhakta, Hanisha AU - Bhakta H AD - Department of Biological Science, College of Engineering and Natural Sciences, University of Tulsa, Tulsa, OK 74104, USA. FAU - Ghanem, Lillian AU - Ghanem L AD - Department of Biological Science, College of Engineering and Natural Sciences, University of Tulsa, Tulsa, OK 74104, USA. FAU - Refai, Fares AU - Refai F AD - Department of Biological Science, College of Engineering and Natural Sciences, University of Tulsa, Tulsa, OK 74104, USA. FAU - Linn, Emma AU - Linn E AD - Department of Biological Science, College of Engineering and Natural Sciences, University of Tulsa, Tulsa, OK 74104, USA. FAU - Avella, Matteo AU - Avella M AD - Department of Biological Science, College of Engineering and Natural Sciences, University of Tulsa, Tulsa, OK 74104, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Hum Reprod JT - Human reproduction (Oxford, England) JID - 8701199 RN - 0 (Nuclear Proteins) RN - 0 (PSMC3IP protein, human) RN - 0 (Trans-Activators) SB - IM MH - Animals MH - Europe MH - Genome, Human MH - *Hominidae/genetics MH - Humans MH - Male MH - *Neanderthals/genetics MH - Nuclear Proteins MH - Reproduction/genetics MH - Trans-Activators OTO - NOTNLM OT - Denisovan OT - Neanderthal OT - development OT - fertilization OT - oogenesis OT - ovary OT - spermatogenesis OT - testis EDAT- 2021/01/09 06:00 MHDA- 2021/05/29 06:00 CRDT- 2021/01/08 17:09 PHST- 2020/08/08 00:00 [received] PHST- 2020/11/12 00:00 [revised] PHST- 2021/01/09 06:00 [pubmed] PHST- 2021/05/29 06:00 [medline] PHST- 2021/01/08 17:09 [entrez] AID - 6071469 [pii] AID - 10.1093/humrep/deaa347 [doi] PST - ppublish SO - Hum Reprod. 2021 Feb 18;36(3):734-755. doi: 10.1093/humrep/deaa347. PMID- 33495362 OWN - NLM STAT- MEDLINE DCOM- 20210623 LR - 20221005 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 118 IP - 6 DP - 2021 Feb 9 TI - Dog domestication and the dual dispersal of people and dogs into the Americas. LID - 10.1073/pnas.2010083118 [doi] LID - e2010083118 AB - Advances in the isolation and sequencing of ancient DNA have begun to reveal the population histories of both people and dogs. Over the last 10,000 y, the genetic signatures of ancient dog remains have been linked with known human dispersals in regions such as the Arctic and the remote Pacific. It is suspected, however, that this relationship has a much deeper antiquity, and that the tandem movement of people and dogs may have begun soon after the domestication of the dog from a gray wolf ancestor in the late Pleistocene. Here, by comparing population genetic results of humans and dogs from Siberia, Beringia, and North America, we show that there is a close correlation in the movement and divergences of their respective lineages. This evidence places constraints on when and where dog domestication took place. Most significantly, it suggests that dogs were domesticated in Siberia by ∼23,000 y ago, possibly while both people and wolves were isolated during the harsh climate of the Last Glacial Maximum. Dogs then accompanied the first people into the Americas and traveled with them as humans rapidly dispersed into the continent beginning ∼15,000 y ago. FAU - Perri, Angela R AU - Perri AR AUID- ORCID: 0000-0002-4349-1060 AD - Department of Archaeology, Durham University, Durham DH1 3LE, United Kingdom; angela.r.perri@durham.ac.uk dmeltzer@smu.edu kelsey_witt_dillon@brown.edu. FAU - Feuerborn, Tatiana R AU - Feuerborn TR AUID- ORCID: 0000-0003-1610-3402 AD - GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark. AD - The Qimmeq Project, University of Greenland, 3905 Nuussuaq, Greenland. AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 114 19 Stockholm, Sweden. AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden. AD - Centre for Palaeogenetics, 114 18 Stockholm, Sweden. FAU - Frantz, Laurent A F AU - Frantz LAF AD - Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich D-80539, Germany. AD - School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom. FAU - Larson, Greger AU - Larson G AUID- ORCID: 0000-0002-4092-0392 AD - The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom. FAU - Malhi, Ripan S AU - Malhi RS AUID- ORCID: 0000-0002-1484-0292 AD - Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801. AD - Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801. FAU - Meltzer, David J AU - Meltzer DJ AUID- ORCID: 0000-0001-8084-9802 AD - Department of Anthropology, Southern Methodist University, Dallas, TX 75205; angela.r.perri@durham.ac.uk dmeltzer@smu.edu kelsey_witt_dillon@brown.edu. AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Witt, Kelsey E AU - Witt KE AUID- ORCID: 0000-0002-3242-2123 AD - Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912; angela.r.perri@durham.ac.uk dmeltzer@smu.edu kelsey_witt_dillon@brown.edu. AD - Center for Computational and Molecular Biology, Brown University, Providence, RI 02912. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - R35 GM128946/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Americas MH - Animal Migration/*physiology MH - Animals MH - Dogs/*physiology MH - *Domestication MH - Geography MH - Haplotypes/genetics MH - *Human Migration MH - Humans MH - Phylogeny MH - Siberia MH - Time Factors PMC - PMC8017920 OTO - NOTNLM OT - archaeology OT - dogs OT - domestication OT - genetics OT - peopling of the Americas COIS- The authors declare no competing interest. EDAT- 2021/01/27 06:00 MHDA- 2021/06/24 06:00 PMCR- 2021/07/25 CRDT- 2021/01/26 05:38 PHST- 2021/01/26 05:38 [entrez] PHST- 2021/01/27 06:00 [pubmed] PHST- 2021/06/24 06:00 [medline] PHST- 2021/07/25 00:00 [pmc-release] AID - 2010083118 [pii] AID - 202010083 [pii] AID - 10.1073/pnas.2010083118 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):e2010083118. doi: 10.1073/pnas.2010083118. PMID- 33547403 OWN - NLM STAT- MEDLINE DCOM- 20210817 LR - 20210817 IS - 2399-3642 (Electronic) IS - 2399-3642 (Linking) VI - 4 IP - 1 DP - 2021 Feb 5 TI - Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt. PG - 169 LID - 10.1038/s42003-021-01689-y [doi] LID - 169 AB - A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals. FAU - Rampelli, Simone AU - Rampelli S AUID- ORCID: 0000-0002-5655-6695 AD - Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy. FAU - Turroni, Silvia AU - Turroni S AUID- ORCID: 0000-0003-2345-9482 AD - Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy. FAU - Mallol, Carolina AU - Mallol C AD - Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain. AD - Archaeological Micromorphology and Biomarker Research Lab, University of La Laguna, Avenida Astrofísico Francisco Sánchez 2, La Laguna, Tenerife, Spain. AD - ICArEHB - Interdisciplinary Center for Archaeology and the Evolution of Human Behaviour, Universidade do Algarve, Campus de Gambelas, Edificio 1, Faro, Portugal. FAU - Hernandez, Cristo AU - Hernandez C AD - Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain. FAU - Galván, Bertila AU - Galván B AD - Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain. FAU - Sistiaga, Ainara AU - Sistiaga A AD - Earth, Atmospheric and Planetary Sciences Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, USA. AD - GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Oester Voldgade 5-7, Copenhagen, Denmark. FAU - Biagi, Elena AU - Biagi E AD - Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy. FAU - Astolfi, Annalisa AU - Astolfi A AD - "Giorgio Prodi" Cancer Research Center, University of Bologna, Via Massarenti 11, Bologna, Italy. AD - Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Via Fossato di Mortara 70, Ferrara, Italy. FAU - Brigidi, Patrizia AU - Brigidi P AD - Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, Bologna, Italy. FAU - Benazzi, Stefano AU - Benazzi S AD - Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, Ravenna, Italy. AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. FAU - Lewis, Cecil M Jr AU - Lewis CM Jr AD - Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, USA. AD - Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA. FAU - Warinner, Christina AU - Warinner C AUID- ORCID: 0000-0002-4528-5877 AD - Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, Jena, Germany. FAU - Hofman, Courtney A AU - Hofman CA AUID- ORCID: 0000-0002-6808-3370 AD - Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, USA. AD - Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA. FAU - Schnorr, Stephanie L AU - Schnorr SL AUID- ORCID: 0000-0002-3742-0565 AD - Konrad Lorenz Institute for Evolution and Cognition Research, Martinstraße 12, Klosterneuburg, Austria. stephanie.schnorr@kli.ac.at. AD - Department of Anthropology, University of Nevada, 4505S. Maryland Pkwy, Las Vegas, NV, USA. stephanie.schnorr@kli.ac.at. FAU - Candela, Marco AU - Candela M AUID- ORCID: 0000-0001-7420-790X AD - Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy. marco.candela@unibo.it. LA - eng GR - R01 GM089886/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20210205 PL - England TA - Commun Biol JT - Communications biology JID - 101719179 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Archaeology MH - DNA, Ancient/isolation & purification MH - Ecosystem MH - Feces/*microbiology MH - Fossils/microbiology MH - *Gastrointestinal Microbiome MH - Geologic Sediments/analysis/microbiology MH - History, Ancient MH - Humans MH - Metagenomics MH - Neanderthals/*microbiology MH - Sequence Analysis, DNA MH - Spain PMC - PMC7864912 COIS- The authors declare no competing interests. EDAT- 2021/02/07 06:00 MHDA- 2021/08/18 06:00 PMCR- 2021/02/05 CRDT- 2021/02/06 05:41 PHST- 2020/04/19 00:00 [received] PHST- 2021/01/05 00:00 [accepted] PHST- 2021/02/06 05:41 [entrez] PHST- 2021/02/07 06:00 [pubmed] PHST- 2021/08/18 06:00 [medline] PHST- 2021/02/05 00:00 [pmc-release] AID - 10.1038/s42003-021-01689-y [pii] AID - 1689 [pii] AID - 10.1038/s42003-021-01689-y [doi] PST - epublish SO - Commun Biol. 2021 Feb 5;4(1):169. doi: 10.1038/s42003-021-01689-y. PMID- 33340848 OWN - NLM STAT- MEDLINE DCOM- 20210608 LR - 20210608 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 319 DP - 2021 Feb TI - Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA. PG - 110638 LID - S0379-0738(20)30500-4 [pii] LID - 10.1016/j.forsciint.2020.110638 [doi] AB - Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites. CI - Copyright © 2020 Elsevier B.V. All rights reserved. FAU - Senovska, Anna AU - Senovska A AD - Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 62500, Czech Republic. Electronic address: anna.senovska@gmail.com. FAU - Drozdova, Eva AU - Drozdova E AD - Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 62500, Czech Republic. FAU - Vaculik, Ondrej AU - Vaculik O AD - Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 62500, Czech Republic. FAU - Pardy, Filip AU - Pardy F AD - CF Genomics CEITEC Masaryk University, Kamenice 753/5, Brno, 62500, Czech Republic. FAU - Brzobohata, Kristyna AU - Brzobohata K AD - Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 62500, Czech Republic. FAU - Fialova, Dana AU - Fialova D AD - Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 62500, Czech Republic. FAU - Smerda, Jaromir AU - Smerda J AD - Masaryk Museum, Zamecke Nam. 27/9, Hodonin, 69501, Czech Republic. FAU - Kos, Petr AU - Kos P AD - Institute for Archaeological Heritage, Kaloudova 1321/30, Brno, 61400, Czech Republic. LA - eng PT - Journal Article DEP - 20201201 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Cost-Benefit Analysis MH - *DNA, Ancient MH - DNA, Mitochondrial/*genetics MH - Forensic Genetics/methods MH - *Genome, Mitochondrial MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Polymerase Chain Reaction OTO - NOTNLM OT - Ancient DNA OT - Capture OT - Enrichment OT - Mitochondrial DNA OT - Mitogenome OT - Sequencing COIS- Declaration of Competing Interest The authors report no declarations of interest. EDAT- 2020/12/20 06:00 MHDA- 2021/06/09 06:00 CRDT- 2020/12/19 20:11 PHST- 2020/06/10 00:00 [received] PHST- 2020/10/28 00:00 [revised] PHST- 2020/11/29 00:00 [accepted] PHST- 2020/12/20 06:00 [pubmed] PHST- 2021/06/09 06:00 [medline] PHST- 2020/12/19 20:11 [entrez] AID - S0379-0738(20)30500-4 [pii] AID - 10.1016/j.forsciint.2020.110638 [doi] PST - ppublish SO - Forensic Sci Int. 2021 Feb;319:110638. doi: 10.1016/j.forsciint.2020.110638. Epub 2020 Dec 1. PMID- 33241578 OWN - NLM STAT- MEDLINE DCOM- 20210318 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 174 IP - 2 DP - 2021 Feb TI - Post-last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans. PG - 363-374 LID - 10.1002/ajpa.24173 [doi] AB - OBJECTIVES: Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins. MATERIALS AND METHODS: Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software. RESULTS: C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves. DISCUSSION: We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM. CI - © 2020 Wiley Periodicals LLC. FAU - Sun, Jin AU - Sun J AD - Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China. AD - Xingyi Normal University for Nationalities, Xingyi, China. FAU - Ma, Peng-Cheng AU - Ma PC AD - School of Life Sciences, Jilin University, Changchun, China. FAU - Cheng, Hui-Zhen AU - Cheng HZ AUID- ORCID: 0000-0002-3965-9895 AD - Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China. FAU - Wang, Chi-Zao AU - Wang CZ AD - Department of Radiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China. FAU - Li, Yong-Lan AU - Li YL AD - School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, China. FAU - Cui, Yin-Qiu AU - Cui YQ AUID- ORCID: 0000-0003-3702-5773 AD - School of Life Sciences, Jilin University, Changchun, China. FAU - Yao, Hong-Bin AU - Yao HB AD - Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, China. FAU - Wen, Shao-Qing AU - Wen SQ AD - Institute of Archaeological Science, Fudan University, Shanghai, China. AD - B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China. FAU - Wei, Lan-Hai AU - Wei LH AUID- ORCID: 0000-0003-3119-7400 AD - Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China. AD - B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201125 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 SB - IM MH - Anthropology, Physical MH - Asia, Northern MH - *Asian People/classification/genetics/history MH - Chromosomes, Human, Y/*genetics MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Male MH - North America MH - Phylogeny MH - *American Indian or Alaska Native/classification/genetics/history OTO - NOTNLM OT - C2a-L1373 OT - Native Americans OT - last glacial maximum OT - northern Asia EDAT- 2020/11/27 06:00 MHDA- 2021/03/19 06:00 CRDT- 2020/11/26 05:51 PHST- 2020/03/08 00:00 [received] PHST- 2020/10/10 00:00 [revised] PHST- 2020/11/04 00:00 [accepted] PHST- 2020/11/27 06:00 [pubmed] PHST- 2021/03/19 06:00 [medline] PHST- 2020/11/26 05:51 [entrez] AID - 10.1002/ajpa.24173 [doi] PST - ppublish SO - Am J Phys Anthropol. 2021 Feb;174(2):363-374. doi: 10.1002/ajpa.24173. Epub 2020 Nov 25. PMID- 33226710 OWN - NLM STAT- MEDLINE DCOM- 20210421 LR - 20210421 IS - 1600-0757 (Electronic) IS - 0906-6713 (Linking) VI - 85 IP - 1 DP - 2021 Feb TI - The evolutionary history of the human oral microbiota and its implications for modern health. PG - 90-100 LID - 10.1111/prd.12353 [doi] AB - Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future. CI - © 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd. FAU - Weyrich, Laura S AU - Weyrich LS AD - Department of Anthropology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA. AD - School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. LA - eng PT - Journal Article PT - Review DEP - 20201123 PL - Denmark TA - Periodontol 2000 JT - Periodontology 2000 JID - 9313276 MH - Diet MH - Humans MH - *Microbiota/genetics MH - *Mouth Diseases MH - Oral Health OTO - NOTNLM OT - Industrialization OT - Neanderthal OT - evolution OT - health OT - oral microbiome OT - oral microbiota EDAT- 2020/11/24 06:00 MHDA- 2021/04/22 06:00 CRDT- 2020/11/23 12:13 PHST- 2020/11/24 06:00 [pubmed] PHST- 2021/04/22 06:00 [medline] PHST- 2020/11/23 12:13 [entrez] AID - 10.1111/prd.12353 [doi] PST - ppublish SO - Periodontol 2000. 2021 Feb;85(1):90-100. doi: 10.1111/prd.12353. Epub 2020 Nov 23. PMID- 33218283 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20211025 IS - 2158-0022 (Electronic) IS - 2158-0014 (Print) IS - 2158-0014 (Linking) VI - 11 IP - 1 DP - 2021 Feb TI - Neanderthal-Derived Genetic Variation is Associated with Functional Connectivity in the Brains of Living Humans. PG - 38-44 LID - 10.1089/brain.2020.0809 [doi] AB - Aim: To determine whether Neanderthal-derived genetic variation relates to functional connectivity patterns in the brains of living modern humans. Introduction: Nearly 50,000 years ago, Neanderthals interbred with ancestors of modern humans, imparting a genetic legacy that lives on today. The vestiges of this Neanderthal-derived genetic variation have been previously shown to be enriched in genes coding for neurogenesis and myelination and to alter skull shape and brain structure in living people. Materials and Methods: Using two independent cohorts totaling 553 healthy individuals, we employed multivariate distance matrix regression (MDMR) to determine whether any brain areas exhibited whole-brain functional connectivity patterns that significantly related to the degree of Neanderthal introgression. Identified clusters were then used as regions of interest in follow-up seed-based functional connectivity analyses to determine the connectivity patterns driving the relationships. Results: The MDMR analysis revealed that the percentage of Neanderthal-originating polymorphisms was significantly associated with the functional connectivity patterns of an area of the intraparietal sulcus (IPS) that was nearly identical in both cohorts. Using these IPS clusters as regions of interest in seed-based connectivity analyses, we found, again in both cohorts, that individuals with a higher proportion of Neanderthal-derived genetic variation showed increased IPS functional connectivity with visual processing regions, but decreased IPS connectivity with regions underlying social cognition. Conclusions: These findings demonstrate that the remnants of Neanderthal admixture continue to influence human brain function today, in ways that are consistent with anthropological conceptualizations of Neanderthal phenotypes, including the possibility that Neanderthals may have depended upon visual processing capabilities at the expense of social cognition, and this may have contributed to the extinction of this species through reduced cultural maintenance and inability to cope with fluctuating resources. This and other studies capitalizing on the emerging science surrounding ancient DNA provide a window through which to view an ancient lineage long past. FAU - Gregory, Michael D AU - Gregory MD AD - Section on Integrative Neuroimaging and Clinical and Translational Neurosciences Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA. FAU - Kippenhan, J Shane AU - Kippenhan JS AD - Section on Integrative Neuroimaging and Clinical and Translational Neurosciences Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA. FAU - Kohn, Philip AU - Kohn P AD - Section on Integrative Neuroimaging and Clinical and Translational Neurosciences Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA. FAU - Eisenberg, Daniel P AU - Eisenberg DP AD - Section on Integrative Neuroimaging and Clinical and Translational Neurosciences Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA. FAU - Callicott, Joseph H AU - Callicott JH AD - Psychosis and Cognitive Studies Section, Clinical and Translational Neurosciences Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA. FAU - Kolachana, Bhaskar AU - Kolachana B AD - Human Brain Collection Core, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA. FAU - Berman, Karen F AU - Berman KF AD - Section on Integrative Neuroimaging and Clinical and Translational Neurosciences Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA. AD - Psychosis and Cognitive Studies Section, Clinical and Translational Neurosciences Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA. LA - eng GR - ZIA MH002942/ImNIH/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't DEP - 20201229 PL - United States TA - Brain Connect JT - Brain connectivity JID - 101550313 SB - IM MH - Animals MH - Brain MH - Genetic Variation/genetics MH - Humans MH - Magnetic Resonance Imaging MH - *Neanderthals/genetics PMC - PMC7891204 OTO - NOTNLM OT - MDMR OT - Neanderthal OT - admixture OT - brain networks OT - intraparietal sulcus OT - introgression COIS- No competing financial interests exist. EDAT- 2020/11/22 06:00 MHDA- 2021/10/26 06:00 PMCR- 2022/02/01 CRDT- 2020/11/21 05:21 PHST- 2020/11/22 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] PHST- 2020/11/21 05:21 [entrez] PHST- 2022/02/01 00:00 [pmc-release] AID - 10.1089/brain.2020.0809 [pii] AID - 10.1089/brain.2020.0809 [doi] PST - ppublish SO - Brain Connect. 2021 Feb;11(1):38-44. doi: 10.1089/brain.2020.0809. Epub 2020 Dec 29. PMID- 32666166 OWN - NLM STAT- MEDLINE DCOM- 20210215 LR - 20221207 IS - 1432-1203 (Electronic) IS - 0340-6717 (Print) IS - 0340-6717 (Linking) VI - 140 IP - 2 DP - 2021 Feb TI - A Southeast Asian origin for present-day non-African human Y chromosomes. PG - 299-307 LID - 10.1007/s00439-020-02204-9 [doi] AB - The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000-70,000 years ago, followed by mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. Here, we show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 50,000-55,000 years ago of all known surviving non-African male lineages (apart from recent migrants). This observation contrasts with the expectation of a West Eurasian origin predicted by a simple model of expansion from a source near Africa, and can be interpreted as resulting from extensive genetic drift in the initial population or replacement of early western Y lineages from the east, thus informing and constraining models of the initial expansion. FAU - Hallast, Pille AU - Hallast P AUID- ORCID: 0000-0002-0588-3987 AD - Institute of Biomedicine and Translational Medicine, University of Tartu, 50411, Tartu, Estonia. pille.hallast@ut.ee. AD - Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. pille.hallast@ut.ee. FAU - Agdzhoyan, Anastasia AU - Agdzhoyan A AD - Vavilov Institute of General Genetics, Moscow, 119991, Russia. AD - Research Centre for Medical Genetics, Moscow, 115522, Russia. FAU - Balanovsky, Oleg AU - Balanovsky O AD - Vavilov Institute of General Genetics, Moscow, 119991, Russia. AD - Research Centre for Medical Genetics, Moscow, 115522, Russia. AD - Biobank of North Eurasia, Moscow, 115201, Russia. FAU - Xue, Yali AU - Xue Y AD - Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. FAU - Tyler-Smith, Chris AU - Tyler-Smith C AD - Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. cts@sanger.ac.uk. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - PUT1036/Eesti Teadusagentuur/ GR - 098051/WT_/Wellcome Trust/United Kingdom PT - Journal Article DEP - 20200714 PL - Germany TA - Hum Genet JT - Human genetics JID - 7613873 RN - 9007-49-2 (DNA) SB - IM MH - Africa MH - Asian People/*genetics MH - Chromosomes, Human, Y/*genetics MH - DNA/genetics MH - Emigration and Immigration MH - Genetics, Population/methods MH - Genome, Human/genetics MH - Haplotypes/genetics MH - Humans MH - Male MH - Phylogeny MH - Phylogeography/methods PMC - PMC7864842 COIS- The authors declare no competing or conflicts of interests. EDAT- 2020/07/16 06:00 MHDA- 2021/02/16 06:00 PMCR- 2020/07/14 CRDT- 2020/07/16 06:00 PHST- 2020/06/02 00:00 [received] PHST- 2020/07/02 00:00 [accepted] PHST- 2020/07/16 06:00 [pubmed] PHST- 2021/02/16 06:00 [medline] PHST- 2020/07/16 06:00 [entrez] PHST- 2020/07/14 00:00 [pmc-release] AID - 10.1007/s00439-020-02204-9 [pii] AID - 2204 [pii] AID - 10.1007/s00439-020-02204-9 [doi] PST - ppublish SO - Hum Genet. 2021 Feb;140(2):299-307. doi: 10.1007/s00439-020-02204-9. Epub 2020 Jul 14. PMID- 33500403 OWN - NLM STAT- MEDLINE DCOM- 20210205 LR - 20220721 IS - 2052-4463 (Electronic) IS - 2052-4463 (Linking) VI - 8 IP - 1 DP - 2021 Jan 26 TI - Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. PG - 31 LID - 10.1038/s41597-021-00816-y [doi] LID - 31 AB - Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833 ) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies. FAU - Fellows Yates, James A AU - Fellows Yates JA AUID- ORCID: 0000-0001-5585-6277 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. fellows@shh.mpg.de. AD - Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, München, 80539, Germany. fellows@shh.mpg.de. FAU - Andrades Valtueña, Aida AU - Andrades Valtueña A AUID- ORCID: 0000-0002-1737-2228 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. FAU - Vågene, Åshild J AU - Vågene ÅJ AUID- ORCID: 0000-0002-7478-8297 AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1350, Denmark. FAU - Cribdon, Becky AU - Cribdon B AUID- ORCID: 0000-0002-3308-0065 AD - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom. FAU - Velsko, Irina M AU - Velsko IM AUID- ORCID: 0000-0001-9810-9917 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. FAU - Borry, Maxime AU - Borry M AUID- ORCID: 0000-0001-9140-7559 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. FAU - Bravo-Lopez, Miriam J AU - Bravo-Lopez MJ AUID- ORCID: 0000-0002-9627-617X AD - International Laboratory for Human Genome Research, National Autonomous University of Mexico, Queretaro, 76230, Mexico. FAU - Fernandez-Guerra, Antonio AU - Fernandez-Guerra A AUID- ORCID: 0000-0002-8679-490X AD - Section for GeoGenetics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1350, Denmark. AD - Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany. FAU - Green, Eleanor J AU - Green EJ AUID- ORCID: 0000-0001-9325-0524 AD - BioArCh, Department of Archaeology, University of York, York, YO10 5DD, United Kingdom. AD - Department of Earth Sciences, Natural History Museum, London, SW7 5BD, United Kingdom. FAU - Ramachandran, Shreya L AU - Ramachandran SL AUID- ORCID: 0000-0001-6760-5053 AD - Human Genetics, University of Chicago, Chicago, IL, 60637, USA. FAU - Heintzman, Peter D AU - Heintzman PD AUID- ORCID: 0000-0002-6449-0219 AD - The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, 9037, Norway. FAU - Spyrou, Maria A AU - Spyrou MA AUID- ORCID: 0000-0002-3615-3936 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. FAU - Hübner, Alexander AU - Hübner A AUID- ORCID: 0000-0003-3572-9996 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. FAU - Gancz, Abigail S AU - Gancz AS AD - Department of Anthropology, Pennsylvania State University, Pennsylvania, PA, 16802, USA. FAU - Hider, Jessica AU - Hider J AUID- ORCID: 0000-0003-3437-7351 AD - Department of Anthropology, McMaster University, Hamilton, L8S4L9, Canada. AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, L8S4L10, Canada. FAU - Allshouse, Aurora F AU - Allshouse AF AD - Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA. FAU - Zaro, Valentina AU - Zaro V AUID- ORCID: 0000-0002-2902-225X AD - Department of Biology, Università degli Studi di Firenze, Florence, 50122, Italy. FAU - Warinner, Christina AU - Warinner C AUID- ORCID: 0000-0002-4528-5877 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. warinner@shh.mpg.de. AD - Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA. warinner@shh.mpg.de. LA - eng GR - 208934/Z/17/Z/Wellcome Trust (Wellcome)/International GR - EXC 2051-Project-ID 390713860/Deutsche Forschungsgemeinschaft (German Research Foundation)/International GR - T32 GM007197/GM/NIGMS NIH HHS/United States GR - DGE1255832/National Science Foundation (NSF)/International GR - ERC-2014-ADG 670518/EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/International GR - IA201219 PAPIIT-DGAPA- UNAM/Universidad Nacional Autónoma de México (National Autonomous University of Mexico)/International GR - AH/N005015/1/RCUK | Arts and Humanities Research Council (AHRC)/International PT - Dataset PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20210126 PL - England TA - Sci Data JT - Scientific data JID - 101640192 SB - IM MH - *Databases, Genetic MH - Humans MH - Metadata MH - *Metagenome MH - *Metagenomics MH - Publications PMC - PMC7838265 COIS- The authors declare no competing interests. EDAT- 2021/01/28 06:00 MHDA- 2021/02/07 06:00 PMCR- 2021/01/26 CRDT- 2021/01/27 05:45 PHST- 2020/09/18 00:00 [received] PHST- 2020/12/13 00:00 [accepted] PHST- 2021/01/27 05:45 [entrez] PHST- 2021/01/28 06:00 [pubmed] PHST- 2021/02/07 06:00 [medline] PHST- 2021/01/26 00:00 [pmc-release] AID - 10.1038/s41597-021-00816-y [pii] AID - 816 [pii] AID - 10.1038/s41597-021-00816-y [doi] PST - epublish SO - Sci Data. 2021 Jan 26;8(1):31. doi: 10.1038/s41597-021-00816-y. PMID- 33514313 OWN - NLM STAT- MEDLINE DCOM- 20210423 LR - 20210423 IS - 2730-7182 (Electronic) IS - 2730-7182 (Linking) VI - 21 IP - 1 DP - 2021 Jan 23 TI - Ancient mitochondrial DNA connects house mice in the British Isles to trade across Europe over three millennia. PG - 9 LID - 10.1186/s12862-021-01746-4 [doi] LID - 9 AB - BACKGROUND: The earliest records in Britain for the western European house mouse (Mus musculus domesticus) date from the Late Bronze Age. The arrival of this commensal species in Britain is thought to be related to human transport and trade with continental Europe. In order to study this arrival, we collected a total of 16 ancient mouse mandibulae from four early British archaeological sites, ranging from the Late Bronze Age to the Roman period. RESULTS: From these, we obtained ancient mitochondrial DNA (mtDNA) house mouse sequences from eight house mice from two of the sites dating from the Late Bronze to Middle Iron Age. We also obtained five ancient mtDNA wood mouse (Apodemus spp.) sequences from all four sites. The ancient house mouse sequences found in this study were from haplogroups E (N = 6) and D (N = 2). Modern British house mouse mtDNA sequences are primarily characterised by haplogroups E and F and, much less commonly, haplogroup D. CONCLUSIONS: The presence of haplogroups D and E in our samples and the dating of the archaeological sites provide evidence of an early house mouse colonisation that may relate to Late Bronze Age/Iron Age trade and/or human expansion. Our results confirm the hypothesis, based on zooarchaeological evidence and modern mtDNA predictions, that house mice, with haplogroups D and E, were established in Britain by the Iron Age and, in the case of haplogroup E, possibly as early as the Late Bronze Age. FAU - García-Rodríguez, Oxala AU - García-Rodríguez O AUID- ORCID: 0000-0003-3211-3790 AD - Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK. oxalagar@gmail.com. FAU - Hardouin, Emilie A AU - Hardouin EA AD - Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK. FAU - Hambleton, Ellen AU - Hambleton E AD - Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK. FAU - Monteith, Jonathan AU - Monteith J AD - Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK. FAU - Randall, Clare AU - Randall C AD - Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK. FAU - Richards, Martin B AU - Richards MB AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK. FAU - Edwards, Ceiridwen J AU - Edwards CJ AD - Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK. FAU - Stewart, John R AU - Stewart JR AD - Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK. LA - eng PT - Journal Article DEP - 20210123 PL - England TA - BMC Ecol Evol JT - BMC ecology and evolution JID - 101775613 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - *DNA, Ancient MH - *DNA, Mitochondrial/genetics MH - Europe MH - Humans MH - Mice MH - Mitochondria MH - United Kingdom PMC - PMC7853306 OTO - NOTNLM OT - Ancient DNA OT - Britain OT - House mouse OT - Mitochondrial DNA OT - Mus musculus OT - Phylogeography COIS- The authors declare that they have no competing interests. EDAT- 2021/01/31 06:00 MHDA- 2021/04/24 06:00 PMCR- 2021/01/23 CRDT- 2021/01/30 05:22 PHST- 2020/08/25 00:00 [received] PHST- 2021/01/13 00:00 [accepted] PHST- 2021/01/30 05:22 [entrez] PHST- 2021/01/31 06:00 [pubmed] PHST- 2021/04/24 06:00 [medline] PHST- 2021/01/23 00:00 [pmc-release] AID - 10.1186/s12862-021-01746-4 [pii] AID - 1746 [pii] AID - 10.1186/s12862-021-01746-4 [doi] PST - epublish SO - BMC Ecol Evol. 2021 Jan 23;21(1):9. doi: 10.1186/s12862-021-01746-4. PMID- 33499220 OWN - NLM STAT- MEDLINE DCOM- 20210728 LR - 20210728 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 12 IP - 2 DP - 2021 Jan 22 TI - Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age. LID - 10.3390/genes12020146 [doi] LID - 146 AB - The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille's overall increased gain of DNA when enough tissue is available and Dabney's improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications. FAU - Xavier, Catarina AU - Xavier C AUID- ORCID: 0000-0003-3522-1631 AD - Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria. FAU - Eduardoff, Mayra AU - Eduardoff M AUID- ORCID: 0000-0002-0974-0609 AD - Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria. FAU - Bertoglio, Barbara AU - Bertoglio B AD - Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, 27100 Pavia, Italy. AD - LABANOF, Laboratory of Forensic Anthropology and Odontology, Department of Biomedical Sciences for Health, Section of Legal Medicine, University of Milan, 20133 Milan, Italy. FAU - Amory, Christina AU - Amory C AD - Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria. FAU - Berger, Cordula AU - Berger C AD - Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria. FAU - Casas-Vargas, Andrea AU - Casas-Vargas A AD - Grupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, Bogotá 11001, Colombia. FAU - Pallua, Johannes AU - Pallua J AD - Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria. AD - University Hospital for Orthopedics and Traumatology, Medical University of Innsbruck, 6020 Innsbruck, Austria. FAU - Parson, Walther AU - Parson W AUID- ORCID: 0000-0002-5692-2392 AD - Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria. AD - Forensic Science Program, The Pennsylvania State University, State College, PA 16802, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20210122 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Age Determination by Skeleton/*methods MH - Age Factors MH - *Bone and Bones/metabolism MH - *DNA, Ancient MH - DNA, Mitochondrial MH - Forensic Genetics/*methods MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Microsatellite Repeats MH - Polymorphism, Single Nucleotide MH - Real-Time Polymerase Chain Reaction MH - Sequence Analysis, DNA PMC - PMC7911526 OTO - NOTNLM OT - DNA quantification OT - ForenSeq OT - Ion S5 sequencing OT - MiSeq FGx OT - SNP sequencing OT - STR typing and sequencing OT - VISAGE Basic Tool OT - bone DNA extraction OT - mtDNA sequencing COIS- The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. EDAT- 2021/01/28 06:00 MHDA- 2021/07/29 06:00 PMCR- 2021/01/22 CRDT- 2021/01/27 01:08 PHST- 2020/12/16 00:00 [received] PHST- 2021/01/14 00:00 [revised] PHST- 2021/01/19 00:00 [accepted] PHST- 2021/01/27 01:08 [entrez] PHST- 2021/01/28 06:00 [pubmed] PHST- 2021/07/29 06:00 [medline] PHST- 2021/01/22 00:00 [pmc-release] AID - genes12020146 [pii] AID - genes-12-00146 [pii] AID - 10.3390/genes12020146 [doi] PST - epublish SO - Genes (Basel). 2021 Jan 22;12(2):146. doi: 10.3390/genes12020146. PMID- 33250022 OWN - NLM STAT- MEDLINE DCOM- 20210913 LR - 20220119 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 376 IP - 1816 DP - 2021 Jan 18 TI - Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories. PG - 20190719 LID - 10.1098/rstb.2019.0719 [doi] LID - 20190719 AB - Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'. FAU - Loog, Liisa AU - Loog L AD - Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20201130 PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA, Ancient) SB - IM MH - *Archaeology MH - DNA, Ancient/*analysis MH - *Demography MH - *Genetic Variation MH - *Genetics, Population MH - Humans MH - *Models, Genetic MH - *Population Density PMC - PMC7741104 OTO - NOTNLM OT - ancient DNA OT - archaeology OT - demographic modelling OT - population genetics OT - population history OT - statistical modelling COIS- I declare I have no competing interests. EDAT- 2020/12/01 06:00 MHDA- 2021/09/14 06:00 PMCR- 2022/01/18 CRDT- 2020/11/30 05:25 PHST- 2020/11/30 05:25 [entrez] PHST- 2020/12/01 06:00 [pubmed] PHST- 2021/09/14 06:00 [medline] PHST- 2022/01/18 00:00 [pmc-release] AID - rstb20190719 [pii] AID - 10.1098/rstb.2019.0719 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2021 Jan 18;376(1816):20190719. doi: 10.1098/rstb.2019.0719. Epub 2020 Nov 30. PMID- 33443182 OWN - NLM STAT- MEDLINE DCOM- 20210507 LR - 20221207 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 118 IP - 1 DP - 2021 Jan 5 TI - The evolution of skin pigmentation-associated variation in West Eurasia. LID - 10.1073/pnas.2009227118 [doi] LID - e2009227118 AB - Skin pigmentation is a classic example of a polygenic trait that has experienced directional selection in humans. Genome-wide association studies have identified well over a hundred pigmentation-associated loci, and genomic scans in present-day and ancient populations have identified selective sweeps for a small number of light pigmentation-associated alleles in Europeans. It is unclear whether selection has operated on all of the genetic variation associated with skin pigmentation as opposed to just a small number of large-effect variants. Here, we address this question using ancient DNA from 1,158 individuals from West Eurasia covering a period of 40,000 y combined with genome-wide association summary statistics from the UK Biobank. We find a robust signal of directional selection in ancient West Eurasians on 170 skin pigmentation-associated variants ascertained in the UK Biobank. However, we also show that this signal is driven by a limited number of large-effect variants. Consistent with this observation, we find that a polygenic selection test in present-day populations fails to detect selection with the full set of variants. Our data allow us to disentangle the effects of admixture and selection. Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation. CI - Copyright © 2021 the Author(s). Published by PNAS. FAU - Ju, Dan AU - Ju D AUID- ORCID: 0000-0002-9614-0045 AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 danju@pennmedicine.upenn.edu mathi@pennmedicine.upenn.edu. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 danju@pennmedicine.upenn.edu mathi@pennmedicine.upenn.edu. LA - eng GR - R35 GM133708/GM/NIGMS NIH HHS/United States GR - T32 GM008216/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Alleles MH - Asia MH - Asian People/genetics MH - Biological Evolution MH - DNA, Ancient/*analysis MH - Databases, Genetic MH - Europe MH - Gene Frequency/genetics MH - Genome-Wide Association Study/methods MH - Genotype MH - Haplotypes/genetics MH - Humans MH - Multifactorial Inheritance/genetics MH - Polymorphism, Single Nucleotide/genetics MH - Selection, Genetic/*genetics MH - Skin Pigmentation/*genetics/physiology MH - White People/genetics PMC - PMC7817156 OTO - NOTNLM OT - ancient DNA OT - complex traits OT - evolution OT - polygenic selection OT - skin pigmentation COIS- The authors declare no competing interest. EDAT- 2021/01/15 06:00 MHDA- 2021/05/08 06:00 PMCR- 2020/12/21 CRDT- 2021/01/14 08:49 PHST- 2021/01/14 08:49 [entrez] PHST- 2021/01/15 06:00 [pubmed] PHST- 2021/05/08 06:00 [medline] PHST- 2020/12/21 00:00 [pmc-release] AID - 2009227118 [pii] AID - 202009227 [pii] AID - 10.1073/pnas.2009227118 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2021 Jan 5;118(1):e2009227118. doi: 10.1073/pnas.2009227118. PMID- 33443177 OWN - NLM STAT- MEDLINE DCOM- 20210430 LR - 20250130 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 118 IP - 1 DP - 2021 Jan 5 TI - Ancient DNA from Guam and the peopling of the Pacific. LID - 10.1073/pnas.2022112118 [doi] LID - e2022112118 AB - Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia. CI - Copyright © 2021 the Author(s). Published by PNAS. FAU - Pugach, Irina AU - Pugach I AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany. FAU - Hübner, Alexander AU - Hübner A AUID- ORCID: 0000-0003-3572-9996 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany. FAU - Hung, Hsiao-Chun AU - Hung HC AUID- ORCID: 0000-0001-5794-3040 AD - Department of Archaeology and Natural History, Australian National University, Canberra, ACT 2601, Australia. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany. FAU - Carson, Mike T AU - Carson MT AUID- ORCID: 0000-0003-3755-9126 AD - Micronesian Area Research Center, University of Guam, 96923 Mangilao, Guam mtcarson@triton.uog.edu stoneking@eva.mpg.de. FAU - Stoneking, Mark AU - Stoneking M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany; mtcarson@triton.uog.edu stoneking@eva.mpg.de. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Humans MH - Archaeology MH - *Chromosomes, Human, Y/genetics MH - Computer Simulation MH - *DNA, Ancient/analysis MH - *DNA, Mitochondrial/genetics MH - Genome MH - Guam MH - Haplotypes MH - History, Ancient MH - *Human Migration/history MH - Indonesia MH - Micronesia MH - New Guinea MH - Philippines MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Polynesia MH - Vanuatu MH - Pacific Island People PMC - PMC7817125 OTO - NOTNLM OT - Micronesia OT - Polynesia OT - ancient DNA OT - human settlement COIS- The authors declare no competing interest. EDAT- 2021/01/15 06:00 MHDA- 2021/05/01 06:00 PMCR- 2020/12/21 CRDT- 2021/01/14 08:49 PHST- 2021/01/14 08:49 [entrez] PHST- 2021/01/15 06:00 [pubmed] PHST- 2021/05/01 06:00 [medline] PHST- 2020/12/21 00:00 [pmc-release] AID - 2022112118 [pii] AID - 202022112 [pii] AID - 10.1073/pnas.2022112118 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2021 Jan 5;118(1):e2022112118. doi: 10.1073/pnas.2022112118. PMID- 34663498 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20211025 IS - 1557-8399 (Electronic) IS - 0065-3527 (Linking) VI - 111 DP - 2021 TI - Molecular archeology of human viruses. PG - 31-61 LID - S0065-3527(21)00020-8 [pii] LID - 10.1016/bs.aivir.2021.07.002 [doi] AB - The evolution of human-virus associations is usually reconstructed from contemporary patterns of genomic diversity. An intriguing, though still rarely implemented, alternative is to search for the genetic material of viruses in archeological and medical archive specimens to document evolution as it happened. In this chapter, we present lessons from ancient DNA research and incorporate insights from virology to explore the potential range of applications and likely limitations of archeovirological approaches. We also highlight the numerous questions archeovirology will hopefully allow us to tackle in the near future, and the main expected roadblocks to these avenues of research. CI - Copyright © 2021 Elsevier Inc. All rights reserved. FAU - Calvignac-Spencer, Sébastien AU - Calvignac-Spencer S AD - Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany. Electronic address: calvignacs@rki.de. FAU - Düx, Ariane AU - Düx A AD - Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany. FAU - Gogarten, Jan F AU - Gogarten JF AD - Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany. FAU - Patrono, Livia V AU - Patrono LV AD - Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany. LA - eng PT - Journal Article DEP - 20210811 PL - United States TA - Adv Virus Res JT - Advances in virus research JID - 0370441 SB - IM MH - *Archaeology MH - Genomics MH - Humans MH - *Viruses/genetics OTO - NOTNLM OT - Ancient DNA OT - Ancient RNA OT - Archeological specimens OT - Archeovirology OT - Paleogenomics OT - Pathology collections OT - Phylogenetics OT - Virus evolution EDAT- 2021/10/20 06:00 MHDA- 2021/10/26 06:00 CRDT- 2021/10/19 05:48 PHST- 2021/10/19 05:48 [entrez] PHST- 2021/10/20 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] AID - S0065-3527(21)00020-8 [pii] AID - 10.1016/bs.aivir.2021.07.002 [doi] PST - ppublish SO - Adv Virus Res. 2021;111:31-61. doi: 10.1016/bs.aivir.2021.07.002. Epub 2021 Aug 11. PMID- 34410642 OWN - NLM STAT- MEDLINE DCOM- 20220113 LR - 20220113 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 2327 DP - 2021 TI - A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus. PG - 93-118 LID - 10.1007/978-1-0716-1518-8_7 [doi] AB - Ancient dental calculus provides a challenging, yet unparalleled, opportunity to reconstruct ancient oral microbial communities and trace the origins of modern microbiota-associated diseases. Metagenomic analysis of ancient dental calculus using high-throughput DNA sequencing has proven itself as an effective method to accurately reconstruct microorganisms that once lived in the mouths of ancient humans. Here, we provide the strategy, methodologies, and approaches used to establish an ancient dental calculus project, from project conception, community engagement, sampling, extracting DNA, and preparing shotgun metagenomic DNA libraries for sequencing on an Illumina platform. We also discuss techniques to minimize background or contaminant DNA by monitoring and reducing contamination in calculus data sets, utilizing appropriate protective gear, and employing the use of sample decontamination strategies. In this methodology chapter, we hope to promote transparency in the ancient dental calculus research field and encourage collaboration across the ancient DNA research community. CI - © 2021. Springer Science+Business Media, LLC, part of Springer Nature. FAU - Moore, Nicole E AU - Moore NE AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, USA. FAU - Weyrich, Laura S AU - Weyrich LS AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, USA. lsw132@psu.edu. AD - School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia. lsw132@psu.edu. LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient MH - *Dental Calculus MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Metagenome MH - Metagenomics MH - Microbiota/genetics MH - Sequence Analysis, DNA OTO - NOTNLM OT - Ancient DNA OT - Bacteria OT - Dental calculus OT - Metagenomics OT - Microbiome OT - Oral microbiota EDAT- 2021/08/20 06:00 MHDA- 2022/01/14 06:00 CRDT- 2021/08/19 12:35 PHST- 2021/08/19 12:35 [entrez] PHST- 2021/08/20 06:00 [pubmed] PHST- 2022/01/14 06:00 [medline] AID - 10.1007/978-1-0716-1518-8_7 [doi] PST - ppublish SO - Methods Mol Biol. 2021;2327:93-118. doi: 10.1007/978-1-0716-1518-8_7. PMID- 33352129 OWN - NLM STAT- MEDLINE DCOM- 20210518 LR - 20250103 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 30 IP - 24 DP - 2020 Dec 21 TI - Human Migrations: Tales of the Pacific. PG - R1478-R1481 LID - S0960-9822(20)31683-3 [pii] LID - 10.1016/j.cub.2020.11.008 [doi] AB - The mode and tempo of human dispersal to the far-flung Pacific Islands has been a source of fascination for centuries. New ancient DNA data from the archipelago of Vanuatu shed light on the ancient migrations that shaped the history of human settlement in the Pacific. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Friedlaender, Jonathan S AU - Friedlaender JS AD - Department of Anthropology, Temple University, Philadelphia, PA, USA. FAU - Tucci, Serena AU - Tucci S AD - Department of Anthropology, Yale University, New Haven, CT, USA. Electronic address: serena.tucci@yale.edu. LA - eng PT - Comment PT - Journal Article PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM CON - Curr Biol. 2020 Dec 21;30(24):4846-4856.e6. doi: 10.1016/j.cub.2020.09.035. PMID: 33065004 MH - *DNA, Ancient MH - *Human Migration MH - Humans MH - Native Hawaiian or Pacific Islander MH - Pacific Islands MH - Vanuatu EDAT- 2020/12/23 06:00 MHDA- 2021/05/19 06:00 CRDT- 2020/12/22 20:08 PHST- 2020/12/22 20:08 [entrez] PHST- 2020/12/23 06:00 [pubmed] PHST- 2021/05/19 06:00 [medline] AID - S0960-9822(20)31683-3 [pii] AID - 10.1016/j.cub.2020.11.008 [doi] PST - ppublish SO - Curr Biol. 2020 Dec 21;30(24):R1478-R1481. doi: 10.1016/j.cub.2020.11.008. PMID- 33065004 OWN - NLM STAT- MEDLINE DCOM- 20210830 LR - 20241205 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 30 IP - 24 DP - 2020 Dec 21 TI - Three Phases of Ancient Migration Shaped the Ancestry of Human Populations in Vanuatu. PG - 4846-4856.e6 LID - S0960-9822(20)31366-X [pii] LID - 10.1016/j.cub.2020.09.035 [doi] AB - The archipelago of Vanuatu has been at the crossroads of human population movements in the Pacific for the past three millennia. To help address several open questions regarding the history of these movements, we generated genome-wide data for 11 ancient individuals from the island of Efate dating from its earliest settlement to the recent past, including five associated with the Chief Roi Mata's Domain World Heritage Area, and analyzed them in conjunction with 34 published ancient individuals from Vanuatu and elsewhere in Oceania, as well as present-day populations. Our results outline three distinct periods of population transformations. First, the four earliest individuals, from the Lapita-period site of Teouma, are concordant with eight previously described Lapita-associated individuals from Vanuatu and Tonga in having almost all of their ancestry from a "First Remote Oceanian" source related to East and Southeast Asians. Second, both the Papuan ancestry predominating in Vanuatu for the past 2,500 years and the smaller component of Papuan ancestry found in Polynesians can be modeled as deriving from a single source most likely originating in New Britain, suggesting that the movement of people carrying this ancestry to Remote Oceania closely followed that of the First Remote Oceanians in time and space. Third, the Chief Roi Mata's Domain individuals descend from a mixture of Vanuatu- and Polynesian-derived ancestry and are related to Polynesian-influenced communities today in central, but not southern, Vanuatu, demonstrating Polynesian genetic input in multiple groups with independent histories. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Lipson, Mark AU - Lipson M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: mlipson@hms.harvard.edu. FAU - Spriggs, Matthew AU - Spriggs M AD - School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, ACT 2601, Australia; Vanuatu National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu. Electronic address: Matthew.Spriggs@anu.edu.au. FAU - Valentin, Frederique AU - Valentin F AD - MSH Mondes, CNRS, UMR 7041, 92023 Nanterre, France. FAU - Bedford, Stuart AU - Bedford S AD - Vanuatu National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu; Department of Archaeology and Natural History, College of Asia-Pacific, The Australian National University, Canberra, ACT 2601, Australia; Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Shing, Richard AU - Shing R AD - Vanuatu National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu. FAU - Zinger, Wanda AU - Zinger W AD - Muséum national d'Histoire naturelle, UMR 7194 (HNHP), MNHN/CNRS/UPVD, Sorbonne Université, Musée de l'Homme, 75016 Paris, France. FAU - Buckley, Hallie AU - Buckley H AD - Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand. FAU - Petchey, Fiona AU - Petchey F AD - Radiocarbon Dating Laboratory, Division of Health, Engineering, Computing and Science, University of Waikato, Hamilton 3240, New Zealand; ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society and Education, James Cook University, Cairns, QLD 4878, Australia. FAU - Matanik, Richard AU - Matanik R AD - Lelema World Heritage Committee and Vanuatu Cultural Centre, Port Vila, Vanuatu. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria. Electronic address: ron.pinhasi@univie.ac.at. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20201015 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM CIN - Curr Biol. 2020 Dec 21;30(24):R1478-R1481. doi: 10.1016/j.cub.2020.11.008. PMID: 33352129 MH - Anthropology/methods MH - Body Remains MH - DNA, Ancient MH - Female MH - Haplotypes MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Male MH - *Phylogeny MH - Vanuatu PMC - PMC7755836 MID - NIHMS1637259 OTO - NOTNLM OT - Lapita OT - Oceania OT - Polynesia OT - Roi Mata OT - Vanuatu OT - ancient DNA COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2020/10/17 06:00 MHDA- 2021/08/31 06:00 PMCR- 2021/12/21 CRDT- 2020/10/16 20:09 PHST- 2020/03/30 00:00 [received] PHST- 2020/07/14 00:00 [revised] PHST- 2020/09/10 00:00 [accepted] PHST- 2020/10/17 06:00 [pubmed] PHST- 2021/08/31 06:00 [medline] PHST- 2020/10/16 20:09 [entrez] PHST- 2021/12/21 00:00 [pmc-release] AID - S0960-9822(20)31366-X [pii] AID - 10.1016/j.cub.2020.09.035 [doi] PST - ppublish SO - Curr Biol. 2020 Dec 21;30(24):4846-4856.e6. doi: 10.1016/j.cub.2020.09.035. Epub 2020 Oct 15. PMID- 32642779 OWN - NLM STAT- MEDLINE DCOM- 20210511 LR - 20210511 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 37 IP - 12 DP - 2020 Dec 16 TI - Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium. PG - 3642-3653 LID - 10.1093/molbev/msaa169 [doi] AB - Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events. CI - © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. FAU - Santiago, Enrique AU - Santiago E AD - Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain. FAU - Novo, Irene AU - Novo I AD - Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, Universidade de Vigo, Vigo, Spain. FAU - Pardiñas, Antonio F AU - Pardiñas AF AD - MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom. FAU - Saura, María AU - Saura M AD - Departamento de Mejora Genética Animal, INIA, Madrid, Spain. FAU - Wang, Jinliang AU - Wang J AD - Institute of Zoology, Zoological Society of London, London, United Kingdom. FAU - Caballero, Armando AU - Caballero A AD - Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, Universidade de Vigo, Vigo, Spain. LA - eng GR - MC_PC_17212/MRC_/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Validation Study PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 SB - IM MH - Algorithms MH - Animals MH - Computer Simulation MH - *Genetic Techniques MH - Humans MH - *Linkage Disequilibrium MH - *Models, Genetic MH - *Population Density MH - *Recombination, Genetic OTO - NOTNLM OT - SNP OT - ancient DNA OT - demography OT - effective population size OT - genetic drift EDAT- 2020/07/10 06:00 MHDA- 2021/05/12 06:00 CRDT- 2020/07/10 06:00 PHST- 2020/07/10 06:00 [pubmed] PHST- 2021/05/12 06:00 [medline] PHST- 2020/07/10 06:00 [entrez] AID - 5869049 [pii] AID - 10.1093/molbev/msaa169 [doi] PST - ppublish SO - Mol Biol Evol. 2020 Dec 16;37(12):3642-3653. doi: 10.1093/molbev/msaa169. PMID- 33299013 OWN - NLM STAT- MEDLINE DCOM- 20210504 LR - 20210504 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 10 IP - 1 DP - 2020 Dec 9 TI - Pluridisciplinary evidence for burial for the La Ferrassie 8 Neandertal child. PG - 21230 LID - 10.1038/s41598-020-77611-z [doi] LID - 21230 AB - The origin of funerary practices has important implications for the emergence of so-called modern cognitive capacities and behaviour. We provide new multidisciplinary information on the archaeological context of the La Ferrassie 8 Neandertal skeleton (grand abri of La Ferrassie, Dordogne, France), including geochronological data -(14)C and OSL-, ZooMS and ancient DNA data, geological and stratigraphic information from the surrounding context, complete taphonomic study of the skeleton and associated remains, spatial information from the 1968-1973 excavations, and new (2014) fieldwork data. Our results show that a pit was dug in a sterile sediment layer and the corpse of a two-year-old child was laid there. A hominin bone from this context, identified through Zooarchaeology by Mass Spectrometry (ZooMS) and associated with Neandertal based on its mitochondrial DNA, yielded a direct (14)C age of 41.7-40.8 ka cal BP (95%), younger than the (14)C dates of the overlying archaeopaleontological layers and the OSL age of the surrounding sediment. This age makes the bone one of the most recent directly dated Neandertals. It is consistent with the age range for the Châtelperronian in the site and in this region and represents the third association of Neandertal taxa to Initial Upper Palaeolithic lithic technocomplex in Western Europe. A detailed multidisciplinary approach, as presented here, is essential to advance understanding of Neandertal behavior, including funerary practices. FAU - Balzeau, Antoine AU - Balzeau A AD - PaleoFED Team, UMR 7194, CNRS, Département Homme et Environnement, Muséum National d'Histoire Naturelle, Musée de l'Homme, 17, Place du Trocadéro, 75016, Paris, France. abalzeau@mnhn.fr. AD - Department of African Zoology, Royal Museum for Central Africa, Tervuren, Belgium. abalzeau@mnhn.fr. FAU - Turq, Alain AU - Turq A AD - Musée National de Préhistoire, 1 Rue du Musée, 24620, Les Eyzies-de-Tayac, France. FAU - Talamo, Sahra AU - Talamo S AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. AD - Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi, 2, 40126, Bologna, Italy. FAU - Daujeard, Camille AU - Daujeard C AD - PaleoFED Team, UMR 7194, CNRS, Département Homme et Environnement, Muséum National d'Histoire Naturelle, Musée de l'Homme, 17, Place du Trocadéro, 75016, Paris, France. FAU - Guérin, Guillaume AU - Guérin G AD - UMR 5060, CNRS-Université Bordeaux Montaigne, IRAMAT-CRP2A, Maison de l'archéologie, Esplanade des Antilles, 33607, Pessac Cedex, France. AD - UMR 6118, CNRS-Univ Rennes, Géosciences Rennes, 35000, Rennes, France. FAU - Welker, Frido AU - Welker F AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Section for Evolutionary Genomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Crevecoeur, Isabelle AU - Crevecoeur I AD - Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600, Pessac, France. FAU - Fewlass, Helen AU - Fewlass H AUID- ORCID: 0000-0002-9093-3490 AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. FAU - Hublin, Jean-Jacques AU - Hublin JJ AUID- ORCID: 0000-0001-6283-8114 AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. FAU - Lahaye, Christelle AU - Lahaye C AD - UMR 5060, CNRS-Université Bordeaux Montaigne, IRAMAT-CRP2A, Maison de l'archéologie, Esplanade des Antilles, 33607, Pessac Cedex, France. FAU - Maureille, Bruno AU - Maureille B AD - Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600, Pessac, France. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Schwab, Catherine AU - Schwab C AD - Musée d'Archéologie Nationale, Saint-Germain-en-Laye, France. FAU - Gómez-Olivencia, Asier AU - Gómez-Olivencia A AD - Department Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain. asier.gomezo@ehu.eus. AD - Sociedad de Ciencias Aranzadi, Zorroagagaina 11, 20014, Donostia-San Sebastián, Spain. asier.gomezo@ehu.eus. AD - Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Avda. Monforte de Lemos 5 (Pabellón 14), 28029, Madrid, Spain. asier.gomezo@ehu.eus. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201209 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Archaeology MH - Bone and Bones/metabolism MH - Burial/*history/*methods MH - Child, Preschool MH - DNA, Mitochondrial/genetics MH - Fossils MH - France MH - Geology MH - History, Ancient MH - Hominidae MH - Humans MH - Mass Spectrometry/methods MH - Neanderthals/*psychology MH - Paleontology PMC - PMC7725784 COIS- The authors declare no competing interests. EDAT- 2020/12/11 06:00 MHDA- 2021/05/05 06:00 PMCR- 2020/12/09 CRDT- 2020/12/10 05:48 PHST- 2020/08/17 00:00 [received] PHST- 2020/10/27 00:00 [accepted] PHST- 2020/12/10 05:48 [entrez] PHST- 2020/12/11 06:00 [pubmed] PHST- 2021/05/05 06:00 [medline] PHST- 2020/12/09 00:00 [pmc-release] AID - 10.1038/s41598-020-77611-z [pii] AID - 77611 [pii] AID - 10.1038/s41598-020-77611-z [doi] PST - epublish SO - Sci Rep. 2020 Dec 9;10(1):21230. doi: 10.1038/s41598-020-77611-z. PMID- 33272282 OWN - NLM STAT- MEDLINE DCOM- 20210406 LR - 20210406 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 21 IP - 1 DP - 2020 Dec 4 TI - Response to Brinkmann et al. "Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States". PG - 287 LID - 10.1186/s13059-020-02203-z [doi] LID - 287 AB - We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with ancient DNA. FAU - Duggan, Ana T AU - Duggan AT AUID- ORCID: 0000-0002-2582-2954 AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, L8S 4L9, Canada. duggana@mcmaster.ca. FAU - Holmes, Edward C AU - Holmes EC AD - Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia. FAU - Poinar, Hendrik N AU - Poinar HN AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, L8S 4L9, Canada. AD - M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, L8S 4L9, Canada. LA - eng PT - Comment PT - Letter PT - Research Support, Non-U.S. Gov't DEP - 20201204 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (Smallpox Vaccine) SB - IM CON - Genome Biol. 2020 Jul 20;21(1):175. doi: 10.1186/s13059-020-02079-z. PMID: 32684155 CON - Genome Biol. 2020 Dec 4;21(1):286. doi: 10.1186/s13059-020-02202-0. PMID: 33272280 MH - American Civil War MH - Genomics MH - Humans MH - *Orthopoxvirus/genetics MH - *Smallpox/prevention & control MH - *Smallpox Vaccine MH - United States PMC - PMC7716422 COIS- The authors declare that they have no competing interests. EDAT- 2020/12/05 06:00 MHDA- 2021/04/07 06:00 PMCR- 2020/12/04 CRDT- 2020/12/04 05:30 PHST- 2020/10/28 00:00 [received] PHST- 2020/11/11 00:00 [accepted] PHST- 2020/12/04 05:30 [entrez] PHST- 2020/12/05 06:00 [pubmed] PHST- 2021/04/07 06:00 [medline] PHST- 2020/12/04 00:00 [pmc-release] AID - 10.1186/s13059-020-02203-z [pii] AID - 2203 [pii] AID - 10.1186/s13059-020-02203-z [doi] PST - epublish SO - Genome Biol. 2020 Dec 4;21(1):287. doi: 10.1186/s13059-020-02203-z. PMID- 33135465 OWN - NLM STAT- MEDLINE DCOM- 20211006 LR - 20211006 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 69 IP - 6 DP - 2020 Dec TI - Comparison of target enrichment strategies for ancient pathogen DNA. PG - 455-459 LID - 10.2144/btn-2020-0100 [doi] AB - In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods - array-based hybridization capture and in-solution capture using either RNA or DNA baits - have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits. FAU - Furtwängler, Anja AU - Furtwängler A AUID- ORCID: 0000-0002-1171-1655 AD - Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany. AD - Senckenberg Centre for Human Evolution & Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany. FAU - Neukamm, Judith AU - Neukamm J AUID- ORCID: 0000-0001-8141-566X AD - Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany. AD - Institute of Evolutionary Medicine, University of Zurich, 8057 Zurich, Switzerland. AD - Institute for Bioinformatics & Medical Informatics, University of Tübingen, 72070 Tübingen, Germany. FAU - Böhme, Lisa AU - Böhme L AD - Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany. FAU - Reiter, Ella AU - Reiter E AD - Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany. FAU - Vollstedt, Melanie AU - Vollstedt M AD - Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany. FAU - Arora, Natasha AU - Arora N AD - Zurich Institute of Forensic Medicine, University of Zurich, 8057 Zurich, Switzerland. FAU - Singh, Pushpendra AU - Singh P AUID- ORCID: 0000-0001-9453-8669 AD - Indian Council of Medical Research National Institute of Research in Tribal Health, Jabalpur 482003, MP, India. FAU - Cole, Stewart T AU - Cole ST AD - Institut Pasteur, 75015 Paris, France. FAU - Knauf, Sascha AU - Knauf S AD - Deutsches Primatenzentrum GmbH, Leibniz-Institute for Primate Research, 37077 Goettingen, Germany. AD - Department for Animal Sciences, Georg-August-University, 37075 Goettingen, Germany. FAU - Calvignac-Spencer, Sébastien AU - Calvignac-Spencer S AUID- ORCID: 0000-0003-4834-0509 AD - Robert Koch Institut, 13353 Berlin, Germany. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AD - Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany. AD - Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Krause, Johannes AU - Krause J AD - Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany. AD - Senckenberg Centre for Human Evolution & Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany. AD - Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Schuenemann, Verena J AU - Schuenemann VJ AUID- ORCID: 0000-0002-8593-3672 AD - Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany. AD - Senckenberg Centre for Human Evolution & Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany. AD - Institute of Evolutionary Medicine, University of Zurich, 8057 Zurich, Switzerland. FAU - Herbig, Alexander AU - Herbig A AUID- ORCID: 0000-0003-1176-1166 AD - Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany. AD - Max Planck Institute for the Science of Human History, 07745 Jena, Germany. LA - eng GR - Senckenberg Centre for Human Evolution and Palaeoenvironment/ GR - Max-Planck Society/ GR - R2STOP Canada/ GR - ICMR, DBT India/ GR - the Leprosy Research Initiative Netherlands/ GR - University of Zurich's University Research Priority Program "Evolution in Action: From Genomes to Ecosystems"/ PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201102 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/*analysis MH - Humans MH - Mycobacterium leprae/*genetics MH - Nucleic Acid Hybridization/*methods MH - Reproducibility of Results MH - Treponema pallidum/*genetics OTO - NOTNLM OT - Mycobacterium leprae OT - Treponema pallidum OT - ancient DNA OT - high-throughput sequencing OT - hybridization capture OT - pathogen DNA OT - target enrichment EDAT- 2020/11/03 06:00 MHDA- 2021/10/07 06:00 CRDT- 2020/11/02 08:39 PHST- 2020/11/03 06:00 [pubmed] PHST- 2021/10/07 06:00 [medline] PHST- 2020/11/02 08:39 [entrez] AID - 10.2144/btn-2020-0100 [doi] PST - ppublish SO - Biotechniques. 2020 Dec;69(6):455-459. doi: 10.2144/btn-2020-0100. Epub 2020 Nov 2. PMID- 32915387 OWN - NLM STAT- MEDLINE DCOM- 20210316 LR - 20210316 IS - 1556-2891 (Electronic) IS - 1547-769X (Linking) VI - 16 IP - 4 DP - 2020 Dec TI - Biological kinship in 750 year old human remains from Central Argentina with signs of interpersonal violence. PG - 649-658 LID - 10.1007/s12024-020-00296-3 [doi] AB - Human skeletal remains of an adult male (20-24 years old) and a juvenile (4-8 years old), dated to 750 ± 85 (14)C years BP, were found on the southern margin of Mar Chiquita Lagoon (Córdoba, Argentina). Both individuals show signs of being victims of interpersonal violence, with arrowheads associated with the remains and perimortem lesions on the juvenile, as well as an unusual form of burial, with the juvenile partially overlapped with the adult. The aim of this work is to study a possible kin relationship between these two individuals through ancient DNA analysis. Biological kinship was evaluated by autosomal and Y-chromosome STR (short tandem repeat) typing, PCR-APLP for SNP determination and hypervariable region I sequencing of the mitochondrial DNA. Genetic analyses indicated that these individuals shared the same Y-chromosomal haplotype but different mitochondrial lineages. The likelihood ratio based on autosomal loci indicates that the genetic profiles of the human remains would be more likely to be that indicating a father-son bond. The paleogenetic approach combined with forensic genetic methods applied to this study allowed us to confirm a hypothesis that originated in bioarchaeological evidence. This study constitutes a unique case in Argentina of kinship determination based on DNA profiles of human remains in an archaeological context of interpersonal violence. It is important to highlight the contribution made by these studies to address topics usually hidden in bioarchaeological studies, such as community organization, cultural customs and mortuary practices. FAU - Nores, Rodrigo AU - Nores R AUID- ORCID: 0000-0002-9153-0626 AD - Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología. CONICET, Instituto de Antropología de Córdoba (IDACOR), Av. Hipólito Yrigoyen 174, 5000, Córdoba, Argentina. rodrigonores@ffyh.unc.edu.ar. FAU - Rena, Viviana AU - Rena V AD - Centro de Genética Forense del Poder Judicial de la Provincia de Córdoba, Ibarbalz 1247, Córdoba, Argentina. FAU - Angeletti, Sofía C AU - Angeletti SC AD - Centro de Genética Forense del Poder Judicial de la Provincia de Córdoba, Ibarbalz 1247, Córdoba, Argentina. FAU - Demarchi, Darío A AU - Demarchi DA AD - Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología. CONICET, Instituto de Antropología de Córdoba (IDACOR), Av. Hipólito Yrigoyen 174, 5000, Córdoba, Argentina. FAU - Modesti, Nidia AU - Modesti N AD - Centro de Genética Forense del Poder Judicial de la Provincia de Córdoba, Ibarbalz 1247, Córdoba, Argentina. FAU - Fabra, Mariana AU - Fabra M AD - Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología. CONICET, Instituto de Antropología de Córdoba (IDACOR), Av. Hipólito Yrigoyen 174, 5000, Córdoba, Argentina. LA - eng GR - FONCyT, PICT 2015-3155/Agencia Nacional de Promoción Científica y Tecnológica/International GR - PID 2018-79/Ministerio de Ciencia y Tecnología de la Provincia de Córdoba/International PT - Historical Article PT - Journal Article DEP - 20200911 PL - United States TA - Forensic Sci Med Pathol JT - Forensic science, medicine, and pathology JID - 101236111 RN - 0 (DNA, Mitochondrial) SB - IM MH - Argentina MH - Burial MH - Child MH - Child, Preschool MH - *Chromosomes, Human, Y MH - *DNA Fingerprinting MH - DNA, Mitochondrial/genetics MH - Electrophoresis, Capillary MH - Forensic Anthropology MH - Forensic Genetics MH - Haplotypes MH - History, Ancient MH - Humans MH - Male MH - *Microsatellite Repeats MH - *Pedigree MH - *Physical Abuse MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Rib Fractures MH - Skull Fracture, Depressed MH - Young Adult OTO - NOTNLM OT - Biological relatedness OT - Córdoba province OT - Forensic genetics OT - Interpersonal violence OT - Paleogenetics OT - perimortem injuries EDAT- 2020/09/12 06:00 MHDA- 2021/03/17 06:00 CRDT- 2020/09/11 12:14 PHST- 2020/07/28 00:00 [accepted] PHST- 2020/09/12 06:00 [pubmed] PHST- 2021/03/17 06:00 [medline] PHST- 2020/09/11 12:14 [entrez] AID - 10.1007/s12024-020-00296-3 [pii] AID - 10.1007/s12024-020-00296-3 [doi] PST - ppublish SO - Forensic Sci Med Pathol. 2020 Dec;16(4):649-658. doi: 10.1007/s12024-020-00296-3. Epub 2020 Sep 11. PMID- 32808278 OWN - NLM STAT- MEDLINE DCOM- 20210226 LR - 20210226 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 173 IP - 4 DP - 2020 Dec TI - Distribution of maternal lineages in hunter-gatherer societies of the southern coast of Tierra del Fuego, Argentina. PG - 709-720 LID - 10.1002/ajpa.24107 [doi] AB - OBJECTIVES: The aim of this work is to explore the maternal genetic diversity of hunter-gatherers of the southern Tierra del Fuego, specifically the north coast of Beagle Channel, the Península Mitre, and Isla de los Estados through ancient mitochondrial DNA analysis. MATERIALS AND METHODS: The hypervariable regions 1 and 2 of the mitochondrial genome of five individuals from the north coast of Beagle Channel, six individuals from Península Mitre, and one individual from Isla de los Estados were analyzed. Through diversity statistics, Analysis of Molecular Variance (AMOVA), and Median Joining networks analyses, maternal relationships in the region were evaluated and phylogenetic similarities between ancient and contemporary populations of Tierra del Fuego were determined. RESULTS: The mitochondrial DNA lineages from the ancient individuals analyzed reveals the presence of subclades C1b and D1g. Pattern of decreasing genetic diversity toward the South is observed. The AMOVAs performed found no statistically significant differences between individuals of the north coast of Beagle Channel and Península Mitre-Isla de los Estados, and modern Yámana populations. Median joining network of haplotypes of clades C1 and D1g, show the same results. DISCUSSION: Ethnohistoric and ethnographic records of Península Mitre show that this region was occupied during the 19th century by Haush or Manekenk populations, although their biological, cultural, and subsistence characterization is unclear. We explore their maternal lineages and encounter low levels of genetic diversity and the absence of population differentiation with modern Yámana groups. We suggest that Península Mitre-Isla de los Estado was part of the same hunting and gathering populations as those of the Beagle Channel. CI - © 2020 Wiley Periodicals LLC. FAU - Crespo, Cristian M AU - Crespo CM AUID- ORCID: 0000-0003-3796-8472 AD - Departamento de Cs. Naturales y Antropológicas, CEBBAD, Universidad Maimónides, CONICET, Equipo de Antropología Biológica, Buenos Aires, Argentina. FAU - Cardozo, Darío G AU - Cardozo DG AUID- ORCID: 0000-0001-8192-259X AD - Departamento de Cs. Naturales y Antropológicas, CEBBAD, Universidad Maimónides, CONICET, Equipo de Antropología Biológica, Buenos Aires, Argentina. FAU - Tessone, Augusto AU - Tessone A AUID- ORCID: 0000-0001-9722-1480 AD - Instituto de Geocronología y Geología Isotópica (INGEIS-CONICET), Pabellón INGEIS, Ciudad Universitaria, Buenos Aires, Argentina. FAU - Vázquez, Martín AU - Vázquez M AUID- ORCID: 0000-0001-5113-4197 AD - Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina. FAU - Kisielinski, Caroline AU - Kisielinski C AUID- ORCID: 0000-0001-6777-8288 AD - Department of Anthropology, University of Kansas, Lawrence, Kansas, USA. FAU - Arencibia, Valeria AU - Arencibia V AUID- ORCID: 0000-0002-5360-2457 AD - Departamento de Cs. Naturales y Antropológicas, CEBBAD, Universidad Maimónides, CONICET, Equipo de Antropología Biológica, Buenos Aires, Argentina. FAU - Tackney, Justin AU - Tackney J AUID- ORCID: 0000-0003-1962-9397 AD - Department of Anthropology, University of Kansas, Lawrence, Kansas, USA. FAU - Zangrando, A Francisco AU - Zangrando AF AUID- ORCID: 0000-0002-5212-0894 AD - Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina. FAU - Dejean, Cristina B AU - Dejean CB AUID- ORCID: 0000-0002-3642-1945 AD - Departamento de Cs. Naturales y Antropológicas, CEBBAD, Universidad Maimónides, Equipo de Antropología Biológica, Buenos Aires, Argentina. AD - UBA, Sección de Antropología Biológica, ICA, FFyL, Buenos Aires, Argentina. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200817 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Argentina MH - *DNA, Mitochondrial/classification/genetics MH - Female MH - Genetic Variation/genetics MH - Genetics, Population MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - *Indians, South American/classification/genetics/history MH - Male MH - Middle Aged MH - Young Adult OTO - NOTNLM OT - Tierra del Fuego OT - hunter-gatherer OT - maternal lineages OT - southern Patagonia EDAT- 2020/08/19 06:00 MHDA- 2021/02/27 06:00 CRDT- 2020/08/19 06:00 PHST- 2020/03/25 00:00 [received] PHST- 2020/05/18 00:00 [revised] PHST- 2020/06/09 00:00 [accepted] PHST- 2020/08/19 06:00 [pubmed] PHST- 2021/02/27 06:00 [medline] PHST- 2020/08/19 06:00 [entrez] AID - 10.1002/ajpa.24107 [doi] PST - ppublish SO - Am J Phys Anthropol. 2020 Dec;173(4):709-720. doi: 10.1002/ajpa.24107. Epub 2020 Aug 17. PMID- 32653893 OWN - NLM STAT- MEDLINE DCOM- 20210618 LR - 20221207 IS - 1435-232X (Electronic) IS - 1434-5161 (Linking) VI - 65 IP - 12 DP - 2020 Dec TI - Paleolithic genetic link between Southern China and Mainland Southeast Asia revealed by ancient mitochondrial genomes. PG - 1125-1128 LID - 10.1038/s10038-020-0796-9 [doi] AB - The genetic history of Southern East Asians is not well-known, especially prior to the Neolithic period. To address this, we successfully sequenced two complete mitochondrial genomes of 11,000-year-old human individuals from Southern China, thus generating the oldest ancient DNA sequences from this area. Integrating published mitochondrial genomes, we characterized M71d, a new subhaplogroup of haplogroup M71. Our results suggest a possible early migration between Southern China and mainland Southeast Asia by at least 22,000 BP. FAU - Bai, Fan AU - Bai F AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, 100044, Beijing, China. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, 100044, Beijing, China. AD - University of Chinese Academy of Sciences, 100049, Beijing, China. FAU - Zhang, Xinglong AU - Zhang X AD - Guizhou Institute of Cultural Relics and Archaeology, Guiyang, 550003, China. FAU - Ji, Xueping AU - Ji X AD - Yunnan Institute of Cultural Relics and Archaeology, Kunming, 650118, China. AD - Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming, 650500, China. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, 100044, Beijing, China. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, 100044, Beijing, China. FAU - Yang, Ruowei AU - Yang R AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, 100044, Beijing, China. FAU - Peng, Minsheng AU - Peng M AUID- ORCID: 0000-0002-6301-9599 AD - University of Chinese Academy of Sciences, 100049, Beijing, China. AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. AD - KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China. FAU - Pei, Shuwen AU - Pei S AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, 100044, Beijing, China. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, 100044, Beijing, China. FAU - Fu, Qiaomei AU - Fu Q AUID- ORCID: 0000-0002-7141-0002 AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, 100044, Beijing, China. fuqiaomei@ivpp.ac.cn. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, 100044, Beijing, China. fuqiaomei@ivpp.ac.cn. AD - University of Chinese Academy of Sciences, 100049, Beijing, China. fuqiaomei@ivpp.ac.cn. LA - eng GR - 91731303/National Natural Science Foundation of China (National Science Foundation of China)/ GR - 41925009/National Natural Science Foundation of China (National Science Foundation of China)/ GR - 41630102/National Natural Science Foundation of China (National Science Foundation of China)/ GR - XDB26000000/Chinese Academy of Sciences (CAS)/ PT - Historical Article PT - Journal Article DEP - 20200711 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Asia, Southeastern MH - Asian People/*genetics MH - China/epidemiology MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/classification/*genetics MH - Genome, Mitochondrial/*genetics MH - Haplotypes/genetics MH - History, Ancient MH - Humans EDAT- 2020/07/13 06:00 MHDA- 2021/06/22 06:00 CRDT- 2020/07/13 06:00 PHST- 2020/05/18 00:00 [received] PHST- 2020/06/27 00:00 [accepted] PHST- 2020/06/21 00:00 [revised] PHST- 2020/07/13 06:00 [pubmed] PHST- 2021/06/22 06:00 [medline] PHST- 2020/07/13 06:00 [entrez] AID - 10.1038/s10038-020-0796-9 [pii] AID - 10.1038/s10038-020-0796-9 [doi] PST - ppublish SO - J Hum Genet. 2020 Dec;65(12):1125-1128. doi: 10.1038/s10038-020-0796-9. Epub 2020 Jul 11. PMID- 32621020 OWN - NLM STAT- MEDLINE DCOM- 20210913 LR - 20210913 IS - 1573-6849 (Electronic) IS - 0967-3849 (Linking) VI - 28 IP - 3-4 DP - 2020 Dec TI - A novel method of male sex identification of human ancient skeletal remains. PG - 277-291 LID - 10.1007/s10577-020-09634-1 [doi] AB - Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in subadult, or fragmented, incomplete skeletons or when the DNA is highly degraded. Most of the methods include the identification of the male and female sexes, but the absence of a specific marker for the males does not mean that the sample obtained was from a female. This study aims (1) to identify new male-specific regions that allow male identification; (2) to contrast the effectiveness of these markers against AMELX/AMELY and anthropometric measurement procedures; and (3) to test the efficacy of these markers in archaeological samples. For the first two aims, we used known sex samples, and for the third aim, we used samples from different archaeological sites. A novel molecular technique to identify male-specific regions by amplification of TTTY7, TSPY3, TTTY2, and TTTY22 genes of the human Y chromosome was developed. The results showed amplification of the specific DNA regions of Y chromosome in male individuals, with no amplification being observed in any of the female samples, confirming their specificity for male individuals. This approach complements the current procedures, such as the AMELX/AMELY test and anthropometric principle. FAU - Navarro-Romero, María Teresa AU - Navarro-Romero MT AD - Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, C.P. 7360, Mexico City, Mexico. FAU - Muñoz, María de Lourdes AU - Muñoz ML AUID- ORCID: 0000-0002-4185-2205 AD - Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, C.P. 7360, Mexico City, Mexico. lmunoz@cinvestav.mx. FAU - Alcala-Castañeda, Enrique AU - Alcala-Castañeda E AD - Department of Archaeological Studies, Instituto Nacional de Antropología e Historia, Lic. Verdad 3, Centro Histórico, 06000, Mexico City, Mexico. FAU - Terreros-Espinosa, Eladio AU - Terreros-Espinosa E AD - Templo Mayor Museum, Instituto Nacional de Antropología e Historia, Seminario 8, Centro Histórico, 06060, Mexico City, Mexico. FAU - Domínguez-de-la-Cruz, Eduardo AU - Domínguez-de-la-Cruz E AD - Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, C.P. 7360, Mexico City, Mexico. FAU - García-Hernández, Normand AU - García-Hernández N AD - Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad Hospital de Pediatría "Dr. Silvestre Frenk Freud", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Av. Cuauhtémoc 330, Doctores, 06720, Mexico City, Mexico. FAU - Moreno-Galeana, Miguel Ángel AU - Moreno-Galeana MÁ AD - Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, C.P. 7360, Mexico City, Mexico. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200703 PL - Netherlands TA - Chromosome Res JT - Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology JID - 9313452 RN - 0 (AMELY protein, human) RN - 0 (Amelogenin) SB - IM MH - Alleles MH - Amelogenin/genetics MH - *Body Remains MH - Chromosomes, Human, X MH - Chromosomes, Human, Y/genetics MH - Female MH - Forensic Anthropology/*methods MH - Forensic Medicine/*methods MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Male OTO - NOTNLM OT - AMEL test; OT - Ancient DNA; OT - Male sex identification; OT - Pre-Hispanic bone remains OT - Y chromosome; EDAT- 2020/07/06 06:00 MHDA- 2021/09/14 06:00 CRDT- 2020/07/05 06:00 PHST- 2020/03/27 00:00 [received] PHST- 2020/06/23 00:00 [accepted] PHST- 2020/06/19 00:00 [revised] PHST- 2020/07/06 06:00 [pubmed] PHST- 2021/09/14 06:00 [medline] PHST- 2020/07/05 06:00 [entrez] AID - 10.1007/s10577-020-09634-1 [pii] AID - 10.1007/s10577-020-09634-1 [doi] PST - ppublish SO - Chromosome Res. 2020 Dec;28(3-4):277-291. doi: 10.1007/s10577-020-09634-1. Epub 2020 Jul 3. PMID- 33012235 OWN - NLM STAT- MEDLINE DCOM- 20210625 LR - 20231112 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 375 IP - 1812 DP - 2020 Nov 23 TI - Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox. PG - 20190572 LID - 10.1098/rstb.2019.0572 [doi] LID - 20190572 AB - Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'. FAU - Ferrari, Giada AU - Ferrari G AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway. AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. FAU - Neukamm, Judith AU - Neukamm J AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. AD - Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany. FAU - Baalsrud, Helle T AU - Baalsrud HT AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway. FAU - Breidenstein, Abagail M AU - Breidenstein AM AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. FAU - Ravinet, Mark AU - Ravinet M AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway. AD - School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. FAU - Phillips, Carina AU - Phillips C AD - The Royal College of Surgeons of England, 35-43 Lincoln's Inn Fields, London WC2A 3PE, UK. FAU - Rühli, Frank AU - Rühli F AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. FAU - Bouwman, Abigail AU - Bouwman A AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. LA - eng SI - figshare/10.6084/m9.figshare.c.5092246 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201005 PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 SB - IM MH - Animals MH - England MH - *Evolution, Molecular MH - *Genome, Viral MH - History, 18th Century MH - Humans MH - Infant MH - Museums MH - Phylogeny MH - Smallpox/*history MH - Variola virus/*genetics PMC - PMC7702794 OTO - NOTNLM OT - ancient DNA OT - metagenomics OT - museum specimens OT - smallpox OT - virus evolution COIS- We declare we have no competing interests. EDAT- 2020/10/06 06:00 MHDA- 2021/06/29 06:00 PMCR- 2020/10/05 CRDT- 2020/10/05 05:28 PHST- 2020/10/05 05:28 [entrez] PHST- 2020/10/06 06:00 [pubmed] PHST- 2021/06/29 06:00 [medline] PHST- 2020/10/05 00:00 [pmc-release] AID - rstb20190572 [pii] AID - 10.1098/rstb.2019.0572 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2020 Nov 23;375(1812):20190572. doi: 10.1098/rstb.2019.0572. Epub 2020 Oct 5. PMID- 33012232 OWN - NLM STAT- MEDLINE DCOM- 20210625 LR - 20211124 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 375 IP - 1812 DP - 2020 Nov 23 TI - Intestinal helminths as a biomolecular complex in archaeological research. PG - 20190570 LID - 10.1098/rstb.2019.0570 [doi] LID - 20190570 AB - Enteric helminths are common parasites in many parts of the world and in the past were much more widespread both geographically and socially. Many enteric helminths are relatively long-lived in the human host, often benign or of low pathogenicity while producing large numbers of environmentally resistant eggs voided in the faeces or found associated with individual remains (skeletons and mummies). The combination of helminth characters offers opportunities to the field of historical pathogen research that are quite different to that of some of the more intensively studied high impact pathogens. Historically, a wealth of studies has employed microscopic techniques to diagnose infection using the morphology of the helminth eggs. More recently, various ancient DNA (aDNA) approaches have been applied in the archaeoparasitological context and these are revolutionizing the field, allowing much more specific diagnosis as well as interrogating the epidemiology of helminths. These advances have enhanced the potential for the field to provide unique information on past populations including using diseases to consider many aspects of life (e.g. sanitation, hygiene, diet, culinary practices and other aspects of society). Here, we consider the impact of helminth archaeoparasitology and more specifically the impact and potential for application of aDNA technologies as a part of the archaeologists' toolkit. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'. FAU - Flammer, Patrik G AU - Flammer PG AD - Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. FAU - Smith, Adrian L AU - Smith AL AD - Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. LA - eng GR - BB/K004468/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/K001388/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20201005 PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Archaeology/*methods MH - DNA, Ancient/*analysis MH - Helminths/*genetics MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, 20th Century MH - History, Ancient MH - History, Medieval MH - Humans MH - Intestinal Diseases, Parasitic/diagnosis/*history/parasitology PMC - PMC7702790 OTO - NOTNLM OT - archaeology OT - epidemiology OT - helminth OT - parasitology COIS- We declare we have no competing interests. EDAT- 2020/10/06 06:00 MHDA- 2021/06/29 06:00 PMCR- 2021/11/23 CRDT- 2020/10/05 05:28 PHST- 2020/10/05 05:28 [entrez] PHST- 2020/10/06 06:00 [pubmed] PHST- 2021/06/29 06:00 [medline] PHST- 2021/11/23 00:00 [pmc-release] AID - rstb20190570 [pii] AID - 10.1098/rstb.2019.0570 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2020 Nov 23;375(1812):20190570. doi: 10.1098/rstb.2019.0570. Epub 2020 Oct 5. PMID- 33012228 OWN - NLM STAT- MEDLINE DCOM- 20210625 LR - 20240331 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 375 IP - 1812 DP - 2020 Nov 23 TI - Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus. PG - 20190573 LID - 10.1098/rstb.2019.0573 [doi] LID - 20190573 AB - We have recently developed bioinformatic tools to accurately assign metagenomic sequence reads to microbial taxa: SPARSE for probabilistic, taxonomic classification of sequence reads; EToKi for assembling and polishing genomes from short-read sequences; and GrapeTree, a graphic visualizer of genetic distances between large numbers of genomes. Together, these methods support comparative analyses of genomes from ancient skeletons and modern humans. Here, we illustrate these capabilities with 784 samples from historical dental calculus, modern saliva and modern dental plaque. The analyses revealed 1591 microbial species within the oral microbiome. We anticipated that the oral complexes of Socransky et al., which were defined in 1998, would predominate among taxa whose frequencies differed by source. However, although some species discriminated between sources, we could not confirm the existence of the complexes. The results also illustrate further functionality of our pipelines with two species that are associated with dental caries, Streptococcus mutans and Streptococcus sobrinus. They were rare in historical dental calculus but common in modern plaque, and even more common in saliva. Reconstructed draft genomes of these two species from metagenomic samples in which they were abundant were combined with modern public genomes to provide a detailed overview of their core genomic diversity. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'. FAU - Achtman, Mark AU - Achtman M AD - Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK. FAU - Zhou, Zhemin AU - Zhou Z AD - Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK. LA - eng SI - figshare/10.6084/m9.figshare.c.5095997 GR - WT_/Wellcome Trust/United Kingdom GR - 202792/Z/16/Z/WT_/Wellcome Trust/United Kingdom GR - BB/L020319/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201005 PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 SB - IM MH - Dental Caries/*history/*microbiology MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, 20th Century MH - History, Ancient MH - History, Medieval MH - Humans MH - *Metagenome MH - *Microbiota MH - Mouth/*microbiology MH - Phylogeny MH - Saliva/microbiology MH - Streptococcus mutans/classification/*genetics MH - Streptococcus sobrinus/classification/*genetics PMC - PMC7702799 OTO - NOTNLM OT - ancient DNA OT - dental calculus OT - dental plaque OT - genomic reconstruction OT - metagenomes OT - saliva COIS- We have no competing interests. EDAT- 2020/10/06 06:00 MHDA- 2021/06/29 06:00 PMCR- 2020/10/05 CRDT- 2020/10/05 05:28 PHST- 2020/10/05 05:28 [entrez] PHST- 2020/10/06 06:00 [pubmed] PHST- 2021/06/29 06:00 [medline] PHST- 2020/10/05 00:00 [pmc-release] AID - rstb20190573 [pii] AID - 10.1098/rstb.2019.0573 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2020 Nov 23;375(1812):20190573. doi: 10.1098/rstb.2019.0573. Epub 2020 Oct 5. PMID- 33012227 OWN - NLM STAT- MEDLINE DCOM- 20210625 LR - 20210625 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 375 IP - 1812 DP - 2020 Nov 23 TI - Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. PG - 20190584 LID - 10.1098/rstb.2019.0584 [doi] LID - 20190584 AB - Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. Mycobacterium leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'. FAU - Fotakis, Anna K AU - Fotakis AK AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway. FAU - Denham, Sean D AU - Denham SD AD - Museum of Archaeology, University of Stavanger, Stavanger, Norway. FAU - Mackie, Meaghan AU - Mackie M AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway. AD - Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark. FAU - Orbegozo, Miren Iraeta AU - Orbegozo MI AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway. FAU - Mylopotamitaki, Dorothea AU - Mylopotamitaki D AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway. FAU - Gopalakrishnan, Shyam AU - Gopalakrishnan S AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway. FAU - Sicheritz-Pontén, Thomas AU - Sicheritz-Pontén T AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway. FAU - Olsen, Jesper V AU - Olsen JV AD - Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark. FAU - Cappellini, Enrico AU - Cappellini E AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway. FAU - Zhang, Guojie AU - Zhang G AD - Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark. AD - BGI-Shenzhen, 518083 Shenzhen, People's Republic of China. AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, People's Republic of China. AD - Centre for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, People's Republic of China. FAU - Christophersen, Axel AU - Christophersen A AD - NTNU University Museum, Trondheim, Norway. FAU - Gilbert, M Thomas P AU - Gilbert MTP AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway. AD - NTNU University Museum, Trondheim, Norway. FAU - Vågene, Åshild J AU - Vågene ÅJ AD - Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway. LA - eng SI - figshare/10.6084/m9.figshare.c.5096246 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201005 PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA, Ancient) SB - IM MH - Adult MH - Archaeology MH - DNA, Ancient/*analysis MH - Dental Calculus/*history/microbiology MH - Female MH - *Genome, Bacterial MH - High-Throughput Nucleotide Sequencing MH - History, 16th Century MH - Humans MH - Leprosy/*history/microbiology MH - Middle Aged MH - Mycobacterium leprae/*genetics MH - Norway MH - Sequence Analysis, DNA PMC - PMC7702802 OTO - NOTNLM OT - Mycobacterium leprae OT - ancient DNA OT - dental calculus OT - leprosy OT - palaeoproteomics COIS- We have no competing interests. EDAT- 2020/10/06 06:00 MHDA- 2021/06/29 06:00 PMCR- 2020/10/05 CRDT- 2020/10/05 05:28 PHST- 2020/10/05 05:28 [entrez] PHST- 2020/10/06 06:00 [pubmed] PHST- 2021/06/29 06:00 [medline] PHST- 2020/10/05 00:00 [pmc-release] AID - rstb20190584 [pii] AID - 10.1098/rstb.2019.0584 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2020 Nov 23;375(1812):20190584. doi: 10.1098/rstb.2019.0584. Epub 2020 Oct 5. PMID- 33012223 OWN - NLM STAT- MEDLINE DCOM- 20210625 LR - 20210625 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 375 IP - 1812 DP - 2020 Nov 23 TI - Investigating the demographic history of Japan using ancient oral microbiota. PG - 20190578 LID - 10.1098/rstb.2019.0578 [doi] LID - 20190578 AB - While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter-gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400-150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species-Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'. FAU - Eisenhofer, Raphael AU - Eisenhofer R AD - Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia. FAU - Kanzawa-Kiriyama, Hideaki AU - Kanzawa-Kiriyama H AD - Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan. FAU - Shinoda, Ken-Ichi AU - Shinoda KI AD - Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan. FAU - Weyrich, Laura S AU - Weyrich LS AD - Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia. AD - Department of Anthropology and the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA. LA - eng SI - figshare/10.6084/m9.figshare.c.5096374 PT - Historical Article PT - Journal Article DEP - 20201005 PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 SB - IM MH - Chloroflexi/classification/*genetics MH - Demography MH - Dental Caries/*history/microbiology MH - *Genome, Bacterial MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, Ancient MH - Humans MH - Japan MH - *Microbiota MH - Mouth/*microbiology MH - Periodontal Diseases/*history/microbiology MH - Phylogeny MH - Population Dynamics PMC - PMC7702792 OTO - NOTNLM OT - Japan OT - ancient DNA OT - microbiome OT - palaeomicrobiology OT - phylogenomics COIS- We declare we have no competing interests. EDAT- 2020/10/06 06:00 MHDA- 2021/06/29 06:00 PMCR- 2020/10/05 CRDT- 2020/10/05 05:28 PHST- 2020/10/05 05:28 [entrez] PHST- 2020/10/06 06:00 [pubmed] PHST- 2021/06/29 06:00 [medline] PHST- 2020/10/05 00:00 [pmc-release] AID - rstb20190578 [pii] AID - 10.1098/rstb.2019.0578 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2020 Nov 23;375(1812):20190578. doi: 10.1098/rstb.2019.0578. Epub 2020 Oct 5. PMID- 33202852 OWN - NLM STAT- MEDLINE DCOM- 20210729 LR - 20240330 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 11 IP - 11 DP - 2020 Nov 13 TI - Ancient DNA Studies in Pre-Columbian Mesoamerica. LID - 10.3390/genes11111346 [doi] LID - 1346 AB - Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE-150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900-1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses. FAU - Roca-Rada, Xavier AU - Roca-Rada X AUID- ORCID: 0000-0001-7502-6270 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. FAU - Souilmi, Yassine AU - Souilmi Y AUID- ORCID: 0000-0001-7543-4864 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. AD - National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia. AD - Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia. FAU - Teixeira, João C AU - Teixeira JC AUID- ORCID: 0000-0001-6417-4702 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. FAU - Llamas, Bastien AU - Llamas B AUID- ORCID: 0000-0002-5550-9176 AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. AD - National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia. AD - Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia. AD - Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20201113 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Central America MH - *DNA, Ancient MH - Genetics, Population/*history MH - History, Ancient MH - Humans MH - Population Dynamics PMC - PMC7696771 OTO - NOTNLM OT - Mesoamerica OT - Native American ancestries OT - Native American founding lineages OT - Native American genetic history OT - Teotihuacan OT - ancient DNA OT - mtDNA COIS- The authors declare no conflict of interest. EDAT- 2020/11/19 06:00 MHDA- 2021/07/30 06:00 PMCR- 2020/11/01 CRDT- 2020/11/18 01:01 PHST- 2020/10/01 00:00 [received] PHST- 2020/11/04 00:00 [revised] PHST- 2020/11/10 00:00 [accepted] PHST- 2020/11/18 01:01 [entrez] PHST- 2020/11/19 06:00 [pubmed] PHST- 2021/07/30 06:00 [medline] PHST- 2020/11/01 00:00 [pmc-release] AID - genes11111346 [pii] AID - genes-11-01346 [pii] AID - 10.3390/genes11111346 [doi] PST - epublish SO - Genes (Basel). 2020 Nov 13;11(11):1346. doi: 10.3390/genes11111346. PMID- 33351947 OWN - NLM STAT- MEDLINE DCOM- 20210121 LR - 20210121 IS - 1937-2345 (Electronic) IS - 0022-3395 (Linking) VI - 106 IP - 6 DP - 2020 Nov 12 TI - Metagonimus yokogawai Ancient DNA Recovered from 16th- to 17th-Century Korean Mummy Feces of the Joseon Dynasty. PG - 802-808 LID - 10.1645/20-42 [doi] AB - Metagonimiasis is foodborne intestinal parasitism occurring by the definitive hosts' ingestion of raw or undercooked fish, mostly commonly sweetfish. Most Metagonimus infection is caused by Metagonimus yokogawai but also rarely by Metagonimus takahashii as well as Metagonimus miyatai. Despite recent molecular work on Metagonimus spp., there are still insufficient data to reveal the genetic characteristics of ancient M. yokogawai in a wide geo-historical scope. In this study, we were successful in the analysis of M. yokogawai ancient DNA (aDNA) using coprolite samples retrieved from 16th- to 17th-century Korean mummies. In BLAST and phylogenetic analyses, M. yokogawai 28S rDNA of Korean mummies were clustered along with the 28S rDNA taxa of M. takahashii and M. miyatai in GenBank. Conversely, the cytochrome c oxidase subunit I (COI) of M. yokogawai aDNA from Korean mummies was distinctly clustered apart from M. takahashii and M. miyatai sequences. This study is the first report of its kind to identify M. yokogawai aDNA retrieved from the archaeological specimens and confirms the usefulness of COI in molecular diagnosis of M. yokogawai. Considering the rarity of reports on the genetics of genus Metagonimus spp., our study will be fundamental for the future study of M. yokogawai paleogenetics. CI - © American Society of Parasitologists 2020. FAU - Hong, Jong Ha AU - Hong JH AD - Institute of Korean Archaeology and Ancient History, Kyung Hee University, Seoul, South Korea. AD - Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, South Korea. FAU - Seo, Min AU - Seo M AD - Department of Parasitology, Dankook University College of Medicine, Cheonan, South Korea. FAU - Oh, Chang Seok AU - Oh CS AD - Department of Mortuary Science, Eulji University, Seongnam-Si, Gyeonggi-Do, South Korea. AD - Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea. FAU - Chai, Jong-Yil AU - Chai JY AD - Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul, South Korea. AD - Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul, South Korea. FAU - Shin, Dong Hoon AU - Shin DH AD - Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, South Korea. AD - Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Parasitol JT - The Journal of parasitology JID - 7803124 RN - 0 (DNA, Helminth) SB - IM MH - Animals MH - DNA, Helminth/history/*isolation & purification MH - Feces/parasitology MH - Female MH - Heterophyidae/*genetics/isolation & purification MH - History, 16th Century MH - History, 17th Century MH - Humans MH - Korea MH - Male MH - Mummies/*history/*parasitology MH - Trematode Infections/*history/parasitology OTO - NOTNLM OT - 28S rDNA OT - COI OT - Metagonimus yokogawai OT - Ancient DNA OT - Parasite OT - Phylogenetic Analysis EDAT- 2020/12/23 06:00 MHDA- 2021/01/22 06:00 CRDT- 2020/12/22 17:14 PHST- 2020/12/22 17:14 [entrez] PHST- 2020/12/23 06:00 [pubmed] PHST- 2021/01/22 06:00 [medline] AID - 449743 [pii] AID - 10.1645/20-42 [doi] PST - ppublish SO - J Parasitol. 2020 Nov 12;106(6):802-808. doi: 10.1645/20-42. PMID- 33157037 OWN - NLM STAT- MEDLINE DCOM- 20210519 LR - 20210519 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 183 IP - 4 DP - 2020 Nov 12 TI - A Dynamic 6,000-Year Genetic History of Eurasia's Eastern Steppe. PG - 890-904.e29 LID - S0092-8674(20)31321-0 [pii] LID - 10.1016/j.cell.2020.10.015 [doi] AB - The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region's population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe. CI - Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Jeong, Choongwon AU - Jeong C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea. Electronic address: cwjeong@snu.ac.kr. FAU - Wang, Ke AU - Wang K AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Wilkin, Shevan AU - Wilkin S AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Taylor, William Timothy Treal AU - Taylor WTT AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology, University of Colorado Boulder, Boulder, CO 80309, USA. FAU - Miller, Bryan K AU - Miller BK AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA. FAU - Bemmann, Jan H AU - Bemmann JH AD - Department of Archaeology and Anthropology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53113, Germany. FAU - Stahl, Raphaela AU - Stahl R AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Chiovelli, Chelsea AU - Chiovelli C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Knolle, Florian AU - Knolle F AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Ulziibayar, Sodnom AU - Ulziibayar S AD - Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar 14200, Mongolia. FAU - Khatanbaatar, Dorjpurev AU - Khatanbaatar D AD - Mongolian University of Science and Technology, Ulaanbaatar 14191, Mongolia. FAU - Erdenebaatar, Diimaajav AU - Erdenebaatar D AD - Department of Archaeology, Ulaanbaatar State University, Bayanzurkh district, Ulaanbaatar 13343, Mongolia. FAU - Erdenebat, Ulambayar AU - Erdenebat U AD - Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14201, Mongolia. FAU - Ochir, Ayudai AU - Ochir A AD - International Institute for the Study of Nomadic Civilizations, Ulaanbaatar 14200, Mongolia. FAU - Ankhsanaa, Ganbold AU - Ankhsanaa G AD - National Centre for Cultural Heritage of Mongolia, Ulaanbaatar 14200, Mongolia. FAU - Vanchigdash, Chuluunkhuu AU - Vanchigdash C AD - Mongolian University of Science and Technology, Ulaanbaatar 14191, Mongolia. FAU - Ochir, Battuga AU - Ochir B AD - Institute of History and Ethnology, Mongolian Academy of Sciences, Ulaanbaatar 14200, Mongolia. FAU - Munkhbayar, Chuluunbat AU - Munkhbayar C AD - University of Khovd, Khovd province, Khovd 84179, Mongolia. FAU - Tumen, Dashzeveg AU - Tumen D AD - Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14201, Mongolia. FAU - Kovalev, Alexey AU - Kovalev A AD - Institute of Archaeology, Russian Academy of Sciences, Moscow 119991, Russia. FAU - Kradin, Nikolay AU - Kradin N AD - Institute of History, Archaeology and Ethnology, Far East Branch of the Russian Academy of Sciences, Vladivostok 690001, Russia; Institute for Mongolian, Buddhist and Tibetan Studies, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude 670047, Russia. FAU - Bazarov, Bilikto A AU - Bazarov BA AD - Institute for Mongolian, Buddhist and Tibetan Studies, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude 670047, Russia. FAU - Miyagashev, Denis A AU - Miyagashev DA AD - Institute for Mongolian, Buddhist and Tibetan Studies, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude 670047, Russia. FAU - Konovalov, Prokopiy B AU - Konovalov PB AD - Institute for Mongolian, Buddhist and Tibetan Studies, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude 670047, Russia. FAU - Zhambaltarova, Elena AU - Zhambaltarova E AD - Department of Museology and Heritage, Faculty of Social and Cultural Activities, Heritage, and Tourism, Federal State Budgetary Educational Institution of Higher Education, East Siberian State Institute of Culture, Ulan-Ude 670031, Russia. FAU - Miller, Alicia Ventresca AU - Miller AV AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology, University of Michigan, Ann Arbor, MI 48109, USA. FAU - Haak, Wolfgang AU - Haak W AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Schiffels, Stephan AU - Schiffels S AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Faculty of Biological Sciences, Friedrich Schiller University, Jena 02134, Germany. FAU - Boivin, Nicole AU - Boivin N AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Erdene, Myagmar AU - Erdene M AD - Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14201, Mongolia. FAU - Hendy, Jessica AU - Hendy J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK. FAU - Warinner, Christina AU - Warinner C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Faculty of Biological Sciences, Friedrich Schiller University, Jena 02134, Germany; Department of Anthropology, Harvard University, Cambridge, MA 02138, USA. Electronic address: warinner@fas.harvard.edu. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201105 PL - United States TA - Cell JT - Cell JID - 0413066 SB - IM MH - Archaeology MH - Europe MH - Female MH - Gene Frequency/genetics MH - Gene Pool MH - Genetic Heterogeneity MH - *Genetics, Population MH - Genome, Human MH - Geography MH - *Grassland MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Male MH - Mongolia MH - Principal Component Analysis MH - Time Factors PMC - PMC7664836 OTO - NOTNLM OT - Eastern Steppe OT - Mongol empire OT - Mongolia OT - Xiongnu empire OT - ancient DNA OT - human population history OT - migration OT - nomadic pastoralists COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2020/11/07 06:00 MHDA- 2021/05/20 06:00 PMCR- 2020/11/12 CRDT- 2020/11/06 20:10 PHST- 2020/01/08 00:00 [received] PHST- 2020/03/12 00:00 [revised] PHST- 2020/10/07 00:00 [accepted] PHST- 2020/11/07 06:00 [pubmed] PHST- 2021/05/20 06:00 [medline] PHST- 2020/11/06 20:10 [entrez] PHST- 2020/11/12 00:00 [pmc-release] AID - S0092-8674(20)31321-0 [pii] AID - 10.1016/j.cell.2020.10.015 [doi] PST - ppublish SO - Cell. 2020 Nov 12;183(4):890-904.e29. doi: 10.1016/j.cell.2020.10.015. Epub 2020 Nov 5. PMID- 33106412 OWN - NLM STAT- MEDLINE DCOM- 20210104 LR - 20210104 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 117 IP - 45 DP - 2020 Nov 10 TI - A genomic and historical synthesis of plague in 18th century Eurasia. PG - 28328-28335 LID - 10.1073/pnas.2009677117 [doi] AB - Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe. CI - Copyright © 2020 the Author(s). Published by PNAS. FAU - Guellil, Meriam AU - Guellil M AUID- ORCID: 0000-0002-7235-4604 AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway; meriam.guellil.ac@gmail.com n.c.stenseth@mn.uio.no barbara.bramanti@ibv.uio.no. AD - Institute of Genomics, University of Tartu, 51010 Tartu, Estonia. FAU - Kersten, Oliver AU - Kersten O AUID- ORCID: 0000-0001-9304-2493 AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway. FAU - Namouchi, Amine AU - Namouchi A AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway. AD - Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, 1430 Ås, Norway. FAU - Luciani, Stefania AU - Luciani S AUID- ORCID: 0000-0002-6078-4041 AD - Laboratory of Molecular Archaeo-Anthropology/ancientDNA, School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy. FAU - Marota, Isolina AU - Marota I AUID- ORCID: 0000-0003-1920-9931 AD - Laboratory of Molecular Archaeo-Anthropology/ancientDNA, School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy. FAU - Arcini, Caroline A AU - Arcini CA AD - Arkeologerna, National Historical Museums, SE-226 60 Lund, Sweden. FAU - Iregren, Elisabeth AU - Iregren E AD - Department of Archaeology and Ancient History, Lund University, SE-221 00, Lund, Sweden. FAU - Lindemann, Robert A AU - Lindemann RA AD - School of Dentistry, University of California Los Angeles, CA 90024. FAU - Warfvinge, Gunnar AU - Warfvinge G AUID- ORCID: 0000-0002-0682-3871 AD - Faculty of Odontology, Malmö University, SE-205 06 Malmö, Sweden. FAU - Bakanidze, Lela AU - Bakanidze L AD - National Center for Disease Control and Public Health, 0198 Tbilisi, Georgia. FAU - Bitadze, Lia AU - Bitadze L AUID- ORCID: 0000-0001-8601-0215 AD - Anthropological Studies of the Institute of History and Ethnology, Ivane Javakhishvili Tbilisi State University, 0177 Tbilisi, Georgia. FAU - Rubini, Mauro AU - Rubini M AUID- ORCID: 0000-0001-5923-0431 AD - Anthropological Service of Soprintendenza Archeologia Belle Arti e Paesaggio per le province di Frosinone, Latina e Rieti (Lazio), Ministry of Cultural Heritage and Activities, 00192 Rome, Italy. AD - Department of Archaeology, University of Foggia, 71122 Foggia, Italy. FAU - Zaio, Paola AU - Zaio P AD - Anthropological Service of Soprintendenza Archeologia Belle Arti e Paesaggio per le province di Frosinone, Latina e Rieti (Lazio), Ministry of Cultural Heritage and Activities, 00192 Rome, Italy. FAU - Zaio, Monica AU - Zaio M AD - Anthropological Service of Soprintendenza Archeologia Belle Arti e Paesaggio per le province di Frosinone, Latina e Rieti (Lazio), Ministry of Cultural Heritage and Activities, 00192 Rome, Italy. FAU - Neri, Damiano AU - Neri D AD - Anthropological Service of Soprintendenza Archeologia Belle Arti e Paesaggio per le province di Frosinone, Latina e Rieti (Lazio), Ministry of Cultural Heritage and Activities, 00192 Rome, Italy. FAU - Stenseth, N C AU - Stenseth NC AUID- ORCID: 0000-0002-1591-5399 AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway; meriam.guellil.ac@gmail.com n.c.stenseth@mn.uio.no barbara.bramanti@ibv.uio.no. FAU - Bramanti, Barbara AU - Bramanti B AUID- ORCID: 0000-0002-5433-663X AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway; meriam.guellil.ac@gmail.com n.c.stenseth@mn.uio.no barbara.bramanti@ibv.uio.no. AD - Institute of Genomics, University of Tartu, 51010 Tartu, Estonia. AD - Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy and Prevention, University of Ferrara, 44121 Ferrara, Italy. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201026 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Bacterial MH - Europe MH - *Genome, Bacterial MH - History, 18th Century MH - History, Medieval MH - Humans MH - Pandemics/history MH - Phylogeny MH - Plague/genetics/*history/*microbiology MH - Russia MH - Yersinia pestis/classification/*genetics PMC - PMC7668095 OTO - NOTNLM OT - Yersinia pestis OT - aDNA OT - ancient DNA OT - pathogen OT - plague COIS- The authors declare no competing interest. EDAT- 2020/10/28 06:00 MHDA- 2021/01/05 06:00 PMCR- 2020/10/26 CRDT- 2020/10/27 05:41 PHST- 2020/10/28 06:00 [pubmed] PHST- 2021/01/05 06:00 [medline] PHST- 2020/10/27 05:41 [entrez] PHST- 2020/10/26 00:00 [pmc-release] AID - 2009677117 [pii] AID - 202009677 [pii] AID - 10.1073/pnas.2009677117 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28328-28335. doi: 10.1073/pnas.2009677117. Epub 2020 Oct 26. PMID- 33077602 OWN - NLM STAT- MEDLINE DCOM- 20210104 LR - 20240330 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 117 IP - 45 DP - 2020 Nov 10 TI - Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic. PG - 28150-28159 LID - 10.1073/pnas.2011696117 [doi] AB - Local wild bovids have been determined to be important prey on the northeastern Tibetan Plateau (NETP), where hunting game was a major subsistence strategy until the late Neolithic, when farming lifestyles dominated in the neighboring Loess Plateau. However, the species affiliation and population ecology of these prehistoric wild bovids in the prehistoric NETP remain unknown. Ancient DNA (aDNA) analysis is highly informative in decoding this puzzle. Here, we applied aDNA analysis to fragmented bovid and rhinoceros specimens dating ∼5,200 y B.P. from the Neolithic site of Shannashuzha located in the marginal area of the NETP. Utilizing both whole genomes and mitochondrial DNA, our results demonstrate that the range of the present-day tropical gaur (Bos gaurus) extended as far north as the margins of the NETP during the late Neolithic from ∼29°N to ∼34°N. Furthermore, comparative analysis with zooarchaeological and paleoclimatic evidence indicated that a high summer temperature in the late Neolithic might have facilitated the northward expansion of tropical animals (at least gaur and Sumatran-like rhinoceros) to the NETP. This enriched the diversity of wildlife, thus providing abundant hunting resources for humans and facilitating the exploration of the Tibetan Plateau as one of the last habitats for hunting game in East Asia. CI - Copyright © 2020 the Author(s). Published by PNAS. FAU - Chen, Ningbo AU - Chen N AUID- ORCID: 0000-0001-6624-5885 AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China. AD - Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100 Yangling, China. FAU - Ren, Lele AU - Ren L AD - School of History and Culture, Lanzhou University, 730000 Lanzhou, China. FAU - Du, Linyao AU - Du L AD - College of Earth and Environmental Sciences, Lanzhou University, 730000 Lanzhou, China. FAU - Hou, Jiawen AU - Hou J AD - Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100 Yangling, China. FAU - Mullin, Victoria E AU - Mullin VE AD - Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom. FAU - Wu, Duo AU - Wu D AD - College of Earth and Environmental Sciences, Lanzhou University, 730000 Lanzhou, China. FAU - Zhao, Xueye AU - Zhao X AD - Gansu Provincial Institute of Cultural Relics and Archaeology, 730000 Lanzhou, China. FAU - Li, Chunmei AU - Li C AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China. AD - Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China. FAU - Huang, Jiahui AU - Huang J AUID- ORCID: 0000-0002-1936-124X AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China. AD - Kunming College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China. FAU - Qi, Xuebin AU - Qi X AUID- ORCID: 0000-0002-7883-4983 AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China. AD - Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China. FAU - Capodiferro, Marco Rosario AU - Capodiferro MR AUID- ORCID: 0000-0003-2494-5423 AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani," Università di Pavia, 27100 Pavia, Italy. FAU - Achilli, Alessandro AU - Achilli A AUID- ORCID: 0000-0001-6871-3451 AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani," Università di Pavia, 27100 Pavia, Italy. FAU - Lei, Chuzhao AU - Lei C AD - Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100 Yangling, China. FAU - Chen, Fahu AU - Chen F AD - CAS Center for Excellence in Tibetan Plateau Earth Sciences, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101 Beijing, China. FAU - Su, Bing AU - Su B AUID- ORCID: 0000-0002-4379-9014 AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China; zhangxiaoming@mail.kiz.ac.cn ghdong@lzu.edu.cn sub@mail.kiz.ac.cn. AD - Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China. FAU - Dong, Guanghui AU - Dong G AD - College of Earth and Environmental Sciences, Lanzhou University, 730000 Lanzhou, China; zhangxiaoming@mail.kiz.ac.cn ghdong@lzu.edu.cn sub@mail.kiz.ac.cn. AD - CAS Center for Excellence in Tibetan Plateau Earth Sciences, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101 Beijing, China. FAU - Zhang, Xiaoming AU - Zhang X AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China; zhangxiaoming@mail.kiz.ac.cn ghdong@lzu.edu.cn sub@mail.kiz.ac.cn. AD - Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201019 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animal Migration MH - Animals MH - *Biodiversity MH - *Cattle/classification/genetics MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial MH - Genome/*genetics MH - History, Ancient MH - Homing Behavior MH - Humans MH - Perissodactyla/classification/genetics MH - Population Dynamics/history MH - Ruminants/classification/genetics MH - Tibet PMC - PMC7668038 OTO - NOTNLM OT - Bos gaurus OT - ancient DNA OT - hunting game OT - late Neolithic OT - northeastern Tibetan Plateau COIS- The authors declare no competing interest. EDAT- 2020/10/21 06:00 MHDA- 2021/01/05 06:00 PMCR- 2020/10/19 CRDT- 2020/10/20 06:17 PHST- 2020/10/21 06:00 [pubmed] PHST- 2021/01/05 06:00 [medline] PHST- 2020/10/20 06:17 [entrez] PHST- 2020/10/19 00:00 [pmc-release] AID - 2011696117 [pii] AID - 202011696 [pii] AID - 10.1073/pnas.2011696117 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28150-28159. doi: 10.1073/pnas.2011696117. Epub 2020 Oct 19. PMID- 33159107 OWN - NLM STAT- MEDLINE DCOM- 20210621 LR - 20240330 IS - 2399-3642 (Electronic) IS - 2399-3642 (Linking) VI - 3 IP - 1 DP - 2020 Nov 6 TI - Ancient DNA reveals monozygotic newborn twins from the Upper Palaeolithic. PG - 650 LID - 10.1038/s42003-020-01372-8 [doi] LID - 650 AB - The Upper Palaeolithic double burial of newborns and the single burial of a ca. 3-month-old infant uncovered at the Gravettian site of Krems-Wachtberg, Austria, are of paramount importance given the rarity of immature human remains from this time. Genome-wide ancient DNA shows that the male infants of the double grave are the earliest reported case of monozygotic twins, while the single grave´s individual was their 3rd-degree male relative. We assessed the individuals´ age at death by applying histological and µCT inspection of the maxillary second incisors (i2) in conjunction with C- and N-isotope ratios and Barium (Ba) intake as biomarker for breastfeeding. The results show that the twins were full-term newborns, and that while individual 2 died at birth, individual 1 survived for about 50 days. The findings show that Gravettian mortuary behaviour also included re-opening of a grave and manipulation of its layout and content. FAU - Teschler-Nicola, Maria AU - Teschler-Nicola M AD - Department of Anthropology, Natural History Museum Vienna, A-1010, Vienna, Austria. maria.teschler@nhm-wien.ac.at. AD - Department of Evolutionary Anthropology, University of Vienna, A-1090, Vienna, Austria. maria.teschler@nhm-wien.ac.at. FAU - Fernandes, Daniel AU - Fernandes D AUID- ORCID: 0000-0002-7434-6552 AD - Department of Evolutionary Anthropology, University of Vienna, A-1090, Vienna, Austria. AD - CIAS, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal. FAU - Händel, Marc AU - Händel M AUID- ORCID: 0000-0003-2472-4006 AD - Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria. FAU - Einwögerer, Thomas AU - Einwögerer T AD - Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria. FAU - Simon, Ulrich AU - Simon U AD - Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria. FAU - Neugebauer-Maresch, Christine AU - Neugebauer-Maresch C AD - Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria. FAU - Tangl, Stefan AU - Tangl S AD - Karl Donath Laboratory for Hard Tissue and Biomaterial Research, University Clinic of Dentistry Vienna, Medical University of Vienna, A-1090, Vienna, Austria. AD - Austrian Cluster for Tissue Regeneration, A-1200, Vienna, Austria. FAU - Heimel, Patrick AU - Heimel P AD - Karl Donath Laboratory for Hard Tissue and Biomaterial Research, University Clinic of Dentistry Vienna, Medical University of Vienna, A-1090, Vienna, Austria. AD - Austrian Cluster for Tissue Regeneration, A-1200, Vienna, Austria. AD - Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, A-1200, Vienna, Austria. FAU - Dobsak, Toni AU - Dobsak T AD - Karl Donath Laboratory for Hard Tissue and Biomaterial Research, University Clinic of Dentistry Vienna, Medical University of Vienna, A-1090, Vienna, Austria. AD - Austrian Cluster for Tissue Regeneration, A-1200, Vienna, Austria. FAU - Retzmann, Anika AU - Retzmann A AD - Chair of General and Analytical Chemistry, Montanuniversität Leoben, A-8700, Leoben, Austria. FAU - Prohaska, Thomas AU - Prohaska T AD - Chair of General and Analytical Chemistry, Montanuniversität Leoben, A-8700, Leoben, Austria. FAU - Irrgeher, Johanna AU - Irrgeher J AD - Chair of General and Analytical Chemistry, Montanuniversität Leoben, A-8700, Leoben, Austria. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA. FAU - Olalde, Iñigo AU - Olalde I AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, A-1090, Vienna, Austria. ron.pinhasi@univie.ac.at. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201106 PL - England TA - Commun Biol JT - Communications biology JID - 101719179 RN - 9007-49-2 (DNA) SB - IM MH - Burial MH - DNA/*genetics MH - History, Ancient MH - Humans MH - Infant, Newborn MH - Paleontology MH - Twins, Monozygotic/*genetics PMC - PMC7648643 COIS- The authors declare no competing interests. EDAT- 2020/11/08 06:00 MHDA- 2021/06/22 06:00 PMCR- 2020/11/06 CRDT- 2020/11/07 05:31 PHST- 2019/12/30 00:00 [received] PHST- 2020/10/01 00:00 [accepted] PHST- 2020/11/07 05:31 [entrez] PHST- 2020/11/08 06:00 [pubmed] PHST- 2021/06/22 06:00 [medline] PHST- 2020/11/06 00:00 [pmc-release] AID - 10.1038/s42003-020-01372-8 [pii] AID - 1372 [pii] AID - 10.1038/s42003-020-01372-8 [doi] PST - epublish SO - Commun Biol. 2020 Nov 6;3(1):650. doi: 10.1038/s42003-020-01372-8. PMID- 33142099 OWN - NLM STAT- MEDLINE DCOM- 20210513 LR - 20221207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 30 IP - 21 DP - 2020 Nov 2 TI - Human Genetics: Lactase Persistence in a Battlefield. PG - R1311-R1313 LID - S0960-9822(20)31277-X [pii] LID - 10.1016/j.cub.2020.08.087 [doi] AB - Lactase persistence is a common genetic trait in Europeans and other pastoralists. New ancient DNA evidence from a Bronze Age battlefield indicates that selection for lactase persistence was strong and on-going in the last 3,000 years. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Saag, Lehti AU - Saag L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia. Electronic address: lehti.saag@ut.ee. LA - eng PT - Comment PT - Journal Article PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - EC 3.2.1.108 (Lactase) SB - IM CON - Curr Biol. 2020 Nov 2;30(21):4307-4315.e13. doi: 10.1016/j.cub.2020.08.033. PMID: 32888485 MH - Child, Preschool MH - Europe MH - Gene Frequency MH - Humans MH - *Lactase/genetics MH - Prevalence MH - *White People EDAT- 2020/11/04 06:00 MHDA- 2021/05/14 06:00 CRDT- 2020/11/03 20:08 PHST- 2020/11/03 20:08 [entrez] PHST- 2020/11/04 06:00 [pubmed] PHST- 2021/05/14 06:00 [medline] AID - S0960-9822(20)31277-X [pii] AID - 10.1016/j.cub.2020.08.087 [doi] PST - ppublish SO - Curr Biol. 2020 Nov 2;30(21):R1311-R1313. doi: 10.1016/j.cub.2020.08.087. PMID- 32939074 OWN - NLM STAT- MEDLINE DCOM- 20210202 LR - 20210216 IS - 1471-0064 (Electronic) IS - 1471-0056 (Linking) VI - 21 IP - 11 DP - 2020 Nov TI - African ancient DNA research requires robust ethics and permission protocols. PG - 645-647 LID - 10.1038/s41576-020-00285-w [doi] FAU - Gibbon, Victoria E AU - Gibbon VE AUID- ORCID: 0000-0001-7875-3297 AD - Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Observatory, Cape Town, South Africa. victoria.gibbon@uct.ac.za. LA - eng PT - Journal Article PL - England TA - Nat Rev Genet JT - Nature reviews. Genetics JID - 100962779 RN - 0 (DNA, Ancient) SB - IM MH - Africa MH - Archaeology/*ethics MH - Body Remains MH - *DNA, Ancient MH - Genetic Research/*ethics MH - Genomics/*ethics MH - Humans MH - Informed Consent EDAT- 2020/09/18 06:00 MHDA- 2021/02/03 06:00 CRDT- 2020/09/17 05:43 PHST- 2020/09/18 06:00 [pubmed] PHST- 2021/02/03 06:00 [medline] PHST- 2020/09/17 05:43 [entrez] AID - 10.1038/s41576-020-00285-w [pii] AID - 10.1038/s41576-020-00285-w [doi] PST - ppublish SO - Nat Rev Genet. 2020 Nov;21(11):645-647. doi: 10.1038/s41576-020-00285-w. PMID- 32318826 OWN - NLM STAT- MEDLINE DCOM- 20210712 LR - 20210712 IS - 1437-1596 (Electronic) IS - 0937-9827 (Linking) VI - 134 IP - 6 DP - 2020 Nov TI - The limitations of kinship determinations using STR data in ill-defined populations. PG - 1981-1990 LID - 10.1007/s00414-020-02298-w [doi] AB - The likelihood ratio (LR) method is commonly used to determine kinship in civil, criminal, or forensic cases. For the past 15 years, our research group has also applied LR to ancient STR data and obtained kinship results for collections of graves or necropolises. Although we were able to reconstruct large genealogies, some pairs of individuals showed ambiguous results. Second-degree relationships, half-sibling pairs for example, were often inconsistent with detected first-degree relationships, such as parent/child or brother/sister pairs. We therefore set about providing empirical estimations of the error rates for the LR method in living populations with STR allelic diversities comparable to that of the ancient populations we had previously studied. We collected biological samples in the field in North-Eastern Siberia and West Africa and studied more than 800 pairs of STR profiles from individuals with known relationships. Because commercial STR panels were constructed for specific regions (namely Europe and North America), their allelic makeup showed a significant deficit in diversity when compared to European populations, replicating a situation often faced in ancient DNA studies. We assessed the capacity of the LR method to confirm known relationships (effectiveness) and its capacity to detect those relationships (reliability). Concerns over the effectiveness of LR determinations are mostly an issue in forensic studies, while the reliability of the detection of kinship is an issue for the study of necropolises or other large gatherings of unidentified individuals, such as disaster victims or mass graves. We show that the application of LR to both test populations highlights specific issues (both false positives and false negatives) that prevent the confirmation of second-degree kinship or even full siblingship in small populations. Up to 29% of detected full sibling relationships were either overestimated half-sibling relationships or underestimated parent-offspring relationships. The error rate for detected half-sibling relationships was even higher, reaching 41%. Only parent-offspring pairs were reliably detected or confirmed. This implies that, in populations that are small, ill-defined, or for which the STR loci analyzed are inappropriate, an examiner might not be able to distinguish a pair of full siblings from a pair of half-siblings. Furthermore, half-sibling pairs might be overlooked altogether, an issue that is exacerbated by the common confusion, in many languages and cultures, between half-siblings and full siblings. Consequently, in the study of ancient populations, human remains of unknown origins, or poorly surveyed modern populations, we recommend a conservative approach to kinship determined by LR. Next-generation sequencing data should be used when possible, but the costs and technology involved might be prohibitive. Therefore, in potentially contentious situations or cases lacking sufficient external information, uniparental markers should be analyzed: ideally, complete mitochondrial genomes and Y-chromosome haplotypes (STR, SNP, and/or sequencing). FAU - Zvénigorosky, Vincent AU - Zvénigorosky V AD - CNRS FRE 2029-BABEL,, Paris Descartes University, Paris, France. z.vincent@live.fr. AD - Strasbourg Institute of Legal Medicine, Strasbourg, France. z.vincent@live.fr. FAU - Sabbagh, Audrey AU - Sabbagh A AD - UMR 261 MERIT, IRD, Paris Descartes University, Paris, France. FAU - Gonzalez, Angéla AU - Gonzalez A AD - Strasbourg Institute of Legal Medicine, Strasbourg, France. FAU - Fausser, Jean-Luc AU - Fausser JL AD - Strasbourg Institute of Legal Medicine, Strasbourg, France. FAU - Palstra, Friso AU - Palstra F AD - UMR 261 MERIT, IRD, Paris Descartes University, Paris, France. FAU - Romanov, Georgii AU - Romanov G AD - Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia. AD - Laboratory of Molecular Genetics, Yakut Science-Centre of Complex Medical Problems, Yakutsk, Sakha Republic, Russia. FAU - Solovyev, Aisen AU - Solovyev A AD - Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia. AD - Institute for Humanitarian Studies and Problems of Indigenous Peoples of the North, Yakutsk, Sakha Republic, Russia. FAU - Barashkov, Nikolay AU - Barashkov N AD - Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia. AD - Laboratory of Molecular Genetics, Yakut Science-Centre of Complex Medical Problems, Yakutsk, Sakha Republic, Russia. FAU - Fedorova, Sardana AU - Fedorova S AD - Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia. AD - Laboratory of Molecular Genetics, Yakut Science-Centre of Complex Medical Problems, Yakutsk, Sakha Republic, Russia. FAU - Crubézy, Éric AU - Crubézy É AD - CNRS UMR 5288 AMIS, Toulouse Paul Sabatier University, Toulouse, France. FAU - Ludes, Bertrand AU - Ludes B AD - CNRS FRE 2029-BABEL,, Paris Descartes University, Paris, France. FAU - Keyser, Christine AU - Keyser C AD - CNRS FRE 2029-BABEL,, Paris Descartes University, Paris, France. AD - Strasbourg Institute of Legal Medicine, Strasbourg, France. LA - eng GR - Travel Grant/Université Toulouse III - Paul Sabatier/ PT - Journal Article DEP - 20200421 PL - Germany TA - Int J Legal Med JT - International journal of legal medicine JID - 9101456 SB - IM MH - Africa, Western/ethnology MH - Benin/ethnology MH - *Family MH - Female MH - Forensic Genetics/*methods MH - Gene Frequency MH - Humans MH - *Likelihood Functions MH - Male MH - Microsatellite Repeats MH - *Pedigree MH - Phylogeny MH - Reproducibility of Results MH - Siberia/ethnology OTO - NOTNLM OT - Ancient DNA OT - Forensic genetics OT - Kinship OT - Likelihood ratios OT - Short tandem repeats EDAT- 2020/04/23 06:00 MHDA- 2021/07/13 06:00 CRDT- 2020/04/23 06:00 PHST- 2019/12/08 00:00 [received] PHST- 2020/04/07 00:00 [accepted] PHST- 2020/04/23 06:00 [pubmed] PHST- 2021/07/13 06:00 [medline] PHST- 2020/04/23 06:00 [entrez] AID - 10.1007/s00414-020-02298-w [pii] AID - 10.1007/s00414-020-02298-w [doi] PST - ppublish SO - Int J Legal Med. 2020 Nov;134(6):1981-1990. doi: 10.1007/s00414-020-02298-w. Epub 2020 Apr 21. PMID- 33122697 OWN - NLM STAT- MEDLINE DCOM- 20210304 LR - 20240330 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 10 IP - 1 DP - 2020 Oct 29 TI - Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes. PG - 18542 LID - 10.1038/s41598-020-75387-w [doi] LID - 18542 AB - Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate genotype imputation from > 1 × coverage data have recently become a routine, a large proportion of ancient samples remain unusable for downstream analyses due to their low coverage. Here, we evaluate a two-step pipeline for the imputation of common variants in ancient genomes at 0.05-1 × coverage. We use the genotype likelihood input mode in Beagle and filter for confident genotypes as the input to impute missing genotypes. This procedure, when tested on ancient genomes, outperforms a single-step imputation from genotype likelihoods, suggesting that current genotype callers do not fully account for errors in ancient sequences and additional quality controls can be beneficial. We compared the effect of various genotype likelihood calling methods, post-calling, pre-imputation and post-imputation filters, different reference panels, as well as different imputation tools. In a Neolithic Hungarian genome, we obtain ~ 90% imputation accuracy for heterozygous common variants at coverage 0.05 × and > 97% accuracy at coverage 0.5 ×. We show that imputation can mitigate, though not eliminate reference bias in ultra-low coverage ancient genomes. FAU - Hui, Ruoyun AU - Hui R AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK. FAU - D'Atanasio, Eugenia AU - D'Atanasio E AD - Department of Human Genetics, Katholieke Universiteit Leuven, Herestraat 49 - box 602, 3000, Leuven, Belgium. AD - Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy. FAU - Cassidy, Lara M AU - Cassidy LM AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. FAU - Scheib, Christiana L AU - Scheib CL AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia. AD - St John's College, St John's Street, Cambridge, CB2 1TP, UK. FAU - Kivisild, Toomas AU - Kivisild T AD - Department of Human Genetics, Katholieke Universiteit Leuven, Herestraat 49 - box 602, 3000, Leuven, Belgium. toomas.kivisild@kuleuven.be. AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia. toomas.kivisild@kuleuven.be. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom GR - 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201029 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/*analysis MH - Genome, Human/*genetics MH - Genotype MH - Humans MH - Polymorphism, Single Nucleotide/genetics MH - Software PMC - PMC7596702 COIS- The authors declare no competing interests. EDAT- 2020/10/31 06:00 MHDA- 2021/03/05 06:00 PMCR- 2020/10/29 CRDT- 2020/10/30 05:48 PHST- 2020/05/13 00:00 [received] PHST- 2020/10/12 00:00 [accepted] PHST- 2020/10/30 05:48 [entrez] PHST- 2020/10/31 06:00 [pubmed] PHST- 2021/03/05 06:00 [medline] PHST- 2020/10/29 00:00 [pmc-release] AID - 10.1038/s41598-020-75387-w [pii] AID - 75387 [pii] AID - 10.1038/s41598-020-75387-w [doi] PST - epublish SO - Sci Rep. 2020 Oct 29;10(1):18542. doi: 10.1038/s41598-020-75387-w. PMID- 33106554 OWN - NLM STAT- MEDLINE DCOM- 20210312 LR - 20231104 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 10 IP - 1 DP - 2020 Oct 26 TI - A systematic investigation of human DNA preservation in medieval skeletons. PG - 18225 LID - 10.1038/s41598-020-75163-w [doi] LID - 18225 AB - Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies. FAU - Parker, Cody AU - Parker C AD - Max Planck Institute for the Science of Human History, Jena, Germany. parker@shh.mpg.de. FAU - Rohrlach, Adam B AU - Rohrlach AB AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA, Australia. FAU - Friederich, Susanne AU - Friederich S AD - Landesamt für Denkmalpflege und Archäologie, Sachsen-Anhalt, Halle (Saale), Germany. FAU - Nagel, Sarah AU - Nagel S AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Meyer, Matthias AU - Meyer M AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena, Germany. krause@shh.mpg.de. FAU - Bos, Kirsten I AU - Bos KI AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Haak, Wolfgang AU - Haak W AD - Max Planck Institute for the Science of Human History, Jena, Germany. haak@shh.mpg.de. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201026 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Bone and Bones/*metabolism MH - DNA, Ancient/analysis/*chemistry/*isolation & purification MH - Ear, Inner/*metabolism MH - Germany MH - History, Medieval MH - Humans MH - Petrous Bone/*metabolism MH - Preservation, Biological/*methods MH - Tooth/*metabolism PMC - PMC7588426 COIS- The authors declare no competing interests. EDAT- 2020/10/28 06:00 MHDA- 2021/03/13 06:00 PMCR- 2020/10/26 CRDT- 2020/10/27 05:44 PHST- 2020/05/23 00:00 [received] PHST- 2020/10/07 00:00 [accepted] PHST- 2020/10/27 05:44 [entrez] PHST- 2020/10/28 06:00 [pubmed] PHST- 2021/03/13 06:00 [medline] PHST- 2020/10/26 00:00 [pmc-release] AID - 10.1038/s41598-020-75163-w [pii] AID - 75163 [pii] AID - 10.1038/s41598-020-75163-w [doi] PST - epublish SO - Sci Rep. 2020 Oct 26;10(1):18225. doi: 10.1038/s41598-020-75163-w. PMID- 33046824 OWN - NLM STAT- MEDLINE DCOM- 20201224 LR - 20211012 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 10 IP - 1 DP - 2020 Oct 12 TI - The first reported case of the rare mitochondrial haplotype H4a1 in ancient Egypt. PG - 17037 LID - 10.1038/s41598-020-74114-9 [doi] LID - 17037 AB - Takabuti, was a female who lived in ancient Egypt during the 25th Dynasty, c.660 BCE. Her mummified remains were brought to Belfast, Northern Ireland, in 1834 and are currently displayed in the Ulster Museum. To gain insight into Takabuti's ancestry, we used deep sampling of vertebral bone, under X-ray control, to obtain non-contaminated bone tissue from which we extracted ancient DNA (aDNA) using established protocols. We targeted the maternally inherited mitochondrial DNA (mtDNA), known to be highly informative for human ancestry, and identified 38 single nucleotide variants using next generation sequencing. The specific combination of these SNVs suggests that Takabuti belonged to mitochondrial haplogroup H4a1. Neither H4 nor H4a1 have been reported in ancient Egyptian samples, prior to this study. The modern distribution of H4a1 is rare and sporadic and has been identified in areas including the Canary Islands, southern Iberia and the Lebanon. H4a1 has also been reported in ancient samples from Bell Beaker and Unetice contexts in Germany, as well as Bronze Age Bulgaria. We believe that this is an important finding because first, it adds to the depth of knowledge about the distribution of the H4a1 haplogroup in existing mtDNA, thus creating a baseline for future occurrences of this haplogroup in ancient Egyptian remains. Second, it is of great importance for archaeological sciences, since a predominantly European haplogroup has been identified in an Egyptian individual in Southern Egypt, prior to the Roman and Greek influx (332BCE). FAU - Drosou, Konstantina AU - Drosou K AD - KNH Centre for Biomedical Egyptology, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, M13 9PG, UK. konstantina.drosou@manchester.ac.uk. AD - Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK. konstantina.drosou@manchester.ac.uk. FAU - Collin, Thomas C AU - Collin TC AD - School of Medicine, University College Dublin, Dublin 4, Ireland. FAU - Freeman, Peter J AU - Freeman PJ AD - Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, M19 9PG, UK. FAU - Loynes, Robert AU - Loynes R AD - KNH Centre for Biomedical Egyptology, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, M13 9PG, UK. FAU - Freemont, Tony AU - Freemont T AD - KNH Centre for Biomedical Egyptology, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, M13 9PG, UK. LA - eng GR - MR/N00583X/1/MRC_/Medical Research Council/United Kingdom PT - Historical Article PT - Journal Article DEP - 20201012 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - Egypt, Ancient MH - Female MH - Haplotypes/*genetics MH - High-Throughput Nucleotide Sequencing MH - History, Ancient MH - Humans MH - Mitochondria/*genetics PMC - PMC7550590 COIS- The authors declare no competing interests. EDAT- 2020/10/14 06:00 MHDA- 2020/12/29 06:00 PMCR- 2020/10/12 CRDT- 2020/10/13 05:36 PHST- 2020/04/21 00:00 [received] PHST- 2020/09/04 00:00 [accepted] PHST- 2020/10/13 05:36 [entrez] PHST- 2020/10/14 06:00 [pubmed] PHST- 2020/12/29 06:00 [medline] PHST- 2020/10/12 00:00 [pmc-release] AID - 10.1038/s41598-020-74114-9 [pii] AID - 74114 [pii] AID - 10.1038/s41598-020-74114-9 [doi] PST - epublish SO - Sci Rep. 2020 Oct 12;10(1):17037. doi: 10.1038/s41598-020-74114-9. PMID- 33022266 OWN - NLM STAT- MEDLINE DCOM- 20210810 LR - 20240807 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 30 IP - 19 DP - 2020 Oct 5 TI - The Recovery, Interpretation and Use of Ancient Pathogen Genomes. PG - R1215-R1231 LID - S0960-9822(20)31271-9 [pii] LID - 10.1016/j.cub.2020.08.081 [doi] AB - The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest - pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) - and for three equally important endemic human disease agents - Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20(th) century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens. CI - Crown Copyright © 2020. Published by Elsevier Inc. All rights reserved. FAU - Duchêne, Sebastián AU - Duchêne S AD - Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia. Electronic address: sebastian.duchene@unimelb.edu.au. FAU - Ho, Simon Y W AU - Ho SYW AD - School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia. FAU - Carmichael, Ann G AU - Carmichael AG AD - History Department, Indiana University, Bloomington, IN, USA. FAU - Holmes, Edward C AU - Holmes EC AD - Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia. Electronic address: edward.holmes@sydney.edu.au. FAU - Poinar, Hendrik AU - Poinar H AD - McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L9, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada. Electronic address: poinarh@mcmaster.ca. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) RN - Treponema pallidum subsp. pallidum SB - IM MH - Animals MH - Bacteria/genetics/*pathogenicity MH - Biological Evolution MH - DNA, Ancient/*analysis MH - DNA, Bacterial/*genetics MH - Evolution, Molecular MH - Genome/genetics MH - Genome, Bacterial/genetics MH - Genomics/methods MH - Humans MH - Microbiota/genetics MH - Mycobacterium leprae/genetics MH - Mycobacterium tuberculosis/genetics MH - Phylogeny MH - Treponema/genetics MH - Variola virus/genetics MH - Vibrio cholerae/genetics MH - Yersinia pestis/genetics PMC - PMC7534838 EDAT- 2020/10/07 06:00 MHDA- 2021/08/11 06:00 PMCR- 2020/10/05 CRDT- 2020/10/06 20:10 PHST- 2020/10/06 20:10 [entrez] PHST- 2020/10/07 06:00 [pubmed] PHST- 2021/08/11 06:00 [medline] PHST- 2020/10/05 00:00 [pmc-release] AID - S0960-9822(20)31271-9 [pii] AID - 10.1016/j.cub.2020.08.081 [doi] PST - ppublish SO - Curr Biol. 2020 Oct 5;30(19):R1215-R1231. doi: 10.1016/j.cub.2020.08.081. PMID- 32795443 OWN - NLM STAT- MEDLINE DCOM- 20210810 LR - 20210810 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 30 IP - 19 DP - 2020 Oct 5 TI - Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe. PG - 3788-3803.e10 LID - S0960-9822(20)31083-6 [pii] LID - 10.1016/j.cub.2020.07.058 [doi] AB - Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15(th) century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood. CI - Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Majander, Kerttu AU - Majander K AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland. Electronic address: kerttu.majander@uzh.ch. FAU - Pfrengle, Saskia AU - Pfrengle S AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany. FAU - Kocher, Arthur AU - Kocher A AD - Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany. FAU - Neukamm, Judith AU - Neukamm J AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany. FAU - du Plessis, Louis AU - du Plessis L AD - Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK. FAU - Pla-Díaz, Marta AU - Pla-Díaz M AD - Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. FAU - Arora, Natasha AU - Arora N AD - Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zurich, Switzerland. FAU - Akgül, Gülfirde AU - Akgül G AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. FAU - Salo, Kati AU - Salo K AD - Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland; Archaeology, Faculty of Arts, University of Helsinki, Unioninkatu 38F, 00014 Helsinki, Finland. FAU - Schats, Rachel AU - Schats R AD - Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333CC Leiden, the Netherlands. FAU - Inskip, Sarah AU - Inskip S AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK. FAU - Oinonen, Markku AU - Oinonen M AD - Laboratory of Chronology, Finnish Museum of Natural History, University of Helsinki, Gustaf Hällströmin katu 2, 00560 Helsinki, Finland. FAU - Valk, Heiki AU - Valk H AD - Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Tartumaa, Estonia. FAU - Malve, Martin AU - Malve M AD - Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Tartumaa, Estonia. FAU - Kriiska, Aivar AU - Kriiska A AD - Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Tartumaa, Estonia. FAU - Onkamo, Päivi AU - Onkamo P AD - Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland; Department of Biology, University of Turku, Vesilinnantie 5, 20500 Turku, Finland. FAU - González-Candelas, Fernando AU - González-Candelas F AD - Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. FAU - Kühnert, Denise AU - Kühnert D AD - Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany. FAU - Krause, Johannes AU - Krause J AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Tübingen, Germany. Electronic address: krause@shh.mpg.de. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Tübingen, Germany. Electronic address: verena.schuenemann@iem.uzh.ch. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200813 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM CIN - Curr Biol. 2020 Oct 5;30(19):R1092-R1095. doi: 10.1016/j.cub.2020.08.022. PMID: 33022244 MH - Archaeology MH - DNA, Ancient/*analysis MH - Europe MH - Genetic Variation/genetics MH - Genome, Bacterial/*genetics MH - History, 15th Century MH - History, Medieval MH - Humans MH - Syphilis/genetics/history/microbiology MH - Treponema pallidum/*genetics/metabolism MH - Yaws/genetics/history/microbiology OTO - NOTNLM OT - Treponema pallidum OT - ancient DNA OT - pathogen evolution OT - syphilis OT - yaws COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2020/08/17 06:00 MHDA- 2021/08/11 06:00 CRDT- 2020/08/16 06:00 PHST- 2020/02/19 00:00 [received] PHST- 2020/04/24 00:00 [revised] PHST- 2020/07/16 00:00 [accepted] PHST- 2020/08/17 06:00 [pubmed] PHST- 2021/08/11 06:00 [medline] PHST- 2020/08/16 06:00 [entrez] AID - S0960-9822(20)31083-6 [pii] AID - 10.1016/j.cub.2020.07.058 [doi] PST - ppublish SO - Curr Biol. 2020 Oct 5;30(19):3788-3803.e10. doi: 10.1016/j.cub.2020.07.058. Epub 2020 Aug 13. PMID- 32963029 OWN - NLM STAT- MEDLINE DCOM- 20211116 LR - 20211116 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 30 IP - 10 DP - 2020 Oct TI - Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples. PG - 1449-1457 LID - 10.1101/gr.263863.120 [doi] AB - Extensive manipulations involved in the preparation of DNA samples for sequencing have hitherto made it impossible to determine the precise structure of double-stranded DNA fragments being sequenced, such as the presence of blunt ends, single-stranded overhangs, or single-strand breaks. We here describe MatchSeq, a method that combines single-stranded DNA library preparation from diluted DNA samples with computational sequence matching, allowing the reconstruction of double-stranded DNA fragments on a single-molecule level. The application of MatchSeq to Neanderthal DNA, a particularly complex source of degraded DNA, reveals that 1- or 2-nt overhangs and blunt ends dominate the ends of ancient DNA molecules and that short gaps exist, which are predominantly caused by the loss of individual purines. We further show that deamination of cytosine to uracil occurs in both single- and double-stranded contexts close to the ends of molecules, and that single-stranded parts of DNA fragments are enriched in pyrimidines. MatchSeq provides unprecedented resolution for interrogating the structures of fragmented double-stranded DNA and can be applied to fragmented double-stranded DNA isolated from any biological source. The method relies on well-established laboratory techniques and can easily be integrated into routine data generation. This possibility is shown by the successful reconstruction of double-stranded DNA fragments from previously published single-stranded sequence data, allowing a more comprehensive characterization of the biochemical properties not only of ancient DNA but also of cell-free DNA from human blood plasma, a clinically relevant marker for the diagnosis and monitoring of disease. CI - © 2020 Bokelmann et al.; Published by Cold Spring Harbor Laboratory Press. FAU - Bokelmann, Lukas AU - Bokelmann L AUID- ORCID: 0000-0001-9170-7236 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Glocke, Isabelle AU - Glocke I AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Meyer, Matthias AU - Meyer M AUID- ORCID: 0000-0002-4760-558X AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200922 PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (Cell-Free Nucleic Acids) RN - 0 (DNA, Ancient) RN - 8J337D1HZY (Cytosine) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Cell-Free Nucleic Acids/blood MH - Cytosine/metabolism MH - DNA/blood MH - DNA, Ancient/*chemistry MH - Deamination MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Neanderthals/genetics MH - Sequence Analysis, DNA/*methods PMC - PMC7605269 EDAT- 2020/09/24 06:00 MHDA- 2021/11/17 06:00 PMCR- 2021/04/01 CRDT- 2020/09/23 06:28 PHST- 2020/03/24 00:00 [received] PHST- 2020/08/07 00:00 [accepted] PHST- 2020/09/24 06:00 [pubmed] PHST- 2021/11/17 06:00 [medline] PHST- 2020/09/23 06:28 [entrez] PHST- 2021/04/01 00:00 [pmc-release] AID - gr.263863.120 [pii] AID - 10.1101/gr.263863.120 [doi] PST - ppublish SO - Genome Res. 2020 Oct;30(10):1449-1457. doi: 10.1101/gr.263863.120. Epub 2020 Sep 22. PMID- 32632332 OWN - NLM STAT- MEDLINE DCOM- 20201201 LR - 20210216 IS - 2397-3374 (Electronic) IS - 2397-3374 (Linking) VI - 4 IP - 10 DP - 2020 Oct TI - Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE. PG - 1004-1010 LID - 10.1038/s41562-020-0897-7 [doi] AB - The Neolithic transition in Europe was driven by the rapid dispersal of Near Eastern farmers who, over a period of 3,500 years, brought food production to the furthest corners of the continent. However, this wave of expansion was far from homogeneous, and climatic factors may have driven a marked slowdown observed at higher latitudes. Here, we test this hypothesis by assembling a large database of archaeological dates of first arrival of farming to quantify the expansion dynamics. We identify four axes of expansion and observe a slowdown along three axes when crossing the same climatic threshold. This threshold reflects the quality of the growing season, suggesting that Near Eastern crops might have struggled under more challenging climatic conditions. This same threshold also predicts the mixing of farmers and hunter-gatherers as estimated from ancient DNA, suggesting that unreliable yields in these regions might have favoured the contact between the two groups. FAU - Betti, Lia AU - Betti L AUID- ORCID: 0000-0003-2895-9718 AD - Centre for Research in Evolutionary, Social and Inter-Disciplinary Anthropology, Department of Life Sciences, University of Roehampton, London, UK. lia.betti@roehampton.ac.uk. FAU - Beyer, Robert M AU - Beyer RM AUID- ORCID: 0000-0003-2673-3096 AD - Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK. rb792@cam.ac.uk. AD - PAVE Research Group, Department of Archaeology, University of Cambridge, Cambridge, UK. rb792@cam.ac.uk. FAU - Jones, Eppie R AU - Jones ER AUID- ORCID: 0000-0002-4590-5415 AD - Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK. FAU - Eriksson, Anders AU - Eriksson A AUID- ORCID: 0000-0003-3436-3726 AD - Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK. AD - Department of Medical and Molecular Genetics, King's College London, Guys Hospital, London, UK. AD - cGEM, Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Tassi, Francesca AU - Tassi F AUID- ORCID: 0000-0001-8310-323X AD - Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy. FAU - Siska, Veronika AU - Siska V AUID- ORCID: 0000-0002-8057-1203 AD - Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK. FAU - Leonardi, Michela AU - Leonardi M AUID- ORCID: 0000-0001-8933-9374 AD - Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK. FAU - Maisano Delser, Pierpaolo AU - Maisano Delser P AUID- ORCID: 0000-0002-1844-1715 AD - Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK. AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. FAU - Bentley, Lily K AU - Bentley LK AUID- ORCID: 0000-0002-0365-6385 AD - Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK. FAU - Nigst, Philip R AU - Nigst PR AUID- ORCID: 0000-0001-7330-8768 AD - Department of Archaeology, University of Cambridge, Cambridge, UK. FAU - Stock, Jay T AU - Stock JT AUID- ORCID: 0000-0003-0147-8631 AD - PAVE Research Group, Department of Archaeology, University of Cambridge, Cambridge, UK. AD - Department of Anthropology, University of Western Ontario, London, Ontario, Canada. AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Manica, Andrea AU - Manica A AUID- ORCID: 0000-0003-1895-450X AD - Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK. am315@cam.ac.uk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200706 PL - England TA - Nat Hum Behav JT - Nature human behaviour JID - 101697750 RN - 0 (DNA, Ancient) SB - IM MH - Agriculture/*history MH - *Climate MH - *DNA, Ancient MH - Europe MH - History, Ancient MH - Humans MH - Middle East MH - *Paleontology MH - Population Dynamics/*history EDAT- 2020/07/08 06:00 MHDA- 2020/12/02 06:00 CRDT- 2020/07/08 06:00 PHST- 2019/01/14 00:00 [received] PHST- 2020/05/18 00:00 [accepted] PHST- 2020/07/08 06:00 [pubmed] PHST- 2020/12/02 06:00 [medline] PHST- 2020/07/08 06:00 [entrez] AID - 10.1038/s41562-020-0897-7 [pii] AID - 10.1038/s41562-020-0897-7 [doi] PST - ppublish SO - Nat Hum Behav. 2020 Oct;4(10):1004-1010. doi: 10.1038/s41562-020-0897-7. Epub 2020 Jul 6. PMID- 32557548 OWN - NLM STAT- MEDLINE DCOM- 20210301 LR - 20210301 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 173 IP - 2 DP - 2020 Oct TI - New insights on Neolithic food and mobility patterns in Mediterranean coastal populations. PG - 218-235 LID - 10.1002/ajpa.24089 [doi] AB - OBJECTIVES: The aims of this research are to explore the diet, mobility, social organization, and environmental exploitation patterns of early Mediterranean farmers, particularly the role of marine and plant resources in these foodways. In addition, this work strives to document possible gendered patterns of behavior linked to the neolithization of this ecologically rich area. To achieve this, a set of multiproxy analyses (isotopic analyses, dental calculus, microremains analysis, ancient DNA) were performed on an exceptional deposit (n = 61) of human remains from the Les Bréguières site (France), dating to the transition of the sixth to the fifth millennium BCE. MATERIALS AND METHODS: The samples used in this study were excavated from the Les Bréguières site (Mougins, Alpes-Maritimes, France), located along the southeastern Mediterranean coastline of France. Stable isotope analyses (C, N) on bone collagen (17 coxal bones, 35 craniofacial elements) were performed as a means to infer protein intake during tissue development. Sulfur isotope ratios were used as indicators of geographical and environmental points of origin. The study of ancient dental calculus helped document the consumption of plants. Strontium isotope analysis on tooth enamel (n = 56) was conducted to infer human provenance and territorial mobility. Finally, ancient DNA analysis was performed to study maternal versus paternal diversity within this Neolithic group (n = 30). RESULTS: Stable isotope ratios for human bones range from -20.3 to -18.1‰ for C, from 8.9 to 11.1‰ for N and from 6.4 to 15‰ for S. Domestic animal data range from -22.0 to -20.2‰ for C, from 4.1 to 6.9‰ for N, and from 10.2 to 12.5‰ for S. Human enamel (87) Sr/(86) Sr range from 0.7081 to 0.7102, slightly wider than the animal range (between 0.7087 and 0.7096). Starch and phytolith microremains were recovered as well as other types of remains (e.g., hairs, diatoms, fungal spores). Starch grains include Triticeae type and phytolith includes dicotyledons and monocot types as panicoid grasses. Mitochondrial DNA characterized eight different maternal lineages: H1, H3, HV (5.26%), J (10.53%), J1, K, T (5.2%), and U5 (10.53%) but no sample yielded reproducible Y chromosome SNPs, preventing paternal lineage characterization. DISCUSSION: Carbon and nitrogen stable isotope ratios indicate a consumption of protein by humans mainly focused on terrestrial animals and possible exploitation of marine resources for one male and one undetermined adult. Sulfur stable isotope ratios allowed distinguishing groups with different geographical origins, including two females possibly more exposed to the sea spray effect. While strontium isotope data do not indicate different origins for the individuals, mitochondrial lineage diversity from petrous bone DNA suggests the burial includes genetically differentiated groups or a group practicing patrilocality. Moreover, the diversity of plant microremains recorded in dental calculus provide the first evidence that the groups of Les Bréguières consumed a wide breadth of plant foods (as cereals and wild taxa) that required access to diverse environments. This transdisciplinary research paves the way for new perspectives and highlights the relevance for novel research of contexts (whether recently discovered or in museum collections) excavated near shorelines, due to the richness of the biodiversity and the wide range of edible resources available. CI - © 2020 Wiley Periodicals, Inc. FAU - Goude, Gwenaëlle AU - Goude G AUID- ORCID: 0000-0002-3008-3607 AD - Aix Marseille Univ, CNRS, Minist. Culture, LAMPEA, Aix-en-Provence, France. FAU - Salazar-García, Domingo C AU - Salazar-García DC AD - Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain. AD - Aix Marseille Univ, IMERA, Marseille, France. AD - Department of Geological Sciences, University of Cape Town, Cape Town, South Africa. AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain. FAU - Power, Robert C AU - Power RC AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Rivollat, Maïté AU - Rivollat M AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Bordeaux University, Pessac, France. FAU - Gourichon, Lionel AU - Gourichon L AD - Université Côte d'Azur, CNRS, CEPAM, France. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - Bordeaux University, Pessac, France. FAU - Pemonge, Marie-Hélène AU - Pemonge MH AD - Bordeaux University, Pessac, France. FAU - Bouby, Laurent AU - Bouby L AD - ISEM-Université Montpellier, CNRS, EPHE, IRD, Montpellier, France. FAU - Binder, Didier AU - Binder D AD - Université Côte d'Azur, CNRS, CEPAM, France. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200618 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - 0 (Isotopes) SB - IM MH - Animals MH - Anthropology, Physical MH - Bone and Bones/chemistry MH - DNA, Ancient/analysis MH - DNA, Mitochondrial MH - Dental Calculus/history MH - Diet/*history MH - Edible Grain/genetics MH - Food/history MH - France MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Isotopes/analysis MH - Mediterranean Region OTO - NOTNLM OT - ancient DNA OT - dental calculus OT - marine resources OT - radiocarbon date OT - stable isotopes EDAT- 2020/06/20 06:00 MHDA- 2021/03/02 06:00 CRDT- 2020/06/20 06:00 PHST- 2019/06/15 00:00 [received] PHST- 2020/05/12 00:00 [revised] PHST- 2020/05/14 00:00 [accepted] PHST- 2020/06/20 06:00 [pubmed] PHST- 2021/03/02 06:00 [medline] PHST- 2020/06/20 06:00 [entrez] AID - 10.1002/ajpa.24089 [doi] PST - ppublish SO - Am J Phys Anthropol. 2020 Oct;173(2):218-235. doi: 10.1002/ajpa.24089. Epub 2020 Jun 18. PMID- 32973032 OWN - NLM STAT- MEDLINE DCOM- 20201204 LR - 20220129 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 369 IP - 6511 DP - 2020 Sep 25 TI - The evolutionary history of Neanderthal and Denisovan Y chromosomes. PG - 1653-1656 LID - 10.1126/science.abb6460 [doi] AB - Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans. CI - Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. FAU - Petr, Martin AU - Petr M AUID- ORCID: 0000-0003-4879-8421 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. mp@bodkan.net kelso@eva.mpg.de. FAU - Hajdinjak, Mateja AU - Hajdinjak M AUID- ORCID: 0000-0002-4064-0331 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. AD - The Francis Crick Institute, NW1 1AT London, UK. FAU - Fu, Qiaomei AU - Fu Q AUID- ORCID: 0000-0002-7141-0002 AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China. AD - CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China. AD - University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Essel, Elena AU - Essel E AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. FAU - Rougier, Hélène AU - Rougier H AUID- ORCID: 0000-0003-0358-0285 AD - Department of Anthropology, California State University, Northridge, Northridge, CA 91330-8244, USA. FAU - Crevecoeur, Isabelle AU - Crevecoeur I AUID- ORCID: 0000-0002-1781-3206 AD - Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France. FAU - Semal, Patrick AU - Semal P AUID- ORCID: 0000-0002-4048-7728 AD - Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium. FAU - Golovanova, Liubov V AU - Golovanova LV AD - ANO Laboratory of Prehistory 14 Linia 3-11, St. Petersburg 1990 34, Russia. FAU - Doronichev, Vladimir B AU - Doronichev VB AD - ANO Laboratory of Prehistory 14 Linia 3-11, St. Petersburg 1990 34, Russia. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AUID- ORCID: 0000-0002-1730-5914 AD - Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, 08003 Barcelona, Spain. FAU - de la Rasilla, Marco AU - de la Rasilla M AUID- ORCID: 0000-0002-5505-0625 AD - Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, 33011 Oviedo, Spain. FAU - Rosas, Antonio AU - Rosas A AUID- ORCID: 0000-0002-5829-9952 AD - Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain. FAU - Shunkov, Michael V AU - Shunkov MV AD - Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. FAU - Kozlikin, Maxim B AU - Kozlikin MB AUID- ORCID: 0000-0001-5082-3345 AD - Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. FAU - Derevianko, Anatoli P AU - Derevianko AP AUID- ORCID: 0000-0003-1156-8331 AD - Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. FAU - Vernot, Benjamin AU - Vernot B AUID- ORCID: 0000-0002-6820-2181 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. FAU - Meyer, Matthias AU - Meyer M AUID- ORCID: 0000-0002-4760-558X AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. FAU - Kelso, Janet AU - Kelso J AUID- ORCID: 0000-0002-3618-322X AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. mp@bodkan.net kelso@eva.mpg.de. LA - eng GR - 694707/ERC_/European Research Council/International PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM CIN - Science. 2020 Sep 25;369(6511):1565-1566. doi: 10.1126/science.abe2766. PMID: 32973019 MH - Animals MH - Chromosomes, Human, Y/genetics MH - DNA, Ancient MH - DNA, Mitochondrial/genetics MH - *Evolution, Molecular MH - Humans MH - *Life History Traits MH - Male MH - Neanderthals/classification/*genetics MH - Phylogeny MH - Y Chromosome/*genetics EDAT- 2020/09/26 06:00 MHDA- 2020/12/15 06:00 CRDT- 2020/09/25 05:53 PHST- 2020/03/09 00:00 [received] PHST- 2020/08/06 00:00 [accepted] PHST- 2020/09/25 05:53 [entrez] PHST- 2020/09/26 06:00 [pubmed] PHST- 2020/12/15 06:00 [medline] AID - 369/6511/1653 [pii] AID - 10.1126/science.abb6460 [doi] PST - ppublish SO - Science. 2020 Sep 25;369(6511):1653-1656. doi: 10.1126/science.abb6460. PMID- 32970680 OWN - NLM STAT- MEDLINE DCOM- 20201027 LR - 20201027 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 15 IP - 9 DP - 2020 TI - Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease. PG - e0233666 LID - 10.1371/journal.pone.0233666 [doi] LID - e0233666 AB - Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics. FAU - Toncheva, Draga AU - Toncheva D AD - Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria. AD - Bulgarian Academy of Sciences-BAS, Sofia, Bulgaria. FAU - Serbezov, Dimitar AU - Serbezov D AD - Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria. FAU - Karachanak-Yankova, Sena AU - Karachanak-Yankova S AD - Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria. AD - Department of Genetics, Faculty of biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria. FAU - Nesheva, Desislava AU - Nesheva D AD - Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria. LA - eng PT - Journal Article DEP - 20200924 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - 9014-25-9 (RNA, Transfer) SB - IM MH - *DNA, Ancient MH - DNA, Mitochondrial/*genetics MH - Databases, Genetic MH - Female MH - *Genes, Mitochondrial MH - Humans MH - Male MH - Mitochondria/genetics MH - Mitochondrial Diseases/*genetics MH - Mutation MH - RNA, Transfer/genetics PMC - PMC7514063 COIS- The authors have declared that no competing interests exist. EDAT- 2020/09/25 06:00 MHDA- 2020/10/28 06:00 PMCR- 2020/09/24 CRDT- 2020/09/24 17:14 PHST- 2020/05/09 00:00 [received] PHST- 2020/08/09 00:00 [accepted] PHST- 2020/09/24 17:14 [entrez] PHST- 2020/09/25 06:00 [pubmed] PHST- 2020/10/28 06:00 [medline] PHST- 2020/09/24 00:00 [pmc-release] AID - PONE-D-20-13726 [pii] AID - 10.1371/journal.pone.0233666 [doi] PST - epublish SO - PLoS One. 2020 Sep 24;15(9):e0233666. doi: 10.1371/journal.pone.0233666. eCollection 2020. PMID- 32943505 OWN - NLM STAT- MEDLINE DCOM- 20201201 LR - 20201201 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 369 IP - 6510 DP - 2020 Sep 18 TI - Ancient DNA tracks Vikings across Europe. PG - 1416-1417 LID - 10.1126/science.369.6510.1416 [doi] FAU - Curry, Andrew AU - Curry A AD - Andrew Curry is a journalist in Berlin. LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Scandinavian and Nordic Countries/ethnology MH - Skeleton EDAT- 2020/09/19 06:00 MHDA- 2020/12/02 06:00 CRDT- 2020/09/18 05:42 PHST- 2020/09/18 05:42 [entrez] PHST- 2020/09/19 06:00 [pubmed] PHST- 2020/12/02 06:00 [medline] AID - 369/6510/1416 [pii] AID - 10.1126/science.369.6510.1416 [doi] PST - ppublish SO - Science. 2020 Sep 18;369(6510):1416-1417. doi: 10.1126/science.369.6510.1416. PMID- 32943086 OWN - NLM STAT- MEDLINE DCOM- 20210611 LR - 20240329 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 21 IP - 1 DP - 2020 Sep 17 TI - Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph. PG - 250 LID - 10.1186/s13059-020-02160-7 [doi] LID - 250 AB - BACKGROUND: During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for aDNA and compare with existing methods. RESULTS: We use vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants and compare with the same data aligned with bwa to the human linear reference genome. Using vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias but can have lower sensitivity than vg, particularly for indels. CONCLUSIONS: Our findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analyzing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed. FAU - Martiniano, Rui AU - Martiniano R AD - Department of Genetics, University of Cambridge, Cambridge, CB3 0DH, UK. FAU - Garrison, Erik AU - Garrison E AD - Wellcome Sanger Institute, Cambridge, CB10 1SA, UK. AD - Genomics Institute, University of California, Santa Cruz, CA 95064, USA. FAU - Jones, Eppie R AU - Jones ER AD - Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK. FAU - Manica, Andrea AU - Manica A AD - Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK. FAU - Durbin, Richard AU - Durbin R AD - Department of Genetics, University of Cambridge, Cambridge, CB3 0DH, UK. richard.durbin@gen.cam.ac.uk. AD - Wellcome Sanger Institute, Cambridge, CB10 1SA, UK. richard.durbin@gen.cam.ac.uk. LA - eng GR - 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom GR - WT207492/WT_/Wellcome Trust/United Kingdom GR - WT206194/WT_/Wellcome Trust/United Kingdom PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200917 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/*analysis MH - *Genome, Human MH - Humans MH - *INDEL Mutation MH - Reference Standards MH - Sequence Analysis, DNA/*methods/standards PMC - PMC7499850 OTO - NOTNLM OT - Ancient DNA OT - Reference bias OT - Sequence alignment OT - Variation graph COIS- The authors declare that they have no competing interests. EDAT- 2020/09/19 06:00 MHDA- 2021/06/12 06:00 PMCR- 2020/09/17 CRDT- 2020/09/18 05:33 PHST- 2019/09/27 00:00 [received] PHST- 2020/08/27 00:00 [accepted] PHST- 2020/09/18 05:33 [entrez] PHST- 2020/09/19 06:00 [pubmed] PHST- 2021/06/12 06:00 [medline] PHST- 2020/09/17 00:00 [pmc-release] AID - 10.1186/s13059-020-02160-7 [pii] AID - 2160 [pii] AID - 10.1186/s13059-020-02160-7 [doi] PST - epublish SO - Genome Biol. 2020 Sep 17;21(1):250. doi: 10.1186/s13059-020-02160-7. PMID- 32938925 OWN - NLM STAT- MEDLINE DCOM- 20201002 LR - 20240329 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 11 IP - 1 DP - 2020 Sep 16 TI - Factor analysis of ancient population genomic samples. PG - 4661 LID - 10.1038/s41467-020-18335-6 [doi] LID - 4661 AB - The recent years have seen a growing number of studies investigating evolutionary questions using ancient DNA. To address these questions, one of the most frequently-used method is principal component analysis (PCA). When PCA is applied to temporal samples, the sample dates are, however, ignored during analysis, leading to imperfect representations of samples in PC plots. Here, we present a factor analysis (FA) method in which individual scores are corrected for the effect of allele frequency drift over time. We obtained exact solutions for the estimates of corrected factors, and we provided a fast algorithm for their computation. Using computer simulations and ancient European samples, we compared geometric representations obtained from FA with PCA and with ancestry estimation programs. In admixture analyses, FA estimates agreed with tree-based statistics, and they were more accurate than those obtained from PCA projections and from ancestry estimation programs. A great advantage of FA over existing approaches is to improve descriptive analyses of ancient DNA samples without requiring inclusion of outgroup or present-day samples. FAU - François, Olivier AU - François O AUID- ORCID: 0000-0003-2402-2442 AD - Université Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble INP, Laboratoire TIMC-IMAG UMR 5525, 38000, Grenoble, France. olivier.francois@univ-grenoble-alpes.fr. FAU - Jay, Flora AU - Jay F AUID- ORCID: 0000-0001-5884-4730 AD - Université Paris-Saclay, Centre National de la Recherche Scientifique, Inria, Laboratoire de Recherche en Informatique UMR 8623, Bâtiment 650 Ada Lovelace, 91405, Orsay Cedex, France. flora.jay@lri.fr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200916 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) SB - IM MH - Algorithms MH - DNA, Ancient/*analysis MH - England MH - Europe MH - *Factor Analysis, Statistical MH - Gene Frequency MH - Genetic Drift MH - Genetics, Population/statistics & numerical data MH - *Genome, Human MH - Humans MH - Metagenomics/*statistics & numerical data MH - Models, Genetic MH - Principal Component Analysis PMC - PMC7494920 COIS- The authors declare no competing interests. EDAT- 2020/09/18 06:00 MHDA- 2020/10/03 06:00 PMCR- 2020/09/16 CRDT- 2020/09/17 05:39 PHST- 2020/01/07 00:00 [received] PHST- 2020/08/18 00:00 [accepted] PHST- 2020/09/17 05:39 [entrez] PHST- 2020/09/18 06:00 [pubmed] PHST- 2020/10/03 06:00 [medline] PHST- 2020/09/16 00:00 [pmc-release] AID - 10.1038/s41467-020-18335-6 [pii] AID - 18335 [pii] AID - 10.1038/s41467-020-18335-6 [doi] PST - epublish SO - Nat Commun. 2020 Sep 16;11(1):4661. doi: 10.1038/s41467-020-18335-6. PMID- 32933569 OWN - NLM STAT- MEDLINE DCOM- 20210611 LR - 20210924 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 21 IP - 1 DP - 2020 Sep 15 TI - AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. PG - 246 LID - 10.1186/s13059-020-02123-y [doi] LID - 246 AB - Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available. FAU - Peyrégne, Stéphane AU - Peyrégne S AUID- ORCID: 0000-0002-9823-9102 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. stephane.peyregne@gmail.com. FAU - Peter, Benjamin M AU - Peter BM AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. LA - eng GR - 694707/ERC_/European Research Council/International PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200915 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (DNA, Ancient) SB - IM MH - *DNA Contamination MH - *DNA Damage MH - DNA, Ancient/*analysis MH - Humans MH - Models, Genetic MH - *Software PMC - PMC7490890 OTO - NOTNLM OT - Ancient DNA OT - Contamination OT - Damage patterns OT - Deamination COIS- The authors declare that they have no competing interests. EDAT- 2020/09/17 06:00 MHDA- 2021/06/12 06:00 PMCR- 2020/09/15 CRDT- 2020/09/16 05:29 PHST- 2020/03/12 00:00 [received] PHST- 2020/07/27 00:00 [accepted] PHST- 2020/09/16 05:29 [entrez] PHST- 2020/09/17 06:00 [pubmed] PHST- 2021/06/12 06:00 [medline] PHST- 2020/09/15 00:00 [pmc-release] AID - 10.1186/s13059-020-02123-y [pii] AID - 2123 [pii] AID - 10.1186/s13059-020-02123-y [doi] PST - epublish SO - Genome Biol. 2020 Sep 15;21(1):246. doi: 10.1186/s13059-020-02123-y. PMID- 32898493 OWN - NLM STAT- MEDLINE DCOM- 20210817 LR - 20241119 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 30 IP - 17 DP - 2020 Sep 7 TI - Increased rate of close-kin unions in the central Andes in the half millennium before European contact. PG - R980-R981 LID - S0960-9822(20)31097-6 [pii] LID - 10.1016/j.cub.2020.07.072 [doi] AB - Analyzing ancient DNA of the central Andes, Ringbauer and colleagues identify a markedly elevated rate of unions of closely related parents after ca. 1000 CE. This change of mating preferences sheds new light on a unique system of social organization based on ancestry ("ayllu") whereby within-group unions were preferred to facilitate sharing of resources. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Ringbauer, Harald AU - Ringbauer H AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Dept. of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA; Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA. FAU - Steinrücken, Matthias AU - Steinrücken M AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA; Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AD - UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Dept. of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Letter PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/*analysis MH - History, Ancient MH - History, Medieval MH - Humans MH - Inbreeding/*history/*methods MH - *Reproduction MH - South America PMC - PMC11571662 MID - NIHMS2033507 COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2020/09/09 06:00 MHDA- 2021/08/18 06:00 PMCR- 2024/11/18 CRDT- 2020/09/08 20:07 PHST- 2020/09/08 20:07 [entrez] PHST- 2020/09/09 06:00 [pubmed] PHST- 2021/08/18 06:00 [medline] PHST- 2024/11/18 00:00 [pmc-release] AID - S0960-9822(20)31097-6 [pii] AID - 10.1016/j.cub.2020.07.072 [doi] PST - ppublish SO - Curr Biol. 2020 Sep 7;30(17):R980-R981. doi: 10.1016/j.cub.2020.07.072. PMID- 32939067 OWN - NLM STAT- MEDLINE DCOM- 20201029 LR - 20210312 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 585 IP - 7825 DP - 2020 Sep TI - Population genomics of the Viking world. PG - 390-396 LID - 10.1038/s41586-020-2688-8 [doi] AB - The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history(1,2). Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent. FAU - Margaryan, Ashot AU - Margaryan A AUID- ORCID: 0000-0002-2576-2429 AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. AD - Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia. AD - Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Lawson, Daniel J AU - Lawson DJ AUID- ORCID: 0000-0002-5311-6213 AD - MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK. AD - School of Statistical Sciences, University of Bristol, Bristol, UK. FAU - Sikora, Martin AU - Sikora M AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Racimo, Fernando AU - Racimo F AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Rasmussen, Simon AU - Rasmussen S AUID- ORCID: 0000-0001-6323-9041 AD - Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Moltke, Ida AU - Moltke I AUID- ORCID: 0000-0001-7052-8554 AD - The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark. FAU - Cassidy, Lara M AU - Cassidy LM AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. FAU - Jørsboe, Emil AU - Jørsboe E AUID- ORCID: 0000-0002-0593-7906 AD - The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark. AD - Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Ingason, Andrés AU - Ingason A AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. AD - Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. AD - Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark. FAU - Pedersen, Mikkel W AU - Pedersen MW AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Korneliussen, Thorfinn AU - Korneliussen T AUID- ORCID: 0000-0001-7576-5380 AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. AD - HSE University, Russian Federation National Research University Higher School of Economics, Moscow, Russia. FAU - Wilhelmson, Helene AU - Wilhelmson H AUID- ORCID: 0000-0002-8422-2369 AD - Department of Archaeology and Ancient History, Lund University, Lund, Sweden. AD - Sydsvensk Arkeologi AB, Kristianstad, Sweden. FAU - Buś, Magdalena M AU - Buś MM AD - Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden. FAU - de Barros Damgaard, Peter AU - de Barros Damgaard P AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Martiniano, Rui AU - Martiniano R AD - Department of Genetics, University of Cambridge, Cambridge, UK. FAU - Renaud, Gabriel AU - Renaud G AUID- ORCID: 0000-0002-0630-027X AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. AD - Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark. FAU - Bhérer, Claude AU - Bhérer C AUID- ORCID: 0000-0002-2744-7246 AD - Department of Human Genetics, McGill University, Montréal, Quebec, Canada. FAU - Moreno-Mayar, J Víctor AU - Moreno-Mayar JV AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. AD - National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico. FAU - Fotakis, Anna K AU - Fotakis AK AD - Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Allen, Marie AU - Allen M AD - Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden. FAU - Allmäe, Raili AU - Allmäe R AD - Archaeological Research Collection, Tallinn University, Tallinn, Estonia. FAU - Molak, Martyna AU - Molak M AUID- ORCID: 0000-0001-5068-8649 AD - Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland. FAU - Cappellini, Enrico AU - Cappellini E AD - Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Scorrano, Gabriele AU - Scorrano G AD - Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - McColl, Hugh AU - McColl H AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Buzhilova, Alexandra AU - Buzhilova A AUID- ORCID: 0000-0001-6398-2177 AD - Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia. FAU - Fox, Allison AU - Fox A AD - Manx National Heritage, Douglas, Isle of Man. FAU - Albrechtsen, Anders AU - Albrechtsen A AUID- ORCID: 0000-0001-7306-031X AD - The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark. FAU - Schütz, Berit AU - Schütz B AD - Upplandsmuseet, Uppsala, Sweden. FAU - Skar, Birgitte AU - Skar B AD - NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway. FAU - Arcini, Caroline AU - Arcini C AD - The Archaeologists, National Historical Museums, Stockholm, Sweden. FAU - Falys, Ceri AU - Falys C AUID- ORCID: 0000-0003-1903-9573 AD - Thames Valley Archaeological Services (TVAS), Reading, UK. FAU - Jonson, Charlotte Hedenstierna AU - Jonson CH AD - Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden. FAU - Błaszczyk, Dariusz AU - Błaszczyk D AD - Institute of Archaeology, University of Warsaw, Warsaw, Poland. FAU - Pezhemsky, Denis AU - Pezhemsky D AD - Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia. FAU - Turner-Walker, Gordon AU - Turner-Walker G AD - Department of Cultural Heritage Conservation, National Yunlin University of Science and Technology, Douliou, Taiwan. FAU - Gestsdóttir, Hildur AU - Gestsdóttir H AD - Institute of Archaeology, Reykjavík, Iceland. FAU - Lundstrøm, Inge AU - Lundstrøm I AD - Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Gustin, Ingrid AU - Gustin I AD - Department of Archaeology and Ancient History, Lund University, Lund, Sweden. FAU - Mainland, Ingrid AU - Mainland I AD - UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK. FAU - Potekhina, Inna AU - Potekhina I AD - Department of Bioarchaeology, Institute of Archaeology of National Academy of Sciences of Ukraine, Kiev, Ukraine. FAU - Muntoni, Italo M AU - Muntoni IM AD - Soprintendenza Archeologia, Belle Arti e Paesaggio per le Province di Barletta, Andria, Trani e Foggia, Foggia, Italy. FAU - Cheng, Jade AU - Cheng J AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Stenderup, Jesper AU - Stenderup J AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Ma, Jilong AU - Ma J AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Gibson, Julie AU - Gibson J AD - UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK. FAU - Peets, Jüri AU - Peets J AD - Archaeological Research Collection, Tallinn University, Tallinn, Estonia. FAU - Gustafsson, Jörgen AU - Gustafsson J AD - Jönköping County Museum, Jönköping, Sweden. FAU - Iversen, Katrine H AU - Iversen KH AD - Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. AD - Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark. FAU - Simpson, Linzi AU - Simpson L AD - Trinity College Dublin, Dublin, Ireland. FAU - Strand, Lisa AU - Strand L AUID- ORCID: 0000-0002-4245-6298 AD - NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway. FAU - Loe, Louise AU - Loe L AD - Heritage Burial Services, Oxford Archaeology, Oxford, UK. FAU - Sikora, Maeve AU - Sikora M AD - National Museum of Ireland, Dublin, Ireland. FAU - Florek, Marek AU - Florek M AUID- ORCID: 0000-0002-9917-710X AD - Institute of Archaeology, Maria Curie-Sklodowska University in Lublin, Lublin, Poland. FAU - Vretemark, Maria AU - Vretemark M AD - Västergötlands Museum, Skara, Sweden. FAU - Redknap, Mark AU - Redknap M AD - Department of History and Archaeology, Amgueddfa Cymru-National Museum Wales, Cardiff, UK. FAU - Bajka, Monika AU - Bajka M AD - Trzy Epoki Archaeological Service, Klimontów, Poland. FAU - Pushkina, Tamara AU - Pushkina T AD - Historical Faculty, Moscow State University, Moscow, Russia. FAU - Søvsø, Morten AU - Søvsø M AD - Museum of Southwest Jutland, Ribe, Denmark. FAU - Grigoreva, Natalia AU - Grigoreva N AD - Department of Slavic-Finnish Archaeology, Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia. FAU - Christensen, Tom AU - Christensen T AD - National Museum of Denmark, Copenhagen, Denmark. FAU - Kastholm, Ole AU - Kastholm O AD - Department of Research and Heritage, Roskilde Museum, Roskilde, Denmark. FAU - Uldum, Otto AU - Uldum O AD - Langelands Museum, Langeland, Denmark. FAU - Favia, Pasquale AU - Favia P AD - Department of Humanities, University of Foggia, Foggia, Italy. FAU - Holck, Per AU - Holck P AD - Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. FAU - Sten, Sabine AU - Sten S AD - Department of Archaeology and Ancient History, Uppsala University Campus Gotland, Visby, Sweden. FAU - Arge, Símun V AU - Arge SV AD - Tjóðsavnið - Faroe Islands National Museum, Tórshavn, Faroe Islands. FAU - Ellingvåg, Sturla AU - Ellingvåg S AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Moiseyev, Vayacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St Petersburg, Russia. FAU - Bogdanowicz, Wiesław AU - Bogdanowicz W AD - Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland. FAU - Magnusson, Yvonne AU - Magnusson Y AUID- ORCID: 0000-0002-7076-2583 AD - Malmö Museum, Malmö, Sweden. FAU - Orlando, Ludovic AU - Orlando L AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France. FAU - Pentz, Peter AU - Pentz P AD - National Museum of Denmark, Copenhagen, Denmark. FAU - Jessen, Mads Dengsø AU - Jessen MD AD - National Museum of Denmark, Copenhagen, Denmark. FAU - Pedersen, Anne AU - Pedersen A AD - National Museum of Denmark, Copenhagen, Denmark. FAU - Collard, Mark AU - Collard M AUID- ORCID: 0000-0002-2725-4989 AD - Department of Archaeology, Simon Fraser University, Burnaby, British Colombia, Canada. FAU - Bradley, Daniel G AU - Bradley DG AUID- ORCID: 0000-0001-7335-7092 AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. FAU - Jørkov, Marie Louise AU - Jørkov ML AD - Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark. FAU - Arneborg, Jette AU - Arneborg J AD - National Museum of Denmark, Copenhagen, Denmark. AD - School of GeoSciences, University of Edinburgh, Edinburgh, UK. FAU - Lynnerup, Niels AU - Lynnerup N AD - Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark. FAU - Price, Neil AU - Price N AD - Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden. FAU - Gilbert, M Thomas P AU - Gilbert MTP AD - Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. AD - Department of Natural History, Norwegian University of Science and Technology (NTNU), Trondheim, Norway. FAU - Allentoft, Morten E AU - Allentoft ME AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. AD - Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia. FAU - Bill, Jan AU - Bill J AD - Museum of Cultural History, University of Oslo, Oslo, Norway. FAU - Sindbæk, Søren M AU - Sindbæk SM AD - Centre for Urban Network Evolutions (UrbNet), School of Culture and Society, Aarhus University, Højbjerg, Denmark. FAU - Hedeager, Lotte AU - Hedeager L AD - Institute of Archaeology, Conservation and History, Oslo, Norway. FAU - Kristiansen, Kristian AU - Kristiansen K AD - Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden. FAU - Nielsen, Rasmus AU - Nielsen R AUID- ORCID: 0000-0003-0513-6591 AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. rasmus_nielsen@berkeley.edu. AD - Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA. rasmus_nielsen@berkeley.edu. AD - Department of Statistics, UC Berkeley, Berkeley, CA, USA. rasmus_nielsen@berkeley.edu. FAU - Werge, Thomas AU - Werge T AUID- ORCID: 0000-0003-1829-0766 AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. Thomas.Werge@regionh.dk. AD - Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. Thomas.Werge@regionh.dk. AD - Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark. Thomas.Werge@regionh.dk. AD - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark. Thomas.Werge@regionh.dk. FAU - Willerslev, Eske AU - Willerslev E AUID- ORCID: 0000-0002-7081-6748 AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. ew482@cam.ac.uk. AD - Department of Zoology, University of Cambridge, Cambridge, UK. ew482@cam.ac.uk. AD - The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark. ew482@cam.ac.uk. AD - The Wellcome Trust Sanger Institute, Cambridge, UK. ew482@cam.ac.uk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200916 PL - England TA - Nature JT - Nature JID - 0410462 RN - EC 3.2.1.108 (Lactase) SB - IM EIN - Nature. 2021 Mar;591(7851):E29. doi: 10.1038/s41586-021-03328-2. PMID: 33707634 MH - Alleles MH - Datasets as Topic MH - England MH - Evolution, Molecular MH - Gene Flow/*genetics MH - *Genetics, Population MH - Genome, Human/*genetics MH - *Genomics MH - Greenland MH - History, Medieval MH - Human Migration/*history MH - Humans MH - Immunity/genetics MH - Ireland MH - Lactase/genetics/metabolism MH - Male MH - Scandinavian and Nordic Countries MH - Selection, Genetic MH - Spatio-Temporal Analysis MH - Young Adult EDAT- 2020/09/18 06:00 MHDA- 2020/10/30 06:00 CRDT- 2020/09/17 05:43 PHST- 2019/07/12 00:00 [received] PHST- 2020/05/21 00:00 [accepted] PHST- 2020/09/17 05:43 [entrez] PHST- 2020/09/18 06:00 [pubmed] PHST- 2020/10/30 06:00 [medline] AID - 10.1038/s41586-020-2688-8 [pii] AID - 10.1038/s41586-020-2688-8 [doi] PST - ppublish SO - Nature. 2020 Sep;585(7825):390-396. doi: 10.1038/s41586-020-2688-8. Epub 2020 Sep 16. PMID- 32674620 OWN - NLM STAT- MEDLINE DCOM- 20210616 LR - 20210616 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 47 IP - 6 DP - 2020 Sep TI - A study of 8,300-year-old Jomon human remains in Japan using complete mitogenome sequences obtained by next-generation sequencing. PG - 555-559 LID - 10.1080/03014460.2020.1797164 [doi] AB - Ancient human remains have been assigned to their mitochondrial DNA (mtDNA) haplogroups. To obtain efficiently deep and reliable nucleotide sequences of ancient DNA of interest, we achieved target enrichment followed by next-generation sequencing (NGS). Complete mitochondrial genome (mitogenome) sequences were obtained for three human remains from the Iyai rock-shelter site of the Initial Jomon Period in Japan. All the Jomon mitogenomes belong to haplogroup N9b, but no sequences among them were identical. High genetic diversity was clarified even among the Jomon human remains belonging to haplogroup N9b, which has been described as a haplogroup representing the Jomon people. FAU - Mizuno, Fuzuki AU - Mizuno F AD - Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan. FAU - Taniguchi, Yasuhiro AU - Taniguchi Y AD - Department of Archaeology, Faculty of Letters, Kokugakuin University, Tokyo, Japan. FAU - Kondo, Osamu AU - Kondo O AD - Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. FAU - Hayashi, Michiko AU - Hayashi M AD - Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan. FAU - Kurosaki, Kunihiko AU - Kurosaki K AD - Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan. FAU - Ueda, Shintaroh AU - Ueda S AD - Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan. AD - Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. LA - eng PT - Journal Article DEP - 20200819 PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - Body Remains MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*analysis MH - *Genome, Mitochondrial MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Japan OTO - NOTNLM OT - Haplogroup N9b OT - Initial jomon period OT - MtDNA OT - ancient DNA OT - mitochondrial genome EDAT- 2020/07/18 06:00 MHDA- 2021/06/17 06:00 CRDT- 2020/07/18 06:00 PHST- 2020/07/18 06:00 [pubmed] PHST- 2021/06/17 06:00 [medline] PHST- 2020/07/18 06:00 [entrez] AID - 10.1080/03014460.2020.1797164 [doi] PST - ppublish SO - Ann Hum Biol. 2020 Sep;47(6):555-559. doi: 10.1080/03014460.2020.1797164. Epub 2020 Aug 19. PMID- 32648350 OWN - NLM STAT- MEDLINE DCOM- 20210818 LR - 20211101 IS - 1521-1878 (Electronic) IS - 0265-9247 (Linking) VI - 42 IP - 9 DP - 2020 Sep TI - Present-Day DNA Contamination in Ancient DNA Datasets. PG - e2000081 LID - 10.1002/bies.202000081 [doi] AB - Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed. CI - © 2020 The Authors. BioEssays published by WILEY Periodicals LLC. FAU - Peyrégne, Stéphane AU - Peyrégne S AUID- ORCID: 0000-0002-9823-9102 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. FAU - Prüfer, Kay AU - Prüfer K AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany. LA - eng GR - 694707/ERC_/European Research Council/International GR - Max-Planck-Gesellschaft/International PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200710 PL - United States TA - Bioessays JT - BioEssays : news and reviews in molecular, cellular and developmental biology JID - 8510851 RN - 0 (DNA, Ancient) SB - IM MH - *DNA Contamination MH - *DNA, Ancient MH - Humans OTO - NOTNLM OT - ancient DNA OT - contamination OT - paleogenomics EDAT- 2020/07/11 06:00 MHDA- 2021/08/19 06:00 CRDT- 2020/07/11 06:00 PHST- 2020/04/14 00:00 [received] PHST- 2020/05/20 00:00 [revised] PHST- 2020/07/11 06:00 [pubmed] PHST- 2021/08/19 06:00 [medline] PHST- 2020/07/11 06:00 [entrez] AID - 10.1002/bies.202000081 [doi] PST - ppublish SO - Bioessays. 2020 Sep;42(9):e2000081. doi: 10.1002/bies.202000081. Epub 2020 Jul 10. PMID- 32369585 OWN - NLM STAT- MEDLINE DCOM- 20210416 LR - 20210507 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 37 IP - 9 DP - 2020 Sep 1 TI - Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions. PG - 2691-2698 LID - 10.1093/molbev/msaa112 [doi] AB - The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research. CI - © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. FAU - Liu, Xiaoming AU - Liu X AD - USF Genomics & College of Public Health, University of South Florida, Tampa, FL. LA - eng GR - R01 HG009524/HG/NHGRI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 SB - IM MH - Agriculture MH - *CpG Islands MH - *Demography MH - *Genome, Human MH - Humans MH - Population Growth PMC - PMC7820361 OTO - NOTNLM OT - demographic history OT - human evolution OT - population genetics EDAT- 2020/05/06 06:00 MHDA- 2021/04/17 06:00 PMCR- 2021/05/05 CRDT- 2020/05/06 06:00 PHST- 2020/05/06 06:00 [pubmed] PHST- 2021/04/17 06:00 [medline] PHST- 2020/05/06 06:00 [entrez] PHST- 2021/05/05 00:00 [pmc-release] AID - 5830537 [pii] AID - msaa112 [pii] AID - 10.1093/molbev/msaa112 [doi] PST - ppublish SO - Mol Biol Evol. 2020 Sep 1;37(9):2691-2698. doi: 10.1093/molbev/msaa112. PMID- 32859198 OWN - NLM STAT- MEDLINE DCOM- 20210407 LR - 20210407 IS - 1741-7007 (Electronic) IS - 1741-7007 (Linking) VI - 18 IP - 1 DP - 2020 Aug 28 TI - 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. PG - 108 LID - 10.1186/s12915-020-00839-8 [doi] LID - 108 AB - BACKGROUND: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging. RESULTS: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed. CONCLUSIONS: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA. FAU - Neukamm, Judith AU - Neukamm J AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. AD - Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany. FAU - Pfrengle, Saskia AU - Pfrengle S AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. FAU - Molak, Martyna AU - Molak M AD - Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland. AD - Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland. FAU - Seitz, Alexander AU - Seitz A AD - Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany. FAU - Francken, Michael AU - Francken M AD - Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. AD - Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. FAU - Eppenberger, Partick AU - Eppenberger P AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. FAU - Avanzi, Charlotte AU - Avanzi C AD - Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, USA. FAU - Reiter, Ella AU - Reiter E AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. FAU - Urban, Christian AU - Urban C AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. FAU - Welte, Beatrix AU - Welte B AD - Institute of Pre- and Protohistory and Medieval Archaeology, Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. FAU - Stockhammer, Philipp W AU - Stockhammer PW AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799, Munich, Germany. AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. FAU - Teßmann, Barbara AU - Teßmann B AD - Berlin Society of Anthropology, Ethnology and Prehistory, 10117, Berlin, Germany. AD - Museum of Prehistory and Early History, SMPK Berlin, 10117, Berlin, Germany. FAU - Herbig, Alexander AU - Herbig A AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. FAU - Harvati, Katerina AU - Harvati K AD - Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. AD - Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. AD - DFG Centre for Advanced Studies Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. FAU - Nieselt, Kay AU - Nieselt K AD - Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany. FAU - Krause, Johannes AU - Krause J AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. krause@shh.mpg.de. AD - Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. krause@shh.mpg.de. AD - Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany. krause@shh.mpg.de. FAU - Schuenemann, Verena J AU - Schuenemann VJ AUID- ORCID: 0000-0002-8593-3672 AD - Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. verena.schuenemann@iem.uzh.ch. AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. verena.schuenemann@iem.uzh.ch. AD - Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. verena.schuenemann@iem.uzh.ch. LA - eng GR - 845479/the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie/International GR - ALTF 1086-2018/European Molecular Biology Organization (EMBO) long-term fellowship/International PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200828 PL - England TA - BMC Biol JT - BMC biology JID - 101190720 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/analysis MH - Egypt MH - *Genome, Bacterial MH - *Genome, Viral MH - Hepatitis B virus/*genetics MH - Humans MH - Metagenomics MH - Microbiota MH - Mummies/*microbiology/virology MH - Mycobacterium leprae/*genetics MH - Sequence Analysis, DNA PMC - PMC7456089 OTO - NOTNLM OT - Ancient DNA OT - Egyptian mummified individuals OT - Hepatitis B virus OT - Leprosy OT - Metagenomics COIS- The authors declare no competing interests. EDAT- 2020/08/30 06:00 MHDA- 2021/04/10 06:00 PMCR- 2020/08/28 CRDT- 2020/08/30 06:00 PHST- 2020/06/05 00:00 [received] PHST- 2020/07/29 00:00 [accepted] PHST- 2020/08/30 06:00 [entrez] PHST- 2020/08/30 06:00 [pubmed] PHST- 2021/04/10 06:00 [medline] PHST- 2020/08/28 00:00 [pmc-release] AID - 10.1186/s12915-020-00839-8 [pii] AID - 839 [pii] AID - 10.1186/s12915-020-00839-8 [doi] PST - epublish SO - BMC Biol. 2020 Aug 28;18(1):108. doi: 10.1186/s12915-020-00839-8. PMID- 33083459 OWN - NLM STAT- MEDLINE DCOM- 20210503 LR - 20221207 IS - 2314-6141 (Electronic) IS - 2314-6133 (Print) VI - 2020 DP - 2020 TI - Skin Pigmentation Differences between Mongolian, Korean, and Uzbekistan Ancient Human DNA Samples. PG - 2585324 LID - 10.1155/2020/2585324 [doi] LID - 2585324 AB - BACKGROUND: This study reports the use of real-time PCR to identify the SNP rs1545397 in the intron region on the OCA2 gene from ancient and degraded DNA isolated from ancient human bones from Mongolia, Korea, and Uzbekistan. This SNP is a marker for skin pigmentation. LightCycler-based probes (HybProbes) were designed. A LightCycler (version 2.0) system was used for the real-time PCR. RESULTS: The results of the real-time PCRs of three different genotypes of SNP rs1545397 were compared with those of the direct sequencing. Melting curve analysis was used for genotype determination. Three genotypes were distinguished: the homozygous T (T/T) SNP type formed a distinct melting peak at 53.3 ± 0.14°C, the homozygous A (A/A) SNP type formed a distinct melting peak at 57.8 ± 0.12°C, and the heterozygous A/T SNP type formed two distinct melting peaks at 53.3 ± 0.17°C and 57.8 ± 0.15°C. Mongolian aDNA samples tested in this study carried all three types of the SNP (A/T, A/A, and T/T) with no distinctly predominant type observed. In contrast, Korean aDNA samples carried the Asian genotype (T/T), while the Uzbekistan aDNA samples carried the European genotype (A/A) more often than the Asian genotype (T/T). CONCLUSIONS: Human Mongolian aDNA samples had A/T, A/A, and T/T SNP rs1545397 with no distinct predominant genotype. When combined with the archeological and aDNA studies of other coupling morphologies with aDNA, our results infer that Mongolia's prehistoric population had considerable heterogeneity of skin color and morphological traits and that in the Neolithic period, a Eurasian or mixed population inhabited the western part of Mongolia. CI - Copyright © 2020 Munkhtsetseg Bazarragchaa et al. FAU - Bazarragchaa, Munkhtsetseg AU - Bazarragchaa M AUID- ORCID: 0000-0003-4051-0251 AD - Department of Molecular Biology and Genetics, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia. FAU - Uuganbayar, Udval AU - Uuganbayar U AUID- ORCID: 0000-0002-2441-3139 AD - Department of Molecular Biology and Genetics, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia. FAU - Lee, Kwang-Ho AU - Lee KH AD - Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, Republic of Korea. FAU - Kim, Kyung-Yong AU - Kim KY AUID- ORCID: 0000-0002-1904-9061 AD - Institute of Gene and Genome Research, College of Medicine, Chung-Ang University, Seoul 06974, Republic of Korea. FAU - Kim, Kijeong AU - Kim K AUID- ORCID: 0000-0002-5132-1774 AD - Institute of Gene and Genome Research, College of Medicine, Chung-Ang University, Seoul 06974, Republic of Korea. LA - eng PT - Journal Article DEP - 20200811 PL - United States TA - Biomed Res Int JT - BioMed research international JID - 101600173 RN - 0 (DNA, Ancient) SB - IM MH - Asian People/*genetics MH - DNA, Ancient/*analysis MH - Genotype MH - Humans MH - Mongolia MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide/genetics MH - Republic of Korea MH - Skin Pigmentation/*genetics MH - Uzbekistan PMC - PMC7559177 COIS- The authors have no conflict of interest to declare. EDAT- 2020/10/22 06:00 MHDA- 2021/05/04 06:00 PMCR- 2020/08/11 CRDT- 2020/10/21 06:04 PHST- 2020/01/23 00:00 [received] PHST- 2020/06/23 00:00 [revised] PHST- 2020/07/10 00:00 [accepted] PHST- 2020/10/21 06:04 [entrez] PHST- 2020/10/22 06:00 [pubmed] PHST- 2021/05/04 06:00 [medline] PHST- 2020/08/11 00:00 [pmc-release] AID - 10.1155/2020/2585324 [doi] PST - epublish SO - Biomed Res Int. 2020 Aug 11;2020:2585324. doi: 10.1155/2020/2585324. eCollection 2020. PMID- 32778135 OWN - NLM STAT- MEDLINE DCOM- 20210712 LR - 20231111 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 21 IP - 1 DP - 2020 Aug 10 TI - A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. PG - 201 LID - 10.1186/s13059-020-02112-1 [doi] LID - 201 AB - BACKGROUND: Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679). RESULTS: A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent. CONCLUSIONS: The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC. FAU - Sabin, Susanna AU - Sabin S AUID- ORCID: 0000-0002-7876-6001 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Herbig, Alexander AU - Herbig A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Vågene, Åshild J AU - Vågene ÅJ AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. AD - Present address: Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark. FAU - Ahlström, Torbjörn AU - Ahlström T AD - Department of Archaeology and Ancient History, Lund University, 221 00, Lund, Sweden. FAU - Bozovic, Gracijela AU - Bozovic G AD - Department of Medical Imaging and Clinical Physiology, Skåne University Hospital Lund and Lund University, 221 00, Lund, Sweden. FAU - Arcini, Caroline AU - Arcini C AD - Arkeologerna, National Historical Museum, 226 60, Lund, Sweden. FAU - Kühnert, Denise AU - Kühnert D AD - Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. kuehnert@shh.mpg.de. FAU - Bos, Kirsten I AU - Bos KI AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. bos@shh.mpg.de. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200810 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 SB - IM MH - Africa MH - Bayes Theorem MH - *Genome, Bacterial MH - History, 17th Century MH - Humans MH - Lung MH - Metagenomics MH - Mycobacterium tuberculosis/classification/*genetics MH - Phylogeny MH - Phylogeography MH - Tuberculosis/history/microbiology PMC - PMC7418204 OTO - NOTNLM OT - Ancient DNA OT - Metagenomics OT - Molecular dating OT - Mycobacterium tuberculosis OT - Tuberculosis COIS- Not applicable. EDAT- 2020/08/12 06:00 MHDA- 2021/07/13 06:00 PMCR- 2020/08/10 CRDT- 2020/08/12 06:00 PHST- 2019/08/09 00:00 [received] PHST- 2020/07/17 00:00 [accepted] PHST- 2020/08/12 06:00 [entrez] PHST- 2020/08/12 06:00 [pubmed] PHST- 2021/07/13 06:00 [medline] PHST- 2020/08/10 00:00 [pmc-release] AID - 10.1186/s13059-020-02112-1 [pii] AID - 2112 [pii] AID - 10.1186/s13059-020-02112-1 [doi] PST - epublish SO - Genome Biol. 2020 Aug 10;21(1):201. doi: 10.1186/s13059-020-02112-1. PMID- 32767894 OWN - NLM STAT- MEDLINE DCOM- 20201127 LR - 20201127 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 91 IP - 4 DP - 2020 Aug 6 TI - New Evidence of Ancient Mitochondrial DNA of the Southern Andes (Calchaquí Valleys, Northwest Argentina, 3,600-1,900 Years before Present). PG - 225-247 LID - 10.13110/humanbiology.91.4.02 [doi] AB - Genetic studies on pre-Hispanic populations of the Southern Andes have been increasing steadily in the last decade. Nevertheless, ancient DNA characterization of Formative Period archaeological human remains is particularly scant, especially for Northwest Argentina. To expand current information on genetic characterization of the first agricultural communities of the southern Calchaquí Valleys, we present and discuss the first mitochondrial ancient DNA information obtained on samples dated to ca. 3,600-1,900 years before present from the Cajón Valley, Catamarca Province. Reproducible mtDNA hypervariable region 1 (HVR-1) sequences were obtained in seven individuals. Mitochondrial HVR-1 haplotypes were assigned to three of the four founding haplogroups, D1 (57.1%), C1 (28.5%), and B2 (14.2%), with absence of A2. Our results show that the Cajón Valley sample, with predominance of D1 and C1, differs from that commonly observed in ancient and modern Andean populations, which usually show a high prevalence of haplogroup B2. The fact that the Cajón Valley and Pampa Grande (Salta Province, Argentina) share a prevalence of haplogroup D1 could provide additional evidence to support possible genetic affinities between the valleys and the eastern sub-Andean region during the Formative Period in Northwest Argentina, expanding the archaeological evidence of contact between both populations. Future complete mitogenomic analysis will provide substantial information to formulate new hypotheses about the origins and phylogenetic relationships between the individuals of the Cajón Valley and other groups from the Andes, Gran Chaco, and the Amazon. FAU - Parolin, María Laura AU - Parolin ML AD - CONICET, Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico (CENPAT), Puerto Madryn, Argentina. FAU - Cortés, Leticia Inés AU - Cortés LI AD - CONICET-Universidad de Buenos Aires, Instituto de las Culturas (IDECU), Buenos Aires, Argentina, leticiacortes@gmail.com. FAU - Basso, Néstor AU - Basso N AD - CONICET, Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico (CENPAT), Puerto Madryn, Argentina. FAU - Scattolin, María Cristina AU - Scattolin MC AD - CONICET-Universidad de Buenos Aires, Instituto de las Culturas (IDECU), Buenos Aires, Argentina. LA - eng PT - Historical Article PT - Journal Article PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Archaeology MH - Argentina/epidemiology MH - Child MH - Child, Preschool MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics/history MH - Female MH - Genetic Variation MH - Haplotypes/*genetics MH - History, Ancient MH - Humans MH - Indians, South American/genetics MH - Male MH - Middle Aged MH - Phylogeny MH - Sequence Analysis, DNA/methods OTO - NOTNLM OT - FORMATIVE PERIOD OT - MITOCHONDRIAL ADNA OT - NORTHWEST ARGENTINA OT - SOUTHERN ANDES EDAT- 2020/08/09 06:00 MHDA- 2020/11/28 06:00 CRDT- 2020/08/09 06:00 PHST- 2019/10/28 00:00 [received] PHST- 2020/02/18 00:00 [accepted] PHST- 2020/08/09 06:00 [entrez] PHST- 2020/08/09 06:00 [pubmed] PHST- 2020/11/28 06:00 [medline] AID - 10.13110/humanbiology.91.4.02 [doi] PST - ppublish SO - Hum Biol. 2020 Aug 6;91(4):225-247. doi: 10.13110/humanbiology.91.4.02. PMID- 32763189 OWN - NLM STAT- MEDLINE DCOM- 20201013 LR - 20240329 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 107 IP - 2 DP - 2020 Aug 6 TI - Fostering Responsible Research on Ancient DNA. PG - 183-195 LID - S0002-9297(20)30205-6 [pii] LID - 10.1016/j.ajhg.2020.06.017 [doi] AB - Anticipating and addressing the social implications of scientific work is a fundamental responsibility of all scientists. However, expectations for ethically sound practices can evolve over time as the implications of science come to be better understood. Contemporary researchers who work with ancient human remains, including those who conduct ancient DNA research, face precisely this challenge as it becomes clear that practices such as community engagement are needed to address the important social implications of this work. To foster and promote ethical engagement between researchers and communities, we offer five practical recommendations for ancient DNA researchers: (1) formally consult with communities; (2) address cultural and ethical considerations; (3) engage communities and support capacity building; (4) develop plans to report results and manage data; and (5) develop plans for long-term responsibility and stewardship. Ultimately, every member of a research team has an important role in fostering ethical research on ancient DNA. CI - Copyright © 2020 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. FAU - Wagner, Jennifer K AU - Wagner JK AD - Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Center for Translational Bioethics and Health Care Policy, Geisinger, Danville, PA 17822, USA. Electronic address: jwagner1@geisinger.edu. FAU - Colwell, Chip AU - Colwell C AD - Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, Denver Museum of Nature and Science, Denver, CO 80205, USA. FAU - Claw, Katrina G AU - Claw KG AD - Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA. FAU - Stone, Anne C AU - Stone AC AD - Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA. FAU - Bolnick, Deborah A AU - Bolnick DA AD - Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA. FAU - Hawks, John AU - Hawks J AD - Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, University of Wisconsin-Madison, Madison, WI 53706, USA. FAU - Brothers, Kyle B AU - Brothers KB AD - Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA. FAU - Garrison, Nanibaa' A AU - Garrison NA AD - Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA. LA - eng GR - K01 HG008818/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA, Ancient/*analysis MH - Foster Home Care MH - Humans PMC - PMC7413888 COIS- The authors have no competing interests to declare. EDAT- 2020/08/09 06:00 MHDA- 2020/10/21 06:00 PMCR- 2021/02/06 CRDT- 2020/08/09 06:00 PHST- 2020/08/09 06:00 [entrez] PHST- 2020/08/09 06:00 [pubmed] PHST- 2020/10/21 06:00 [medline] PHST- 2021/02/06 00:00 [pmc-release] AID - S0002-9297(20)30205-6 [pii] AID - 10.1016/j.ajhg.2020.06.017 [doi] PST - ppublish SO - Am J Hum Genet. 2020 Aug 6;107(2):183-195. doi: 10.1016/j.ajhg.2020.06.017. PMID- 32661160 OWN - NLM STAT- MEDLINE DCOM- 20200922 LR - 20211204 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 117 IP - 31 DP - 2020 Aug 4 TI - Integration of ancient DNA with transdisciplinary dataset finds strong support for Inca resettlement in the south Peruvian coast. PG - 18359-18368 LID - 10.1073/pnas.2005965117 [doi] AB - Ancient DNA (aDNA) analysis provides a powerful means of investigating human migration, social organization, and a plethora of other crucial questions about humanity's past. Recently, specialists have suggested that the ideal research design involving aDNA would include multiple independent lines of evidence. In this paper, we adopt a transdisciplinary approach integrating aDNA with archaeological, biogeochemical, and historical data to investigate six individuals found in two cemeteries that date to the Late Horizon (1400 to 1532 CE) and Colonial (1532 to 1825 CE) periods in the Chincha Valley of southern Peru. Genomic analyses indicate that these individuals are genetically most similar to ancient and present-day populations from the north Peruvian coast located several hundred kilometers away. These genomic data are consistent with 16th century written records as well as ceramic, textile, and isotopic data. These results provide some of the strongest evidence yet of state-sponsored resettlement in the pre-Colonial Andes. This study highlights the power of transdisciplinary research designs when using aDNA data and sets a methodological standard for investigating ancient mobility in complex societies. CI - Copyright © 2020 the Author(s). Published by PNAS. FAU - Bongers, Jacob L AU - Bongers JL AD - Sainsbury Research Unit, University of East Anglia, NR4 7TJ Norwich, United Kingdom; J.Bongers@uea.ac.uk stanish.charles@gmail.com. AD - Cotsen Institute of Archaeology, University of California, Los Angeles, CA 90024. FAU - Nakatsuka, Nathan AU - Nakatsuka N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. FAU - O'Shea, Colleen AU - O'Shea C AD - Conservation Department, Fine Arts Museums of San Francisco, San Francisco, CA 94118. FAU - Harper, Thomas K AU - Harper TK AUID- ORCID: 0000-0002-4969-1653 AD - Department of Anthropology, The Pennsylvania State University, University Park, PA 16802. FAU - Tantaleán, Henry AU - Tantaleán H AUID- ORCID: 0000-0002-3087-7968 AD - Escuela Profesional de Arqueología, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru. FAU - Stanish, Charles AU - Stanish C AD - Institute for the Advanced Study of Culture and the Environment, University of South Florida, Tampa, FL 33620-8100; J.Bongers@uea.ac.uk stanish.charles@gmail.com. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AUID- ORCID: 0000-0001-5510-1114 AD - University of California, Santa Cruz (UCSC) Paleogenomics, Department of Anthropology, University of California, Santa Cruz, CA 95064. AD - UCSC Genomics Institute, University of California, Santa Cruz, CA 95064. LA - eng GR - T32 GM007753/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20200713 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - *Archaeology MH - DNA, Ancient/*chemistry MH - Hispanic or Latino MH - History, Ancient MH - *Human Migration MH - Humans MH - Indians, South American/*genetics/*history MH - Peru PMC - PMC7414190 OTO - NOTNLM OT - Andes OT - Inca OT - ancient DNA OT - mobility OT - transdisciplinary approach COIS- The authors declare no competing interest. EDAT- 2020/07/15 06:00 MHDA- 2020/09/23 06:00 PMCR- 2020/07/13 CRDT- 2020/07/15 06:00 PHST- 2020/07/15 06:00 [pubmed] PHST- 2020/09/23 06:00 [medline] PHST- 2020/07/15 06:00 [entrez] PHST- 2020/07/13 00:00 [pmc-release] AID - 2005965117 [pii] AID - 202005965 [pii] AID - 10.1073/pnas.2005965117 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2020 Aug 4;117(31):18359-18368. doi: 10.1073/pnas.2005965117. Epub 2020 Jul 13. PMID- 32747648 OWN - NLM STAT- MEDLINE DCOM- 20200908 LR - 20231111 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 11 IP - 1 DP - 2020 Aug 3 TI - Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography. PG - 3868 LID - 10.1038/s41467-020-17656-w [doi] LID - 3868 AB - Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast. FAU - Nakatsuka, Nathan AU - Nakatsuka N AUID- ORCID: 0000-0002-5091-4914 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. nathan_nakatsuka@hms.harvard.edu. AD - Harvard-MIT Division of Health Sciences and Technology, Boston, MA, 02115, USA. nathan_nakatsuka@hms.harvard.edu. FAU - Luisi, Pierre AU - Luisi P AUID- ORCID: 0000-0002-2542-3689 AD - Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, 5000, Córdoba, Argentina. pierre.luisi@unc.edu.ar. FAU - Motti, Josefina M B AU - Motti JMB AUID- ORCID: 0000-0002-6624-1822 AD - NEIPHPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7631, Quequén, Argentina. FAU - Salemme, Mónica AU - Salemme M AD - Centro Austral de Investigaciones Científicas (CADIC-CONICET), 9410, Ushuaia, Tierra del Fuego, Argentina. AD - Instituto de Cultura, Sociedad y Estado (ICSE), Universidad Nacional de Tierra del Fuego, 9410, Ushuaia, Tierra del Fuego, Argentina. FAU - Santiago, Fernando AU - Santiago F AUID- ORCID: 0000-0002-0357-9965 AD - Centro Austral de Investigaciones Científicas (CADIC-CONICET), 9410, Ushuaia, Tierra del Fuego, Argentina. FAU - D'Angelo Del Campo, Manuel D AU - D'Angelo Del Campo MD AD - NEIPHPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7631, Quequén, Argentina. AD - Laboratorio de Poblaciones del Pasado (LAPP), Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid (UAM), E-28049, Madrid, Spain. FAU - Vecchi, Rodrigo J AU - Vecchi RJ AD - CONICET-Departamento de Humanidades, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina. FAU - Espinosa-Parrilla, Yolanda AU - Espinosa-Parrilla Y AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain. AD - School of Medicine and Laboratory of Molecular Medicine-LMM, Center for Education, Healthcare and Investigation-CADI, Universidad de Magallanes, Punta Arenas, Chile. FAU - Prieto, Alfredo AU - Prieto A AUID- ORCID: 0000-0001-7622-2353 AD - Universidad de Magallanes, Avenida Bulnes 01855, Punta Arenas, Chile. FAU - Adamski, Nicole AU - Adamski N AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02446, USA. FAU - Lawson, Ann Marie AU - Lawson AM AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02446, USA. FAU - Harper, Thomas K AU - Harper TK AUID- ORCID: 0000-0002-4969-1653 AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA. FAU - Culleton, Brendan J AU - Culleton BJ AD - Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA, 16802, USA. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AUID- ORCID: 0000-0002-1730-5914 AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02446, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - Guichón, Ricardo A AU - Guichón RA AD - NEIPHPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7631, Quequén, Argentina. FAU - Cabana, Graciela S AU - Cabana GS AUID- ORCID: 0000-0002-5399-1173 AD - Molecular Anthropology Laboratories, Department of Anthropology, University of Tennessee, Knoxville, TN, 37996, USA. FAU - Nores, Rodrigo AU - Nores R AUID- ORCID: 0000-0002-9153-0626 AD - Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, 5000, Córdoba, Argentina. rodrigonores@ffyh.unc.edu.ar. AD - Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, 5000, Córdoba, Argentina. rodrigonores@ffyh.unc.edu.ar. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02446, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. reich@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. reich@genetics.med.harvard.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - T32 GM007753/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20200803 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology/methods MH - Argentina MH - Bone and Bones/metabolism MH - Chile MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/classification/genetics MH - *Fossils MH - *Gene Flow MH - Genetic Variation MH - Genome, Human/*genetics MH - Geography MH - *Human Migration MH - Humans MH - Phylogeny MH - Radiometric Dating/methods MH - Sequence Analysis, DNA/methods MH - Tooth/metabolism PMC - PMC7400565 COIS- P.L. provides consulting services to myDNAmap S.L. The remaining authors declare no competing interests. EDAT- 2020/08/05 06:00 MHDA- 2020/09/09 06:00 PMCR- 2020/08/03 CRDT- 2020/08/05 06:00 PHST- 2020/01/20 00:00 [received] PHST- 2020/07/10 00:00 [accepted] PHST- 2020/08/05 06:00 [entrez] PHST- 2020/08/05 06:00 [pubmed] PHST- 2020/09/09 06:00 [medline] PHST- 2020/08/03 00:00 [pmc-release] AID - 10.1038/s41467-020-17656-w [pii] AID - 17656 [pii] AID - 10.1038/s41467-020-17656-w [doi] PST - epublish SO - Nat Commun. 2020 Aug 3;11(1):3868. doi: 10.1038/s41467-020-17656-w. PMID- 32815536 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20241117 IS - 2047-217X (Electronic) IS - 2047-217X (Linking) VI - 9 IP - 8 DP - 2020 Aug 1 TI - A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level. LID - 10.1093/gigascience/giaa086 [doi] LID - giaa086 AB - BACKGROUND: Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data. FINDINGS: TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs. CONCLUSIONS: TRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe. CI - © The Author(s) 2020. Published by Oxford University Press. FAU - Pratas, Diogo AU - Pratas D AD - Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland. AD - Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal. AD - Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal. FAU - Toppinen, Mari AU - Toppinen M AD - Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland. FAU - Pyöriä, Lari AU - Pyöriä L AD - Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland. FAU - Hedman, Klaus AU - Hedman K AD - Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland. AD - HUSLAB, Helsinki University Hospital, Topeliuksenkatu 32, 00290 Helsinki, Finland. FAU - Sajantila, Antti AU - Sajantila A AD - Department of Forensic Medicine, University of Helsinki, Kytösuontie 11, 00300, Helsinki, Finland. AD - Forensic Medicine Unit, Finnish Institute of Health and Welfare, PO Box 30 FI-00271 Helsinki, Finland. FAU - Perdomo, Maria F AU - Perdomo MF AD - Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Gigascience JT - GigaScience JID - 101596872 SB - IM MH - Base Sequence MH - *Genome, Viral MH - Genomics MH - Humans MH - Sequence Alignment MH - *Software PMC - PMC7439602 OTO - NOTNLM OT - JC polyomavirus OT - efficient pipeline OT - genome analysis OT - mitochondrial DNA OT - multi-organ sequencing OT - parvovirus B19 OT - viral genomes COIS- The authors declare that they have no competing interests. EDAT- 2020/08/21 06:00 MHDA- 2021/10/26 06:00 PMCR- 2020/08/20 CRDT- 2020/08/21 06:00 PHST- 2020/01/17 00:00 [received] PHST- 2020/05/25 00:00 [revised] PHST- 2020/07/23 00:00 [accepted] PHST- 2020/08/21 06:00 [entrez] PHST- 2020/08/21 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] PHST- 2020/08/20 00:00 [pmc-release] AID - 5894824 [pii] AID - giaa086 [pii] AID - 10.1093/gigascience/giaa086 [doi] PST - ppublish SO - Gigascience. 2020 Aug 1;9(8):giaa086. doi: 10.1093/gigascience/giaa086. PMID- 32603999 OWN - NLM STAT- MEDLINE DCOM- 20211004 LR - 20211004 IS - 1879-0372 (Electronic) IS - 0952-7915 (Linking) VI - 65 DP - 2020 Aug TI - An ancient view on host pathogen interaction across time and space. PG - 65-69 LID - S0952-7915(20)30057-1 [pii] LID - 10.1016/j.coi.2020.05.004 [doi] AB - The ancient DNA revolution provided diverse fields with an unprecedented opportunity to look back into the past and shed light on research aspects that were until now subject to speculation and inference from modern data. In particular enrichment methods that allow the targeted retrieval of millions of SNP positions from ancient human genomes, or even complete bacterial and viral genomes have the potential to revolutionize our understanding of host pathogen interactions. Ancient DNA combined with new bioinformatic tools now even allows actual allele calling for immunogenetic systems such as Human Leukocyte Antigen (HLA) across time and space. The coming years will provide us with frequency data of human immunity genes, such as HLA, as well as genome wide data of ancient pathogens from many time periods of human history, and will therefore provide us with a dynamic view on historical human adaptation to pathogen exposure on a population wide scale. CI - Copyright © 2020 Elsevier Ltd. All rights reserved. FAU - Barquera, Rodrigo AU - Barquera R AD - Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745, Jena, Germany. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745, Jena, Germany. Electronic address: krause@shh.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200627 PL - England TA - Curr Opin Immunol JT - Current opinion in immunology JID - 8900118 RN - 0 (HLA Antigens) SB - IM MH - HLA Antigens/genetics/*immunology MH - Host-Pathogen Interactions/genetics/*immunology MH - Humans EDAT- 2020/07/01 06:00 MHDA- 2021/10/05 06:00 CRDT- 2020/07/01 06:00 PHST- 2020/05/15 00:00 [received] PHST- 2020/05/18 00:00 [accepted] PHST- 2020/07/01 06:00 [pubmed] PHST- 2021/10/05 06:00 [medline] PHST- 2020/07/01 06:00 [entrez] AID - S0952-7915(20)30057-1 [pii] AID - 10.1016/j.coi.2020.05.004 [doi] PST - ppublish SO - Curr Opin Immunol. 2020 Aug;65:65-69. doi: 10.1016/j.coi.2020.05.004. Epub 2020 Jun 27. PMID- 32497286 OWN - NLM STAT- MEDLINE DCOM- 20210211 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 172 IP - 4 DP - 2020 Aug TI - The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders. PG - 638-649 LID - 10.1002/ajpa.24079 [doi] AB - OBJECTIVES: In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences. METHODS: We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools. RESULTS: The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style. CONCLUSION: We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange. CI - © 2020 The Authors. American Journal of Physical Anthropology published by Wiley Periodicals, Inc. FAU - Coutinho, Alexandra AU - Coutinho A AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. FAU - Günther, Torsten AU - Günther T AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. FAU - Munters, Arielle R AU - Munters AR AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. FAU - Svensson, Emma M AU - Svensson EM AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. FAU - Götherström, Anders AU - Götherström A AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Storå, Jan AU - Storå J AD - Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Malmström, Helena AU - Malmström H AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. AD - Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, Auckland Park, South Africa. FAU - Jakobsson, Mattias AU - Jakobsson M AUID- ORCID: 0000-0001-7840-7853 AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. AD - Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, Auckland Park, South Africa. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200604 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Burial/history MH - Chromosomes, Human, Y/genetics MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/genetics MH - Female MH - Genetics, Population MH - Genome, Human/genetics MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Male MH - Scandinavian and Nordic Countries/ethnology MH - Tooth/chemistry MH - *White People/ethnology/genetics OTO - NOTNLM OT - Stone Age OT - admixture OT - ancient DNA OT - migration EDAT- 2020/06/05 06:00 MHDA- 2021/02/12 06:00 CRDT- 2020/06/05 06:00 PHST- 2019/12/18 00:00 [received] PHST- 2020/03/26 00:00 [revised] PHST- 2020/04/17 00:00 [accepted] PHST- 2020/06/05 06:00 [pubmed] PHST- 2021/02/12 06:00 [medline] PHST- 2020/06/05 06:00 [entrez] AID - 10.1002/ajpa.24079 [doi] PST - ppublish SO - Am J Phys Anthropol. 2020 Aug;172(4):638-649. doi: 10.1002/ajpa.24079. Epub 2020 Jun 4. PMID- 32393839 OWN - NLM STAT- MEDLINE DCOM- 20201113 LR - 20210216 IS - 2397-3374 (Electronic) IS - 2397-3374 (Linking) VI - 4 IP - 8 DP - 2020 Aug TI - Chemical evidence of dairying by hunter-gatherers in highland Lesotho in the late first millennium AD. PG - 791-799 LID - 10.1038/s41562-020-0859-0 [doi] AB - The recovery of Early Iron Age artefacts and domestic animal remains from hunter-gatherer contexts at Likoaeng, Lesotho, has been argued to indicate contact between highland hunter-gatherers and Early Iron Age agropastoralist communities settled in lowland areas of southeastern Africa during the second half of the first millennium AD. However, disagreement between archaeozoological studies and ancient DNA means that the possibility that those hunter-gatherers kept livestock themselves remains controversial. Here we report analyses of pottery-absorbed organic residues from two hunter-gatherer sites and one agriculturalist site in highland Lesotho to reconstruct prehistoric subsistence practices. Our results demonstrate the exploitation of secondary products from domestic livestock by hunter-gatherers in Lesotho, directly dated to the seventh century AD at Likoaeng and the tenth century AD at the nearby site of Sehonghong. The data provide compelling evidence for the keeping of livestock by hunter-gatherer groups and their probable incorporation as ancillary resources into their subsistence strategies. FAU - Fewlass, Helen AU - Fewlass H AUID- ORCID: 0000-0002-9093-3490 AD - Department of Anthropology and Archaeology, University of Bristol, Bristol, UK. helen_fewlass@eva.mpg.de. AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. helen_fewlass@eva.mpg.de. FAU - Mitchell, Peter J AU - Mitchell PJ AD - School of Archaeology, University of Oxford and St Hugh's College, Oxford, UK. AD - School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa. FAU - Casanova, Emmanuelle AU - Casanova E AUID- ORCID: 0000-0003-1417-3060 AD - Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK. FAU - Cramp, Lucy J E AU - Cramp LJE AUID- ORCID: 0000-0003-2012-2753 AD - Department of Anthropology and Archaeology, University of Bristol, Bristol, UK. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200511 PL - England TA - Nat Hum Behav JT - Nature human behaviour JID - 101697750 RN - 0 (CD36 Antigens) RN - 0 (Lipids) SB - IM MH - Animals MH - CD36 Antigens/analysis MH - Cattle MH - Ceramics/history MH - Dairying/*history MH - History, Ancient MH - Humans MH - Lesotho MH - Lipids/analysis MH - Radiometric Dating MH - Sheep EDAT- 2020/05/13 06:00 MHDA- 2020/11/18 06:00 CRDT- 2020/05/13 06:00 PHST- 2019/07/02 00:00 [received] PHST- 2020/03/13 00:00 [accepted] PHST- 2020/05/13 06:00 [pubmed] PHST- 2020/11/18 06:00 [medline] PHST- 2020/05/13 06:00 [entrez] AID - 10.1038/s41562-020-0859-0 [pii] AID - 10.1038/s41562-020-0859-0 [doi] PST - ppublish SO - Nat Hum Behav. 2020 Aug;4(8):791-799. doi: 10.1038/s41562-020-0859-0. Epub 2020 May 11. PMID- 32409524 OWN - NLM STAT- MEDLINE DCOM- 20200810 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 369 IP - 6501 DP - 2020 Jul 17 TI - Ancient DNA indicates human population shifts and admixture in northern and southern China. PG - 282-288 LID - 10.1126/science.aba0909 [doi] AB - Human genetic history in East Asia is poorly understood. To clarify population relationships, we obtained genome-wide data from 26 ancient individuals from northern and southern East Asia spanning 9500 to 300 years ago. Genetic differentiation in this region was higher in the past than the present, which reflects a major episode of admixture involving northern East Asian ancestry spreading across southern East Asia after the Neolithic, thereby transforming the genetic ancestry of southern China. Mainland southern East Asian and Taiwan Strait island samples from the Neolithic show clear connections with modern and ancient individuals with Austronesian-related ancestry, which supports an origin in southern China for proto-Austronesians. Connections among Neolithic coastal groups from Siberia and Japan to Vietnam indicate that migration and gene flow played an important role in the prehistory of coastal Asia. CI - Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. FAU - Yang, Melinda A AU - Yang MA AUID- ORCID: 0000-0001-9004-7563 AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. AD - Department of Biology, University of Richmond, Richmond, VA 23173. FAU - Fan, Xuechun AU - Fan X AD - International Research Center for Austronesian Archaeology, Pingtan 350000. AD - Fujian Museum, Fuzhou 350001. FAU - Sun, Bo AU - Sun B AD - Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012. FAU - Chen, Chungyu AU - Chen C AD - Institute of History and Philology, Academia Sinica, Taipei 11529. FAU - Lang, Jianfeng AU - Lang J AD - School of History and Culture, Shandong University, Jinan 250100. FAU - Ko, Ying-Chin AU - Ko YC AD - Environment-Omics-Disease Research Center, China Medical University and Hospital, Taichung 40402. FAU - Tsang, Cheng-Hwa AU - Tsang CH AUID- ORCID: 0000-0002-1549-2234 AD - Institute of Anthropology, National Tsinghua University, Hsinchu 30013. FAU - Chiu, Hunglin AU - Chiu H AUID- ORCID: 0000-0002-7027-8601 AD - Institute of Anthropology, National Tsinghua University, Hsinchu 30013. FAU - Wang, Tianyi AU - Wang T AUID- ORCID: 0000-0002-4790-7668 AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. AD - School of Cultural Heritage, Northwest University, Xi'an 710069. FAU - Bao, Qingchuan AU - Bao Q AD - The Institute of Cultural Relics and Archaeology, Inner Mongolia Autonomous Region 010011. FAU - Wu, Xiaohong AU - Wu X AUID- ORCID: 0000-0002-3819-0829 AD - School of Archaeology and Museology, Peking University, Beijing 100871. FAU - Hajdinjak, Mateja AU - Hajdinjak M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig. FAU - Ko, Albert Min-Shan AU - Ko AM AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. FAU - Ding, Manyu AU - Ding M AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. AD - University of Chinese Academy of Sciences, Beijing 100049. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. FAU - Yang, Ruowei AU - Yang R AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. FAU - Liu, Feng AU - Liu F AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. FAU - Nickel, Birgit AU - Nickel B AD - School of Archaeology and Museology, Peking University, Beijing 100871. FAU - Dai, Qingyan AU - Dai Q AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. FAU - Zhang, Lizhao AU - Zhang L AUID- ORCID: 0000-0001-6983-8053 AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. FAU - Sun, Chengkai AU - Sun C AD - Shandong Museum, Jinan 250014. FAU - Ning, Chao AU - Ning C AUID- ORCID: 0000-0002-8848-3961 AD - School of Life Sciences, Jilin University, Changchun 130023. FAU - Zeng, Wen AU - Zeng W AD - Institute of Cultural Heritage, Shandong University, Qingdao 266237. FAU - Zhao, Yongsheng AU - Zhao Y AD - Institute of Cultural Heritage, Shandong University, Qingdao 266237. FAU - Zhang, Ming AU - Zhang M AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. AD - University of Chinese Academy of Sciences, Beijing 100049. FAU - Gao, Xing AU - Gao X AUID- ORCID: 0000-0001-5295-3629 AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. AD - University of Chinese Academy of Sciences, Beijing 100049. FAU - Cui, Yinqiu AU - Cui Y AUID- ORCID: 0000-0003-3702-5773 AD - School of Life Sciences, Jilin University, Changchun 130023. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138. AD - Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115. FAU - Stoneking, Mark AU - Stoneking M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig. FAU - Fu, Qiaomei AU - Fu Q AUID- ORCID: 0000-0002-7141-0002 AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044. fuqiaomei@ivpp.ac.cn. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044. AD - University of Chinese Academy of Sciences, Beijing 100049. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200514 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Asia, Southeastern MH - Asian People/genetics MH - China MH - *DNA, Ancient MH - Gene Flow MH - *Genetics, Population MH - Genome, Human MH - *Human Migration MH - Humans MH - Siberia MH - Vietnam EDAT- 2020/05/16 06:00 MHDA- 2020/08/11 06:00 CRDT- 2020/05/16 06:00 PHST- 2019/11/04 00:00 [received] PHST- 2020/05/01 00:00 [accepted] PHST- 2020/05/16 06:00 [pubmed] PHST- 2020/08/11 06:00 [medline] PHST- 2020/05/16 06:00 [entrez] AID - science.aba0909 [pii] AID - 10.1126/science.aba0909 [doi] PST - ppublish SO - Science. 2020 Jul 17;369(6501):282-288. doi: 10.1126/science.aba0909. Epub 2020 May 14. PMID- 32678112 OWN - NLM STAT- MEDLINE DCOM- 20201214 LR - 20220104 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 10 IP - 1 DP - 2020 Jul 16 TI - Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images. PG - 11850 LID - 10.1038/s41598-020-68259-w [doi] LID - 11850 AB - Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case-control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively. FAU - Li, Jiarui AU - Li J AD - Medical Imaging Research Center, MIRC, University Hospitals Leuven, Leuven, Belgium. jiarui.li@kuleuven.be. AD - Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium. jiarui.li@kuleuven.be. FAU - Zarzar, Tomás González AU - Zarzar TG AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, USA. FAU - White, Julie D AU - White JD AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, USA. FAU - Indencleef, Karlijne AU - Indencleef K AD - Medical Imaging Research Center, MIRC, University Hospitals Leuven, Leuven, Belgium. AD - Department of Neurosciences, Experimental Otorhinolaryngology, KU Leuven, Leuven, Belgium. FAU - Hoskens, Hanne AU - Hoskens H AD - Medical Imaging Research Center, MIRC, University Hospitals Leuven, Leuven, Belgium. AD - Department of Human Genetics, KU Leuven, Leuven, Belgium. FAU - Matthews, Harry AU - Matthews H AD - Medical Imaging Research Center, MIRC, University Hospitals Leuven, Leuven, Belgium. AD - Department of Human Genetics, KU Leuven, Leuven, Belgium. AD - Murdoch Childrens Research Institute, Melbourne, VIC, Australia. FAU - Nauwelaers, Nele AU - Nauwelaers N AD - Medical Imaging Research Center, MIRC, University Hospitals Leuven, Leuven, Belgium. AD - Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium. FAU - Zaidi, Arslan AU - Zaidi A AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, USA. FAU - Eller, Ryan J AU - Eller RJ AD - Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, USA. FAU - Herrick, Noah AU - Herrick N AD - Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, USA. FAU - Günther, Torsten AU - Günther T AD - Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden. FAU - Svensson, Emma M AU - Svensson EM AD - Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden. FAU - Walsh, Susan AU - Walsh S AD - Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, USA. FAU - Van Steen, Kristel AU - Van Steen K AD - Department of Human Genetics, KU Leuven, Leuven, Belgium. AD - Medical Genomics Research Unit, GIGA-R, University of Liège, Liège, Belgium. AD - Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Liège, Belgium. FAU - Shriver, Mark D AU - Shriver MD AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, USA. FAU - Claes, Peter AU - Claes P AD - Medical Imaging Research Center, MIRC, University Hospitals Leuven, Leuven, Belgium. peter.claes@kuleuven.be. AD - Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium. peter.claes@kuleuven.be. AD - Department of Human Genetics, KU Leuven, Leuven, Belgium. peter.claes@kuleuven.be. AD - Murdoch Childrens Research Institute, Melbourne, VIC, Australia. peter.claes@kuleuven.be. LA - eng GR - R01 DE027023/DE/NIDCR NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20200716 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Biometric Identification/*methods MH - Datasets as Topic MH - Face/*anatomy & histology MH - Facial Recognition/physiology MH - Female MH - Genetics, Population/methods MH - *Genome, Human MH - Genome-Wide Association Study MH - History, 21st Century MH - History, Ancient MH - Human Genetics/*methods MH - Humans MH - Image Processing, Computer-Assisted MH - *Inheritance Patterns MH - Male MH - *Models, Statistical MH - Racial Groups/history PMC - PMC7367291 COIS- The authors declare no competing interests. EDAT- 2020/07/18 06:00 MHDA- 2020/12/15 06:00 PMCR- 2020/07/16 CRDT- 2020/07/18 06:00 PHST- 2020/02/09 00:00 [received] PHST- 2020/06/19 00:00 [accepted] PHST- 2020/07/18 06:00 [entrez] PHST- 2020/07/18 06:00 [pubmed] PHST- 2020/12/15 06:00 [medline] PHST- 2020/07/16 00:00 [pmc-release] AID - 10.1038/s41598-020-68259-w [pii] AID - 68259 [pii] AID - 10.1038/s41598-020-68259-w [doi] PST - epublish SO - Sci Rep. 2020 Jul 16;10(1):11850. doi: 10.1038/s41598-020-68259-w. PMID- 32664326 OWN - NLM STAT- MEDLINE DCOM- 20210319 LR - 20210319 IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 11 IP - 7 DP - 2020 Jul 10 TI - Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population. LID - 10.3390/genes11070775 [doi] LID - 775 AB - A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. F(ST) ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese. FAU - Iwasaki, Risa L AU - Iwasaki RL AUID- ORCID: 0000-0002-6728-9721 AD - Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan. FAU - Ishiya, Koji AU - Ishiya K AUID- ORCID: 0000-0002-8715-0452 AD - Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan. FAU - Kanzawa-Kiriyama, Hideaki AU - Kanzawa-Kiriyama H AUID- ORCID: 0000-0002-7442-5736 AD - Department of Anthropology, National Museum of Nature and Science, Ibaraki 305-0005, Japan. FAU - Kawai, Yosuke AU - Kawai Y AD - Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan. FAU - Gojobori, Jun AU - Gojobori J AUID- ORCID: 0000-0002-7699-7746 AD - Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan. FAU - Satta, Yoko AU - Satta Y AUID- ORCID: 0000-0002-5305-493X AD - Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200710 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (Antigens, Neoplasm) RN - 0 (GPI-Linked Proteins) RN - 0 (Neoplasm Proteins) RN - 0 (PSCA protein, human) SB - IM MH - Antigens, Neoplasm/*genetics MH - *Evolution, Molecular MH - GPI-Linked Proteins/genetics MH - Gene Frequency MH - Humans MH - Japan MH - Neoplasm Proteins/*genetics MH - *Polymorphism, Single Nucleotide MH - Population/*genetics MH - Selection, Genetic MH - Stomach Neoplasms/*genetics PMC - PMC7396988 OTO - NOTNLM OT - Japanese OT - Jomon people OT - PSCA OT - Yayoi people OT - diffuse-type gastric cancer OT - dual-structure model OT - genetic differentiation OT - hardening selective sweep OT - rs2294008 OT - selection target change OT - soft sweep COIS- The authors declare no conflict of interest. EDAT- 2020/07/16 06:00 MHDA- 2021/03/20 06:00 PMCR- 2020/07/01 CRDT- 2020/07/16 06:00 PHST- 2020/06/11 00:00 [received] PHST- 2020/07/02 00:00 [revised] PHST- 2020/07/08 00:00 [accepted] PHST- 2020/07/16 06:00 [entrez] PHST- 2020/07/16 06:00 [pubmed] PHST- 2021/03/20 06:00 [medline] PHST- 2020/07/01 00:00 [pmc-release] AID - genes11070775 [pii] AID - genes-11-00775 [pii] AID - 10.3390/genes11070775 [doi] PST - epublish SO - Genes (Basel). 2020 Jul 10;11(7):775. doi: 10.3390/genes11070775. PMID- 32650941 OWN - NLM STAT- MEDLINE DCOM- 20220414 LR - 20220414 IS - 1876-4452 (Electronic) IS - 1355-0306 (Linking) VI - 60 IP - 4 DP - 2020 Jul TI - Assessing the performance of quantity and quality metrics using the QIAGEN Investigator® Quantiplex® pro RGQ kit. PG - 388-397 LID - S1355-0306(19)30166-2 [pii] LID - 10.1016/j.scijus.2020.03.002 [doi] AB - The Quantiplex® Pro RGQ kit quantifies DNA in a sample, supports the detection of mixtures and assesses the extent of DNA degradation based on relative ratios of amplified autosomal and male markers. Data show no significant difference in the accuracy and sensitivity of quantification between this and the Promega PowerQuant® System, both detecting the lowest amount of DNA tested, 4 pg. Laboratory controlled mixed male:female DNA samples together with mock sexual assault samples were quantified across a range of mixture ratios. Analysis software detected mixed DNA samples across all ratios for both quantification kits. Subsequent STR analysis using the Investigator® 24Plex QS Kit was able to corroborate mixture detection down to 1:25 male:female DNA ratios, past which point mixtures appeared identical to single-source female samples. Analysis software also detected laboratory degraded DNA samples, with data showing a positive trend between the Degradation Index (DI) and length of time of sonication. When used on ancient remains the assay was able to triage samples for further analysis, and STR profiles were concordant with DNA quantification results in all instances. STR analyses of laboratory-controlled sensitivity, mixture, and degradation studies supports the quality metric obtained from quantification. These data support the use of the Quantiplex® Pro RGQ kit for sample screening and quantification in forensic casework and ancient DNA studies. CI - Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved. FAU - Morrison, Jack AU - Morrison J AD - School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom. FAU - McColl, Suzzanne AU - McColl S AD - School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom. FAU - Louhelainen, Jari AU - Louhelainen J AD - School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom. FAU - Sheppard, Kayleigh AU - Sheppard K AD - School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom. FAU - May, Ashley AU - May A AD - Research Centre in Evolutionary Anthropology and Palaeoecology, School of Natural Sciences and Psychology, Liverpool John Moores University, Life Sciences Building, Byrom Street, Liverpool L3 3AF, United Kingdom. FAU - Girdland-Flink, Linus AU - Girdland-Flink L AD - Research Centre in Evolutionary Anthropology and Palaeoecology, School of Natural Sciences and Psychology, Liverpool John Moores University, Life Sciences Building, Byrom Street, Liverpool L3 3AF, United Kingdom. FAU - Watts, Giles AU - Watts G AD - School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom. FAU - Dawnay, Nick AU - Dawnay N AD - School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom. Electronic address: n.m.dawnay@ljmu.ac.uk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200326 PL - England TA - Sci Justice JT - Science & justice : journal of the Forensic Science Society JID - 9508563 RN - 9007-49-2 (DNA) SB - IM MH - *Benchmarking MH - DNA/analysis MH - *DNA Fingerprinting/methods MH - Female MH - Humans MH - Male MH - Microsatellite Repeats OTO - NOTNLM OT - DNA degradation OT - DNA typing OT - Forensic science OT - Quantification OT - Real-time PCR OT - Validation studies EDAT- 2020/07/12 06:00 MHDA- 2022/04/15 06:00 CRDT- 2020/07/12 06:00 PHST- 2019/06/07 00:00 [received] PHST- 2020/02/28 00:00 [revised] PHST- 2020/03/23 00:00 [accepted] PHST- 2020/07/12 06:00 [entrez] PHST- 2020/07/12 06:00 [pubmed] PHST- 2022/04/15 06:00 [medline] AID - S1355-0306(19)30166-2 [pii] AID - 10.1016/j.scijus.2020.03.002 [doi] PST - ppublish SO - Sci Justice. 2020 Jul;60(4):388-397. doi: 10.1016/j.scijus.2020.03.002. Epub 2020 Mar 26. PMID- 32598277 OWN - NLM STAT- MEDLINE DCOM- 20210615 LR - 20240211 IS - 2057-5858 (Electronic) IS - 2057-5858 (Linking) VI - 6 IP - 7 DP - 2020 Jul TI - The past, present and future of ancient bacterial DNA. LID - 10.1099/mgen.0.000384 [doi] LID - mgen000384 AB - Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered. FAU - Arning, Nicolas AU - Arning N AD - Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK. FAU - Wilson, Daniel J AU - Wilson DJ AD - Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom GR - 101237/Z/13/B/WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Microb Genom JT - Microbial genomics JID - 101671820 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Bacteria/*classification/genetics MH - Bone and Bones/microbiology MH - DNA, Ancient/*analysis MH - Dental Pulp/microbiology MH - Feces/microbiology MH - Genome, Bacterial MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Mummies/microbiology MH - Sequence Analysis, DNA/*methods PMC - PMC7478633 OTO - NOTNLM OT - ancient bacterial DNA OT - ancient pathogens OT - bacterial evolution OT - paleogenetics OT - paleomicrobiology COIS- The authors declare that there are no conflicts of interest. EDAT- 2020/07/01 06:00 MHDA- 2021/06/16 06:00 PMCR- 2020/06/29 CRDT- 2020/06/30 06:00 PHST- 2020/07/01 06:00 [pubmed] PHST- 2021/06/16 06:00 [medline] PHST- 2020/06/30 06:00 [entrez] PHST- 2020/06/29 00:00 [pmc-release] AID - 000384 [pii] AID - 10.1099/mgen.0.000384 [doi] PST - ppublish SO - Microb Genom. 2020 Jul;6(7):mgen000384. doi: 10.1099/mgen.0.000384. PMID- 32406954 OWN - NLM STAT- MEDLINE DCOM- 20210125 LR - 20211204 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 172 IP - 3 DP - 2020 Jul TI - Ancient DNA reveals two paternal lineages C2a1a1b1a/F3830 and C2b1b/F845 in past nomadic peoples distributed on the Mongolian Plateau. PG - 402-411 LID - 10.1002/ajpa.24076 [doi] AB - OBJECTIVES: Since the third century CE, a series of nomadic tribes have been active on the eastern part of the Mongolian Plateau. Characterizing the genetic compositions of past nomadic people is significant for research on the nomadic cultures of the Eurasian Steppe region. Ancient DNA analysis facilitates a deeper understanding of the relationship between historical and modern nomadic populations. MATERIALS AND METHODS: Whole-genome shotgun sequencing and capture sequencing of the nonrecombining region of the Y chromosome were performed for six ancient Hg C2/M217 individuals. The individuals were interred at six separate sites on the Mongolian Plateau and represent dates spanning the late Neolithic to Yuan Dynasty (~3,500-700 BP). RESULTS: After NRY capture sequencing, three of the six ancient samples were attributed to C2b1b/F845 and the other three ancient samples belonged to C2a1a1b1a/F3830. Analysis of whole-genome shotgun sequencing data shows that the ancient C2b1b/F845 individuals are closely related to She, Han and other East Asian populations, while the ancient C2a1a1b1a/F3830 individuals are more similar to modern Northeast Asian peoples, such as the Ulchi and Yakut. DISCUSSION: Hg C2/M217, widely distributed in the eastern part of the Eurasian continent, was discovered in the ancient Central Steppe and Baikal region. This study shows that there were two important subclades of Hg C2/M217 among the ancient nomadic peoples: C2a1a1b1a/F3830, which has made important genetic contributions to modern Mongolic- and Manchu-speaking populations, and C2b1b/F845, which probably originated in the farming populations of southern East Asia and made certain genetic contributions to past nomadic peoples on the Mongolian Plateau. CI - © 2020 Wiley Periodicals, Inc. FAU - Li, Jiawei AU - Li J AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China. FAU - Cai, Dawei AU - Cai D AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China. FAU - Zhang, Ye AU - Zhang Y AD - College of Life Science, Jilin University, Changchun, People's Republic of China. FAU - Zhu, Hong AU - Zhu H AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China. FAU - Zhou, Hui AU - Zhou H AUID- ORCID: 0000-0001-5858-5636 AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China. AD - College of Life Science, Jilin University, Changchun, People's Republic of China. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200514 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) SB - IM MH - Anthropology, Physical MH - Chromosomes, Human, Y/*genetics MH - DNA, Ancient/*analysis MH - Ethnicity/*genetics/history MH - Genome, Human/genetics MH - Genomics/methods MH - History, Ancient MH - Humans MH - Male MH - Mongolia MH - Sequence Analysis, DNA/methods MH - Transients and Migrants/*history OTO - NOTNLM OT - NRY capture OT - ancient DNA OT - nomadic population OT - shotgun sequencing EDAT- 2020/05/15 06:00 MHDA- 2021/01/26 06:00 CRDT- 2020/05/15 06:00 PHST- 2019/07/04 00:00 [received] PHST- 2020/04/09 00:00 [revised] PHST- 2020/04/17 00:00 [accepted] PHST- 2020/05/15 06:00 [pubmed] PHST- 2021/01/26 06:00 [medline] PHST- 2020/05/15 06:00 [entrez] AID - 10.1002/ajpa.24076 [doi] PST - ppublish SO - Am J Phys Anthropol. 2020 Jul;172(3):402-411. doi: 10.1002/ajpa.24076. Epub 2020 May 14. PMID- 32283039 OWN - NLM STAT- MEDLINE DCOM- 20210112 LR - 20210112 IS - 1480-3321 (Electronic) IS - 0831-2796 (Linking) VI - 63 IP - 7 DP - 2020 Jul TI - Evidence for the persistence of ancient Beothuk and Maritime Archaic mitochondrial DNA genome lineages among modern Native American peoples. PG - 349-355 LID - 10.1139/gen-2019-0149 [doi] AB - The Beothuk were a Native American people who formerly occupied the island of Newfoundland, and who are generally accepted to have become culturally extinct in 1829. The Beothuk succeeded the Maritime Archaic people on the island after a hiatus of ca. 1.4 ka, and were themselves succeeded by the extant Mi'kmaq within historic times. Genetic continuity between ancient and modern Native Americans remains of interest. Complete aDNA mitogenomes from ancient Beothuk and Maritime Archaic were compared with the most closely related modern mitogenomes as obtained by BLAST search of GenBank. Beothuk mitogenomes in five clades are in one case identical to and otherwise differ by minima of three to eight SNPs from the most closely related modern mitogenomes. Maritime Archaic mitogenomes in 12 clades are in one case identical to and otherwise differ by minima of one to nine SNPs from the most similar modern mitogenomes. The single available modern Mi'kmaq mitogenome differs from the most similar Beothuk and Maritime Archaic mitogenomes by 12 and 22 SNPs, respectively. Phylogenetic analysis and sequence similarities imply lineage extinction of most ancient clades, as well as continuity of two Beothuk and at least one Maritime Archaic lineages in modern Native Americans and their descendants. FAU - Carr, Steven M AU - Carr SM AD - Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada. AD - Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada. LA - eng PT - Journal Article DEP - 20200413 PL - Canada TA - Genome JT - Genome JID - 8704544 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Ancient MH - *DNA, Mitochondrial MH - *Evolution, Molecular MH - Genome, Human MH - Humans MH - Indigenous Canadians/*genetics OTO - NOTNLM OT - ADN ancien OT - Amérindiens OT - Beothuk OT - Béothuks OT - Maritime Archaic OT - Native Americans OT - ancient DNA OT - haplogroupes A, B, C, D et X OT - haplogroups A, B, C, D, and X OT - peuples Maritimes Archaïques EDAT- 2020/04/14 06:00 MHDA- 2021/01/13 06:00 CRDT- 2020/04/14 06:00 PHST- 2020/04/14 06:00 [pubmed] PHST- 2021/01/13 06:00 [medline] PHST- 2020/04/14 06:00 [entrez] AID - 10.1139/gen-2019-0149 [doi] PST - ppublish SO - Genome. 2020 Jul;63(7):349-355. doi: 10.1139/gen-2019-0149. Epub 2020 Apr 13. PMID- 32145021 OWN - NLM STAT- MEDLINE DCOM- 20210401 LR - 20221207 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 37 IP - 7 DP - 2020 Jul 1 TI - Limited Evidence for Selection at the FADS Locus in Native American Populations. PG - 2029-2033 LID - 10.1093/molbev/msaa064 [doi] AB - The FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids. This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of long-chain polyunsaturated fatty acids varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals are confounded by independent selection-postdating the split from Native Americans-in the European and, possibly, the East Asian populations used in the population branch statistic test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. An explanation for the present-day distribution of the haplotype that is more consistent with the data is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown. CI - © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA. LA - eng GR - R35 GM133708/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (Delta-5 Fatty Acid Desaturase) RN - EC 1.14.19.- (Fatty Acid Desaturases) RN - EC 1.14.19.3 (FADS1 protein, human) RN - EC 1.14.19.3 (FADS2 protein, human) SB - IM MH - Adaptation, Biological MH - Delta-5 Fatty Acid Desaturase MH - *Evolution, Molecular MH - Fatty Acid Desaturases/*genetics MH - Haplotypes MH - Humans MH - Phylogeography MH - *Selection, Genetic MH - American Indian or Alaska Native/*genetics PMC - PMC7306688 OTO - NOTNLM OT - FADS OT - PBS OT - ancient DNA OT - diet OT - selection EDAT- 2020/03/08 06:00 MHDA- 2021/04/02 06:00 PMCR- 2020/03/07 CRDT- 2020/03/08 06:00 PHST- 2020/03/08 06:00 [pubmed] PHST- 2021/04/02 06:00 [medline] PHST- 2020/03/08 06:00 [entrez] PHST- 2020/03/07 00:00 [pmc-release] AID - 5799087 [pii] AID - msaa064 [pii] AID - 10.1093/molbev/msaa064 [doi] PST - ppublish SO - Mol Biol Evol. 2020 Jul 1;37(7):2029-2033. doi: 10.1093/molbev/msaa064. PMID- 32584871 OWN - NLM STAT- MEDLINE DCOM- 20200831 LR - 20200831 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 15 IP - 6 DP - 2020 TI - Screening archaeological bone for palaeogenetic and palaeoproteomic studies. PG - e0235146 LID - 10.1371/journal.pone.0235146 [doi] LID - e0235146 AB - The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals' size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology. FAU - Kontopoulos, Ioannis AU - Kontopoulos I AUID- ORCID: 0000-0001-5591-8917 AD - Department of Archaeology, BioArCh, University of York, York, United Kingdom. FAU - Penkman, Kirsty AU - Penkman K AD - Department of Chemistry, BioArCh, University of York, York, United Kingdom. FAU - Mullin, Victoria E AU - Mullin VE AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. AD - Department of Earth Sciences, Natural History Museum, London, United Kingdom. FAU - Winkelbach, Laura AU - Winkelbach L AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany. FAU - Unterländer, Martina AU - Unterländer M AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany. AD - Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece. AD - German Federal Criminal Police Office, Wiesbaden, Germany. FAU - Scheu, Amelie AU - Scheu A AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany. FAU - Kreutzer, Susanne AU - Kreutzer S AUID- ORCID: 0000-0001-6286-534X AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany. FAU - Hansen, Henrik B AU - Hansen HB AD - Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Margaryan, Ashot AU - Margaryan A AD - Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Teasdale, Matthew D AU - Teasdale MD AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. AD - Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom. FAU - Gehlen, Birgit AU - Gehlen B AUID- ORCID: 0000-0003-1345-8072 AD - Collaborative Research Centre, project D4, Cologne University, Cologne, Germany. FAU - Street, Martin AU - Street M AD - MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM Leibniz Research Institute for Archaeology, Neuwied, Germany. FAU - Lynnerup, Niels AU - Lynnerup N AD - Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark. FAU - Liritzis, Ioannis AU - Liritzis I AD - Laboratory of Archaeometry, Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece. AD - Center on Yellow River Civilization of Henan Province, Key Research Institute of Yellow River Civilization and Sustainable Development and Collaborative Innovation, Henan University, Kaifeng, China. FAU - Sampson, Adamantios AU - Sampson A AD - Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece. FAU - Papageorgopoulou, Christina AU - Papageorgopoulou C AD - Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece. FAU - Allentoft, Morten E AU - Allentoft ME AD - Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. FAU - Burger, Joachim AU - Burger J AD - Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany. FAU - Bradley, Daniel G AU - Bradley DG AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. FAU - Collins, Matthew J AU - Collins MJ AD - Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom. AD - Centre for Evogenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. LA - eng SI - figshare/10.6084/m9.figshare.11653170 SI - figshare/10.6084/m9.figshare.11653194 SI - figshare/10.6084/m9.figshare.11653197 SI - figshare/10.6084/m9.figshare.12187575 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200625 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *Archaeology MH - Bone and Bones/*chemistry/metabolism MH - DNA, Ancient/*analysis/chemistry MH - *Fossils MH - Humans MH - *Proteomics MH - Spectroscopy, Fourier Transform Infrared PMC - PMC7316274 COIS- The authors have declared that no competing interests exist. EDAT- 2020/06/26 06:00 MHDA- 2020/09/01 06:00 PMCR- 2020/06/25 CRDT- 2020/06/26 06:00 PHST- 2020/01/19 00:00 [received] PHST- 2020/06/09 00:00 [accepted] PHST- 2020/06/26 06:00 [entrez] PHST- 2020/06/26 06:00 [pubmed] PHST- 2020/09/01 06:00 [medline] PHST- 2020/06/25 00:00 [pmc-release] AID - PONE-D-20-01701 [pii] AID - 10.1371/journal.pone.0235146 [doi] PST - epublish SO - PLoS One. 2020 Jun 25;15(6):e0235146. doi: 10.1371/journal.pone.0235146. eCollection 2020. PMID- 32572090 OWN - NLM STAT- MEDLINE DCOM- 20201210 LR - 20211204 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 10 IP - 1 DP - 2020 Jun 22 TI - Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data. PG - 10075 LID - 10.1038/s41598-020-66953-3 [doi] LID - 10075 AB - The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe. FAU - Debortoli, Guilherme AU - Debortoli G AD - Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada. FAU - Abbatangelo, Cristina AU - Abbatangelo C AD - Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada. FAU - Ceballos, Francisco AU - Ceballos F AD - Department of Biological Sciences, Middle East Technical University, Çankaya, Turkey. FAU - Fortes-Lima, Cesar AU - Fortes-Lima C AD - Sub-department of Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. FAU - Norton, Heather L AU - Norton HL AD - Department of Anthropology, University of Cincinnati, Cincinnati, OH, USA. FAU - Ozarkar, Shantanu AU - Ozarkar S AD - Department of Anthropology, Savitribai Phule Pune University, Pune, India. FAU - Parra, Esteban J AU - Parra EJ AD - Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada. FAU - Jonnalagadda, Manjari AU - Jonnalagadda M AD - Symbiosis School for Liberal Arts, Symbiosis International (Deemed University), Pune, India. manjari.jonnalagadda@ssla.edu.in. LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200622 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Ethnicity/*genetics MH - Genetic Drift MH - Genotyping Techniques MH - Humans MH - India/ethnology MH - Population Density MH - Social Class MH - Whole Genome Sequencing/*methods PMC - PMC7308293 COIS- The authors declare no competing interests. EDAT- 2020/06/24 06:00 MHDA- 2020/12/15 06:00 PMCR- 2020/06/22 CRDT- 2020/06/24 06:00 PHST- 2020/02/25 00:00 [received] PHST- 2020/05/27 00:00 [accepted] PHST- 2020/06/24 06:00 [entrez] PHST- 2020/06/24 06:00 [pubmed] PHST- 2020/12/15 06:00 [medline] PHST- 2020/06/22 00:00 [pmc-release] AID - 10.1038/s41598-020-66953-3 [pii] AID - 66953 [pii] AID - 10.1038/s41598-020-66953-3 [doi] PST - epublish SO - Sci Rep. 2020 Jun 22;10(1):10075. doi: 10.1038/s41598-020-66953-3. PMID- 32539695 OWN - NLM STAT- MEDLINE DCOM- 20210308 LR - 20240426 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 21 IP - 1 DP - 2020 Jun 15 TI - Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia. PG - 402 LID - 10.1186/s12864-020-06810-9 [doi] LID - 402 AB - BACKGROUND: Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death. RESULTS: In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. forsythia-containing samples were obtained revealed the pathogenic alveolar bone loss in tooth areas characteristic for advanced periodontitis. Finally, we analyzed the genetic material of ancient T. forsythia strains. As a result, we assembled four ancient T. forsythia genomes - one 2000- and three 1000- year-old. Their comparison with contemporary T. forsythia genomes revealed a lower genetic diversity within the four ancient strains than within contemporary strains. We also investigated the genes of T. forsythia virulence factors and found that several of them (KLIKK protease and bspA genes) differ significantly between ancient and modern bacteria. CONCLUSIONS: In summary, we showed that NGS screening of the ancient human microbiome is a valid approach for the identification of disease-associated microbes. Following this protocol, we provided a new set of information on the emergence, evolution and virulence factors of T. forsythia, the member of the oral dysbiotic microbiome. FAU - Philips, Anna AU - Philips A AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. FAU - Stolarek, Ireneusz AU - Stolarek I AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. FAU - Handschuh, Luiza AU - Handschuh L AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. FAU - Nowis, Katarzyna AU - Nowis K AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. FAU - Juras, Anna AU - Juras A AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland. FAU - Trzciński, Dawid AU - Trzciński D AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland. FAU - Nowaczewska, Wioletta AU - Nowaczewska W AD - Department of Human Biology, Faculty of Biological Sciences, Wroclaw University, 50-138, Wroclaw, Poland. FAU - Wrzesińska, Anna AU - Wrzesińska A AD - Anthropological Laboratory, Museum of the First Piasts at Lednica, 62-261, Lednogora, Poland. FAU - Potempa, Jan AU - Potempa J AD - Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland. AD - Department of Oral Immunity and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, 40202, USA. FAU - Figlerowicz, Marek AU - Figlerowicz M AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. marekf@ibch.poznan.pl. AD - Institute of Computing Science, Poznan University of Technology, 60-965, Poznan, Poland. marekf@ibch.poznan.pl. LA - eng GR - R21 DE026280/DE/NIDCR NIH HHS/United States GR - R21DE026280/DE/NIDCR NIH HHS/United States PT - Journal Article DEP - 20200615 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (Virulence Factors) SB - IM MH - Body Remains/*microbiology MH - Fossils/*microbiology MH - *Gastrointestinal Microbiome MH - Genome, Bacterial MH - Genomics MH - Humans MH - Metagenome MH - Mouth/*microbiology MH - Periodontitis/microbiology MH - Periodontium/microbiology MH - Tannerella forsythia/*genetics/*pathogenicity MH - Tooth/microbiology MH - Virulence Factors/*genetics PMC - PMC7296668 OTO - NOTNLM OT - Ancient genomics OT - Comparative genomics OT - Oral microbiome OT - T. forsythia OT - aDNA COIS- The authors declare that they have no competing interests. EDAT- 2020/06/17 06:00 MHDA- 2021/03/09 06:00 PMCR- 2020/06/15 CRDT- 2020/06/17 06:00 PHST- 2020/02/12 00:00 [received] PHST- 2020/06/08 00:00 [accepted] PHST- 2020/06/17 06:00 [entrez] PHST- 2020/06/17 06:00 [pubmed] PHST- 2021/03/09 06:00 [medline] PHST- 2020/06/15 00:00 [pmc-release] AID - 10.1186/s12864-020-06810-9 [pii] AID - 6810 [pii] AID - 10.1186/s12864-020-06810-9 [doi] PST - epublish SO - BMC Genomics. 2020 Jun 15;21(1):402. doi: 10.1186/s12864-020-06810-9. PMID- 32511234 OWN - NLM STAT- MEDLINE DCOM- 20200729 LR - 20211204 IS - 1545-7885 (Electronic) IS - 1544-9173 (Print) IS - 1544-9173 (Linking) VI - 18 IP - 6 DP - 2020 Jun TI - Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA. PG - e3000742 LID - 10.1371/journal.pbio.3000742 [doi] LID - e3000742 AB - The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all? FAU - Segurel, Laure AU - Segurel L AUID- ORCID: 0000-0001-7339-0976 AD - Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris, Paris, France. FAU - Guarino-Vignon, Perle AU - Guarino-Vignon P AUID- ORCID: 0000-0002-7852-0538 AD - Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris, Paris, France. FAU - Marchi, Nina AU - Marchi N AUID- ORCID: 0000-0001-6624-5922 AD - Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris, Paris, France. FAU - Lafosse, Sophie AU - Lafosse S AD - Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris, Paris, France. FAU - Laurent, Romain AU - Laurent R AUID- ORCID: 0000-0003-0363-2954 AD - Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris, Paris, France. FAU - Bon, Céline AU - Bon C AUID- ORCID: 0000-0001-5422-3232 AD - Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris, Paris, France. FAU - Fabre, Alexandre AU - Fabre A AUID- ORCID: 0000-0001-5155-6437 AD - Aix Marseille University, INSERM, MMG, Marseille, France. AD - APHM, Hôpital de la Timone Enfant, Service de Pédiatrie Multidisciplinaire, Marseille, France. FAU - Hegay, Tatyana AU - Hegay T AUID- ORCID: 0000-0003-4764-0841 AD - Institute of Immunology and Human Genomics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan. FAU - Heyer, Evelyne AU - Heyer E AUID- ORCID: 0000-0002-0266-3196 AD - Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris, Paris, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200608 PL - United States TA - PLoS Biol JT - PLoS biology JID - 101183755 RN - 0 (DNA, Ancient) RN - EC 3.2.1.108 (Lactase) SB - IM MH - Animals MH - Asia MH - *DNA, Ancient MH - Ethnicity/genetics MH - Europe MH - Fermentation MH - Gene Frequency/genetics MH - Genotype MH - Humans MH - Lactase/*genetics MH - Milk MH - *Selection, Genetic MH - Time Factors PMC - PMC7302802 COIS- The authors have declared that no competing interests exist. EDAT- 2020/06/09 06:00 MHDA- 2020/07/30 06:00 PMCR- 2020/06/08 CRDT- 2020/06/09 06:00 PHST- 2020/06/18 00:00 [revised] PHST- 2020/06/09 06:00 [pubmed] PHST- 2020/07/30 06:00 [medline] PHST- 2020/06/09 06:00 [entrez] PHST- 2020/06/08 00:00 [pmc-release] AID - PBIOLOGY-D-20-00891 [pii] AID - 10.1371/journal.pbio.3000742 [doi] PST - epublish SO - PLoS Biol. 2020 Jun 8;18(6):e3000742. doi: 10.1371/journal.pbio.3000742. eCollection 2020 Jun. PMID- 32359431 OWN - NLM STAT- MEDLINE DCOM- 20210810 LR - 20221207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 30 IP - 11 DP - 2020 Jun 8 TI - Origin and Health Status of First-Generation Africans from Early Colonial Mexico. PG - 2078-2091.e11 LID - S0960-9822(20)30482-6 [pii] LID - 10.1016/j.cub.2020.04.002 [doi] AB - The forced relocation of several thousand Africans during Mexico's historic period has so far been documented mostly through archival sources, which provide only sparse detail on their origins and lived experience. Here, we employ a bioarchaeological approach to explore the life history of three 16(th) century Africans from a mass burial at the San José de los Naturales Royal Hospital in Mexico City. Our approach draws together ancient genomic data, osteological analysis, strontium isotope data from tooth enamel, δ(13)C and δ(15)N isotope data from dentine, and ethnohistorical information to reveal unprecedented detail on their origins and health. Analyses of skeletal features, radiogenic isotopes, and genetic data from uniparental, genome-wide, and human leukocyte antigen (HLA) markers are consistent with a Sub-Saharan African origin for all three individuals. Complete genomes of Treponema pallidum sub. pertenue (causative agent of yaws) and hepatitis B virus (HBV) recovered from these individuals provide insight into their health as related to infectious disease. Phylogenetic analysis of both pathogens reveals their close relationship to strains circulating in current West African populations, lending support to their origins in this region. The further relationship between the treponemal genome retrieved and a treponemal genome previously typed in an individual from Colonial Mexico highlights the role of the transatlantic slave trade in the introduction and dissemination of pathogens into the New World. Putting together all lines of evidence, we were able to create a biological portrait of three individuals whose life stories have long been silenced by disreputable historical events. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Barquera, Rodrigo AU - Barquera R AD - Department of Archaeogenetics (DAG), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany; Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Periférico Sur y Zapote s/n. Col. Isidro Fabela, Tlalpan, 14030 Mexico City, Mexico. FAU - Lamnidis, Thiseas C AU - Lamnidis TC AD - Department of Archaeogenetics (DAG), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany. FAU - Lankapalli, Aditya Kumar AU - Lankapalli AK AD - Department of Archaeogenetics (DAG), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany. FAU - Kocher, Arthur AU - Kocher A AD - Transmission, Infection, Diversification & Evolution Group (TIDE), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany. FAU - Hernández-Zaragoza, Diana I AU - Hernández-Zaragoza DI AD - Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Periférico Sur y Zapote s/n. Col. Isidro Fabela, Tlalpan, 14030 Mexico City, Mexico; Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Calz. del Hueso 714, Coapa, Los Sauces, Coyoacán, 04940 Mexico City, CDMX, Mexico. FAU - Nelson, Elizabeth A AU - Nelson EA AD - Department of Archaeogenetics (DAG), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany; Institute for the Archaeological Sciences, University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany. FAU - Zamora-Herrera, Adriana C AU - Zamora-Herrera AC AD - Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Periférico Sur y Zapote s/n. Col. Isidro Fabela, Tlalpan, 14030 Mexico City, Mexico. FAU - Ramallo, Patxi AU - Ramallo P AD - Department of Archaeology (DA), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany; Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Arriola Pasealekua, 2, 20018 Donostia, Gipuzkoa, Spain. FAU - Bernal-Felipe, Natalia AU - Bernal-Felipe N AD - Escuela Nacional de Antropología e Historia (ENAH), Periférico Sur y Zapote s/n. Col. Isidro Fabela, Tlalpan, 14030 Mexico City, Mexico. FAU - Immel, Alexander AU - Immel A AD - Department of Archaeogenetics (DAG), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany; Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany. FAU - Bos, Kirsten AU - Bos K AD - Department of Archaeogenetics (DAG), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany. FAU - Acuña-Alonzo, Víctor AU - Acuña-Alonzo V AD - Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Periférico Sur y Zapote s/n. Col. Isidro Fabela, Tlalpan, 14030 Mexico City, Mexico. FAU - Barbieri, Chiara AU - Barbieri C AD - Department of Linguistic and Cultural Evolution (DLCE), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland. FAU - Roberts, Patrick AU - Roberts P AD - Department of Archaeology (DA), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany. FAU - Herbig, Alexander AU - Herbig A AD - Department of Archaeogenetics (DAG), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany. FAU - Kühnert, Denise AU - Kühnert D AD - Transmission, Infection, Diversification & Evolution Group (TIDE), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany. Electronic address: kuehnert@shh.mpg.de. FAU - Márquez-Morfín, Lourdes AU - Márquez-Morfín L AD - Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Periférico Sur y Zapote s/n. Col. Isidro Fabela, Tlalpan, 14030 Mexico City, Mexico. Electronic address: rlmorfin@gmail.com. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics (DAG), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745 Jena, Germany. Electronic address: krause@shh.mpg.de. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200430 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - Treponema pallidum subsp. pertenue SB - IM MH - Adult MH - Archaeology MH - Black People/history MH - DNA, Ancient/*analysis MH - Enslaved Persons/*history MH - *Health Status MH - Hepatitis B/*history MH - Hepatitis B virus/isolation & purification MH - History, 16th Century MH - Humans MH - Male MH - Mexico MH - Treponema/isolation & purification MH - Yaws/*history MH - Young Adult OTO - NOTNLM OT - African ancestry OT - New Spain OT - Treponema pallidum OT - ancient DNA OT - hepatitis B virus OT - transatlantic slave trade COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2020/05/04 06:00 MHDA- 2021/08/11 06:00 CRDT- 2020/05/04 06:00 PHST- 2020/01/17 00:00 [received] PHST- 2020/03/03 00:00 [revised] PHST- 2020/04/01 00:00 [accepted] PHST- 2020/05/04 06:00 [pubmed] PHST- 2021/08/11 06:00 [medline] PHST- 2020/05/04 06:00 [entrez] AID - S0960-9822(20)30482-6 [pii] AID - 10.1016/j.cub.2020.04.002 [doi] PST - ppublish SO - Curr Biol. 2020 Jun 8;30(11):2078-2091.e11. doi: 10.1016/j.cub.2020.04.002. Epub 2020 Apr 30. PMID- 32745952 OWN - NLM STAT- MEDLINE DCOM- 20210702 LR - 20231112 IS - 1879-0380 (Electronic) IS - 0959-437X (Print) IS - 0959-437X (Linking) VI - 62 DP - 2020 Jun TI - Human adaptation over the past 40,000 years. PG - 97-104 LID - S0959-437X(20)30101-5 [pii] LID - 10.1016/j.gde.2020.06.003 [doi] AB - Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits. CI - Copyright © 2020 Elsevier Ltd. All rights reserved. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States. Electronic address: mathi@pennmedicine.upenn.edu. LA - eng GR - R35 GM133708/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200801 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) SB - IM MH - *Adaptation, Physiological MH - DNA, Ancient/*analysis MH - *Evolution, Molecular MH - Genomics/*history MH - History, Ancient MH - Humans MH - *Multifactorial Inheritance MH - Phenotype MH - *Selection, Genetic PMC - PMC7484260 MID - NIHMS1608180 EDAT- 2020/08/04 06:00 MHDA- 2021/07/03 06:00 PMCR- 2021/08/01 CRDT- 2020/08/04 06:00 PHST- 2020/03/16 00:00 [received] PHST- 2020/05/10 00:00 [revised] PHST- 2020/06/01 00:00 [accepted] PHST- 2020/08/04 06:00 [pubmed] PHST- 2021/07/03 06:00 [medline] PHST- 2020/08/04 06:00 [entrez] PHST- 2021/08/01 00:00 [pmc-release] AID - S0959-437X(20)30101-5 [pii] AID - 10.1016/j.gde.2020.06.003 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2020 Jun;62:97-104. doi: 10.1016/j.gde.2020.06.003. Epub 2020 Aug 1. PMID- 32688244 OWN - NLM STAT- MEDLINE DCOM- 20210702 LR - 20221207 IS - 1879-0380 (Electronic) IS - 0959-437X (Linking) VI - 62 DP - 2020 Jun TI - Human evolutionary history in Eastern Eurasia using insights from ancient DNA. PG - 78-84 LID - S0959-437X(20)30109-X [pii] LID - 10.1016/j.gde.2020.06.009 [doi] AB - Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia-some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia. CI - Copyright © 2020 Elsevier Ltd. All rights reserved. FAU - Zhang, Ming AU - Zhang M AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng GR - 55008731/HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200717 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Asian People/*genetics MH - *Biological Evolution MH - DNA, Ancient/*analysis MH - *Genetic Variation MH - *Genetics, Population MH - *Genome, Human MH - History, Ancient MH - Human Migration/*history MH - Humans EDAT- 2020/07/21 06:00 MHDA- 2021/07/03 06:00 CRDT- 2020/07/21 06:00 PHST- 2020/02/26 00:00 [received] PHST- 2020/05/22 00:00 [revised] PHST- 2020/06/17 00:00 [accepted] PHST- 2020/07/21 06:00 [pubmed] PHST- 2021/07/03 06:00 [medline] PHST- 2020/07/21 06:00 [entrez] AID - S0959-437X(20)30109-X [pii] AID - 10.1016/j.gde.2020.06.009 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2020 Jun;62:78-84. doi: 10.1016/j.gde.2020.06.009. Epub 2020 Jul 17. PMID- 32659643 OWN - NLM STAT- MEDLINE DCOM- 20210702 LR - 20210702 IS - 1879-0380 (Electronic) IS - 0959-437X (Linking) VI - 62 DP - 2020 Jun TI - The history behind the mosaic of the Americas. PG - 72-77 LID - S0959-437X(20)30107-6 [pii] LID - 10.1016/j.gde.2020.06.007 [doi] AB - Focusing on literature published in 2018-2020, we review inferences about: (i) how ancient DNA is contributing to clarify the peopling of the Americas and the dispersal of its first inhabitants, (ii) how the interplay between environmental diversity and culture has influenced the genetic structure and adaptation of Andean and Amazon populations, (iii) how genetics has contributed to our understanding of the Pre-Columbian Tupi expansion in Eastern South America, (iv) the subcontinental origins and dynamics of Post-Columbian admixture in the Americas, and finally, (v) episodes of adaptive natural selection in the American continent, particularly in the high altitudes of the Andes. CI - Copyright © 2020 Elsevier Ltd. All rights reserved. FAU - Mendes, Marla AU - Mendes M AD - Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. FAU - Alvim, Isabela AU - Alvim I AD - Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. FAU - Borda, Victor AU - Borda V AD - Laboratório de Bioinformática, LABINFO, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil. FAU - Tarazona-Santos, Eduardo AU - Tarazona-Santos E AD - Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. Electronic address: edutars@icb.ufmg.br. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200710 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) SB - IM MH - Americas MH - Colombia MH - DNA, Ancient/*analysis MH - *Genetic Variation MH - *Genetics, Population MH - *Genome, Human MH - Haplotypes MH - History, Ancient MH - Human Migration/*history MH - Humans MH - *Mosaicism MH - *Selection, Genetic EDAT- 2020/07/14 06:00 MHDA- 2021/07/03 06:00 CRDT- 2020/07/14 06:00 PHST- 2020/02/23 00:00 [received] PHST- 2020/06/09 00:00 [revised] PHST- 2020/06/11 00:00 [accepted] PHST- 2020/07/14 06:00 [pubmed] PHST- 2021/07/03 06:00 [medline] PHST- 2020/07/14 06:00 [entrez] AID - S0959-437X(20)30107-6 [pii] AID - 10.1016/j.gde.2020.06.007 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2020 Jun;62:72-77. doi: 10.1016/j.gde.2020.06.007. Epub 2020 Jul 10. PMID- 32610222 OWN - NLM STAT- MEDLINE DCOM- 20210702 LR - 20221207 IS - 1879-0380 (Electronic) IS - 0959-437X (Linking) VI - 62 DP - 2020 Jun TI - Latest trends in archaeogenetic research of west Eurasians. PG - 36-43 LID - S0959-437X(20)30072-1 [pii] LID - 10.1016/j.gde.2020.05.021 [doi] AB - During the past ten years, archaeogenetic research has exponentially grown to study the genetic history of human populations, using genome-wide data from large numbers of ancient individuals. Of the entire globe, Europe and the Near East are the regions where ancient DNA data is by far most abundant with over 2500 genomes published at present. In this review, we focus on archaeological contexts that have received less attention in the literature, specifically those associated with west Eurasian hunter-gatherers as well as populations from the Iron Age and later historical periods. In addition, we emphasize a recent shift from continent-wide to regional and even site-specific studies, which is starting to provide novel insights into sociocultural aspects of past societies. CI - Copyright © 2020 Elsevier Ltd. All rights reserved. FAU - Olalde, Iñigo AU - Olalde I AD - Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain. FAU - Posth, Cosimo AU - Posth C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany. Electronic address: posth@shh.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200628 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology/*methods MH - DNA, Ancient/*analysis MH - *Gene Flow MH - *Genetic Variation MH - *Genome, Human MH - Human Migration/*trends MH - Humans MH - White People/*genetics EDAT- 2020/07/02 06:00 MHDA- 2021/07/03 06:00 CRDT- 2020/07/02 06:00 PHST- 2020/02/01 00:00 [received] PHST- 2020/05/11 00:00 [revised] PHST- 2020/05/22 00:00 [accepted] PHST- 2020/07/02 06:00 [pubmed] PHST- 2021/07/03 06:00 [medline] PHST- 2020/07/02 06:00 [entrez] AID - S0959-437X(20)30072-1 [pii] AID - 10.1016/j.gde.2020.05.021 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2020 Jun;62:36-43. doi: 10.1016/j.gde.2020.05.021. Epub 2020 Jun 28. PMID- 32574964 OWN - NLM STAT- MEDLINE DCOM- 20210702 LR - 20210702 IS - 1879-0380 (Electronic) IS - 0959-437X (Linking) VI - 62 DP - 2020 Jun TI - Harnessing epigenetics to study human evolution. PG - 23-29 LID - S0959-437X(20)30074-5 [pii] LID - 10.1016/j.gde.2020.05.023 [doi] AB - Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates. CI - Copyright © 2020 Elsevier Ltd. All rights reserved. FAU - Mathov, Yoav AU - Mathov Y AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190400, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190400, Israel. FAU - Batyrev, Daniel AU - Batyrev D AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190400, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190400, Israel. FAU - Meshorer, Eran AU - Meshorer E AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190400, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190400, Israel. Electronic address: eran.meshorer@mail.huji.ac.il. FAU - Carmel, Liran AU - Carmel L AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190400, Israel. Electronic address: liran.carmel@huji.ac.il. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200620 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 SB - IM MH - *DNA Methylation MH - *Epigenesis, Genetic MH - *Evolution, Molecular MH - *Genetic Variation MH - *Genome, Human MH - Humans EDAT- 2020/06/24 06:00 MHDA- 2021/07/03 06:00 CRDT- 2020/06/24 06:00 PHST- 2020/02/14 00:00 [received] PHST- 2020/05/18 00:00 [revised] PHST- 2020/05/22 00:00 [accepted] PHST- 2020/06/24 06:00 [pubmed] PHST- 2021/07/03 06:00 [medline] PHST- 2020/06/24 06:00 [entrez] AID - S0959-437X(20)30074-5 [pii] AID - 10.1016/j.gde.2020.05.023 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2020 Jun;62:23-29. doi: 10.1016/j.gde.2020.05.023. Epub 2020 Jun 20. PMID- 32563853 OWN - NLM STAT- MEDLINE DCOM- 20210702 LR - 20221207 IS - 1879-0380 (Electronic) IS - 0959-437X (Linking) VI - 62 DP - 2020 Jun TI - African population history: an ancient DNA perspective. PG - 8-15 LID - S0959-437X(20)30059-9 [pii] LID - 10.1016/j.gde.2020.05.008 [doi] AB - The history of human populations in Africa is complex and includes various demographic events that influenced patterns of genetic variation across the continent. Through genetic studies of modern-day, and most recently, ancient African genetic variation, it became evident that deep African history is captured by the relationships among hunter-gatherers. Furthermore, it was shown that agriculture had a large influence on the distribution of current-day Africans. These later population movements changed the demographic face of the continent and descendants of farming groups today form the majority populations across Africa. Ancient DNA methods are continually evolving, and we see evidence of this in how research has advanced in the last decade. With the increased availability of full genomic data from diverse sets of modern-day and prehistoric Africans we now have more power to infer human demography. Future ancient DNA research promises to reveal more detailed stories of human prehistory in Africa. CI - Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Vicente, Mário AU - Vicente M AD - Human Evolution, Department of Organismal Biology, Uppsala University, Sweden. FAU - Schlebusch, Carina M AU - Schlebusch CM AD - Human Evolution, Department of Organismal Biology, Uppsala University, Sweden; Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa; Science for Life Laboratory, Uppsala, Sweden. Electronic address: carina.schlebusch@ebc.uu.se. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200618 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) SB - IM MH - Black People/*genetics MH - DNA, Ancient/*analysis MH - *Genetic Variation MH - *Genetics, Population MH - *Genome, Human MH - Humans MH - *Population Dynamics EDAT- 2020/06/22 06:00 MHDA- 2021/07/03 06:00 CRDT- 2020/06/22 06:00 PHST- 2020/02/09 00:00 [received] PHST- 2020/05/04 00:00 [revised] PHST- 2020/05/06 00:00 [accepted] PHST- 2020/06/22 06:00 [pubmed] PHST- 2021/07/03 06:00 [medline] PHST- 2020/06/22 06:00 [entrez] AID - S0959-437X(20)30059-9 [pii] AID - 10.1016/j.gde.2020.05.008 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2020 Jun;62:8-15. doi: 10.1016/j.gde.2020.05.008. Epub 2020 Jun 18. PMID- 32405770 OWN - NLM STAT- MEDLINE DCOM- 20211022 LR - 20211022 IS - 1420-9144 (Electronic) IS - 0036-6978 (Linking) VI - 28 IP - 2 DP - 2020 Jun TI - [About Media Presence and Prominence of DNA-Supported Research of the Past]. PG - 181-192 LID - 10.1007/s00048-020-00249-5 [doi] AB - In recent years molecular genetics has provided a completely new approach/access to the human past. The still new and quite dynamic research field of archaeogenetics (also known as palaeogenetics or genetic history) claims to be able to write history using ancient DNA. Through numerous remarkable publications it has generated and received much interest not only in scientific discourse but also in the media. So far, however, scientists have not paid much attention to this coverage-a research desideratum this paper cannot resolve. But by looking at selected press clippings it seeks to capture first trends according to the following three theses: telling success stories, drawing boundaries, and writing in a conformist manner. FAU - Samida, Stefanie AU - Samida S AD - Historisches Seminar, Ruprecht-Karls-Universität Heidelberg, 69117, Heidelberg, Germany. stefanie.samida@zegk.uni-heidelberg.de. LA - ger PT - Journal Article PT - Research Support, Non-U.S. Gov't TT - Über mediale Präsenz und Prominenz DNA-gestützter Vergangenheitsforschung. PL - Switzerland TA - NTM JT - NTM JID - 0347631 RN - 9007-49-2 (DNA) MH - Archaeology/*methods MH - *Communications Media MH - *DNA MH - Genetic Techniques MH - Humans MH - Molecular Biology/*methods MH - Publishing MH - *Research MH - Science MH - Writing OTO - NOTNLM OT - ancient DNA OT - archaeogenetics/genetic history OT - media EDAT- 2020/05/15 06:00 MHDA- 2023/02/25 06:00 CRDT- 2020/05/15 06:00 PHST- 2020/05/15 06:00 [pubmed] PHST- 2023/02/25 06:00 [medline] PHST- 2020/05/15 06:00 [entrez] AID - 10.1007/s00048-020-00249-5 [pii] AID - 10.1007/s00048-020-00249-5 [doi] PST - ppublish SO - NTM. 2020 Jun;28(2):181-192. doi: 10.1007/s00048-020-00249-5. PMID- 32396835 OWN - NLM STAT- MEDLINE DCOM- 20210527 LR - 20210527 IS - 0168-9525 (Print) IS - 0168-9525 (Linking) VI - 36 IP - 6 DP - 2020 Jun TI - The Genomics of Human Local Adaptation. PG - 415-428 LID - S0168-9525(20)30070-6 [pii] LID - 10.1016/j.tig.2020.03.006 [doi] AB - Modern humans inhabit a variety of environments and are exposed to a plethora of selective pressures, leading to multiple genetic adaptations to local environmental conditions. These include adaptations to climate, UV exposure, disease, diet, altitude, or cultural practice and have generated important genetic and phenotypic differences amongst populations. In recent years, new methods to identify the genomic signatures of natural selection underlying these adaptations, combined with novel types of genetic data (e.g., ancient DNA), have provided unprecedented insights into the origin of adaptive alleles and the modes of adaptation. As a result, numerous instances of local adaptation have been identified in humans. Here, we review the most exciting recent developments and discuss, in our view, the future of this field. CI - Copyright © 2020. Published by Elsevier Ltd. FAU - Rees, Jasmin S AU - Rees JS AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK; Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London, London, UK. FAU - Castellano, Sergi AU - Castellano S AD - Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London, London, UK; UCL Genomics, Great Ormond Street Institute of Child Health, University College London, London, UK. FAU - Andrés, Aida M AU - Andrés AM AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK. Electronic address: a.andres@ucl.ac.uk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200415 PL - England TA - Trends Genet JT - Trends in genetics : TIG JID - 8507085 SB - IM MH - *Adaptation, Physiological MH - Animals MH - *Biological Evolution MH - *Genetic Variation MH - Genomics/*methods MH - Humans MH - *Selection, Genetic OTO - NOTNLM OT - adaptive introgression OT - genealogical methods OT - genetic adaptation OT - genetic-environmental correlation OT - polygenic selection OT - positive selection OT - selection on de novo mutation (SDN) OT - selection on standing variation (SSV) EDAT- 2020/05/13 06:00 MHDA- 2021/05/28 06:00 CRDT- 2020/05/13 06:00 PHST- 2020/01/27 00:00 [received] PHST- 2020/03/16 00:00 [revised] PHST- 2020/03/18 00:00 [accepted] PHST- 2020/05/13 06:00 [entrez] PHST- 2020/05/13 06:00 [pubmed] PHST- 2021/05/28 06:00 [medline] AID - S0168-9525(20)30070-6 [pii] AID - 10.1016/j.tig.2020.03.006 [doi] PST - ppublish SO - Trends Genet. 2020 Jun;36(6):415-428. doi: 10.1016/j.tig.2020.03.006. Epub 2020 Apr 15. PMID- 32297323 OWN - NLM STAT- MEDLINE DCOM- 20210203 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 172 IP - 2 DP - 2020 Jun TI - Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations. PG - 176-188 LID - 10.1002/ajpa.24057 [doi] AB - OBJECTIVE: In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes. MATERIALS AND METHODS: We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzyżow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS (14) C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples. RESULTS: Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzyżów people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study. DISCUSSION: Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzyżów-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group. CI - © 2020 Wiley Periodicals, Inc. FAU - Juras, Anna AU - Juras A AUID- ORCID: 0000-0002-2585-127X AD - Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland. FAU - Makarowicz, Przemysław AU - Makarowicz P AD - Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poland. FAU - Chyleński, Maciej AU - Chyleński M AD - Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland. FAU - Ehler, Edvard AU - Ehler E AUID- ORCID: 0000-0003-1774-0091 AD - Department of Biology and Environmental Studies, Charles University, Faculty of Education, Praha 1, Czech Republic. FAU - Malmström, Helena AU - Malmström H AD - Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, UPpSala, Sweden. AD - Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa. FAU - Krzewińska, Maja AU - Krzewińska M AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. FAU - Pospieszny, Łukasz AU - Pospieszny Ł AD - Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland. AD - Department of Anthropology and Archaeology, University of Bristol, Bristol, UK. FAU - Górski, Jacek AU - Górski J AD - Department of History and Cultural Heritage, University of Pope Jan Paweł II, Kraków, Poland. AD - Archaeological Museum in Cracow, Kraków, Poland. FAU - Taras, Halina AU - Taras H AD - Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland. FAU - Szczepanek, Anita AU - Szczepanek A AD - Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland. FAU - Polańska, Marta AU - Polańska M AD - Department of Material and Spiritual Culture, Lublin Museum, Lublin, Poland. FAU - Włodarczak, Piotr AU - Włodarczak P AD - Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland. FAU - Szyca, Agnieszka AU - Szyca A AD - Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland. FAU - Lasota-Kuś, Anna AU - Lasota-Kuś A AD - Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland. FAU - Wójcik, Irena AU - Wójcik I AD - Archaeological Museum in Cracow, Kraków, Poland. FAU - Jakobsson, Mattias AU - Jakobsson M AUID- ORCID: 0000-0001-7840-7853 AD - Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, UPpSala, Sweden. AD - Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa. FAU - Dabert, Miroslawa AU - Dabert M AD - Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200415 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) SB - IM MH - Adult MH - Anthropology, Physical MH - Cemeteries MH - Child MH - DNA, Ancient/*analysis MH - Female MH - *Genetics, Population MH - Genome, Mitochondrial/*genetics MH - Haplotypes/genetics MH - History, Ancient MH - Human Migration MH - Humans MH - Male MH - Poland MH - White People/*genetics OTO - NOTNLM OT - Bronze Age OT - Late Neolithic OT - ancient DNA OT - human population OT - mitochondrial genome EDAT- 2020/04/17 06:00 MHDA- 2021/02/04 06:00 CRDT- 2020/04/17 06:00 PHST- 2019/11/15 00:00 [received] PHST- 2020/03/13 00:00 [revised] PHST- 2020/03/21 00:00 [accepted] PHST- 2020/04/17 06:00 [pubmed] PHST- 2021/02/04 06:00 [medline] PHST- 2020/04/17 06:00 [entrez] AID - 10.1002/ajpa.24057 [doi] PST - ppublish SO - Am J Phys Anthropol. 2020 Jun;172(2):176-188. doi: 10.1002/ajpa.24057. Epub 2020 Apr 15. PMID- 32233019 OWN - NLM STAT- MEDLINE DCOM- 20210413 LR - 20210413 IS - 2324-9269 (Electronic) IS - 2324-9269 (Linking) VI - 8 IP - 6 DP - 2020 Jun TI - Ancient dental pulp: Masterpiece tissue for paleomicrobiology. PG - e1202 LID - 10.1002/mgg3.1202 [doi] LID - e1202 AB - INTRODUCTION: Dental pulp with special structure has become a good reference sample in paleomicrobiology-related blood-borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins. OBJECTIVES: This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe. METHODS: The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: "ancient," "dental pulp," "teeth," "anatomy," "structure," "collection," "preservation," "selection," "photography," "radiography," "contamination," "decontamination," "DNA," "protein," "extraction," "bone," "paleomicrobiology," "bacteria," "virus," "pathogen," "molecular biology," "proteomics," "PCR," "MALDI-TOF," "LC/MS," "ELISA," "immunology," "immunochromatography," "genome," "microbiome," "metagenomics." RESULTS: The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty-seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species. CONCLUSIONS: Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics. CI - © 2020 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc. FAU - Mai, Ba Hoang Anh AU - Mai BHA AD - Aix-Marseille Université, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France. AD - Hue University of Medicine and Pharmacy, Thua Thien Hue, Vietnam. FAU - Drancourt, Michel AU - Drancourt M AD - Aix-Marseille Université, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France. FAU - Aboudharam, Gérard AU - Aboudharam G AUID- ORCID: 0000-0003-4472-9154 AD - Aix-Marseille Université, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France. AD - UFR Odontologie, Aix-Marseille Université, Marseille, France. LA - eng PT - Journal Article PT - Review DEP - 20200331 PL - United States TA - Mol Genet Genomic Med JT - Molecular genetics & genomic medicine JID - 101603758 RN - 0 (DNA, Ancient) SB - IM MH - Bacterial Infections/epidemiology/*microbiology MH - *DNA, Ancient MH - Dental Pulp/*microbiology MH - Fossils/*microbiology MH - Humans MH - Metagenome MH - Microbiota PMC - PMC7284042 OTO - NOTNLM OT - ancient dental pulp OT - infectious diseases OT - nucleic acids OT - paleomicrobiology OT - proteins EDAT- 2020/04/02 06:00 MHDA- 2021/04/14 06:00 PMCR- 2020/03/31 CRDT- 2020/04/02 06:00 PHST- 2020/01/15 00:00 [received] PHST- 2020/02/21 00:00 [accepted] PHST- 2020/04/02 06:00 [pubmed] PHST- 2021/04/14 06:00 [medline] PHST- 2020/04/02 06:00 [entrez] PHST- 2020/03/31 00:00 [pmc-release] AID - MGG31202 [pii] AID - 10.1002/mgg3.1202 [doi] PST - ppublish SO - Mol Genet Genomic Med. 2020 Jun;8(6):e1202. doi: 10.1002/mgg3.1202. Epub 2020 Mar 31. PMID- 32127690 OWN - NLM STAT- MEDLINE DCOM- 20200722 LR - 20230519 IS - 1471-0064 (Electronic) IS - 1471-0056 (Linking) VI - 21 IP - 6 DP - 2020 Jun TI - Beyond broad strokes: sociocultural insights from the study of ancient genomes. PG - 355-366 LID - 10.1038/s41576-020-0218-z [doi] AB - In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from mostly large-scale supraregional studies to a more local perspective, shedding light on socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies showcasing these types of insights, focusing on methods used to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines - such as anthropology, archaeology, linguistics and genetics - that have until recently evolved in separation. Multidisciplinary dialogue is important for an integrated reconstruction of human history, which can yield extraordinary insights about past societies, reproductive behaviours and even lifestyle habits that would not be possible to obtain otherwise. FAU - Racimo, Fernando AU - Racimo F AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. fracimo@sund.ku.dk. FAU - Sikora, Martin AU - Sikora M AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Vander Linden, Marc AU - Vander Linden M AD - Department of Archaeology, Cambridge University, Cambridge, UK. FAU - Schroeder, Hannes AU - Schroeder H AUID- ORCID: 0000-0002-6743-0270 AD - Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AUID- ORCID: 0000-0002-1730-5914 AD - Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain. carles.lalueza@upf.edu. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200303 PL - England TA - Nat Rev Genet JT - Nature reviews. Genetics JID - 100962779 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology/methods MH - DNA, Ancient/*analysis MH - Emigration and Immigration/statistics & numerical data MH - Genetics, Population/*methods MH - History, Ancient MH - Humans MH - Metagenomics/*methods MH - Socioeconomic Factors EDAT- 2020/03/05 06:00 MHDA- 2020/07/23 06:00 CRDT- 2020/03/05 06:00 PHST- 2020/02/04 00:00 [accepted] PHST- 2020/03/05 06:00 [pubmed] PHST- 2020/07/23 06:00 [medline] PHST- 2020/03/05 06:00 [entrez] AID - 10.1038/s41576-020-0218-z [pii] AID - 10.1038/s41576-020-0218-z [doi] PST - ppublish SO - Nat Rev Genet. 2020 Jun;21(6):355-366. doi: 10.1038/s41576-020-0218-z. Epub 2020 Mar 3. PMID- 32004756 OWN - NLM STAT- MEDLINE DCOM- 20210616 LR - 20240214 IS - 1567-7257 (Electronic) IS - 1567-1348 (Print) IS - 1567-1348 (Linking) VI - 80 DP - 2020 Jun TI - Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793). PG - 104209 LID - S1567-1348(20)30041-1 [pii] LID - 10.1016/j.meegid.2020.104209 [doi] AB - The French revolutionary Jean-Paul Marat (1743-1793) was assassinated in 1793 in his bathtub, where he was trying to find relief from the debilitating skin disease he was suffering from. At the time of his death, Marat was annotating newspapers, which got stained with his blood and were subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain and also from another section of the newspaper, which we used for comparison. Results from the human DNA sequence analyses were compatible with a heterogeneous ancestry of Marat, with his mother being of French origin and his father born in Sardinia. Metagenomic analyses of the non-human reads uncovered the presence of fungal, bacterial and low levels of viral DNA. Relying on the presence/absence of microbial species in the samples, we could cast doubt on several putative infectious agents that have been previously hypothesised as the cause of his condition but for which we detect not a single sequencing read. Conversely, some of the species we detect are uncommon as environmental contaminants and may represent plausible infective agents. Based on all the available evidence, we hypothesize that Marat may have suffered from a fungal infection (seborrheic dermatitis), possibly superinfected with bacterial opportunistic pathogens. CI - Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved. FAU - de-Dios, Toni AU - de-Dios T AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain. FAU - van Dorp, Lucy AU - van Dorp L AD - UCL Genetics Institute, University College London, London WC1E 6BT, UK. Electronic address: lucy.dorp.12@ucl.ac.uk. FAU - Charlier, Philippe AU - Charlier P AD - Département de la Recherche et de l'Enseignement, Musée du Quai Branly - Jacques Chirac, 75007 Paris, France; Université Paris-Saclay (UVSQ), Laboratory Anthropology, Archaeology, Biology (LAAB), 78180 Montigny-le-bretonneux, France. FAU - Morfopoulou, Sofia AU - Morfopoulou S AD - UCL Genetics Institute, University College London, London WC1E 6BT, UK; Division of Infection and Immunity, University College London, London WC1E 6BT, UK. FAU - Lizano, Esther AU - Lizano E AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain. FAU - Bon, Celine AU - Bon C AD - Département Hommes, Natures, Sociétés, Muséum National d'Histoire Naturelle, 75116 Paris, France. FAU - Le Bitouzé, Corinne AU - Le Bitouzé C AD - Archives Nationales, 75004 Paris, France. FAU - Alvarez-Estape, Marina AU - Alvarez-Estape M AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain. FAU - Marquès-Bonet, Tomas AU - Marquès-Bonet T AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain. FAU - Balloux, François AU - Balloux F AD - UCL Genetics Institute, University College London, London WC1E 6BT, UK. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain. LA - eng GR - 206478/Z/17/Z/WT_/Wellcome Trust/United Kingdom GR - 206478/WT_/Wellcome Trust/United Kingdom GR - BB/R01356X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom GR - HHMI/Howard Hughes Medical Institute/United States GR - U01 MH106874/MH/NIMH NIH HHS/United States GR - MR/P007597/1/MRC_/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20200129 PL - Netherlands TA - Infect Genet Evol JT - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JID - 101084138 RN - 0 (DNA, Mitochondrial) SB - IM MH - *Blood Stains MH - DNA, Mitochondrial MH - Forensic Genetics/*methods MH - Genetics, Population MH - Humans MH - *Metagenome MH - *Metagenomics/methods MH - Phylogeny MH - Polymorphism, Single Nucleotide PMC - PMC7615110 MID - EMS187490 OTO - NOTNLM OT - Ancient DNA OT - Infection OT - Metagenomics COIS- Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. EDAT- 2020/02/01 06:00 MHDA- 2021/06/17 06:00 PMCR- 2023/09/19 CRDT- 2020/02/01 06:00 PHST- 2019/11/08 00:00 [received] PHST- 2020/01/24 00:00 [revised] PHST- 2020/01/26 00:00 [accepted] PHST- 2020/02/01 06:00 [pubmed] PHST- 2021/06/17 06:00 [medline] PHST- 2020/02/01 06:00 [entrez] PHST- 2023/09/19 00:00 [pmc-release] AID - S1567-1348(20)30041-1 [pii] AID - 10.1016/j.meegid.2020.104209 [doi] PST - ppublish SO - Infect Genet Evol. 2020 Jun;80:104209. doi: 10.1016/j.meegid.2020.104209. Epub 2020 Jan 29. PMID- 31964606 OWN - NLM STAT- MEDLINE DCOM- 20210706 LR - 20210706 IS - 1879-9825 (Electronic) IS - 1879-9817 (Linking) VI - 29 DP - 2020 Jun TI - Advances in the molecular detection of tuberculosis in pre-contact Andean South America. PG - 128-140 LID - S1879-9817(19)30153-6 [pii] LID - 10.1016/j.ijpp.2019.12.006 [doi] AB - Andean paleopathological research has significantly enhanced knowledge about the geographical distribution and evolution of tuberculosis (TB) in pre-Columbian South America. In this paper, we review the history and progress of research on ancient tuberculosis (TB) in the Andean region, focusing on the strengths and limitations of current approaches for the molecular detection of ancient pathogens, with special attention to TB. As a case study, we describe a molecular screening approach for the detection of ancient Mycobacterium tuberculosis in individuals from Late Intermediate Period (1000-1400 CE) contexts at the site of Huari, Peru. We evaluate 34 commingled human vertebrae and combine morphological assessments of pathology with high throughput sequencing and a non-selective approach to ancient pathogen DNA screening. Our method enabled the simultaneous detection of ancient M. tuberculosis DNA and an evaluation of the environmental microbial composition of each sample. Our results show that despite the dominance of environmental DNA, molecular signatures of M. tuberculosis were identified in eight vertebrae, six of which had no observable skeletal pathology classically associated tuberculosis infection. This screening approach will assist in the identification of candidate samples for downstream genomic analyses. The method permits higher resolution disease identification in cases where pathology may be absent, or where the archaeological context may necessitate a broad differential diagnosis based on morphology alone. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Nelson, Elizabeth A AU - Nelson EA AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str 10, 07745 Jena, Germany; Eberhard Karls Universität Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany. Electronic address: nelson@shh.mpg.de. FAU - Buikstra, Jane E AU - Buikstra JE AD - Center for Bioarchaeological Research, Arizona State University, 1151 S. Forest Ave., Tempe, AZ, 85281, USA. Electronic address: buikstra@asu.edu. FAU - Herbig, Alexander AU - Herbig A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str 10, 07745 Jena, Germany. Electronic address: herbig@shh.mpg.de. FAU - Tung, Tiffiny A AU - Tung TA AD - Department of Anthropology, Vanderbilt University, VU Station B #356050, Nashville, TN 37235, USA. Electronic address: t.tung@vanderbilt.edu. FAU - Bos, Kirsten I AU - Bos KI AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str 10, 07745 Jena, Germany. Electronic address: bos@shh.mpg.de. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20200120 PL - Netherlands TA - Int J Paleopathol JT - International journal of paleopathology JID - 101562474 RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Bacterial/genetics/*history MH - Diffusion of Innovation MH - Forecasting MH - High-Throughput Nucleotide Sequencing/trends MH - History, Ancient MH - Humans MH - Metagenomics/trends MH - *Mycobacterium tuberculosis/genetics MH - *Paleopathology/trends MH - *Research Design/trends MH - Sequence Analysis, DNA/*trends MH - South America MH - Tuberculosis/genetics/*history/microbiology OTO - NOTNLM OT - Ancient DNA OT - Andean South America OT - Huari OT - Molecular paleopathology OT - Tuberculosis EDAT- 2020/01/23 06:00 MHDA- 2021/07/07 06:00 CRDT- 2020/01/23 06:00 PHST- 2019/02/28 00:00 [received] PHST- 2019/12/06 00:00 [revised] PHST- 2019/12/13 00:00 [accepted] PHST- 2020/01/23 06:00 [pubmed] PHST- 2021/07/07 06:00 [medline] PHST- 2020/01/23 06:00 [entrez] AID - S1879-9817(19)30153-6 [pii] AID - 10.1016/j.ijpp.2019.12.006 [doi] PST - ppublish SO - Int J Paleopathol. 2020 Jun;29:128-140. doi: 10.1016/j.ijpp.2019.12.006. Epub 2020 Jan 20. PMID- 32470401 OWN - NLM STAT- MEDLINE DCOM- 20201216 LR - 20211204 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 181 IP - 5 DP - 2020 May 28 TI - Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus. PG - 1158-1175.e28 LID - S0092-8674(20)30509-2 [pii] LID - 10.1016/j.cell.2020.04.044 [doi] AB - Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6(th) millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today's Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age. VIDEO ABSTRACT. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Skourtanioti, Eirini AU - Skourtanioti E AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Erdal, Yilmaz S AU - Erdal YS AD - Department of Anthropology, Hacettepe University, Ankara 06800, Turkey. FAU - Frangipane, Marcella AU - Frangipane M AD - Department of Classics, Sapienza University of Rome, Rome 00185, Italy. FAU - Balossi Restelli, Francesca AU - Balossi Restelli F AD - Department of Classics, Sapienza University of Rome, Rome 00185, Italy. FAU - Yener, K Aslıhan AU - Yener KA AD - Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA. FAU - Pinnock, Frances AU - Pinnock F AD - Department of Classics, Sapienza University of Rome, Rome 00185, Italy. FAU - Matthiae, Paolo AU - Matthiae P AD - Department of Classics, Sapienza University of Rome, Rome 00185, Italy. FAU - Özbal, Rana AU - Özbal R AD - Department of Archaeology and History of Art, Koç University, Istanbul 34450, Turkey. FAU - Schoop, Ulf-Dietrich AU - Schoop UD AD - School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK. FAU - Guliyev, Farhad AU - Guliyev F AD - Institute of Archaeology and Ethnography, Azerbaijan National Academy of Sciences, Baku AZ1073, Azerbaijan. FAU - Akhundov, Tufan AU - Akhundov T AD - Institute of Archaeology and Ethnography, Azerbaijan National Academy of Sciences, Baku AZ1073, Azerbaijan. FAU - Lyonnet, Bertille AU - Lyonnet B AD - PROCLAC/UMR Laboratory, French National Centre for Scientific Research, UMR 7192, Paris 75005, France. FAU - Hammer, Emily L AU - Hammer EL AD - Near Eastern Languages and Civilizations, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Nugent, Selin E AU - Nugent SE AD - School of Anthropology and Museum Ethnography, University of Oxford, Oxford OX2 6PE, UK. FAU - Burri, Marta AU - Burri M AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Neumann, Gunnar U AU - Neumann GU AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Penske, Sandra AU - Penske S AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Ingman, Tara AU - Ingman T AD - Department of Archaeology and History of Art, Koç University, Istanbul 34450, Turkey. FAU - Akar, Murat AU - Akar M AD - Department of Archaeology, Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey. FAU - Shafiq, Rula AU - Shafiq R AD - History Department, Ibn Haldun University, Istanbul 34494, Turkey. FAU - Palumbi, Giulio AU - Palumbi G AD - Université Nice Sophia Antipolis, CEPAM (Cultures et Environnements. Préhistoire, Antiquité, Moyen Âge), CNRS-UMR 7264, Nice 06357, France. FAU - Eisenmann, Stefanie AU - Eisenmann S AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - D'Andrea, Marta AU - D'Andrea M AD - Department of Classics, Sapienza University of Rome, Rome 00185, Italy. FAU - Rohrlach, Adam B AU - Rohrlach AB AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; ARC Centre of Excellence for the Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA 5005, Australia. FAU - Warinner, Christina AU - Warinner C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology, Harvard University, Cambridge, MA 02138, USA. Electronic address: warinner@fas.harvard.edu. FAU - Jeong, Choongwon AU - Jeong C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea. Electronic address: cwjeong@snu.ac.kr. FAU - Stockhammer, Philipp W AU - Stockhammer PW AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich 80539, Germany. Electronic address: philipp.stockhammer@lmu.de. FAU - Haak, Wolfgang AU - Haak W AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. Electronic address: haak@shh.mpg.de. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. Electronic address: krause@shh.mpg.de. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM CIN - Cell. 2020 May 28;181(5):966-968. doi: 10.1016/j.cell.2020.05.010. PMID: 32470405 MH - Archaeology/methods MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/genetics MH - Ethnicity/*genetics/history MH - Gene Flow/*genetics/physiology MH - Genetic Variation/genetics MH - Genetics, Population/methods MH - Genome, Human/genetics MH - Genomics/methods MH - Haplotypes MH - History, Ancient MH - Human Migration/history MH - Humans MH - Mediterranean Region MH - Middle East MH - Sequence Analysis, DNA OTO - NOTNLM OT - Eastern Mediterranean OT - Kura-Araxes OT - Near East OT - Ubaid OT - Uruk OT - admixture OT - ancient DNA OT - archaeogenetics OT - genetic continuity OT - genome-wide data OT - human population history COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2020/05/30 06:00 MHDA- 2020/12/17 06:00 CRDT- 2020/05/30 06:00 PHST- 2019/11/29 00:00 [received] PHST- 2020/03/18 00:00 [revised] PHST- 2020/04/22 00:00 [accepted] PHST- 2020/05/30 06:00 [entrez] PHST- 2020/05/30 06:00 [pubmed] PHST- 2020/12/17 06:00 [medline] AID - S0092-8674(20)30509-2 [pii] AID - 10.1016/j.cell.2020.04.044 [doi] PST - ppublish SO - Cell. 2020 May 28;181(5):1158-1175.e28. doi: 10.1016/j.cell.2020.04.044. PMID- 32470400 OWN - NLM STAT- MEDLINE DCOM- 20201216 LR - 20230526 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 181 IP - 5 DP - 2020 May 28 TI - The Genomic History of the Bronze Age Southern Levant. PG - 1146-1157.e11 LID - S0092-8674(20)30487-6 [pii] LID - 10.1016/j.cell.2020.04.024 [doi] AB - We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the "Canaanite" material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different "Canaanite" groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze-Age migrations into the region over the past 3,000 years. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Agranat-Tamir, Lily AU - Agranat-Tamir L AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; Department of Statistics, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel. FAU - Waldman, Shamam AU - Waldman S AD - Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Martin, Mario A S AU - Martin MAS AD - Institute of Archaeology, Tel Aviv University, Tel Aviv 6997801, Israel. FAU - Gokhman, David AU - Gokhman D AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. FAU - Mishol, Nadav AU - Mishol N AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. FAU - Eshel, Tzilla AU - Eshel T AD - The Fredy and Nadine Herrmann Institute of Earth Sciences, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02138, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Adamski, Nicole AU - Adamski N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Lawson, Ann Marie AU - Lawson AM AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Mah, Matthew AU - Mah M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Candilio, Francesca AU - Candilio F AD - School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland; Soprintendenza ABAP per la città metropolitana di Cagliari e le province di Oristano e Sud Sardegna, Cagliari, Italy. FAU - Keating, Denise AU - Keating D AD - School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland. FAU - Gamarra, Beatriz AU - Gamarra B AD - School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland; Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain; Universitat Rovira i Virgili, Àrea de Prehistòria, Tarragona, Spain. FAU - Tzur, Shay AU - Tzur S AD - Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Novak, Mario AU - Novak M AD - Institute for Anthropological Research, Zagreb, Croatia. Electronic address: mario.novak@inantro.hr. FAU - Kalisher, Rachel AU - Kalisher R AD - Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, RI 02912, USA. FAU - Bechar, Shlomit AU - Bechar S AD - The Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel. FAU - Eshed, Vered AU - Eshed V AD - Israel Antiquities Authority, P.O.B 586, Jerusalem 91004, Israel. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology, University of California, Santa Barbara, CA 93106, USA. FAU - Faerman, Marina AU - Faerman M AD - Laboratory of Bioanthropology and Ancient DNA, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel. FAU - Yahalom-Mack, Naama AU - Yahalom-Mack N AD - The Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel. FAU - Monge, Janet M AU - Monge JM AD - University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA. FAU - Govrin, Yehuda AU - Govrin Y AD - The Nelson Glueck School of Biblical Archaeology, Hebrew Union College, Jerusalem 9410125, Israel. FAU - Erel, Yigal AU - Erel Y AD - The Fredy and Nadine Herrmann Institute of Earth Sciences, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. FAU - Yakir, Benjamin AU - Yakir B AD - Department of Statistics, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. Electronic address: ron.pinhasi@univie.ac.at. FAU - Carmi, Shai AU - Carmi S AD - Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel. Electronic address: shai.carmi@mail.huji.ac.il. FAU - Finkelstein, Israel AU - Finkelstein I AD - Institute of Archaeology, Tel Aviv University, Tel Aviv 6997801, Israel. Electronic address: fink2@tauex.tau.ac.il. FAU - Carmel, Liran AU - Carmel L AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. Electronic address: liran.carmel@huji.ac.il. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM CIN - Cell. 2020 May 28;181(5):966-968. doi: 10.1016/j.cell.2020.05.010. PMID: 32470405 MH - Archaeology/methods MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/genetics MH - Ethnicity/*genetics/history MH - Gene Flow/*genetics/physiology MH - Genetic Variation/genetics MH - Genetics, Population/methods MH - Genome, Human/genetics MH - Genomics/methods MH - Haplotypes MH - History, Ancient MH - Human Migration/history MH - Humans MH - Mediterranean Region MH - Middle East MH - Sequence Analysis, DNA PMC - PMC10212583 MID - NIHMS1586612 OTO - NOTNLM OT - Abel Beth Maacah OT - Baq‛ah OT - Tel Megiddo OT - Tel Shadud OT - Yehud OT - ancient DNA OT - archaeology OT - demographic inference OT - genetic ancestry OT - population genetics COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2020/05/30 06:00 MHDA- 2020/12/17 06:00 PMCR- 2023/05/25 CRDT- 2020/05/30 06:00 PHST- 2019/09/25 00:00 [received] PHST- 2020/02/10 00:00 [revised] PHST- 2020/04/15 00:00 [accepted] PHST- 2020/05/30 06:00 [entrez] PHST- 2020/05/30 06:00 [pubmed] PHST- 2020/12/17 06:00 [medline] PHST- 2023/05/25 00:00 [pmc-release] AID - S0092-8674(20)30487-6 [pii] AID - 10.1016/j.cell.2020.04.024 [doi] PST - ppublish SO - Cell. 2020 May 28;181(5):1146-1157.e11. doi: 10.1016/j.cell.2020.04.024. PMID- 32386546 OWN - NLM STAT- MEDLINE DCOM- 20201216 LR - 20240330 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 181 IP - 5 DP - 2020 May 28 TI - A Paleogenomic Reconstruction of the Deep Population History of the Andes. PG - 1131-1145.e21 LID - S0092-8674(20)30477-3 [pii] LID - 10.1016/j.cell.2020.04.015 [doi] AB - There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT. CI - Copyright © 2020 Elsevier Inc. All rights reserved. FAU - Nakatsuka, Nathan AU - Nakatsuka N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA. Electronic address: nathan_nakatsuka@hms.harvard.edu. FAU - Lazaridis, Iosif AU - Lazaridis I AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Barbieri, Chiara AU - Barbieri C AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland. FAU - Skoglund, Pontus AU - Skoglund P AD - Francis Crick Institute, London NW1 1AT, UK. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. FAU - Posth, Cosimo AU - Posth C AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Harkins-Kinkaid, Kelly AU - Harkins-Kinkaid K AD - UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA. FAU - Harney, Éadaoin AU - Harney É AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA. FAU - Novak-Forst, Jannine AU - Novak-Forst J AD - UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. FAU - Capriles, José M AU - Capriles JM AD - Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Durruty, Marta Alfonso AU - Durruty MA AD - Department of Sociology, Anthropology and Social Work, Kansas State University, Manhattan, KS 66506, USA. FAU - Álvarez, Karina Aranda AU - Álvarez KA AD - Sociedad de Arqueología de La Paz, 5294 La Paz, Bolivia. FAU - Beresford-Jones, David AU - Beresford-Jones D AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing St., Cambridge, CB2 3ER, UK. FAU - Burger, Richard AU - Burger R AD - Department of Anthropology, Yale University, New Haven, CT 06511, USA. FAU - Cadwallader, Lauren AU - Cadwallader L AD - Office of Scholarly Communication, Cambridge University Library, Cambridge CB3 9DR, UK. FAU - Fujita, Ricardo AU - Fujita R AD - Centro de Genética y Biología Molecular, Facultdad de Medicina, Universidad de San Martín de Porres, Lima 15011, Peru. FAU - Isla, Johny AU - Isla J AD - Peruvian Ministry of Culture, DDC Ica, Directos of the Nasca-Palpa Management Plan, Calle Juan Matta 880, Nasca 11401, Peru. FAU - Lau, George AU - Lau G AD - Sainsbury Research Unit, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK. FAU - Aguirre, Carlos Lémuz AU - Aguirre CL AD - Carrera de Arqueología, Universidad Mayor de San Andrés, Edificio Facultad de Ciencias Sociales 3er Piso, La Paz 1995, Bolivia. FAU - LeBlanc, Steven AU - LeBlanc S AD - Harvard Peabody Museum, Harvard University, Cambridge, MA 02138, USA. FAU - Maldonado, Sergio Calla AU - Maldonado SC AD - Carrera de Arqueología, Universidad Mayor de San Andrés, Edificio Facultad de Ciencias Sociales 3er Piso, La Paz 1995, Bolivia. FAU - Meddens, Frank AU - Meddens F AD - School of Archaeology, Geography and Environmental Sciences, University of Reading, Reading, Berkshire, RG6 6AH, UK. FAU - Messineo, Pablo G AU - Messineo PG AD - INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina. FAU - Culleton, Brendan J AU - Culleton BJ AD - Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Harper, Thomas K AU - Harper TK AD - Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Quilter, Jeffrey AU - Quilter J AD - Harvard Peabody Museum, Harvard University, Cambridge, MA 02138, USA. FAU - Politis, Gustavo AU - Politis G AD - INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina. FAU - Rademaker, Kurt AU - Rademaker K AD - Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA. FAU - Reindel, Markus AU - Reindel M AD - Commission for Archaeology of Non-European Cultures, German Archaeological Institute, Berlin 14195, Germany. FAU - Rivera, Mario AU - Rivera M AD - Universidad de Magallanes, Punta Arenas 6210427, Chile; Field Museum Natural History 1400 S Lake Shore Dr., Chicago, IL 60605, USA. FAU - Salazar, Lucy AU - Salazar L AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing St., Cambridge, CB2 3ER, UK. FAU - Sandoval, José R AU - Sandoval JR AD - Centro de Genética y Biología Molecular, Facultdad de Medicina, Universidad de San Martín de Porres, Lima 15011, Peru. FAU - Santoro, Calogero M AU - Santoro CM AD - Instituto de Alta Investigation, Universidad de Tarapaca, Antafogasta 1520, Arica, 1000000, Chile. FAU - Scheifler, Nahuel AU - Scheifler N AD - INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina. FAU - Standen, Vivien AU - Standen V AD - Departamento de Antropología, Universidad de Tarapacá, Antafogasta 1520, Arica, 1000000, Chile. FAU - Barreto, Maria Ines AU - Barreto MI AD - Museo de Sitio Huaca Pucllana, Calle General Borgoño, Cuadra 8, Miraflores, Lima 18, Peru. FAU - Espinoza, Isabel Flores AU - Espinoza IF AD - Museo de Sitio Huaca Pucllana, Calle General Borgoño, Cuadra 8, Miraflores, Lima 18, Peru. FAU - Tomasto-Cagigao, Elsa AU - Tomasto-Cagigao E AD - Department of Humanities, Pontifical Catholic University of Peru, San Miguel 15088, Peru. FAU - Valverde, Guido AU - Valverde G AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia. FAU - Kennett, Douglas J AU - Kennett DJ AD - Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Haak, Wolfgang AU - Haak W AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: reich@genetics.med.harvard.edu. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AD - UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. Electronic address: lfehrens@ucsc.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States GR - T32 GM007753/GM/NIGMS NIH HHS/United States GR - MRC_/Medical Research Council/United Kingdom GR - WT_/Wellcome Trust/United Kingdom GR - FC001595/ARC_/Arthritis Research UK/United Kingdom GR - CRUK_/Cancer Research UK/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20200507 PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology/*methods MH - Central America MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/genetics MH - Gene Flow/*genetics/physiology MH - Genetics, Population/methods MH - Haplotypes MH - Humans MH - Sequence Analysis, DNA MH - South America PMC - PMC7304944 MID - NIHMS1585754 OTO - NOTNLM OT - Andes OT - ancient DNA OT - anthropology OT - archaeology OT - population genetics COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2020/05/11 06:00 MHDA- 2020/12/17 06:00 PMCR- 2020/05/28 CRDT- 2020/05/11 06:00 PHST- 2019/08/29 00:00 [received] PHST- 2020/01/11 00:00 [revised] PHST- 2020/04/13 00:00 [accepted] PHST- 2020/05/11 06:00 [pubmed] PHST- 2020/12/17 06:00 [medline] PHST- 2020/05/11 06:00 [entrez] PHST- 2020/05/28 00:00 [pmc-release] AID - S0092-8674(20)30477-3 [pii] AID - 10.1016/j.cell.2020.04.015 [doi] PST - ppublish SO - Cell. 2020 May 28;181(5):1131-1145.e21. doi: 10.1016/j.cell.2020.04.015. Epub 2020 May 7. PMID- 32428013 OWN - NLM STAT- MEDLINE DCOM- 20200803 LR - 20200803 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 15 IP - 5 DP - 2020 TI - A three-population wave-of-advance model for the European early Neolithic. PG - e0233184 LID - 10.1371/journal.pone.0233184 [doi] LID - e0233184 AB - Ancient DNA studies have shown that early farming spread through most of Europe by the range expansion of farmers of Anatolian origin rather than by the conversion to farming of the local hunter-gatherers, and have confirmed that these hunter-gatherers continued to coexist with the incoming farmers. In this short report, I extend a previous three-population wave-of-advance model to accommodate these new findings, and derive the conditions supportive of such a scenario in terms of the relative magnitudes of the parameters. The revised model predicts that the conversion rate must, not surprisingly, be low, but also that the hunter-gatherers must compete more strongly with the converted farmers than with the alien farmers. Moreover, competition with the hunter-gatherers diminishes the speed of the wave-of advance of the farmers. In addition, I briefly consider how the wave-of-advance approach may contribute to interpreting the results of archaeological studies using the summed probability distribution of radiocarbon dates. FAU - Aoki, Kenichi AU - Aoki K AUID- ORCID: 0000-0002-8426-4091 AD - Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Nakano-ku, Tokyo, Japan. LA - eng PT - Historical Article PT - Journal Article DEP - 20200519 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) SB - IM MH - Agriculture/*history MH - *DNA, Ancient MH - History, Ancient MH - Human Migration/*history MH - Humans MH - *Models, Biological PMC - PMC7237037 COIS- The author declares no competing interests. EDAT- 2020/05/20 06:00 MHDA- 2020/08/04 06:00 PMCR- 2020/05/19 CRDT- 2020/05/20 06:00 PHST- 2020/01/19 00:00 [received] PHST- 2020/04/29 00:00 [accepted] PHST- 2020/05/20 06:00 [entrez] PHST- 2020/05/20 06:00 [pubmed] PHST- 2020/08/04 06:00 [medline] PHST- 2020/05/19 00:00 [pmc-release] AID - PONE-D-20-01744 [pii] AID - 10.1371/journal.pone.0233184 [doi] PST - epublish SO - PLoS One. 2020 May 19;15(5):e0233184. doi: 10.1371/journal.pone.0233184. eCollection 2020. PMID- 32427845 OWN - NLM STAT- MEDLINE DCOM- 20201204 LR - 20231103 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 10 IP - 1 DP - 2020 May 19 TI - Tracking the Near Eastern origins and European dispersal of the western house mouse. PG - 8276 LID - 10.1038/s41598-020-64939-9 [doi] LID - 8276 AB - The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks - 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe - which in turn may have driven the first human mediated dispersal of cats in Europe. FAU - Cucchi, Thomas AU - Cucchi T AD - Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France. cucchi@mnhn.fr. FAU - Papayianni, Katerina AU - Papayianni K AD - Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France. AD - Malcolm H. Wiener Laboratory for Archaeological Science, American School of Classical Studies, Souidias 54, 10676, Athens, Greece. FAU - Cersoy, Sophie AU - Cersoy S AD - Centre de Recherche sur la Conservation (CRC), Muséum national d'Histoire naturelle, CNRS, Ministère de la Culture, CP 21, 36 rue Geoffroy Saint-Hilaire, 75005, Paris, France. FAU - Aznar-Cormano, Laetitia AU - Aznar-Cormano L AD - Centre de recherche en Paléontologie Paris, UMR7207, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, 8 rue Buffon, 75005, Paris, France. FAU - Zazzo, Antoine AU - Zazzo A AD - Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France. FAU - Debruyne, Régis AU - Debruyne R AD - DGD-REVE, Muséum national d'Histoire naturelle, 17 Place du Trocadéro, bureau E205, 75016, Paris, France. FAU - Berthon, Rémi AU - Berthon R AD - Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France. FAU - Bălășescu, Adrian AU - Bălășescu A AD - Vasile Pârvan, Institute of Archaeology, Romanian Academy, 11 Henri Coandă Street, Bucarest, Romania. FAU - Simmons, Alan AU - Simmons A AD - Department of Anthropology, University of Nevada, Las Vegas/Desert Research Institute, Reno, Nevada, USA. FAU - Valla, François AU - Valla F AD - Archéologies et Sciences de l'Antiquité (Arscan), UMR 7041 CNRS, Université de Paris Nanterre, Paris I, 92023, Nanterre, France. FAU - Hamilakis, Yannis AU - Hamilakis Y AD - Joukowsky Institute for Archaeology and the Ancient World, Brown University, Box 1837, 60 George Street, Providence, RI, 02912, USA. FAU - Mavridis, Fanis AU - Mavridis F AD - Ephorate of Palaeoanthropology and Speleology, Hellenic Ministry of Culture and Sports, Ardittou 34B, 11636, Athens, Greece. FAU - Mashkour, Marjan AU - Mashkour M AD - Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France. FAU - Darvish, Jamshid AU - Darvish J AD - Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran. FAU - Siahsarvi, Roohollah AU - Siahsarvi R AD - Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran. FAU - Biglari, Fereidoun AU - Biglari F AD - Paleolithic Department, National Museum of Iran, Tehran, Iran. FAU - Petrie, Cameron A AU - Petrie CA AD - Department of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK. FAU - Weeks, Lloyd AU - Weeks L AD - Archaeology, School of HASS, University of New England, Armidale, NSW, 2351, Australia. FAU - Sardari, Alireza AU - Sardari A AD - Research Institute of Cultural Heritage and Tourism (RICHT), Iranian Center for Archaeological Research (ICAR), Tehran, Iran. FAU - Maziar, Sepideh AU - Maziar S AD - Near Eastern Archaeology, Institute für Archäologie Wissenschaften, Johann Wolfgang Goethe Universität, Frankfurt am Main, Germany. FAU - Denys, Christiane AU - Denys C AD - Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205, Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France. FAU - Orton, David AU - Orton D AD - BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK. FAU - Jenkins, Emma AU - Jenkins E AD - Institute for the Modelling of Socio-Environmental Transitions, Bournemouth University, Talbot Campus, Poole, BH12 5BB, UK. FAU - Zeder, Melinda AU - Zeder M AD - Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA. FAU - Searle, Jeremy B AU - Searle JB AD - Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY, 14853-2701, USA. FAU - Larson, Greger AU - Larson G AD - Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK. FAU - Bonhomme, François AU - Bonhomme F AD - Institut des Sciences de l'Evolution (ISEM), UMR 4554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France. FAU - Auffray, Jean-Christophe AU - Auffray JC AD - Institut des Sciences de l'Evolution (ISEM), UMR 4554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France. FAU - Vigne, Jean-Denis AU - Vigne JD AD - Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200519 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Archaeology MH - Asia, Western MH - Cyprus MH - DNA, Mitochondrial/*genetics MH - Europe, Eastern MH - Humans MH - Introduced Species MH - Mice/*classification/genetics MH - Mitochondria/*genetics MH - Radiometric Dating MH - Sequence Analysis, DNA/*veterinary PMC - PMC7237409 COIS- The authors declare no competing interests. EDAT- 2020/05/20 06:00 MHDA- 2020/12/15 06:00 PMCR- 2020/05/19 CRDT- 2020/05/20 06:00 PHST- 2019/11/22 00:00 [received] PHST- 2020/04/24 00:00 [accepted] PHST- 2020/05/20 06:00 [entrez] PHST- 2020/05/20 06:00 [pubmed] PHST- 2020/12/15 06:00 [medline] PHST- 2020/05/19 00:00 [pmc-release] AID - 10.1038/s41598-020-64939-9 [pii] AID - 64939 [pii] AID - 10.1038/s41598-020-64939-9 [doi] PST - epublish SO - Sci Rep. 2020 May 19;10(1):8276. doi: 10.1038/s41598-020-64939-9. PMID- 32421727 OWN - NLM STAT- MEDLINE DCOM- 20200817 LR - 20200817 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 15 IP - 5 DP - 2020 TI - A tale of textiles: Genetic characterization of historical paper mulberry barkcloth from Oceania. PG - e0233113 LID - 10.1371/journal.pone.0233113 [doi] LID - e0233113 AB - Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past. FAU - Peña-Ahumada, Bárbara AU - Peña-Ahumada B AD - Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile. FAU - Saldarriaga-Córdoba, Mónica AU - Saldarriaga-Córdoba M AD - Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile. AD - Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Santiago, Chile. FAU - Kardailsky, Olga AU - Kardailsky O AD - Department of Anatomy, University of Otago, Dunedin, New Zealand. FAU - Moncada, Ximena AU - Moncada X AD - Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile. FAU - Moraga, Mauricio AU - Moraga M AD - Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile. AD - Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile. FAU - Matisoo-Smith, Elizabeth AU - Matisoo-Smith E AUID- ORCID: 0000-0002-3500-8307 AD - Department of Anatomy, University of Otago, Dunedin, New Zealand. FAU - Seelenfreund, Daniela AU - Seelenfreund D AD - Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile. FAU - Seelenfreund, Andrea AU - Seelenfreund A AUID- ORCID: 0000-0002-9319-083X AD - Escuela de Antropología, Facultad de Ciencias Sociales, Universidad Academia de Humanismo Cristiano, Santiago, Chile. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200518 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - Broussonetia/*genetics MH - Genotyping Techniques MH - Humans MH - Microsatellite Repeats/genetics MH - Pacific Islands MH - Taiwan MH - *Textiles PMC - PMC7233582 COIS- The authors have declared that no competing interests exist. EDAT- 2020/05/19 06:00 MHDA- 2020/08/18 06:00 PMCR- 2020/05/18 CRDT- 2020/05/19 06:00 PHST- 2019/11/15 00:00 [received] PHST- 2020/04/28 00:00 [accepted] PHST- 2020/05/19 06:00 [entrez] PHST- 2020/05/19 06:00 [pubmed] PHST- 2020/08/18 06:00 [medline] PHST- 2020/05/18 00:00 [pmc-release] AID - PONE-D-19-31840 [pii] AID - 10.1371/journal.pone.0233113 [doi] PST - epublish SO - PLoS One. 2020 May 18;15(5):e0233113. doi: 10.1371/journal.pone.0233113. eCollection 2020. PMID- 32375874 OWN - NLM STAT- MEDLINE DCOM- 20210204 LR - 20231113 IS - 2049-2618 (Electronic) IS - 2049-2618 (Linking) VI - 8 IP - 1 DP - 2020 May 6 TI - Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome. PG - 62 LID - 10.1186/s40168-020-00832-x [doi] LID - 62 AB - BACKGROUND: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. METHODS: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. RESULTS: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. CONCLUSIONS: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract. FAU - Rifkin, Riaan F AU - Rifkin RF AD - Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. riaanrifkin@gmail.com. AD - Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK. riaanrifkin@gmail.com. FAU - Vikram, Surendra AU - Vikram S AD - Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. FAU - Ramond, Jean-Baptiste AU - Ramond JB AD - Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. AD - Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK. AD - Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile. FAU - Rey-Iglesia, Alba AU - Rey-Iglesia A AD - Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark. FAU - Brand, Tina B AU - Brand TB AD - Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark. FAU - Porraz, Guillaume AU - Porraz G AD - CNRS, UMR 7041 ArScAn-AnTET, Université Paris-Nanterre, Paris, France. AD - Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa. FAU - Val, Aurore AU - Val A AD - Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa. AD - Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany. FAU - Hall, Grant AU - Hall G AD - Mammal Research Institute, University of Pretoria, Hatfield, South Africa. FAU - Woodborne, Stephan AU - Woodborne S AD - Mammal Research Institute, University of Pretoria, Hatfield, South Africa. AD - iThemba LABS, Braamfontein Johannesburg, South Africa. FAU - Le Bailly, Matthieu AU - Le Bailly M AD - University of Bourgogne France-Comte, CNRS UMR 6249 Chrono-environment, Besancon, France. FAU - Potgieter, Marnie AU - Potgieter M AD - Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. FAU - Underdown, Simon J AU - Underdown SJ AD - Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. AD - Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK. FAU - Koopman, Jessica E AU - Koopman JE AD - Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. FAU - Cowan, Don A AU - Cowan DA AD - Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. FAU - Van de Peer, Yves AU - Van de Peer Y AD - Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa. AD - VIB Centre for Plant Systems Biology, Ghent, Belgium. AD - Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark. AD - GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. AD - Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. FAU - Hansen, Anders J AU - Hansen AJ AD - Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark. ajhansen@snm.ku.dk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Video-Audio Media DEP - 20200506 PL - England TA - Microbiome JT - Microbiome JID - 101615147 SB - IM MH - Africa South of the Sahara MH - *Archaeology MH - Feces/*microbiology MH - *Gastrointestinal Microbiome MH - History, 15th Century MH - Humans MH - Metagenomics PMC - PMC7204047 OTO - NOTNLM OT - Ancient DNA OT - Human evolution OT - Intestinal microbiome OT - Metabolic capacity OT - Molecular ecology OT - Taxonomic composition COIS- The authors declare that they have no competing interests. The funding sponsors had no role in the design of the study, the collection, analyses and interpretation of data, in the writing of the manuscript or in the decision to distribute the results. EDAT- 2020/05/08 06:00 MHDA- 2021/02/05 06:00 PMCR- 2020/05/06 CRDT- 2020/05/08 06:00 PHST- 2019/11/26 00:00 [received] PHST- 2020/03/18 00:00 [accepted] PHST- 2020/05/08 06:00 [entrez] PHST- 2020/05/08 06:00 [pubmed] PHST- 2021/02/05 06:00 [medline] PHST- 2020/05/06 00:00 [pmc-release] AID - 10.1186/s40168-020-00832-x [pii] AID - 832 [pii] AID - 10.1186/s40168-020-00832-x [doi] PST - epublish SO - Microbiome. 2020 May 6;8(1):62. doi: 10.1186/s40168-020-00832-x. PMID- 31957867 OWN - NLM STAT- MEDLINE DCOM- 20210108 LR - 20210108 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 172 IP - 1 DP - 2020 May TI - Genome-wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains. PG - 99-109 LID - 10.1002/ajpa.23996 [doi] AB - OBJECTIVE: A genome-wide high-throughput single nucleotide polymorphism (SNP) typing method was tested with respect of the applicability to ancient and degraded DNA. The results were compared to mini-sequencing data achieved through single base extension (SBE) typing. The SNPs chosen for the study allow to determine the hair colors and eye colors of humans. MATERIAL AND METHODS: The DNA samples were extracted from the skeletal remains of 59 human individuals dating back to the Late Bronze Age. The 3,000 years old bones had been discovered in the Lichtenstein Cave in Lower Saxony, Germany. The simultaneous typing of 24 SNPs for each of the ancient DNA samples was carried out using the 192.24 Dynamic Array™ by Fluidigm®. RESULTS: Thirty-eight of the ancient samples (=64%) revealed full and reproducible SNP genotypes allowing hair and eye color phenotyping. In 10 samples (=17%) at least half of the SNPs were unambiguously determined, in 11 samples (=19%) the SNP typing failed. For 23 of the 59 individuals, a comparison of the SNP typing results with genotypes from an earlier performed SBE typing approach was possible. The comparison confirmed the full concordance of the results for 90% of the SNP typings. In the remaining 10% allelic dropouts were identified. DISCUSSION: The high genotyping success rate could be achieved by introducing modifications to the preamplification protocol mainly by increasing the DNA input and the amplification cycle number. The occurrence of allelic dropouts indicates that a further increase of DNA input to the preamplification step is desirable. CI - © 2020 The Authors. American Journal of Physical Anthropology published by Wiley Periodicals, Inc. FAU - Schmidt, Nicole AU - Schmidt N AD - Department of Historical Anthropology and Human Ecology, University of Göttingen, Göttingen, Germany. FAU - Schücker, Katharina AU - Schücker K AD - Department of Historical Anthropology and Human Ecology, University of Göttingen, Göttingen, Germany. AD - Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany. FAU - Krause, Ina AU - Krause I AD - Department of Historical Anthropology and Human Ecology, University of Göttingen, Göttingen, Germany. FAU - Dörk, Thilo AU - Dörk T AD - Gynaecological Research Unit, Hannover Medical School, Hannover, Germany. FAU - Klintschar, Michael AU - Klintschar M AD - Hannover Medical School, Institute for Legal Medicine, Hannover, Germany. FAU - Hummel, Susanne AU - Hummel S AUID- ORCID: 0000-0002-3647-8968 AD - Department of Historical Anthropology and Human Ecology, University of Göttingen, Göttingen, Germany. LA - eng PT - Historical Article PT - Journal Article DEP - 20200120 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Body Remains MH - DNA, Ancient/*analysis MH - Eye Color/*genetics MH - *Genotype MH - Germany MH - Hair Color/*genetics MH - History, Ancient MH - Humans MH - *Polymorphism, Single Nucleotide OTO - NOTNLM OT - ancient and degraded DNA OT - eye color OT - genome wide OT - hair color OT - high-throughput SNP typing OT - phenotype EDAT- 2020/01/21 06:00 MHDA- 2021/01/09 06:00 CRDT- 2020/01/21 06:00 PHST- 2019/06/03 00:00 [received] PHST- 2019/11/21 00:00 [revised] PHST- 2019/12/13 00:00 [accepted] PHST- 2020/01/21 06:00 [pubmed] PHST- 2021/01/09 06:00 [medline] PHST- 2020/01/21 06:00 [entrez] AID - 10.1002/ajpa.23996 [doi] PST - ppublish SO - Am J Phys Anthropol. 2020 May;172(1):99-109. doi: 10.1002/ajpa.23996. Epub 2020 Jan 20. PMID- 32355290 OWN - NLM STAT- MEDLINE DCOM- 20210106 LR - 20210430 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 10 IP - 1 DP - 2020 Apr 30 TI - Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations. PG - 7339 LID - 10.1038/s41598-020-64312-w [doi] LID - 7339 AB - The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations. FAU - Pierini, Federica AU - Pierini F AD - Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany. AD - Université Paris-Saclay, CNRS, Inria, Laboratoire de recherche en informatique, 91405, Orsay, France. FAU - Nutsua, Marcel AU - Nutsua M AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Böhme, Lisa AU - Böhme L AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Özer, Onur AU - Özer O AD - Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany. FAU - Bonczarowska, Joanna AU - Bonczarowska J AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Susat, Julian AU - Susat J AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Franke, Andre AU - Franke A AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Nebel, Almut AU - Nebel A AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AD - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany. FAU - Lenz, Tobias L AU - Lenz TL AD - Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany. lenz@post.harvard.edu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200430 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (Genetic Markers) RN - 0 (HLA Antigens) RN - 0 (Histocompatibility Antigens Class II) SB - IM MH - Alleles MH - DNA, Ancient/*analysis MH - Denmark MH - Genetic Markers MH - Genetics, Population MH - Genome, Human MH - *Genotype MH - HLA Antigens/*genetics MH - Haplotypes MH - *High-Throughput Nucleotide Sequencing MH - Histocompatibility Antigens Class II/*genetics MH - Humans MH - Pattern Recognition, Automated MH - *Polymorphism, Single Nucleotide PMC - PMC7193575 COIS- The authors declare no competing interests. EDAT- 2020/05/02 06:00 MHDA- 2021/01/07 06:00 PMCR- 2020/04/30 CRDT- 2020/05/02 06:00 PHST- 2019/12/12 00:00 [received] PHST- 2020/04/14 00:00 [accepted] PHST- 2020/05/02 06:00 [entrez] PHST- 2020/05/02 06:00 [pubmed] PHST- 2021/01/07 06:00 [medline] PHST- 2020/04/30 00:00 [pmc-release] AID - 10.1038/s41598-020-64312-w [pii] AID - 64312 [pii] AID - 10.1038/s41598-020-64312-w [doi] PST - epublish SO - Sci Rep. 2020 Apr 30;10(1):7339. doi: 10.1038/s41598-020-64312-w. PMID- 32321996 OWN - NLM STAT- MEDLINE DCOM- 20201124 LR - 20221207 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 10 IP - 1 DP - 2020 Apr 22 TI - Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans. PG - 6843 LID - 10.1038/s41598-020-64007-2 [doi] LID - 6843 AB - Historical genetic links among similar populations can be difficult to establish. Identity by descent (IBD) analyses find genomic blocks that represent direct genealogical relationships among individuals. However, this method has rarely been applied to ancient genomes because IBD stretches are progressively fragmented by recombination and thus not recognizable after few tens of generations. To explore such genealogical relationships, we estimated long IBD blocks among modern Europeans, generating networks to uncover the genetic structures. We found that Basques, Sardinians, Icelanders and Orcadians form, each of them, highly intraconnected sub-clusters in a European network, indicating dense genealogical links within small, isolated populations. We also exposed individual genealogical links -such as the connection between one Basque and one Icelandic individual- that cannot be uncovered with other, widely used population genetics methods such as PCA or ADMIXTURE. Moreover, using ancient DNA technology we sequenced a Late Medieval individual (Barcelona, Spain) to high genomic coverage and identified IBD blocks shared between her and modern Europeans. The Medieval IBD blocks are statistically overrepresented only in modern Spaniards, which is the geographically closest population. This approach can be used to produce a fine-scale reflection of shared ancestry across different populations of the world, offering a direct genetic link from the past to the present. FAU - Ferrando-Bernal, Manuel AU - Ferrando-Bernal M AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain. FAU - Morcillo-Suarez, Carlos AU - Morcillo-Suarez C AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain. FAU - de-Dios, Toni AU - de-Dios T AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain. FAU - Gelabert, Pere AU - Gelabert P AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain. AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Civit, Sergi AU - Civit S AD - Departament d'Estadística, Facultat de Biologia, Universitat de Barcelona, 08028, Barcelona, Spain. FAU - Díaz-Carvajal, Antonia AU - Díaz-Carvajal A AD - Grup de Recerca d'Arqueologia Medieval i Postmedieval (GRAMP-UB), Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, 08001, Barcelona, Spain. FAU - Ollich-Castanyer, Imma AU - Ollich-Castanyer I AD - Grup de Recerca d'Arqueologia Medieval i Postmedieval (GRAMP-UB), Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, 08001, Barcelona, Spain. FAU - Allentoft, Morten E AU - Allentoft ME AD - Lundbeck Foundation GeoGenetics Centre, The Globe Institute, University of Copenhagen, 1350, Copenhagen, Denmark. FAU - Valverde, Sergi AU - Valverde S AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain. carles.lalueza@upf.edu. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200422 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - Ethnicity/*genetics MH - Europe MH - Female MH - *Genetic Variation MH - History, Medieval MH - Humans MH - Male MH - *Polymorphism, Single Nucleotide MH - White People/*genetics/history PMC - PMC7176696 COIS- The authors declare no competing interests. EDAT- 2020/04/24 06:00 MHDA- 2020/11/25 06:00 PMCR- 2020/04/22 CRDT- 2020/04/24 06:00 PHST- 2019/09/13 00:00 [received] PHST- 2020/04/06 00:00 [accepted] PHST- 2020/04/24 06:00 [entrez] PHST- 2020/04/24 06:00 [pubmed] PHST- 2020/11/25 06:00 [medline] PHST- 2020/04/22 00:00 [pmc-release] AID - 10.1038/s41598-020-64007-2 [pii] AID - 64007 [pii] AID - 10.1038/s41598-020-64007-2 [doi] PST - epublish SO - Sci Rep. 2020 Apr 22;10(1):6843. doi: 10.1038/s41598-020-64007-2. PMID- 32238559 OWN - NLM STAT- MEDLINE DCOM- 20200727 LR - 20231103 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 117 IP - 16 DP - 2020 Apr 21 TI - The spatiotemporal spread of human migrations during the European Holocene. PG - 8989-9000 LID - 10.1073/pnas.1920051117 [doi] AB - The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. We aim to test to what extent vegetation change through time is associated with changes in population composition as a consequence of these migrations, or with changes in climate. Using ancient DNA in combination with geostatistical techniques, we produce detailed maps of ancient population movements, which allow us to visualize how these migrations unfolded through time and space. We find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings on the cultural spread of farming from radiocarbon-dated archaeological sites. This movement, however, did not have a strong association with changes in the vegetational landscape. In contrast, the Yamnaya migration speed was at least twice as fast and coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture and natural grasslands in the continent. We demonstrate the utility of integrating ancient genomes with archaeometric datasets in a spatiotemporal statistical framework, which we foresee will enable future studies of ancient populations' movements, and their putative effects on local fauna and flora. CI - Copyright © 2020 the Author(s). Published by PNAS. FAU - Racimo, Fernando AU - Racimo F AUID- ORCID: 0000-0002-5025-2607 AD - Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark; fracimo@sund.ku.dk. FAU - Woodbridge, Jessie AU - Woodbridge J AUID- ORCID: 0000-0003-0756-3538 AD - School of Geography, Earth, and Environmental Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom. FAU - Fyfe, Ralph M AU - Fyfe RM AUID- ORCID: 0000-0002-5676-008X AD - School of Geography, Earth, and Environmental Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom. FAU - Sikora, Martin AU - Sikora M AD - Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Sjögren, Karl-Göran AU - Sjögren KG AUID- ORCID: 0000-0003-1791-3175 AD - Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. FAU - Kristiansen, Kristian AU - Kristiansen K AD - Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. FAU - Vander Linden, Marc AU - Vander Linden M AUID- ORCID: 0000-0002-0120-7754 AD - Department of Archaeology, University of Cambridge, Cambridge CB2 1TN, United Kingdom. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200401 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Agriculture/history MH - Animal Distribution MH - Archaeology/*methods MH - DNA, Ancient/analysis MH - Datasets as Topic MH - Europe MH - Farmers MH - Feasibility Studies MH - Forests MH - *Genome, Human MH - Geography MH - Grassland MH - History, Ancient MH - Human Migration/*history MH - Humans MH - *Models, Genetic MH - Plant Dispersal MH - Radiometric Dating MH - *Spatio-Temporal Analysis PMC - PMC7183159 OTO - NOTNLM OT - Bronze Age OT - Neolithic OT - ancient DNA OT - land cover OT - migrations COIS- The authors declare no competing interest. EDAT- 2020/04/03 06:00 MHDA- 2020/07/28 06:00 PMCR- 2020/04/01 CRDT- 2020/04/03 06:00 PHST- 2020/04/03 06:00 [pubmed] PHST- 2020/07/28 06:00 [medline] PHST- 2020/04/03 06:00 [entrez] PHST- 2020/04/01 00:00 [pmc-release] AID - 1920051117 [pii] AID - 201920051 [pii] AID - 10.1073/pnas.1920051117 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2020 Apr 21;117(16):8989-9000. doi: 10.1073/pnas.1920051117. Epub 2020 Apr 1. PMID- 32297957 OWN - NLM STAT- MEDLINE DCOM- 20210818 LR - 20210818 IS - 1424-3997 (Electronic) IS - 0036-7672 (Linking) VI - 150 DP - 2020 Apr 6 TI - A review of HLA allele and SNP associations with highly prevalent infectious diseases in human populations. PG - w20214 LID - Swiss Med Wkly. 2020;150:w20214 [pii] LID - 10.4414/smw.2020.20214 [doi] AB - Human leucocyte antigen (HLA) alleles and single nucleotide polymorphisms (SNPs) lying in the HLA region are known to be associated with several infectious diseases among which acquired immunodeficiency syndrome, hepatitis B, hepatitis C, tuberculosis, leprosy and malaria are highly prevalent in many human populations worldwide. Distinct approaches such as case-control comparisons, immunogenetic analyses, bioinformatic peptide-binding predictions, ancient DNA and genome-wide association studies (GWAS) have contributed to improving this knowledge during the last decade, although many results still need stronger statistical and/or functional support. The present review updates the information regarding the main HLA allele and SNP associations observed to date for six of the most widespread and some other infectious diseases, and provides a synthetic illustration of these findings on a schematic HLA genomic map. It then discusses these results by stressing the importance of integrating information on HLA population diversity in disease-association studies. FAU - Sanchez-Mazas, Alicia AU - Sanchez-Mazas A AD - Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Switzerland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20200416 PL - Switzerland TA - Swiss Med Wkly JT - Swiss medical weekly JID - 100970884 SB - IM CIN - Swiss Med Wkly. 2020 Apr 16;150:w20248. doi: 10.4414/smw.2020.20248. PMID: 32297958 MH - Alleles MH - Case-Control Studies MH - Genetic Predisposition to Disease/genetics MH - Genome-Wide Association Study MH - *Hepatitis B MH - Humans MH - *Polymorphism, Single Nucleotide/genetics EDAT- 2020/04/17 06:00 MHDA- 2021/08/19 06:00 CRDT- 2020/04/17 06:00 PHST- 2020/04/17 06:00 [entrez] PHST- 2020/04/17 06:00 [pubmed] PHST- 2021/08/19 06:00 [medline] AID - Swiss Med Wkly. 2020;150:w20214 [pii] AID - 10.4414/smw.2020.20214 [doi] PST - epublish SO - Swiss Med Wkly. 2020 Apr 16;150:w20214. doi: 10.4414/smw.2020.20214. eCollection 2020 Apr 6. PMID- 32064591 OWN - NLM STAT- MEDLINE DCOM- 20201217 LR - 20201217 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 171 IP - 4 DP - 2020 Apr TI - Historical human remains identification through maternal and paternal genetic signatures in a founder population with extensive genealogical record. PG - 645-658 LID - 10.1002/ajpa.24024 [doi] AB - OBJECTIVES: We describe a method to identify human remains excavated from unmarked graves in historical Québec cemeteries by combining parental-lineage genetic markers with the whole-population genealogy of Québec contained in the BALSAC database. MATERIALS AND METHODS: The remains of six men were exhumed from four historical cemeteries in the province of Québec, Canada. DNA was extracted from the remains and genotyped to reveal their mitochondrial and Y-chromosome haplotypes, which were compared to a collection of haplotypes of genealogically-anchored modern volunteers. Maternal and paternal genealogies were searched in the BALSAC genealogical record for parental couples matching the mitochondrial and the Y-chromosome haplotypic signatures, to identify candidate sons from whom the remains could have originated. RESULTS: Analysis of the matching genealogies identified the parents of one man inhumed in the cemetery of the investigated parish during its operating time. The candidate individual died in 1833 at the age of 58, a plausible age at death in light of osteological analysis of the remains. DISCUSSION: This study demonstrates the promising potential of coupling genetic information from living individuals to genealogical data in BALSAC to identify historical human remains. If genetic coverage is increased, the genealogical information in BALSAC could enable the identification of 87% of the men (n = 178,435) married in Québec before 1850, with high discriminatory power in most cases since >75% of the parental couples have unique biparental signatures in most regions. Genotyping and identifying Québec's historical human remains are a key to reconstructing the genomes of the founders of Québec and reinhuming archeological remains with a marked grave. CI - © 2020 Wiley Periodicals, Inc. FAU - Harding, Tommy AU - Harding T AUID- ORCID: 0000-0002-7823-2755 AD - Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada. AD - Laboratoire de recherche en criminalistique, Département de chimie, biochimie et sciences de l'énergie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada. FAU - Milot, Emmanuel AU - Milot E AD - Laboratoire de recherche en criminalistique, Département de chimie, biochimie et sciences de l'énergie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada. AD - Centre international de criminologie comparée and Centre interuniversitaire d'études québécoises, Université du Québec à Trois-Rivières, Trois-Rivières, Canada. FAU - Moreau, Claudia AU - Moreau C AD - Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada. AD - Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Canada. FAU - Lefebvre, Jean-Francois AU - Lefebvre JF AD - Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada. FAU - Bournival, Jean-Sébastien AU - Bournival JS AD - Projet BALSAC, Université du Québec à Chicoutimi, Chicoutimi, Canada. FAU - Vézina, Hélène AU - Vézina H AD - Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Canada. AD - Projet BALSAC, Université du Québec à Chicoutimi, Chicoutimi, Canada. AD - Département des sciences humaines et sociales, Université du Québec à Chicoutimi, Chicoutimi, Canada. FAU - Laprise, Catherine AU - Laprise C AD - Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Canada. AD - Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Canada. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain. FAU - Anglada, Roger AU - Anglada R AD - Genomics Core Facility, Universitat Pompeu Fabra, Barcelona, Spain. FAU - Loewen, Brad AU - Loewen B AD - Département d'anthropologie, Université de Montréal, Montréal, Canada. FAU - Casals, Ferran AU - Casals F AD - Genomics Core Facility, Universitat Pompeu Fabra, Barcelona, Spain. FAU - Ribot, Isabelle AU - Ribot I AD - Département d'anthropologie, Université de Montréal, Montréal, Canada. FAU - Labuda, Damian AU - Labuda D AD - Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada. AD - Département de pédiatrie, Université de Montréal, Montréal, Canada. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200216 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Genetic Markers) SB - IM MH - Adult MH - Anthropology, Physical/*methods MH - Body Remains MH - *Genetic Markers MH - Humans MH - Male MH - *Maternal Inheritance MH - Middle Aged MH - *Paternal Inheritance MH - Quebec MH - Young Adult OTO - NOTNLM OT - ancient DNA OT - buried's identification OT - uniparental DNA markers OT - whole-population genealogy EDAT- 2020/02/18 06:00 MHDA- 2020/12/18 06:00 CRDT- 2020/02/18 06:00 PHST- 2019/10/26 00:00 [received] PHST- 2020/01/13 00:00 [revised] PHST- 2020/02/04 00:00 [accepted] PHST- 2020/02/18 06:00 [pubmed] PHST- 2020/12/18 06:00 [medline] PHST- 2020/02/18 06:00 [entrez] AID - 10.1002/ajpa.24024 [doi] PST - ppublish SO - Am J Phys Anthropol. 2020 Apr;171(4):645-658. doi: 10.1002/ajpa.24024. Epub 2020 Feb 16. PMID- 31869003 OWN - NLM STAT- MEDLINE DCOM- 20210621 LR - 20210621 IS - 1521-6551 (Electronic) IS - 1521-6543 (Linking) VI - 72 IP - 4 DP - 2020 Apr TI - Contaminations in (meta)genome data: An open issue for the scientific community. PG - 698-705 LID - 10.1002/iub.2216 [doi] AB - In recent years, the high throughput and the low cost of next-generation sequencing (NGS) technologies have led to an increase of the amount of (meta)genomic data, revolutionizing genomic research studies. However, the quality of sequencing data could be affected by experimental errors derived from defective methods and protocols. This represents a serious problem for the scientific community with a negative impact on the correctness of studies that involve genomic sequence analysis. As a countermeasure, several alignment and taxonomic classification tools have been developed to uncover and correct errors. In this critical review some of these integrated software tools and pipelines used to detect contaminations in reference genome databases and sequenced samples are reported. In particular, case studies of bacterial contaminations, contaminations of human origin, mitochondrial contaminations of ancient DNA, and cross contaminations are examined. CI - © 2019 International Union of Biochemistry and Molecular Biology. FAU - De Simone, Giovanna AU - De Simone G AD - Department of Sciences, Roma Tre University, Roma, Italy. FAU - Pasquadibisceglie, Andrea AU - Pasquadibisceglie A AD - Department of Sciences, Roma Tre University, Roma, Italy. FAU - Proietto, Roberta AU - Proietto R AD - Department of Sciences, Roma Tre University, Roma, Italy. FAU - Polticelli, Fabio AU - Polticelli F AD - Department of Sciences, Roma Tre University, Roma, Italy. FAU - Aime, Silvio AU - Aime S AD - Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy. FAU - J M Op den Camp, Huub AU - J M Op den Camp H AD - Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, The Netherlands. FAU - Ascenzi, Paolo AU - Ascenzi P AUID- ORCID: 0000-0002-6449-2150 AD - Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Roma, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20191223 PL - England TA - IUBMB Life JT - IUBMB life JID - 100888706 RN - 0 (DNA, Ancient) SB - IM MH - Bacteria/genetics MH - DNA, Ancient MH - Genomics/*methods MH - High-Throughput Nucleotide Sequencing/methods MH - Humans MH - Metagenome/*genetics MH - Mitochondria/genetics MH - *Software OTO - NOTNLM OT - (meta)genome data OT - bacterial contaminations OT - contaminations of human origin OT - cross contaminations OT - genomic sequence analysis OT - mitochondrial contaminations of ancient DNA EDAT- 2019/12/24 06:00 MHDA- 2021/06/22 06:00 CRDT- 2019/12/24 06:00 PHST- 2019/11/26 00:00 [received] PHST- 2019/11/30 00:00 [accepted] PHST- 2019/12/24 06:00 [pubmed] PHST- 2021/06/22 06:00 [medline] PHST- 2019/12/24 06:00 [entrez] AID - 10.1002/iub.2216 [doi] PST - ppublish SO - IUBMB Life. 2020 Apr;72(4):698-705. doi: 10.1002/iub.2216. Epub 2019 Dec 23. PMID- 32183622 OWN - NLM STAT- MEDLINE DCOM- 20200701 LR - 20221207 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 287 IP - 1923 DP - 2020 Mar 25 TI - Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans. PG - 20192968 LID - 10.1098/rspb.2019.2968 [doi] LID - 20192968 AB - The clarification of the genetic origins of present-day Tibetans requires an understanding of their past relationships with the ancient populations of the Tibetan Plateau. Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogroups D4j1b and M9a1a1c1b1a) that suggest some ancestors of Tibetans came from low-altitude areas 4750 to 2775 years ago and that some were involved in an expansion of people moving between high-altitude areas 2125 to 1100 years ago, we found limited evidence of recent matrilineal continuity on the plateau. Furthermore, deep learning of the ancient data incorporated into simulation models with an accuracy of 97% supports that present-day Tibetan matrilineal ancestry received partial contribution rather than complete continuity from the plateau populations of the last 5200 years. FAU - Ding, Manyu AU - Ding M AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. AD - Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. AD - University of Chinese Academy of Sciences, 100049, People's Republic of China. AD - Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, People's Republic of China. FAU - Wang, Tianyi AU - Wang T AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. AD - School of Cultural Heritage, Northwest University, Xi'an 710069, People's Republic of China. FAU - Ko, Albert Min-Shan AU - Ko AM AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. FAU - Chen, Honghai AU - Chen H AD - School of Cultural Heritage, Northwest University, Xi'an 710069, People's Republic of China. FAU - Wang, Hui AU - Wang H AD - Fudan Archaeological Science Institute, Fudan University, Shanghai 200433, People's Republic of China. AD - Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou 730030, People's Republic of China. FAU - Dong, Guanghui AU - Dong G AD - Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China. FAU - Lu, Hongliang AU - Lu H AD - Department of Archaeology, Sichuan University, Chengdu 610064, People's Republic of China. FAU - He, Wei AU - He W AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, People's Republic of China. FAU - Wangdue, Shargan AU - Wangdue S AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, People's Republic of China. FAU - Yuan, Haibing AU - Yuan H AD - National Demonstration Center for Experimental Archaeology Education and Department of Archaeology, Sichuan University, Chengdu 610064, People's Republic of China. FAU - He, Yuanhong AU - He Y AD - Department of Archaeology, Sichuan University, Chengdu 610064, People's Republic of China. FAU - Cai, Linhai AU - Cai L AD - Qinghai Provincial Cultural Relics and Archaeology Institute, Xining 810007, People's Republic of China. FAU - Chen, Zujun AU - Chen Z AD - Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, People's Republic of China. FAU - Hou, Guangliang AU - Hou G AD - Department of Life and Geography, Qinghai Normal University, Xining 810000, People's Republic of China. FAU - Zhang, Dongju AU - Zhang D AD - Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China. FAU - Zhang, Zhaoxia AU - Zhang Z AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. FAU - Cao, Peng AU - Cao P AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. FAU - Dai, Qingyan AU - Dai Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. FAU - Feng, Xiaotian AU - Feng X AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. FAU - Zhang, Ming AU - Zhang M AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. FAU - Wang, Hongru AU - Wang H AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. FAU - Yang, Melinda A AU - Yang MA AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. AD - Department of Biology, University of Richmond, Richmond, VA, USA. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. AD - University of Chinese Academy of Sciences, 100049, People's Republic of China. AD - Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, People's Republic of China. LA - eng SI - figshare/10.6084/m9.figshare.c.4886247 GR - 55008731/HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200318 PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 SB - IM MH - Altitude MH - Asian People/*genetics MH - Genetic Variation MH - *Genome, Mitochondrial MH - Humans MH - Tibet PMC - PMC7126037 OTO - NOTNLM OT - Tibetan prehistory OT - ancient DNA OT - population genetics of humans COIS- We declare we have no competing interests. EDAT- 2020/03/19 06:00 MHDA- 2020/07/02 06:00 PMCR- 2021/03/25 CRDT- 2020/03/19 06:00 PHST- 2020/03/19 06:00 [entrez] PHST- 2020/03/19 06:00 [pubmed] PHST- 2020/07/02 06:00 [medline] PHST- 2021/03/25 00:00 [pmc-release] AID - rspb20192968 [pii] AID - 10.1098/rspb.2019.2968 [doi] PST - ppublish SO - Proc Biol Sci. 2020 Mar 25;287(1923):20192968. doi: 10.1098/rspb.2019.2968. Epub 2020 Mar 18. PMID- 32130218 OWN - NLM STAT- MEDLINE DCOM- 20200527 LR - 20200527 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 15 IP - 3 DP - 2020 TI - Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan. PG - e0226654 LID - 10.1371/journal.pone.0226654 [doi] LID - e0226654 AB - Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th-19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis. FAU - Sawafuji, Rikai AU - Sawafuji R AUID- ORCID: 0000-0002-8174-2326 AD - Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nakagami, Okinawa, Japan. AD - Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. FAU - Saso, Aiko AU - Saso A AD - The University Museum, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. AD - Department of Physical Therapy, Faculty of Rehabilitation, Niigata University of Health and Welfare, Kita-ku, Niigata, Japan. FAU - Suda, Wataru AU - Suda W AD - RIKEN Center for Integrative Medical Sciences (IMS), Laboratory for Microbiome Sciences, Yokohama, Kanagawa, Japan. FAU - Hattori, Masahira AU - Hattori M AD - RIKEN Center for Integrative Medical Sciences (IMS), Laboratory for Microbiome Sciences, Yokohama, Kanagawa, Japan. AD - Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo, Japan. FAU - Ueda, Shintaroh AU - Ueda S AD - Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. AD - School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, People's Republic of China. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200304 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Fungal) RN - 0 (DNA, Plant) SB - IM MH - Archaeology/*methods MH - Body Remains MH - DNA Barcoding, Taxonomic MH - DNA, Ancient/*isolation & purification MH - DNA, Fungal/isolation & purification MH - DNA, Plant/isolation & purification MH - Dental Calculus/*chemistry MH - *Feeding Behavior MH - Female MH - Fungi/genetics MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Japan MH - Male MH - Oryza/*genetics MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA PMC - PMC7055813 COIS- The authors have declared that no competing interests exist. EDAT- 2020/03/05 06:00 MHDA- 2020/05/28 06:00 PMCR- 2020/03/04 CRDT- 2020/03/05 06:00 PHST- 2019/09/09 00:00 [received] PHST- 2019/12/01 00:00 [accepted] PHST- 2020/03/05 06:00 [entrez] PHST- 2020/03/05 06:00 [pubmed] PHST- 2020/05/28 06:00 [medline] PHST- 2020/03/04 00:00 [pmc-release] AID - PONE-D-19-25288 [pii] AID - 10.1371/journal.pone.0226654 [doi] PST - epublish SO - PLoS One. 2020 Mar 4;15(3):e0226654. doi: 10.1371/journal.pone.0226654. eCollection 2020. PMID- 32098773 OWN - NLM STAT- MEDLINE DCOM- 20210224 LR - 20210926 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 30 IP - 3 DP - 2020 Mar TI - Human auditory ossicles as an alternative optimal source of ancient DNA. PG - 427-436 LID - 10.1101/gr.260141.119 [doi] AB - DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results. CI - © 2020 Sirak et al.; Published by Cold Spring Harbor Laboratory Press. FAU - Sirak, Kendra AU - Sirak K AUID- ORCID: 0000-0003-2347-3479 AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland. FAU - Fernandes, Daniel AU - Fernandes D AUID- ORCID: 0000-0002-7434-6552 AD - Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland. AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria. AD - CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal. FAU - Cheronet, Olivia AU - Cheronet O AD - Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland. AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria. FAU - Harney, Eadaoin AU - Harney E AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena, D-07745, Germany. FAU - Mah, Matthew AU - Mah M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Adamski, Nicole AU - Adamski N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Callan, Kimberly AU - Callan K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Candilio, Francesca AU - Candilio F AD - Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland. FAU - Lawson, Ann Marie AU - Lawson AM AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Mandl, Kirsten AU - Mandl K AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Zalzala, Fatma AU - Zalzala F AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Anders, Alexandra AU - Anders A AD - Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary. FAU - Bartík, Juraj AU - Bartík J AD - Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic. FAU - Coppa, Alfredo AU - Coppa A AD - Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy. FAU - Dashtseveg, Tumen AU - Dashtseveg T AD - Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia. FAU - Évinger, Sándor AU - Évinger S AD - Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary. FAU - Farkaš, Zdeněk AU - Farkaš Z AD - Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic. FAU - Hajdu, Tamás AU - Hajdu T AD - Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary. AD - Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary. FAU - Bayarsaikhan, Jamsranjav AU - Bayarsaikhan J AD - Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia. AD - National Museum of Mongolia, Ulaanbaatar 210146, Mongolia. FAU - McIntyre, Lauren AU - McIntyre L AD - Oxford Archaeology, Oxford OX2 0ES, United Kingdom. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia. FAU - Okumura, Mercedes AU - Okumura M AD - Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Cidade Universitária 05508-090 São Paulo, Brazil. FAU - Pap, Ildikó AU - Pap I AD - Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary. FAU - Pietrusewsky, Michael AU - Pietrusewsky M AD - Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA. FAU - Raczky, Pál AU - Raczky P AD - Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary. FAU - Šefčáková, Alena AU - Šefčáková A AD - Department of Anthropology, Slovak National Museum-Natural History Museum, 810 06 Bratislava 16, Slovak Republic. FAU - Soficaru, Andrei AU - Soficaru A AD - "Fr. J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania. FAU - Szeniczey, Tamás AU - Szeniczey T AD - Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary. AD - Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary. FAU - Szőke, Béla Miklós AU - Szőke BM AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary. FAU - Van Gerven, Dennis AU - Van Gerven D AD - Department of Anthropology, University of Colorado at Boulder, Boulder, Colorado 80309, USA. FAU - Vasilyev, Sergey AU - Vasilyev S AD - Institute of Ethnology and Anthropology, RAS, Moscow, 119991, Russia. FAU - Bell, Lynne AU - Bell L AD - Centre for Forensic Research, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria. LA - eng GR - 263441/ERC_/European Research Council/International PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20200225 PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (DNA, Ancient) SB - IM MH - Cochlea/chemistry MH - DNA, Ancient/*analysis MH - Ear Ossicles/anatomy & histology/*chemistry/embryology MH - Humans MH - Sequence Analysis, DNA PMC - PMC7111520 EDAT- 2020/02/27 06:00 MHDA- 2021/02/25 06:00 PMCR- 2020/09/01 CRDT- 2020/02/27 06:00 PHST- 2019/12/10 00:00 [received] PHST- 2020/02/11 00:00 [accepted] PHST- 2020/02/27 06:00 [pubmed] PHST- 2021/02/25 06:00 [medline] PHST- 2020/02/27 06:00 [entrez] PHST- 2020/09/01 00:00 [pmc-release] AID - gr.260141.119 [pii] AID - 10.1101/gr.260141.119 [doi] PST - ppublish SO - Genome Res. 2020 Mar;30(3):427-436. doi: 10.1101/gr.260141.119. Epub 2020 Feb 25. PMID- 32094539 OWN - NLM STAT- MEDLINE DCOM- 20200331 LR - 20220531 IS - 2397-334X (Electronic) IS - 2397-334X (Linking) VI - 4 IP - 3 DP - 2020 Mar TI - The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean. PG - 334-345 LID - 10.1038/s41559-020-1102-0 [doi] AB - Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people. FAU - Fernandes, Daniel M AU - Fernandes DM AUID- ORCID: 0000-0002-7434-6552 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. daniel.fernandes@univie.ac.at. AD - Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland. daniel.fernandes@univie.ac.at. AD - CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. daniel.fernandes@univie.ac.at. FAU - Mittnik, Alissa AU - Mittnik A AUID- ORCID: 0000-0002-6963-4824 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Olalde, Iñigo AU - Olalde I AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Lazaridis, Iosif AU - Lazaridis I AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAU - Bernardos, Rebecca AU - Bernardos R AUID- ORCID: 0000-0003-4625-3727 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AUID- ORCID: 0000-0001-5350-1608 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. AD - Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA, USA. FAU - Carlsson, Jens AU - Carlsson J AD - Area 52 Research Group, School of Biology and Environmental Science/Earth Institute, University College Dublin, Dublin, Ireland. FAU - Culleton, Brendan J AU - Culleton BJ AD - Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Gamarra, Beatriz AU - Gamarra B AD - Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland. AD - Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain. AD - Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain. FAU - Lari, Martina AU - Lari M AD - Dipartimento di Biologia, Università di Firenze, Florence, Italy. FAU - Mah, Matthew AU - Mah M AUID- ORCID: 0000-0001-8987-6436 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. FAU - Modi, Alessandra AU - Modi A AUID- ORCID: 0000-0001-9514-9868 AD - Dipartimento di Biologia, Università di Firenze, Florence, Italy. FAU - Novak, Mario AU - Novak M AD - Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland. AD - Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. AD - Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA. FAU - Sirak, Kendra A AU - Sirak KA AD - Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Mandl, Kirsten AU - Mandl K AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Schattke, Constanze AU - Schattke C AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Özdoğan, Kadir T AU - Özdoğan KT AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. FAU - Lucci, Michaela AU - Lucci M AD - DANTE Laboratory of Diet and Ancient Technology, Sapienza University of Rome, Rome, Italy. FAU - Gasperetti, Gabriella AU - Gasperetti G AD - Superintendency of Archaeology, Fine Arts and Landscape for the provinces of Sassari and Nuoro, Sassari, Italy. FAU - Candilio, Francesca AU - Candilio F AUID- ORCID: 0000-0002-4668-1361 AD - Superintendency of Archaeology, Fine Arts and Landscape for the city of Cagliari and the provinces of Oristano and South Sardinia, Cagliari, Italy. FAU - Salis, Gianfranca AU - Salis G AD - Superintendency of Archaeology, Fine Arts and Landscape for the city of Cagliari and the provinces of Oristano and South Sardinia, Cagliari, Italy. FAU - Vai, Stefania AU - Vai S AUID- ORCID: 0000-0003-3844-5147 AD - Dipartimento di Biologia, Università di Firenze, Florence, Italy. FAU - Camarós, Edgard AU - Camarós E AUID- ORCID: 0000-0002-0119-3807 AD - Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain. FAU - Calò, Carla AU - Calò C AD - Dipartimento di Scienze della Vita e dell' Ambiente, Sezione di Neuroscienze e Antropologia, Universita' di Cagliari, Cagliari, Italy. FAU - Catalano, Giulio AU - Catalano G AD - Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy. FAU - Cueto, Marián AU - Cueto M AUID- ORCID: 0000-0001-7989-9925 AD - Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain. FAU - Forgia, Vincenza AU - Forgia V AUID- ORCID: 0000-0003-1121-2706 AD - Dipartimento Culture e Società, Università di Palermo, Palermo, Italy. FAU - Lozano, Marina AU - Lozano M AUID- ORCID: 0000-0002-6304-7848 AD - Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain. AD - Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain. FAU - Marini, Elisabetta AU - Marini E AD - Dipartimento di Scienze della Vita e dell' Ambiente, Sezione di Neuroscienze e Antropologia, Universita' di Cagliari, Cagliari, Italy. FAU - Micheletti, Margherita AU - Micheletti M AD - Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Torino, Italy. FAU - Miccichè, Roberto M AU - Miccichè RM AUID- ORCID: 0000-0002-2485-2019 AD - Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy. FAU - Palombo, Maria R AU - Palombo MR AD - CNR-Istituto di Geologia Ambientale e Geoingegneria c/o Dipartimento di Scienze della Terra, Sapienza Università di Roma, Rome, Italy. FAU - Ramis, Damià AU - Ramis D AD - Independent researcher, Palma de Mallorca, Spain. FAU - Schimmenti, Vittoria AU - Schimmenti V AD - Museo Archeologico Regionale Antonino Salinas, Palermo, Italy. FAU - Sureda, Pau AU - Sureda P AUID- ORCID: 0000-0003-4366-6489 AD - Instituto de Ciencias del Patrimonio (Incipit-CSIC), Santiago de Compostela, Spain. AD - McDonald Institute for Archaeological Research and Homerton College, University of Cambridge, Cambridge, UK. FAU - Teira, Luís AU - Teira L AD - Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain. FAU - Teschler-Nicola, Maria AU - Teschler-Nicola M AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Department of Anthropology, Natural History Museum Vienna, Vienna, Austria. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA, USA. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AUID- ORCID: 0000-0002-1730-5914 AD - Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. FAU - Sineo, Luca AU - Sineo L AUID- ORCID: 0000-0001-8634-2295 AD - Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy. FAU - Coppa, Alfredo AU - Coppa A AD - Department of Environmental Biology, Sapienza University of Rome, Rome, Italy. FAU - Caramelli, David AU - Caramelli D AUID- ORCID: 0000-0001-6468-1675 AD - Dipartimento di Biologia, Università di Firenze, Florence, Italy. david.caramelli@unifi.it. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at. AD - Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland. ron.pinhasi@univie.ac.at. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. reich@genetics.med.harvard.edu. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, USA. reich@genetics.med.harvard.edu. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States GR - R01 GM100233/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20200224 PL - England TA - Nat Ecol Evol JT - Nature ecology & evolution JID - 101698577 RN - 0 (DNA, Ancient) SB - IM EIN - Nat Ecol Evol. 2020 May;4(5):764. doi: 10.1038/s41559-020-1197-3. PMID: 32296139 MH - Africa MH - *Agriculture MH - Anthropology MH - *DNA, Ancient MH - Emigration and Immigration MH - Europe MH - *Genome-Wide Association Study MH - Humans MH - Iran MH - Islands MH - Sicily MH - Spain PMC - PMC7080320 MID - NIHMS1548654 COIS- Competing Interests The authors declare no competing financial interests. EDAT- 2020/02/26 06:00 MHDA- 2020/04/01 06:00 PMCR- 2020/08/24 CRDT- 2020/02/26 06:00 PHST- 2019/03/21 00:00 [received] PHST- 2020/01/08 00:00 [accepted] PHST- 2020/02/26 06:00 [pubmed] PHST- 2020/04/01 06:00 [medline] PHST- 2020/02/26 06:00 [entrez] PHST- 2020/08/24 00:00 [pmc-release] AID - 10.1038/s41559-020-1102-0 [pii] AID - 10.1038/s41559-020-1102-0 [doi] PST - ppublish SO - Nat Ecol Evol. 2020 Mar;4(3):334-345. doi: 10.1038/s41559-020-1102-0. Epub 2020 Feb 24. PMID- 31710665 OWN - NLM STAT- MEDLINE DCOM- 20201112 LR - 20201112 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 37 IP - 3 DP - 2020 Mar 1 TI - Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities. PG - 611-626 LID - 10.1093/molbev/msz267 [doi] AB - Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders. CI - © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. FAU - Nieves-Colón, Maria A AU - Nieves-Colón MA AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ. AD - National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico. FAU - Pestle, William J AU - Pestle WJ AD - Department of Anthropology, University of Miami, Coral Gables, FL. FAU - Reynolds, Austin W AU - Reynolds AW AD - Department of Anthropology, University of California, Davis, CA. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Biological Sciences and Environment Institute, The University of Adelaide, Adelaide, SA, Australia. FAU - de la Fuente, Constanza AU - de la Fuente C AD - Department of Human Genetics, University of Chicago, Chicago, IL. FAU - Fowler, Kathleen AU - Fowler K AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ. FAU - Skerry, Katherine M AU - Skerry KM AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ. AD - School of Life Sciences, Arizona State University, Tempe, AZ. FAU - Crespo-Torres, Edwin AU - Crespo-Torres E AD - Forensic Anthropology and Bioarcheology Laboratory, University of Puerto Rico, Rio Piedras, Puerto Rico. FAU - Bustamante, Carlos D AU - Bustamante CD AD - Department of Biomedical Data Science, Stanford University, Stanford, CA. FAU - Stone, Anne C AU - Stone AC AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Bone and Bones MH - Chromosomes, Human/*genetics MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics MH - Dental Calculus/*genetics MH - Fossils MH - Genetics, Population MH - Haplotypes MH - High-Throughput Nucleotide Sequencing MH - Human Migration MH - Humans MH - Indigenous Peoples/*genetics MH - Puerto Rico/ethnology MH - Tooth OTO - NOTNLM OT - Caribbean OT - ancient DNA OT - human genetics OT - mitochondrial DNA EDAT- 2019/11/12 06:00 MHDA- 2020/11/13 06:00 CRDT- 2019/11/12 06:00 PHST- 2019/11/12 06:00 [pubmed] PHST- 2020/11/13 06:00 [medline] PHST- 2019/11/12 06:00 [entrez] AID - 5618728 [pii] AID - 10.1093/molbev/msz267 [doi] PST - ppublish SO - Mol Biol Evol. 2020 Mar 1;37(3):611-626. doi: 10.1093/molbev/msz267. PMID- 32094358 OWN - NLM STAT- MEDLINE DCOM- 20200505 LR - 20240922 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 11 IP - 1 DP - 2020 Feb 24 TI - Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. PG - 939 LID - 10.1038/s41467-020-14523-6 [doi] LID - 939 AB - The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time. FAU - Marcus, Joseph H AU - Marcus JH AUID- ORCID: 0000-0002-0923-9881 AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. FAU - Posth, Cosimo AU - Posth C AUID- ORCID: 0000-0002-8206-3907 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Ringbauer, Harald AU - Ringbauer H AUID- ORCID: 0000-0002-4884-9682 AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. FAU - Lai, Luca AU - Lai L AD - Department of Anthropology, University of South Florida, Tampa, FL, USA. AD - Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA. FAU - Skeates, Robin AU - Skeates R AD - Department of Archaeology, Durham University, Durham, UK. FAU - Sidore, Carlo AU - Sidore C AUID- ORCID: 0000-0001-7504-7477 AD - Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy. AD - Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy. FAU - Beckett, Jessica AU - Beckett J AD - Private contractor, Cagliari, Sardinia, Italy. FAU - Furtwängler, Anja AU - Furtwängler A AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Olivieri, Anna AU - Olivieri A AUID- ORCID: 0000-0002-3941-8098 AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy. FAU - Chiang, Charleston W K AU - Chiang CWK AUID- ORCID: 0000-0002-0668-7865 AD - Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. AD - Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA. FAU - Al-Asadi, Hussein AU - Al-Asadi H AD - Department of Statistics, University of Chicago, Chicago, IL, USA. AD - Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA. FAU - Dey, Kushal AU - Dey K AD - Department of Statistics, University of Chicago, Chicago, IL, USA. AD - Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA. FAU - Joseph, Tyler A AU - Joseph TA AD - Department of Computer Science, Columbia University, New York, NY, USA. FAU - Liu, Chi-Chun AU - Liu CC AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. FAU - Der Sarkissian, Clio AU - Der Sarkissian C AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse 3, Toulouse, France. FAU - Radzevičiūtė, Rita AU - Radzevičiūtė R AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Michel, Megan AU - Michel M AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. FAU - Gradoli, Maria Giuseppina AU - Gradoli MG AD - School of Archaeology and Ancient History, University of Leicester, Leicester, UK. FAU - Marongiu, Patrizia AU - Marongiu P AD - Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy. FAU - Rubino, Salvatore AU - Rubino S AD - Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy. FAU - Mazzarello, Vittorio AU - Mazzarello V AD - Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy. FAU - Rovina, Daniela AU - Rovina D AD - Soprintendenza Archeologia, belle arti e paesaggio delle province di Sassari e Nuoro, Sassari, Italy. FAU - La Fragola, Alessandra AU - La Fragola A AD - Departamento de Geografía, Historia y Humanidades Escuela Internacional de Doctorado de la Universidad de Almería, Almería, Spain. FAU - Serra, Rita Maria AU - Serra RM AD - Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy. AD - Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, University of Sassari, Sassari, Italy. FAU - Bandiera, Pasquale AU - Bandiera P AUID- ORCID: 0000-0002-0589-4539 AD - Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy. AD - Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, University of Sassari, Sassari, Italy. FAU - Bianucci, Raffaella AU - Bianucci R AD - Department of Sciences and Technological Innovation, University of Eastern Piedmont, 15121, Alessandria, Italy. AD - Legal Medicine Section, Department of Public Health and Paediatric Sciences, University of Turin, 10126, Turin, Italy. FAU - Pompianu, Elisa AU - Pompianu E AD - Department of History, Human Sciences and Education, University of Sassari, 07100, Sassari, Italy. FAU - Murgia, Clizia AU - Murgia C AD - Universitat Autònoma de Barcelona, Departament de Biologia Animal, Biologia Vegetal i Ecologia, 08193, Barcelona, Spain. FAU - Guirguis, Michele AU - Guirguis M AUID- ORCID: 0000-0001-9222-5124 AD - Department of History, Human Sciences and Education, University of Sassari, 07100, Sassari, Italy. FAU - Orquin, Rosana Pla AU - Orquin RP AUID- ORCID: 0000-0002-6448-015X AD - Department of History, Human Sciences and Education, University of Sassari, 07100, Sassari, Italy. FAU - Tuross, Noreen AU - Tuross N AUID- ORCID: 0000-0002-3080-4005 AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. FAU - van Dommelen, Peter AU - van Dommelen P AUID- ORCID: 0000-0003-0970-6651 AD - Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, RI, 02912, USA. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Munich, Germany. FAU - Schlessinger, David AU - Schlessinger D AD - Laboratory of Genetics, NIA, NIH, Baltimore, MD, USA. FAU - Cucca, Francesco AU - Cucca F AD - Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy. fcucca@uniss.it. AD - Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy. fcucca@uniss.it. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Max Planck Institute for the Science of Human History, Jena, Germany. krause@shh.mpg.de. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. krause@shh.mpg.de. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Munich, Germany. krause@shh.mpg.de. FAU - Novembre, John AU - Novembre J AUID- ORCID: 0000-0001-5345-0214 AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. jnovembre@uchicago.edu. AD - Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA. jnovembre@uchicago.edu. LA - eng GR - HHSN271201100005C/DA/NIDA NIH HHS/United States GR - R01 GM132383/GM/NIGMS NIH HHS/United States GR - R01 HG007089/HG/NHGRI NIH HHS/United States GR - T32 GM007197/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20200224 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology/methods MH - Body Remains MH - Chromosomes, Human, X/genetics MH - Chromosomes, Human, Y/genetics MH - *DNA, Ancient MH - DNA, Mitochondrial/*genetics MH - Datasets as Topic MH - Female MH - Genetics, Population/*history MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, 20th Century MH - History, 21st Century MH - History, Ancient MH - History, Medieval MH - *Human Migration MH - Humans MH - Italy MH - Male MH - *Models, Genetic MH - Sequence Analysis, DNA PMC - PMC7039977 COIS- The authors declare no competing interests. EDAT- 2020/02/26 06:00 MHDA- 2020/05/06 06:00 PMCR- 2020/02/24 CRDT- 2020/02/26 06:00 PHST- 2019/03/21 00:00 [received] PHST- 2020/01/08 00:00 [accepted] PHST- 2020/02/26 06:00 [entrez] PHST- 2020/02/26 06:00 [pubmed] PHST- 2020/05/06 06:00 [medline] PHST- 2020/02/24 00:00 [pmc-release] AID - 10.1038/s41467-020-14523-6 [pii] AID - 14523 [pii] AID - 10.1038/s41467-020-14523-6 [doi] PST - epublish SO - Nat Commun. 2020 Feb 24;11(1):939. doi: 10.1038/s41467-020-14523-6. PMID- 31939994 OWN - NLM STAT- MEDLINE DCOM- 20201120 LR - 20221207 IS - 1618-1301 (Electronic) IS - 0018-442X (Linking) VI - 71 IP - 1 DP - 2020 Feb 13 TI - Analysis of maternal lineage structure of individuals from chamber graves placed in medieval cemetery in Kałdus, Central Poland. PG - 43-50 LID - 10.1127/homo/2020/1008 [doi] AB - The beginning of the early Middle Ages period in Poland (10(th)-14(th) century) has been widely debated in the context of an active demographic inflow from other countries and its contribution to the creation of the new country. Finding chamber graves which are considered typical for the Scandinavian ethnic group in a few cemeteries in Poland has become the basis for the anthropological inference on the potential participation of North European people in forming the social elite of medieval Poland. However, the question of whether this fact was the result of presence of people from other countries lacks an unambiguous answer. We attempted to isolate ancient DNA from the medieval necropolis in Kałdus where several chamber graves have been found and analysed the genetic diversity of maternal lineage of this population. We analysed the HVR I fragment and coding regions to assess the mitochondrial DNA haplogroup. We have identified a few relatively rare haplogroups (A2, T2b4a, HV, K1a11, J2b1a, and X2) which were previously found in early medieval sites in Norway and Denmark. Obtained results might suggest genetic relation between the people of Kałdus and past northern Europe populations. Present and further research can undoubtedly shed new light on the aspect of the formation of the early medieval Polish population. FAU - Płoszaj, Tomasz AU - Płoszaj T AD - Department of Molecular Biology, Medical University of Lodz, Narutowicza 60, 90-136 Łódź, Poland. FAU - Jędrychowska-Dańska, Krystyna AU - Jędrychowska-Dańska K AD - Department of Molecular Biology, Medical University of Lodz, Narutowicza 60, 90-136 Łódź, Poland. FAU - Zamerska, Alicja AU - Zamerska A AD - Department of Molecular Biology, Medical University of Lodz, Narutowicza 60, 90-136 Łódź, Poland. FAU - Lewandowska, Magda AU - Lewandowska M AD - Department of Molecular Biology, Medical University of Lodz, Narutowicza 60, 90-136 Łódź, Poland. FAU - Bojarski, Jacek AU - Bojarski J AD - Institute of Archaeology, Nicolaus Copernicus University, Szosa Bydgoska 44/48, 87-100 Toruń, Poland. FAU - Chudziak, Wojciech AU - Chudziak W AD - Institute of Archaeology, Nicolaus Copernicus University, Szosa Bydgoska 44/48, 87-100 Toruń, Poland. FAU - Drozd-Lipińska, Alicja AU - Drozd-Lipińska A AD - Department of Anthropology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland. FAU - Robaszkiewicz, Agnieszka AU - Robaszkiewicz A AD - Department of General Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland. FAU - Witas, Henryk W AU - Witas HW AD - Department of Molecular Biology, Medical University of Lodz, Narutowicza 60, 90-136 Łódź, Poland. LA - eng PT - Historical Article PT - Journal Article PL - Germany TA - Homo JT - Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen JID - 0374655 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Anthropology, Physical MH - Cemeteries/*history MH - Child MH - DNA, Mitochondrial/*genetics MH - Female MH - Haplotypes/*genetics MH - History, Medieval MH - Humans MH - Male MH - Poland MH - White People/*genetics EDAT- 2020/01/16 06:00 MHDA- 2020/11/21 06:00 CRDT- 2020/01/16 06:00 PHST- 2019/02/06 00:00 [received] PHST- 2019/10/04 00:00 [revised] PHST- 2019/10/04 00:00 [accepted] PHST- 2020/01/16 06:00 [pubmed] PHST- 2020/11/21 06:00 [medline] PHST- 2020/01/16 06:00 [entrez] AID - 10.1127/homo/2020/1008 [doi] PST - ppublish SO - Homo. 2020 Feb 13;71(1):43-50. doi: 10.1127/homo/2020/1008. PMID- 31504166 OWN - NLM STAT- MEDLINE DCOM- 20200917 LR - 20230130 IS - 1367-4811 (Electronic) IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 36 IP - 3 DP - 2020 Feb 1 TI - A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data. PG - 828-841 LID - 10.1093/bioinformatics/btz660 [doi] AB - MOTIVATION: The presence of present-day human contaminating DNA fragments is one of the challenges defining ancient DNA (aDNA) research. This is especially relevant to the ancient human DNA field where it is difficult to distinguish endogenous molecules from human contaminants due to their genetic similarity. Recently, with the advent of high-throughput sequencing and new aDNA protocols, hundreds of ancient human genomes have become available. Contamination in those genomes has been measured with computational methods often developed specifically for these empirical studies. Consequently, some of these methods have not been implemented and tested for general use while few are aimed at low-depth nuclear data, a common feature in aDNA datasets. RESULTS: We develop a new X-chromosome-based maximum likelihood method for estimating present-day human contamination in low-depth sequencing data from male individuals. We implement our method for general use, assess its performance under conditions typical of ancient human DNA research, and compare it to previous nuclear data-based methods through extensive simulations. For low-depth data, we show that existing methods can produce unusable estimates or substantially underestimate contamination. In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5× on the X-chromosome when contamination is below 25%. Moreover, our method still yields meaningful estimates in very challenging situations, i.e. when the contaminant and the target come from closely related populations or with increased error rates. With a running time below 5 min, our method is applicable to large scale aDNA genomic studies. AVAILABILITY AND IMPLEMENTATION: The method is implemented in C++ and R and is available in github.com/sapfo/contaminationX and popgen.dk/angsd. CI - © The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. FAU - Moreno-Mayar, J Víctor AU - Moreno-Mayar JV AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. AD - National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico. FAU - Korneliussen, Thorfinn Sand AU - Korneliussen TS AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen. FAU - Dalal, Jyoti AU - Dalal J AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. FAU - Renaud, Gabriel AU - Renaud G AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen. FAU - Albrechtsen, Anders AU - Albrechtsen A AD - Department of Biology, The Bioinformatics Centre, University of Copenhagen, 2200 Copenhagen, Denmark. FAU - Nielsen, Rasmus AU - Nielsen R AD - Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen. AD - Department of Statistics, CA 94720, USA. AD - Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. LA - eng GR - R01 GM116044/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (DNA, Ancient) SB - IM MH - Chromosomes MH - *DNA, Ancient MH - *High-Throughput Nucleotide Sequencing MH - Humans MH - Likelihood Functions MH - Male MH - Sequence Analysis, DNA PMC - PMC8215924 EDAT- 2019/09/11 06:00 MHDA- 2020/09/18 06:00 PMCR- 2020/08/26 CRDT- 2019/09/11 06:00 PHST- 2019/03/14 00:00 [received] PHST- 2019/08/05 00:00 [revised] PHST- 2019/08/22 00:00 [accepted] PHST- 2019/09/11 06:00 [pubmed] PHST- 2020/09/18 06:00 [medline] PHST- 2019/09/11 06:00 [entrez] PHST- 2020/08/26 00:00 [pmc-release] AID - 5554699 [pii] AID - btz660 [pii] AID - 10.1093/bioinformatics/btz660 [doi] PST - ppublish SO - Bioinformatics. 2020 Feb 1;36(3):828-841. doi: 10.1093/bioinformatics/btz660. PMID- 31990948 OWN - NLM STAT- MEDLINE DCOM- 20200406 LR - 20200408 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 15 IP - 1 DP - 2020 TI - A multidisciplinary approach for investigating dietary and medicinal habits of the Medieval population of Santa Severa (7th-15th centuries, Rome, Italy). PG - e0227433 LID - 10.1371/journal.pone.0227433 [doi] LID - e0227433 AB - A multidisciplinary approach, combining stable isotope analysis from bone proteins and investigations on dental calculus using DNA analysis, light microscopy, and gas chromatography coupled with mass spectrometry, was applied to reconstruct dietary and medicinal habits of the individuals recovered in the cemetery of the Castle of Santa Severa (7th-15th centuries CE; Rome, Italy). Stable isotope analysis was performed on 120 humans, 41 faunal specimens and 8 charred seeds. Dental calculus analyses were carried out on 94 samples. Overall, isotope data indicated an omnivorous diet based on C3-terrestrial protein, although some individuals possessed carbon values indicative of C4 plant consumption. In terms of animal protein, the diet was probably based on cattle, sheep, pig and chicken products, as witnessed by the archaeozoological findings. Evidence from calculus suggested the consumption of C3 cereals, Fabaceae, Fagaceae, milk and dairy products. Secondary metabolites of herbs and wine were also detected. The detection of marine fish ancient DNA, as well as of ω3 fatty acids in calculus, hypothesized the consumption of marine foodstuffs for this coastal population, despite the lack of a clear marine isotopic signal and the presence of polyunsaturated fatty acids in plant tissues. Moreover, the knowledge of ethnopharmacological tradition and the application of medicinal plants (e.g. Punica granatum L., Ephedra sp. L.) were also identified. The detection of artemisinin, known to have antimalarial properties, led to hypothesize the presence of malaria in the area. Altogether, the combined application of microscopy and biomolecular techniques provided an innovative reconstruction of Medieval lifeways in Central Italy. FAU - Gismondi, Angelo AU - Gismondi A AD - Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - Baldoni, Marica AU - Baldoni M AD - Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - Gnes, Micaela AU - Gnes M AD - Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - Scorrano, Gabriele AU - Scorrano G AD - Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - D'Agostino, Alessia AU - D'Agostino A AD - Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - Di Marco, Gabriele AU - Di Marco G AD - Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - Calabria, Giulietta AU - Calabria G AD - Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - Petrucci, Michela AU - Petrucci M AD - Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - Müldner, Gundula AU - Müldner G AD - Department of Archaeology, University of Reading, Reading, England, United Kingdom. FAU - Von Tersch, Matthew AU - Von Tersch M AD - Department of Archaeology, BioArCh, University of York, York, England, United Kingdom. FAU - Nardi, Alessandra AU - Nardi A AD - Department of Mathematics, University of Rome "Tor Vergata", Rome, Italy. FAU - Enei, Flavio AU - Enei F AD - Museo Civico di Santa Marinella "Museo del Mare e della Navigazione Antica", Castello di Santa Severa (Roma-Italia). FAU - Canini, Antonella AU - Canini A AD - Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - Rickards, Olga AU - Rickards O AD - Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. FAU - Alexander, Michelle AU - Alexander M AUID- ORCID: 0000-0001-8000-3639 AD - Department of Archaeology, BioArCh, University of York, York, England, United Kingdom. FAU - Martínez-Labarga, Cristina AU - Martínez-Labarga C AUID- ORCID: 0000-0003-0439-0379 AD - Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome "Tor Vergata", Rome, Italy. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200128 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *Archaeology MH - Bone and Bones/*chemistry/metabolism MH - *Cemeteries MH - DNA, Ancient/*analysis MH - Diet/*history MH - History, Medieval MH - Humans MH - Rome PMC - PMC6986732 COIS- The authors declare no conflict of interest. EDAT- 2020/01/29 06:00 MHDA- 2020/04/09 06:00 PMCR- 2020/01/28 CRDT- 2020/01/29 06:00 PHST- 2019/07/30 00:00 [received] PHST- 2019/12/18 00:00 [accepted] PHST- 2020/01/29 06:00 [entrez] PHST- 2020/01/29 06:00 [pubmed] PHST- 2020/04/09 06:00 [medline] PHST- 2020/01/28 00:00 [pmc-release] AID - PONE-D-19-21430 [pii] AID - 10.1371/journal.pone.0227433 [doi] PST - epublish SO - PLoS One. 2020 Jan 28;15(1):e0227433. doi: 10.1371/journal.pone.0227433. eCollection 2020. PMID- 31892727 OWN - NLM STAT- MEDLINE DCOM- 20201110 LR - 20210110 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 9 IP - 1 DP - 2019 Dec 31 TI - Environmental factors modulated ancient mitochondrial DNA variability and the prevalence of rheumatic diseases in the Basque Country. PG - 20380 LID - 10.1038/s41598-019-56921-x [doi] LID - 20380 AB - Among the factors that would explain the distribution of mitochondrial lineages in Europe, climate and diseases may have played an important role. A possible explanation lies in the nature of the mitochondrion, in which the energy generation process produces reactive oxygen species that may influence the development of different diseases. The present study is focused on the medieval necropolis of San Miguel de Ereñozar (13(th)-16(th) centuries, Basque Country), whose inhabitants presented a high prevalence of rheumatic diseases and lived during the Little Ice Age (LIA). Our results indicate a close relationship between rheumatic diseases and mitochondrial haplogroup H, and specifically between spondyloarthropathies and sub-haplogroup H2. One possible explanation may be the climate change that took place in the LIA that favoured those haplogroups that were more energy-efficient, such as haplogroup H, to endure lower temperatures and food shortage. However, it had a biological trade-off: the increased risk of developing rheumatic diseases. FAU - Laza, I M AU - Laza IM AUID- ORCID: 0000-0002-2996-4861 AD - Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV-EHU), 48940, Leioa, Bizkaia, Basque Country, Spain. imanol.martinl@ehu.eus. FAU - Hervella, M AU - Hervella M AD - Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV-EHU), 48940, Leioa, Bizkaia, Basque Country, Spain. FAU - Neira Zubieta, M AU - Neira Zubieta M AD - QarK Arqueología, 01006, Vitoria-Gasteiz, Álava, Basque Country, Spain. FAU - de-la-Rúa, C AU - de-la-Rúa C AD - Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV-EHU), 48940, Leioa, Bizkaia, Basque Country, Spain. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20191231 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - *DNA, Ancient MH - DNA, Mitochondrial/*genetics MH - *Evolution, Molecular MH - Genetic Predisposition to Disease MH - Humans MH - Prevalence MH - Rheumatic Diseases/epidemiology/*genetics MH - Spain PMC - PMC6938509 COIS- The authors declare no competing interests. EDAT- 2020/01/02 06:00 MHDA- 2020/11/11 06:00 PMCR- 2019/12/31 CRDT- 2020/01/02 06:00 PHST- 2019/04/08 00:00 [received] PHST- 2019/12/17 00:00 [accepted] PHST- 2020/01/02 06:00 [entrez] PHST- 2020/01/02 06:00 [pubmed] PHST- 2020/11/11 06:00 [medline] PHST- 2019/12/31 00:00 [pmc-release] AID - 10.1038/s41598-019-56921-x [pii] AID - 56921 [pii] AID - 10.1038/s41598-019-56921-x [doi] PST - epublish SO - Sci Rep. 2019 Dec 31;9(1):20380. doi: 10.1038/s41598-019-56921-x. PMID- 31878147 OWN - NLM STAT- MEDLINE DCOM- 20200916 LR - 20200916 IS - 2073-4409 (Electronic) IS - 2073-4409 (Linking) VI - 9 IP - 1 DP - 2019 Dec 24 TI - Predicted Archaic 3D Genome Organization Reveals Genes Related to Head and Spinal Cord Separating Modern from Archaic Humans. LID - 10.3390/cells9010048 [doi] LID - 48 AB - High coverage sequences of archaic humans enabled the reconstruction of their DNA methylation patterns. This allowed comparing gene regulation between human groups, and linking such regulatory changes to phenotypic differences. In a previous work, a detailed comparison of DNA methylation in modern humans, archaic humans, and chimpanzees revealed 873 modern human-derived differentially methylated regions (DMRs). To understand the regulatory implications of these DMRs, we defined differentially methylated genes (DMGs) as genes that harbor DMRs in their promoter or gene body. While most of the modern human-derived DMRs could be linked to DMGs, many others remained unassigned. Here, we used information on 3D genome organization to link ~70 out of the remaining 288 unassigned DMRs to genes. Combined with the previously identified DMGs, we reinforce the enrichment of these genes with vocal and facial anatomy, and additionally find significant enrichment with the spinal column, chin, hair, and scalp. These results reveal the importance of 3D genomic organization in understanding gene regulation by DNA methylation. FAU - Batyrev, Daniel AU - Batyrev D AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. AD - The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. FAU - Lapid, Elisheva AU - Lapid E AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. AD - The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. FAU - Carmel, Liran AU - Carmel L AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. FAU - Meshorer, Eran AU - Meshorer E AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. AD - The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel. LA - eng GR - 1140/17/Israel Science Foundation/International PT - Journal Article DEP - 20191224 PL - Switzerland TA - Cells JT - Cells JID - 101600052 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA Methylation/genetics MH - DNA, Ancient/analysis MH - Databases, Genetic MH - Epigenesis, Genetic/genetics MH - Genome/genetics MH - Genomics/methods MH - Head/*anatomy & histology MH - Hominidae/*genetics MH - Humans MH - Neanderthals/genetics MH - Promoter Regions, Genetic/genetics MH - Spinal Cord/*anatomy & histology PMC - PMC7017363 OTO - NOTNLM OT - DNA methylation OT - ancient DNA OT - archaic humans OT - comparative epigenomics OT - epigenetics OT - gene regulation OT - genome organization COIS- The authors declare no conflict of interest. EDAT- 2019/12/28 06:00 MHDA- 2020/09/17 06:00 PMCR- 2020/01/01 CRDT- 2019/12/28 06:00 PHST- 2019/10/29 00:00 [received] PHST- 2019/12/16 00:00 [revised] PHST- 2019/12/20 00:00 [accepted] PHST- 2019/12/28 06:00 [entrez] PHST- 2019/12/28 06:00 [pubmed] PHST- 2020/09/17 06:00 [medline] PHST- 2020/01/01 00:00 [pmc-release] AID - cells9010048 [pii] AID - cells-09-00048 [pii] AID - 10.3390/cells9010048 [doi] PST - epublish SO - Cells. 2019 Dec 24;9(1):48. doi: 10.3390/cells9010048. PMID- 31848342 OWN - NLM STAT- MEDLINE DCOM- 20200225 LR - 20231020 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 10 IP - 1 DP - 2019 Dec 17 TI - A 5700 year-old human genome and oral microbiome from chewed birch pitch. PG - 5520 LID - 10.1038/s41467-019-13549-9 [doi] LID - 5520 AB - The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA. FAU - Jensen, Theis Z T AU - Jensen TZT AUID- ORCID: 0000-0002-7166-7975 AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. AD - BioArch, Department of Archaeology, University of York, York, YO10 5DD, UK. FAU - Niemann, Jonas AU - Niemann J AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. AD - BioArch, Department of Archaeology, University of York, York, YO10 5DD, UK. FAU - Iversen, Katrine Højholt AU - Iversen KH AUID- ORCID: 0000-0002-7134-7672 AD - Department of Bio and Health Informatics, Technical University of Denmark, Kongens, Lyngby, 2800, Denmark. AD - Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark. FAU - Fotakis, Anna K AU - Fotakis AK AUID- ORCID: 0000-0002-4585-4662 AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Gopalakrishnan, Shyam AU - Gopalakrishnan S AUID- ORCID: 0000-0002-2004-6810 AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Vågene, Åshild J AU - Vågene ÅJ AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Pedersen, Mikkel Winther AU - Pedersen MW AUID- ORCID: 0000-0002-7291-8887 AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Sinding, Mikkel-Holger S AU - Sinding MS AUID- ORCID: 0000-0003-1371-219X AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Ellegaard, Martin R AU - Ellegaard MR AUID- ORCID: 0000-0001-5777-091X AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Allentoft, Morten E AU - Allentoft ME AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Lanigan, Liam T AU - Lanigan LT AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Taurozzi, Alberto J AU - Taurozzi AJ AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Nielsen, Sofie Holtsmark AU - Nielsen SH AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Dee, Michael W AU - Dee MW AD - Centre for Isotope Research, University of Groningen, Groningen, 9747 AG, The Netherlands. FAU - Mortensen, Martin N AU - Mortensen MN AUID- ORCID: 0000-0002-8914-9463 AD - The National Museum of Denmark, I.C. Modewegs Vej, Brede, Kongens Lyngby, 2800, Denmark. FAU - Christensen, Mads C AU - Christensen MC AD - The National Museum of Denmark, I.C. Modewegs Vej, Brede, Kongens Lyngby, 2800, Denmark. FAU - Sørensen, Søren A AU - Sørensen SA AD - Museum Lolland-Falster, Frisegade 40, Nykøbing Falster, 4800, Denmark. FAU - Collins, Matthew J AU - Collins MJ AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, CB2 3ER, UK. FAU - Gilbert, M Thomas P AU - Gilbert MTP AUID- ORCID: 0000-0002-5805-7195 AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. AD - University Museum, NTNU, 7012, Trondheim, Norway. FAU - Sikora, Martin AU - Sikora M AUID- ORCID: 0000-0003-2818-8319 AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. FAU - Rasmussen, Simon AU - Rasmussen S AUID- ORCID: 0000-0001-6323-9041 AD - Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark. FAU - Schroeder, Hannes AU - Schroeder H AUID- ORCID: 0000-0002-6743-0270 AD - The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark. hschroeder@bio.ku.dk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20191217 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - Animals MH - Betula/*physiology MH - DNA, Ancient/*analysis MH - DNA, Bacterial/analysis MH - Denmark MH - *Genome, Human MH - Geography MH - Humans MH - Microbiota/*genetics MH - Mouth/*microbiology MH - Phenotype MH - Radiometric Dating MH - Sex Determination Analysis MH - Time Factors PMC - PMC6917805 COIS- The authors declare no competing interests. EDAT- 2019/12/19 06:00 MHDA- 2020/02/26 06:00 PMCR- 2019/12/17 CRDT- 2019/12/19 06:00 PHST- 2019/06/17 00:00 [received] PHST- 2019/11/15 00:00 [accepted] PHST- 2019/12/19 06:00 [entrez] PHST- 2019/12/19 06:00 [pubmed] PHST- 2020/02/26 06:00 [medline] PHST- 2019/12/17 00:00 [pmc-release] AID - 10.1038/s41467-019-13549-9 [pii] AID - 13549 [pii] AID - 10.1038/s41467-019-13549-9 [doi] PST - epublish SO - Nat Commun. 2019 Dec 17;10(1):5520. doi: 10.1038/s41467-019-13549-9. PMID- 31792176 OWN - NLM STAT- MEDLINE DCOM- 20200413 LR - 20231027 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 116 IP - 51 DP - 2019 Dec 17 TI - The Justinianic Plague: An inconsequential pandemic? PG - 25546-25554 LID - 10.1073/pnas.1903797116 [doi] AB - Existing mortality estimates assert that the Justinianic Plague (circa 541 to 750 CE) caused tens of millions of deaths throughout the Mediterranean world and Europe, helping to end antiquity and start the Middle Ages. In this article, we argue that this paradigm does not fit the evidence. We examine a series of independent quantitative and qualitative datasets that are directly or indirectly linked to demographic and economic trends during this two-century period: Written sources, legislation, coinage, papyri, inscriptions, pollen, ancient DNA, and mortuary archaeology. Individually or together, they fail to support the maximalist paradigm: None has a clear independent link to plague outbreaks and none supports maximalist reconstructions of late antique plague. Instead of large-scale, disruptive mortality, when contextualized and examined together, the datasets suggest continuity across the plague period. Although demographic, economic, and political changes continued between the 6th and 8th centuries, the evidence does not support the now commonplace claim that the Justinianic Plague was a primary causal factor of them. CI - Copyright © 2019 the Author(s). Published by PNAS. FAU - Mordechai, Lee AU - Mordechai L AUID- ORCID: 0000-0002-8474-0473 AD - National Socio-Environmental Synthesis Center, Annapolis, MD 21401; lee.mordechai@mail.huji.ac.il. AD - History Department, Hebrew University of Jerusalem, Mount Scopus, 9190501 Jerusalem, Israel. FAU - Eisenberg, Merle AU - Eisenberg M AUID- ORCID: 0000-0003-1556-5752 AD - National Socio-Environmental Synthesis Center, Annapolis, MD 21401. AD - History Department, Princeton University, Princeton, NJ 08544. FAU - Newfield, Timothy P AU - Newfield TP AUID- ORCID: 0000-0003-1451-5024 AD - History Department, Georgetown University, NW, Washington, DC 20057. AD - Biology Department, Georgetown University, NW, Washington, DC 20057. FAU - Izdebski, Adam AU - Izdebski A AUID- ORCID: 0000-0002-3456-5478 AD - Paleo-Science & History Independent Research Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Institute of History, Jagiellonian University, 31-007 Kraków, Poland. FAU - Kay, Janet E AU - Kay JE AUID- ORCID: 0000-0002-7253-8294 AD - Society of Fellows in the Liberal Arts, Princeton University, Princeton, NJ 08544. FAU - Poinar, Hendrik AU - Poinar H AUID- ORCID: 0000-0002-0314-4160 AD - Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada. AD - Department of Biochemistry, McMaster University, Hamilton, ON L8S 4L9, Canada. AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada. AD - Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L9, Canada. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20191202 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Byzantium MH - History, Medieval MH - Humans MH - Pandemics/*history MH - Plague/*history MH - Population Dynamics/*history MH - Yersinia pestis PMC - PMC6926030 OTO - NOTNLM OT - Justinianic Plague OT - Late Antiquity OT - Yersinia pestis OT - first plague pandemic OT - plague COIS- The authors declare no competing interest. EDAT- 2019/12/04 06:00 MHDA- 2020/04/14 06:00 PMCR- 2019/12/02 CRDT- 2019/12/04 06:00 PHST- 2019/12/04 06:00 [pubmed] PHST- 2020/04/14 06:00 [medline] PHST- 2019/12/04 06:00 [entrez] PHST- 2019/12/02 00:00 [pmc-release] AID - 1903797116 [pii] AID - 201903797 [pii] AID - 10.1073/pnas.1903797116 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2019 Dec 17;116(51):25546-25554. doi: 10.1073/pnas.1903797116. Epub 2019 Dec 2. PMID- 31697016 OWN - NLM STAT- MEDLINE DCOM- 20200518 LR - 20240722 IS - 1469-3178 (Electronic) IS - 1469-221X (Print) IS - 1469-221X (Linking) VI - 20 IP - 12 DP - 2019 Dec 5 TI - Ancient DNA and contemporary politics: The analysis of ancient DNA challenges long-held beliefs about identity and history with potential for political abuse. PG - e49507 LID - 10.15252/embr.201949507 [doi] LID - e49507 AB - The sequencing and analysis of ancient human DNA has helped to rewrite human history. But it is also tempting politicians, nationalists and supremacists to abuse this research for their agendas. CI - © 2019 The Author. FAU - Wolinsky, Howard AU - Wolinsky H AD - Chicago, IL, USA. LA - eng PT - Historical Article PT - Journal Article DEP - 20191107 PL - England TA - EMBO Rep JT - EMBO reports JID - 100963049 RN - 0 (DNA, Ancient) SB - IM MH - Americas MH - *DNA, Ancient MH - Emigration and Immigration/history MH - Europe MH - Genetics, Population/history MH - History, Ancient MH - Human Genetics MH - Human Migration/*history MH - Humans MH - *Politics MH - Racism PMC - PMC6893318 EDAT- 2019/11/08 06:00 MHDA- 2020/05/19 06:00 PMCR- 2020/12/05 CRDT- 2019/11/08 06:00 PHST- 2019/11/08 06:00 [pubmed] PHST- 2020/05/19 06:00 [medline] PHST- 2019/11/08 06:00 [entrez] PHST- 2020/12/05 00:00 [pmc-release] AID - EMBR201949507 [pii] AID - 10.15252/embr.201949507 [doi] PST - ppublish SO - EMBO Rep. 2019 Dec 5;20(12):e49507. doi: 10.15252/embr.201949507. Epub 2019 Nov 7. PMID- 31424543 OWN - NLM STAT- MEDLINE DCOM- 20200217 LR - 20200217 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 36 IP - 12 DP - 2019 Dec 1 TI - Direct Evidence of an Increasing Mutational Load in Humans. PG - 2823-2829 LID - 10.1093/molbev/msz192 [doi] AB - The extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. Although the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes, and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations. CI - © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. FAU - Aris-Brosou, Stéphane AU - Aris-Brosou S AD - Department of Biology, University of Ottawa, Ottawa, ON, Canada. AD - Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada. LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 SB - IM MH - Alleles MH - Disease/*genetics MH - Gene Frequency MH - *Genetic Load MH - *Genome, Human MH - Homozygote MH - Humans MH - Mutation OTO - NOTNLM OT - Combined Annotation Dependent Depletion (CADD) OT - Genome-Wide Association Study (GWAS) OT - ancient DNA OT - range expansion OT - selection OT - single nucleotide polymorphism (SNP) EDAT- 2019/08/20 06:00 MHDA- 2020/02/18 06:00 CRDT- 2019/08/20 06:00 PHST- 2019/08/20 06:00 [pubmed] PHST- 2020/02/18 06:00 [medline] PHST- 2019/08/20 06:00 [entrez] AID - 5551346 [pii] AID - 10.1093/molbev/msz192 [doi] PST - ppublish SO - Mol Biol Evol. 2019 Dec 1;36(12):2823-2829. doi: 10.1093/molbev/msz192. PMID- 31679935 OWN - NLM STAT- MEDLINE DCOM- 20200909 LR - 20221207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 29 IP - 22 DP - 2019 Nov 18 TI - Heterogeneity in Palaeolithic Population Continuity and Neolithic Expansion in North Africa. PG - 3953-3959.e4 LID - S0960-9822(19)31241-2 [pii] LID - 10.1016/j.cub.2019.09.050 [doi] AB - North Africa is located at the crossroads of the Mediterranean Sea, the Middle East, and the Sahara Desert. Extensive migrations and gene flow in the region have shaped many different cultures and ancestral genetic components through time [1-6]. DNA data from ancient Moroccan sites [7, 8] has recently shed some light to the population continuity-versus-replacement debate, i.e., the question of whether current North African populations descend from Palaeolithic groups or, on the contrary, subsequent migrations swept away all pre-existing genetic signal in the region. In the present study, we analyze 21 complete North African genomes and compare them with extant and ancient genome data in order to address the demographic continuity-versus-replacement debate, to assess whether these demographic events were homogeneous (including Berber and Arabic-speaking groups), and to explore the effect of Neolithization and posterior migration waves. The North African genetic pool is defined as a melting pot of genetic components, including an endemic North African Epipalaeolithic component at low frequency that forms a declining gradient from Western to Eastern North Africa. This scenario is consistent with Neolithization having shaped most of the current genetic variation in the region when compared to posterior back-to-North-Africa migration waves such as the Arabization. A common and distinct genetic history of the region is shown, with internal different proportions of genetic components owing to differential admixture with surrounding groups as well as to genetic drift due to isolation and endogamy in certain populations. CI - Copyright © 2019 Elsevier Ltd. All rights reserved. FAU - Serra-Vidal, Gerard AU - Serra-Vidal G AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Departament de Ciencies Experimentals i de la Salut, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain. FAU - Lucas-Sanchez, Marcel AU - Lucas-Sanchez M AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Departament de Ciencies Experimentals i de la Salut, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain. FAU - Fadhlaoui-Zid, Karima AU - Fadhlaoui-Zid K AD - College of Science, Department of Biology, Taibah University, Street Janadah Bin Umayyah Road, Al Madinah Al Monawarah 42353, Saudi Arabia; Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Street Tolede, Tunis 2092, Tunisia. FAU - Bekada, Asmahan AU - Bekada A AD - Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), 1524 El M'Naouer, Oran 31000, Algeria. FAU - Zalloua, Pierre AU - Zalloua P AD - The Lebanese American University, Chouran, School of Medicine, Chouran Street, Beirut 1102-2801, Lebanon. FAU - Comas, David AU - Comas D AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Departament de Ciencies Experimentals i de la Salut, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain. Electronic address: david.comas@upf.edu. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20191031 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Africa South of the Sahara MH - Africa, Northern MH - Black People/*genetics MH - Fossils MH - Gene Flow/*genetics MH - Gene Pool MH - Genetic Variation MH - Genetics, Population/methods MH - Genome/genetics MH - Haplotypes MH - History, Ancient MH - Human Migration/history MH - Humans MH - Polymorphism, Single Nucleotide MH - White People/genetics OTO - NOTNLM OT - North Africa OT - admixture OT - human population genetics OT - population structure OT - whole-genome sequences EDAT- 2019/11/05 06:00 MHDA- 2020/09/10 06:00 CRDT- 2019/11/05 06:00 PHST- 2018/10/11 00:00 [received] PHST- 2019/08/02 00:00 [revised] PHST- 2019/09/19 00:00 [accepted] PHST- 2019/11/05 06:00 [pubmed] PHST- 2020/09/10 06:00 [medline] PHST- 2019/11/05 06:00 [entrez] AID - S0960-9822(19)31241-2 [pii] AID - 10.1016/j.cub.2019.09.050 [doi] PST - ppublish SO - Curr Biol. 2019 Nov 18;29(22):3953-3959.e4. doi: 10.1016/j.cub.2019.09.050. Epub 2019 Oct 31. PMID- 31744094 OWN - NLM STAT- MEDLINE DCOM- 20200403 LR - 20231020 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 20 IP - 22 DP - 2019 Nov 16 TI - Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case. LID - 10.3390/ijms20225763 [doi] LID - 5763 AB - Many anthropological, linguistic, genetic and genomic analyses have been carried out to evaluate the potential impact that evolutionary forces had in shaping the present-day Sardinian gene pool, the main outlier in the genetic landscape of Europe. However, due to the homogenizing effect of internal movements, which have intensified over the past fifty years, only partial information has been obtained about the main demographic events. To overcome this limitation, we analyzed the male-specific region of the Y chromosome in three population samples obtained by reallocating a large number of Sardinian subjects to the place of origin of their monophyletic surnames, which are paternally transmitted through generations in most of the populations, much like the Y chromosome. Three Y-chromosome founding lineages, G2-L91, I2-M26 and R1b-V88, were identified as strongly contributing to the definition of the outlying position of Sardinians in the European genetic context and marking a significant differentiation within the island. The present distribution of these lineages does not always mirror that detected in ancient DNAs. Our results show that the analysis of the Y-chromosome gene pool coupled with a sampling method based on the origin of the family name, is an efficient approach to unravelling past heterogeneity, often hidden by recent movements, in the gene pool of modern populations. Furthermore, the reconstruction and comparison of past genetic isolates represent a starting point to better assess the genetic information deriving from the increasing number of available ancient DNA samples. FAU - Grugni, Viola AU - Grugni V AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Raveane, Alessandro AU - Raveane A AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Colombo, Giulia AU - Colombo G AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Nici, Carmen AU - Nici C AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Crobu, Francesca AU - Crobu F AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Italy. FAU - Ongaro, Linda AU - Ongaro L AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. AD - Estonian Biocentre, Institute of Genomics, Riia 23, 51010 Tartu, Estonia. AD - Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, 51010 Tartu, Estonia. FAU - Battaglia, Vincenza AU - Battaglia V AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Sanna, Daria AU - Sanna D AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. AD - Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy. FAU - Al-Zahery, Nadia AU - Al-Zahery N AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Fiorani, Ornella AU - Fiorani O AD - Istituto di Genetica Molecolare "L.L. Cavalli-Sforza", Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy. FAU - Lisa, Antonella AU - Lisa A AD - Istituto di Genetica Molecolare "L.L. Cavalli-Sforza", Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy. FAU - Ferretti, Luca AU - Ferretti L AUID- ORCID: 0000-0001-5044-8442 AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Achilli, Alessandro AU - Achilli A AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Olivieri, Anna AU - Olivieri A AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Francalacci, Paolo AU - Francalacci P AD - Dipartimento di Scienza della Vita e dell'Ambiente, Università di Cagliari, 09123 Cagliari, Italy. FAU - Piazza, Alberto AU - Piazza A AD - Dipartimento di Scienze Mediche, Scuola di Medicina, Università di Torino, 10124 Torino, Italy. FAU - Torroni, Antonio AU - Torroni A AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. FAU - Semino, Ornella AU - Semino O AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy. LA - eng GR - 2006.194/Compagnia di San Paolo/ PT - Journal Article DEP - 20191116 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (DNA, Ancient) SB - IM MH - Chromosomes, Human, Y/classification/*genetics MH - DNA, Ancient/analysis MH - Gene Frequency MH - Genetic Linkage MH - *Genetics, Population MH - Haplotypes MH - Humans MH - Islands MH - Italy MH - Male MH - Phylogeny MH - Principal Component Analysis MH - White People/genetics PMC - PMC6888588 OTO - NOTNLM OT - Human Y-chromosome variation OT - family name origin OT - haplogroups OT - migrations OT - peopling of Sardinia OT - phylogenetics COIS- The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. EDAT- 2019/11/21 06:00 MHDA- 2020/04/04 06:00 PMCR- 2019/11/01 CRDT- 2019/11/21 06:00 PHST- 2019/10/16 00:00 [received] PHST- 2019/11/11 00:00 [revised] PHST- 2019/11/14 00:00 [accepted] PHST- 2019/11/21 06:00 [entrez] PHST- 2019/11/21 06:00 [pubmed] PHST- 2020/04/04 06:00 [medline] PHST- 2019/11/01 00:00 [pmc-release] AID - ijms20225763 [pii] AID - ijms-20-05763 [pii] AID - 10.3390/ijms20225763 [doi] PST - epublish SO - Int J Mol Sci. 2019 Nov 16;20(22):5763. doi: 10.3390/ijms20225763. PMID- 31729399 OWN - NLM STAT- MEDLINE DCOM- 20201112 LR - 20221207 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 9 IP - 1 DP - 2019 Nov 15 TI - Human mitochondrial DNA lineages in Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry. PG - 16883 LID - 10.1038/s41598-019-51045-8 [doi] LID - 16883 AB - Human ancient DNA studies have revealed high mobility in Europe's past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300-1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns. FAU - Översti, Sanni AU - Översti S AD - Department of Biosciences, University of Helsinki, Helsinki, Finland. sanni.oversti@helsinki.fi. FAU - Majander, Kerttu AU - Majander K AD - Department of Biosciences, University of Helsinki, Helsinki, Finland. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Salmela, Elina AU - Salmela E AUID- ORCID: 0000-0003-1326-4462 AD - Department of Biosciences, University of Helsinki, Helsinki, Finland. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Salo, Kati AU - Salo K AD - Department of Cultures, University of Helsinki, Helsinki, Finland. FAU - Arppe, Laura AU - Arppe L AD - Laboratory of Chronology, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland. FAU - Belskiy, Stanislav AU - Belskiy S AD - Peter the Great Museum of World Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg, Russia. FAU - Etu-Sihvola, Heli AU - Etu-Sihvola H AUID- ORCID: 0000-0001-6669-797X AD - Laboratory of Chronology, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland. FAU - Laakso, Ville AU - Laakso V AD - Department of Archaeology, University of Turku, Turku, Finland. FAU - Mikkola, Esa AU - Mikkola E AD - Finnish Heritage Agency, Helsinki, Finland. FAU - Pfrengle, Saskia AU - Pfrengle S AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Putkonen, Mikko AU - Putkonen M AD - Department of Forensic Medicine, University of Helsinki, Helsinki, Finland. FAU - Taavitsainen, Jussi-Pekka AU - Taavitsainen JP AD - Department of Archaeology, University of Turku, Turku, Finland. FAU - Vuoristo, Katja AU - Vuoristo K AD - Finnish Heritage Agency, Helsinki, Finland. FAU - Wessman, Anna AU - Wessman A AUID- ORCID: 0000-0001-6886-5455 AD - Department of Cultures, University of Helsinki, Helsinki, Finland. AD - Department of Archaeology, University of Turku, Turku, Finland. FAU - Sajantila, Antti AU - Sajantila A AD - Department of Forensic Medicine, University of Helsinki, Helsinki, Finland. FAU - Oinonen, Markku AU - Oinonen M AUID- ORCID: 0000-0002-0881-7643 AD - Laboratory of Chronology, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. AD - Institute of Evolutionary Medicine, University of Zürich, Zürich, Switzerland. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Palo, Jukka U AU - Palo JU AD - Department of Forensic Medicine, University of Helsinki, Helsinki, Finland. AD - Forensic Genetics Unit, National Institute for Health and Welfare, Helsinki, Finland. FAU - Onkamo, Päivi AU - Onkamo P AD - Department of Biosciences, University of Helsinki, Helsinki, Finland. AD - Department of Biology, University of Turku, Turku, Finland. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20191115 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - E1UOL152H7 (Iron) SB - IM MH - Agriculture MH - *Crosses, Genetic MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*analysis/genetics MH - Europe MH - Farmers/statistics & numerical data MH - Farms MH - Finland MH - Genome, Mitochondrial/genetics MH - History, Ancient MH - *Human Migration/history MH - Humans MH - Iron MH - Maternal Inheritance/*genetics MH - Oceans and Seas MH - White People/*genetics PMC - PMC6858343 COIS- The authors declare no competing interests. EDAT- 2019/11/16 06:00 MHDA- 2020/11/13 06:00 PMCR- 2019/11/15 CRDT- 2019/11/16 06:00 PHST- 2019/04/03 00:00 [received] PHST- 2019/09/19 00:00 [accepted] PHST- 2019/11/16 06:00 [entrez] PHST- 2019/11/16 06:00 [pubmed] PHST- 2020/11/13 06:00 [medline] PHST- 2019/11/15 00:00 [pmc-release] AID - 10.1038/s41598-019-51045-8 [pii] AID - 51045 [pii] AID - 10.1038/s41598-019-51045-8 [doi] PST - epublish SO - Sci Rep. 2019 Nov 15;9(1):16883. doi: 10.1038/s41598-019-51045-8. PMID- 31754290 OWN - NLM STAT- MEDLINE DCOM- 20200512 LR - 20200512 IS - 2219-2840 (Electronic) IS - 1007-9327 (Print) IS - 1007-9327 (Linking) VI - 25 IP - 42 DP - 2019 Nov 14 TI - Helicobacter pylori in ancient human remains. PG - 6289-6298 LID - 10.3748/wjg.v25.i42.6289 [doi] AB - The bacterium Helicobacter pylori (H. pylori) infects the stomachs of approximately 50% of all humans. With its universal occurrence, high infectivity and virulence properties it is considered as one of the most severe global burdens of modern humankind. It has accompanied humans for many thousands of years, and due to its high genetic variability and vertical transmission, its population genetics reflects the history of human migrations. However, especially complex demographic events such as the colonisation of Europe cannot be resolved with population genetic analysis of modern H. pylori strains alone. This is best exemplified with the reconstruction of the 5300-year-old H. pylori genome of the Iceman, a European Copper Age mummy. Our analysis provided precious insights into the ancestry and evolution of the pathogen and underlined the high complexity of ancient European population history. In this review we will provide an overview on the molecular analysis of H. pylori in mummified human remains that were done so far and we will outline methodological advancements in the field of ancient DNA research that support the reconstruction and authentication of ancient H. pylori genome sequences. CI - ©The Author(s) 2019. Published by Baishideng Publishing Group Inc. All rights reserved. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, EURAC Research, Bolzano 39100, Italy. frank.maixner@eurac.edu. FAU - Thorell, Kaisa AU - Thorell K AD - Department of Infectious Diseases, University of Gothenburg, Göteborg SE405 30, Sweden. FAU - Granehäll, Lena AU - Granehäll L AD - Institute for Mummy Studies, EURAC Research, Bolzano 39100, Italy. FAU - Linz, Bodo AU - Linz B AD - Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, United States. FAU - Moodley, Yoshan AU - Moodley Y AD - Department of Zoology, University of Venda, Thohoyandou 0950, South Africa. FAU - Rattei, Thomas AU - Rattei T AD - Department of Microbiology and Ecosystem Science, University of Vienna, Vienna 1090, Austria. FAU - Engstrand, Lars AU - Engstrand L AD - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 141 83, Sweden. FAU - Zink, Albert AU - Zink A AD - Institute for Mummy Studies, EURAC Research, Bolzano 39100, Italy. LA - eng PT - Journal Article PT - Review PL - United States TA - World J Gastroenterol JT - World journal of gastroenterology JID - 100883448 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - Body Remains/*microbiology MH - DNA, Ancient/*analysis MH - DNA, Bacterial/analysis MH - Genome, Bacterial MH - Helicobacter Infections/*microbiology MH - Helicobacter pylori/isolation & purification MH - Humans MH - *Mummies MH - Stomach/microbiology MH - Virulence PMC - PMC6861846 OTO - NOTNLM OT - Helicobacter pylori OT - Ancient DNA OT - Ancient gut contents OT - Coprolites OT - Evolution OT - Iceman COIS- Conflict-of-interest statement: No potential conflicts of interest. EDAT- 2019/11/23 06:00 MHDA- 2020/05/13 06:00 PMCR- 2019/11/14 CRDT- 2019/11/23 06:00 PHST- 2019/06/28 00:00 [received] PHST- 2019/09/13 00:00 [revised] PHST- 2019/11/01 00:00 [accepted] PHST- 2019/11/23 06:00 [entrez] PHST- 2019/11/23 06:00 [pubmed] PHST- 2020/05/13 06:00 [medline] PHST- 2019/11/14 00:00 [pmc-release] AID - 10.3748/wjg.v25.i42.6289 [doi] PST - ppublish SO - World J Gastroenterol. 2019 Nov 14;25(42):6289-6298. doi: 10.3748/wjg.v25.i42.6289. PMID- 31607556 OWN - NLM STAT- MEDLINE DCOM- 20200304 LR - 20240722 IS - 1934-6069 (Electronic) IS - 1931-3128 (Print) IS - 1931-3128 (Linking) VI - 26 IP - 5 DP - 2019 Nov 13 TI - The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. PG - 666-679.e7 LID - S1931-3128(19)30427-5 [pii] LID - 10.1016/j.chom.2019.08.018 [doi] AB - Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations. CI - Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Tett, Adrian AU - Tett A AD - CIBIO Department, University of Trento, 38123 Trento, Italy. Electronic address: adrianjames.tett@unitn.it. FAU - Huang, Kun D AU - Huang KD AD - CIBIO Department, University of Trento, 38123 Trento, Italy; Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 1 38010 S, San Michele all'Adige, Italy. FAU - Asnicar, Francesco AU - Asnicar F AD - CIBIO Department, University of Trento, 38123 Trento, Italy. FAU - Fehlner-Peach, Hannah AU - Fehlner-Peach H AD - Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA. FAU - Pasolli, Edoardo AU - Pasolli E AD - CIBIO Department, University of Trento, 38123 Trento, Italy. FAU - Karcher, Nicolai AU - Karcher N AD - CIBIO Department, University of Trento, 38123 Trento, Italy. FAU - Armanini, Federica AU - Armanini F AD - CIBIO Department, University of Trento, 38123 Trento, Italy. FAU - Manghi, Paolo AU - Manghi P AD - CIBIO Department, University of Trento, 38123 Trento, Italy. FAU - Bonham, Kevin AU - Bonham K AD - The Broad Institute of MIT and Harvard, Cambridge, MA 02115, USA; Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy. FAU - Zolfo, Moreno AU - Zolfo M AD - CIBIO Department, University of Trento, 38123 Trento, Italy. FAU - De Filippis, Francesca AU - De Filippis F AD - Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy. FAU - Magnabosco, Cara AU - Magnabosco C AD - Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA. FAU - Bonneau, Richard AU - Bonneau R AD - Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA; Departments of Biology and Computer Science, New York University, New York, NY 10003, USA. FAU - Lusingu, John AU - Lusingu J AD - National Institute for Medical Research, Tanga Centre, Tanzania. FAU - Amuasi, John AU - Amuasi J AD - Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Ghana. FAU - Reinhard, Karl AU - Reinhard K AD - Hardin Hall, School of Natural Resources, University of Nebraska, Lincoln, NE 68583-0987, USA. FAU - Rattei, Thomas AU - Rattei T AD - CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. FAU - Boulund, Fredrik AU - Boulund F AD - Centre for Translational Microbiome Research, Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden. FAU - Engstrand, Lars AU - Engstrand L AD - Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy. FAU - Zink, Albert AU - Zink A AD - Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy. FAU - Collado, Maria Carmen AU - Collado MC AD - Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain. FAU - Littman, Dan R AU - Littman DR AD - Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA. FAU - Eibach, Daniel AU - Eibach D AD - Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, 20359 Hamburg, Germany. FAU - Ercolini, Danilo AU - Ercolini D AD - Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy. FAU - Rota-Stabelli, Omar AU - Rota-Stabelli O AD - Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 1 38010 S, San Michele all'Adige, Italy. FAU - Huttenhower, Curtis AU - Huttenhower C AD - The Broad Institute of MIT and Harvard, Cambridge, MA 02115, USA; Biostatistics Department, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy. FAU - Segata, Nicola AU - Segata N AD - CIBIO Department, University of Trento, 38123 Trento, Italy. Electronic address: nicola.segata@unitn.it. LA - eng GR - TL1 TR001447/TR/NCATS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States GR - U54 DE023798/DE/NIDCR NIH HHS/United States GR - 716575/ERC_/European Research Council/International GR - R24 DK110499/DK/NIDDK NIH HHS/United States GR - R01 DK103358/DK/NIDDK NIH HHS/United States GR - R01 HG005220/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20191010 PL - United States TA - Cell Host Microbe JT - Cell host & microbe JID - 101302316 RN - Prevotella copri SB - IM CIN - Cell Host Microbe. 2019 Nov 13;26(5):577-578. doi: 10.1016/j.chom.2019.10.020. PMID: 31726027 MH - Diet MH - Ethiopia MH - Feces/microbiology MH - Fossils/*microbiology MH - Gastrointestinal Microbiome/*genetics MH - Genetic Variation MH - Genome, Bacterial/*genetics MH - Ghana MH - Humans MH - Prevotella/*classification/*genetics/isolation & purification MH - Tanzania PMC - PMC6854460 OTO - NOTNLM OT - Iceman OT - Prevotella copri OT - Westernization OT - ancient DNA OT - bacterial pangenome OT - bacterial phylogenetics OT - comparative microbial genomics OT - gut microbes OT - human microbiome OT - metagenomic assembly OT - metagenomics COIS- The authors declare no competing interests. EDAT- 2019/10/15 06:00 MHDA- 2020/03/05 06:00 PMCR- 2019/11/13 CRDT- 2019/10/15 06:00 PHST- 2019/04/15 00:00 [received] PHST- 2019/07/05 00:00 [revised] PHST- 2019/08/28 00:00 [accepted] PHST- 2019/10/15 06:00 [pubmed] PHST- 2020/03/05 06:00 [medline] PHST- 2019/10/15 06:00 [entrez] PHST- 2019/11/13 00:00 [pmc-release] AID - S1931-3128(19)30427-5 [pii] AID - 10.1016/j.chom.2019.08.018 [doi] PST - ppublish SO - Cell Host Microbe. 2019 Nov 13;26(5):666-679.e7. doi: 10.1016/j.chom.2019.08.018. Epub 2019 Oct 10. PMID- 31486822 OWN - NLM STAT- MEDLINE DCOM- 20200423 LR - 20200423 IS - 1618-1301 (Electronic) IS - 0018-442X (Linking) VI - 70 IP - 2 DP - 2019 Oct 24 TI - Osteoarcheological and biomolecular evidence of leprosy from an 11-13(th) century CE Muslim cemetery in Europe (Orosháza, Southeast Hungary). PG - 105-118 LID - 10.1127/homo/2019/1071 [doi] AB - Orosháza site no. 10 (Southeast Hungary) contains the partially excavated archaeological remains of an 11-13(th) century CE Muslim merchant village and its cemetery located in close proximity to Christian villages of the same era. The skeleton of a young woman (grave no. 16) from the last phase of the cemetery use was identified with rhinomaxillary lesions associated with lepromatous leprosy. The right parietal bone also exhibited signs of cranial trauma, possibly caused by symbolic trepanation, a well-known ritual practice in the 9-11(th) century CE Carpathian Basin. The retrospective diagnosis of the disease was supported by ancient DNA analysis, as the samples were positive for Mycobacterium leprae aDNA, shown to be of genotype 3. Contrary to the general practice of the era, the body of the young female with severe signs of leprosy was interred among the regular graves of the Muslim cemetery in Orosháza, which may reflect the unique cultural background of the community. FAU - Balázs, János AU - Balázs J AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Rózsa, Zoltán AU - Rózsa Z AD - Nagy Gyula Museum, Orosháza, Hungary. FAU - Bereczki, Zsolt AU - Bereczki Z AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Marcsik, Antónia AU - Marcsik A AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Tihanyi, Balázs AU - Tihanyi B AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Karlinger, Kinga AU - Karlinger K AD - Department of Radiology, Semmelweis University, Budapest, Hungary. FAU - Pölöskei, Gergely AU - Pölöskei G AD - Department of Radiology, Semmelweis University, Budapest, Hungary. FAU - Molnár, Erika AU - Molnár E AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. LA - eng PT - Historical Article PT - Journal Article PL - Germany TA - Homo JT - Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen JID - 0374655 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - Adult MH - Bone and Bones/microbiology/pathology MH - Cemeteries/*history MH - DNA, Ancient/analysis MH - DNA, Bacterial/analysis/genetics MH - Female MH - History, Medieval MH - Humans MH - Hungary MH - Islam/*history MH - Leprosy/*history/microbiology MH - Male MH - Mycobacterium leprae/genetics MH - Paleopathology MH - Young Adult EDAT- 2019/09/06 06:00 MHDA- 2020/04/24 06:00 CRDT- 2019/09/06 06:00 PHST- 2018/08/07 00:00 [received] PHST- 2019/05/13 00:00 [revised] PHST- 2019/05/18 00:00 [accepted] PHST- 2019/09/06 06:00 [pubmed] PHST- 2020/04/24 06:00 [medline] PHST- 2019/09/06 06:00 [entrez] AID - 10.1127/homo/2019/1071 [doi] PST - ppublish SO - Homo. 2019 Oct 24;70(2):105-118. doi: 10.1127/homo/2019/1071. PMID- 31594846 OWN - NLM STAT- MEDLINE DCOM- 20200331 LR - 20221207 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 116 IP - 43 DP - 2019 Oct 22 TI - Genetic contributions to variation in human stature in prehistoric Europe. PG - 21484-21492 LID - 10.1073/pnas.1910606116 [doi] AB - The relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 y in European height predicted using DNA from 1,071 ancient individuals are consistent with changes observed in 1,159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height-consistent with genetic predictions-although genetics predicts a small post-Neolithic increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change. CI - Copyright © 2019 the Author(s). Published by PNAS. FAU - Cox, Samantha L AU - Cox SL AUID- ORCID: 0000-0003-2557-6711 AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. FAU - Ruff, Christopher B AU - Ruff CB AD - Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine, Baltimore, MD 21205. FAU - Maier, Robert M AU - Maier RM AD - Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142. AD - Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142. AD - Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; mathi@pennmedicine.upenn.edu. LA - eng GR - R35 GM133708/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20191008 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - *Body Height MH - DNA, Ancient/*chemistry MH - Europe MH - *Genetic Variation MH - Genetics, Population/history MH - History, Ancient MH - Human Genetics/*history MH - Humans MH - Paleontology MH - Phenotype MH - Polymorphism, Single Nucleotide MH - White People/*genetics/*history PMC - PMC6815153 OTO - NOTNLM OT - ancient DNA OT - evolution OT - height OT - stature COIS- The authors declare no competing interest. EDAT- 2019/10/09 06:00 MHDA- 2020/04/01 06:00 PMCR- 2019/10/08 CRDT- 2019/10/10 06:00 PHST- 2019/10/09 06:00 [pubmed] PHST- 2020/04/01 06:00 [medline] PHST- 2019/10/10 06:00 [entrez] PHST- 2019/10/08 00:00 [pmc-release] AID - 1910606116 [pii] AID - 201910606 [pii] AID - 10.1073/pnas.1910606116 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21484-21492. doi: 10.1073/pnas.1910606116. Epub 2019 Oct 8. PMID- 31626767 OWN - NLM STAT- MEDLINE DCOM- 20200519 LR - 20200519 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 179 IP - 3 DP - 2019 Oct 17 TI - An Ancient Genome from the Indus Valley Civilization. PG - 586-588 LID - S0092-8674(19)31078-5 [pii] LID - 10.1016/j.cell.2019.09.027 [doi] AB - Shinde et al. report the first genome-wide data from an ancient individual from the Indus Valley Civilization in South Asia. Their findings have implications for the origins and spread of farming and Indo-European languages in the region and the makings of the South Asian gene pool. CI - Copyright © 2019 Elsevier Inc. All rights reserved. FAU - Raghavan, Maanasa AU - Raghavan M AD - Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. FAU - Schroeder, Hannes AU - Schroeder H AD - Section for Evolutionary Genomics, The Globe Institute, University of Copenhagen, 1553 Copenhagen, Denmark. FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Department of Computational Biology, University of Lausanne & Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. Electronic address: annasapfo.malaspinas@unil.ch. LA - eng PT - Comment PT - Journal Article PL - United States TA - Cell JT - Cell JID - 0413066 SB - IM CON - PLoS One. 2018 Feb 21;13(2):e0192299. doi: 10.1371/journal.pone.0192299. PMID: 29466426 MH - Archaeology MH - Asia MH - *Cemeteries MH - *Civilization MH - Humans MH - India EDAT- 2019/10/19 06:00 MHDA- 2020/05/20 06:00 CRDT- 2019/10/19 06:00 PHST- 2019/10/19 06:00 [entrez] PHST- 2019/10/19 06:00 [pubmed] PHST- 2020/05/20 06:00 [medline] AID - S0092-8674(19)31078-5 [pii] AID - 10.1016/j.cell.2019.09.027 [doi] PST - ppublish SO - Cell. 2019 Oct 17;179(3):586-588. doi: 10.1016/j.cell.2019.09.027. PMID- 31495572 OWN - NLM STAT- MEDLINE DCOM- 20200527 LR - 20231104 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 179 IP - 3 DP - 2019 Oct 17 TI - An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers. PG - 729-735.e10 LID - S0092-8674(19)30967-5 [pii] LID - 10.1016/j.cell.2019.08.048 [doi] AB - We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people. CI - Copyright © 2019 Elsevier Inc. All rights reserved. FAU - Shinde, Vasant AU - Shinde V AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. Electronic address: vasant.shinde@dcpune.ac.in. FAU - Narasimhan, Vagheesh M AU - Narasimhan VM AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: vagheesh@mail.harvard.edu. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. FAU - Mah, Matthew AU - Mah M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. FAU - Lipson, Mark AU - Lipson M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Nakatsuka, Nathan AU - Nakatsuka N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Adamski, Nicole AU - Adamski N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Lawson, Ann Marie AU - Lawson AM AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Jadhav, Nilesh AU - Jadhav N AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. FAU - Kim, Yong Jun AU - Kim YJ AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. FAU - Chatterjee, Malavika AU - Chatterjee M AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. FAU - Munshi, Avradeep AU - Munshi A AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. FAU - Panyam, Amrithavalli AU - Panyam A AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. FAU - Waghmare, Pranjali AU - Waghmare P AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. FAU - Yadav, Yogesh AU - Yadav Y AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. FAU - Patel, Himani AU - Patel H AD - Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India. FAU - Kaushik, Amit AU - Kaushik A AD - Amity Institute of Biotechnology, Amity University, Noida 201313, India. FAU - Thangaraj, Kumarasamy AU - Thangaraj K AD - CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. FAU - Meyer, Matthias AU - Meyer M AD - Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Rai, Niraj AU - Rai N AD - Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. Electronic address: nirajrai@bsip.res.in. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - HHMI_/Howard Hughes Medical Institute/United States GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - T32 GM007753/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20190905 PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) SB - IM MH - Asian People/genetics MH - DNA, Ancient/*chemistry MH - Evolution, Molecular MH - *Genome, Human MH - *Human Migration MH - Humans MH - Iran MH - Pakistan MH - *Pedigree MH - Population/*genetics PMC - PMC6800651 MID - NIHMS1538584 OTO - NOTNLM OT - Harappan Civilization OT - Indus Valley Civilization OT - South Asia OT - ancient DNA OT - anthropology OT - archaeology OT - population genetics COIS- Declaration of Interests The authors declare no competing interests. EDAT- 2019/09/10 06:00 MHDA- 2020/05/28 06:00 PMCR- 2020/10/17 CRDT- 2019/09/10 06:00 PHST- 2019/08/09 00:00 [received] PHST- 2019/08/26 00:00 [revised] PHST- 2019/08/27 00:00 [accepted] PHST- 2019/09/10 06:00 [pubmed] PHST- 2020/05/28 06:00 [medline] PHST- 2019/09/10 06:00 [entrez] PHST- 2020/10/17 00:00 [pmc-release] AID - S0092-8674(19)30967-5 [pii] AID - 10.1016/j.cell.2019.08.048 [doi] PST - ppublish SO - Cell. 2019 Oct 17;179(3):729-735.e10. doi: 10.1016/j.cell.2019.08.048. Epub 2019 Sep 5. PMID- 31611588 OWN - NLM STAT- MEDLINE DCOM- 20201030 LR - 20221207 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 9 IP - 1 DP - 2019 Oct 14 TI - Rare human mitochondrial HV lineages spread from the Near East and Caucasus during post-LGM and Neolithic expansions. PG - 14751 LID - 10.1038/s41598-019-48596-1 [doi] LID - 14751 AB - Of particular significance to human population history in Eurasia are the migratory events that connected the Near East to Europe after the Last Glacial Maximum (LGM). Utilizing 315 HV*(xH,V) mitogenomes, including 27 contemporary lineages first reported here, we found the genetic signatures for distinctive movements out of the Near East and South Caucasus both westward into Europe and eastward into South Asia. The parallel phylogeographies of rare, yet widely distributed HV*(xH,V) subclades reveal a connection between the Italian Peninsula and South Caucasus, resulting from at least two (post-LGM, Neolithic) waves of migration. Many of these subclades originated in a population ancestral to contemporary Armenians and Assyrians. One such subclade, HV1b-152, supports a postexilic, northern Mesopotamian origin for the Ashkenazi HV1b2 lineages. In agreement with ancient DNA findings, our phylogenetic analysis of HV12 and HV14, the two exclusively Asian subclades of HV*(xH,V), point to the migration of lineages originating in Iran to South Asia before and during the Neolithic period. With HV12 being one of the oldest HV subclades, our results support an origin of HV haplogroup in the region defined by Western Iran, Mesopotamia, and the South Caucasus, where the highest prevalence of HV has been found. FAU - Shamoon-Pour, Michel AU - Shamoon-Pour M AD - Department of Anthropology, Binghamton University, Binghamton, NY, 13902, USA. mshamoon@binghamton.edu. FAU - Li, Mian AU - Li M AD - Department of Biology, Binghamton University, Binghamton, NY, 13902, USA. FAU - Merriwether, D Andrew AU - Merriwether DA AD - Department of Anthropology, Binghamton University, Binghamton, NY, 13902, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20191014 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) SB - IM MH - Armenia MH - Asia MH - Asian People/genetics MH - DNA, Mitochondrial/*genetics MH - Europe MH - Genetic Variation MH - Genetics, Population MH - Haplotypes MH - Humans MH - Middle East MH - Mitochondria/genetics MH - Phylogeography MH - White People/genetics PMC - PMC6791841 COIS- The authors declare no competing interests. EDAT- 2019/10/16 06:00 MHDA- 2020/10/31 06:00 PMCR- 2019/10/14 CRDT- 2019/10/16 06:00 PHST- 2019/01/11 00:00 [received] PHST- 2019/06/21 00:00 [accepted] PHST- 2019/10/16 06:00 [entrez] PHST- 2019/10/16 06:00 [pubmed] PHST- 2020/10/31 06:00 [medline] PHST- 2019/10/14 00:00 [pmc-release] AID - 10.1038/s41598-019-48596-1 [pii] AID - 48596 [pii] AID - 10.1038/s41598-019-48596-1 [doi] PST - epublish SO - Sci Rep. 2019 Oct 14;9(1):14751. doi: 10.1038/s41598-019-48596-1. PMID- 31594508 OWN - NLM STAT- MEDLINE DCOM- 20200528 LR - 20221207 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 286 IP - 1912 DP - 2019 Oct 9 TI - The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon. PG - 20191528 LID - 10.1098/rspb.2019.1528 [doi] LID - 20191528 AB - The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24× coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers. FAU - Malmström, Helena AU - Malmström H AD - Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden. AD - Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, 2006 Auckland Park, South Africa. FAU - Günther, Torsten AU - Günther T AD - Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden. FAU - Svensson, Emma M AU - Svensson EM AD - Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden. FAU - Juras, Anna AU - Juras A AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland. FAU - Fraser, Magdalena AU - Fraser M AD - Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden. AD - Department of Archaeology and Ancient History, Uppsala University-Campus Gotland, 621 67 Visby, Sweden. FAU - Munters, Arielle R AU - Munters AR AD - Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden. FAU - Pospieszny, Łukasz AU - Pospieszny Ł AD - Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, UK. AD - Institute of Archaeology and Ethnology, Centre for Studies into Late Antiquity and Early Medieval Times, Polish Academy of Sciences, 61-612 Poznań, Poland. FAU - Tõrv, Mari AU - Tõrv M AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, 50090 Tartu, Estonia. FAU - Lindström, Jonathan AU - Lindström J AD - Graduate School of Contract Archaeology, Department of Archaeology, Linneaus University, 391 82 Kalmar, Sweden. FAU - Götherström, Anders AU - Götherström A AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden. FAU - Storå, Jan AU - Storå J AD - Osteoarchaeological Research Laboratory, Department of Archaeology, and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden. AD - Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, 2006 Auckland Park, South Africa. LA - eng SI - figshare/10.6084/m9.figshare.c.4682318 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20191009 PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Ancient) SB - IM MH - Baltic States MH - Base Sequence MH - *Culture MH - DNA, Ancient MH - Europe MH - Farmers MH - Genomics MH - *History, Ancient MH - *Human Migration MH - Humans MH - Poland MH - Population Dynamics MH - Scandinavian and Nordic Countries MH - Sweden MH - White People PMC - PMC6790770 OTO - NOTNLM OT - Battle Axe Culture OT - Corded Ware Culture OT - European Neolithic OT - ancient DNA OT - demography OT - migration COIS- We declare we have no competing interests. EDAT- 2019/10/09 06:00 MHDA- 2020/05/29 06:00 PMCR- 2019/10/09 CRDT- 2019/10/10 06:00 PHST- 2019/10/10 06:00 [entrez] PHST- 2019/10/09 06:00 [pubmed] PHST- 2020/05/29 06:00 [medline] PHST- 2019/10/09 00:00 [pmc-release] AID - rspb20191528 [pii] AID - 10.1098/rspb.2019.1528 [doi] PST - ppublish SO - Proc Biol Sci. 2019 Oct 9;286(1912):20191528. doi: 10.1098/rspb.2019.1528. Epub 2019 Oct 9. PMID- 31437436 OWN - NLM STAT- MEDLINE DCOM- 20191003 LR - 20191007 IS - 1090-2449 (Electronic) IS - 0014-4894 (Linking) VI - 205 DP - 2019 Oct TI - Are immunoenzymatic tests for intestinal protozoans reliable when used on archaeological material? PG - 107739 LID - S0014-4894(19)30159-6 [pii] LID - 10.1016/j.exppara.2019.107739 [doi] AB - Intestinal protozoans found in ancient human samples have been studied primarily by microscopy and immunodiagnostic assays. However, such methods are not suitable for the detection of zoonotic genotypes. The objectives of the present study were to utilize immunoenzimatic assays for coproantigen detection of Cryptosporidium sp., Giardia duodenalis, and Entamoeba histolytica/Entamoeba dispar in sixty ancient human and animal samples collected from 14 archaeological sites in South America, and to carry out a critical analysis of G. duodenalis according to results obtained from three diagnostic methodologies: microscopy, immunodiagnostic tests (immunoenzymatic and immunofluorescence), and molecular biology (PCR and sequencing). More than half (31/60) of the samples analyzed using immunoenzymatic tests were positive for at least one of the intestinal protozoans, with 46.6% (28/60) corresponding to G. duodenalis, 26.6% (16/60) to Cryptosporidium sp., and 5% (3/60) to E. histolytica/E. dispar. Cryptosporidium sp. and G. duodenalis coinfection was observed in 15% (9/60) of the samples, whereas all three protozoans were found in 5% (3/60) of samples. In the Northeast Region of Brazil, by immunoenzymatic tests there is evidence that G. duodenlais and Cryptosporidium sp. have infected humans and rodents for at least 7150 years. However, for G. duodenalis, the results from the three diagnostic tests were discordant. Specifically, despite the efficiency of the molecular biology assay in the experimental models, G. duodenalis DNA could not be amplified from the ancient samples. These results raise the following question: Are all ancient samples positive for coproantigen of G. duodenalis by immunoenzymatic tests truly positive? This scenario highlights the importance of further studies to evaluate the sensitivity and specificity of the immunoenzymatic method in the archaeological context. CI - Copyright © 2019 Elsevier Inc. All rights reserved. FAU - Leles, Daniela AU - Leles D AD - Laboratório de Biologia Molecular de Parasitos, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense. Rua Professor Hernani Melo, 101, São Domingos, Niterói-RJ, CEP, 21041-210, Brazil. Electronic address: dleles@id.uff.br. FAU - Frías, Liesbeth AU - Frías L AD - Escola Nacional de Saúde Pública Sérgio Arouca - Fundação Owaldo Cruz, Rua Leopoldo Bulhões, 1480, Manguinhos, Rio de Janeiro - RJ, CEP, 21041-210, Brazil. FAU - Araújo, Adauto AU - Araújo A AD - Escola Nacional de Saúde Pública Sérgio Arouca - Fundação Owaldo Cruz, Rua Leopoldo Bulhões, 1480, Manguinhos, Rio de Janeiro - RJ, CEP, 21041-210, Brazil. FAU - Brener, Beatriz AU - Brener B AD - Laboratório de Biologia Molecular de Parasitos, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense. Rua Professor Hernani Melo, 101, São Domingos, Niterói-RJ, CEP, 21041-210, Brazil. FAU - Sudré, Adriana AU - Sudré A AD - Laboratório de Biologia Molecular de Parasitos, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense. Rua Professor Hernani Melo, 101, São Domingos, Niterói-RJ, CEP, 21041-210, Brazil. FAU - Chame, Márcia AU - Chame M AD - Escola Nacional de Saúde Pública Sérgio Arouca - Fundação Owaldo Cruz, Rua Leopoldo Bulhões, 1480, Manguinhos, Rio de Janeiro - RJ, CEP, 21041-210, Brazil. FAU - Laurentino, Valmir AU - Laurentino V AD - Escola Nacional de Saúde Pública Sérgio Arouca - Fundação Owaldo Cruz, Rua Leopoldo Bulhões, 1480, Manguinhos, Rio de Janeiro - RJ, CEP, 21041-210, Brazil; Fundação Benedito Pereira Nunes - Faculdade de Medicina de Campos, Av. Alberto Torres, 206, Centro, Campos dos Goytacazes - RJ, CEP 28035-582, Brazil. LA - eng PT - Journal Article DEP - 20190819 PL - United States TA - Exp Parasitol JT - Experimental parasitology JID - 0370713 RN - 0 (Antigens, Protozoan) SB - IM MH - Animals MH - Antigens, Protozoan/analysis/genetics MH - Archaeology/*methods MH - Cryptosporidium/genetics/immunology/*isolation & purification MH - Entamoeba/genetics/immunology/*isolation & purification MH - Entamoeba histolytica/genetics/immunology/isolation & purification MH - Feces/*parasitology MH - Giardia lamblia/genetics/immunology/*isolation & purification MH - Humans MH - Immunoenzyme Techniques/*standards MH - Intestinal Diseases, Parasitic/parasitology MH - Rodentia MH - Sensitivity and Specificity MH - South America OTO - NOTNLM OT - Ancient DNA OT - Coprolite OT - Cryptosporidium sp. OT - Entamoeba histolytica/dispar OT - Giardia duodenalis OT - Paleoparasitology EDAT- 2019/08/23 06:00 MHDA- 2019/10/08 06:00 CRDT- 2019/08/23 06:00 PHST- 2019/04/04 00:00 [received] PHST- 2019/08/15 00:00 [revised] PHST- 2019/08/18 00:00 [accepted] PHST- 2019/08/23 06:00 [pubmed] PHST- 2019/10/08 06:00 [medline] PHST- 2019/08/23 06:00 [entrez] AID - S0014-4894(19)30159-6 [pii] AID - 10.1016/j.exppara.2019.107739 [doi] PST - ppublish SO - Exp Parasitol. 2019 Oct;205:107739. doi: 10.1016/j.exppara.2019.107739. Epub 2019 Aug 19. PMID- 31270812 OWN - NLM STAT- MEDLINE DCOM- 20200416 LR - 20240712 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 170 IP - 2 DP - 2019 Oct TI - Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier. PG - 232-245 LID - 10.1002/ajpa.23887 [doi] AB - OBJECTIVES: Ancient DNA (aDNA) and standard osteological analyses applied to 11 skeletons at a late 17th to early 18th century farmstead site in Delaware to investigate the biological and social factors of settlement and slavery in colonial America. MATERIALS AND METHODS: Osteological analysis and mitochondrial DNA (mtDNA) sequencing were conducted for all individuals and the resulting data contextualized with archaeological and documentary evidence. RESULTS: Individuals of European and African descent were spatially separated in this colonial cemetery. The skeletal remains exhibited differences in osteological features and maternal genetic ancestry. A specific mtDNA haplotype appeared in a subset of the European-descended individuals suggesting they were maternally related. Individuals of African descent were not maternally related, and instead showed a diversity of haplotypes affiliated with present-day Western, Central, and Eastern regions of Africa. DISCUSSION: Along with the bioarchaeological and documentary evidence, the aDNA findings contribute to our understanding of life on the colonial Delaware frontier. Evidence of maternal relatedness among European-descended individuals at the site demonstrates kin-based settlements in 17th century Delaware and provides preliminary identifications of individuals. The maternal genetic diversity of the individuals with African descent aligns with the routes of the trans-Atlantic slave trade but broadens our understanding of the ancestries of persons involved in it. Burial positioning, osteological pathology, and lack of maternal kinship among individuals of African descent provide tangible evidence for the emergence of racialized labor and society in Delaware during the late 17th century. CI - © 2019 Wiley Periodicals, Inc. FAU - Fleskes, Raquel E AU - Fleskes RE AUID- ORCID: 0000-0002-2875-6286 AD - Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania. FAU - Bruwelheide, Karin S AU - Bruwelheide KS AD - Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, D.C. FAU - West, Frankie L AU - West FL AD - Department of Anthropology, University of Tennessee, Knoxville, Tennessee. FAU - Owsley, Douglas W AU - Owsley DW AD - Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, D.C. FAU - Griffith, Daniel R AU - Griffith DR AD - Archaeological Society of Delaware, Inc., Dover, Delaware. FAU - Barca, Kathryn G AU - Barca KG AUID- ORCID: 0000-0001-6487-7926 AD - Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, D.C. FAU - Cabana, Graciela S AU - Cabana GS AUID- ORCID: 0000-0002-5399-1173 AD - Department of Anthropology, University of Tennessee, Knoxville, Tennessee. FAU - Schurr, Theodore G AU - Schurr TG AUID- ORCID: 0000-0001-9323-9237 AD - Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania. LA - eng GR - The University of Pennsylvania/International PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190704 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Archaeology MH - *Black People/ethnology/genetics/history MH - Cemeteries/history MH - Child, Preschool MH - Colonialism/*history MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/genetics MH - Delaware MH - Enslavement/*history MH - Female MH - History, 17th Century MH - History, 18th Century MH - Humans MH - Infant MH - Male MH - Middle Aged MH - *White People/ethnology/genetics/history MH - Black or African American OTO - NOTNLM OT - bioarchaeology OT - colonization OT - mitochondrial DNA OT - trans-Atlantic slavery EDAT- 2019/07/05 06:00 MHDA- 2020/04/17 06:00 CRDT- 2019/07/05 06:00 PHST- 2019/03/05 00:00 [received] PHST- 2019/06/07 00:00 [revised] PHST- 2019/06/13 00:00 [accepted] PHST- 2019/07/05 06:00 [pubmed] PHST- 2020/04/17 06:00 [medline] PHST- 2019/07/05 06:00 [entrez] AID - 10.1002/ajpa.23887 [doi] PST - ppublish SO - Am J Phys Anthropol. 2019 Oct;170(2):232-245. doi: 10.1002/ajpa.23887. Epub 2019 Jul 4. PMID- 31537848 OWN - NLM STAT- MEDLINE DCOM- 20201026 LR - 20221207 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 9 IP - 1 DP - 2019 Sep 19 TI - Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy. PG - 13581 LID - 10.1038/s41598-019-49901-8 [doi] LID - 13581 AB - Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians. FAU - Tamm, Erika AU - Tamm E AD - Institute of Genomics, University of Tartu, Tartu, Estonia. erika.tamm@gmail.com. FAU - Di Cristofaro, Julie AU - Di Cristofaro J AUID- ORCID: 0000-0001-7867-6455 AD - Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France. AD - Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France. FAU - Mazières, Stéphane AU - Mazières S AD - Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France. FAU - Pennarun, Erwan AU - Pennarun E AD - Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Kushniarevich, Alena AU - Kushniarevich A AD - Institute of Genomics, University of Tartu, Tartu, Estonia. AD - Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Belarus. FAU - Raveane, Alessandro AU - Raveane A AUID- ORCID: 0000-0002-8322-5461 AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy. FAU - Semino, Ornella AU - Semino O AD - Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy. FAU - Chiaroni, Jacques AU - Chiaroni J AD - Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France. AD - Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France. FAU - Pereira, Luisa AU - Pereira L AD - i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal. AD - Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), 4200-135, Porto, Portugal. FAU - Metspalu, Mait AU - Metspalu M AUID- ORCID: 0000-0003-3099-9161 AD - Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Montinaro, Francesco AU - Montinaro F AUID- ORCID: 0000-0002-4506-963X AD - Institute of Genomics, University of Tartu, Tartu, Estonia. francesco.montinaro@gmail.com. AD - Department of Zoology, University of Oxford, Oxford, UK. francesco.montinaro@gmail.com. LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190919 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM EIN - Sci Rep. 2019 Dec 6;9(1):18827. doi: 10.1038/s41598-019-55185-9. PMID: 31806867 MH - Africa, Northern MH - France/ethnology MH - Gene Frequency MH - Genetics, Population MH - Haplotypes MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Italy/ethnology MH - Phylogeny MH - Population Dynamics MH - Selection, Genetic MH - White People/ethnology/*genetics MH - Whole Genome Sequencing/*methods PMC - PMC6753063 COIS- The authors declare no competing interests. EDAT- 2019/09/21 06:00 MHDA- 2020/10/27 06:00 PMCR- 2019/09/19 CRDT- 2019/09/21 06:00 PHST- 2019/04/24 00:00 [received] PHST- 2019/08/31 00:00 [accepted] PHST- 2019/09/21 06:00 [entrez] PHST- 2019/09/21 06:00 [pubmed] PHST- 2020/10/27 06:00 [medline] PHST- 2019/09/19 00:00 [pmc-release] AID - 10.1038/s41598-019-49901-8 [pii] AID - 49901 [pii] AID - 10.1038/s41598-019-49901-8 [doi] PST - epublish SO - Sci Rep. 2019 Sep 19;9(1):13581. doi: 10.1038/s41598-019-49901-8. PMID- 31481615 OWN - NLM STAT- MEDLINE DCOM- 20200410 LR - 20220129 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 116 IP - 38 DP - 2019 Sep 17 TI - The genetic landscape of Scotland and the Isles. PG - 19064-19070 LID - 10.1073/pnas.1904761116 [doi] AB - Britain and Ireland are known to show population genetic structure; however, large swathes of Scotland, in particular, have yet to be described. Delineating the structure and ancestry of these populations will allow variant discovery efforts to focus efficiently on areas not represented in existing cohorts. Thus, we assembled genotype data for 2,554 individuals from across the entire archipelago with geographically restricted ancestry, and performed population structure analyses and comparisons to ancient DNA. Extensive geographic structuring is revealed, from broad scales such as a NE to SW divide in mainland Scotland, through to the finest scale observed to date: across 3 km in the Northern Isles. Many genetic boundaries are consistent with Dark Age kingdoms of Gaels, Picts, Britons, and Norse. Populations in the Hebrides, the Highlands, Argyll, Donegal, and the Isle of Man show characteristics of isolation. We document a pole of Norwegian ancestry in the north of the archipelago (reaching 23 to 28% in Shetland) which complements previously described poles of Germanic ancestry in the east, and "Celtic" to the west. This modern genetic structure suggests a northwestern British or Irish source population for the ancient Gaels that contributed to the founding of Iceland. As rarer variants, often with larger effect sizes, become the focus of complex trait genetics, more diverse rural cohorts may be required to optimize discoveries in British and Irish populations and their considerable global diaspora. CI - Copyright © 2019 the Author(s). Published by PNAS. FAU - Gilbert, Edmund AU - Gilbert E AD - School of Pharmacy and Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland. AD - FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland. FAU - O'Reilly, Seamus AU - O'Reilly S AD - Genealogical Society of Ireland, Dún Laoghaire, Co. Dublin A96 AD76, Ireland. FAU - Merrigan, Michael AU - Merrigan M AD - Genealogical Society of Ireland, Dún Laoghaire, Co. Dublin A96 AD76, Ireland. FAU - McGettigan, Darren AU - McGettigan D AD - Genealogical Society of Ireland, Dún Laoghaire, Co. Dublin A96 AD76, Ireland. FAU - Vitart, Veronique AU - Vitart V AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland. FAU - Joshi, Peter K AU - Joshi PK AUID- ORCID: 0000-0002-6361-5059 AD - Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland. FAU - Clark, David W AU - Clark DW AD - Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland. FAU - Campbell, Harry AU - Campbell H AD - Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland. FAU - Hayward, Caroline AU - Hayward C AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland. FAU - Ring, Susan M AU - Ring SM AUID- ORCID: 0000-0003-3103-9330 AD - Bristol Bioresource Laboratories, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, United Kingdom. AD - Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, United Kingdom. FAU - Golding, Jean AU - Golding J AUID- ORCID: 0000-0003-2826-3307 AD - Centre for Academic Child Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1NU, United Kingdom. FAU - Goodfellow, Stephanie AU - Goodfellow S AD - Private address, Isle of Man IM7 2EA, Isle of Man. FAU - Navarro, Pau AU - Navarro P AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland. FAU - Kerr, Shona M AU - Kerr SM AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland. FAU - Amador, Carmen AU - Amador C AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland. FAU - Campbell, Archie AU - Campbell A AUID- ORCID: 0000-0003-0198-5078 AD - Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland. FAU - Haley, Chris S AU - Haley CS AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland. AD - The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh EH25 9RG, Scotland. FAU - Porteous, David J AU - Porteous DJ AD - Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland. FAU - Cavalleri, Gianpiero L AU - Cavalleri GL AD - School of Pharmacy and Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland. AD - FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland. FAU - Wilson, James F AU - Wilson JF AD - Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland; jim.wilson@ed.ac.uk. AD - Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland. LA - eng GR - G0700704/MRC_/Medical Research Council/United Kingdom GR - ARC_/Arthritis Research UK/United Kingdom GR - WT_/Wellcome Trust/United Kingdom GR - CSO_/Chief Scientist Office/United Kingdom GR - MR/K026992/1/MRC_/Medical Research Council/United Kingdom GR - MC_PC_U127592696/MRC_/Medical Research Council/United Kingdom GR - MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190903 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/*analysis MH - Ethnicity/*genetics MH - *Genetic Variation MH - *Genetics, Population MH - *Genome, Human MH - Humans MH - Ireland MH - Islands MH - Scotland PMC - PMC6754546 OTO - NOTNLM OT - fine-scale structure OT - history OT - migration OT - population genetics COIS- The authors declare no conflict of interest. EDAT- 2019/09/05 06:00 MHDA- 2020/04/11 06:00 PMCR- 2019/09/03 CRDT- 2019/09/05 06:00 PHST- 2019/09/05 06:00 [pubmed] PHST- 2020/04/11 06:00 [medline] PHST- 2019/09/05 06:00 [entrez] PHST- 2019/09/03 00:00 [pmc-release] AID - 1904761116 [pii] AID - 201904761 [pii] AID - 10.1073/pnas.1904761116 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):19064-19070. doi: 10.1073/pnas.1904761116. Epub 2019 Sep 3. PMID- 31513651 OWN - NLM STAT- MEDLINE DCOM- 20200129 LR - 20231014 IS - 1553-7374 (Electronic) IS - 1553-7366 (Print) IS - 1553-7366 (Linking) VI - 15 IP - 9 DP - 2019 Sep TI - The molecular clock of Mycobacterium tuberculosis. PG - e1008067 LID - 10.1371/journal.ppat.1008067 [doi] LID - e1008067 AB - The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations. FAU - Menardo, Fabrizio AU - Menardo F AUID- ORCID: 0000-0002-7885-4482 AD - Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. AD - University of Basel, Basel, Switzerland. FAU - Duchêne, Sebastian AU - Duchêne S AUID- ORCID: 0000-0002-2863-0907 AD - Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia. FAU - Brites, Daniela AU - Brites D AUID- ORCID: 0000-0002-8090-2287 AD - Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. AD - University of Basel, Basel, Switzerland. FAU - Gagneux, Sebastien AU - Gagneux S AD - Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. AD - University of Basel, Basel, Switzerland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190912 PL - United States TA - PLoS Pathog JT - PLoS pathogens JID - 101238921 RN - 0 (DNA, Bacterial) SB - IM MH - Bayes Theorem MH - Biological Clocks/*genetics/physiology MH - DNA, Bacterial/genetics MH - Evolution, Molecular MH - Genome, Bacterial MH - Humans MH - Models, Biological MH - Molecular Epidemiology MH - Mycobacterium bovis/genetics/physiology MH - Mycobacterium tuberculosis/*genetics/pathogenicity/physiology MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Time Factors MH - Tuberculosis/epidemiology/microbiology PMC - PMC6759198 COIS- The authors have declared that no competing interests exist. EDAT- 2019/09/13 06:00 MHDA- 2020/01/30 06:00 PMCR- 2019/09/12 CRDT- 2019/09/13 06:00 PHST- 2019/04/24 00:00 [received] PHST- 2019/09/03 00:00 [accepted] PHST- 2019/09/24 00:00 [revised] PHST- 2019/09/13 06:00 [pubmed] PHST- 2020/01/30 06:00 [medline] PHST- 2019/09/13 06:00 [entrez] PHST- 2019/09/12 00:00 [pmc-release] AID - PPATHOGENS-D-19-00781 [pii] AID - 10.1371/journal.ppat.1008067 [doi] PST - epublish SO - PLoS Pathog. 2019 Sep 12;15(9):e1008067. doi: 10.1371/journal.ppat.1008067. eCollection 2019 Sep. PMID- 31480978 OWN - NLM STAT- MEDLINE DCOM- 20200603 LR - 20240720 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 286 IP - 1910 DP - 2019 Sep 11 TI - Early integration of pastoralism and millet cultivation in Bronze Age Eurasia. PG - 20191273 LID - 10.1098/rspb.2019.1273 [doi] LID - 20191273 AB - Mobile pastoralists are thought to have facilitated the first trans-Eurasian dispersals of domesticated plants during the Early Bronze Age (ca 2500-2300 BC). Problematically, the earliest seeds of wheat, barley and millet in Inner Asia were recovered from human mortuary contexts and do not inform on local cultivation or subsistence use, while contemporaneous evidence for the use and management of domesticated livestock in the region remains ambiguous. We analysed mitochondrial DNA and multi-stable isotopic ratios (δ(13)C, δ(15)N and δ(18)O) of faunal remains from key pastoralist sites in the Dzhungar Mountains of southeastern Kazakhstan. At ca 2700 BC, Near Eastern domesticated sheep and goat were present at the settlement of Dali, which were also winter foddered with the region's earliest cultivated millet spreading from its centre of domestication in northern China. In the following centuries, millet cultivation and caprine management became increasingly intertwined at the nearby site of Begash. Cattle, on the other hand, received low levels of millet fodder at the sites for millennia. By primarily examining livestock dietary intake, this study reveals that the initial transmission of millet across the mountains of Inner Asia coincided with a substantial connection between pastoralism and plant cultivation, suggesting that pastoralist livestock herding was integral for the westward dispersal of millet from farming societies in China. FAU - Hermes, Taylor R AU - Hermes TR AD - Graduate School 'Human Development in Landscapes', Kiel University, Leibniz Straße 3, 24118 Kiel, Germany. AD - Institute of Prehistoric and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Straße 2-6, 24118 Kiel, Germany. FAU - Frachetti, Michael D AU - Frachetti MD AD - Department of Anthropology, Washington University in St Louis, One Brookings Drive, St Louis 63130, USA. FAU - Doumani Dupuy, Paula N AU - Doumani Dupuy PN AD - Institute of Prehistoric and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Straße 2-6, 24118 Kiel, Germany. AD - School of Humanities and Social Sciences, Nazarbayev University, Kabanbay Batyr Avenue 53, Astana 010000, Kazakhstan. FAU - Mar'yashev, Alexei AU - Mar'yashev A AD - Margulan Institute of Archaeology, Dostyk Avenue 44, Almaty 480100, Kazakhstan. FAU - Nebel, Almut AU - Nebel A AD - Graduate School 'Human Development in Landscapes', Kiel University, Leibniz Straße 3, 24118 Kiel, Germany. AD - Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Rosalind-Franklin Straße 12, 24105, Kiel, Germany. FAU - Makarewicz, Cheryl A AU - Makarewicz CA AD - Graduate School 'Human Development in Landscapes', Kiel University, Leibniz Straße 3, 24118 Kiel, Germany. AD - Institute of Prehistoric and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Straße 2-6, 24118 Kiel, Germany. LA - eng SI - figshare/10.6084/m9.figshare.c.4614116 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20190904 PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 SB - IM MH - Agriculture/*history MH - Animals MH - Archaeology MH - Cattle MH - China MH - Crops, Agricultural/*history MH - Domestication MH - Goats MH - History, Ancient MH - Humans MH - Kazakhstan MH - Livestock MH - *Millets MH - Radiometric Dating MH - Sheep PMC - PMC6743000 OTO - NOTNLM OT - ancient DNA OT - isotope analysis OT - millet OT - pastoralism OT - steppe archaeology COIS- We declare we have no competing interests. EDAT- 2019/09/05 06:00 MHDA- 2020/06/04 06:00 PMCR- 2019/09/04 CRDT- 2019/09/05 06:00 PHST- 2019/09/05 06:00 [entrez] PHST- 2019/09/05 06:00 [pubmed] PHST- 2020/06/04 06:00 [medline] PHST- 2019/09/04 00:00 [pmc-release] AID - rspb20191273 [pii] AID - 10.1098/rspb.2019.1273 [doi] PST - ppublish SO - Proc Biol Sci. 2019 Sep 11;286(1910):20191273. doi: 10.1098/rspb.2019.1273. Epub 2019 Sep 4. PMID- 31283430 OWN - NLM STAT- MEDLINE DCOM- 20200710 LR - 20200710 IS - 1545-3251 (Electronic) IS - 0066-4227 (Linking) VI - 73 DP - 2019 Sep 8 TI - Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. PG - 639-666 LID - 10.1146/annurev-micro-090817-062436 [doi] AB - The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation. FAU - Bos, Kirsten I AU - Bos KI AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. FAU - Kühnert, Denise AU - Kühnert D AD - Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Herbig, Alexander AU - Herbig A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. FAU - Esquivel-Gomez, Luis Roger AU - Esquivel-Gomez LR AD - Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Andrades Valtueña, Aida AU - Andrades Valtueña A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. FAU - Barquera, Rodrigo AU - Barquera R AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. FAU - Giffin, Karen AU - Giffin K AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. FAU - Kumar Lankapalli, Aditya AU - Kumar Lankapalli A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. FAU - Nelson, Elizabeth A AU - Nelson EA AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. FAU - Sabin, Susanna AU - Sabin S AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. FAU - Spyrou, Maria A AU - Spyrou MA AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; email: bos@shh.mpg.de. AD - Faculty of Biological Sciences, Friedrich Schiller University, 07737 Jena, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20190705 PL - United States TA - Annu Rev Microbiol JT - Annual review of microbiology JID - 0372370 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - Biological Evolution MH - Communicable Diseases/*history MH - DNA, Ancient/*analysis MH - DNA, Bacterial MH - Fossils/*microbiology/parasitology MH - Genome, Bacterial MH - Genomics/methods MH - Helicobacter pylori/genetics MH - High-Throughput Nucleotide Sequencing/methods MH - History, Ancient MH - Humans MH - Mycobacterium leprae/genetics MH - Mycobacterium tuberculosis/genetics MH - Paleontology/methods MH - Paleopathology/*methods MH - Phylogeny MH - Yersinia pestis/genetics OTO - NOTNLM OT - ancient DNA OT - disease emergence OT - molecular dating OT - paleopathology OT - pathogen evolution EDAT- 2019/07/10 06:00 MHDA- 2020/07/11 06:00 CRDT- 2019/07/09 06:00 PHST- 2019/07/10 06:00 [pubmed] PHST- 2020/07/11 06:00 [medline] PHST- 2019/07/09 06:00 [entrez] AID - 10.1146/annurev-micro-090817-062436 [doi] PST - ppublish SO - Annu Rev Microbiol. 2019 Sep 8;73:639-666. doi: 10.1146/annurev-micro-090817-062436. Epub 2019 Jul 5. PMID- 31517046 OWN - NLM STAT- MEDLINE DCOM- 20200514 LR - 20200514 IS - 2375-2548 (Electronic) IS - 2375-2548 (Linking) VI - 5 IP - 9 DP - 2019 Sep TI - Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals. PG - eaaw3950 LID - 10.1126/sciadv.aaw3950 [doi] LID - eaaw3950 AB - A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans. FAU - Bennett, E Andrew AU - Bennett EA AUID- ORCID: 0000-0003-3827-0711 AD - Institut Jacques Monod, CNRS, University Paris Diderot, 75013 Paris, France. FAU - Crevecoeur, Isabelle AU - Crevecoeur I AD - UMR 5199 PACEA, Université de Bordeaux, 33615 Pessac, France. FAU - Viola, Bence AU - Viola B AUID- ORCID: 0000-0001-8052-707X AD - Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada. AD - Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk RU-630090, Russia. FAU - Derevianko, Anatoly P AU - Derevianko AP AUID- ORCID: 0000-0003-1156-8331 AD - Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk RU-630090, Russia. AD - Altai State University, Barnaul RU-656049, Russia. FAU - Shunkov, Michael V AU - Shunkov MV AUID- ORCID: 0000-0003-1388-2308 AD - Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk RU-630090, Russia. AD - Novosibirsk National Research State University, Novosibirsk RU-630090, Russia. FAU - Grange, Thierry AU - Grange T AUID- ORCID: 0000-0001-8700-3092 AD - Institut Jacques Monod, CNRS, University Paris Diderot, 75013 Paris, France. FAU - Maureille, Bruno AU - Maureille B AUID- ORCID: 0000-0002-7616-0073 AD - UMR 5199 PACEA, Université de Bordeaux, 33615 Pessac, France. FAU - Geigl, Eva-Maria AU - Geigl EM AUID- ORCID: 0000-0001-6376-2094 AD - Institut Jacques Monod, CNRS, University Paris Diderot, 75013 Paris, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190904 PL - United States TA - Sci Adv JT - Science advances JID - 101653440 SB - IM CIN - Nature. 2019 Sep;573(7773):175-176. doi: 10.1038/d41586-019-02647-9. PMID: 31506618 MH - Animals MH - Finger Phalanges/*anatomy & histology MH - *Genome, Human MH - Humans MH - Molar/*anatomy & histology MH - *Neanderthals/anatomy & histology/genetics MH - Species Specificity PMC - PMC6726440 EDAT- 2019/09/14 06:00 MHDA- 2020/05/15 06:00 PMCR- 2019/09/04 CRDT- 2019/09/14 06:00 PHST- 2018/12/17 00:00 [received] PHST- 2019/07/11 00:00 [accepted] PHST- 2019/09/14 06:00 [entrez] PHST- 2019/09/14 06:00 [pubmed] PHST- 2020/05/15 06:00 [medline] PHST- 2019/09/04 00:00 [pmc-release] AID - aaw3950 [pii] AID - 10.1126/sciadv.aaw3950 [doi] PST - epublish SO - Sci Adv. 2019 Sep 4;5(9):eaaw3950. doi: 10.1126/sciadv.aaw3950. eCollection 2019 Sep. PMID- 31328768 OWN - NLM STAT- MEDLINE DCOM- 20200316 LR - 20200316 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 11 IP - 9 DP - 2019 Sep 1 TI - Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry. PG - 2593-2604 LID - 10.1093/gbe/evz161 [doi] AB - After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population. CI - © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Mas-Sandoval, Alex AU - Mas-Sandoval A AD - Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil. AD - Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain. FAU - Arauna, Lara R AU - Arauna LR AD - Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain. FAU - Gouveia, Mateus H AU - Gouveia MH AD - Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. AD - Center for Research on Genomics and Global Health, National Institutes of Health, Bethesda, Maryland. FAU - Barreto, Mauricio L AU - Barreto ML AD - Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil. AD - Center for Data and Knowledge Integration for Health, Institute Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil. FAU - Horta, Bernardo L AU - Horta BL AD - Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Rio Grande do Sul, Brazil. FAU - Lima-Costa, Maria Fernanda AU - Lima-Costa MF AD - Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil. FAU - Pereira, Alexandre C AU - Pereira AC AD - Instituto do Coração, Universidade de São Paulo, São Paulo, Brazil. FAU - Salzano, Francisco M AU - Salzano FM AD - Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil. FAU - Hünemeier, Tábita AU - Hünemeier T AD - Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil. FAU - Tarazona-Santos, Eduardo AU - Tarazona-Santos E AD - Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. FAU - Bortolini, Maria Cátira AU - Bortolini MC AD - Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil. FAU - Comas, David AU - Comas D AD - Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 SB - IM MH - Brazil MH - Genetic Variation MH - Genome, Human MH - Geography MH - Haplotypes MH - Humans MH - Indians, South American/*genetics MH - Population Density PMC - PMC6756188 OTO - NOTNLM OT - Brazil OT - Native American groups OT - human genome diversity EDAT- 2019/07/23 06:00 MHDA- 2020/03/17 06:00 PMCR- 2019/07/22 CRDT- 2019/07/23 06:00 PHST- 2019/07/17 00:00 [accepted] PHST- 2019/07/23 06:00 [pubmed] PHST- 2020/03/17 06:00 [medline] PHST- 2019/07/23 06:00 [entrez] PHST- 2019/07/22 00:00 [pmc-release] AID - 5536765 [pii] AID - evz161 [pii] AID - 10.1093/gbe/evz161 [doi] PST - ppublish SO - Genome Biol Evol. 2019 Sep 1;11(9):2593-2604. doi: 10.1093/gbe/evz161. PMID- 31216503 OWN - NLM STAT- MEDLINE DCOM- 20191219 LR - 20191219 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 42 DP - 2019 Sep TI - SD quants-Sensitive detection tetraplex-system for nuclear and mitochondrial DNA quantification and degradation inference. PG - 39-44 LID - S1872-4973(19)30178-4 [pii] LID - 10.1016/j.fsigen.2019.06.004 [doi] AB - Measuring the quantity of DNA present in a forensic sample is relevant in a number of ways. First, it informs the analyst about the general DNA content to adjust the volume of DNA extract used for the genotyping assay to the optimal conditions (when possible). Second, quantification values can serve as plausibility checks for the performance of the DNA extraction method used as extraction positive and negative controls demand expected values. Third and relevant to highly compromised specimens, DNA quantification can inform about the degradation state of the DNA extracted from the unknown biological sample and aid the choice of downstream genotyping assays. While there are different, commercial products for the quantification of nuclear DNA available, commercial mitochondrial DNA (mtDNA) quantification systems are rare. Even more so, the simultaneous quantification of nuclear and mtDNA that is of relevance in highly degraded forensic specimens has rarely been described. We present here a novel real-time qPCR based tetraplex system termed SD quants that targets two different-sized mtDNA and a nuclear DNA region and includes an internal positive control to monitor potential inhibition. SD quants was compared to other existing quantification systems and subjected to analysis of severely degraded DNA present in ancient DNA and aged forensic specimens. This study complies with the MIQE (Bustin et al., 2009) guidelines (when applicable). CI - Copyright © 2019 Elsevier B.V. All rights reserved. FAU - Xavier, Catarina AU - Xavier C AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria. Electronic address: catarina.gomes@i-med.ac.at. FAU - Eduardoff, Mayra AU - Eduardoff M AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria. FAU - Strobl, Christina AU - Strobl C AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria. FAU - Parson, Walther AU - Parson W AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA. LA - eng PT - Journal Article DEP - 20190610 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Bone and Bones/chemistry MH - Cell Nucleus/*genetics MH - DNA/*analysis MH - *DNA Degradation, Necrotic MH - *DNA Fingerprinting MH - DNA, Mitochondrial/*analysis MH - Hair/chemistry MH - Humans MH - Real-Time Polymerase Chain Reaction/*methods MH - Tooth/chemistry OTO - NOTNLM OT - DNA degradation inference OT - Internal positive control OT - Nuclear and mitochondrial DNA quantification OT - Real time quantitative PCR EDAT- 2019/06/20 06:00 MHDA- 2019/12/20 06:00 CRDT- 2019/06/20 06:00 PHST- 2019/04/15 00:00 [received] PHST- 2019/06/06 00:00 [revised] PHST- 2019/06/07 00:00 [accepted] PHST- 2019/06/20 06:00 [pubmed] PHST- 2019/12/20 06:00 [medline] PHST- 2019/06/20 06:00 [entrez] AID - S1872-4973(19)30178-4 [pii] AID - 10.1016/j.fsigen.2019.06.004 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2019 Sep;42:39-44. doi: 10.1016/j.fsigen.2019.06.004. Epub 2019 Jun 10. PMID- 31433816 OWN - NLM STAT- MEDLINE DCOM- 20200228 LR - 20200228 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 14 IP - 8 DP - 2019 TI - Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia. PG - e0216366 LID - 10.1371/journal.pone.0216366 [doi] LID - e0216366 AB - Three individuals dating to the Great Migration Period (5th century CE) were discovered in a pit at the Hermanov vinograd site in Osijek, Croatia. We were inspired to study these individuals based on their unusual burial context as well as the identification of two different types of artificial cranial deformation in two of the individuals. We combine bioarchaeological analysis with radiographic imaging, stable isotopes analysis, and ancient DNA to analyze their dietary patterns, molecular sex, and genetic affinities in the context of the archaeological data and their bioarchaeological attributes. While all three individuals were adolescent males with skeletal evidence of severe malnutrition and similar diets, the most striking observation is that they had major differences in their genetic ancestry. Results of the genetic analyses of the nuclear ancient DNA data for these individuals indicate that the individual without artificial cranial deformation shows broadly West Eurasian associated-ancestry, the individual with tabular oblique-type has East Asian ancestry and the third individual with circular erect-type has Near Eastern associated-ancestry. Based on these results, we speculate that artificial cranial deformation type may have been a visual indicator membership in a specific cultural group, and that these groups were interacting intimately on the Pannonian Plain during the Migration Period. FAU - Fernandes, Daniel AU - Fernandes D AUID- ORCID: 0000-0002-7434-6552 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - School of Archaeology, University College Dublin, Dublin, Ireland. AD - CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. FAU - Sirak, Kendra AU - Sirak K AD - Department of Genetics, Harvard Medical School, Boston, MA, United States of America. FAU - Cheronet, Olivia AU - Cheronet O AUID- ORCID: 0000-0001-6760-1204 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - School of Archaeology, University College Dublin, Dublin, Ireland. FAU - Howcroft, Rachel AU - Howcroft R AD - School of Archaeology, University College Dublin, Dublin, Ireland. FAU - Čavka, Mislav AU - Čavka M AD - Department of Diagnostic and Interventional Radiology, University Hospital Center Zagreb, Zagreb, Croatia. FAU - Los, Dženi AU - Los D AD - Kaducej Ltd., Split, Croatia. FAU - Burmaz, Josip AU - Burmaz J AD - Kaducej Ltd., Split, Croatia. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - School of Archaeology, University College Dublin, Dublin, Ireland. FAU - Novak, Mario AU - Novak M AUID- ORCID: 0000-0002-4567-8742 AD - School of Archaeology, University College Dublin, Dublin, Ireland. AD - Institute for Anthropological Research, Zagreb, Croatia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190821 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - Adolescent MH - *Archaeology MH - Croatia MH - *Genetic Variation MH - *Human Migration MH - Humans MH - Male MH - Skull/*abnormalities/diagnostic imaging MH - Tomography, X-Ray Computed PMC - PMC6703674 COIS- The authors have declared that no competing interests exist. Two of the co-authors (Dženi Los and Josip Burmaz) are employed by a commercial company Kaducej Ltd. This commercial affiliation does not alter our adherence to PLOS ONE policies on sharing data and materials. EDAT- 2019/08/23 06:00 MHDA- 2020/02/29 06:00 PMCR- 2019/08/21 CRDT- 2019/08/22 06:00 PHST- 2019/01/11 00:00 [received] PHST- 2019/07/16 00:00 [accepted] PHST- 2019/08/22 06:00 [entrez] PHST- 2019/08/23 06:00 [pubmed] PHST- 2020/02/29 06:00 [medline] PHST- 2019/08/21 00:00 [pmc-release] AID - PONE-D-19-00982 [pii] AID - 10.1371/journal.pone.0216366 [doi] PST - epublish SO - PLoS One. 2019 Aug 21;14(8):e0216366. doi: 10.1371/journal.pone.0216366. eCollection 2019. PMID- 31431628 OWN - NLM STAT- MEDLINE DCOM- 20191216 LR - 20211204 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 10 IP - 1 DP - 2019 Aug 20 TI - Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India. PG - 3670 LID - 10.1038/s41467-019-11357-9 [doi] LID - 3670 AB - Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups. FAU - Harney, Éadaoin AU - Harney É AD - Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - Nayak, Ayushi AU - Nayak A AD - Department of Archaeology, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of Harvard and MIT, Cambridge, MA, 02142 USA, USA. AD - Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. FAU - Joglekar, Pramod AU - Joglekar P AD - Deccan College, Pune, 411006, India. FAU - Mushrif-Tripathy, Veena AU - Mushrif-Tripathy V AUID- ORCID: 0000-0002-4749-1316 AD - Deccan College, Pune, 411006, India. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, 02142 USA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - Sedig, Jakob AU - Sedig J AUID- ORCID: 0000-0001-6642-7734 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - Adamski, Nicole AU - Adamski N AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. FAU - Bernardos, Rebecca AU - Bernardos R AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AUID- ORCID: 0000-0001-5350-1608 AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. FAU - Culleton, Brendan J AU - Culleton BJ AD - Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, 16802, USA. AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. FAU - Harper, Thomas K AU - Harper TK AD - Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, D-07745, Jena, Germany. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. FAU - Zhang, Zhao AU - Zhang Z AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - Harashawaradhana AU - Harashawaradhana AD - Anthropological Survey of India, North West Regional Centre, Dehradun, 248195, India. FAU - Bartwal, Maanwendra Singh AU - Bartwal MS AD - Anthropological Survey of India, North West Regional Centre, Dehradun, 248195, India. FAU - Kumar, Sachin AU - Kumar S AD - CSIR Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India. AD - Birbal Sahni Institute of Palaeosciences, Lucknow, Uttar Pradesh, 226007, India. FAU - Diyundi, Subhash Chandra AU - Diyundi SC AUID- ORCID: 0000-0001-9172-5944 AD - Gautam Budh Health Care Foundation, Noida, Uttar Pradesh, 201301, India. FAU - Roberts, Patrick AU - Roberts P AUID- ORCID: 0000-0002-4403-7548 AD - Department of Archaeology, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany. FAU - Boivin, Nicole AU - Boivin N AD - Department of Archaeology, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA. FAU - Thangaraj, Kumarasamy AU - Thangaraj K AD - CSIR Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India. FAU - Reich, David AU - Reich D AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA. reich@genetics.med.harvard.edu. AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu. AD - Broad Institute of Harvard and MIT, Cambridge, MA, 02142 USA, USA. reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. reich@genetics.med.harvard.edu. FAU - Rai, Niraj AU - Rai N AD - CSIR Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India. AD - Birbal Sahni Institute of Palaeosciences, Lucknow, Uttar Pradesh, 226007, India. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20190820 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 9007-49-2 (DNA) SB - IM MH - Body Remains/*cytology MH - DNA/*genetics MH - Diet MH - *Fossils MH - Human Migration MH - Humans MH - India MH - Mediterranean Region MH - Polymorphism, Single Nucleotide/genetics MH - Racial Groups/*genetics MH - Radiometric Dating PMC - PMC6702210 COIS- The authors declare no competing interests. EDAT- 2019/08/23 06:00 MHDA- 2019/12/18 06:00 PMCR- 2019/08/20 CRDT- 2019/08/22 06:00 PHST- 2019/04/18 00:00 [received] PHST- 2019/06/26 00:00 [accepted] PHST- 2019/08/22 06:00 [entrez] PHST- 2019/08/23 06:00 [pubmed] PHST- 2019/12/18 06:00 [medline] PHST- 2019/08/20 00:00 [pmc-release] AID - 10.1038/s41467-019-11357-9 [pii] AID - 11357 [pii] AID - 10.1038/s41467-019-11357-9 [doi] PST - epublish SO - Nat Commun. 2019 Aug 20;10(1):3670. doi: 10.1038/s41467-019-11357-9. PMID- 31353181 OWN - NLM STAT- MEDLINE DCOM- 20200720 LR - 20221207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 29 IP - 15 DP - 2019 Aug 5 TI - Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan. PG - 2526-2532.e4 LID - S0960-9822(19)30771-7 [pii] LID - 10.1016/j.cub.2019.06.044 [doi] AB - Recent studies of early Bronze Age human genomes revealed a massive population expansion by individuals-related to the Yamnaya culture, from the Pontic Caspian steppe into Western and Eastern Eurasia, likely accompanied by the spread of Indo-European languages [1-5]. The south eastern extent of this migration is currently not known. Modern-day human populations from the Xinjiang region in northwestern China show a complex population history, with genetic links to both Eastern and Western Eurasia [6-10]. However, due to the lack of ancient genomic data, it remains unclear which source populations contributed to the Xinjiang population and what was the timing and the number of admixture events. Here, we report the first genome-wide data of 10 ancient individuals from northeastern Xinjiang. They are dated to around 2,200 years ago and were found at the Iron Age Shirenzigou site. We find them to be already genetically admixed between Eastern and Western Eurasians. We also find that the majority of the East Eurasian ancestry in the Shirenzigou individuals is-related to northeastern Asian populations, while the West Eurasian ancestry is best presented by ∼20% to 80% Yamnaya-like ancestry. Our data thus suggest a Western Eurasian steppe origin for at least part of the ancient Xinjiang population. Our findings furthermore support a Yamnaya-related origin for the now extinct Tocharian languages in the Tarim Basin, in southern Xinjiang. CI - Copyright © 2019 Elsevier Ltd. All rights reserved. FAU - Ning, Chao AU - Ning C AD - School of Life Sciences, Jilin University, Changchun 130012, China; Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Wang, Chuan-Chao AU - Wang CC AD - Department of Anthropology & Ethnology, Institute of Anthropology, Xiamen University, Xiamen 361005, China; Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Gao, Shizhu AU - Gao S AD - College of Pharmacia Sciences, Jilin University, Changchun 130021, China. FAU - Yang, Yang AU - Yang Y AD - College of Pharmacia Sciences, Jilin University, Changchun 130021, China. FAU - Zhang, Xue AU - Zhang X AD - College of Pharmacia Sciences, Jilin University, Changchun 130021, China. FAU - Wu, Xiyan AU - Wu X AD - School of Life Sciences, Jilin University, Changchun 130012, China. FAU - Zhang, Fan AU - Zhang F AD - School of Life Sciences, Jilin University, Changchun 130012, China. FAU - Nie, Zhongzhi AU - Nie Z AD - Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, China. FAU - Tang, Yunpeng AU - Tang Y AD - School of Cultural Heritage, Northwest University, Xi'an 710069, China. FAU - Robbeets, Martine AU - Robbeets M AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Ma, Jian AU - Ma J AD - School of Cultural Heritage, Northwest University, Xi'an 710069, China. Electronic address: eurasiansteppes@126.com. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany. Electronic address: krause@shh.mpg.de. FAU - Cui, Yinqiu AU - Cui Y AD - School of Life Sciences, Jilin University, Changchun 130012, China; Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, China; Key Laboratory for Evolution of Past Life and Environment in Northeast Asia (Jilin University), Ministry of Education, Changchun 130021, China. Electronic address: cuiyq@jlu.edu.cn. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190725 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Asian People/genetics MH - China MH - DNA, Ancient/*analysis MH - *Genome, Human MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Language MH - White People/genetics OTO - NOTNLM OT - Indo-European language OT - Iron Age OT - Northwest China OT - Tarim Basin OT - ancient genome EDAT- 2019/07/30 06:00 MHDA- 2020/07/21 06:00 CRDT- 2019/07/30 06:00 PHST- 2019/03/03 00:00 [received] PHST- 2019/04/08 00:00 [revised] PHST- 2019/06/13 00:00 [accepted] PHST- 2019/07/30 06:00 [pubmed] PHST- 2020/07/21 06:00 [medline] PHST- 2019/07/30 06:00 [entrez] AID - S0960-9822(19)30771-7 [pii] AID - 10.1016/j.cub.2019.06.044 [doi] PST - ppublish SO - Curr Biol. 2019 Aug 5;29(15):2526-2532.e4. doi: 10.1016/j.cub.2019.06.044. Epub 2019 Jul 25. PMID- 31455916 OWN - NLM STAT- MEDLINE DCOM- 20191231 LR - 20220531 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 572 IP - 7771 DP - 2019 Aug TI - 'Paralysed by anxiety': researchers speak about life in troubled ancient-DNA lab. PG - 571-572 LID - 10.1038/d41586-019-02540-5 [doi] FAU - Lewis, Dyani AU - Lewis D LA - eng PT - Comment PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM CON - Nat Genet. 2013 Apr;45(4):450-5, 455e1. doi: 10.1038/ng.2536. PMID: 23416520 MH - DNA, Ancient MH - *Dental Plaque MH - *Diet MH - Humans MH - *Microbiota MH - Mouth/microbiology OTO - NOTNLM OT - Culture OT - Lab life EDAT- 2019/08/29 06:00 MHDA- 2020/01/01 06:00 CRDT- 2019/08/29 06:00 PHST- 2019/08/29 06:00 [entrez] PHST- 2019/08/29 06:00 [pubmed] PHST- 2020/01/01 06:00 [medline] AID - 10.1038/d41586-019-02540-5 [pii] AID - 10.1038/d41586-019-02540-5 [doi] PST - ppublish SO - Nature. 2019 Aug;572(7771):571-572. doi: 10.1038/d41586-019-02540-5. PMID- 31310584 OWN - NLM STAT- MEDLINE DCOM- 20200410 LR - 20210405 IS - 1937-2345 (Electronic) IS - 0022-3395 (Linking) VI - 105 IP - 4 DP - 2019 Aug TI - Genetic Analysis of Small-Subunit Ribosomal RNA, Internal Transcribed Spacer 2, and ATP Synthase Subunit 8 of Trichuris trichiura Ancient DNA Retrieved from the 15th to 18th Century Joseon Dynasty Mummies' Coprolites from Korea. PG - 539-545 AB - Although parasitic infection by Trichuris trichiura is a very common intestinal helminthic disease worldwide, there is still insufficient information on the genetic characteristics of ancient T. trichiura in different spatiotemporal perspectives. Utilizing coprolite specimens obtained from 15th-18th century mummies dating to the Joseon Dynasty, we analyzed small-subunit ribosomal RNA, internal transcribed spacer 2, and ATP synthase subunit 8 of T. trichiura ancient DNA (aDNA). In BLAST and phylogenetic analyses, the T. trichiura aDNA sequences of this study belong to a separate cluster that is evidently distinct from the other genus Trichuris spp. reported in GenBank. This report characterizes T. trichiura aDNA of pre-20th century East Asia, and in so doing, it also proves the potential of aDNA analysis for differential diagnosis of T. trichiura in cases where ancient parasite eggs are morphologically indeterminate for species identification. FAU - Hong, Jong Ha AU - Hong JH AD - 1   Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul 03080, South Korea. FAU - Seo, Min AU - Seo M AD - 2   Department of Parasitology, Dankook University College of Medicine, Cheonan 31116, South Korea. FAU - Oh, Chang Seok AU - Oh CS AD - 1   Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul 03080, South Korea. AD - 3   Institute of Forensic Science, Seoul National University College of Medicine, Seoul 03080, South Korea. FAU - Shin, Dong Hoon AU - Shin DH AD - 1   Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul 03080, South Korea. AD - 3   Institute of Forensic Science, Seoul National University College of Medicine, Seoul 03080, South Korea. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Parasitol JT - The Journal of parasitology JID - 7803124 RN - 0 (DNA, Helminth) RN - 0 (RNA, Ribosomal) RN - EC 3.6.3.- (MT-ATP8 protein, human) RN - EC 3.6.3.- (Mitochondrial Proton-Translocating ATPases) SB - IM MH - Animals MH - DNA, Helminth/analysis/genetics/history MH - Feces/parasitology MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - Humans MH - Korea MH - Mitochondrial Proton-Translocating ATPases/analysis/genetics/history MH - Mummies/*history MH - Phylogeny MH - RNA, Ribosomal/genetics/history MH - Trichuriasis/*history MH - Trichuris/classification/genetics/*isolation & purification OTO - NOTNLM OT - Ancient Parasite OT - Ancient DNA OT - Mummy Feces OT - South Korea EDAT- 2019/07/17 06:00 MHDA- 2020/04/11 06:00 CRDT- 2019/07/17 06:00 PHST- 2019/07/17 06:00 [entrez] PHST- 2019/07/17 06:00 [pubmed] PHST- 2020/04/11 06:00 [medline] AID - 10.1645/19-31 [pii] PST - ppublish SO - J Parasitol. 2019 Aug;105(4):539-545. PMID- 31256878 OWN - NLM STAT- MEDLINE DCOM- 20200316 LR - 20240719 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 105 IP - 2 DP - 2019 Aug 1 TI - Inference of Population Structure from Time-Series Genotype Data. PG - 317-333 LID - S0002-9297(19)30227-7 [pii] LID - 10.1016/j.ajhg.2019.06.002 [doi] AB - Sequencing ancient DNA can offer direct probing of population history. Yet, such data are commonly analyzed with standard tools that assume DNA samples are all contemporary. We present DyStruct, a model and inference algorithm for inferring shared ancestry from temporally sampled genotype data. DyStruct explicitly incorporates temporal dynamics by modeling individuals as mixtures of unobserved populations whose allele frequencies drift over time. We develop an efficient inference algorithm for our model using stochastic variational inference. On simulated data, we show that DyStruct outperforms the current state of the art when individuals are sampled over time. Using a dataset of 296 modern and 80 ancient samples, we demonstrate DyStruct is able to capture a well-supported admixture event of steppe ancestry into modern Europe. We further apply DyStruct to a genome-wide dataset of 2,067 modern and 262 ancient samples used to study the origin of farming in the Near East. We show that DyStruct provides new insight into population history when compared with alternate approaches, within feasible run time. CI - Copyright © 2019 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. FAU - Joseph, Tyler A AU - Joseph TA AD - Department of Computer Science, Columbia University, New York, NY 10027, USA. Electronic address: tjoseph@cs.columbia.edu. FAU - Pe'er, Itsik AU - Pe'er I AD - Department of Computer Science, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10027, USA; Data Science Institute, Columbia University, New York, NY 10027, USA. Electronic address: itsik@cs.columbia.edu. LA - eng GR - U01 CA217858/CA/NCI NIH HHS/United States GR - U54 CA209997/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20190627 PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 SB - IM MH - *Algorithms MH - Europe MH - Gene Frequency MH - Genetic Predisposition to Disease MH - *Genetic Variation MH - *Genetics, Population MH - Genome-Wide Association Study MH - Genotype MH - Humans MH - Middle East MH - *Models, Genetic MH - *Models, Statistical MH - Population Groups/*genetics MH - Time Factors PMC - PMC6698887 OTO - NOTNLM OT - ancient DNA OT - population structure OT - time-series OT - variational inference COIS- The authors declare no competing interests. EDAT- 2019/07/02 06:00 MHDA- 2020/03/17 06:00 PMCR- 2020/02/01 CRDT- 2019/07/02 06:00 PHST- 2019/01/22 00:00 [received] PHST- 2019/06/04 00:00 [accepted] PHST- 2019/07/02 06:00 [pubmed] PHST- 2020/03/17 06:00 [medline] PHST- 2019/07/02 06:00 [entrez] PHST- 2020/02/01 00:00 [pmc-release] AID - S0002-9297(19)30227-7 [pii] AID - 10.1016/j.ajhg.2019.06.002 [doi] PST - ppublish SO - Am J Hum Genet. 2019 Aug 1;105(2):317-333. doi: 10.1016/j.ajhg.2019.06.002. Epub 2019 Jun 27. PMID- 31092597 OWN - NLM STAT- MEDLINE DCOM- 20200722 LR - 20210109 IS - 1098-660X (Electronic) IS - 0095-1137 (Print) IS - 0095-1137 (Linking) VI - 57 IP - 8 DP - 2019 Aug TI - Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes. LID - 10.1128/JCM.00100-19 [doi] LID - e00100-19 AB - Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens. CI - Copyright © 2019 American Society for Microbiology. FAU - Bennett, Rebecca J AU - Bennett RJ AD - Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom. FAU - Baker, Kate S AU - Baker KS AD - Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom kate.baker@liverpool.ac.uk. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom GR - 106690/A/14/Z/WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20190726 PL - United States TA - J Clin Microbiol JT - Journal of clinical microbiology JID - 7505564 RN - 0 (Anti-Bacterial Agents) RN - 0 (DNA, Ancient) SB - IM MH - Anti-Bacterial Agents/pharmacology MH - Bacteria/drug effects/*genetics/pathogenicity MH - DNA, Ancient/*analysis MH - Drug Resistance, Multiple, Bacterial/genetics MH - Evolution, Molecular MH - Genetic Variation MH - *Genome, Bacterial MH - Humans MH - Mycobacterium leprae/genetics/pathogenicity MH - Mycobacterium tuberculosis/genetics/pathogenicity MH - Phylogeny MH - *Sequence Analysis, DNA MH - Yersinia pestis/genetics/pathogenicity PMC - PMC6663899 OTO - NOTNLM OT - Murray Collection OT - ancient DNA OT - historical isolates OT - whole-genome sequencing EDAT- 2019/05/17 06:00 MHDA- 2020/07/23 06:00 PMCR- 2020/01/26 CRDT- 2019/05/17 06:00 PHST- 2019/05/17 06:00 [pubmed] PHST- 2020/07/23 06:00 [medline] PHST- 2019/05/17 06:00 [entrez] PHST- 2020/01/26 00:00 [pmc-release] AID - JCM.00100-19 [pii] AID - 00100-19 [pii] AID - 10.1128/JCM.00100-19 [doi] PST - epublish SO - J Clin Microbiol. 2019 Jul 26;57(8):e00100-19. doi: 10.1128/JCM.00100-19. Print 2019 Aug. PMID- 30952160 OWN - NLM STAT- MEDLINE DCOM- 20200203 LR - 20200309 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 36 IP - 8 DP - 2019 Aug 1 TI - Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations. PG - 1628-1642 LID - 10.1093/molbev/msz037 [doi] AB - Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high-quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations and showed our approach to be robust via coalescent simulations. Our f3 and f4 statistics-based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex interpopulation relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively. CI - © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Yelmen, Burak AU - Yelmen B AD - Institute of Genomics, University of Tartu, Tartu, Estonia. AD - Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. FAU - Mondal, Mayukh AU - Mondal M AD - Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Marnetto, Davide AU - Marnetto D AD - Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Pathak, Ajai K AU - Pathak AK AD - Institute of Genomics, University of Tartu, Tartu, Estonia. AD - Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. FAU - Montinaro, Francesco AU - Montinaro F AD - Institute of Genomics, University of Tartu, Tartu, Estonia. AD - Department of Zoology, University of Oxford, Oxford, United Kingdom. FAU - Gallego Romero, Irene AU - Gallego Romero I AD - Melbourne Integrative Genomics and School of BioSciences, University of Melbourne, Parkville, Australia. FAU - Kivisild, Toomas AU - Kivisild T AD - Institute of Genomics, University of Tartu, Tartu, Estonia. AD - Department of Human Genetics, KU Leuven, Leuven, Belgium. FAU - Metspalu, Mait AU - Metspalu M AD - Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Pagani, Luca AU - Pagani L AD - Institute of Genomics, University of Tartu, Tartu, Estonia. AD - APE Lab, Department of Biology, University of Padova, Padova, Italy. LA - eng PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 SB - IM CIN - Mol Biol Evol. 2019 Aug 1;36(8):1846. doi: 10.1093/molbev/msz095. PMID: 31124570 MH - Adaptation, Biological MH - Demography MH - *Genome, Human MH - Genomics/*methods MH - Haplotypes MH - Humans MH - India MH - Pakistan MH - Phylogeography MH - Polymorphism, Single Nucleotide MH - Principal Component Analysis MH - Selection, Genetic PMC - PMC6657728 OTO - NOTNLM OT - South Asia OT - ancestry deconvolution OT - post-admixture selection OT - skin color EDAT- 2019/04/06 06:00 MHDA- 2020/02/06 06:00 PMCR- 2019/04/05 CRDT- 2019/04/06 06:00 PHST- 2019/04/06 06:00 [pubmed] PHST- 2020/02/06 06:00 [medline] PHST- 2019/04/06 06:00 [entrez] PHST- 2019/04/05 00:00 [pmc-release] AID - 5364274 [pii] AID - msz037 [pii] AID - 10.1093/molbev/msz037 [doi] PST - ppublish SO - Mol Biol Evol. 2019 Aug 1;36(8):1628-1642. doi: 10.1093/molbev/msz037. PMID- 31308224 OWN - NLM STAT- MEDLINE DCOM- 20200324 LR - 20240214 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 116 IP - 31 DP - 2019 Jul 30 TI - A genetic analysis of the Gibraltar Neanderthals. PG - 15610-15615 LID - 10.1073/pnas.1903984116 [doi] AB - The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation. FAU - Bokelmann, Lukas AU - Bokelmann L AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; lukas_bokelmann@eva.mpg.de paabo@eva.mpg.de c.stringer@nhm.ac.uk. FAU - Hajdinjak, Mateja AU - Hajdinjak M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Peyrégne, Stéphane AU - Peyrégne S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Brace, Selina AU - Brace S AD - Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom. FAU - Essel, Elena AU - Essel E AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - de Filippo, Cesare AU - de Filippo C AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Glocke, Isabelle AU - Glocke I AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Grote, Steffi AU - Grote S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Mafessoni, Fabrizio AU - Mafessoni F AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Nagel, Sarah AU - Nagel S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Kelso, Janet AU - Kelso J AUID- ORCID: 0000-0002-3618-322X AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Prüfer, Kay AU - Prüfer K AUID- ORCID: 0000-0001-6242-3058 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Vernot, Benjamin AU - Vernot B AUID- ORCID: 0000-0002-6820-2181 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Barnes, Ian AU - Barnes I AUID- ORCID: 0000-0001-8322-6918 AD - Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom. FAU - Pääbo, Svante AU - Pääbo S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; lukas_bokelmann@eva.mpg.de paabo@eva.mpg.de c.stringer@nhm.ac.uk. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Stringer, Chris AU - Stringer C AD - Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom lukas_bokelmann@eva.mpg.de paabo@eva.mpg.de c.stringer@nhm.ac.uk. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190715 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *DNA, Ancient MH - Gibraltar MH - History, Ancient MH - Humans MH - Neanderthals/*genetics MH - *Oligonucleotide Array Sequence Analysis PMC - PMC6681707 OTO - NOTNLM OT - Forbes’ Quarry OT - Gibraltar Neanderthal OT - ancient DNA OT - library preparation OT - paleogenetics COIS- The authors declare no conflict of interest. EDAT- 2019/07/17 06:00 MHDA- 2020/03/25 06:00 PMCR- 2020/01/15 CRDT- 2019/07/17 06:00 PHST- 2019/07/17 06:00 [pubmed] PHST- 2020/03/25 06:00 [medline] PHST- 2019/07/17 06:00 [entrez] PHST- 2020/01/15 00:00 [pmc-release] AID - 1903984116 [pii] AID - 201903984 [pii] AID - 10.1073/pnas.1903984116 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2019 Jul 30;116(31):15610-15615. doi: 10.1073/pnas.1903984116. Epub 2019 Jul 15. PMID- 31348818 OWN - NLM STAT- MEDLINE DCOM- 20191217 LR - 20231013 IS - 1553-7404 (Electronic) IS - 1553-7390 (Print) IS - 1553-7390 (Linking) VI - 15 IP - 7 DP - 2019 Jul TI - The presence and impact of reference bias on population genomic studies of prehistoric human populations. PG - e1008302 LID - 10.1371/journal.pgen.1008302 [doi] LID - e1008302 AB - Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially. FAU - Günther, Torsten AU - Günther T AUID- ORCID: 0000-0001-9460-390X AD - Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. FAU - Nettelblad, Carl AU - Nettelblad C AUID- ORCID: 0000-0003-0458-6902 AD - Division of Scientific Computing, Department of Information Technology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190726 PL - United States TA - PLoS Genet JT - PLoS genetics JID - 101239074 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Bias MH - DNA, Ancient/*analysis MH - Genome, Human MH - High-Throughput Nucleotide Sequencing/methods MH - Hominidae/*genetics MH - Humans MH - Metagenomics/*methods MH - Sequence Analysis, DNA/methods MH - Software PMC - PMC6685638 COIS- The authors have declared that no competing interests exist. EDAT- 2019/07/28 06:00 MHDA- 2019/12/18 06:00 PMCR- 2019/07/26 CRDT- 2019/07/27 06:00 PHST- 2019/01/15 00:00 [received] PHST- 2019/07/10 00:00 [accepted] PHST- 2019/08/07 00:00 [revised] PHST- 2019/07/28 06:00 [pubmed] PHST- 2019/12/18 06:00 [medline] PHST- 2019/07/27 06:00 [entrez] PHST- 2019/07/26 00:00 [pmc-release] AID - PGENETICS-D-19-00061 [pii] AID - 10.1371/journal.pgen.1008302 [doi] PST - epublish SO - PLoS Genet. 2019 Jul 26;15(7):e1008302. doi: 10.1371/journal.pgen.1008302. eCollection 2019 Jul. PMID- 31303491 OWN - NLM STAT- MEDLINE DCOM- 20200710 LR - 20211204 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 29 IP - 14 DP - 2019 Jul 22 TI - Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance. PG - 2430-2441.e10 LID - S0960-9822(19)30712-2 [pii] LID - 10.1016/j.cub.2019.06.019 [doi] AB - The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component. CI - Copyright © 2019 Elsevier Ltd. All rights reserved. FAU - Järve, Mari AU - Järve M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. Electronic address: mari.jarve@ut.ee. FAU - Saag, Lehti AU - Saag L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Scheib, Christiana Lyn AU - Scheib CL AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Pathak, Ajai K AU - Pathak AK AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Montinaro, Francesco AU - Montinaro F AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Pagani, Luca AU - Pagani L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi 58/B, Padova 35121, Italy. FAU - Flores, Rodrigo AU - Flores R AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Guellil, Meriam AU - Guellil M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Saag, Lauri AU - Saag L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Tambets, Kristiina AU - Tambets K AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Kushniarevich, Alena AU - Kushniarevich A AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Solnik, Anu AU - Solnik A AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Varul, Liivi AU - Varul L AD - School of Humanities, Tallinn University, 29 Narva Street, Tallinn 10120, Estonia. FAU - Zadnikov, Stanislav AU - Zadnikov S AD - Museum of Archaeology, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine. FAU - Petrauskas, Oleg AU - Petrauskas O AD - Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine. FAU - Avramenko, Maryana AU - Avramenko M AD - Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine. FAU - Magomedov, Boris AU - Magomedov B AD - Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine. FAU - Didenko, Serghii AU - Didenko S AD - National Museum of History of Ukraine, 2 Volodymyrs'ka Street, Kyiv 02000, Ukraine. FAU - Toshev, Gennadi AU - Toshev G AD - Zaporizhzhya National University, 33A Dniprovska Street, Zaporizhzhya 69061, Ukraine. FAU - Bruyako, Igor AU - Bruyako I AD - Odessa Archaeological Museum, 4 Lanzheronivs'ka Street, Odessa 65000, Ukraine. FAU - Grechko, Denys AU - Grechko D AD - Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine. FAU - Okatenko, Vitalii AU - Okatenko V AD - SC SRC "Protective Archeological Service of Ukraine," Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine. FAU - Gorbenko, Kyrylo AU - Gorbenko K AD - Mykolaiv V.O. Sukhomlynskyi National University, 24 Nikolska Street, Mykolaiv 54030, Ukraine. FAU - Smyrnov, Oleksandr AU - Smyrnov O AD - Mykolaiv V.O. Sukhomlynskyi National University, 24 Nikolska Street, Mykolaiv 54030, Ukraine. FAU - Heiko, Anatolii AU - Heiko A AD - National Museum of Ukrainian Pottery in Opishne, 102 Partyzanska Street, Opishne 38164, Ukraine. FAU - Reida, Roman AU - Reida R AD - Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine. FAU - Sapiehin, Serheii AU - Sapiehin S AD - Anton Makarenko Museum, Poltava Regional Makarenko Scientific Lyceum, 1-2 Makarenko Lane, Kovalivka 38701, Ukraine. FAU - Sirotin, Sergey AU - Sirotin S AD - Institute of Archaeology, Russian Academy of Sciences, 19 Dmitri Ulyanov Street, Moscow 117292, Russia. FAU - Tairov, Aleksandr AU - Tairov A AD - South Ural State University, 76 Lenin Avenue, Chelyabinsk 454080, Russia. FAU - Beisenov, Arman AU - Beisenov A AD - A. Kh. Margulan Institute of Archaeology, 44 Dostyk Avenue, Almaty 480100, Kazakhstan. FAU - Starodubtsev, Maksim AU - Starodubtsev M AD - Sterlitamak Museum of Local History, 100 Karl Marx Street, Sterlitamak 453124, Russia. FAU - Vasilev, Vitali AU - Vasilev V AD - LoCom Medien Akademie Europäisches Bildungsinstitut, Bachstraße 4, Bonn 53115, Germany. FAU - Nechvaloda, Alexei AU - Nechvaloda A AD - Institute of History, Language and Literature, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia. FAU - Atabiev, Biyaslan AU - Atabiev B AD - Institute for Caucasus Archaeology, 30 Katkhanova Street, Nalchik 361401, Russia. FAU - Litvinov, Sergey AU - Litvinov S AD - Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia. FAU - Ekomasova, Natalia AU - Ekomasova N AD - Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, 32 Zaki Validi Street, Ufa 450076, Russia. FAU - Dzhaubermezov, Murat AU - Dzhaubermezov M AD - Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, 32 Zaki Validi Street, Ufa 450076, Russia. FAU - Voroniatov, Sergey AU - Voroniatov S AD - Department of Archaeology of Eastern Europe and Siberia, State Hermitage Museum, 34 Dvortsovaya Embankment, St. Petersburg 190000, Russia. FAU - Utevska, Olga AU - Utevska O AD - Department of Genetics and Cytology, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine. FAU - Shramko, Irina AU - Shramko I AD - Museum of Archaeology, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine. FAU - Khusnutdinova, Elza AU - Khusnutdinova E AD - Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, 32 Zaki Validi Street, Ufa 450076, Russia. FAU - Metspalu, Mait AU - Metspalu M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. FAU - Savelev, Nikita AU - Savelev N AD - Institute of History, Language and Literature, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia. FAU - Kriiska, Aivar AU - Kriiska A AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, 2 Jakobi Street, Tartu 51014, Estonia. FAU - Kivisild, Toomas AU - Kivisild T AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, O&N IV Herestraat 49, Leuven 3000, Belgium. FAU - Villems, Richard AU - Villems R AD - Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, Tartu 51010, Estonia. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190711 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*analysis MH - Ethnicity/genetics MH - *Genetic Drift MH - Genome, Human MH - History, Ancient MH - *Human Migration MH - Humans MH - Male MH - Ukraine OTO - NOTNLM OT - Chernyakhiv culture OT - Eurasian Steppe OT - Iron Age OT - Sarmatians OT - Scythians OT - aDNA EDAT- 2019/07/16 06:00 MHDA- 2020/07/11 06:00 CRDT- 2019/07/16 06:00 PHST- 2019/02/23 00:00 [received] PHST- 2019/05/03 00:00 [revised] PHST- 2019/06/07 00:00 [accepted] PHST- 2019/07/16 06:00 [pubmed] PHST- 2020/07/11 06:00 [medline] PHST- 2019/07/16 06:00 [entrez] AID - S0960-9822(19)30712-2 [pii] AID - 10.1016/j.cub.2019.06.019 [doi] PST - ppublish SO - Curr Biol. 2019 Jul 22;29(14):2430-2441.e10. doi: 10.1016/j.cub.2019.06.019. Epub 2019 Jul 11. PMID- 31284503 OWN - NLM STAT- MEDLINE DCOM- 20200106 LR - 20231013 IS - 2073-4425 (Print) IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 10 IP - 7 DP - 2019 Jul 5 TI - Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data. LID - 10.3390/genes10070509 [doi] LID - 509 AB - The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub. FAU - Lan, Tian Ming AU - Lan TM AD - Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark. AD - BGI-Shenzhen, Shenzhen 518083, China. FAU - Lin, Yu AU - Lin Y AUID- ORCID: 0000-0002-6181-939X AD - BGI-Shenzhen, Shenzhen 518083, China. AD - China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. FAU - Njaramba-Ngatia, Jacob AU - Njaramba-Ngatia J AD - College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China. FAU - Guo, Xiao Sen AU - Guo XS AD - BGI-Shenzhen, Shenzhen 518083, China. FAU - Li, Ren Gui AU - Li RG AD - Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China. FAU - Li, Hai Meng AU - Li HM AD - BGI-Shenzhen, Shenzhen 518083, China. AD - School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China. FAU - Kumar-Sahu, Sunil AU - Kumar-Sahu S AD - BGI-Shenzhen, Shenzhen 518083, China. AD - China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. FAU - Wang, Xie AU - Wang X AD - China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. FAU - Yang, Xiu Juan AU - Yang XJ AD - Heilongjiang Provincial Museum, Harbin 150001, China. FAU - Guo, Hua Bing AU - Guo HB AD - Forest Inventory and Planning Institute of Jilin Province, Changchun 130022, China. FAU - Xu, Wen Hao AU - Xu WH AD - College of Informatics, Huazhong Agricultural University, Wuhan 430070, China. FAU - Kristiansen, Karsten AU - Kristiansen K AD - Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark. AD - BGI-Shenzhen, Shenzhen 518083, China. FAU - Liu, Huan AU - Liu H AUID- ORCID: 0000-0003-3909-0931 AD - BGI-Shenzhen, Shenzhen 518083, China. liuhuan@genomics.cn. AD - State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China. liuhuan@genomics.cn. FAU - Xu, Yan Chun AU - Xu YC AD - Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China. xu_daniel@nefu.edu.cn. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190705 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Mitochondrial) SB - IM MH - Algorithms MH - Animals MH - DNA, Mitochondrial MH - Genome MH - Goats/*genetics MH - High-Throughput Nucleotide Sequencing MH - Horses/*genetics MH - Humans MH - Mammoths/*genetics MH - Paleontology MH - Ruminants/*genetics PMC - PMC6679096 OTO - NOTNLM OT - BLAST OT - ancient DNA OT - next-generation sequencing OT - species identification COIS- The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. EDAT- 2019/07/10 06:00 MHDA- 2019/07/10 06:01 PMCR- 2019/07/01 CRDT- 2019/07/10 06:00 PHST- 2019/05/14 00:00 [received] PHST- 2019/06/26 00:00 [revised] PHST- 2019/07/03 00:00 [accepted] PHST- 2019/07/10 06:00 [entrez] PHST- 2019/07/10 06:00 [pubmed] PHST- 2019/07/10 06:01 [medline] PHST- 2019/07/01 00:00 [pmc-release] AID - genes10070509 [pii] AID - genes-10-00509 [pii] AID - 10.3390/genes10070509 [doi] PST - epublish SO - Genes (Basel). 2019 Jul 5;10(7):509. doi: 10.3390/genes10070509. PMID- 31147405 OWN - NLM STAT- MEDLINE DCOM- 20200325 LR - 20200325 IS - 1095-9203 (Electronic) IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 365 IP - 6448 DP - 2019 Jul 5 TI - Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. LID - 10.1126/science.aaw6275 [doi] LID - eaaw6275 AB - How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts. CI - Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. FAU - Prendergast, Mary E AU - Prendergast ME AUID- ORCID: 0000-0003-0275-6795 AD - Division of Humanities, Saint Louis University, 28003 Madrid, Spain. mary.prendergast@slu.edu mlipson@genetics.med.harvard.edu elizabeth.sawchuk@stonybrook.edu reich@genetics.med.harvard.edu. AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Lipson, Mark AU - Lipson M AUID- ORCID: 0000-0001-5346-9329 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. mary.prendergast@slu.edu mlipson@genetics.med.harvard.edu elizabeth.sawchuk@stonybrook.edu reich@genetics.med.harvard.edu. FAU - Sawchuk, Elizabeth A AU - Sawchuk EA AUID- ORCID: 0000-0003-4398-2174 AD - Department of Anthropology, Stony Brook University, Stony Brook, NY 11790, USA. mary.prendergast@slu.edu mlipson@genetics.med.harvard.edu elizabeth.sawchuk@stonybrook.edu reich@genetics.med.harvard.edu. FAU - Olalde, Iñigo AU - Olalde I AUID- ORCID: 0000-0002-2660-6807 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Ogola, Christine A AU - Ogola CA AD - Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Sirak, Kendra A AU - Sirak KA AUID- ORCID: 0000-0003-2347-3479 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Adamski, Nicole AU - Adamski N AUID- ORCID: 0000-0002-2268-1359 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Bernardos, Rebecca AU - Bernardos R AUID- ORCID: 0000-0003-4625-3727 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AUID- ORCID: 0000-0001-5350-1608 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Callan, Kimberly AU - Callan K AUID- ORCID: 0000-0003-3170-8514 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Culleton, Brendan J AU - Culleton BJ AD - Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA. FAU - Eccles, Laurie AU - Eccles L AD - Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA. FAU - Harper, Thomas K AU - Harper TK AD - Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA. FAU - Lawson, Ann Marie AU - Lawson AM AUID- ORCID: 0000-0003-0990-2329 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Mah, Matthew AU - Mah M AUID- ORCID: 0000-0001-8987-6436 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AUID- ORCID: 0000-0001-7973-6173 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Zalzala, Fatma AU - Zalzala F AUID- ORCID: 0000-0002-8981-1277 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Ambrose, Stanley H AU - Ambrose SH AUID- ORCID: 0000-0002-8785-0512 AD - Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA. FAU - Ayodo, George AU - Ayodo G AD - Department of Public and Community Health, School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya. FAU - Gates, Henry Louis Jr AU - Gates HL Jr AD - Hutchins Center for African and African American Research, Harvard University, Cambridge, MA 02138, USA. FAU - Gidna, Agness O AU - Gidna AO AD - National Museums of Tanzania, Dar es Salaam, Tanzania. FAU - Katongo, Maggie AU - Katongo M AUID- ORCID: 0000-0002-5286-1350 AD - Livingstone Museum, Livingstone, Zambia. FAU - Kwekason, Amandus AU - Kwekason A AD - National Museums of Tanzania, Dar es Salaam, Tanzania. FAU - Mabulla, Audax Z P AU - Mabulla AZP AD - National Museums of Tanzania, Dar es Salaam, Tanzania. FAU - Mudenda, George S AU - Mudenda GS AUID- ORCID: 0000-0003-0014-260X AD - Livingstone Museum, Livingstone, Zambia. FAU - Ndiema, Emmanuel K AU - Ndiema EK AD - Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya. FAU - Nelson, Charles AU - Nelson C AUID- ORCID: 0000-0002-2157-6610 AD - Academy for Lifelong Learning, Western Washington University, Bellingham, WA 98225, USA. FAU - Robertshaw, Peter AU - Robertshaw P AUID- ORCID: 0000-0002-2286-1464 AD - Department of Anthropology, California State University, San Bernardino, CA 92407, USA. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology, University of California, Santa Barbara, CA 93106, USA. FAU - Manthi, Fredrick K AU - Manthi FK AD - Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya. FAU - Reich, David AU - Reich D AUID- ORCID: 0000-0002-7037-5292 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. mary.prendergast@slu.edu mlipson@genetics.med.harvard.edu elizabeth.sawchuk@stonybrook.edu reich@genetics.med.harvard.edu. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20190530 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Agriculture/*history MH - DNA, Ancient MH - *Genome, Human MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Kenya MH - Occupations/*history MH - Tanzania PMC - PMC6827346 MID - NIHMS1055228 COIS- Competing interests: Authors declare no competing interests. EDAT- 2019/05/31 06:00 MHDA- 2020/03/26 06:00 PMCR- 2019/11/04 CRDT- 2019/06/01 06:00 PHST- 2019/01/10 00:00 [received] PHST- 2019/05/13 00:00 [accepted] PHST- 2019/05/31 06:00 [pubmed] PHST- 2020/03/26 06:00 [medline] PHST- 2019/06/01 06:00 [entrez] PHST- 2019/11/04 00:00 [pmc-release] AID - science.aaw6275 [pii] AID - 10.1126/science.aaw6275 [doi] PST - ppublish SO - Science. 2019 Jul 5;365(6448):eaaw6275. doi: 10.1126/science.aaw6275. Epub 2019 May 30. PMID- 31281897 OWN - NLM STAT- MEDLINE DCOM- 20200625 LR - 20221207 IS - 2375-2548 (Electronic) IS - 2375-2548 (Linking) VI - 5 IP - 7 DP - 2019 Jul TI - Ancient DNA sheds light on the genetic origins of early Iron Age Philistines. PG - eaax0061 LID - 10.1126/sciadv.aax0061 [doi] LID - eaax0061 AB - The ancient Mediterranean port city of Ashkelon, identified as "Philistine" during the Iron Age, underwent a marked cultural change between the Late Bronze and the early Iron Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called "Sea Peoples." Here, we report genome-wide data of 10 Bronze and Iron Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European-related admixture. This genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze to Iron Age transition in Ashkelon but did not leave a long-lasting genetic signature. FAU - Feldman, Michal AU - Feldman M AUID- ORCID: 0000-0003-4618-1460 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Strasse 10, D-07745 Jena, Germany. FAU - Master, Daniel M AU - Master DM AD - Wheaton Archaeology Museum, Wheaton College, Wheaton, IL 60187, USA. AD - Harvard Semitic Museum, Harvard University, Cambridge, MA 02138, USA. FAU - Bianco, Raffaela A AU - Bianco RA AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Strasse 10, D-07745 Jena, Germany. FAU - Burri, Marta AU - Burri M AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Strasse 10, D-07745 Jena, Germany. FAU - Stockhammer, Philipp W AU - Stockhammer PW AUID- ORCID: 0000-0003-4702-9372 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Strasse 10, D-07745 Jena, Germany. AD - Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität, Schellingstrasse 12, D-80799 München, Germany. FAU - Mittnik, Alissa AU - Mittnik A AUID- ORCID: 0000-0002-6963-4824 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Strasse 10, D-07745 Jena, Germany. AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Aja, Adam J AU - Aja AJ AD - Harvard Semitic Museum, Harvard University, Cambridge, MA 02138, USA. FAU - Jeong, Choongwon AU - Jeong C AUID- ORCID: 0000-0003-3049-2352 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Strasse 10, D-07745 Jena, Germany. AD - School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Strasse 10, D-07745 Jena, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190703 PL - United States TA - Sci Adv JT - Science advances JID - 101653440 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - *Genetics, Population MH - Genome-Wide Association Study MH - History, Ancient MH - *Human Migration MH - Humans MH - White People/history/*legislation & jurisprudence PMC - PMC6609216 EDAT- 2019/07/10 06:00 MHDA- 2020/06/26 06:00 PMCR- 2019/07/03 CRDT- 2019/07/09 06:00 PHST- 2019/02/13 00:00 [received] PHST- 2019/05/23 00:00 [accepted] PHST- 2019/07/09 06:00 [entrez] PHST- 2019/07/10 06:00 [pubmed] PHST- 2020/06/26 06:00 [medline] PHST- 2019/07/03 00:00 [pmc-release] AID - aax0061 [pii] AID - 10.1126/sciadv.aax0061 [doi] PST - epublish SO - Sci Adv. 2019 Jul 3;5(7):eaax0061. doi: 10.1126/sciadv.aax0061. eCollection 2019 Jul. PMID- 31389359 OWN - NLM STAT- MEDLINE DCOM- 20200102 LR - 20221207 IS - 0973-7138 (Electronic) IS - 0250-5991 (Linking) VI - 44 IP - 3 DP - 2019 Jul TI - Peopling of India: Ancient DNA perspectives. LID - 70 [pii] AB - To reconstruct and explain patterns of genetic diversity of modern humans, understanding their past and present genetic profile is crucial. While genomes of contemporary people can provide information about present day population structure, analysis of ancient genomes may provide unprecedented insights about the past demographic events that have shaped the contemporary gene pool. Population genetics has recently witnessed an explosion in studies on ancient human population histories, primarily from Europe and America. South Asia has no representation in the ancient genomics literature, despite the wealth of archaeological richness in the form of human skeletal remains that exist in collections all over the country. Representing one-fifth of present day humanity calls for understanding the demographic history of south Asia not merely as a prerequisite but as an urgent need to understand its genetic variations on a global scale. Although the overall picture is taking form, new archaeological and genetic information from the region has started to reveal a more complex scenario of ancient human migrations and admixtures than was ever known before. In this article, we discuss a meaningful insight on the current status of ancient DNA (aDNA) research in India. We have also summarized a few but important aDNA studies, which have been successfully carried out in India. Furthermore, we have highlighted the potential opportunity of aDNA research in the Indian subcontinent. FAU - Thangaraj, K AU - Thangaraj K AD - CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India, thangs@ccmb.res.in. FAU - Rai, Niraj AU - Rai N LA - eng PT - Historical Article PT - Journal Article PL - India TA - J Biosci JT - Journal of biosciences JID - 8100809 RN - 0 (DNA, Ancient) SB - IM CIN - J Biosci. 2019 Jul;44(3):71. PMID: 31389360 MH - Anthropology/methods MH - Archaeology/methods MH - Asian People/*history MH - Biological Evolution MH - DNA, Ancient/*analysis MH - Ethnicity MH - Female MH - Genetic Variation MH - *Genetics, Population MH - History, Ancient MH - Human Migration/*trends MH - Humans MH - India/ethnology MH - Language/*history MH - Male MH - Selection, Genetic MH - White People/*history EDAT- 2019/08/08 06:00 MHDA- 2020/01/03 06:00 CRDT- 2019/08/08 06:00 PHST- 2019/08/08 06:00 [entrez] PHST- 2019/08/08 06:00 [pubmed] PHST- 2020/01/03 06:00 [medline] AID - 70 [pii] PST - ppublish SO - J Biosci. 2019 Jul;44(3):70. PMID- 31109769 OWN - NLM STAT- MEDLINE DCOM- 20200414 LR - 20200414 IS - 0168-9525 (Print) IS - 0168-9525 (Linking) VI - 35 IP - 7 DP - 2019 Jul TI - Horse Paleogenomes and Human-Animal Interactions in Prehistory. PG - 473-475 LID - S0168-9525(19)30077-0 [pii] LID - 10.1016/j.tig.2019.04.006 [doi] AB - A new analysis of paleogenomic data from 278 ancient horses (Fages et al. Cellhttp://doi.org/10.1016/j.cell.2019.03.049) finds that this animal - crucially important to many ancient and contemporary human societies for subsistence, transportation, conflict, and more - was domesticated in at least two different regions, but with the geographic and cultural origins of the modern domestic horse lineage remaining unknown. By tracing ancient horse population movements and inferring the spatiotemporal trajectories of phenotypic adaptations, this study provides fresh perspectives on past human group interactions and activities. CI - Copyright © 2019 Elsevier Ltd. All rights reserved. FAU - Perry, George H AU - Perry GH AD - Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; 'Words, Bones, Genes, Tools' Deutsche Forschungsgemeinschaft (DFG) Center for Advanced Studies, University of Tübingen, Tübingen 72076, Germany. Electronic address: ghp3@psu.edu. FAU - Makarewicz, Cheryl A AU - Makarewicz CA AD - Institute for Prehistoric and Protohistoric Archaeology, University of Kiel, Kiel 24418, Germany; University of Haifa, Abba Khoushy Avenue 199, Haifa 3498838, Israel. Electronic address: c.makarewicz@ufg.uni-kiel.de. LA - eng PT - Comment PT - Journal Article DEP - 20190517 PL - England TA - Trends Genet JT - Trends in genetics : TIG JID - 8507085 SB - IM CON - Cell. 2019 May 30;177(6):1419-1435.e31. doi: 10.1016/j.cell.2019.03.049. PMID: 31056281 MH - Animals MH - *Genome MH - Horses MH - Humans OTO - NOTNLM OT - ancient DNA OT - domestication OT - equid OT - evolutionary genomics OT - population history EDAT- 2019/05/22 06:00 MHDA- 2020/04/15 06:00 CRDT- 2019/05/22 06:00 PHST- 2019/04/22 00:00 [received] PHST- 2019/04/25 00:00 [accepted] PHST- 2019/05/22 06:00 [pubmed] PHST- 2020/04/15 06:00 [medline] PHST- 2019/05/22 06:00 [entrez] AID - S0168-9525(19)30077-0 [pii] AID - 10.1016/j.tig.2019.04.006 [doi] PST - ppublish SO - Trends Genet. 2019 Jul;35(7):473-475. doi: 10.1016/j.tig.2019.04.006. Epub 2019 May 17. PMID- 31088861 OWN - NLM STAT- MEDLINE DCOM- 20200113 LR - 20240229 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 212 IP - 3 DP - 2019 Jul TI - Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples. PG - 587-614 LID - 10.1534/genetics.119.302057 [doi] AB - Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6× and down to 7-8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses. CI - Copyright © 2019 by the Genetics Society of America. FAU - Renaud, Gabriel AU - Renaud G AUID- ORCID: 0000-0002-0630-027X AD - Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark gabriel.reno@gmail.com. FAU - Hanghøj, Kristian AU - Hanghøj K AD - Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark. AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, France. FAU - Korneliussen, Thorfinn Sand AU - Korneliussen TS AD - Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark. AD - Department of Zoology, University of Cambridge, CB2 3EJ, UK. AD - The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. AD - The Danish Institute for Advanced Study at The University of Southern Denmark, DK-5230 Odense M, Denmark. FAU - Orlando, Ludovic AU - Orlando L AUID- ORCID: 0000-0003-3936-1850 AD - Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark. AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190514 PL - United States TA - Genetics JT - Genetics JID - 0374636 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Bayes Theorem MH - *DNA, Ancient MH - Genotyping Techniques/*methods/standards MH - *Heterozygote MH - *Homozygote MH - Humans MH - Markov Chains PMC - PMC6614887 OTO - NOTNLM OT - Ancient DNA OT - Runs of homozygosity OT - effective population size OT - heterozygosity OT - inbreeding EDAT- 2019/05/16 06:00 MHDA- 2020/01/14 06:00 PMCR- 2019/05/14 CRDT- 2019/05/16 06:00 PHST- 2019/02/26 00:00 [received] PHST- 2019/05/01 00:00 [accepted] PHST- 2019/05/16 06:00 [pubmed] PHST- 2020/01/14 06:00 [medline] PHST- 2019/05/16 06:00 [entrez] PHST- 2019/05/14 00:00 [pmc-release] AID - genetics.119.302057 [pii] AID - 302057 [pii] AID - 10.1534/genetics.119.302057 [doi] PST - ppublish SO - Genetics. 2019 Jul;212(3):587-614. doi: 10.1534/genetics.119.302057. Epub 2019 May 14. PMID- 31216315 OWN - NLM STAT- MEDLINE DCOM- 20200213 LR - 20200309 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 14 IP - 6 DP - 2019 TI - Habitat suitability and the genetic structure of human populations during the Last Glacial Maximum (LGM) in Western Europe. PG - e0217996 LID - 10.1371/journal.pone.0217996 [doi] LID - e0217996 AB - Human populations in Western Europe during the Last Glacial Maximum were geographically constrained to glacial refugia by the severity of the climate and ecological risk factors. In this research we use an agent-based model of human mobility and interaction, based on ethnographic and archaeological data, to explore the impact of ecological risk on human population structure via a reconstructed landscape of habitat suitability. The agent-based model allows us to evaluate the size and location of glacial refugia, the size of the populations occupying them and the degree of genetic relatedness between people occupying these areas. To do this, we model the probability of an agent foraging groups' survival as a function of habitat suitability. The model's simulated "genomes" (composed of regionally specific genetic markers) allow us to track long-term trends of inter-regional interaction and mobility. The results agree with previous archaeological studies situating a large glacial refugium spanning southern France and northeastern Spain, but we expand on those studies by demonstrating that higher rates of population growth in this central refugium led to continuous out-migration and therefore genetic homogeneity across Western Europe, with the possible exception of the Italian peninsula. These results concur with material culture data from known archaeological sites dating to the Last Glacial Maximum and make predictions for future ancient DNA studies. FAU - Wren, Colin D AU - Wren CD AUID- ORCID: 0000-0003-4940-3997 AD - Department of Anthropology, University of Colorado Colorado Springs, Colorado Springs, Colorado, United States of America. FAU - Burke, Ariane AU - Burke A AD - Département d'Anthropologie, Université de Montréal, Montreal, Québec, Canada. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190619 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - *Biological Evolution MH - Climate MH - DNA, Mitochondrial/*genetics MH - Ecosystem MH - Europe MH - France MH - *Genetics, Population MH - Haplotypes MH - Humans MH - Italy MH - Paleontology MH - Phylogeny MH - *Phylogeography MH - Population Density MH - Refugium MH - Sequence Analysis, DNA MH - Spain PMC - PMC6583941 COIS- The authors have declared that no competing interests exist. EDAT- 2019/06/20 06:00 MHDA- 2020/02/14 06:00 PMCR- 2019/06/19 CRDT- 2019/06/20 06:00 PHST- 2019/01/30 00:00 [received] PHST- 2019/05/22 00:00 [accepted] PHST- 2019/06/20 06:00 [entrez] PHST- 2019/06/20 06:00 [pubmed] PHST- 2020/02/14 06:00 [medline] PHST- 2019/06/19 00:00 [pmc-release] AID - PONE-D-19-02959 [pii] AID - 10.1371/journal.pone.0217996 [doi] PST - epublish SO - PLoS One. 2019 Jun 19;14(6):e0217996. doi: 10.1371/journal.pone.0217996. eCollection 2019. PMID- 31164419 OWN - NLM STAT- MEDLINE DCOM- 20200406 LR - 20231012 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 116 IP - 25 DP - 2019 Jun 18 TI - Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750). PG - 12363-12372 LID - 10.1073/pnas.1820447116 [doi] AB - The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic. CI - Copyright © 2019 the Author(s). Published by PNAS. FAU - Keller, Marcel AU - Keller M AUID- ORCID: 0000-0001-9668-6817 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; marcel.keller@ut.ee harbeck@snsb.de herbig@shh.mpg.de krause@shh.mpg.de. AD - State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany. FAU - Spyrou, Maria A AU - Spyrou MA AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Scheib, Christiana L AU - Scheib CL AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom. AD - Institute of Genomics, University of Tartu, 51010 Tartu, Estonia. FAU - Neumann, Gunnar U AU - Neumann GU AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Kröpelin, Andreas AU - Kröpelin A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Friedrich Schiller University Jena, 07743 Jena, Germany. FAU - Haas-Gebhard, Brigitte AU - Haas-Gebhard B AD - Archaeological Collection of the Bavarian State, 80538 Munich, Germany. FAU - Päffgen, Bernd AU - Päffgen B AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799 Munich, Germany. FAU - Haberstroh, Jochen AU - Haberstroh J AD - Bavarian State Department of Monuments and Sites, 80539 Munich, Germany. FAU - Ribera I Lacomba, Albert AU - Ribera I Lacomba A AD - Department for Municipal Archaeology, Valencia City Council, 46014 Valencia, Spain. FAU - Raynaud, Claude AU - Raynaud C AD - CNRS, UMR5140, Archéologie des Sociétés Méditerranéennes, 34199 Montpellier, France. FAU - Cessford, Craig AU - Cessford C AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom. FAU - Durand, Raphaël AU - Durand R AD - Service d'Archéologie Préventive de l'Agglomération de Bourges Plus, 18023 Bourges Cedex, France. FAU - Stadler, Peter AU - Stadler P AD - Department of Pre- and Protohistory, University of Vienna, 1190 Vienna, Austria. FAU - Nägele, Kathrin AU - Nägele K AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Bates, Jessica S AU - Bates JS AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom. FAU - Trautmann, Bernd AU - Trautmann B AD - State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany. FAU - Inskip, Sarah A AU - Inskip SA AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, United Kingdom. FAU - Peters, Joris AU - Peters J AD - State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany. AD - ArchaeoBioCenter, Ludwig Maximilian University Munich, 80539 Munich, Germany. AD - Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig Maximilian University Munich, 80539 Munich, Germany. FAU - Robb, John E AU - Robb JE AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom. FAU - Kivisild, Toomas AU - Kivisild T AUID- ORCID: 0000-0002-6297-7808 AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom. AD - Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium. FAU - Castex, Dominique AU - Castex D AD - UMR 5199, PACEA, CNRS Institute, 33615 Pessac Cedex, France. FAU - McCormick, Michael AU - McCormick M AD - Initiative for the Science of the Human Past, Department of History, Harvard University, Cambridge, MA 02138. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 07745 Jena, Germany. FAU - Bos, Kirsten I AU - Bos KI AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Harbeck, Michaela AU - Harbeck M AD - State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany; marcel.keller@ut.ee harbeck@snsb.de herbig@shh.mpg.de krause@shh.mpg.de. FAU - Herbig, Alexander AU - Herbig A AUID- ORCID: 0000-0003-1176-1166 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; marcel.keller@ut.ee harbeck@snsb.de herbig@shh.mpg.de krause@shh.mpg.de. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; marcel.keller@ut.ee harbeck@snsb.de herbig@shh.mpg.de krause@shh.mpg.de. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 07745 Jena, Germany. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom GR - 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190604 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Disease Outbreaks/*history MH - Europe/epidemiology MH - *Genome, Bacterial MH - History, Medieval MH - Humans MH - Plague/epidemiology/history/*microbiology MH - Yersinia pestis/*genetics/pathogenicity PMC - PMC6589673 OTO - NOTNLM OT - Anglo-Saxons OT - Justinianic Plague OT - Merovingians OT - ancient DNA OT - bacterial evolution COIS- The authors declare no conflict of interest. EDAT- 2019/06/06 06:00 MHDA- 2020/04/09 06:00 PMCR- 2019/06/04 CRDT- 2019/06/06 06:00 PHST- 2019/06/06 06:00 [pubmed] PHST- 2020/04/09 06:00 [medline] PHST- 2019/06/06 06:00 [entrez] PHST- 2019/06/04 00:00 [pmc-release] AID - 1820447116 [pii] AID - 201820447 [pii] AID - 10.1073/pnas.1820447116 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12363-12372. doi: 10.1073/pnas.1820447116. Epub 2019 Jun 4. PMID- 31220249 OWN - NLM STAT- MEDLINE DCOM- 20200204 LR - 20210109 IS - 2047-217X (Electronic) IS - 2047-217X (Linking) VI - 8 IP - 6 DP - 2019 Jun 1 TI - Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples. LID - 10.1093/gigascience/giz065 [doi] LID - giz065 AB - BACKGROUND: Recent advances in ancient DNA studies, especially in increasing isolated DNA yields and quality, have opened the possibility of analysis of ancient host microbiome. However, such pitfalls as spurious identification of pathogens based on fragmentary data or environmental contamination could lead to incorrect epidaemiological conclusions. Within the Mycobacterium genus, Mycobacterium tuberculosis complex members responsible for tuberculosis share up to ∼99% genomic sequence identity, while other more distantly related Mycobacteria other than M. tuberculosis can be causative agents for pulmonary diseases or soil dwellers. Therefore, reliable determination of species complex is crucial for interpretation of sequencing results. RESULTS: Here we present a novel bioinformatical approach, used for screening of ancient tuberculosis in sequencing data, derived from 28 individuals (dated 4400-4000 and 3100-2900 BC) from central Poland. We demonstrate that cost-effective next-generation screening sequencing data (∼20M reads per sample) could yield enough information to provide statistically supported identification of probable ancient disease cases. CONCLUSIONS: Application of appropriate bioinformatic tools, including an unbiased selection of genomic alignment targets for species specificity, makes it possible to extract valid data from full-sample sequencing results (without subjective targeted enrichment procedures). This approach broadens the potential scope of palaeoepidaemiology both to older, suboptimally preserved samples and to pathogens with difficult intrageneric taxonomy. CI - © The Author(s) 2019. Published by Oxford University Press. FAU - Borówka, Paulina AU - Borówka P AD - Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland. FAU - Pułaski, Łukasz AU - Pułaski Ł AD - Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland. AD - Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Łódź, Poland. FAU - Marciniak, Błażej AU - Marciniak B AD - Biobank Lab, Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, 14 Pilarskiego Street, 90-231 Łódź, Poland. AD - BBMRI.pl Consortium, 147 Stabłowicka Street, 54-066 Wrocław, Poland. FAU - Borowska-Strugińska, Beata AU - Borowska-Strugińska B AD - Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland. FAU - Dziadek, Jarosław AU - Dziadek J AD - Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Łódź, Poland. FAU - Żądzińska, Elżbieta AU - Żądzińska E AD - Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland. FAU - Lorkiewicz, Wiesław AU - Lorkiewicz W AD - Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland. FAU - Strapagiel, Dominik AU - Strapagiel D AD - Biobank Lab, Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, 14 Pilarskiego Street, 90-231 Łódź, Poland. AD - BBMRI.pl Consortium, 147 Stabłowicka Street, 54-066 Wrocław, Poland. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Gigascience JT - GigaScience JID - 101596872 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - Body Remains/*microbiology MH - Bone and Bones/microbiology MH - DNA Barcoding, Taxonomic/*methods MH - *DNA, Ancient MH - DNA, Bacterial MH - Female MH - High-Throughput Nucleotide Sequencing/*methods MH - History, Ancient MH - Humans MH - Male MH - Mycobacterium tuberculosis/genetics/*isolation & purification PMC - PMC6586198 OTO - NOTNLM OT - NGS OT - aTB OT - ancient DNA OT - ancient tuberculosis EDAT- 2019/06/21 06:00 MHDA- 2020/02/06 06:00 PMCR- 2019/06/20 CRDT- 2019/06/21 06:00 PHST- 2019/01/11 00:00 [received] PHST- 2019/04/07 00:00 [revised] PHST- 2019/05/10 00:00 [accepted] PHST- 2019/06/21 06:00 [entrez] PHST- 2019/06/21 06:00 [pubmed] PHST- 2020/02/06 06:00 [medline] PHST- 2019/06/20 00:00 [pmc-release] AID - 5521156 [pii] AID - giz065 [pii] AID - 10.1093/gigascience/giz065 [doi] PST - ppublish SO - Gigascience. 2019 Jun 1;8(6):giz065. doi: 10.1093/gigascience/giz065. PMID- 30964548 OWN - NLM STAT- MEDLINE DCOM- 20200327 LR - 20200327 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 169 IP - 2 DP - 2019 Jun TI - Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark. PG - 240-252 LID - 10.1002/ajpa.23820 [doi] AB - OBJECTIVES: In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isotope data. This study uses ancient DNA (aDNA) isolated from skeletal remains to examine whether evidence for large-scale population movement can be gleaned from the complete mitochondrial genomes of 264 medieval individuals from England (London) and Denmark. MATERIALS AND METHODS: Using a novel library-conserving approach to targeted capture, we recovered 264 full mitochondrial genomes from the petrous portion of the temporal bones and teeth and compared genetic diversity across the medieval period within and between English (London) and Danish populations and with contemporary populations through population pairwise Φ(ST) analysis. RESULTS: We find no evidence of significant differences in genetic diversity spatially or temporally in our dataset, yet there is a high degree of haplotype diversity in our medieval samples with little exact sequence sharing. DISCUSSION: The mitochondrial genomes of both medieval Londoners and medieval Danes suggest high mitochondrial diversity before, during and after the Black Death. While our mitochondrial genomic data lack geographically correlated signals, these data could be the result of high, continual female migration before and after the Black Death or may simply indicate a large female effective population size unaffected by the upheaval of the medieval period. Either scenario suggests a genetic resiliency in areas of northwestern medieval Europe. CI - © 2019 Wiley Periodicals, Inc. FAU - Klunk, Jennifer AU - Klunk J AUID- ORCID: 0000-0002-6521-8516 AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada. AD - Department of Biology, McMaster University, Hamilton, Ontario, Canada. FAU - Duggan, Ana T AU - Duggan AT AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada. AD - Department of Anthropology, McMaster University, Hamilton, Ontario, Canada. FAU - Redfern, Rebecca AU - Redfern R AD - Center for Human Bioarchaeology, Museum of London, London, UK. FAU - Gamble, Julia AU - Gamble J AD - Department of Anthropology, University of Manitoba, Winnipeg, Manitoba. FAU - Boldsen, Jesper L AU - Boldsen JL AD - Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense, Denmark. FAU - Golding, G Brian AU - Golding GB AD - Department of Biology, McMaster University, Hamilton, Ontario, Canada. FAU - Walter, Brittany S AU - Walter BS AD - Defense POW/MIA Accounting Agency Laboratory, Offutt AFB, Omaha, Nebraska. FAU - Eaton, Katherine AU - Eaton K AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada. AD - Department of Anthropology, McMaster University, Hamilton, Ontario, Canada. FAU - Stangroom, Julianna AU - Stangroom J AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada. AD - Department of Anthropology, McMaster University, Hamilton, Ontario, Canada. FAU - Rouillard, Jean-Marie AU - Rouillard JM AD - Arbor Biosciences, Ann Arbor, Michigan. AD - Department of Chemical Engineering, University of Michigan Ann Arbor, Ann Arbor, Michigan. FAU - Devault, Alison AU - Devault A AD - Arbor Biosciences, Ann Arbor, Michigan. FAU - DeWitte, Sharon N AU - DeWitte SN AD - Department of Anthropology, University of South Carolina, Columbia, South Carolina. FAU - Poinar, Hendrik N AU - Poinar HN AUID- ORCID: 0000-0002-0314-4160 AD - McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada. AD - Department of Biology, McMaster University, Hamilton, Ontario, Canada. AD - Department of Anthropology, McMaster University, Hamilton, Ontario, Canada. AD - Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada. AD - Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada. LA - eng GR - APP1065106/National Health and Medical Research Council (NHMRC)/International GR - RGPIN-2015-04477/Natural Sciences and Engineering Research Council of Canada (NSERC)/International GR - 430-2017-01193/Social Sciences and Humanities Research Council of Canada (SSHRC)/International GR - 435-2018-0465/Social Sciences and Humanities Research Council of Canada (SSHRC)/International GR - Arbor Biosciences/International GR - McMaster University/International GR - Canada Research Chair Program/International GR - University of Toronto/International PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190409 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Bone and Bones/chemistry MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/analysis MH - Denmark MH - Female MH - Genetic Variation/*genetics MH - Genome, Mitochondrial/*genetics MH - History, Medieval MH - Human Migration/history MH - Humans MH - London MH - Male MH - Plague/*history MH - Tooth/chemistry OTO - NOTNLM OT - ancient DNA OT - medieval London and Denmark OT - migration OT - mitochondrial DNA EDAT- 2019/04/10 06:00 MHDA- 2020/03/28 06:00 CRDT- 2019/04/10 06:00 PHST- 2018/10/22 00:00 [received] PHST- 2019/02/08 00:00 [revised] PHST- 2019/03/02 00:00 [accepted] PHST- 2019/04/10 06:00 [pubmed] PHST- 2020/03/28 06:00 [medline] PHST- 2019/04/10 06:00 [entrez] AID - 10.1002/ajpa.23820 [doi] PST - ppublish SO - Am J Phys Anthropol. 2019 Jun;169(2):240-252. doi: 10.1002/ajpa.23820. Epub 2019 Apr 9. PMID- 30953039 OWN - NLM STAT- MEDLINE DCOM- 20190724 LR - 20210109 IS - 1471-0064 (Electronic) IS - 1471-0056 (Print) IS - 1471-0056 (Linking) VI - 20 IP - 6 DP - 2019 Jun TI - Ancient pathogen genomics as an emerging tool for infectious disease research. PG - 323-340 LID - 10.1038/s41576-019-0119-1 [doi] AB - Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes. FAU - Spyrou, Maria A AU - Spyrou MA AUID- ORCID: 0000-0002-3615-3936 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. spyrou@shh.mpg.de. FAU - Bos, Kirsten I AU - Bos KI AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Herbig, Alexander AU - Herbig A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. krause@shh.mpg.de. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Nat Rev Genet JT - Nature reviews. Genetics JID - 100962779 RN - 0 (DNA, Ancient) CIN - Nat Rev Genet. 2019 Jun;20(6):311. doi: 10.1038/s41576-019-0131-5. PMID: 31101903 MH - Archaea/genetics/isolation & purification MH - Bacteria/genetics/isolation & purification MH - Biological Evolution MH - Communicable Diseases/*history/microbiology/parasitology/virology MH - DNA, Ancient/*analysis/isolation & purification MH - Fossils MH - *Genome MH - Genomics/*methods MH - Global Health/history MH - High-Throughput Nucleotide Sequencing/*methods MH - History, 19th Century MH - History, 21st Century MH - History, Ancient MH - History, Medieval MH - Humans MH - Public Health Surveillance/methods MH - Viruses/genetics/isolation & purification PMC - PMC7097038 COIS- The authors declare no competing interests. EDAT- 2019/04/07 06:00 MHDA- 2019/07/25 06:00 PMCR- 2020/03/26 CRDT- 2019/04/07 06:00 PHST- 2019/04/07 06:00 [pubmed] PHST- 2019/07/25 06:00 [medline] PHST- 2019/04/07 06:00 [entrez] PHST- 2020/03/26 00:00 [pmc-release] AID - 10.1038/s41576-019-0119-1 [pii] AID - 119 [pii] AID - 10.1038/s41576-019-0119-1 [doi] PST - ppublish SO - Nat Rev Genet. 2019 Jun;20(6):323-340. doi: 10.1038/s41576-019-0119-1. PMID- 30913508 OWN - NLM STAT- MEDLINE DCOM- 20200210 LR - 20200210 IS - 1879-9825 (Electronic) IS - 1879-9817 (Linking) VI - 25 DP - 2019 Jun TI - Multi-analytic study of a probable case of fibrous dysplasia (FD) from certosa monumental cemetery (Bologna, Italy). PG - 1-8 LID - S1879-9817(18)30110-4 [pii] LID - 10.1016/j.ijpp.2019.03.003 [doi] AB - OBJECTIVE: To evaluate, via a multidisciplinary approach, a distinctive paleopathological condition believed to be fibrous dysplasia, found on a 19th/20th century skeleton from Certosa Monumental Cemetery, Bologna, Italy. MATERIALS: A skeletonized cranium and mandible recovered from an ossuary in 2014. METHODS: Pathological alterations were analysed by radiological examination, dental macrowear, histopathological and genetic analyses. RESULT: The skeleton is believed to be an adult male. Differential diagnoses include Paget's disease, McCune-Albright syndrome, osteochondroma and osteosarcoma. The radiographic findings, along with the solitary nature of the lesions, are strong evidence for the diagnosis of fibrous dysplasia (FD). Genetic analysis further revealed a frequency of ˜1% of mutant alleles with the R201C substitution, one of the post-zygotic activating mutation frequently associated with FD. CONCLUSIONS: The multi-analytical method employed suggests a diagnosis of monostotic form of FD. The diagnostic design incorporates multiple lines of evidence, including macroscopic, histopathological, and genetic analyses. SIGNIFICANCE: Through the use of a multi-analytic approach, robust diagnoses can be offered. This case serves as one of the oldest examples of FD from an historical context. The genetic mutation detected, associated with FD, has not been previously reported in historical/ancient samples. CI - Copyright © 2019 Elsevier Inc. All rights reserved. FAU - Traversari, Mirko AU - Traversari M AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy. Electronic address: mirko.traversari2@unibo.it. FAU - Serrangeli, Maria Cristina AU - Serrangeli MC AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy; UCD School of Medicine, Health Science Centre, University College Dublin, Belfield, Dublin 4, Ireland. FAU - Catalano, Giulio AU - Catalano G AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy. FAU - Petrella, Enrico AU - Petrella E AD - Department of Radiology, AUSL Romagna, Morgagni-Pierantoni city hospital, via Carlo Forlanini 34, 47121, Forlì, Italy. FAU - Piciucchi, Sara AU - Piciucchi S AD - Department of Radiology, AUSL Romagna, Morgagni-Pierantoni city hospital, via Carlo Forlanini 34, 47121, Forlì, Italy. FAU - Feletti, Francesco AU - Feletti F AD - Department of Diagnostic Imaging Ausl Romagna, Santa Maria delle Croci Hospital, Viale Randi, 5, 48121 Ravenna, Italy. FAU - Oxilia, Gregorio AU - Oxilia G AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy. FAU - Cristiani, Emanuela AU - Cristiani E AD - Department of Oral and Maxillofacial Sciences, School of Dentistry, Sapienza University of Rome, Via Caserta, 6, 00161 Rome. FAU - Vazzana, Antonino AU - Vazzana A AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy. FAU - Sorrentino, Rita AU - Sorrentino R AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy; Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, Bologna, Italy. FAU - De Fanti, Sara AU - De Fanti S AD - Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, Bologna, Italy. FAU - Luiselli, Donata AU - Luiselli D AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy. FAU - Calcagnile, Lucio AU - Calcagnile L AD - CEDAD - CEnter for DAting and Diagnostics Department of Mathematics and Physics "Ennio De Giorgi", University of Salento and INFN-National Institute for Nuclear Physics, Via Monteroni, 73100, Lecce, Italy. FAU - Saragoni, Luca AU - Saragoni L AD - Department of Pathological Anatomy, AUSL Romagna, Morgagni-Pierantoni city hospital, via Carlo Forlanini 34, 47121, Forlì, Italy. FAU - Feeney, Robin N M AU - Feeney RNM AD - UCD School of Medicine, Health Science Centre, University College Dublin, Belfield, Dublin 4, Ireland. FAU - Gruppioni, Giorgio AU - Gruppioni G AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy. FAU - Cilli, Elisabetta AU - Cilli E AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy. FAU - Benazzi, Stefano AU - Benazzi S AD - Department of Cultural Heritage, University of Bologna, via degli Ariani 1, 48121, Ravenna, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190323 PL - Netherlands TA - Int J Paleopathol JT - International journal of paleopathology JID - 101562474 SB - IM MH - Adult MH - Amino Acid Substitution MH - Cemeteries/history MH - Craniofacial Fibrous Dysplasia/*diagnostic imaging/genetics/history/pathology MH - Fibrous Dysplasia, Polyostotic/diagnostic imaging/history/pathology MH - History, 19th Century MH - History, 20th Century MH - Humans MH - Italy MH - Male MH - Mutation MH - Osteitis Deformans/diagnostic imaging/pathology MH - Osteosarcoma/diagnostic imaging/history/pathology MH - Tomography, X-Ray Computed/history OTO - NOTNLM OT - Ancient DNA OT - Developmental anomaly OT - Para-functional facets OT - Pseudo-tumor EDAT- 2019/03/27 06:00 MHDA- 2020/02/11 06:00 CRDT- 2019/03/27 06:00 PHST- 2018/06/13 00:00 [received] PHST- 2019/03/08 00:00 [revised] PHST- 2019/03/08 00:00 [accepted] PHST- 2019/03/27 06:00 [pubmed] PHST- 2020/02/11 06:00 [medline] PHST- 2019/03/27 06:00 [entrez] AID - S1879-9817(18)30110-4 [pii] AID - 10.1016/j.ijpp.2019.03.003 [doi] PST - ppublish SO - Int J Paleopathol. 2019 Jun;25:1-8. doi: 10.1016/j.ijpp.2019.03.003. Epub 2019 Mar 23. PMID- 30471018 OWN - NLM STAT- MEDLINE DCOM- 20191202 LR - 20200225 IS - 1590-3478 (Electronic) IS - 1590-1874 (Linking) VI - 40 IP - 6 DP - 2019 Jun TI - The antiquity of hydrocephalus: the first full palaeo-neuropathological description. PG - 1315-1322 LID - 10.1007/s10072-018-3643-4 [doi] AB - The Pathology Museum of the University of Florence houses a rich collection of anatomical specimens and over a hundred waxworks portraying pathological conditions occurring in the nineteenth century, when the museum was established. Clinical and autopsy findings of these cases can still be retrieved from the original museum catalogue, offering a rare opportunity for retrospective palaeo-pathological diagnostics. We present a historical case of severe hydrocephalus backed by modern-day anthropological, radiological and molecular analyses conducted on the skeleton of an 18-month-old male infant deceased in 1831. Luigi Calamai (1796-1851), a wax craftsman of La Specola workshop in Florence, was commissioned to create a life-sized wax model of the child's head, neck and upper thorax. This artwork allows us to appreciate the cranial and facial alterations determined by 30 lb of cerebrospinal fluid (CSF) accumulated within the cerebral ventricular system. Based on the autopsy report, gross malformations of the neural tube, tumours and haemorrhage could be excluded. A molecular approach proved helpful in confirming sex. We present this case as the so-far most compelling case of hydrocephalus in palaeo-pathological research. FAU - Santi, Raffaella AU - Santi R AD - Division of Pathological Anatomy, Department of Surgery and Translational Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy. FAU - Rizzolo, Piera AU - Rizzolo P AD - Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy. FAU - Pietragalla, Michele AU - Pietragalla M AD - Radiology Section, University of Florence, Florence, Italy. FAU - Valentini, Virginia AU - Valentini V AD - Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy. FAU - Zelli, Veronica AU - Zelli V AD - Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy. FAU - Galassi, Francesco Maria AU - Galassi FM AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Ottini, Laura AU - Ottini L AD - Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy. FAU - Nesi, Gabriella AU - Nesi G AUID- ORCID: 0000-0002-2614-944X AD - Division of Pathological Anatomy, Department of Surgery and Translational Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy. gabriella.nesi@unifi.it. LA - eng GR - no grant number/Mäxi Foundation/ PT - Historical Article PT - Journal Article DEP - 20181123 PL - Italy TA - Neurol Sci JT - Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology JID - 100959175 RN - 0 (DNA, Ancient) RN - 0 (Waxes) SB - IM MH - DNA, Ancient MH - History, 19th Century MH - Humans MH - Hydrocephalus/diagnostic imaging/*genetics/history/*pathology MH - Infant MH - Italy MH - Male MH - *Models, Anatomic MH - Museums MH - Sculpture MH - Waxes OTO - NOTNLM OT - Ancient DNA OT - Hydrocephalus OT - Palaeo-radiology OT - Palaeoneurology OT - Pathology museum OT - Wax models EDAT- 2018/11/25 06:00 MHDA- 2019/12/04 06:00 CRDT- 2018/11/25 06:00 PHST- 2018/06/12 00:00 [received] PHST- 2018/11/08 00:00 [accepted] PHST- 2018/11/25 06:00 [pubmed] PHST- 2019/12/04 06:00 [medline] PHST- 2018/11/25 06:00 [entrez] AID - 10.1007/s10072-018-3643-4 [pii] AID - 10.1007/s10072-018-3643-4 [doi] PST - ppublish SO - Neurol Sci. 2019 Jun;40(6):1315-1322. doi: 10.1007/s10072-018-3643-4. Epub 2018 Nov 23. PMID- 31061125 OWN - NLM STAT- MEDLINE DCOM- 20200330 LR - 20200330 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 116 IP - 22 DP - 2019 May 28 TI - Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave. PG - 10705-10710 LID - 10.1073/pnas.1820210116 [doi] AB - The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300-2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community. CI - Copyright © 2019 the Author(s). Published by PNAS. FAU - Schroeder, Hannes AU - Schroeder H AUID- ORCID: 0000-0002-6743-0270 AD - Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1353 Copenhagen K, Denmark; hschroeder@bio.ku.dk nnj@cas.au.dk meallentoft@bio.ku.dk. FAU - Margaryan, Ashot AU - Margaryan A AD - Lundbeck Foundation GeoGenetics Centre, Department of Biology, University of Copenhagen, 1350 Copenhagen K, Denmark. AD - Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, 0014 Yerevan, Armenia. FAU - Szmyt, Marzena AU - Szmyt M AD - Institute of Eastern Studies, Adam Mickiewicz University, 61-614 Poznań, Poland. AD - Archaeological Museum, 61-781 Poznań, Poland. FAU - Theulot, Bertrand AU - Theulot B AD - Lundbeck Foundation GeoGenetics Centre, Department of Biology, University of Copenhagen, 1350 Copenhagen K, Denmark. FAU - Włodarczak, Piotr AU - Włodarczak P AD - Institute of Archaeology and Ethnology, Polish Academy of Sciences, Centre for Mountains and Uplands Archaeology, 31-016 Kraków, Poland. FAU - Rasmussen, Simon AU - Rasmussen S AUID- ORCID: 0000-0001-6323-9041 AD - Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark. AD - Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark. FAU - Gopalakrishnan, Shyam AU - Gopalakrishnan S AD - Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1353 Copenhagen K, Denmark. FAU - Szczepanek, Anita AU - Szczepanek A AUID- ORCID: 0000-0003-0936-767X AD - Institute of Archaeology and Ethnology, Polish Academy of Sciences, Centre for Mountains and Uplands Archaeology, 31-016 Kraków, Poland. AD - Department of Anatomy, Jagiellonian University Medical College, 31-034 Kraków, Poland. FAU - Konopka, Tomasz AU - Konopka T AD - Department of Forensic Medicine, Jagiellonian University Collegium Medicum, 31-008 Kraków, Poland. FAU - Jensen, Theis Z T AU - Jensen TZT AD - Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1353 Copenhagen K, Denmark. AD - BioArCh, Department of Archaeology, University of York, York YO10 5NG, United Kingdom. FAU - Witkowska, Barbara AU - Witkowska B AD - Institute of Eastern Studies, Adam Mickiewicz University, 61-614 Poznań, Poland. AD - Archaeological Museum, 61-781 Poznań, Poland. AD - Institute of Archaeology, Jagiellonian University, 31-007 Kraków, Poland. FAU - Wilk, Stanisław AU - Wilk S AD - Institute of Archaeology, Jagiellonian University, 31-007 Kraków, Poland. FAU - Przybyła, Marcin M AU - Przybyła MM AD - Dolmen S.C., 30-512 Kraków, Poland. FAU - Pospieszny, Łukasz AU - Pospieszny Ł AD - Institute of Archaeology and Ethnology, Centre for Studies into Late Antiquity and Early Medieval Times, Polish Academy of Sciences, 61-612 Poznań, Poland. AD - Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, United Kingdom. FAU - Sjögren, Karl-Göran AU - Sjögren KG AD - Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. FAU - Belka, Zdzislaw AU - Belka Z AUID- ORCID: 0000-0001-9634-610X AD - Isotope Laboratory, Adam Mickiewicz University, 61-680 Poznań, Poland. FAU - Olsen, Jesper AU - Olsen J AD - Aarhus AMS Centre, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark. FAU - Kristiansen, Kristian AU - Kristiansen K AD - Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. FAU - Willerslev, Eske AU - Willerslev E AD - Lundbeck Foundation GeoGenetics Centre, Department of Biology, University of Copenhagen, 1350 Copenhagen K, Denmark. AD - Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdom. AD - Wellcome Trust Sanger Institute, CB10 1SA Hinxton, United Kingdom. FAU - Frei, Karin M AU - Frei KM AUID- ORCID: 0000-0001-5198-073X AD - Unit for Environmental Archaeology and Materials Science, National Museum of Denmark, 1220 Copenhagen K, Denmark. FAU - Sikora, Martin AU - Sikora M AD - Lundbeck Foundation GeoGenetics Centre, Department of Biology, University of Copenhagen, 1350 Copenhagen K, Denmark. FAU - Johannsen, Niels N AU - Johannsen NN AD - Department of Archaeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark hschroeder@bio.ku.dk nnj@cas.au.dk meallentoft@bio.ku.dk. FAU - Allentoft, Morten E AU - Allentoft ME AD - Lundbeck Foundation GeoGenetics Centre, Department of Biology, University of Copenhagen, 1350 Copenhagen K, Denmark; hschroeder@bio.ku.dk nnj@cas.au.dk meallentoft@bio.ku.dk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190506 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Adolescent MH - Adult MH - Archaeology MH - Burial/*history MH - Child MH - Child, Preschool MH - DNA, Ancient/*analysis MH - Female MH - History, Ancient MH - Human Migration MH - Humans MH - Infant MH - Male MH - Middle Aged MH - Pedigree MH - Poland MH - Violence/*history MH - Young Adult PMC - PMC6561172 OTO - NOTNLM OT - ancient DNA OT - archaeology OT - kinship OT - migration OT - violence COIS- The authors declare no conflict of interest. EDAT- 2019/05/08 06:00 MHDA- 2020/03/31 06:00 PMCR- 2019/05/06 CRDT- 2019/05/08 06:00 PHST- 2019/05/08 06:00 [pubmed] PHST- 2020/03/31 06:00 [medline] PHST- 2019/05/08 06:00 [entrez] PHST- 2019/05/06 00:00 [pmc-release] AID - 1820210116 [pii] AID - 201820210 [pii] AID - 10.1073/pnas.1820210116 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2019 May 28;116(22):10705-10710. doi: 10.1073/pnas.1820210116. Epub 2019 May 6. PMID- 31124326 OWN - NLM STAT- MEDLINE DCOM- 20191114 LR - 20200225 IS - 1598-6357 (Electronic) IS - 1011-8934 (Print) IS - 1011-8934 (Linking) VI - 34 IP - 20 DP - 2019 May 27 TI - Cytochrome C Oxidase Subunit 1, Internal Transcribed Spacer 1, Nicotinamide Adenine Dinucleotide Hydrogen Dehydrogenase Subunits 2 and 5 of Clonorchis sinensis Ancient DNA Retrieved from Joseon Dynasty Mummy Specimens. PG - e149 LID - 10.3346/jkms.2019.34.e149 [doi] LID - e149 AB - We analyzed Clonorchis sinensis ancient DNA (aDNA) acquired from the specimens of the Joseon mummies. The target regions were cytochrome C oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits 2 (NAD2) and 5 (NAD5). The sequences of C. sinensis aDNA was completely or almost identical to modern C. sinensis sequences in GenBank. We also found that ITS1, NAD2 and NAD5 could be good markers for molecular diagnosis between C. sinensis and the other trematode parasite species. The current result could improve our knowledge about genetic history of C. sinensis. CI - © 2019 The Korean Academy of Medical Sciences. FAU - Hong, Jong Ha AU - Hong JH AUID- ORCID: 0000-0002-9104-3908 AD - Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, Korea. FAU - Oh, Chang Seok AU - Oh CS AUID- ORCID: 0000-0001-6913-1832 AD - Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, Korea. AD - Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea. FAU - Chai, Jong Yil AU - Chai JY AUID- ORCID: 0000-0002-8366-0674 AD - Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul, Korea. AD - Institute of Parasitic Diseases, Korean Association of Health Promotion, Seoul, Korea. FAU - Seo, Min AU - Seo M AUID- ORCID: 0000-0002-1765-0240 AD - Department of Parasitology, Dankook University College of Medicine, Cheonan, Korea. bbbenji@naver.com. FAU - Shin, Dong Hoon AU - Shin DH AUID- ORCID: 0000-0001-8032-1266 AD - Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, Korea. AD - Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea. cuteminjae@gmail.com. LA - eng GR - NRF-2016R1A2B4015669/NRF/National Research Foundation of Korea/Korea PT - Journal Article DEP - 20190527 PL - Korea (South) TA - J Korean Med Sci JT - Journal of Korean medical science JID - 8703518 RN - 0 (DNA, Ancient) RN - 0 (Protein Subunits) RN - EC 1.- (Oxidoreductases) RN - EC 1.12.1.2 (hydrogen dehydrogenase) RN - EC 1.9.3.1 (Electron Transport Complex IV) SB - IM MH - Animals MH - Clonorchiasis/diagnosis/epidemiology MH - Clonorchis sinensis/classification/*genetics MH - DNA, Ancient/*chemistry/isolation & purification MH - Electron Transport Complex IV/chemistry/classification/*genetics MH - Humans MH - Mummies/parasitology MH - Oxidoreductases/chemistry/classification/*genetics MH - Phylogeny MH - Protein Subunits/chemistry/classification/genetics MH - Republic of Korea MH - Sequence Analysis, DNA PMC - PMC6535405 OTO - NOTNLM OT - Ancient DNA OT - Clonorchis sinensis OT - Mummies OT - Phylogenetic Analysis OT - Republic of Korea COIS- The authors have no potential conflicts of interest to disclose. EDAT- 2019/05/28 06:00 MHDA- 2019/11/15 06:00 PMCR- 2019/05/27 CRDT- 2019/05/25 06:00 PHST- 2019/04/10 00:00 [received] PHST- 2019/05/06 00:00 [accepted] PHST- 2019/05/25 06:00 [entrez] PHST- 2019/05/28 06:00 [pubmed] PHST- 2019/11/15 06:00 [medline] PHST- 2019/05/27 00:00 [pmc-release] AID - 34.e149 [pii] AID - 10.3346/jkms.2019.34.e149 [doi] PST - epublish SO - J Korean Med Sci. 2019 May 27;34(20):e149. doi: 10.3346/jkms.2019.34.e149. PMID- 31036632 OWN - NLM STAT- MEDLINE DCOM- 20200330 LR - 20220129 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 116 IP - 21 DP - 2019 May 21 TI - Molecular insights into an ancient form of Paget's disease of bone. PG - 10463-10472 LID - 10.1073/pnas.1820556116 [doi] AB - Paget's disease of bone (PDB) is a chronic skeletal disorder that can affect one or several bones in individuals older than 55 y of age. PDB-like changes have been reported in archaeological remains as old as Roman, although accurate diagnosis and natural history of the disease is lacking. Six skeletons from a collection of 130 excavated at Norton Priory in the North West of England, which dates to medieval times, show atypical and extensive pathological changes resembling contemporary PDB affecting as many as 75% of individual skeletons. Disease prevalence in the remaining collection is high, at least 16% of adults, with age at death estimations as low as 35 y. Despite these atypical features, paleoproteomic analysis identified sequestosome 1 (SQSTM1) or p62, a protein central to the pathological milieu of PDB, as one of the few noncollagenous human sequences preserved in skeletal samples. Targeted proteomic analysis detected >60% of the ancient p62 primary sequence, with Western blotting indicating p62 abnormalities, including in dentition. Direct sequencing of ancient DNA excluded contemporary PDB-associated SQSTM1 mutations. Our observations indicate that the ancient p62 protein is likely modified within its C-terminal ubiquitin-associated domain. Ancient miRNAs were remarkably preserved in an osteosarcoma from a skeleton with extensive disease, with miR-16 expression consistent with that reported in contemporary PDB-associated bone tumors. Our work displays the use of proteomics to inform diagnosis of ancient diseases such as atypical PDB, which has unusual features presumably potentiated by yet-unidentified environmental or genetic factors. CI - Copyright © 2019 the Author(s). Published by PNAS. FAU - Shaw, Barry AU - Shaw B AD - School of Life Sciences, University of Nottingham, NG7 2UH Nottingham, United Kingdom. FAU - Burrell, Carla L AU - Burrell CL AD - Research Centre for Evolutionary Anthropology and Paleoecology, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom. AD - Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands. FAU - Green, Darrell AU - Green D AUID- ORCID: 0000-0002-0217-3322 AD - Norwich Medical School, University of East Anglia, NR4 7TJ Norwich, United Kingdom. FAU - Navarro-Martinez, Ana AU - Navarro-Martinez A AD - School of Life Sciences, University of Nottingham, NG7 2UH Nottingham, United Kingdom. FAU - Scott, Daniel AU - Scott D AD - School of Life Sciences, University of Nottingham, NG7 2UH Nottingham, United Kingdom. FAU - Daroszewska, Anna AU - Daroszewska A AD - Institute of Ageing and Chronic Disease, University of Liverpool, L7 8TX Liverpool, United Kingdom. AD - Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool and Broadgreen University Hospitals National Health Service Trust, L7 8XP Liverpool, United Kingdom. AD - Department of Rheumatology, Royal Liverpool and Broadgreen University Hospitals National Health Service Trust, L7 8XP Liverpool, United Kingdom. FAU - van 't Hof, Rob AU - van 't Hof R AD - Institute of Ageing and Chronic Disease, University of Liverpool, L7 8TX Liverpool, United Kingdom. FAU - Smith, Lynn AU - Smith L AD - Norton Priory Museum and Gardens, WA7 1SX Runcorn, United Kingdom. FAU - Hargrave, Frank AU - Hargrave F AD - Norton Priory Museum and Gardens, WA7 1SX Runcorn, United Kingdom. FAU - Mistry, Sharad AU - Mistry S AD - Protein & Nucleic Acid Chemistry Laboratory, University of Leicester, LE1 9HN Leicester, United Kingdom. FAU - Bottrill, Andrew AU - Bottrill A AD - Protein & Nucleic Acid Chemistry Laboratory, University of Leicester, LE1 9HN Leicester, United Kingdom. FAU - Kessler, Benedikt M AU - Kessler BM AD - Target Discovery Institute, University of Oxford, OX3 7FZ Oxford, United Kingdom. FAU - Fischer, Roman AU - Fischer R AD - Target Discovery Institute, University of Oxford, OX3 7FZ Oxford, United Kingdom. FAU - Singh, Archana AU - Singh A AUID- ORCID: 0000-0002-5027-4582 AD - School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, United Kingdom. FAU - Dalmay, Tamas AU - Dalmay T AD - School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, United Kingdom. FAU - Fraser, William D AU - Fraser WD AD - Norwich Medical School, University of East Anglia, NR4 7TJ Norwich, United Kingdom. AD - Department of Clinical Biochemistry, Norfolk and Norwich University Hospital, NR4 7UY Norwich, United Kingdom. FAU - Henneberger, Kirstin AU - Henneberger K AD - Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany. FAU - King, Turi AU - King T AD - Department of Genetics and Genome Biology, University of Leicester, LE1 7RH Leicester, United Kingdom. FAU - Gonzalez, Silvia AU - Gonzalez S AD - Research Centre for Evolutionary Anthropology and Paleoecology, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom. FAU - Layfield, Robert AU - Layfield R AD - School of Life Sciences, University of Nottingham, NG7 2UH Nottingham, United Kingdom; robert.layfield@nottingham.ac.uk. LA - eng GR - Wellcome Trust/United Kingdom GR - MR/P020941/1/MRC_/Medical Research Council/United Kingdom GR - 107720/Z/15/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190429 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (MicroRNAs) RN - 0 (Proteome) RN - 0 (SQSTM1 protein, human) RN - 0 (Sequestosome-1 Protein) SB - IM MH - Bone and Bones/*metabolism/pathology MH - History, Medieval MH - Humans MH - MicroRNAs/metabolism MH - Osteitis Deformans/complications/*metabolism/pathology MH - Osteosarcoma/etiology/metabolism MH - Paleopathology MH - *Proteome MH - Sequence Analysis, DNA MH - Sequestosome-1 Protein/chemistry/*metabolism PMC - PMC6535003 OTO - NOTNLM OT - Paget’s disease OT - SQSTM1 OT - osteosarcoma OT - p62 OT - paleoproteomic COIS- The authors declare no conflict of interest. EDAT- 2019/05/01 06:00 MHDA- 2020/03/31 06:00 PMCR- 2019/04/29 CRDT- 2019/05/01 06:00 PHST- 2019/05/01 06:00 [pubmed] PHST- 2020/03/31 06:00 [medline] PHST- 2019/05/01 06:00 [entrez] PHST- 2019/04/29 00:00 [pmc-release] AID - 1820556116 [pii] AID - 201820556 [pii] AID - 10.1073/pnas.1820556116 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2019 May 21;116(21):10463-10472. doi: 10.1073/pnas.1820556116. Epub 2019 Apr 29. PMID- 31080083 OWN - NLM STAT- MEDLINE DCOM- 20200615 LR - 20231012 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 29 IP - 10 DP - 2019 May 20 TI - The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East. PG - 1701-1711.e16 LID - S0960-9822(19)30424-5 [pii] LID - 10.1016/j.cub.2019.04.026 [doi] AB - In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200-400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC-50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC-450 AD) (IngIA) and 7 Middle Age Estonian (1200-1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1-5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic. VIDEO ABSTRACT. CI - Copyright © 2019 Elsevier Ltd. All rights reserved. FAU - Saag, Lehti AU - Saag L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia. Electronic address: lehti.saag@ut.ee. FAU - Laneman, Margot AU - Laneman M AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia. FAU - Varul, Liivi AU - Varul L AD - School of Humanities, Tallinn University, Tallinn 10120, Estonia. FAU - Malve, Martin AU - Malve M AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia. FAU - Valk, Heiki AU - Valk H AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia. FAU - Razzak, Maria A AU - Razzak MA AD - Department of Slavic and Finnic Archaeology, Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia. FAU - Shirobokov, Ivan G AU - Shirobokov IG AD - Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg 199034, Russia. FAU - Khartanovich, Valeri I AU - Khartanovich VI AD - Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg 199034, Russia. FAU - Mikhaylova, Elena R AU - Mikhaylova ER AD - Saint Petersburg State University, St. Petersburg 199034, Russia. FAU - Kushniarevich, Alena AU - Kushniarevich A AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Scheib, Christiana Lyn AU - Scheib CL AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Solnik, Anu AU - Solnik A AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Reisberg, Tuuli AU - Reisberg T AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Parik, Jüri AU - Parik J AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia. FAU - Saag, Lauri AU - Saag L AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Metspalu, Ene AU - Metspalu E AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Rootsi, Siiri AU - Rootsi S AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Montinaro, Francesco AU - Montinaro F AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Remm, Maido AU - Remm M AD - Department of Bioinformatics, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia. FAU - Mägi, Reedik AU - Mägi R AD - Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - D'Atanasio, Eugenia AU - D'Atanasio E AD - Department of Human Genetics, KU Leuven, Leuven 3000, Belgium. FAU - Crema, Enrico Ryunosuke AU - Crema ER AD - Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, UK. FAU - Díez-Del-Molino, David AU - Díez-Del-Molino D AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 104 05, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Stockholm 106 91, Sweden. FAU - Thomas, Mark G AU - Thomas MG AD - Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; UCL Genetics Institute, University College London, London WC1E 6BT, UK. FAU - Kriiska, Aivar AU - Kriiska A AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia. FAU - Kivisild, Toomas AU - Kivisild T AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven 3000, Belgium. FAU - Villems, Richard AU - Villems R AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia. FAU - Lang, Valter AU - Lang V AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia. FAU - Metspalu, Mait AU - Metspalu M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. FAU - Tambets, Kristiina AU - Tambets K AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia. Electronic address: kristiina.tambets@ut.ee. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 261213/ERC_/European Research Council/International GR - 100719/Z/12/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190509 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - DNA, Ancient/*analysis MH - Estonia MH - Female MH - *Gene Flow MH - History, Ancient MH - History, Medieval MH - *Human Migration MH - Humans MH - Male MH - *Phenotype PMC - PMC6544527 MID - EMS82666 OTO - NOTNLM OT - Bronze Age OT - Eastern Baltic OT - Estonia OT - Iron Age OT - Middle Ages OT - ancient DNA OT - kinship OT - phenotype OT - population genetics OT - shotgun sequencing COIS- Declaration of Interests The authors declare no competing financial interests. EDAT- 2019/05/14 06:00 MHDA- 2020/06/17 06:00 PMCR- 2019/05/31 CRDT- 2019/05/14 06:00 PHST- 2019/02/05 00:00 [received] PHST- 2019/03/18 00:00 [revised] PHST- 2019/04/09 00:00 [accepted] PHST- 2019/05/14 06:00 [pubmed] PHST- 2020/06/17 06:00 [medline] PHST- 2019/05/14 06:00 [entrez] PHST- 2019/05/31 00:00 [pmc-release] AID - S0960-9822(19)30424-5 [pii] AID - 10.1016/j.cub.2019.04.026 [doi] PST - ppublish SO - Curr Biol. 2019 May 20;29(10):1701-1711.e16. doi: 10.1016/j.cub.2019.04.026. Epub 2019 May 9. PMID- 31123709 OWN - NLM STAT- MEDLINE DCOM- 20200420 LR - 20240716 IS - 2399-3642 (Electronic) IS - 2399-3642 (Linking) VI - 2 DP - 2019 TI - Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia. PG - 185 LID - 10.1038/s42003-019-0399-1 [doi] LID - 185 AB - Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations. FAU - Kashuba, Natalija AU - Kashuba N AD - 1Museum of Cultural History, University of Oslo, P.O. Box 6762. St. Olavs Plass, NO-0130 Oslo, Norway. AD - 2Department of Archaeology and Ancient History, Uppsala University, P.O. Box 626, SE-751 26 Uppsala, Sweden. FAU - Kırdök, Emrah AU - Kırdök E AD - 3Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden. FAU - Damlien, Hege AU - Damlien H AD - 1Museum of Cultural History, University of Oslo, P.O. Box 6762. St. Olavs Plass, NO-0130 Oslo, Norway. FAU - Manninen, Mikael A AU - Manninen MA AUID- ORCID: 0000-0002-8906-6502 AD - 1Museum of Cultural History, University of Oslo, P.O. Box 6762. St. Olavs Plass, NO-0130 Oslo, Norway. FAU - Nordqvist, Bengt AU - Nordqvist B AD - Foundation War-Booty Site Finnestorp, Klarinettvägen 75, SE-434 75 Kungsbacka, Sweden. FAU - Persson, Per AU - Persson P AD - 1Museum of Cultural History, University of Oslo, P.O. Box 6762. St. Olavs Plass, NO-0130 Oslo, Norway. FAU - Götherström, Anders AU - Götherström A AD - 3Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden. LA - eng SI - Dryad/10.5061/dryad.j3k19p9 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190515 PL - England TA - Commun Biol JT - Communications biology JID - 101719179 RN - 0 (Chewing Gum) RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - 0 (Mastic Resin) RN - 0 (Resins, Plant) RN - 88S87KL877 (rosin) MH - Anthropology, Cultural/history MH - Betula/chemistry MH - Chewing Gum/history MH - DNA, Ancient/*isolation & purification MH - DNA, Mitochondrial/genetics/history MH - Genetics, Population/history MH - History, Ancient MH - Human Migration/history MH - Humans MH - Mastic Resin/history MH - Resins, Plant/history MH - Scandinavian and Nordic Countries PMC - PMC6520363 OTO - NOTNLM OT - Genomics OT - Population genetics COIS- The authors declare no competing interests. EDAT- 2019/05/28 06:00 MHDA- 2019/05/28 06:01 PMCR- 2019/05/15 CRDT- 2019/05/25 06:00 PHST- 2018/11/15 00:00 [received] PHST- 2019/03/21 00:00 [accepted] PHST- 2019/05/25 06:00 [entrez] PHST- 2019/05/28 06:00 [pubmed] PHST- 2019/05/28 06:01 [medline] PHST- 2019/05/15 00:00 [pmc-release] AID - 399 [pii] AID - 10.1038/s42003-019-0399-1 [doi] PST - epublish SO - Commun Biol. 2019 May 15;2:185. doi: 10.1038/s42003-019-0399-1. eCollection 2019. PMID- 31075917 OWN - NLM STAT- MEDLINE DCOM- 20191219 LR - 20200309 IS - 2073-4409 (Print) IS - 2073-4409 (Electronic) IS - 2073-4409 (Linking) VI - 8 IP - 5 DP - 2019 May 9 TI - Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases. LID - 10.3390/cells8050433 [doi] LID - 433 AB - Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases-and profiling, in certain conditions-especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven's grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge. FAU - Merheb, Maxime AU - Merheb M AD - Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah 10021, UAE. maximemerheb@yahoo.fr. FAU - Matar, Rachel AU - Matar R AD - Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah 10021, UAE. rachel.matar@aurak.ac.ae. FAU - Hodeify, Rawad AU - Hodeify R AD - Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah 10021, UAE. rawad.hodeify@aurak.ac.ae. FAU - Siddiqui, Shoib Sarwar AU - Siddiqui SS AD - Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah 10021, UAE. shoib.siddiqui@aurak.ac.ae. FAU - Vazhappilly, Cijo George AU - Vazhappilly CG AD - Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah 10021, UAE. cijo.vazhappilly@aurak.ac.ae. FAU - Marton, John AU - Marton J AD - Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah 10021, UAE. jmarton@aurak.ac.ae. FAU - Azharuddin, Syed AU - Azharuddin S AD - Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah 10021, UAE. azharuddin.syed@aurak.ac.ae. FAU - Al Zouabi, Hussain AU - Al Zouabi H AD - Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah 10021, UAE. hussain.zouabi@aurak.ac.ae. LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20190509 PL - Switzerland TA - Cells JT - Cells JID - 101600052 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - *Civilization MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics MH - *Domestication MH - History, 18th Century MH - Homicide/*history MH - Humans MH - *Music PMC - PMC6562384 OTO - NOTNLM OT - Beethoven OT - Erard OT - Louis XVII OT - Tsar Nicholas II OT - ancient DNA OT - ancient glue OT - ancient human diet OT - ancient leather OT - ancient trade routes OT - burnt human remains OT - domestication OT - mitochondrial DNA OT - mummies COIS- The authors declare no conflict of interest. EDAT- 2019/05/12 06:00 MHDA- 2019/05/12 06:01 PMCR- 2019/05/01 CRDT- 2019/05/12 06:00 PHST- 2019/02/27 00:00 [received] PHST- 2019/04/17 00:00 [revised] PHST- 2019/05/07 00:00 [accepted] PHST- 2019/05/12 06:00 [entrez] PHST- 2019/05/12 06:00 [pubmed] PHST- 2019/05/12 06:01 [medline] PHST- 2019/05/01 00:00 [pmc-release] AID - cells8050433 [pii] AID - cells-08-00433 [pii] AID - 10.3390/cells8050433 [doi] PST - epublish SO - Cells. 2019 May 9;8(5):433. doi: 10.3390/cells8050433. PMID- 31006515 OWN - NLM STAT- MEDLINE DCOM- 20200206 LR - 20221207 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 104 IP - 5 DP - 2019 May 2 TI - A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences. PG - 977-984 LID - S0002-9297(19)30111-9 [pii] LID - 10.1016/j.ajhg.2019.03.015 [doi] AB - During the medieval period, hundreds of thousands of Europeans migrated to the Near East to take part in the Crusades, and many of them settled in the newly established Christian states along the Eastern Mediterranean coast. Here, we present a genetic snapshot of these events and their aftermath by sequencing the whole genomes of 13 individuals who lived in what is today known as Lebanon between the 3(rd) and 13(th) centuries CE. These include nine individuals from the "Crusaders' pit" in Sidon, a mass burial in South Lebanon identified from the archaeology as the grave of Crusaders killed during a battle in the 13(th) century CE. We show that all of the Crusaders' pit individuals were males; some were Western Europeans from diverse origins, some were locals (genetically indistinguishable from present-day Lebanese), and two individuals were a mixture of European and Near Eastern ancestries, providing direct evidence that the Crusaders admixed with the local population. However, these mixtures appear to have had limited genetic consequences since signals of admixture with Europeans are not significant in any Lebanese group today-in particular, Lebanese Christians are today genetically similar to local people who lived during the Roman period which preceded the Crusades by more than four centuries. CI - Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved. FAU - Haber, Marc AU - Haber M AD - Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Electronic address: mh25@sanger.ac.uk. FAU - Doumet-Serhal, Claude AU - Doumet-Serhal C AD - The Sidon excavation, Saida, Lebanon. FAU - Scheib, Christiana L AU - Scheib CL AD - Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK. FAU - Xue, Yali AU - Xue Y AD - Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. FAU - Mikulski, Richard AU - Mikulski R AD - Department of Archaeology, Anthropology, and Forensic Science, Bournemouth University, Talbot Campus, Poole BH12 5BB, UK. FAU - Martiniano, Rui AU - Martiniano R AD - Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK. FAU - Fischer-Genz, Bettina AU - Fischer-Genz B AD - Publication Department, Orient-Institut Beirut, Beirut 11-2988, Lebanon. FAU - Schutkowski, Holger AU - Schutkowski H AD - Department of Archaeology, Anthropology, and Forensic Science, Bournemouth University, Talbot Campus, Poole BH12 5BB, UK. FAU - Kivisild, Toomas AU - Kivisild T AD - Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK. FAU - Tyler-Smith, Chris AU - Tyler-Smith C AD - Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Electronic address: cts@sanger.ac.uk. LA - eng GR - WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190418 PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Mitochondrial) SB - IM MH - Chromosomes, Human, Y/genetics MH - DNA, Mitochondrial/analysis/genetics MH - Ethnicity/*genetics/*history MH - Female MH - *Gene Flow MH - *Genetics, Population MH - *Genome, Human MH - History, Ancient MH - Humans MH - Lebanon/ethnology MH - Male MH - White People/*genetics PMC - PMC6506814 OTO - NOTNLM OT - Lebanon OT - Roman period OT - Sidon OT - aDNA OT - medieval period OT - population history OT - whole-genome sequences EDAT- 2019/04/23 06:00 MHDA- 2020/02/07 06:00 PMCR- 2019/11/02 CRDT- 2019/04/23 06:00 PHST- 2019/01/14 00:00 [received] PHST- 2019/03/18 00:00 [accepted] PHST- 2019/04/23 06:00 [pubmed] PHST- 2020/02/07 06:00 [medline] PHST- 2019/04/23 06:00 [entrez] PHST- 2019/11/02 00:00 [pmc-release] AID - S0002-9297(19)30111-9 [pii] AID - 10.1016/j.ajhg.2019.03.015 [doi] PST - ppublish SO - Am J Hum Genet. 2019 May 2;104(5):977-984. doi: 10.1016/j.ajhg.2019.03.015. Epub 2019 Apr 18. PMID- 30994442 OWN - NLM STAT- MEDLINE DCOM- 20190514 LR - 20190924 IS - 1473-5644 (Electronic) IS - 0022-2615 (Linking) VI - 68 IP - 5 DP - 2019 May TI - Molecular detection of Treponema pallidum subspecies pallidum in 150-year-old foetal remains, southeastern France. PG - 761-769 LID - 10.1099/jmm.0.000978 [doi] AB - PURPOSE: Syphilis, caused by Treponema pallidum subspecies pallidum , is considered as an old disease affecting humans; traces of such infections, including congenital syphilis, are potentially identifiable in archaeological samples. The aim of this research was to perform macroscopic and molecular investigations of T. pallidum on six infant remains, buried between 1837 and 1867, from the cemetery of 'Les Crottes' in Marseille city (southeastern France). METHODOLOGY: Pathological analysis of bones from individuals, aged from the twenty-ninth week of amenorrhea to 4-9 months, was performed. Samples served also as a source of ancient DNA (aDNA) for PCR-based molecular investigations targeting T. pallidum DNA; all samples were also tested for Mycobacterium tuberculosis and Plasmodium falciparum DNA. Sequences characterized were cloned and sequenced, and compared to those available in databases.Results/Key findings. All samples tested displayed widespread osteoporotic lesions across the skeleton possibly related to some metabolic or infectious disorders. Subsequent molecular analysis revealed that one individual, SP332 (unborn, 29 amenorrhea weeks, inhumation date 1864-1866), exhibited positive signals for the five T. pallidum amplification systems tested; sequence analysis provided strong evidence for the effective detection of T. pallidum subspecies pallidum DNA. CONCLUSIONS: Individual SP332 is the first PCR-confirmed palaeopathological case of syphilis identified in France, and the youngest specimen ever to be diagnosed with certainty for congenital syphilis. Future research aimed at better characterizing this 150-year-old treponeme genome and exploring new archaelogical cases of syphilis in the very young should contribute to a better comprehension of the disease's history. FAU - Meffray, Avril AU - Meffray A AD - Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France. FAU - Perrin, Marie AU - Perrin M AD - Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France. FAU - Richier, Anne AU - Richier A AD - Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France. AD - INRAP Mediterranee, Marseille, France. FAU - Schmitt, Aurore AU - Schmitt A AD - Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France. FAU - Ardagna, Yann AU - Ardagna Y AD - Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France. FAU - Biagini, Philippe AU - Biagini P AD - Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France. LA - eng PT - Historical Article PT - Journal Article DEP - 20190417 PL - England TA - J Med Microbiol JT - Journal of medical microbiology JID - 0224131 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Cemeteries MH - DNA, Ancient/*isolation & purification MH - Fetus/microbiology MH - France MH - History, 19th Century MH - Humans MH - Infant MH - Mycobacterium tuberculosis/genetics MH - Plasmodium falciparum/genetics MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA MH - Syphilis, Congenital/history/*microbiology MH - Treponema pallidum/classification/*isolation & purification OTO - NOTNLM OT - PCR OT - ancient DNA OT - congenital syphilis OT - palaeomicrobiology OT - palaeopathology OT - skeletal treponematosis EDAT- 2019/04/18 06:00 MHDA- 2019/05/15 06:00 CRDT- 2019/04/18 06:00 PHST- 2019/04/18 06:00 [pubmed] PHST- 2019/05/15 06:00 [medline] PHST- 2019/04/18 06:00 [entrez] AID - 10.1099/jmm.0.000978 [doi] PST - ppublish SO - J Med Microbiol. 2019 May;68(5):761-769. doi: 10.1099/jmm.0.000978. Epub 2019 Apr 17. PMID- 30988490 OWN - NLM STAT- MEDLINE DCOM- 20191011 LR - 20230615 IS - 2397-334X (Electronic) IS - 2397-334X (Linking) VI - 3 IP - 5 DP - 2019 May TI - Ancient genomes indicate population replacement in Early Neolithic Britain. PG - 765-771 LID - 10.1038/s41559-019-0871-9 [doi] AB - The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC. FAU - Brace, Selina AU - Brace S AD - Department of Earth Sciences, Natural History Museum, London, UK. FAU - Diekmann, Yoan AU - Diekmann Y AD - Research Department of Genetics, Evolution and Environment, University College London, London, UK. FAU - Booth, Thomas J AU - Booth TJ AD - Department of Earth Sciences, Natural History Museum, London, UK. FAU - van Dorp, Lucy AU - van Dorp L AUID- ORCID: 0000-0002-6211-2310 AD - UCL Genetics Institute, University College London, London, UK. FAU - Faltyskova, Zuzana AU - Faltyskova Z AD - Research Department of Genetics, Evolution and Environment, University College London, London, UK. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Mallick, Swapan AU - Mallick S AD - UCL Genetics Institute, University College London, London, UK. AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Olalde, Iñigo AU - Olalde I AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Martiniano, Rui AU - Martiniano R AUID- ORCID: 0000-0003-0216-778X AD - Department of Genetics, University of Cambridge, Cambridge, UK. FAU - Walsh, Susan AU - Walsh S AD - Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA. FAU - Kayser, Manfred AU - Kayser M AUID- ORCID: 0000-0002-4958-847X AD - Department of Genetic Identification, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands. FAU - Charlton, Sophy AU - Charlton S AUID- ORCID: 0000-0001-7487-2635 AD - Department of Earth Sciences, Natural History Museum, London, UK. AD - Bioarch, University of York, York, UK. FAU - Hellenthal, Garrett AU - Hellenthal G AD - UCL Genetics Institute, University College London, London, UK. FAU - Armit, Ian AU - Armit I AUID- ORCID: 0000-0001-8669-3810 AD - School of Archaeological and Forensic Sciences, University of Bradford, Bradford, UK. FAU - Schulting, Rick AU - Schulting R AD - Institute of Archaeology, University of Oxford, Oxford, UK. FAU - Craig, Oliver E AU - Craig OE AUID- ORCID: 0000-0002-4296-8402 AD - Bioarch, University of York, York, UK. FAU - Sheridan, Alison AU - Sheridan A AD - National Museums Scotland, Edinburgh, UK. FAU - Parker Pearson, Mike AU - Parker Pearson M AD - Institute of Archaeology, University College London, London, UK. FAU - Stringer, Chris AU - Stringer C AUID- ORCID: 0000-0002-9183-7337 AD - Department of Earth Sciences, Natural History Museum, London, UK. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Broad Institute of MIT and Harvard, Cambridge, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Thomas, Mark G AU - Thomas MG AUID- ORCID: 0000-0002-2452-981X AD - Research Department of Genetics, Evolution and Environment, University College London, London, UK. m.thomas@ucl.ac.uk. AD - UCL Genetics Institute, University College London, London, UK. m.thomas@ucl.ac.uk. FAU - Barnes, Ian AU - Barnes I AUID- ORCID: 0000-0001-8322-6918 AD - Department of Earth Sciences, Natural History Museum, London, UK. I.Barnes@nhm.ac.uk. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 100713/WT_/Wellcome Trust/United Kingdom GR - R01 GM100233/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20190415 PL - England TA - Nat Ecol Evol JT - Nature ecology & evolution JID - 101698577 RN - 0 (DNA, Ancient) SB - IM EIN - Nat Ecol Evol. 2019 Jun;3(6):986-987. doi: 10.1038/s41559-019-0912-4. PMID: 31068681 MH - *DNA, Ancient MH - Europe MH - *Genome MH - Humans MH - Population Dynamics MH - United Kingdom PMC - PMC6520225 MID - EMS82120 COIS- Competing Interests Statement We confirm that none of the authors have a competing financial and/or non-financial interest in relation to the work described. EDAT- 2019/04/17 06:00 MHDA- 2019/10/12 06:00 PMCR- 2019/11/01 CRDT- 2019/04/17 06:00 PHST- 2018/12/17 00:00 [received] PHST- 2019/03/06 00:00 [accepted] PHST- 2019/04/17 06:00 [pubmed] PHST- 2019/10/12 06:00 [medline] PHST- 2019/04/17 06:00 [entrez] PHST- 2019/11/01 00:00 [pmc-release] AID - 10.1038/s41559-019-0871-9 [pii] AID - 10.1038/s41559-019-0871-9 [doi] PST - ppublish SO - Nat Ecol Evol. 2019 May;3(5):765-771. doi: 10.1038/s41559-019-0871-9. Epub 2019 Apr 15. PMID- 30954285 OWN - NLM STAT- MEDLINE DCOM- 20200630 LR - 20200630 IS - 0168-9525 (Print) IS - 0168-9525 (Linking) VI - 35 IP - 5 DP - 2019 May TI - The Promise of Paleogenomics Beyond Our Own Species. PG - 319-329 LID - S0168-9525(19)30035-6 [pii] LID - 10.1016/j.tig.2019.02.006 [doi] AB - Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions. CI - Copyright © 2019 Elsevier Ltd. All rights reserved. FAU - Brunson, Katherine AU - Brunson K AD - Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, RI 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA. Electronic address: katherine_brunson@brown.edu. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review DEP - 20190404 PL - England TA - Trends Genet JT - Trends in genetics : TIG JID - 8507085 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Biological Evolution MH - DNA, Ancient MH - Genome-Wide Association Study MH - *Genomics/methods MH - Geography MH - Horses MH - Humans MH - *Paleontology/methods MH - Species Specificity MH - Zea mays/genetics OTO - NOTNLM OT - cave bear OT - domestication OT - horse OT - maize OT - paleogenomics EDAT- 2019/04/08 06:00 MHDA- 2020/07/01 06:00 CRDT- 2019/04/08 06:00 PHST- 2019/01/03 00:00 [received] PHST- 2019/02/18 00:00 [revised] PHST- 2019/02/25 00:00 [accepted] PHST- 2019/04/08 06:00 [pubmed] PHST- 2020/07/01 06:00 [medline] PHST- 2019/04/08 06:00 [entrez] AID - S0168-9525(19)30035-6 [pii] AID - 10.1016/j.tig.2019.02.006 [doi] PST - ppublish SO - Trends Genet. 2019 May;35(5):319-329. doi: 10.1016/j.tig.2019.02.006. Epub 2019 Apr 4. PMID- 30942856 OWN - NLM STAT- MEDLINE DCOM- 20190829 LR - 20210620 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 11 IP - 5 DP - 2019 May 1 TI - Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World. PG - 1417-1430 LID - 10.1093/gbe/evz071 [doi] AB - The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (>20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations. CI - © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Harris, Daniel N AU - Harris DN AD - Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland. AD - Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland. AD - Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland. FAU - Ruczinski, Ingo AU - Ruczinski I AD - Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland. FAU - Yanek, Lisa R AU - Yanek LR AD - GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, Maryland. FAU - Becker, Lewis C AU - Becker LC AD - GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, Maryland. FAU - Becker, Diane M AU - Becker DM AD - GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, Maryland. FAU - Guio, Heinner AU - Guio H AD - Laboratorio de Biología Molecular, Instituto Nacional de Salud, Lima, Perú. FAU - Cui, Tao AU - Cui T AD - Department of Urology, Wake Forest School of Medicine, Winston-Salem, North Carolina. FAU - Chilton, Floyd H AU - Chilton FH AD - Department of Nutritional Sciences, University of Arizona, Tucson, Arizona. FAU - Mathias, Rasika A AU - Mathias RA AD - GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, Maryland. FAU - O'Connor, Timothy D AU - O'Connor TD AD - Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland. AD - Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland. AD - Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland. LA - eng GR - R01 AT008621/AT/NCCIH NIH HHS/United States GR - R01 HL087698/HL/NHLBI NIH HHS/United States GR - R01 HL112064/HL/NHLBI NIH HHS/United States GR - U01 HL072518/HL/NHLBI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 RN - 0 (Fatty Acids, Unsaturated) RN - EC 1.14.19.- (Fatty Acid Desaturases) SB - IM CIN - Genome Biol Evol. 2019 May 1;11(5):1512-1513. doi: 10.1093/gbe/evz105. PMID: 31150061 MH - Animals MH - *Evolution, Molecular MH - Fatty Acid Desaturases/*genetics/metabolism MH - Fatty Acids, Unsaturated/*metabolism MH - Hominidae/*genetics/metabolism MH - Humans MH - Indians, North American/genetics MH - Selection, Genetic MH - Siberia PMC - PMC6514828 OTO - NOTNLM OT - ancient DNA OT - evolution OT - polyunsaturated fatty acids OT - population genetics EDAT- 2019/04/04 06:00 MHDA- 2019/08/30 06:00 PMCR- 2019/04/03 CRDT- 2019/04/04 06:00 PHST- 2019/04/01 00:00 [accepted] PHST- 2019/04/04 06:00 [pubmed] PHST- 2019/08/30 06:00 [medline] PHST- 2019/04/04 06:00 [entrez] PHST- 2019/04/03 00:00 [pmc-release] AID - 5426762 [pii] AID - evz071 [pii] AID - 10.1093/gbe/evz071 [doi] PST - ppublish SO - Genome Biol Evol. 2019 May 1;11(5):1417-1430. doi: 10.1093/gbe/evz071. PMID- 30723959 OWN - NLM STAT- MEDLINE DCOM- 20200212 LR - 20200212 IS - 1365-294X (Electronic) IS - 0962-1083 (Linking) VI - 28 IP - 10 DP - 2019 May TI - Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA. PG - 2636-2652 LID - 10.1111/mec.15038 [doi] AB - Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high-throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft-bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft-bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales. CI - © 2019 John Wiley & Sons Ltd. FAU - Del Carmen Gomez Cabrera, Maria AU - Del Carmen Gomez Cabrera M AUID- ORCID: 0000-0001-9665-2123 AD - Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia. FAU - Young, Jennifer M AU - Young JM AD - Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia. FAU - Roff, George AU - Roff G AD - Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia. FAU - Staples, Timothy AU - Staples T AD - Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia. FAU - Ortiz, Juan Carlos AU - Ortiz JC AD - Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia. AD - Australian Institute for Marine Science, Townsville, Queensland, Australia. FAU - Pandolfi, John M AU - Pandolfi JM AD - Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190514 PL - England TA - Mol Ecol JT - Molecular ecology JID - 9214478 RN - 0 (DNA, Ancient) RN - 0 (RNA, Ribosomal, 18S) SB - IM MH - Animals MH - Anthozoa/*genetics MH - *Biodiversity MH - *Coral Reefs MH - DNA Barcoding, Taxonomic MH - DNA, Ancient/*analysis MH - Ecology MH - Ecosystem MH - Humans MH - Paleontology MH - RNA, Ribosomal, 18S/genetics MH - Seaweed/classification/genetics OTO - NOTNLM OT - ancient DNA OT - coral reef OT - environmental DNA OT - macroalgae OT - marine palaeoecology OT - metabarcoding EDAT- 2019/02/07 06:00 MHDA- 2020/02/13 06:00 CRDT- 2019/02/07 06:00 PHST- 2017/08/10 00:00 [received] PHST- 2019/01/10 00:00 [revised] PHST- 2019/01/18 00:00 [accepted] PHST- 2019/02/07 06:00 [pubmed] PHST- 2020/02/13 06:00 [medline] PHST- 2019/02/07 06:00 [entrez] AID - 10.1111/mec.15038 [doi] PST - ppublish SO - Mol Ecol. 2019 May;28(10):2636-2652. doi: 10.1111/mec.15038. Epub 2019 May 14. PMID- 30261278 OWN - NLM STAT- MEDLINE DCOM- 20190813 LR - 20190813 IS - 1872-8278 (Electronic) IS - 1567-7249 (Linking) VI - 46 DP - 2019 May TI - Development of a triplex mtDNA qPCR assay to assess quantification, degradation, inhibition, and amplification target copy numbers. PG - 41-50 LID - S1567-7249(18)30080-1 [pii] LID - 10.1016/j.mito.2018.09.007 [doi] AB - A hybrid absolute/relative qPCR assay which provides information regarding the condition of mitochondrial DNA (mtDNA) in a DNA sample is described. MtDNA concentration (copy number/μL) is determined via absolute quantification using a standard curve of a synthetic duplex DNA previously described (Kavlick et al., 2011). The state of mtDNA degradation is determined via the relative quantification of a mtDNA target found within the 16 s rRNA gene which is 3× longer than that of the short target in the former duplex assay, using the delta, delta Ct (ΔΔCt) method. The presence or absence of PCR inhibitors in the sample is qualitatively determined using a custom internal positive control (IPC) system which targets a unique and non-naturally occurring duplex DNA sequence. This IPC effectively detected inhibition by humic acid, tannic acid, melanin, and EDTA. All three assay components utilize sensitive and specific hydrolysis probes. The utility of ΔΔCt method was demonstrated in a series of experiments involving laboratory-fragmented DNA. Also described is a method for estimating copy number of any mtDNA target longer than the two targets amplified. The described triplex assay works well for intact and for fragmented or degraded mtDNA and therefore may be useful in forensic and ancient DNA disciplines as well as in biomedical research or practice. CI - Published by Elsevier B.V. FAU - Kavlick, Mark F AU - Kavlick MF AD - Counterterrorism and Forensic Science Research Unit, Laboratory Division, Federal Bureau of Investigation, 2501 Investigation Parkway, Quantico, VA 22135, United States. Electronic address: Mfkavlick@fbi.gov. LA - eng PT - Journal Article DEP - 20180925 PL - Netherlands TA - Mitochondrion JT - Mitochondrion JID - 100968751 RN - 0 (DNA, Mitochondrial) MH - Animals MH - DNA, Mitochondrial/*analysis/genetics MH - Female MH - Humans MH - Male MH - Multiplex Polymerase Chain Reaction/*methods/standards MH - Real-Time Polymerase Chain Reaction/*methods/standards MH - Reference Standards OTO - NOTNLM OT - Copy numbers OT - Degradation OT - Fragmentation OT - Mitochondrial DNA OT - Quantification OT - mtDNA OT - qPCR EDAT- 2018/09/28 06:00 MHDA- 2019/08/14 06:00 CRDT- 2018/09/28 06:00 PHST- 2018/03/23 00:00 [received] PHST- 2018/05/11 00:00 [revised] PHST- 2018/09/18 00:00 [accepted] PHST- 2018/09/28 06:00 [pubmed] PHST- 2019/08/14 06:00 [medline] PHST- 2018/09/28 06:00 [entrez] AID - S1567-7249(18)30080-1 [pii] AID - 10.1016/j.mito.2018.09.007 [doi] PST - ppublish SO - Mitochondrion. 2019 May;46:41-50. doi: 10.1016/j.mito.2018.09.007. Epub 2018 Sep 25. PMID- 30192911 OWN - NLM STAT- MEDLINE DCOM- 20200214 LR - 20200415 IS - 1367-4811 (Electronic) IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 35 IP - 8 DP - 2019 Apr 15 TI - Inference and visualization of DNA damage patterns using a grade of membership model. PG - 1292-1298 LID - 10.1093/bioinformatics/bty779 [doi] AB - MOTIVATION: Quality control plays a major role in the analysis of ancient DNA (aDNA). One key step in this quality control is assessment of DNA damage: aDNA contains unique signatures of DNA damage that distinguish it from modern DNA, and so analyses of damage patterns can help confirm that DNA sequences obtained are from endogenous aDNA rather than from modern contamination. Predominant signatures of DNA damage include a high frequency of cytosine to thymine substitutions (C-to-T) at the ends of fragments, and elevated rates of purines (A & G) before the 5' strand-breaks. Existing QC procedures help assess damage by simply plotting for each sample, the C-to-T mismatch rate along the read and the composition of bases before the 5' strand-breaks. Here we present a more flexible and comprehensive model-based approach to infer and visualize damage patterns in aDNA, implemented in an R package aRchaic. This approach is based on a 'grade of membership' model (also known as 'admixture' or 'topic' model) in which each sample has an estimated grade of membership in each of K damage profiles that are estimated from the data. RESULTS: We illustrate aRchaic on data from several aDNA studies and modern individuals from 1000 Genomes Project Consortium (2012). Here, aRchaic clearly distinguishes modern from ancient samples irrespective of DNA extraction, lab and sequencing protocols. Additionally, through an in-silico contamination experiment, we show that the aRchaic grades of membership reflect relative levels of exogenous modern contamination. Together, the outputs of aRchaic provide a concise visual summary of DNA damage patterns, as well as other processes generating mismatches in the data. AVAILABILITY AND IMPLEMENTATION: aRchaic is available for download from https://www.github.com/kkdey/aRchaic. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CI - © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. FAU - Al-Asadi, Hussein AU - Al-Asadi H AD - Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA. AD - Department of Statistics, University of Chicago, Chicago, IL, USA. FAU - Dey, Kushal K AU - Dey KK AD - Department of Statistics, University of Chicago, Chicago, IL, USA. FAU - Novembre, John AU - Novembre J AD - Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA. AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. FAU - Stephens, Matthew AU - Stephens M AD - Department of Statistics, University of Chicago, Chicago, IL, USA. AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. LA - eng GR - R01 HG002585/HG/NHGRI NIH HHS/United States GR - U01 CA198933/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (DNA, Ancient) RN - 8J337D1HZY (Cytosine) SB - IM MH - Cytosine MH - *DNA Damage MH - DNA, Ancient MH - *Genome MH - Humans MH - Sequence Analysis, DNA PMC - PMC6821257 EDAT- 2018/09/08 06:00 MHDA- 2020/02/15 06:00 PMCR- 2020/04/15 CRDT- 2018/09/08 06:00 PHST- 2018/06/06 00:00 [received] PHST- 2018/08/11 00:00 [revised] PHST- 2018/09/04 00:00 [accepted] PHST- 2018/09/08 06:00 [pubmed] PHST- 2020/02/15 06:00 [medline] PHST- 2018/09/08 06:00 [entrez] PHST- 2020/04/15 00:00 [pmc-release] AID - 5091332 [pii] AID - bty779 [pii] AID - 10.1093/bioinformatics/bty779 [doi] PST - ppublish SO - Bioinformatics. 2019 Apr 15;35(8):1292-1298. doi: 10.1093/bioinformatics/bty779. PMID- 31004132 OWN - NLM STAT- MEDLINE DCOM- 20191206 LR - 20240716 IS - 2047-217X (Electronic) IS - 2047-217X (Linking) VI - 8 IP - 4 DP - 2019 Apr 1 TI - DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage. LID - 10.1093/gigascience/giz025 [doi] LID - giz025 AB - BACKGROUND: Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons. FINDINGS: Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data. It builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post-mortem cytosine deamination rates at both methylated and unmethylated sites. To validate DamMet, we extended gargammel, a sequence simulator for ancient DNA data, by introducing methylation-dependent features of post-mortem DNA decay. This new simulator provides direct validation of DamMet predictions. Additionally, the methylation levels inferred by DamMet were found to be correlated to those inferred by epiPALEOMIX and both on par and directly comparable to those measured from whole-genome bisulphite sequencing experiments of fresh tissues. CONCLUSIONS: DamMet provides genuine estimates for local DNA methylation levels in ancient individual genomes. The returned estimates are directly cross-sample comparable, and the software is available as an open-source C++ program hosted at https://gitlab.com/KHanghoj/DamMet along with a manual and tutorial. CI - © The Author(s) 2019. Published by Oxford University Press. FAU - Hanghøj, Kristian AU - Hanghøj K AD - Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark. AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse III, Paul Sabatier (UPS), 31000 Toulouse, France. FAU - Renaud, Gabriel AU - Renaud G AD - Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark. FAU - Albrechtsen, Anders AU - Albrechtsen A AD - Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark, Øster voldgade 5-7, 1350k. FAU - Orlando, Ludovic AU - Orlando L AD - Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark. AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse III, Paul Sabatier (UPS), 31000 Toulouse, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Gigascience JT - GigaScience JID - 101596872 SB - IM MH - Algorithms MH - Autopsy MH - *Computational Biology/methods MH - CpG Islands MH - DNA Damage MH - *DNA Methylation MH - Epigenomics/*methods MH - Gene Expression Profiling/methods MH - High-Throughput Nucleotide Sequencing MH - Humans MH - *Software PMC - PMC6474913 OTO - NOTNLM OT - CpG dinucleotide OT - ancient DNA OT - epigenetics OT - high-throughput DNA sequencing OT - methylome EDAT- 2019/04/21 06:00 MHDA- 2019/12/18 06:00 PMCR- 2019/04/20 CRDT- 2019/04/21 06:00 PHST- 2018/10/29 00:00 [received] PHST- 2019/02/07 00:00 [revised] PHST- 2019/02/27 00:00 [accepted] PHST- 2019/04/21 06:00 [entrez] PHST- 2019/04/21 06:00 [pubmed] PHST- 2019/12/18 06:00 [medline] PHST- 2019/04/20 00:00 [pmc-release] AID - 5475519 [pii] AID - giz025 [pii] AID - 10.1093/gigascience/giz025 [doi] PST - ppublish SO - Gigascience. 2019 Apr 1;8(4):giz025. doi: 10.1093/gigascience/giz025. PMID- 30992585 OWN - NLM STAT- MEDLINE DCOM- 20191022 LR - 20220420 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 568 IP - 7752 DP - 2019 Apr TI - Indigenous groups look to ancient DNA to bring their ancestors home. PG - 294-297 LID - 10.1038/d41586-019-01167-w [doi] FAU - Phillips, Nicky AU - Phillips N LA - eng PT - Comment PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM CON - Sci Adv. 2018 Dec 19;4(12):eaau5064. doi: 10.1126/sciadv.aau5064. PMID: 30585290 MH - Archaeology MH - *Body Remains MH - *DNA, Ancient MH - DNA, Mitochondrial MH - Humans OTO - NOTNLM OT - Anthropology OT - Archaeology OT - Genetics OT - Genomics EDAT- 2019/04/18 06:00 MHDA- 2019/10/23 06:00 CRDT- 2019/04/18 06:00 PHST- 2019/04/18 06:00 [entrez] PHST- 2019/04/18 06:00 [pubmed] PHST- 2019/10/23 06:00 [medline] AID - 10.1038/d41586-019-01167-w [pii] AID - 10.1038/d41586-019-01167-w [doi] PST - ppublish SO - Nature. 2019 Apr;568(7752):294-297. doi: 10.1038/d41586-019-01167-w. PMID- 30880015 OWN - NLM STAT- MEDLINE DCOM- 20200413 LR - 20200413 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 29 IP - 7 DP - 2019 Apr 1 TI - Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula. PG - 1169-1177.e7 LID - S0960-9822(19)30145-9 [pii] LID - 10.1016/j.cub.2019.02.006 [doi] AB - The Iberian Peninsula in southwestern Europe represents an important test case for the study of human population movements during prehistoric periods. During the Last Glacial Maximum (LGM), the peninsula formed a periglacial refugium [1] for hunter-gatherers (HGs) and thus served as a potential source for the re-peopling of northern latitudes [2]. The post-LGM genetic signature was previously described as a cline from Western HG (WHG) to Eastern HG (EHG), further shaped by later Holocene expansions from the Near East and the North Pontic steppes [3-9]. Western and central Europe were dominated by ancestry associated with the ∼14,000-year-old individual from Villabruna, Italy, which had largely replaced earlier genetic ancestry, represented by 19,000-15,000-year-old individuals associated with the Magdalenian culture [2]. However, little is known about the genetic diversity in southern European refugia, the presence of distinct genetic clusters, and correspondence with geography. Here, we report new genome-wide data from 11 HGs and Neolithic individuals that highlight the late survival of Paleolithic ancestry in Iberia, reported previously in Magdalenian-associated individuals. We show that all Iberian HGs, including the oldest, a ∼19,000-year-old individual from El Mirón in Spain, carry dual ancestry from both Villabruna and the Magdalenian-related individuals. Thus, our results suggest an early connection between two potential refugia, resulting in a genetic ancestry that survived in later Iberian HGs. Our new genomic data from Iberian Early and Middle Neolithic individuals show that the dual Iberian HG genomic legacy pertains in the peninsula, suggesting that expanding farmers mixed with local HGs. VIDEO ABSTRACT. CI - Copyright © 2019 Elsevier Ltd. All rights reserved. FAU - Villalba-Mouco, Vanessa AU - Villalba-Mouco V AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany; Departamento de Ciencias de la Antigüedad, Grupo Primeros Pobladores del Valle del Ebro (PPVE), Instituto de Investigación en Ciencias Ambientales (IUCA), Universidad de Zaragoza, Pedro Cerbuna, 50009 Zaragoza, Spain. FAU - van de Loosdrecht, Marieke S AU - van de Loosdrecht MS AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany. FAU - Posth, Cosimo AU - Posth C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany. FAU - Mora, Rafael AU - Mora R AD - Centre d'Estudis del Patrimoni Arqueològic de la Prehistòria (CEPAP), Facultat de Lletres, Universitat Autònoma Barcelona, 08190 Bellaterra, Spain. FAU - Martínez-Moreno, Jorge AU - Martínez-Moreno J AD - Centre d'Estudis del Patrimoni Arqueològic de la Prehistòria (CEPAP), Facultat de Lletres, Universitat Autònoma Barcelona, 08190 Bellaterra, Spain. FAU - Rojo-Guerra, Manuel AU - Rojo-Guerra M AD - Department of Prehistory, University of Valladolid, Plaza del Campus, 47011 Valladolid, Spain. FAU - Salazar-García, Domingo C AU - Salazar-García DC AD - Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Euskal Herriko Unibertsitatea, Francisco Tomas y Valiente s/n., 01006 Vitoria, Spain. FAU - Royo-Guillén, José I AU - Royo-Guillén JI AD - Dirección General de Cultura y Patrimonio, Gobierno de Aragón, Avenida de Ranillas, 5 D., 50018 Zaragoza, Spain. FAU - Kunst, Michael AU - Kunst M AD - Instituto Arqueológico Alemán, Calle Serrano 159, E-28002 Madrid, Spain. FAU - Rougier, Hélène AU - Rougier H AD - Department of Anthropology, California State University, Northridge, Northridge, California 91330, USA. FAU - Crevecoeur, Isabelle AU - Crevecoeur I AD - Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France. FAU - Arcusa-Magallón, Héctor AU - Arcusa-Magallón H AD - Arcadia-FUNGE, Fundación General de la Universidad de Valladolid, 47002 Valladolid, Spain. FAU - Tejedor-Rodríguez, Cristina AU - Tejedor-Rodríguez C AD - Juan de la Cierva-Formación Program, Institute of Heritage Sciences, Spanish National Research Council (Incipit, CSIC), Av. de Vigo, 15705 Santiago de Compostela, Spain. FAU - García-Martínez de Lagrán, Iñigo AU - García-Martínez de Lagrán I AD - Juan de la Cierva-Incorporación Program, Department of Prehistory, Valladolid University, Plaza del Campus, 47011 Valladolid, Spain. FAU - Garrido-Pena, Rafael AU - Garrido-Pena R AD - Department of Prehistory, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain. FAU - Alt, Kurt W AU - Alt KW AD - Center of Natural and Cultural Human History, Danube Private University, Steiner Landstr. 124, A-3500 Krems, Austria; Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14-16, CH-4123 Allschwil, Switzerland. FAU - Jeong, Choongwon AU - Jeong C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany. FAU - Schiffels, Stephan AU - Schiffels S AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany. FAU - Utrilla, Pilar AU - Utrilla P AD - Departamento de Ciencias de la Antigüedad, Grupo Primeros Pobladores del Valle del Ebro (PPVE), Instituto de Investigación en Ciencias Ambientales (IUCA), Universidad de Zaragoza, Pedro Cerbuna, 50009 Zaragoza, Spain. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany. FAU - Haak, Wolfgang AU - Haak W AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany. Electronic address: haak@shh.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190314 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/*analysis MH - *Genome, Human MH - *Human Migration MH - Humans MH - Spain OTO - NOTNLM OT - Europe OT - Iberia OT - Last Glacial Maximum OT - Mesolithic OT - Neolithic OT - Paleolithic OT - ancestry OT - ancient DNA OT - genome OT - human EDAT- 2019/03/19 06:00 MHDA- 2020/04/14 06:00 CRDT- 2019/03/19 06:00 PHST- 2018/10/16 00:00 [received] PHST- 2019/01/04 00:00 [revised] PHST- 2019/02/01 00:00 [accepted] PHST- 2019/03/19 06:00 [pubmed] PHST- 2020/04/14 06:00 [medline] PHST- 2019/03/19 06:00 [entrez] AID - S0960-9822(19)30145-9 [pii] AID - 10.1016/j.cub.2019.02.006 [doi] PST - ppublish SO - Curr Biol. 2019 Apr 1;29(7):1169-1177.e7. doi: 10.1016/j.cub.2019.02.006. Epub 2019 Mar 14. PMID- 30842617 OWN - NLM STAT- MEDLINE DCOM- 20190416 LR - 20210603 IS - 1750-2799 (Electronic) IS - 1750-2799 (Linking) VI - 14 IP - 4 DP - 2019 Apr TI - Isolating the human cochlea to generate bone powder for ancient DNA analysis. PG - 1194-1205 LID - 10.1038/s41596-019-0137-7 [doi] AB - The cortical bone that forms the structure of the cochlea, part of the osseous labyrinth of the inner ear, is now one of the most frequently used skeletal elements in analyses of human ancient DNA. However, there is currently no published, standardized method for its sampling. This protocol describes the preparation of bone powder from the cochlea of fragmented skulls in which the petrous pyramid of the temporal bone is accessible. Using a systematic process of bone removal based on distinct anatomical landmarks and the identification of relevant morphological features, a petrous pyramid is cleaned with a sandblaster, and the cochlea is located, isolated, and reduced to a homogeneous bone powder. All steps are carried out in dedicated ancient DNA facilities, thus reducing the introduction of contamination. This protocol requires an understanding of ancient DNA clean-room procedures and basic knowledge of petrous pyramid anatomy. In 50-65 min, it results in bone powder with endogenous DNA yields that can exceed those from teeth and other bones by up to two orders of magnitude. Compared with drilling methods, this method facilitates a more precise targeting of the cochlea, allows the user to visually inspect the cochlea and remove any residual sediment before the generation of bone powder, and confines the damage to the inner ear region and surface of the petrous portion of fragmentary crania. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. ron.pinhasi@univie.ac.at. FAU - Fernandes, Daniel M AU - Fernandes DM AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. FAU - Sirak, Kendra AU - Sirak K AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Cheronet, Olivia AU - Cheronet O AUID- ORCID: 0000-0001-6760-1204 AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190306 PL - England TA - Nat Protoc JT - Nature protocols JID - 101284307 RN - 0 (DNA, Ancient) RN - 0 (Powders) SB - IM MH - Cochlea/anatomy & histology/*chemistry MH - DNA, Ancient/*analysis/isolation & purification MH - Gene Library MH - History, Ancient MH - Humans MH - Liquid-Liquid Extraction/*methods MH - Petrous Bone/anatomy & histology/*chemistry MH - Powders MH - Sequence Analysis, DNA/methods EDAT- 2019/03/08 06:00 MHDA- 2019/04/17 06:00 CRDT- 2019/03/08 06:00 PHST- 2018/05/14 00:00 [received] PHST- 2019/01/10 00:00 [accepted] PHST- 2019/03/08 06:00 [pubmed] PHST- 2019/04/17 06:00 [medline] PHST- 2019/03/08 06:00 [entrez] AID - 10.1038/s41596-019-0137-7 [pii] AID - 10.1038/s41596-019-0137-7 [doi] PST - ppublish SO - Nat Protoc. 2019 Apr;14(4):1194-1205. doi: 10.1038/s41596-019-0137-7. Epub 2019 Mar 6. PMID- 30884759 OWN - NLM STAT- MEDLINE DCOM- 20200109 LR - 20200309 IS - 2073-4425 (Print) IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 10 IP - 3 DP - 2019 Mar 15 TI - The Genetic Variability of APOE in Different Human Populations and Its Implications for Longevity. LID - 10.3390/genes10030222 [doi] LID - 222 AB - Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer's disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved. FAU - Abondio, Paolo AU - Abondio P AD - Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy. paolo.abondio2@unibo.it. FAU - Sazzini, Marco AU - Sazzini M AD - Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy. marco.sazzini2@unibo.it. FAU - Garagnani, Paolo AU - Garagnani P AD - Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy. paolo.garagnani2@unibo.it. FAU - Boattini, Alessio AU - Boattini A AD - Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy. alessio.boattini2@unibo.it. FAU - Monti, Daniela AU - Monti D AD - Department of Biomedical, Clinical and Experimental Sciences "Mario Serio", University of Florence, 50134 Florence, Italy. daniela.monti@unifi.it. FAU - Franceschi, Claudio AU - Franceschi C AD - IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy. claudio.franceschi@unibo.it. FAU - Luiselli, Donata AU - Luiselli D AD - Department of Cultural Heritage (DBC), University of Bologna, Ravenna Campus, 48121 Ravenna, Italy. donata.luiselli@unibo.it. FAU - Giuliani, Cristina AU - Giuliani C AD - Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy. cristina.giuliani2@unibo.it. AD - School of Anthropology and Museum Ethnography, University of Oxford, OX2 6PE Oxford, UK. cristina.giuliani2@unibo.it. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20190315 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (ApoE protein, human) RN - 0 (Apolipoproteins E) SB - IM MH - Apolipoproteins E/*genetics MH - *Genetic Variation MH - Genetics, Population MH - Haplotypes MH - Humans MH - *Longevity MH - Multifactorial Inheritance PMC - PMC6471373 OTO - NOTNLM OT - APOE OT - apolipoprotein E OT - genomics OT - longevity OT - populations COIS- The authors declare no conflict of interest. EDAT- 2019/03/20 06:00 MHDA- 2019/03/20 06:01 PMCR- 2019/03/01 CRDT- 2019/03/20 06:00 PHST- 2019/01/31 00:00 [received] PHST- 2019/03/01 00:00 [revised] PHST- 2019/03/12 00:00 [accepted] PHST- 2019/03/20 06:00 [entrez] PHST- 2019/03/20 06:00 [pubmed] PHST- 2019/03/20 06:01 [medline] PHST- 2019/03/01 00:00 [pmc-release] AID - genes10030222 [pii] AID - genes-10-00222 [pii] AID - 10.3390/genes10030222 [doi] PST - epublish SO - Genes (Basel). 2019 Mar 15;10(3):222. doi: 10.3390/genes10030222. PMID- 30862131 OWN - NLM STAT- MEDLINE DCOM- 20191216 LR - 20200309 IS - 2073-4425 (Print) IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 10 IP - 3 DP - 2019 Mar 11 TI - Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities. LID - 10.3390/genes10030207 [doi] LID - 207 AB - Çatalhöyük is one of the most widely recognized and extensively researched Neolithic settlements. The site has been used to discuss a wide range of aspects associated with the spread of the Neolithic lifestyle and the social organization of Neolithic societies. Here, we address both topics using newly generated mitochondrial genomes, obtained by direct sequencing and capture-based enrichment of genomic libraries, for a group of individuals buried under a cluster of neighboring houses from the classical layer of the site's occupation. Our data suggests a lack of maternal kinship between individuals interred under the floors of Çatalhöyük buildings. The findings could potentially be explained either by a high variability of maternal lineages within a larger kin group, or alternatively, an intentional selection of individuals for burial based on factors other than biological kinship. Our population analyses shows that Neolithic Central Anatolian groups, including Çatalhöyük, share the closest affinity with the population from the Marmara Region and are, in contrast, set further apart from the Levantine populations. Our findings support the hypothesis about the emergence and the direction of spread of the Neolithic within Anatolian Peninsula and beyond, emphasizing a significant role of Central Anatolia in this process. FAU - Chyleński, Maciej AU - Chyleński M AUID- ORCID: 0000-0003-1347-1904 AD - Institute of Archaeology, Faculty of Historical Studies, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland. maciej.ch@amu.edu.pl. FAU - Ehler, Edvard AU - Ehler E AUID- ORCID: 0000-0003-1774-0091 AD - Department of Biology and Environmental Studies, Faculty of Education, Charles University, Magdalény Rettigové 4, 116 39 Prague, Czech Republic. edvard.ehler@pedf.cuni.cz. FAU - Somel, Mehmet AU - Somel M AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. somel.mehmet@googlemail.com. FAU - Yaka, Reyhan AU - Yaka R AUID- ORCID: 0000-0002-9359-4391 AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. yakaryhn@gmail.com. FAU - Krzewińska, Maja AU - Krzewińska M AUID- ORCID: 0000-0002-6702-8724 AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden. maja.krzewinska@arklab.su.se. FAU - Dabert, Mirosława AU - Dabert M AD - Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznań, Poland. mirkad@amu.edu.pl. FAU - Juras, Anna AU - Juras A AUID- ORCID: 0000-0002-2585-127X AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland. annaj@amu.edu.pl. FAU - Marciniak, Arkadiusz AU - Marciniak A AUID- ORCID: 0000-0001-6933-3290 AD - Institute of Archaeology, Faculty of Historical Studies, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland. arekmar@amu.edu.pl. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190311 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Ancient) SB - IM MH - *DNA, Ancient MH - Evolution, Molecular MH - *Genome, Mitochondrial MH - Humans MH - *Maternal Inheritance MH - *Pedigree MH - Turkey PMC - PMC6471721 OTO - NOTNLM OT - Neolithic OT - ancient DNA OT - kinship COIS- The authors declare no conflict of interest. EDAT- 2019/03/14 06:00 MHDA- 2019/03/14 06:01 PMCR- 2019/03/01 CRDT- 2019/03/14 06:00 PHST- 2019/01/25 00:00 [received] PHST- 2019/03/04 00:00 [revised] PHST- 2019/03/04 00:00 [accepted] PHST- 2019/03/14 06:00 [entrez] PHST- 2019/03/14 06:00 [pubmed] PHST- 2019/03/14 06:01 [medline] PHST- 2019/03/01 00:00 [pmc-release] AID - genes10030207 [pii] AID - genes-10-00207 [pii] AID - 10.3390/genes10030207 [doi] PST - epublish SO - Genes (Basel). 2019 Mar 11;10(3):207. doi: 10.3390/genes10030207. PMID- 31303107 OWN - NLM STAT- MEDLINE DCOM- 20191031 LR - 20191031 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 46 IP - 2 DP - 2019 Mar TI - Human biology and ancient DNA: exploring disease, domestication and movement. PG - 95-98 LID - 10.1080/03014460.2019.1629536 [doi] FAU - Houldcroft, Charlotte J AU - Houldcroft CJ AUID- ORCID: 0000-0002-1833-5285 AD - a Department of Medicine , Addenbrooke's Hospital, University of Cambridge , Cambridge , UK. AD - b Parasites and Microbes , Wellcome Sanger Institute , Hinxton , UK. AD - c Department of Archaeology , University of Cambridge , Cambridge , UK. FAU - Rifkin, Riaan F AU - Rifkin RF AUID- ORCID: 0000-0003-1791-3706 AD - d Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology , University of Pretoria , Hatfield , South Africa. AD - e Human Origins and Palaeo-Environments Research Group, Department of Anthropology and Geography , Oxford Brookes University , Oxford , UK. FAU - Underdown, Simon J AU - Underdown SJ AUID- ORCID: 0000-0001-6056-2353 AD - e Human Origins and Palaeo-Environments Research Group, Department of Anthropology and Geography , Oxford Brookes University , Oxford , UK. LA - eng PT - Editorial PT - Historical Article PT - Introductory Journal Article PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - *Biological Evolution MH - DNA, Ancient/*analysis MH - Domestication MH - Genetic Predisposition to Disease/*etiology/history MH - History, Ancient MH - Human Migration/*history MH - Humans EDAT- 2019/07/16 06:00 MHDA- 2019/11/02 06:00 CRDT- 2019/07/16 06:00 PHST- 2019/07/16 06:00 [entrez] PHST- 2019/07/16 06:00 [pubmed] PHST- 2019/11/02 06:00 [medline] AID - 10.1080/03014460.2019.1629536 [doi] PST - ppublish SO - Ann Hum Biol. 2019 Mar;46(2):95-98. doi: 10.1080/03014460.2019.1629536. PMID- 31184205 OWN - NLM STAT- MEDLINE DCOM- 20191101 LR - 20210317 IS - 1464-5033 (Electronic) IS - 0301-4460 (Print) IS - 0301-4460 (Linking) VI - 46 IP - 2 DP - 2019 Mar TI - East Anglian early Neolithic monument burial linked to contemporary Megaliths. PG - 145-149 LID - 10.1080/03014460.2019.1623912 [doi] AB - In the fourth millennium BCE a cultural phenomenon of monumental burial structures spread along the Atlantic façade. Megalithic burials have been targeted for aDNA analyses, but a gap remains in East Anglia, where Neolithic structures were generally earthen or timber. An early Neolithic (3762-3648 cal. BCE) burial monument at the site of Trumpington Meadows, Cambridgeshire, UK, contained the partially articulated remains of at least three individuals. To determine whether this monument fits a pattern present in megalithic burials regarding sex bias, kinship, diet and relationship to modern populations, teeth and ribs were analysed for DNA and carbon and nitrogen isotopic values, respectively. Whole ancient genomes were sequenced from two individuals to a mean genomic coverage of 1.6 and 1.2X and genotypes imputed. Results show that they were brothers from a small population genetically and isotopically similar to previously published British Neolithic individuals, with a level of genome-wide homozygosity consistent with a small island population sourced from continental Europe, but bearing no signs of recent inbreeding. The first Neolithic whole genomes from a monumental burial in East Anglia confirm that this region was connected with the larger pattern of Neolithic megaliths in the British Isles and the Atlantic façade. FAU - Scheib, Christiana L AU - Scheib CL AUID- ORCID: 0000-0003-4158-8296 AD - a Estonian Biocentre, Institute of Genomics , University of Tartu , Tartu , Estonia. AD - b McDonald Institute for Archaeological Research , University of Cambridge , Cambridge , UK. FAU - Hui, Ruoyun AU - Hui R AD - b McDonald Institute for Archaeological Research , University of Cambridge , Cambridge , UK. FAU - D'Atanasio, Eugenia AU - D'Atanasio E AD - c Department of Human Genetics , KU Leuven , Leuven , Belgium. FAU - Wohns, Anthony Wilder AU - Wohns AW AD - d Big Data Institute , University of Oxford , Oxford , UK. FAU - Inskip, Sarah A AU - Inskip SA AD - b McDonald Institute for Archaeological Research , University of Cambridge , Cambridge , UK. FAU - Rose, Alice AU - Rose A AD - b McDonald Institute for Archaeological Research , University of Cambridge , Cambridge , UK. FAU - Cessford, Craig AU - Cessford C AUID- ORCID: 0000-0001-7291-7828 AD - b McDonald Institute for Archaeological Research , University of Cambridge , Cambridge , UK. AD - e Cambridge Archaeological Unit , Cambridge , UK. FAU - O'Connell, Tamsin C AU - O'Connell TC AD - f Department of Archaeology , University of Cambridge , Cambridge , UK. FAU - Robb, John E AU - Robb JE AD - f Department of Archaeology , University of Cambridge , Cambridge , UK. FAU - Evans, Christopher AU - Evans C AD - e Cambridge Archaeological Unit , Cambridge , UK. FAU - Patten, Ricky AU - Patten R AD - e Cambridge Archaeological Unit , Cambridge , UK. FAU - Kivisild, Toomas AU - Kivisild T AUID- ORCID: 0000-0002-6297-7808 AD - a Estonian Biocentre, Institute of Genomics , University of Tartu , Tartu , Estonia. AD - b McDonald Institute for Archaeological Research , University of Cambridge , Cambridge , UK. AD - c Department of Human Genetics , KU Leuven , Leuven , Belgium. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - Burial/*history MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*analysis MH - England MH - History, Ancient MH - Humans MH - Male MH - Whole Genome Sequencing PMC - PMC6816495 OTO - NOTNLM OT - Ancient DNA OT - Britain OT - isotope analysis OT - kinship EDAT- 2019/06/12 06:00 MHDA- 2019/11/02 06:00 PMCR- 2019/10/28 CRDT- 2019/06/12 06:00 PHST- 2019/06/12 06:00 [pubmed] PHST- 2019/11/02 06:00 [medline] PHST- 2019/06/12 06:00 [entrez] PHST- 2019/10/28 00:00 [pmc-release] AID - 1623912 [pii] AID - 10.1080/03014460.2019.1623912 [doi] PST - ppublish SO - Ann Hum Biol. 2019 Mar;46(2):145-149. doi: 10.1080/03014460.2019.1623912. PMID- 31163991 OWN - NLM STAT- MEDLINE DCOM- 20191101 LR - 20221207 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 46 IP - 2 DP - 2019 Mar TI - Searching for archaic contribution in Africa. PG - 129-139 LID - 10.1080/03014460.2019.1624823 [doi] AB - Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence of Homo sapiens. However, once humans dispersed beyond Africa, the history of those who stayed remains vastly under-studied, lacking the proper attention the birthplace of both modern and archaic humans deserves. The sequencing of Neanderthal and Denisovan genomes has elucidated evidence of admixture between archaic and modern humans outside of Africa, but has not aided efforts in answering whether archaic admixture happened within Africa. Objectives: This article reviews the state of research for archaic introgression in African populations and discusses recent insights into this topic. Methods: Gathering published sources and recently released preprints, this review reports on the different methods developed for detecting archaic introgression. Particularly it discusses how relevant these are when implemented on African populations and what findings these studies have shown so far. Results: Methods for detecting archaic introgression have been predominantly developed and implemented on non-African populations. Recent preprints present new methods considering African populations. While a number of studies using these methods suggest archaic introgression in Africa, without an African archaic genome to validate these results, such findings remain as putative archaic introgression. Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent. FAU - Santander, Cindy AU - Santander C AUID- ORCID: 0000-0003-3021-6809 AD - a Department of Zoology , University of Oxford , Oxford , UK. FAU - Montinaro, Francesco AU - Montinaro F AD - a Department of Zoology , University of Oxford , Oxford , UK. AD - b Estonian Biocentre , University of Tartu , Tartu , Estonia. FAU - Capelli, Cristian AU - Capelli C AD - a Department of Zoology , University of Oxford , Oxford , UK. LA - eng PT - Journal Article PT - Review DEP - 20190626 PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) SB - IM MH - Africa MH - Animals MH - Black People/*genetics MH - DNA, Ancient/*analysis MH - Genome, Human MH - Hominidae/*genetics MH - Humans MH - *Hybridization, Genetic OTO - NOTNLM OT - Africa OT - ancient admixture OT - archaic introgression OT - human evolution EDAT- 2019/06/06 06:00 MHDA- 2019/11/02 06:00 CRDT- 2019/06/06 06:00 PHST- 2019/06/06 06:00 [pubmed] PHST- 2019/11/02 06:00 [medline] PHST- 2019/06/06 06:00 [entrez] AID - 10.1080/03014460.2019.1624823 [doi] PST - ppublish SO - Ann Hum Biol. 2019 Mar;46(2):129-139. doi: 10.1080/03014460.2019.1624823. Epub 2019 Jun 26. PMID- 31137975 OWN - NLM STAT- MEDLINE DCOM- 20191101 LR - 20191101 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 46 IP - 2 DP - 2019 Mar TI - Tuberculosis and leprosy associated with historical human population movements in Europe and beyond - an overview based on mycobacterial ancient DNA. PG - 120-128 LID - 10.1080/03014460.2019.1624822 [doi] AB - Context: Tuberculosis and leprosy are readily recognised in human remains due to their typical palaeopathology. Both Mycobacterium tuberculosis (MTB) and Mycobacterium leprae (ML) are obligate pathogens and have been detected in ancient human populations. Objective: To demonstrate historical tuberculosis and leprosy cases in Europe and beyond using molecular methods, as human populations are associated with different mycobacterial genotypes. Methods: MTB and ML ancient DNA (aDNA) has been detected by DNA amplification using PCR, or by whole genome sequencing. Mycobacterial cell wall lipids also provide specific markers for identification. Results: In 18th century Hungary, the European indigenous MTB genotype 4 strains have been found. However, many individuals were co-infected with up to three MTB sub-genotypes. In 8th-14th century Europe significant differences in ML genotypes were found between northwest Europe compared with central, southern, or eastern Europe. In addition, several co-infections of MTB and ML were detected in historical samples. Conclusion: Both MTB and ML strain types differ between geographically separate populations. This is associated with ancient human migration after an evolutionary bottleneck and clonal expansion. The absence of indigenous leprosy in Europe today may be due to the greater mortality of tuberculosis in individuals who are co-infected with both organisms. FAU - Donoghue, Helen D AU - Donoghue HD AUID- ORCID: 0000-0003-3918-5252 AD - a Centre for Clinical Microbiology , University College London (UCL) , London , UK. LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20190620 PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/*analysis MH - Europe MH - Genotype MH - History, 17th Century MH - History, 18th Century MH - History, Medieval MH - Human Migration/*history MH - Humans MH - Leprosy/*history/microbiology MH - Mycobacterium leprae/*genetics MH - Mycobacterium tuberculosis/*genetics MH - Paleopathology MH - Polymerase Chain Reaction MH - Tuberculosis/*history/microbiology MH - Whole Genome Sequencing OTO - NOTNLM OT - Ancient DNA (aDNA) OT - genotyping EDAT- 2019/05/30 06:00 MHDA- 2019/11/02 06:00 CRDT- 2019/05/30 06:00 PHST- 2019/05/30 06:00 [pubmed] PHST- 2019/11/02 06:00 [medline] PHST- 2019/05/30 06:00 [entrez] AID - 10.1080/03014460.2019.1624822 [doi] PST - ppublish SO - Ann Hum Biol. 2019 Mar;46(2):120-128. doi: 10.1080/03014460.2019.1624822. Epub 2019 Jun 20. PMID- 30586168 OWN - NLM STAT- MEDLINE DCOM- 20200107 LR - 20240716 IS - 1096-8644 (Electronic) IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 168 IP - 3 DP - 2019 Mar TI - The efficacy of whole human genome capture on ancient dental calculus and dentin. PG - 496-509 LID - 10.1002/ajpa.23763 [doi] AB - OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples. CI - © 2018 The Authors. American Journal of Physical Anthropology published by Wiley Periodicals, Inc. FAU - Ziesemer, Kirsten A AU - Ziesemer KA AD - Faculty of Archaeology, Leiden University, Leiden, The Netherlands. FAU - Ramos-Madrigal, Jazmín AU - Ramos-Madrigal J AD - Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Mann, Allison E AU - Mann AE AD - Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma. FAU - Brandt, Bernd W AU - Brandt BW AD - Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands. FAU - Sankaranarayanan, Krithivasan AU - Sankaranarayanan K AD - Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma. AD - Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma. FAU - Ozga, Andrew T AU - Ozga AT AD - School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona. AD - Institute for Human Origins, Arizona State University, Tempe, Arizona. AD - Center for Evolution and Medicine, Arizona State University, Tempe, Arizona. FAU - Hoogland, Menno AU - Hoogland M AD - Faculty of Archaeology, Leiden University, Leiden, The Netherlands. FAU - Hofman, Courtney A AU - Hofman CA AD - Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma. FAU - Salazar-García, Domingo C AU - Salazar-García DC AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. AD - Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain. FAU - Frohlich, Bruno AU - Frohlich B AD - Department of Anthropology, Hanover, New Hampshire. FAU - Milner, George R AU - Milner GR AD - Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania. FAU - Stone, Anne C AU - Stone AC AD - School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona. AD - Institute for Human Origins, Arizona State University, Tempe, Arizona. AD - Center for Evolution and Medicine, Arizona State University, Tempe, Arizona. FAU - Aldenderfer, Mark AU - Aldenderfer M AD - Department of Anthropology and Heritage Studies, University of California, Merced, California. FAU - Lewis, Cecil M Jr AU - Lewis CM Jr AD - Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma. FAU - Hofman, Corinne L AU - Hofman CL AD - Faculty of Archaeology, Leiden University, Leiden, The Netherlands. FAU - Warinner, Christina AU - Warinner C AD - Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Schroeder, Hannes AU - Schroeder H AUID- ORCID: 0000-0002-6743-0270 AD - Faculty of Archaeology, Leiden University, Leiden, The Netherlands. AD - Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. LA - eng GR - 319209/H2020 European Research Council/International GR - 649307DK-TAF 5662/Horizon 2020 Framework Programme/International GR - BCS 1516633/National Science Foundation/International GR - BCS‐1528698/National Science Foundation/International PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20181226 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - *DNA, Ancient/analysis/isolation & purification MH - Dental Calculus/*chemistry/microbiology MH - Dentin/*chemistry MH - Female MH - Genome, Human/*genetics MH - Genomics/*methods MH - Humans MH - Male MH - Sequence Analysis, DNA PMC - PMC6519167 OTO - NOTNLM OT - ancient DNA OT - genomics OT - hybridization capture OT - target enrichment EDAT- 2018/12/27 06:00 MHDA- 2020/01/08 06:00 PMCR- 2019/05/15 CRDT- 2018/12/27 06:00 PHST- 2018/05/29 00:00 [received] PHST- 2018/09/09 00:00 [revised] PHST- 2018/11/10 00:00 [accepted] PHST- 2018/12/27 06:00 [pubmed] PHST- 2020/01/08 06:00 [medline] PHST- 2018/12/27 06:00 [entrez] PHST- 2019/05/15 00:00 [pmc-release] AID - AJPA23763 [pii] AID - 10.1002/ajpa.23763 [doi] PST - ppublish SO - Am J Phys Anthropol. 2019 Mar;168(3):496-509. doi: 10.1002/ajpa.23763. Epub 2018 Dec 26. PMID- 30399480 OWN - NLM STAT- MEDLINE DCOM- 20200109 LR - 20200109 IS - 1879-9825 (Electronic) IS - 1879-9817 (Linking) VI - 24 DP - 2019 Mar TI - The people behind the samples: Biographical features of Past Hunter-Gatherers from KwaZulu-Natal who yielded aDNA. PG - 158-164 LID - S1879-9817(18)30050-0 [pii] LID - 10.1016/j.ijpp.2018.10.008 [doi] AB - PURPOSE: Skeletons sampled for ancient human DNA analysis are sometimes complete enough to provide information about the lives of the people they represent. We focus on three Later Stone Age skeletons, ca. 2000 B.P., from coastal KwaZulu-Natal, South Africa, whose ancient genomes have been sequenced (Schlebusch et al., 2017). METHODS: Bioarchaeological approaches are integrated with aDNA information. RESULTS: All skeletons are male. Dental development shows that the boy, with prominent cribra orbitalia, died at age 6-7 years. Two men show cranial and spinal trauma, extensive tooth wear, plus mild cribra orbitalia in one. CONCLUSIONS: Dental wear and trauma of the adults are consistent with hunter-gatherer lives. Even partial aDNA evidence contributes to sex determination. Parasitic infection such as schistosomiasis is the best-fit cause for the child's anemia in this case. CONTRIBUTION TO KNOWLEDGE: The convergence of genomic and bioarchaeological approaches expands our knowledge of the past lives of a boy and two men whose lives as hunter-gatherers included episodes of trauma and disease. LIMITATIONS: The skeletons are incomplete, in variable condition, and from poorly characterized local cultural contexts. SUGGESTIONS FOR FURTHER RESEARCH: Thorough osteobiographic analysis should accompany paleogenomic investigations. Such disciplinary collaboration enriches our understanding of the human past. CI - Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Pfeiffer, Susan AU - Pfeiffer S AD - Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, M5S 2S2, Canada; Department of Archaeology, University of Cape Town, Rondebosch 7701, South Africa; Department of Anthropology, George Washington University, D.C., USA. Electronic address: susan.pfeiffer@utoronto.ca. FAU - Harrington, Lesley AU - Harrington L AD - Department of Anthropology, University of Alberta, 13-15 H.M. Tory Building, Edmonton, T6G 2H4, Canada. FAU - Lombard, Marlize AU - Lombard M AD - Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181103 PL - Netherlands TA - Int J Paleopathol JT - International journal of paleopathology JID - 101562474 RN - 0 (DNA, Ancient) SB - IM MH - Adult MH - Base Sequence/genetics MH - Bone and Bones/*pathology MH - Child MH - DNA, Ancient/*analysis MH - Humans MH - Malaria MH - Male MH - Schistosomiasis/diagnosis/*pathology MH - Skull/*pathology MH - South Africa OTO - NOTNLM OT - Child growth OT - Cribra orbitalia OT - Hookworm OT - Khoe-San OT - Later Stone age OT - Malaria OT - Schistosomiasis EDAT- 2018/11/07 06:00 MHDA- 2020/01/10 06:00 CRDT- 2018/11/07 06:00 PHST- 2018/03/27 00:00 [received] PHST- 2018/10/18 00:00 [revised] PHST- 2018/10/25 00:00 [accepted] PHST- 2018/11/07 06:00 [pubmed] PHST- 2020/01/10 06:00 [medline] PHST- 2018/11/07 06:00 [entrez] AID - S1879-9817(18)30050-0 [pii] AID - 10.1016/j.ijpp.2018.10.008 [doi] PST - ppublish SO - Int J Paleopathol. 2019 Mar;24:158-164. doi: 10.1016/j.ijpp.2018.10.008. Epub 2018 Nov 3. PMID- 32073242 OWN - NLM STAT- MEDLINE DCOM- 20200729 LR - 20200729 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 91 IP - 1 DP - 2019 Feb 17 TI - Mitochondrial Genome of an 8,400-Year-Old Individual from Northern China Reveals a Novel Subclade Under C5d. PG - 21-30 LID - 10.13110/humanbiology.91.1.04 [doi] AB - Ancient DNA studies have always refreshed our understanding of the human past that cannot be tracked by modern DNA alone. Until recently, ancient mitochondrial genomic studies in East Asia were still very limited. Here, we retrieved the whole mitochondrial genome of an 8,400-year-old individual from Inner Mongolia, China. Phylogenetic analyses show that the individual belongs to a previously undescribed clade under haplogroup C5d that most probably originated in northern Asia and may have a very low frequency in extant populations that have not yet been sampled. We further characterized the demographic history of mitochondrial haplogroups C5 and C5d and found that C5 experienced a sharp increase in population size starting around 4,000 years before present, the time when intensive millet farming was developed by populations who are associated with the Lower Xiajiadian culture and was widely adopted in northern China. We caution that people related to haplogroup C5 may have added this farming technology to their original way of life and that the various forms of subsistence may have provided abundant food sources and further contributed to the increase in population size. FAU - Wu, Xiyan AU - Wu X AD - Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China. AD - School of Life Sciences, Jilin University, Changchun, People's Republic of China. FAU - Ning, Chao AU - Ning C AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Bao, Qingchuan AU - Bao Q AD - Institute of Cultural Relics and Archaeology, Inner Mongolia Autonomous Region, Hohhot, People's Republic of China. FAU - Gao, Shizhu AU - Gao S AD - College of Pharmaceutical Sciences, Jilin University, Changchun, People's Republic of China. FAU - Zhang, Fan AU - Zhang F AD - School of Life Sciences, Jilin University, Changchun, People's Republic of China. FAU - Wu, Sihao AU - Wu S AD - School of Life Sciences, Jilin University, Changchun, People's Republic of China. FAU - Li, Tianjiao AU - Li T AD - School of Life Sciences, Jilin University, Changchun, People's Republic of China. FAU - Fan, Linyuan AU - Fan L AD - School of Life Sciences, Jilin University, Changchun, People's Republic of China. FAU - Li, Tao AU - Li T AD - Department of Archaeology, College of History, Wuhan University, Wuhan, People's Republic of China. FAU - Yang, Xuan AU - Yang X AD - School of Life Sciences, Jilin University, Changchun, People's Republic of China. FAU - Cai, Dawei AU - Cai D AD - Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China, caidw@jlu.edu.cn. AD - School of Archaeology, Jilin University, Changchun, People's Republic of China. FAU - Cui, Yinqiu AU - Cui Y AD - Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China. AD - School of Life Sciences, Jilin University, Changchun, People's Republic of China, cuiyq@jlu.edu.cn. AD - Key Laboratory for Evolution of Past Life and Environment in Northeast Asia, Jilin University, Ministry of Education, Changchun, China. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Ancient MH - DNA, Mitochondrial MH - Genome, Mitochondrial/*genetics MH - Genotyping Techniques MH - Haplotypes/*genetics MH - History, Ancient MH - Humans MH - Mongolia/epidemiology MH - Phylogeny OTO - NOTNLM OT - ANCIENT DNA OT - INNER MONGOLIA OT - MILLET FARMING OT - MITOCHONDRIAL GENOME OT - MTDNA HAPLOGROUP C5D OT - PHYLOGENETIC ANALYSIS EDAT- 2020/02/20 06:00 MHDA- 2020/07/30 06:00 CRDT- 2020/02/20 06:00 PHST- 2019/07/12 00:00 [received] PHST- 2019/10/04 00:00 [accepted] PHST- 2020/02/20 06:00 [entrez] PHST- 2020/02/20 06:00 [pubmed] PHST- 2020/07/30 06:00 [medline] AID - 10.13110/humanbiology.91.1.04 [doi] PST - ppublish SO - Hum Biol. 2019 Feb 17;91(1):21-30. doi: 10.13110/humanbiology.91.1.04. PMID- 30963935 OWN - NLM STAT- MEDLINE DCOM- 20200211 LR - 20241121 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 286 IP - 1896 DP - 2019 Feb 13 TI - Inferring the model and onset of natural selection under varying population size from the site frequency spectrum and haplotype structure. PG - 20182541 LID - 10.1098/rspb.2018.2541 [doi] LID - 20182541 AB - A fundamental question about adaptation in a population is the time of onset of the selective pressure acting on beneficial alleles. Inferring this time, in turn, depends on the selection model. We develop a framework of approximate Bayesian computation (ABC) that enables the use of the full site frequency spectrum and haplotype structure to test the goodness-of-fit of selection models and estimate the timing of selection under varying population size scenarios. We show that our method has sufficient power to distinguish natural selection from neutrality even if relatively old selection increased the frequency of a pre-existing allele from 20% to 50% or from 40% to 80%. Our ABC can accurately estimate the time of onset of selection on a new mutation. However, estimates are prone to bias under the standing variation model, possibly due to the uncertainty in the allele frequency at the onset of selection. We further extend our approach to take advantage of ancient DNA data that provides information on the allele frequency path of the beneficial allele. Applying our ABC, including both modern and ancient human DNA data, to four pigmentation alleles in Europeans, we detected selection on standing variants that occurred after the dispersal from Africa even though models of selection on a new mutation were initially supported for two of these alleles without the ancient data. FAU - Nakagome, Shigeki AU - Nakagome S AD - 1 Department of Human Genetics, University of Chicago , Chicago, IL , USA. AD - 3 School of Medicine, Faculty of Health Sciences, Trinity College Dublin, the University of Dublin , Dublin , Ireland. FAU - Hudson, Richard R AU - Hudson RR AD - 1 Department of Human Genetics, University of Chicago , Chicago, IL , USA. AD - 2 Department of Ecology & Evolution, University of Chicago , Chicago, IL , USA. FAU - Di Rienzo, Anna AU - Di Rienzo A AD - 1 Department of Human Genetics, University of Chicago , Chicago, IL , USA. LA - eng SI - figshare/10.6084/m9.figshare.c.4385147 GR - R01 GM101682/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Ancient) SB - IM MH - Bayes Theorem MH - DNA, Ancient/*analysis MH - Europe MH - *Gene Frequency MH - Haplotypes/*genetics MH - *Human Migration MH - Humans MH - Models, Genetic MH - Population Density MH - *Selection, Genetic MH - Skin Pigmentation/*genetics MH - Time Factors PMC - PMC6408616 OTO - NOTNLM OT - approximate Bayesian computation OT - natural selection on standing variation OT - selective sweep OT - timing of natural selection COIS- We declare we have no competing interests. EDAT- 2019/04/10 06:00 MHDA- 2020/02/12 06:00 PMCR- 2020/02/13 CRDT- 2019/04/10 06:00 PHST- 2019/04/10 06:00 [entrez] PHST- 2019/04/10 06:00 [pubmed] PHST- 2020/02/12 06:00 [medline] PHST- 2020/02/13 00:00 [pmc-release] AID - rspb20182541 [pii] AID - 10.1098/rspb.2018.2541 [doi] PST - ppublish SO - Proc Biol Sci. 2019 Feb 13;286(1896):20182541. doi: 10.1098/rspb.2018.2541. PMID- 30628076 OWN - NLM STAT- MEDLINE DCOM- 20191220 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 168 IP - 2 DP - 2019 Feb TI - Molecular analysis of an ancient Thule population at Nuvuk, Point Barrow, Alaska. PG - 303-317 LID - 10.1002/ajpa.23746 [doi] AB - OBJECTIVES: The North American archaeological record supports a Holocene origin of Arctic Indigenous peoples. Although the Paleo-Inuit were present for millennia, archaeological and genetic studies suggest that modern peoples descend from a second, more recent tradition known as the Neo-Inuit. Origins of the Neo-Inuit and their relations to the earlier and later Indigenous peoples are an area of active study. Here, we genetically analyze the maternal lineages present at Nuvuk, once the northernmost community in Alaska and located in a region identified as a possible origin point of the Neo-Inuit Thule. The cemetery at Nuvuk contains human remains representing a nearly one thousand year uninterrupted occupation from early Thule to post-contact Iñupiat. MATERIALS AND METHODS: We selected 44 individuals from Nuvuk with calibrated dates between 981 AD and 1885 AD for molecular analysis. We amplified and sequenced the hypervariable segment I of the mitogenome. We compared the Nuvuk data with previously published sequences from 68 modern and ancient communities from across Asia and North America. Phylogeographic analyses suggest possible scenarios of Holocene Arctic and sub-Arctic population movements. RESULTS: We successfully retrieved sequence data from 39 individuals. Haplogroup frequencies in Nuvuk were typed as 66.7% A2b1, 25.6% A2a, and 7.7% D4b1a2a1a. These results suggest that the population at Nuvuk was closest to the ancient Thule and modern Inuit of Canada, and to the Siberian Naukan people. We confirm that haplogroups A2a, A2b1, D2a, and D4b1a2a1a appear at high frequency in Arctic and sub-Arctic populations of North America and Chukotka. Sister clades D2b and D4b1a2a1b are present in Asian and Eastern European populations. DISCUSSION: The ancient mitochondrial sequences from Nuvuk confirm the link between the North Slope and the Thule who later spread east, and the maternal discontinuity between the Neo-Inuit and Paleo-Inuit. We suggest haplogroups A2a, A2b, and D4b1a2a1a are linked to the ancestors of the Thule in eastern Beringia, whereas the D2 and D4b1a2a1 clades appear to have Asian Holocene origins. Further Siberian and Alaskan genomes are necessary to clarify these population migrations beyond a simple two-wave scenario of Neo-Inuit and Paleo-Inuit. CI - © 2019 Wiley Periodicals, Inc. FAU - Tackney, Justin AU - Tackney J AUID- ORCID: 0000-0003-1962-9397 AD - Department of Anthropology, University of Kansas, Lawrence, Kansas. FAU - Jensen, Anne M AU - Jensen AM AUID- ORCID: 0000-0002-8947-5859 AD - UIC Science LLC, Barrow, Alaska. AD - Department of Anthropology, University of Alaska Fairbanks, Fairbanks, Alaska. FAU - Kisielinski, Caroline AU - Kisielinski C AUID- ORCID: 0000-0001-6777-8288 AD - Department of Anthropology, University of Kansas, Lawrence, Kansas. FAU - O'Rourke, Dennis H AU - O'Rourke DH AUID- ORCID: 0000-0001-5196-3577 AD - Department of Anthropology, University of Kansas, Lawrence, Kansas. LA - eng GR - OPP-0732846/Office of Polar Programs/International GR - OPP-0732857/Office of Polar Programs/International GR - OPP-0637246/Office of Polar Programs/International GR - OPP-0535356/Office of Polar Programs/International GR - OPP-1460387/Office of Polar Programs/International GR - OPP-0820790/Office of Polar Programs/International GR - OPP-0726253/Office of Polar Programs/International GR - OPP-0820790/National Science Foundation (NSF)/International GR - ARC-0726253/National Science Foundation (NSF)/International GR - OPP-1460387/National Science Foundation (NSF)/International GR - OPP-0535356/National Science Foundation (NSF)/International GR - OPP-0637246/National Science Foundation (NSF)/International GR - OPP-0732857/International Polar Year grant/International GR - OPP-0732846/International Polar Year grant/International PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Alaska MH - Anthropology, Physical MH - Arctic Regions MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/*genetics MH - Haplotypes/genetics MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, Medieval MH - Humans MH - Inuit/*genetics/*history MH - Phylogeography OTO - NOTNLM OT - Arctic OT - Neo-Inuit OT - Thule OT - ancient DNA OT - mtDNA EDAT- 2019/01/11 06:00 MHDA- 2019/12/21 06:00 CRDT- 2019/01/11 06:00 PHST- 2018/06/16 00:00 [received] PHST- 2018/10/05 00:00 [revised] PHST- 2018/10/16 00:00 [accepted] PHST- 2019/01/11 06:00 [entrez] PHST- 2019/01/11 06:00 [pubmed] PHST- 2019/12/21 06:00 [medline] AID - 10.1002/ajpa.23746 [doi] PST - ppublish SO - Am J Phys Anthropol. 2019 Feb;168(2):303-317. doi: 10.1002/ajpa.23746. PMID- 30700787 OWN - NLM STAT- MEDLINE DCOM- 20200810 LR - 20200810 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 9 IP - 1 DP - 2019 Jan 30 TI - Mitochondrial ancestry of medieval individuals carelessly interred in a multiple burial from southeastern Romania. PG - 961 LID - 10.1038/s41598-018-37760-8 [doi] LID - 961 AB - The historical province of Dobruja, located in southeastern Romania, has experienced intense human population movement, invasions, and conflictual episodes during the Middle Ages, being an important intersection point between Asia and Europe. The most informative source of maternal population histories is the complete mitochondrial genome of archaeological specimens, but currently, there is insufficient ancient DNA data available for the medieval period in this geographical region to complement the archaeological findings. In this study, we reconstructed, by using Next Generation Sequencing, the entire mitochondrial genomes (mitogenomes) of six medieval individuals neglectfully buried in a multiple burial from Capidava necropolis (Dobruja), some presenting signs of a violent death. Six distinct maternal lineages (H11a1, U4d2, J1c15, U6a1a1, T2b, and N1a3a) with different phylogenetic background were identified, pointing out the heterogeneous genetic aspect of the analyzed medieval group. Using population genetic analysis based on high-resolution mitochondrial data, we inferred the genetic affinities of the available medieval dataset from Capidava to other ancient Eurasian populations. The genetic data were integrated with the archaeological and anthropological information in order to sketch a small, local piece of the mosaic that is the image of medieval European population history. FAU - Rusu, Ioana AU - Rusu I AUID- ORCID: 0000-0002-6152-8832 AD - Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania. rusu.n.ioana@gmail.com. AD - Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj, Napoca, Romania. rusu.n.ioana@gmail.com. FAU - Modi, Alessandra AU - Modi A AD - Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy. alessandra.modi@unifi.it. FAU - Radu, Claudia AU - Radu C AD - Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania. AD - Department of Ancient History and Archaeology, Faculty of History and Philosophy, Babeș-Bolyai University, 400084, Cluj, Napoca, Romania. FAU - Mircea, Cristina AU - Mircea C AD - Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania. AD - Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj, Napoca, Romania. FAU - Vulpoi, Adriana AU - Vulpoi A AD - Nanostructured Materials and Bio-Nano-Interfaces Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania. FAU - Dobrinescu, Cătălin AU - Dobrinescu C AD - Department of Research-Development and Projects, Museum of National History and Archeology, 900745, Constanța, Romania. FAU - Bodolică, Vitalie AU - Bodolică V AD - Department of Research-Development and Projects, Museum of National History and Archeology, 900745, Constanța, Romania. FAU - Potârniche, Tiberiu AU - Potârniche T AD - Department of Research-Development and Projects, Museum of National History and Archeology, 900745, Constanța, Romania. FAU - Popescu, Octavian AU - Popescu O AD - Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania. AD - Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj, Napoca, Romania. AD - Institute of Biology Bucharest, Romanian Academy, 060031, Bucharest, Romania. FAU - Caramelli, David AU - Caramelli D AD - Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy. FAU - Kelemen, Beatrice AU - Kelemen B AUID- ORCID: 0000-0002-2989-2941 AD - Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania. AD - Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj, Napoca, Romania. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190130 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - Bone and Bones/metabolism MH - Burial/*history MH - DNA, Mitochondrial/genetics MH - Female MH - Genetics, Population MH - Genome, Human MH - Genome, Mitochondrial MH - Geography MH - Haplotypes/genetics MH - History, Medieval MH - Humans MH - Male MH - Mitochondria/*genetics MH - *Phylogeny MH - Romania PMC - PMC6353917 COIS- The authors declare no competing interests. EDAT- 2019/02/01 06:00 MHDA- 2020/08/11 06:00 PMCR- 2019/01/30 CRDT- 2019/02/01 06:00 PHST- 2018/06/12 00:00 [received] PHST- 2018/12/13 00:00 [accepted] PHST- 2019/02/01 06:00 [entrez] PHST- 2019/02/01 06:00 [pubmed] PHST- 2020/08/11 06:00 [medline] PHST- 2019/01/30 00:00 [pmc-release] AID - 10.1038/s41598-018-37760-8 [pii] AID - 37760 [pii] AID - 10.1038/s41598-018-37760-8 [doi] PST - epublish SO - Sci Rep. 2019 Jan 30;9(1):961. doi: 10.1038/s41598-018-37760-8. PMID- 30682121 OWN - NLM STAT- MEDLINE DCOM- 20191018 LR - 20240607 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 14 IP - 1 DP - 2019 TI - Medieval mummies of Zeleny Yar burial ground in the Arctic Zone of Western Siberia. PG - e0210718 LID - 10.1371/journal.pone.0210718 [doi] LID - e0210718 AB - Notwithstanding the pioneering achievements of studies on arctic mummies in Siberia, there are insufficient data for any comprehensive understanding of the bio-cultural details of medieval people living in the region. In the Western Siberian arctic, permafrost mummies have been found in 12th to 13th century graves located in the Zeleny Yar (Z-Y) burial ground (66°19'4.54"С; 67°21'13.54"В). In 2013-2016, we were fortunate to be able to excavate that cemetery, locating a total of 47 burials, including cases of mummification. Some of these mummies had been wrapped in a multi-layered birch-bark cocoon. After removal of the cocoon, we conducted interdisciplinary studies using various scientific techniques. Gross anatomical examination and CT radiography showed that the internal organs were still well preserved inside the body cavities. Under light and electron microscopy, the histological findings were very similar to those for naturally mummified specimens discovered in other countries. Ancient DNA analysis showed that the Z-Y mummies' mtDNA haplotypes belong to five different haplogroups, namely U5a (#34), H3ao (#53), D (#67-1), U4b1b1 (#67-2), and D4j8 (#68), which distinguish them for their unique combination of Western- and Eastern Siberia-specific mtDNA haplogroups. Our interdisciplinary study obtained fundamental information that will form the foundation of successful future investigations on medieval mummies found in the Western Siberian arctic. FAU - Slepchenko, Sergey Mikhailovich AU - Slepchenko SM AD - Tyumen Scientific Center of the Siberian Branch of the Russian Academy of Sciences, Tyumen, Russia. FAU - Gusev, Alexander Vasilyevich AU - Gusev AV AUID- ORCID: 0000-0003-1157-7983 AD - Arctic Research Center, Archeology Department, Archeology and Ethnology Sector, Salekhard, Russia. FAU - Svyatova, Evgenia Olegovna AU - Svyatova EO AD - Institution of Culture of Sverdlovsk Region, Center for Protection and Use of Monuments of History and Culture of Sverdlovsk Region, Scientific and Production Center, Ekaterinburg, Russia. FAU - Hong, Jong Ha AU - Hong JH AD - Lab of Bioanthropology, Paleopathology, and History of Diseases, Department of Anatomy/Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea. FAU - Oh, Chang Seok AU - Oh CS AD - Lab of Bioanthropology, Paleopathology, and History of Diseases, Department of Anatomy/Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea. FAU - Lim, Do Seon AU - Lim DS AD - Department of Dental Hygiene, College of Health Science, Eulji University, Seongnam, South Korea. FAU - Shin, Dong Hoon AU - Shin DH AUID- ORCID: 0000-0001-8032-1266 AD - Lab of Bioanthropology, Paleopathology, and History of Diseases, Department of Anatomy/Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190125 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Arctic Regions MH - Burial MH - Cemeteries MH - DNA, Mitochondrial/genetics MH - Haplotypes MH - Humans MH - *Mummies MH - Siberia PMC - PMC6347368 COIS- The authors have declared that no competing interests exist. EDAT- 2019/01/27 06:00 MHDA- 2019/10/19 06:00 PMCR- 2019/01/25 CRDT- 2019/01/26 06:00 PHST- 2018/06/15 00:00 [received] PHST- 2019/01/01 00:00 [accepted] PHST- 2019/01/26 06:00 [entrez] PHST- 2019/01/27 06:00 [pubmed] PHST- 2019/10/19 06:00 [medline] PHST- 2019/01/25 00:00 [pmc-release] AID - PONE-D-18-17918 [pii] AID - 10.1371/journal.pone.0210718 [doi] PST - epublish SO - PLoS One. 2019 Jan 25;14(1):e0210718. doi: 10.1371/journal.pone.0210718. eCollection 2019. PMID- 30528431 OWN - NLM STAT- MEDLINE DCOM- 20191113 LR - 20191113 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 176 IP - 1-2 DP - 2019 Jan 10 TI - Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline. PG - 295-305.e10 LID - S0092-8674(18)31464-8 [pii] LID - 10.1016/j.cell.2018.11.005 [doi] AB - Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe. CI - Copyright © 2018 Elsevier Inc. All rights reserved. FAU - Rascovan, Nicolás AU - Rascovan N AD - Aix Marseille Université, UMR MEPHI, CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France. Electronic address: nicorasco@gmail.com. FAU - Sjögren, Karl-Göran AU - Sjögren KG AD - Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. FAU - Kristiansen, Kristian AU - Kristiansen K AD - Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. FAU - Nielsen, Rasmus AU - Nielsen R AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA. FAU - Willerslev, Eske AU - Willerslev E AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK. FAU - Desnues, Christelle AU - Desnues C AD - Aix Marseille Université, UMR MEPHI, CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France. FAU - Rasmussen, Simon AU - Rasmussen S AD - Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, 2800 Kongens Lyngby, Denmark. Electronic address: simon.rasmussen@cpr.ku.dk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181206 PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Bacterial) SB - IM MH - Biological Evolution MH - DNA, Bacterial/genetics MH - Europe MH - Genome, Bacterial MH - History, Ancient MH - Humans MH - Pandemics MH - Phylogeny MH - Plague/*history MH - Yersinia pestis/*classification/*pathogenicity OTO - NOTNLM OT - Neolithic decline OT - Yersinia pestis OT - ancient DNA OT - emergence and spread of infectious diseases OT - mega settlements OT - metagenomics OT - pathogen evolution OT - plague EDAT- 2018/12/12 06:00 MHDA- 2019/11/14 06:00 CRDT- 2018/12/12 06:00 PHST- 2018/08/09 00:00 [received] PHST- 2018/10/10 00:00 [revised] PHST- 2018/11/01 00:00 [accepted] PHST- 2018/12/12 06:00 [pubmed] PHST- 2019/11/14 06:00 [medline] PHST- 2018/12/12 06:00 [entrez] AID - S0092-8674(18)31464-8 [pii] AID - 10.1016/j.cell.2018.11.005 [doi] PST - ppublish SO - Cell. 2019 Jan 10;176(1-2):295-305.e10. doi: 10.1016/j.cell.2018.11.005. Epub 2018 Dec 6. PMID- 30247677 OWN - NLM STAT- MEDLINE DCOM- 20200511 LR - 20200511 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 47 IP - D1 DP - 2019 Jan 8 TI - AmtDB: a database of ancient human mitochondrial genomes. PG - D29-D32 LID - 10.1093/nar/gky843 [doi] AB - Ancient mitochondrial DNA is used for tracing human past demographic events due to its population-level variability. The number of published ancient mitochondrial genomes has increased in recent years, alongside with the development of high-throughput sequencing and capture enrichment methods. Here, we present AmtDB, the first database of ancient human mitochondrial genomes. Release version contains 1107 hand-curated ancient samples, freely accessible for download, together with the individual descriptors, including geographic location, radiocarbon dating, and archaeological culture affiliation. The database also features an interactive map for sample location visualization. AmtDB is a key platform for ancient population genetic studies and is available at https://amtdb.org. FAU - Ehler, Edvard AU - Ehler E AD - Institute of Molecular Genetics of the ASCR, Vídeňská 1083, 142 20 Prague 4, Czech Republic. AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznań, Poland. FAU - Novotný, Jirí AU - Novotný J AD - Institute of Molecular Genetics of the ASCR, Vídeňská 1083, 142 20 Prague 4, Czech Republic. AD - Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Technická 5, 166 28 Prague 6, Dejvice, Czech Republic. FAU - Juras, Anna AU - Juras A AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland. FAU - Chylenski, Maciej AU - Chylenski M AD - Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614 Poznan, Poland. FAU - Moravcík, Ondrej AU - Moravcík O AD - Institute of Molecular Genetics of the ASCR, Vídenská 1083, 142 20 Prague 4, Czech Republic. FAU - Paces, Jan AU - Paces J AD - Institute of Molecular Genetics of the ASCR, Vídeňská 1083, 142 20 Prague 4, Czech Republic. AD - Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Technická 5, 166 28 Prague 6, Dejvice, Czech Republic. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 SB - IM MH - *Databases, Genetic MH - *Genome, Mitochondrial MH - *Genomics/methods MH - Humans MH - Mitochondria/genetics MH - Web Browser PMC - PMC6324066 EDAT- 2018/09/25 06:00 MHDA- 2020/05/12 06:00 PMCR- 2018/09/24 CRDT- 2018/09/25 06:00 PHST- 2018/08/03 00:00 [received] PHST- 2018/09/21 00:00 [accepted] PHST- 2018/09/25 06:00 [pubmed] PHST- 2020/05/12 06:00 [medline] PHST- 2018/09/25 06:00 [entrez] PHST- 2018/09/24 00:00 [pmc-release] AID - 5106144 [pii] AID - gky843 [pii] AID - 10.1093/nar/gky843 [doi] PST - ppublish SO - Nucleic Acids Res. 2019 Jan 8;47(D1):D29-D32. doi: 10.1093/nar/gky843. PMID- 30875055 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20190904 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence. PG - 195-213 LID - 10.1007/978-1-4939-9176-1_18 [doi] AB - Recent methodological advances have transformed the field of ancient DNA (aDNA). Basic bioinformatics skills are becoming essential requirements to process and analyze the sheer amounts of data generated by current aDNA studies and in biomedical research in general. This chapter is intended as a practical guide to the assembly of ancient mitochondrial genomes, directly from genomic DNA-derived next-generation sequencing (NGS) data, specifically in the absence of closely related reference genomes. In a hands-on tutorial suitable for readers with little to no prior bioinformatics experience, we reconstruct the mitochondrial genome of a woolly mammoth deposited ~45,000 years ago. We introduce key software tools and outline general strategies for mitogenome assembly, including the critical quality assessment of assembly results without a reference genome. FAU - Hahn, Christoph AU - Hahn C AD - Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria. chr.j.hahn@gmail.com. LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics MH - *Genome, Mitochondrial MH - Genomics/*methods MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Reference Standards MH - Sequence Analysis, DNA/methods/*standards MH - Software OTO - NOTNLM OT - Ancient DNA OT - Bioinformatics OT - Genome assembly OT - Mitogenomics OT - Next-generation sequencing EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_18 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:195-213. doi: 10.1007/978-1-4939-9176-1_18. PMID- 30875054 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20190904 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Authentication and Assessment of Contamination in Ancient DNA. PG - 163-194 LID - 10.1007/978-1-4939-9176-1_17 [doi] AB - Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination. FAU - Renaud, Gabriel AU - Renaud G AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. FAU - Schubert, Mikkel AU - Schubert M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. FAU - Sawyer, Susanna AU - Sawyer S AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. ludovic.orlando@univ-tlse3.fr. AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, Toulouse, France. ludovic.orlando@univ-tlse3.fr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Cell Nucleus/*genetics MH - *DNA Contamination MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics MH - Genome, Mitochondrial MH - Humans MH - Sequence Analysis, DNA/*methods OTO - NOTNLM OT - Ancient DNA OT - Contamination OT - DICE OT - Postmortem damage OT - Schmutzi OT - mapDamage2.0 EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_17 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:163-194. doi: 10.1007/978-1-4939-9176-1_17. PMID- 30875052 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20190904 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis. PG - 141-147 LID - 10.1007/978-1-4939-9176-1_15 [doi] AB - The analysis of single-nucleotide polymorphisms (SNPs) has proven to be advantageous for addressing variation within samples of highly degraded or low-quality DNA samples. This is because only short fragments need to be amplified to analyze SNPs, and this can be achieved by multiplex PCR. Here, we present a sensitive method for the targeted sequencing of SNP loci that requires only small amounts of template DNA. The approach combines multiplex amplification of very short fragments covering SNP positions followed by sample barcoding and next-generation sequencing. This method allows generation of data from large sample sets of poorly preserved specimens, such as fossil remains, forensic samples, and museum specimens. The approach is cost-effective, rapid, and applicable to forensics, population genetics, and phylogenetic research questions. FAU - Wutke, Saskia AU - Wutke S AD - Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland. FAU - Ludwig, Arne AU - Ludwig A AD - Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany. ludwig@izw-berlin.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) SB - IM MH - DNA Fingerprinting/*methods MH - DNA, Ancient/*analysis MH - Forensic Genetics MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Multiplex Polymerase Chain Reaction/*methods MH - *Polymorphism, Single Nucleotide OTO - NOTNLM OT - Ancient DNA OT - Library preparation OT - Multiplex PCR OT - Next-generation sequencing OT - Single-nucleotide polymorphism EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_15 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:141-147. doi: 10.1007/978-1-4939-9176-1_15. PMID- 30875051 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20190904 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA. PG - 129-139 LID - 10.1007/978-1-4939-9176-1_14 [doi] AB - Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted "contaminant" DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment. FAU - Paijmans, Johanna L A AU - Paijmans JLA AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. paijmans.jla@gmail.com. FAU - González Fortes, Gloria AU - González Fortes G AD - Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy. FAU - Förster, Daniel W AU - Förster DW AD - Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany. LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) RN - 63231-63-0 (RNA) SB - IM MH - DNA, Ancient/chemistry/*isolation & purification MH - *Gene Library MH - *Genome, Mitochondrial MH - Genomics MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Nucleic Acid Hybridization/*methods MH - RNA/*chemistry/*genetics MH - Sequence Analysis, DNA/methods OTO - NOTNLM OT - Ancient DNA OT - Hybridization capture OT - Microarray capture OT - Next-generation sequencing OT - Target enrichment EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_14 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:129-139. doi: 10.1007/978-1-4939-9176-1_14. PMID- 30875050 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20190904 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Hybridization Capture of Ancient DNA Using RNA Baits. PG - 121-128 LID - 10.1007/978-1-4939-9176-1_13 [doi] AB - The majority of DNA recovered from ancient remains is derived from organisms that colonize the remains post-mortem, such as soil microbes, or from contaminants, such as DNA from living humans. Additionally, some ancient DNA research projects aim to target specific genomic regions, such as mitochondrial genomes or variable single nucleotide polymorphisms (SNPs). To overcome the challenge of targeting specific fragments of DNA from within a complex DNA extract, methods have been developed to enrich ancient DNA extracts for target DNA relative to nontarget DNA. This chapter describes a method for target DNA enrichment that uses hybridization to biotinylated RNA baits to capture and amplify specific ancient DNA fragments from within the pool of extracted fragments. FAU - Soares, André E R AU - Soares AER AD - Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil. aersoares@gmail.com. LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) RN - 63231-63-0 (RNA) SB - IM MH - *DNA Contamination MH - DNA, Ancient/chemistry/*isolation & purification MH - Gene Library MH - Genomics MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Nucleic Acid Hybridization/*methods MH - RNA/chemistry/*genetics MH - Sequence Analysis, DNA/methods OTO - NOTNLM OT - Ancient DNA OT - DNA capture OT - Hybridization OT - RNA bait EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_13 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:121-128. doi: 10.1007/978-1-4939-9176-1_13. PMID- 30875049 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20190904 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Generating RNA Baits for Capture-Based Enrichment. PG - 107-120 LID - 10.1007/978-1-4939-9176-1_12 [doi] AB - Capture-based enrichment techniques have revolutionized genomic analysis of species and populations for which only low-quality or contaminated DNA samples (e.g., ancient DNA, noninvasively collected DNA, environmental DNA) are available. This chapter outlines an optimized laboratory protocol for generating RNA "baits" for genome-wide capture of target DNA from a larger pool of DNA. This method relies on the in vitro transcription of biotinylated RNA baits, which has the dual benefit of eliminating the high cost of synthesizing custom baits and producing a bait set that targets the majority of regions genome-wide. We provide a detailed protocol for the three main steps involved in bait library construction: (1) making a DNA library from a high-quality DNA sample for the organism of interest or a closely related species; (2) using duplex-specific nuclease digestion to reduce the representation of repetitive regions in the DNA library; and (3) performing in vitro transcription of the repetitive region-depleted DNA library to generate biotinylated RNA baits. Where applicable, we include notes and recommendations based on our own experiences. FAU - Snyder-Mackler, Noah AU - Snyder-Mackler N AD - Department of Evolutionary Anthropology, Duke University, Durham, NC, USA. AD - Department of Psychology, University of Washington, Seattle, WA, USA. FAU - Voyles, Tawni AU - Voyles T AD - Department of Evolutionary Anthropology, Duke University, Durham, NC, USA. FAU - Tung, Jenny AU - Tung J AD - Department of Evolutionary Anthropology, Duke University, Durham, NC, USA. jt5@duke.edu. LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) RN - 63231-63-0 (RNA) RN - 6SO6U10H04 (Biotin) SB - IM MH - Biotin/*chemistry MH - DNA, Ancient/chemistry/*isolation & purification MH - *Gene Library MH - *Genome, Human MH - Genomics MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - RNA/*chemistry/*genetics MH - Sequence Analysis, DNA/methods OTO - NOTNLM OT - Biotinylated RNA baits OT - Capture-based enrichment OT - Genome resequencing OT - Repetitive regions OT - Targeted enrichment OT - Whole-genome capture EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_12 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:107-120. doi: 10.1007/978-1-4939-9176-1_12. PMID- 30875048 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20190904 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Whole-Genome Capture of Ancient DNA Using Homemade Baits. PG - 93-105 LID - 10.1007/978-1-4939-9176-1_11 [doi] AB - For many archaeological and paleontological samples, the relative content of endogenous compared to contaminant DNA is low. In such cases, enriching sequencing libraries for endogenous DNA, prior to sequencing can make the final research project more cost-effective. Here, we present an in-solution enrichment protocol based on homemade baits that can be applied to recover complete nuclear genomes from ancient remains. The approach is based on the preparation of DNA baits by biotinylated adapter ligation. The procedure has been developed for use with human remains but can be adapted to other species or target regions by choosing the appropriate template DNA from which to build the capture baits. By using homemade rather than commercially acquired baits, this protocol may offer increased flexibility and cost efficiency. FAU - González Fortes, Gloria AU - González Fortes G AD - Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy. ggfortes14@gmail.com. FAU - Paijmans, Johanna L A AU - Paijmans JLA AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) RN - 6SO6U10H04 (Biotin) SB - IM MH - Biotin/*chemistry MH - DNA, Ancient/chemistry/*isolation & purification MH - *Gene Library MH - *Genome, Human MH - Genomics MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Sequence Analysis, DNA/*methods OTO - NOTNLM OT - Ancient DNA OT - Homemade capture baits OT - Hybridization capture OT - Whole-genome target enrichment EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_11 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:93-105. doi: 10.1007/978-1-4939-9176-1_11. PMID- 30875041 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20190904 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Extraction of Highly Degraded DNA from Ancient Bones and Teeth. PG - 25-29 LID - 10.1007/978-1-4939-9176-1_4 [doi] AB - We provide a DNA extraction protocol optimized for the recovery of highly fragmented molecules preserved within bones and teeth. In this method, the hard tissue matrix is degraded using an EDTA/Proteinase K lysis buffer, and the DNA is purified using spin columns with silica membranes. This method efficiently recovers molecules as short as 35 base-pairs long. FAU - Dabney, Jesse AU - Dabney J AD - Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. mmeyer@eva.mpg.de. LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) RN - 7631-86-9 (Silicon Dioxide) RN - 9G34HU7RV0 (Edetic Acid) RN - EC 3.4.21.64 (Endopeptidase K) SB - IM MH - Bone and Bones/*metabolism MH - *DNA Degradation, Necrotic MH - DNA, Ancient/*isolation & purification MH - Edetic Acid/*metabolism MH - Endopeptidase K/*metabolism MH - Humans MH - Silicon Dioxide/chemistry MH - Tooth/*metabolism OTO - NOTNLM OT - Ancient DNA OT - DNA extraction OT - Degraded DNA OT - Paleogenomics OT - Silica purification EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_4 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:25-29. doi: 10.1007/978-1-4939-9176-1_4. PMID- 30875040 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20190904 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step. PG - 21-24 LID - 10.1007/978-1-4939-9176-1_3 [doi] AB - Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction. FAU - Schroeder, Hannes AU - Schroeder H AD - Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. hschroeder@snm.ku.dk. FAU - de Barros Damgaard, Peter AU - de Barros Damgaard P AD - Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Allentoft, Morten E AU - Allentoft ME AD - Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) RN - 9G34HU7RV0 (Edetic Acid) RN - EC 3.4.21.64 (Endopeptidase K) SB - IM MH - Bone and Bones/*metabolism MH - *DNA Contamination MH - DNA, Ancient/*analysis/*isolation & purification MH - Edetic Acid/*metabolism MH - Endopeptidase K/*metabolism MH - Humans MH - Tooth/*metabolism OTO - NOTNLM OT - Ancient DNA OT - Contamination OT - EDTA OT - Pretreatment OT - Proteinase K EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_3 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:21-24. doi: 10.1007/978-1-4939-9176-1_3. PMID- 30875038 OWN - NLM STAT- MEDLINE DCOM- 20190904 LR - 20200511 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1963 DP - 2019 TI - Setting Up an Ancient DNA Laboratory. PG - 1-13 LID - 10.1007/978-1-4939-9176-1_1 [doi] AB - Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential is high for contamination of ancient samples, ancient DNA extracts, and genomic sequencing libraries prepared from these extracts with non-degraded DNA from the present-day environment. To minimize the risk of contamination in ancient DNA environments, experimental protocols specific to handling ancient specimens, including those that outline the design and layout of laboratory space, have been introduced. Here, we outline challenges associated with working with ancient samples, including providing guidelines for setting up a new ancient DNA laboratory. We also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination of ancient DNA experiments with exogenous sources of DNA. FAU - Fulton, Tara L AU - Fulton TL AD - Environment and Climate Change Canada, Edmonton, AB, Canada. FAU - Shapiro, Beth AU - Shapiro B AD - Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA. bashapir@ucsc.edu. LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *DNA Contamination MH - DNA Damage MH - DNA, Ancient/*analysis/chemistry/isolation & purification MH - Fossils MH - Humans MH - Laboratories/standards MH - Sequence Analysis, DNA/*methods/standards OTO - NOTNLM OT - Ancient DNA OT - Contamination OT - DNA damage OT - Guidelines OT - Laboratory setup OT - Sample preparation OT - Subsampling OT - aDNA EDAT- 2019/03/16 06:00 MHDA- 2019/09/05 06:00 CRDT- 2019/03/16 06:00 PHST- 2019/03/16 06:00 [entrez] PHST- 2019/03/16 06:00 [pubmed] PHST- 2019/09/05 06:00 [medline] AID - 10.1007/978-1-4939-9176-1_1 [doi] PST - ppublish SO - Methods Mol Biol. 2019;1963:1-13. doi: 10.1007/978-1-4939-9176-1_1. PMID- 30408154 OWN - NLM STAT- MEDLINE DCOM- 20200113 LR - 20210130 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 168 Suppl 67 DP - 2019 Jan TI - Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. PG - 4-26 LID - 10.1002/ajpa.23737 [doi] AB - Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits. CI - © 2018 American Association of Physical Anthropologists. FAU - Quillen, Ellen E AU - Quillen EE AUID- ORCID: 0000-0003-2033-8693 AD - Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina. AD - Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina. FAU - Norton, Heather L AU - Norton HL AD - Department of Anthropology, University of Cincinnati, Cincinnati, Ohio. FAU - Parra, Esteban J AU - Parra EJ AD - Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada. FAU - Lona-Durazo, Frida AU - Lona-Durazo F AD - Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada. FAU - Ang, Khai C AU - Ang KC AD - Department of Pathology and Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania. FAU - Illiescu, Florin Mircea AU - Illiescu FM AD - Department of Zoology, University of Cambridge, Cambridge, United Kingdom. AD - Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile. FAU - Pearson, Laurel N AU - Pearson LN AD - Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania. FAU - Shriver, Mark D AU - Shriver MD AD - Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania. FAU - Lasisi, Tina AU - Lasisi T AD - Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania. FAU - Gokcumen, Omer AU - Gokcumen O AD - Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York. FAU - Starr, Izzy AU - Starr I AD - Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York. FAU - Lin, Yen-Lung AU - Lin YL AD - Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York. FAU - Martin, Alicia R AU - Martin AR AD - Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts. AD - Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts. AD - Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts. FAU - Jablonski, Nina G AU - Jablonski NG AD - Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania. LA - eng GR - 1714867/National Science Foundation/International PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20181108 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Antiporters) RN - 0 (Guanine Nucleotide Exchange Factors) RN - 0 (MC1R protein, human) RN - 0 (MFSD12 protein, human) RN - 0 (Membrane Proteins) RN - 0 (Membrane Transport Proteins) RN - 0 (OCA2 protein, human) RN - 0 (Receptor, Melanocortin, Type 1) RN - 0 (SLC24A5 protein, human) RN - EC 2.3.2.27 (HERC2 protein, human) RN - EC 2.3.2.27 (Ubiquitin-Protein Ligases) SB - IM MH - Anthropology, Physical MH - Antiporters/genetics MH - *Biological Evolution MH - Genetics, Population MH - Guanine Nucleotide Exchange Factors/genetics MH - Humans MH - Membrane Proteins/genetics MH - Membrane Transport Proteins/genetics MH - Receptor, Melanocortin, Type 1/genetics MH - Skin/metabolism MH - *Skin Physiological Phenomena MH - *Skin Pigmentation/genetics/physiology MH - Ubiquitin-Protein Ligases OTO - NOTNLM OT - genetics OT - human evolution OT - skin pigmentation EDAT- 2018/11/09 06:00 MHDA- 2020/01/14 06:00 CRDT- 2018/11/09 06:00 PHST- 2018/07/02 00:00 [received] PHST- 2018/09/17 00:00 [revised] PHST- 2018/09/20 00:00 [accepted] PHST- 2018/11/09 06:00 [pubmed] PHST- 2020/01/14 06:00 [medline] PHST- 2018/11/09 06:00 [entrez] AID - 10.1002/ajpa.23737 [doi] PST - ppublish SO - Am J Phys Anthropol. 2019 Jan;168 Suppl 67:4-26. doi: 10.1002/ajpa.23737. Epub 2018 Nov 8. PMID- 29595343 OWN - NLM STAT- MEDLINE DCOM- 20190212 LR - 20210112 IS - 2470-1408 (Electronic) IS - 2470-1394 (Linking) VI - 30 IP - 1 DP - 2019 Jan TI - On the persistence and detectability of ancient Beothuk mitochondrial DNA genomes in living First Nations peoples. PG - 68-74 LID - 10.1080/24701394.2018.1455190 [doi] AB - Claims have long been made as to the survival to the present day of descendants of the Newfoundland Beothuk, a group generally accepted to have become extinct with the death of the last known member, Shanawdithit, in 1829. Interest has recently been revived by the availability of commercial genetic testing, which some claim can assign living individuals to specific Native American groups. We compare complete mitogenome sequences (16569 bp) from aDNA of eight distinct Beothuk lineages, including Shanawdithit's uncle Nonosabasut and his wife Demasduit, with three Newfoundland Mi'kmaq lineages and 21 other living Native Americans drawn from GenBank. A Newfoundland Mi'kmaq lineage in Haplogroup A is more similar to three Native Americans (1-3 SNPs) than to the most closely related Beothuk (24 SNPs). Nonosabasut in Haplogroup X is identical to a non-Beothuk Native American. Demasduit in Haplogroup C differs from three other Native Americans by 1-4 substitutions. Within a 2168 bp region of the HVS sequences available from living Mi'kmaq of the Miawpukek First Nation in Newfoundland, lineages in Haplogroups C, X, and A differ by 1, 4, and 8 substitutions, from the most similar Beothuk, and are more similar to other Native Americans. MtDNA genome sequences in living persons identical or similar to those of Beothuk do not necessarily indicate Beothuk ancestry. Mi'kmaq lineages cannot at this time be associated with any Beothuk lineages more closely than those of other Native Americans. FAU - Collier, Ashley AU - Collier A AD - a Department of Biology, Genetics, Evolution, and Molecular Systematics Laboratory , Memorial University of Newfoundland , St. John's , Canada. FAU - Carr, Steven M AU - Carr SM AD - a Department of Biology, Genetics, Evolution, and Molecular Systematics Laboratory , Memorial University of Newfoundland , St. John's , Canada. LA - eng PT - Journal Article DEP - 20180329 PL - England TA - Mitochondrial DNA A DNA Mapp Seq Anal JT - Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis JID - 101679980 SB - IM ECI - Mitochondrial DNA A DNA Mapp Seq Anal. 2021 Mar;32(2):76. doi: 10.1080/24701394.2020.1857198. PMID: 33427537 MH - *Genome, Mitochondrial MH - Genotyping Techniques/methods/standards MH - Haplotypes MH - Humans MH - Indians, North American/*genetics MH - Limit of Detection MH - Polymorphism, Genetic OTO - NOTNLM OT - Beothuk OT - C and X OT - Haplogroups A OT - Mi’kmaq OT - Norse OT - ancient DNA EDAT- 2018/03/30 06:00 MHDA- 2019/02/13 06:00 CRDT- 2018/03/30 06:00 PHST- 2018/03/30 06:00 [pubmed] PHST- 2019/02/13 06:00 [medline] PHST- 2018/03/30 06:00 [entrez] AID - 10.1080/24701394.2018.1455190 [doi] PST - ppublish SO - Mitochondrial DNA A DNA Mapp Seq Anal. 2019 Jan;30(1):68-74. doi: 10.1080/24701394.2018.1455190. Epub 2018 Mar 29. PMID- 29931305 OWN - NLM STAT- MEDLINE DCOM- 20191022 LR - 20191022 IS - 1367-4811 (Electronic) IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 34 IP - 24 DP - 2018 Dec 15 TI - snpAD: an ancient DNA genotype caller. PG - 4165-4171 LID - 10.1093/bioinformatics/bty507 [doi] AB - MOTIVATION: The study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling. RESULTS: I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals. AVAILABILITY AND IMPLEMENTATION: The C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. FAU - Prüfer, Kay AU - Prüfer K AD - Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (DNA, Ancient) SB - IM MH - Computational Biology MH - *DNA, Ancient MH - *Genome MH - Genotype MH - *Genotyping Techniques MH - Humans MH - Sequence Analysis, DNA MH - *Software PMC - PMC6289138 EDAT- 2018/06/23 06:00 MHDA- 2019/10/23 06:00 PMCR- 2018/06/21 CRDT- 2018/06/23 06:00 PHST- 2018/03/23 00:00 [received] PHST- 2018/06/19 00:00 [accepted] PHST- 2018/06/23 06:00 [pubmed] PHST- 2019/10/23 06:00 [medline] PHST- 2018/06/23 06:00 [entrez] PHST- 2018/06/21 00:00 [pmc-release] AID - 5042170 [pii] AID - bty507 [pii] AID - 10.1093/bioinformatics/bty507 [doi] PST - ppublish SO - Bioinformatics. 2018 Dec 15;34(24):4165-4171. doi: 10.1093/bioinformatics/bty507. PMID- 30478041 OWN - NLM STAT- MEDLINE DCOM- 20190204 LR - 20240719 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 115 IP - 50 DP - 2018 Dec 11 TI - Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. PG - E11790-E11797 LID - 10.1073/pnas.1812865115 [doi] AB - Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement. CI - Copyright © 2018 the Author(s). Published by PNAS. FAU - Namouchi, Amine AU - Namouchi A AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; amine.namouchi@ibv.uio.no n.c.stenseth@ibv.uio.no barbara.bramanti@ibv.uio.no. FAU - Guellil, Meriam AU - Guellil M AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway. FAU - Kersten, Oliver AU - Kersten O AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway. FAU - Hänsch, Stephanie AU - Hänsch S AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway. FAU - Ottoni, Claudio AU - Ottoni C AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway. FAU - Schmid, Boris V AU - Schmid BV AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway. FAU - Pacciani, Elsa AU - Pacciani E AD - Soprintendenza Archeologia, Belle Arti e Paesaggio di Firenze, Pistoia e Prato, 50125 Florence, Italy. FAU - Quaglia, Luisa AU - Quaglia L AD - Soprintendenza Archeologia, Belle Arti e Paesaggio di Firenze, Pistoia e Prato, 50125 Florence, Italy. FAU - Vermunt, Marco AU - Vermunt M AD - Department of Monuments and Archaeology, Municipality of Bergen op Zoom, 4611BT-59 Bergen op Zoom, The Netherlands. FAU - Bauer, Egil L AU - Bauer EL AD - Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway. FAU - Derrick, Michael AU - Derrick M AD - Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway. FAU - Jensen, Anne Ø AU - Jensen AØ AD - Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway. FAU - Kacki, Sacha AU - Kacki S AD - Department of Archaeology, Durham University, DH1 3LE Durham, United Kingdom. AD - UMR 5199 De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie, Centre National de la Recherche Scientifique, University of Bordeaux, 33615 Pessac, France. FAU - Cohn, Samuel K Jr AU - Cohn SK Jr AD - School of Humanities, University of Glasgow, G12 8QQ Glasgow, United Kingdom. FAU - Stenseth, Nils C AU - Stenseth NC AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; amine.namouchi@ibv.uio.no n.c.stenseth@ibv.uio.no barbara.bramanti@ibv.uio.no. AD - Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Ministry of Education, 100084 Beijing, China. FAU - Bramanti, Barbara AU - Bramanti B AUID- ORCID: 0000-0002-5433-663X AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; amine.namouchi@ibv.uio.no n.c.stenseth@ibv.uio.no barbara.bramanti@ibv.uio.no. AD - Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy, and Prevention, University of Ferrara, 35-441221 Ferrara, Italy. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181126 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Bacterial) SB - IM EIN - Proc Natl Acad Sci U S A. 2019 Jan 2;116(1):338. doi: 10.1073/pnas.1820659116. PMID: 30584097 CIN - Proc Natl Acad Sci U S A. 2019 Apr 16;116(16):7622-7623. doi: 10.1073/pnas.1902274116. PMID: 30948635 CIN - Proc Natl Acad Sci U S A. 2019 Apr 16;116(16):7620-7621. doi: 10.1073/pnas.1901145116. PMID: 30948636 EIN - Proc Natl Acad Sci U S A. 2020 Jun 2;117(22):12500. doi: 10.1073/pnas.2007983117. PMID: 32457145 MH - DNA, Bacterial/genetics/isolation & purification MH - Europe/epidemiology MH - Evolution, Molecular MH - Fossils/microbiology MH - Genome, Bacterial MH - History, Medieval MH - Humans MH - Pandemics/*history MH - Phylogeny MH - Plague/epidemiology/*history/microbiology MH - Polymorphism, Single Nucleotide MH - Time Factors MH - Yersinia pestis/classification/*genetics PMC - PMC6294933 OTO - NOTNLM OT - Medieval OT - Second Pandemic OT - Yersinia pestis OT - ancient DNA OT - plague COIS- The authors declare no conflict of interest. EDAT- 2018/11/28 06:00 MHDA- 2019/02/05 06:00 PMCR- 2018/11/26 CRDT- 2018/11/28 06:00 PHST- 2018/11/28 06:00 [pubmed] PHST- 2019/02/05 06:00 [medline] PHST- 2018/11/28 06:00 [entrez] PHST- 2018/11/26 00:00 [pmc-release] AID - 1812865115 [pii] AID - 201812865 [pii] AID - 10.1073/pnas.1812865115 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):E11790-E11797. doi: 10.1073/pnas.1812865115. Epub 2018 Nov 26. PMID- 30521562 OWN - NLM STAT- MEDLINE DCOM- 20190508 LR - 20221207 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 13 IP - 12 DP - 2018 TI - The multiple maternal legacy of the Late Iron Age group of Urville-Nacqueville (France, Normandy) documents a long-standing genetic contact zone in northwestern France. PG - e0207459 LID - 10.1371/journal.pone.0207459 [doi] LID - e0207459 AB - The compilation of archaeological and genetic data for ancient European human groups has provided persuasive evidence for a complex series of migrations, population replacements and admixture until the Bronze Age. If the Bronze-to-Iron Age transition has been well documented archaeologically, ancient DNA (aDNA) remains rare for the latter period and does not precisely reflect the genetic diversity of European Celtic groups. In order to document the evolution of European communities, we analysed 45 individuals from the Late Iron Age (La Tène) Urville-Nacqueville necropolis in northwestern France, a region recognized as a major cultural contact zone between groups from both sides of the Channel. The characterization of 37 HVS-I mitochondrial sequences and 40 haplogroups provided the largest maternal gene pool yet recovered for the European Iron Age. First, descriptive analyses allowed us to demonstrate the presence of substantial amounts of steppe-related mitochondrial ancestry in the community, which is consistent with the expansion of Bell Beaker groups bearing an important steppe legacy in northwestern Europe at approximately 2500 BC. Second, maternal genetic affinities highlighted with Bronze Age groups from Great Britain and the Iberian Peninsula regions tends to support the idea that the continuous cultural exchanges documented archaeologically across the Channel and along the Atlantic coast (during and after the Bronze Age period) were accompanied by significant gene flow. Lastly, our results suggest a maternal genetic continuity between Bronze Age and Iron Age groups that would argue in favour of a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. The palaeogenetic data gathered for the Urville-Nacqueville group constitute an important step in the biological characterization of European Iron age groups. Clearly, more numerous and diachronic aDNA data are needed to fully understand the complex relationship between the cultural and biological evolution of groups from the period. FAU - Fischer, Claire-Elise AU - Fischer CE AUID- ORCID: 0000-0003-4513-1031 AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France. FAU - Lefort, Anthony AU - Lefort A AD - Inrap Grand-Ouest, Boulevard de l'Europe, Bourguébus, France. FAU - Pemonge, Marie-Hélène AU - Pemonge MH AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France. FAU - Couture-Veschambre, Christine AU - Couture-Veschambre C AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France. FAU - Rottier, Stéphane AU - Rottier S AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181206 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM EIN - PLoS One. 2019 Jan 25;14(1):e0211519. doi: 10.1371/journal.pone.0211519. PMID: 30682189 MH - Archaeology/methods MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/analysis/*genetics MH - Europe/ethnology MH - France/ethnology MH - Gene Pool MH - Genetic Variation/genetics MH - Genetics, Population/methods MH - Genotype MH - Haplotypes MH - History, Ancient MH - Humans MH - United Kingdom MH - White People/*genetics PMC - PMC6283558 COIS- The authors have declared that no competing interests exist. EDAT- 2018/12/07 06:00 MHDA- 2019/05/09 06:00 PMCR- 2018/12/06 CRDT- 2018/12/07 06:00 PHST- 2018/03/18 00:00 [received] PHST- 2018/10/31 00:00 [accepted] PHST- 2018/12/07 06:00 [entrez] PHST- 2018/12/07 06:00 [pubmed] PHST- 2019/05/09 06:00 [medline] PHST- 2018/12/06 00:00 [pmc-release] AID - PONE-D-18-08273 [pii] AID - 10.1371/journal.pone.0207459 [doi] PST - epublish SO - PLoS One. 2018 Dec 6;13(12):e0207459. doi: 10.1371/journal.pone.0207459. eCollection 2018. PMID- 30514893 OWN - NLM STAT- MEDLINE DCOM- 20191025 LR - 20231104 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 8 IP - 1 DP - 2018 Dec 4 TI - Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza. PG - 17567 LID - 10.1038/s41598-018-35667-y [doi] LID - 17567 AB - Ibiza was permanently settled around the 7(th) century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4(th) century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island's modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated. FAU - Zalloua, Pierre AU - Zalloua P AD - School of Medicine, Lebanese American University, Byblos, Lebanon. pierre.zalloua@lau.edu.lb. FAU - Collins, Catherine J AU - Collins CJ AD - Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand. FAU - Gosling, Anna AU - Gosling A AD - Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand. FAU - Biagini, Simone Andrea AU - Biagini SA AUID- ORCID: 0000-0002-4488-3162 AD - Department de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain. FAU - Costa, Benjamí AU - Costa B AD - Museu Arqueològic d'Eivissa i Formentera, Universitat de Barcelona, Illes Balears, Spain. FAU - Kardailsky, Olga AU - Kardailsky O AD - Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand. FAU - Nigro, Lorenzo AU - Nigro L AD - Facoltà di Lettere e Filosofia, Università di Roma, La Sapienza, Rome, Italy. FAU - Khalil, Wissam AU - Khalil W AD - Department of Arts and Archaeology, Lebanese University, Beirut, Lebanon. FAU - Calafell, Francesc AU - Calafell F AUID- ORCID: 0000-0002-1083-9438 AD - Department de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain. FAU - Matisoo-Smith, Elizabeth AU - Matisoo-Smith E AD - Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand. matisoo-smith@otago.ac.nz. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181204 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - Black People/genetics/*history MH - Body Remains MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Emigration and Immigration/*history MH - Genetic Variation MH - Genome, Mitochondrial/genetics MH - History, Ancient MH - Humans MH - Male MH - Phylogeography MH - Spain MH - White People/genetics/*history PMC - PMC6279797 COIS- The authors declare no competing interests. EDAT- 2018/12/06 06:00 MHDA- 2019/10/28 06:00 PMCR- 2018/12/04 CRDT- 2018/12/06 06:00 PHST- 2018/04/09 00:00 [received] PHST- 2018/11/09 00:00 [accepted] PHST- 2018/12/06 06:00 [entrez] PHST- 2018/12/06 06:00 [pubmed] PHST- 2019/10/28 06:00 [medline] PHST- 2018/12/04 00:00 [pmc-release] AID - 10.1038/s41598-018-35667-y [pii] AID - 35667 [pii] AID - 10.1038/s41598-018-35667-y [doi] PST - epublish SO - Sci Rep. 2018 Dec 4;8(1):17567. doi: 10.1038/s41598-018-35667-y. PMID- 30286387 OWN - NLM STAT- MEDLINE DCOM- 20190813 LR - 20190813 IS - 1879-0380 (Electronic) IS - 0959-437X (Linking) VI - 53 DP - 2018 Dec TI - The genetic makings of South Asia. PG - 128-133 LID - S0959-437X(17)30175-2 [pii] LID - 10.1016/j.gde.2018.09.003 [doi] AB - South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for disentangling the genetic makings of South Asia. In this review we shall give brief account on the recent developments in the field. Advances are made in two fronts simultaneously. Whole genome characterisation of many extant South Asians paint the picture of the genetic diversity and its implications to health-care. On the other hand ancient DNA studies, which are finally reaching South Asia, provide new incites to the demographic history of the subcontinent. Before the spread of agriculture, South Asia was likely inhabited by hunter-gatherer groups deriving much of their ancestry from a population that split from the rest of humanity soon after expanding from Africa. Early Iranian agriculturalists mixing with these local hunter-gatherers probably formed the population that flourished during the blossoming of the Indus Valley Civilisation. Further admixture with the still persisting HG groups and population(s) from the Eurasian Steppe, formed the two ancestral populations (ANI and ASI), the north-south mixing pattern of whom is known today as the 'Indian Cline'. Studies on natural selection in South Asia have so far revealed strong signals of sweeps that are shared with West Eurasians. Future studies will have to fully unlock the aDNA promise for South Asia. CI - Copyright © 2018 Elsevier Ltd. All rights reserved. FAU - Metspalu, Mait AU - Metspalu M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Mondal, Mayukh AU - Mondal M AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia. FAU - Chaubey, Gyaneshwer AU - Chaubey G AD - Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia; Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20181001 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) MH - Asia MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - *Genetics, Population MH - Genome, Human/*genetics MH - Human Migration MH - Humans MH - Iran MH - Selection, Genetic/*genetics EDAT- 2018/10/05 06:00 MHDA- 2019/08/14 06:00 CRDT- 2018/10/05 06:00 PHST- 2018/05/10 00:00 [received] PHST- 2018/09/13 00:00 [accepted] PHST- 2018/10/05 06:00 [pubmed] PHST- 2019/08/14 06:00 [medline] PHST- 2018/10/05 06:00 [entrez] AID - S0959-437X(17)30175-2 [pii] AID - 10.1016/j.gde.2018.09.003 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2018 Dec;53:128-133. doi: 10.1016/j.gde.2018.09.003. Epub 2018 Oct 1. PMID- 30272210 OWN - NLM STAT- MEDLINE DCOM- 20190718 LR - 20231004 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 35 IP - 12 DP - 2018 Dec 1 TI - FADS1 and the Timing of Human Adaptation to Agriculture. PG - 2957-2970 LID - 10.1093/molbev/msy180 [doi] AB - Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced ∼8,500 years ago by Early Neolithic farming populations. However, we also show that it was not under strong selection in these populations. We find that this allele, and other proposed agricultural adaptations at LCT/MCM6 and SLC22A4, were not strongly selected until much later, perhaps as late as the Bronze Age. Similarly, increased copy number variation at the salivary amylase gene AMY1 is not linked to the development of agriculture although, in this case, the putative adaptation precedes the agricultural transition. Our analysis shows that selection at the FADS locus was not tightly linked to the initial introduction of agriculture and the Neolithic transition. Further, it suggests that the strongest signals of recent human adaptation in Europe did not coincide with the Neolithic transition but with more recent changes in environment, diet, or efficiency of selection due to increases in effective population size. FAU - Mathieson, Sara AU - Mathieson S AD - Department of Computer Science, Swarthmore College, Swarthmore, PA. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA. LA - eng PT - Journal Article PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (Delta-5 Fatty Acid Desaturase) RN - EC 1.14.19.- (Fatty Acid Desaturases) RN - EC 1.14.19.3 (FADS1 protein, human) SB - IM MH - *Adaptation, Biological MH - *Agriculture MH - Biological Evolution MH - Delta-5 Fatty Acid Desaturase MH - Diet MH - Fatty Acid Desaturases/*genetics MH - Genome, Human MH - Haplotypes MH - Humans MH - Lipid Metabolism/genetics MH - *Selection, Genetic MH - White People/*genetics PMC - PMC6278866 EDAT- 2018/10/03 06:00 MHDA- 2019/07/19 06:00 PMCR- 2018/10/01 CRDT- 2018/10/02 06:00 PHST- 2018/10/03 06:00 [pubmed] PHST- 2019/07/19 06:00 [medline] PHST- 2018/10/02 06:00 [entrez] PHST- 2018/10/01 00:00 [pmc-release] AID - 5112969 [pii] AID - msy180 [pii] AID - 10.1093/molbev/msy180 [doi] PST - ppublish SO - Mol Biol Evol. 2018 Dec 1;35(12):2957-2970. doi: 10.1093/molbev/msy180. PMID- 29960127 OWN - NLM STAT- MEDLINE DCOM- 20190813 LR - 20221207 IS - 1879-0380 (Electronic) IS - 0959-437X (Linking) VI - 53 DP - 2018 Dec TI - The evolutionary history of human populations in Europe. PG - 21-27 LID - S0959-437X(18)30058-3 [pii] LID - 10.1016/j.gde.2018.06.007 [doi] AB - I review the evolutionary history of human populations in Europe with an emphasis on what has been learned in recent years through the study of ancient DNA. Human populations in Europe ∼430-39kya (archaic Europeans) included Neandertals and their ancestors, who were genetically differentiated from other archaic Eurasians (such as the Denisovans of Siberia), as well as modern humans. Modern humans arrived to Europe by ∼45kya, and are first genetically attested by ∼39kya when they were still mixing with Neandertals. The first Europeans who were recognizably genetically related to modern ones appeared in the genetic record shortly thereafter at ∼37kya. At ∼15kya a largely homogeneous set of hunter-gatherers became dominant in most of Europe, but with some admixture from Siberian hunter-gatherers in the eastern part of the continent. These hunter-gatherers were joined by migrants from the Near East beginning at ∼8-9kya: Anatolian farmers settled most of mainland Europe, and migrants from the Caucasus reached eastern Europe, forming steppe populations. After ∼5kya there was migration from the steppe into mainland Europe and vice versa. Present-day Europeans (ignoring the long-distance migrations of the modern era) are largely the product of this Bronze Age collision of steppe pastoralists with Neolithic farmers. CI - Copyright © 2018 Elsevier Ltd. All rights reserved. FAU - Lazaridis, Iosif AU - Lazaridis I AD - Department of Genetics, 77 Avenue Louis Pasteur, New Research Building 260, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: lazaridis@genetics.med.harvard.edu. LA - eng PT - Journal Article PT - Review DEP - 20180628 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) MH - Animals MH - DNA, Ancient MH - Europe MH - *Genetics, Population MH - Genome, Human/*genetics MH - *Genomics MH - Human Migration MH - Humans MH - Neanderthals/genetics MH - White People/*genetics EDAT- 2018/07/01 06:00 MHDA- 2019/08/14 06:00 CRDT- 2018/07/01 06:00 PHST- 2018/05/02 00:00 [received] PHST- 2018/06/07 00:00 [revised] PHST- 2018/06/08 00:00 [accepted] PHST- 2018/07/01 06:00 [pubmed] PHST- 2019/08/14 06:00 [medline] PHST- 2018/07/01 06:00 [entrez] AID - S0959-437X(18)30058-3 [pii] AID - 10.1016/j.gde.2018.06.007 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2018 Dec;53:21-27. doi: 10.1016/j.gde.2018.06.007. Epub 2018 Jun 28. PMID- 29894925 OWN - NLM STAT- MEDLINE DCOM- 20190813 LR - 20190813 IS - 1879-0380 (Electronic) IS - 0959-437X (Linking) VI - 53 DP - 2018 Dec TI - Something old, something borrowed: admixture and adaptation in human evolution. PG - 1-8 LID - S0959-437X(17)30185-5 [pii] LID - 10.1016/j.gde.2018.05.009 [doi] AB - The sequencing of ancient DNA from archaic humans-Neanderthals and Denisovans-has revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Was the introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full. Here, we review the recent literature characterizing introgressed DNA and the likely biological consequences for their modern human carriers. We focus particularly on archaic human haplotypes that were beneficial to modern humans as they expanded across the globe, and on ways to understand how populations harboring these haplotypes evolved over time. CI - Copyright © 2018 Elsevier Ltd. All rights reserved. FAU - Dannemann, Michael AU - Dannemann M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Racimo, Fernando AU - Racimo F AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. Electronic address: fracimo@snm.ku.dk. LA - eng PT - Journal Article PT - Review DEP - 20180609 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) MH - Adaptation, Physiological/*genetics MH - Animals MH - *Biological Evolution MH - DNA, Ancient MH - *Evolution, Molecular MH - Genetics, Population MH - Genome, Human/genetics MH - Haplotypes MH - Hominidae/*genetics MH - Humans MH - Neanderthals/genetics EDAT- 2018/06/13 06:00 MHDA- 2019/08/14 06:00 CRDT- 2018/06/13 06:00 PHST- 2018/04/23 00:00 [received] PHST- 2018/05/21 00:00 [revised] PHST- 2018/05/24 00:00 [accepted] PHST- 2018/06/13 06:00 [pubmed] PHST- 2019/08/14 06:00 [medline] PHST- 2018/06/13 06:00 [entrez] AID - S0959-437X(17)30185-5 [pii] AID - 10.1016/j.gde.2018.05.009 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2018 Dec;53:1-8. doi: 10.1016/j.gde.2018.05.009. Epub 2018 Jun 9. PMID- 30479341 OWN - NLM STAT- MEDLINE DCOM- 20181231 LR - 20191127 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 9 IP - 1 DP - 2018 Nov 27 TI - Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe. PG - 5018 LID - 10.1038/s41467-018-07483-5 [doi] LID - 5018 AB - European population history has been shaped by migrations of people, and their subsequent admixture. Recently, ancient DNA has brought new insights into European migration events linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland. FAU - Lamnidis, Thiseas C AU - Lamnidis TC AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Majander, Kerttu AU - Majander K AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, 72070, Tübingen, Germany. AD - Department of Biosciences, University of Helsinki, PL 56 (Viikinkaari 9), 00014, Helsinki, Finland. FAU - Jeong, Choongwon AU - Jeong C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. AD - The Eurasia3angle Project, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Salmela, Elina AU - Salmela E AUID- ORCID: 0000-0003-1326-4462 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. AD - Department of Biosciences, University of Helsinki, PL 56 (Viikinkaari 9), 00014, Helsinki, Finland. FAU - Wessman, Anna AU - Wessman A AD - Department of Cultures, Archaeology, University of Helsinki, PL 59 (Unioninkatu 38), 00014, Helsinki, Finland. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia. FAU - Khartanovich, Valery AU - Khartanovich V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia. FAU - Balanovsky, Oleg AU - Balanovsky O AD - Vavilov Institute of General Genetics, Ulitsa Gubkina, 3, Moscow, 117971, Russia. AD - Research Centre for Medical Genetics, Moskvorech'ye Ulitsa, 1, Moscow, 115478, Russia. AD - Biobank of North Eurasia, Kotlyakovskaya Ulitsa, 3 строение 12, Moscow, 115201, Russia. FAU - Ongyerth, Matthias AU - Ongyerth M AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103, Leipzig, Germany. FAU - Weihmann, Antje AU - Weihmann A AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103, Leipzig, Germany. FAU - Sajantila, Antti AU - Sajantila A AD - Department of Forensic Medicine, University of Helsinki, PL 40 (Kytösuontie 11), Helsinki, 00014, Finland. FAU - Kelso, Janet AU - Kelso J AUID- ORCID: 0000-0002-3618-322X AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103, Leipzig, Germany. FAU - Pääbo, Svante AU - Pääbo S AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103, Leipzig, Germany. FAU - Onkamo, Päivi AU - Onkamo P AD - Department of Biosciences, University of Helsinki, PL 56 (Viikinkaari 9), 00014, Helsinki, Finland. paivi.onkamo@helsinki.fi. AD - Department of Biology, University of Turku, Turku, 20014, Finland. paivi.onkamo@helsinki.fi. FAU - Haak, Wolfgang AU - Haak W AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. haak@shh.mpg.de. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. FAU - Schiffels, Stephan AU - Schiffels S AUID- ORCID: 0000-0002-1017-9150 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. schiffels@shh.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181127 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 SB - IM MH - Archaeology MH - Female MH - Finland MH - *Genealogy and Heraldry MH - Genetics, Population MH - *Genome, Human MH - Geography MH - Humans MH - Male MH - Principal Component Analysis MH - Siberia PMC - PMC6258758 COIS- The authors declare no competing interests. EDAT- 2018/11/28 06:00 MHDA- 2019/01/01 06:00 PMCR- 2018/11/27 CRDT- 2018/11/28 06:00 PHST- 2017/12/08 00:00 [received] PHST- 2018/10/31 00:00 [accepted] PHST- 2018/11/28 06:00 [entrez] PHST- 2018/11/28 06:00 [pubmed] PHST- 2019/01/01 06:00 [medline] PHST- 2018/11/27 00:00 [pmc-release] AID - 10.1038/s41467-018-07483-5 [pii] AID - 7483 [pii] AID - 10.1038/s41467-018-07483-5 [doi] PST - epublish SO - Nat Commun. 2018 Nov 27;9(1):5018. doi: 10.1038/s41467-018-07483-5. PMID- 30445034 OWN - NLM STAT- MEDLINE DCOM- 20190820 LR - 20190820 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 175 IP - 5 DP - 2018 Nov 15 TI - Native American Genomic Diversity through Ancient DNA. PG - 1173-1174 LID - S0092-8674(18)31457-0 [pii] LID - 10.1016/j.cell.2018.10.058 [doi] AB - Ancient DNA is a powerful tool to understand the evolutionary dynamics of both current and ancestral populations. Posth et al. use ancient DNA to elucidate important questions surrounding the peopling of Central and South America, giving us greater insights into the ancestry of genetically understudied populations. CI - Copyright © 2018 Elsevier Inc. All rights reserved. FAU - O'Connor, Timothy D AU - O'Connor TD AD - Institute for Genome Sciences, Program for Personalized and Genomic Medicine, University of Maryland, School of Medicine, Baltimore, MD, USA. Electronic address: timothydoconnor@gmail.com. LA - eng PT - Comment PT - Journal Article PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) CON - Cell. 2018 Nov 15;175(5):1185-1197.e22. doi: 10.1016/j.cell.2018.10.027. PMID: 30415837 EIN - Cell. 2019 Jan 10;176(1-2):405-406. doi: 10.1016/j.cell.2018.12.033. PMID: 30633908 MH - *DNA, Ancient MH - Genetics, Population MH - Genomics MH - Humans MH - *Indians, North American MH - South America EDAT- 2018/11/18 06:00 MHDA- 2019/08/21 06:00 CRDT- 2018/11/17 06:00 PHST- 2018/11/17 06:00 [entrez] PHST- 2018/11/18 06:00 [pubmed] PHST- 2019/08/21 06:00 [medline] AID - S0092-8674(18)31457-0 [pii] AID - 10.1016/j.cell.2018.10.058 [doi] PST - ppublish SO - Cell. 2018 Nov 15;175(5):1173-1174. doi: 10.1016/j.cell.2018.10.058. PMID- 30415837 OWN - NLM STAT- MEDLINE DCOM- 20190827 LR - 20240527 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 175 IP - 5 DP - 2018 Nov 15 TI - Reconstructing the Deep Population History of Central and South America. PG - 1185-1197.e22 LID - S0092-8674(18)31380-1 [pii] LID - 10.1016/j.cell.2018.10.027 [doi] AB - We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions. CI - Published by Elsevier Inc. FAU - Posth, Cosimo AU - Posth C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany. Electronic address: posth@shh.mpg.de. FAU - Nakatsuka, Nathan AU - Nakatsuka N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA. Electronic address: nathan_nakatsuka@hms.harvard.edu. FAU - Lazaridis, Iosif AU - Lazaridis I AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Francis Crick Institute, London NW1 1AT, UK. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Lamnidis, Thiseas C AU - Lamnidis TC AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Nägele, Kathrin AU - Nägele K AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Adamski, Nicole AU - Adamski N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Bertolini, Emilie AU - Bertolini E AD - Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia 27100, Italy. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia. FAU - Culleton, Brendan J AU - Culleton BJ AD - Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Ferraz, Tiago AU - Ferraz T AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Furtwängler, Anja AU - Furtwängler A AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany. FAU - Haak, Wolfgang AU - Haak W AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Harkins, Kelly AU - Harkins K AD - UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. FAU - Harper, Thomas K AU - Harper TK AD - Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Hünemeier, Tábita AU - Hünemeier T AD - Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil. FAU - Lawson, Ann Marie AU - Lawson AM AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Nelson, Elizabeth AU - Nelson E AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. FAU - Schiffels, Stephan AU - Schiffels S AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Sedig, Jakob AU - Sedig J AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Talamo, Sahra AU - Talamo S AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Wang, Chuan-Chao AU - Wang CC AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology and Ethnology, Xiamen University, Xiamen 361005, China. FAU - Hublin, Jean-Jacques AU - Hublin JJ AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Hubbe, Mark AU - Hubbe M AD - Department of Anthropology, The Ohio State University, Columbus, OH 43210, USA; Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Región de Antofagasta, Antofagasta CP 1410000, Chile. FAU - Harvati, Katerina AU - Harvati K AD - Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany. FAU - Nuevo Delaunay, Amalia AU - Nuevo Delaunay A AD - Centro de Investigación en Ecosistemas de la Patagonia, Coyhaique 5951601, Chile. FAU - Beier, Judith AU - Beier J AD - Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany. FAU - Francken, Michael AU - Francken M AD - Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany. FAU - Kaulicke, Peter AU - Kaulicke P AD - Pontifical Catholic University of Peru, San Miguel, Lima 32, Peru. FAU - Reyes-Centeno, Hugo AU - Reyes-Centeno H AD - Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany. FAU - Rademaker, Kurt AU - Rademaker K AD - Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA. FAU - Trask, Willa R AU - Trask WR AD - Central Identification Laboratory, Defense POW/MIA Accounting Agency, Department of Defense, Joint Base Pearl Harbor-Hickam, HI 96853, USA. FAU - Robinson, Mark AU - Robinson M AD - Department of Archaeology, Exeter University, Exeter EX4 4QJ, UK. FAU - Gutierrez, Said M AU - Gutierrez SM AD - Ya'axché Conservation Trust, Punta Gorda Town, Belize. FAU - Prufer, Keith M AU - Prufer KM AD - Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA; Center for Stable Isotopes, University of New Mexico, Albuquerque, NM 87131, USA. FAU - Salazar-García, Domingo C AU - Salazar-García DC AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany; Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria, Spain. FAU - Chim, Eliane N AU - Chim EN AD - Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil. FAU - Müller Plumm Gomes, Lisiane AU - Müller Plumm Gomes L AD - Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil. FAU - Alves, Marcony L AU - Alves ML AD - Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil. FAU - Liryo, Andersen AU - Liryo A AD - Museu Nacional da Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, Brazil. FAU - Inglez, Mariana AU - Inglez M AD - Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil. FAU - Oliveira, Rodrigo E AU - Oliveira RE AD - Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Departamento de Estomatologia, Faculdade de Odontologia, Universidade de São Paulo, São Paulo 05508-000, Brazil. FAU - Bernardo, Danilo V AU - Bernardo DV AD - Laboratório de Estudos em Antropologia Biológica, Bioarqueologia e Evolução Humana, Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande, Rio Grande do Sul 96203-900, Brazil. FAU - Barioni, Alberto AU - Barioni A AD - Faculdade de Filosofia Ciencias e Letras, Universidade de São Paulo, São Paulo 05508-080, Brazil. FAU - Wesolowski, Veronica AU - Wesolowski V AD - Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil. FAU - Scheifler, Nahuel A AU - Scheifler NA AD - INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina. FAU - Rivera, Mario A AU - Rivera MA AD - Comité Chileno del Consejo Internacional de Monumentos y Sitios, Santiago 8320000, Chile; Field Museum of Natural History, Chicago, IL 60605, USA; Universidad de Magallanes, Punta Arenas 6200000, Chile. FAU - Plens, Claudia R AU - Plens CR AD - Escola De Filosofia, Letras E Ciências Humanas, Universidade Federal de São Paulo, São Paulo 07252-312, Brazil. FAU - Messineo, Pablo G AU - Messineo PG AD - INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina. FAU - Figuti, Levy AU - Figuti L AD - Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil. FAU - Corach, Daniel AU - Corach D AD - Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires y CONICET, Ciudad Autonoma de Buenos Aires, Junin 954, Argentina. FAU - Scabuzzo, Clara AU - Scabuzzo C AD - CONICET-División Arqueología, Facultad de Ciencias Naturales y Museo, La Plata 1900, Argentina. FAU - Eggers, Sabine AU - Eggers S AD - Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Naturhistorisches Museum Wien, Vienna 1010, Austria. FAU - DeBlasis, Paulo AU - DeBlasis P AD - Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil. FAU - Reindel, Markus AU - Reindel M AD - German Archaeological Institute, Commission for Archaeology of Non-European Cultures, Bonn 53173, Germany. FAU - Méndez, César AU - Méndez C AD - Centro de Investigación en Ecosistemas de la Patagonia, Coyhaique 5951601, Chile. FAU - Politis, Gustavo AU - Politis G AD - INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina. FAU - Tomasto-Cagigao, Elsa AU - Tomasto-Cagigao E AD - Pontifical Catholic University of Peru, San Miguel, Lima 32, Peru. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Strauss, André AU - Strauss A AD - Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil; Centro de Arqueologia Annette Laming Emperaire, Miguel A Salomão, Lagoa Santa, MG 33400-000, Brazil. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AD - UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - FC001595/MRC_/Medical Research Council/United Kingdom GR - T32 GM007753/GM/NIGMS NIH HHS/United States GR - FC001595/WT_/Wellcome Trust/United Kingdom GR - WT_/Wellcome Trust/United Kingdom GR - HHMI/Howard Hughes Medical Institute/United States GR - R01 HG006399/HG/NHGRI NIH HHS/United States GR - FC001595/ARC_/Arthritis Research UK/United Kingdom GR - FC001595/CRUK_/Cancer Research UK/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20181108 PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM CIN - Cell. 2018 Nov 15;175(5):1173-1174. doi: 10.1016/j.cell.2018.10.058. PMID: 30445034 MH - Central America MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/genetics MH - Gene Flow MH - Genetics, Population/*history MH - *Genome, Human MH - History, Ancient MH - Humans MH - Models, Theoretical MH - South America PMC - PMC6327247 OTO - NOTNLM OT - Central America OT - South America OT - anthropology OT - archaeology OT - population genetics EDAT- 2018/11/13 06:00 MHDA- 2019/08/28 06:00 PMCR- 2018/11/15 CRDT- 2018/11/13 06:00 PHST- 2018/08/30 00:00 [received] PHST- 2018/09/15 00:00 [revised] PHST- 2018/10/11 00:00 [accepted] PHST- 2018/11/13 06:00 [pubmed] PHST- 2019/08/28 06:00 [medline] PHST- 2018/11/13 06:00 [entrez] PHST- 2018/11/15 00:00 [pmc-release] AID - S0092-8674(18)31380-1 [pii] AID - 10.1016/j.cell.2018.10.027 [doi] PST - ppublish SO - Cell. 2018 Nov 15;175(5):1185-1197.e22. doi: 10.1016/j.cell.2018.10.027. Epub 2018 Nov 8. PMID- 30409866 OWN - NLM STAT- MEDLINE DCOM- 20190508 LR - 20190508 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 362 IP - 6415 DP - 2018 Nov 9 TI - Ancient DNA tracks migrations around Americas. PG - 627-628 LID - 10.1126/science.362.6415.627 [doi] FAU - Wade, Lizzie AU - Wade L LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Americas MH - DNA, Ancient/*analysis MH - History, Ancient MH - Human Migration/*history MH - Humans EDAT- 2018/11/10 06:00 MHDA- 2019/05/09 06:00 CRDT- 2018/11/10 06:00 PHST- 2018/11/10 06:00 [entrez] PHST- 2018/11/10 06:00 [pubmed] PHST- 2019/05/09 06:00 [medline] AID - 362/6415/627 [pii] AID - 10.1126/science.362.6415.627 [doi] PST - ppublish SO - Science. 2018 Nov 9;362(6415):627-628. doi: 10.1126/science.362.6415.627. PMID- 31714695 OWN - NLM STAT- MEDLINE DCOM- 20191202 LR - 20200108 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 90 IP - 4 DP - 2018 Nov TI - Genetic Overview of the Maya Populations: Mitochondrial DNA Haplogroups. PG - 281-300 LID - 10.13110/humanbiology.90.4.03 [doi] AB - We identified mitochondrial DNA haplogroups A, B, C, and D in 75 present-day Maya individuals, 24 Maya individuals of the colonial period, and 1 pre-Columbian Maya individual from Quintana Roo, Mexico. We examined these data together with those of 21 Maya populations reported in the literature, comprising 647 present-day Maya individuals and 71 ancient Maya individuals. A demographic study based on analysis of fertility and endogamy was carried out in two modern Maya populations to identify cultural factors that influence the mitochondrial haplogroup genetic diversity. Most present-day and ancient Maya populations show a distribution pattern of mitochondrial haplogroup frequencies A, C, B, and D in decreasing order, with haplogroup D absent in several populations. Considering only modern Maya populations with at least 50 individuals analyzed, the present-day Tzotzil and Lacandon populations from Chiapas show the highest and lowest genetic diversity, 0.706 and 0.025, respectively. Our results show small genetic differences between the Maya populations, with the exception of the present-day Tojolabal and Lacandon populations from Chiapas. The present-day Lacandon population from Chiapas differs from other Maya populations in showing almost only haplogroup A. This result suggests a long history of isolation and endogamy as well as a possible founder effect inside the Lacandonian rain forest. The contemporary Tojolabal population is the only one with an unusual mitochondrial haplogroup pattern, exhibiting a frequency of haplogroup B higher than A and the absence of haplogroup C. With a small sample size, the pre-Columbian Copán Maya show a high content of haplogroup C and a low frequency of haplogroup D. The genetic homogeneity of the Maya populations is indicative of a common origin and nearly continuous gene flow in the long term within a general isolation of the whole group, in contrast to the Nahua populations that had different origins. Our demographic study showed high fertility rates and high levels of endogamy in the present-day Maya populations from Quintana Roo that are consistent with their general low genetic diversity. We propose that the genetic similarity among ancient and present-day Maya populations persists due to a strong sense of social cohesion and identity that impacts their marriage practices, keeping this cultural group isolated. These factors have constrained gene flow inside the Maya region and have impeded the differentiation among the Maya. Discernment of genetic differentiation within the peninsula is constrained by the lack of sampling documentation in the literature. FAU - González-Oliver, Angélica AU - González-Oliver A AD - Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México, goliver@unam.mx. FAU - Pineda-Vázquez, Dircé AU - Pineda-Vázquez D AD - Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México. FAU - Garfias-Morales, Ernesto AU - Garfias-Morales E AD - Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México. FAU - La Cruz-Laina, Isabel De AU - La Cruz-Laina I AD - Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México. FAU - Medrano-González, Luis AU - Medrano-González L AD - Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México. FAU - Márquez-Morfín, Lourdes AU - Márquez-Morfín L AD - Escuela Nacional de Antropología e Historia, Instituto Nacional de Antropología e Historia, Ciudad de México, México. FAU - Ortega-Muñoz, Allan AU - Ortega-Muñoz A AD - Centro INAH, Chetumal, Quintana Roo, México. LA - eng PT - Journal Article PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adolescent MH - Adult MH - DNA, Mitochondrial/*genetics MH - Evolution, Molecular MH - Female MH - *Gene Flow MH - Genetic Variation/genetics MH - Genetics, Population/*statistics & numerical data MH - Haplotypes/*genetics MH - Humans MH - Indians, North American/*genetics MH - Male MH - Mexico/ethnology MH - Phylogeny MH - Young Adult OTO - NOTNLM OT - ancient dna OT - maya populations OT - mitochondrial dna OT - mitochondrial haplogroups EDAT- 2019/11/13 06:00 MHDA- 2019/12/04 06:00 CRDT- 2019/11/13 06:00 PHST- 2019/03/07 00:00 [received] PHST- 2019/06/24 00:00 [accepted] PHST- 2019/11/13 06:00 [entrez] PHST- 2019/11/13 06:00 [pubmed] PHST- 2019/12/04 06:00 [medline] AID - 10.13110/humanbiology.90.4.03 [doi] PST - ppublish SO - Hum Biol. 2018 Nov;90(4):281-300. doi: 10.13110/humanbiology.90.4.03. PMID- 30187463 OWN - NLM STAT- MEDLINE DCOM- 20191007 LR - 20191007 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 167 IP - 3 DP - 2018 Nov TI - The female ancestor's tale: Long-term matrilineal continuity in a nonisolated region of Tuscany. PG - 497-506 LID - 10.1002/ajpa.23679 [doi] AB - OBJECTIVES: With the advent of ancient DNA analyses, it has been possible to disentangle the contribution of ancient populations to the genetic pool of the modern inhabitants of many regions. Reconstructing the maternal ancestry has often highlighted genetic continuity over several millennia, but almost always in isolated areas. Here we analyze North-western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast. MATERIALS AND METHODS: We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000 years: Prehistory, Etruscan age, Roman age, Renaissance, and Present-day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups. RESULTS: Our analyses always favor continuity over discontinuity for all groups considered, with the Etruscans being part of the genealogy. Moreover, the posterior distributions of the parameters support very small female effective population sizes. CONCLUSIONS: The observed signals of long-term genetic continuity and isolation are in contrast with the history of the region, conquered several times (Etruscans, Romans, Lombards, and French). While the Etruscans appear as a local population, intermediate between the prehistoric and the other samples, we suggest that the other conquerors-arriving from far-had a consistent social or sex bias, hence only marginally affecting the maternal lineages. At the same time, our results show that long-term genealogical continuity is not necessarily linked to geographical isolation. CI - © 2018 Wiley Periodicals, Inc. FAU - Leonardi, Michela AU - Leonardi M AUID- ORCID: 0000-0001-8933-9374 AD - Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy. FAU - Sandionigi, Anna AU - Sandionigi A AD - Dipartimento di Biologia, Università di Firenze, Florence, Italy. FAU - Conzato, Annalisa AU - Conzato A AD - Dipartimento di Biologia, Università di Firenze, Florence, Italy. FAU - Vai, Stefania AU - Vai S AD - Dipartimento di Biologia, Università di Firenze, Florence, Italy. FAU - Lari, Martina AU - Lari M AD - Dipartimento di Biologia, Università di Firenze, Florence, Italy. FAU - Tassi, Francesca AU - Tassi F AD - Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy. FAU - Ghirotto, Silvia AU - Ghirotto S AD - Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy. FAU - Caramelli, David AU - Caramelli D AD - Dipartimento di Biologia, Università di Firenze, Florence, Italy. FAU - Barbujani, Guido AU - Barbujani G AD - Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy. LA - eng PT - Journal Article DEP - 20180906 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - Bayes Theorem MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/genetics MH - *Evolution, Molecular MH - Female MH - Genetic Variation MH - *Genotype MH - Genotyping Techniques MH - Humans MH - Italy OTO - NOTNLM OT - Approximate Bayesian Computation OT - ancient DNA OT - coalescent simulations OT - human evolutionary history EDAT- 2018/09/07 06:00 MHDA- 2019/10/08 06:00 CRDT- 2018/09/07 06:00 PHST- 2018/01/19 00:00 [received] PHST- 2018/05/14 00:00 [revised] PHST- 2018/06/19 00:00 [accepted] PHST- 2018/09/07 06:00 [pubmed] PHST- 2019/10/08 06:00 [medline] PHST- 2018/09/07 06:00 [entrez] AID - 10.1002/ajpa.23679 [doi] PST - ppublish SO - Am J Phys Anthropol. 2018 Nov;167(3):497-506. doi: 10.1002/ajpa.23679. Epub 2018 Sep 6. PMID- 29993816 OWN - NLM STAT- MEDLINE DCOM- 20190701 LR - 20191113 IS - 1557-9964 (Electronic) IS - 1545-5963 (Linking) VI - 15 IP - 6 DP - 2018 Nov-Dec TI - Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. PG - 2094-2100 AB - Ancestral genome reconstruction is an important task to analyze the evolution of genomes. Recent progress in sequencing ancient DNA led to the publication of so-called paleogenomes and allows the integration of this sequencing data in genome evolution analysis. However, the de novo assembly of ancient genomes is usually fragmented due to DNA degradation over time among others. Integrated phylogenetic assembly addresses the issue of genome fragmentation in the ancient DNA assembly while aiming to improve the reconstruction of all ancient genomes in the phylogeny simultaneously. The fragmented assembly of the ancient genome can be represented as an assembly graph, indicating contradicting ordering information of contigs. In this setting, our approach is to compare the ancient data with extant finished genomes. We generalize a reconstruction approach minimizing the Single-Cut-or-Join rearrangement distance towards multifurcating trees and include edge lengths to improve the reconstruction in practice. This results in a polynomial time algorithm that includes additional ancient DNA data at one node in the tree, resulting in consistent reconstructions of ancestral genomes. FAU - Luhmann, Nina AU - Luhmann N FAU - Chauve, Cedric AU - Chauve C FAU - Stoye, Jens AU - Stoye J FAU - Wittler, Roland AU - Wittler R LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180315 PL - United States TA - IEEE/ACM Trans Comput Biol Bioinform JT - IEEE/ACM transactions on computational biology and bioinformatics JID - 101196755 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Algorithms MH - Animals MH - *DNA/analysis/classification/genetics MH - DNA, Ancient/*analysis MH - Evolution, Molecular MH - Genomics/*methods MH - History, Ancient MH - History, Medieval MH - Humans MH - Models, Genetic MH - Paleontology MH - Phylogeny MH - Plague/history/microbiology MH - Rats MH - Sequence Alignment/methods MH - Sequence Analysis, DNA/*methods MH - Yersinia pestis/classification/genetics EDAT- 2018/07/12 06:00 MHDA- 2019/07/02 06:00 CRDT- 2018/07/12 06:00 PHST- 2018/07/12 06:00 [pubmed] PHST- 2019/07/02 06:00 [medline] PHST- 2018/07/12 06:00 [entrez] AID - 10.1007/978-3-319-12418-6_17 [doi] PST - ppublish SO - IEEE/ACM Trans Comput Biol Bioinform. 2018 Nov-Dec;15(6):2094-2100. doi: 10.1007/978-3-319-12418-6_17. Epub 2018 Mar 15. PMID- 29877032 OWN - NLM STAT- MEDLINE DCOM- 20181217 LR - 20181217 IS - 1755-0998 (Electronic) IS - 1755-098X (Linking) VI - 18 IP - 6 DP - 2018 Nov TI - Optimized DNA sampling of ancient bones using Computed Tomography scans. PG - 1196-1208 LID - 10.1111/1755-0998.12911 [doi] AB - The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era. CI - © 2018 John Wiley & Sons Ltd. FAU - Alberti, Federica AU - Alberti F AUID- ORCID: 0000-0002-1065-7490 AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. FAU - Gonzalez, Javier AU - Gonzalez J AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. FAU - Paijmans, Johanna L A AU - Paijmans JLA AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. FAU - Basler, Nikolas AU - Basler N AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. FAU - Preick, Michaela AU - Preick M AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. FAU - Henneberger, Kirstin AU - Henneberger K AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. FAU - Trinks, Alexandra AU - Trinks A AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. AD - Evolutionary Biology, IRI for the Life Sciences, Humboldt University Berlin, Berlin, Germany. FAU - Rabeder, Gernot AU - Rabeder G AD - Department of Palaeontology, Geozentrum, University of Vienna, Vienna, Austria. FAU - Conard, Nicholas J AU - Conard NJ AD - Institute for Archaeological Sciences, Archaeozoology, University of Tübingen, Tübingen, Germany. FAU - Münzel, Susanne C AU - Münzel SC AD - Institute for Archaeological Sciences, Archaeozoology, University of Tübingen, Tübingen, Germany. FAU - Joger, Ulrich AU - Joger U AD - Staatliches Naturhistorisches Museum Braunschweig, Braunschweig, Germany. FAU - Fritsch, Guido AU - Fritsch G AD - Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany. FAU - Hildebrandt, Thomas AU - Hildebrandt T AD - Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany. FAU - Hofreiter, Michael AU - Hofreiter M AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. FAU - Barlow, Axel AU - Barlow A AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. LA - eng SI - GENBANK/PRJEB25493 GR - 310763/ERC consolidator grant GeneFlow/ GR - 00.298.2016/Klaus Tschira foundation/ PT - Journal Article DEP - 20180627 PL - England TA - Mol Ecol Resour JT - Molecular ecology resources JID - 101465604 RN - 0 (DNA, Ancient) SB - IM CIN - Mol Ecol Resour. 2018 Nov;18(6):1185-1187. doi: 10.1111/1755-0998.12931. PMID: 30375193 MH - Bone and Bones/*chemistry MH - DNA, Ancient/*analysis/*isolation & purification MH - *Fossils MH - Humans MH - Tomography, X-Ray Computed/*methods OTO - NOTNLM OT - ancient DNA OT - computer tomography OT - palaeogenomics OT - paleogenetics OT - petrous bone EDAT- 2018/06/08 06:00 MHDA- 2018/12/18 06:00 CRDT- 2018/06/08 06:00 PHST- 2017/12/11 00:00 [received] PHST- 2018/03/14 00:00 [revised] PHST- 2018/03/19 00:00 [accepted] PHST- 2018/06/08 06:00 [pubmed] PHST- 2018/12/18 06:00 [medline] PHST- 2018/06/08 06:00 [entrez] AID - 10.1111/1755-0998.12911 [doi] PST - ppublish SO - Mol Ecol Resour. 2018 Nov;18(6):1196-1208. doi: 10.1111/1755-0998.12911. Epub 2018 Jun 27. PMID- 30379865 OWN - NLM STAT- MEDLINE DCOM- 20190326 LR - 20190326 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 13 IP - 10 DP - 2018 TI - Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan. PG - e0205646 LID - 10.1371/journal.pone.0205646 [doi] LID - e0205646 AB - The Silk Road was an important trade route that channeled trade goods, people, plants, animals, and ideas across the continental interior of Eurasia, fueling biotic exchange and key social developments across the Old World. Nestled between the Pamir and Alay ranges at a baseline elevation of nearly 3000m, Kyrgyzstan's high Alay Valley forms a wide geographic corridor that comprised one of the primary channels of the ancient Silk Road. Recent archaeological survey reveals a millennia-long history of pastoral occupation of Alay from the early Bronze Age through the Medieval period, and a stratified Holocene sequence at the site of Chegirtke Cave. Faunal remains were recovered from test excavations as well as surface collection of material from recent marmot activity. Although recovered specimens were highly fragmented and mostly unidentifiable using traditional zooarchaeological methods, species identification via collagen mass fingerprinting (ZooMS) coupled with sex and first-generation hybrid identification through ancient DNA enabled preliminary characterization of the animal economy of Alay herders. Our new results indicate primary reliance on sheep at Chegirtke Cave (ca. 2200 BCE), with cattle and goat also present. The discovery of a large grinding stone at a spatially associated Bronze or Iron Age habitation structure suggests a mixed agropastoral economic strategy, rather than a unique reliance on domestic animals. Radiocarbon-dated faunal assemblages from habitation structures at nearby localities in the Alay Valley demonstrate the presence of domestic horse, as well as Bactrian camel during later periods. The current study reveals that agropastoral occupation of the high-mountain Alay corridor started millennia before the formal establishment of the Silk Road, and posits that ZooMS, when paired with radiocarbon dates and ancient DNA, is a powerful and cost-effective tool for investigating shifts in the use of animal domesticates in early pastoral economies. FAU - Taylor, William AU - Taylor W AUID- ORCID: 0000-0002-0836-7814 AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Shnaider, Svetlana AU - Shnaider S AD - Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. AD - Altai State University, Barnaul, Russia. FAU - Abdykanova, Aida AU - Abdykanova A AD - American University of Central Asia, Bishkek, Kyrgyz Republic. FAU - Fages, Antoine AU - Fages A AD - Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Université de Toulouse, Université Paul Sabatier, Toulouse, France. AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. FAU - Welker, Frido AU - Welker F AD - Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Irmer, Franziska AU - Irmer F AUID- ORCID: 0000-0002-9887-4368 AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Seguin-Orlando, Andaine AU - Seguin-Orlando A AD - Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Université de Toulouse, Université Paul Sabatier, Toulouse, France. AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. FAU - Khan, Naveed AU - Khan N AUID- ORCID: 0000-0002-6502-9774 AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. AD - Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan. FAU - Douka, Katerina AU - Douka K AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Kolobova, Ksenia AU - Kolobova K AD - Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. FAU - Orlando, Ludovic AU - Orlando L AD - Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Université de Toulouse, Université Paul Sabatier, Toulouse, France. AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. FAU - Krivoshapkin, Andrei AU - Krivoshapkin A AUID- ORCID: 0000-0002-5327-3438 AD - Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. AD - Novosibirsk State University, Novosibirsk, Russia. FAU - Boivin, Nicole AU - Boivin N AD - Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181031 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - *Animal Husbandry/economics/history MH - Animals MH - Camelus/*genetics MH - Cattle MH - *DNA Fingerprinting MH - History, Ancient MH - Horses/*genetics MH - Humans MH - Kyrgyzstan MH - Selective Breeding/*history MH - Sheep/*genetics PMC - PMC6209189 COIS- The authors have declared that no competing interests exist. EDAT- 2018/11/01 06:00 MHDA- 2019/03/27 06:00 PMCR- 2018/10/31 CRDT- 2018/11/01 06:00 PHST- 2018/07/11 00:00 [received] PHST- 2018/09/29 00:00 [accepted] PHST- 2018/11/01 06:00 [entrez] PHST- 2018/11/01 06:00 [pubmed] PHST- 2019/03/27 06:00 [medline] PHST- 2018/10/31 00:00 [pmc-release] AID - PONE-D-18-20515 [pii] AID - 10.1371/journal.pone.0205646 [doi] PST - epublish SO - PLoS One. 2018 Oct 31;13(10):e0205646. doi: 10.1371/journal.pone.0205646. eCollection 2018. PMID- 30369466 OWN - NLM STAT- MEDLINE DCOM- 20190328 LR - 20221207 IS - 0253-9772 (Print) IS - 0253-9772 (Linking) VI - 40 IP - 10 DP - 2018 Oct 20 TI - [The origin and evolution history of East Asian populations from genetic perspectives]. PG - 814-824 LID - 10.16288/j.yczz.18-202 [doi] AB - East Asia is widely concerned as one of the important places for the dispersal and evolution of the Anatomically Modern Human (AMH). How the diverse ethnic groups in East Asia originated and diversified is also widely focused by different disciplines of Anthropology. The adoption of genetic data had provided new clues for reconstructing the genetic history of East Asian populations. Genetic studies supported the hypothesis that the AMHs originated from Africa's Homo sapiens at about 200 kilo years ago (kya) and then migrated out of Africa at ~100 kya, followed by expansions into the whole East Asia since their arrival in Southern East Asia at 5~6 kya along the coastal route. Early Homo Sapiens might have genetic contribution to the non-African AMHs. Early settlement, cultural assimilation, population migration and genetic exchanges are crucial in the origination and evolution of East Asia populations. Previous studies made detailed analysis for the genetic history of East Asian populations, which largely resolved the longstanding divergence between archaeology and history. However, this needs further verification by whole-genome sequencing and ancient DNA studies. Here we briefly reviewed the progresses of genetic studies in exploring the population origin, dispersal and diversification in East Asia, which improved understanding of the evolution of East Asian populations. We also prospected the future of genetic studies in revealing the prehistory of East Asians. FAU - Tian, Jiao Yang AU - Tian JY AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. FAU - Li, Yu Chun AU - Li YC AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. FAU - Kong, Qing Peng AU - Kong QP AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. FAU - Zhang, Ya Ping AU - Zhang YP AD - State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. LA - chi PT - Journal Article PT - Review PL - China TA - Yi Chuan JT - Yi chuan = Hereditas JID - 9436478 SB - IM MH - Asia MH - Asian People/*genetics MH - Evolution, Molecular MH - *Genetics, Population MH - Human Genetics MH - Humans MH - Phylogeny EDAT- 2018/10/30 06:00 MHDA- 2019/03/29 06:00 CRDT- 2018/10/30 06:00 PHST- 2018/10/30 06:00 [entrez] PHST- 2018/10/30 06:00 [pubmed] PHST- 2019/03/29 06:00 [medline] AID - 10.16288/j.yczz.18-202 [doi] PST - ppublish SO - Yi Chuan. 2018 Oct 20;40(10):814-824. doi: 10.16288/j.yczz.18-202. PMID- 30333260 OWN - NLM STAT- MEDLINE DCOM- 20190827 LR - 20240403 IS - 1744-957X (Electronic) IS - 1744-9561 (Print) IS - 1744-9561 (Linking) VI - 14 IP - 10 DP - 2018 Oct 17 TI - Dogs accompanied humans during the Neolithic expansion into Europe. LID - 10.1098/rsbl.2018.0286 [doi] LID - 20180286 AB - Near Eastern Neolithic farmers introduced several species of domestic plants and animals as they dispersed into Europe. Dogs were the only domestic species present in both Europe and the Near East prior to the Neolithic. Here, we assessed whether early Near Eastern dogs possessed a unique mitochondrial lineage that differentiated them from Mesolithic European populations. We then analysed mitochondrial DNA sequences from 99 ancient European and Near Eastern dogs spanning the Upper Palaeolithic to the Bronze Age to assess if incoming farmers brought Near Eastern dogs with them, or instead primarily adopted indigenous European dogs after they arrived. Our results show that European pre-Neolithic dogs all possessed the mitochondrial haplogroup C, and that the Neolithic and Post-Neolithic dogs associated with farmers from Southeastern Europe mainly possessed haplogroup D. Thus, the appearance of haplogroup D most probably resulted from the dissemination of dogs from the Near East into Europe. In Western and Northern Europe, the turnover is incomplete and haplogroup C persists well into the Chalcolithic at least. These results suggest that dogs were an integral component of the Neolithic farming package and a mitochondrial lineage associated with the Near East was introduced into Europe alongside pigs, cows, sheep and goats. It got diluted into the native dog population when reaching the Western and Northern margins of Europe. CI - © 2018 The Author(s). FAU - Ollivier, Morgane AU - Ollivier M AUID- ORCID: 0000-0002-8361-4221 AD - CNRS/ENS de Lyon, PALGENE, ENS de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France morgane.ollivier@univ-rennes1.fr. FAU - Tresset, Anne AU - Tresset A AUID- ORCID: 0000-0002-8391-059X AD - CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France anne.tresset@mnhn.fr. FAU - Frantz, Laurent A F AU - Frantz LAF AD - Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3QY, UK. AD - School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK. FAU - Bréhard, Stéphanie AU - Bréhard S AD - CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France. FAU - Bălăşescu, Adrian AU - Bălăşescu A AD - Romanian Academy of Sciences, 11 Henri Coandă St., Sector 1, 010667 Bucharest, Romania. FAU - Mashkour, Marjan AU - Mashkour M AD - CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France. FAU - Boroneanţ, Adina AU - Boroneanţ A AD - Romanian Academy of Sciences, 11 Henri Coandă St., Sector 1, 010667 Bucharest, Romania. FAU - Pionnier-Capitan, Maud AU - Pionnier-Capitan M AD - CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France. FAU - Lebrasseur, Ophélie AU - Lebrasseur O AD - Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3QY, UK. FAU - Arbogast, Rose-Marie AU - Arbogast RM AD - CNRS - UMR 7044 MISHA, 5 allée du Général Rouvillois, 67083 Strasbourg, France. FAU - Bartosiewicz, László AU - Bartosiewicz L AD - Osteoarchaeological Research Laboratory, University of Stockholm, Stockholm, Sweden. FAU - Debue, Karyne AU - Debue K AD - CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France. FAU - Rabinovich, Rivka AU - Rabinovich R AD - Institute of Archaeology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel. FAU - Sablin, Mikhail V AU - Sablin MV AD - Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint Petersburg, Russia. FAU - Larson, Greger AU - Larson G AUID- ORCID: 0000-0002-4092-0392 AD - Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3QY, UK. FAU - Hänni, Catherine AU - Hänni C AD - LECA CNRS UMR 5553, 38000 Grenoble, France. FAU - Hitte, Christophe AU - Hitte C AD - Univ Rennes, CNRS, IGDR, UMR 6290, 35000 Rennes, France. FAU - Vigne, Jean-Denis AU - Vigne JD AD - CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France. LA - eng SI - Dryad/10.5061/dryad.h55p1q5 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181017 PL - England TA - Biol Lett JT - Biology letters JID - 101247722 RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture MH - Animals MH - *Archaeology MH - *DNA, Mitochondrial MH - Dogs/classification/*genetics MH - Europe MH - Fossils MH - Haplotypes MH - Humans MH - Sequence Analysis, DNA PMC - PMC6227856 OTO - NOTNLM OT - Neolithic OT - ancient DNA OT - dog OT - domestication COIS- We have no competing interests. EDAT- 2018/10/20 06:00 MHDA- 2019/08/28 06:00 PMCR- 2019/10/01 CRDT- 2018/10/19 06:00 PHST- 2018/04/23 00:00 [received] PHST- 2018/09/24 00:00 [accepted] PHST- 2018/10/19 06:00 [entrez] PHST- 2018/10/20 06:00 [pubmed] PHST- 2019/08/28 06:00 [medline] PHST- 2019/10/01 00:00 [pmc-release] AID - rsbl.2018.0286 [pii] AID - rsbl20180286 [pii] AID - 10.1098/rsbl.2018.0286 [doi] PST - epublish SO - Biol Lett. 2018 Oct 17;14(10):20180286. doi: 10.1098/rsbl.2018.0286. PMID- 30406142 OWN - NLM STAT- MEDLINE DCOM- 20190218 LR - 20230928 IS - 2314-6141 (Electronic) IS - 2314-6133 (Print) VI - 2018 DP - 2018 TI - First Paleogenetic Evidence of Probable Syphilis and Treponematoses Cases in the Brazilian Colonial Period. PG - 8304129 LID - 10.1155/2018/8304129 [doi] LID - 8304129 AB - Despite interest in the origins of syphilis, paleopathological analysis has not provided answers, and paleogenetic diagnosis remains a challenge. Even venereal syphilis has low infectivity which means there are few circulating bacteria for most of the individual's life. Human remains recovered from the Nossa Senhora do Carmo Church (17th to 19th centuries) and the Praça XV Cemetery (18th to 19th centuries), Rio de Janeiro, Brazil, were subjected to Treponema paleogenetic analysis. Historical data point to endemic treponemal infections in the city, including venereal syphilis. Based on the physiopathology of Treponema pallidum infection, 25 samples, mostly from skull remains of young adults, with no visible paleopathological evidence of treponematoses, were analyzed. PCR with three molecular targets, tpp47, polA, and tpp15, were applied. Ancient DNA tpp15 sequences were recovered from two young adults from each archaeological site and revealed the polymorphism that characterizes T. p. subsp. pallidum in a female up to 18 years old, suggesting a probable case of syphilis infection. The results indicated that the epidemiological context and the physiopathology of the disease should be considered in syphilis paleogenetic detection. The findings of Treponema sp. aDNA are consistent with historical documents that describe venereal syphilis and yaws as endemic diseases in Rio de Janeiro. Data on the epidemiological characteristics of the disease and its pathophysiology offer new perspectives in paleopathology. FAU - Guedes, Lucélia AU - Guedes L AD - Laboratório de Biologia de Tripanosomatídeos (LABTRIP), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro, RJ 21040-900, Brazil. FAU - Dias, Ondemar AU - Dias O AD - Instituto de Arqueologia Brasileira, Estr. Cruz Vermelha, 45 - Vila Santa Teresa, Belford Roxo, Rio de Janeiro, RJ 26193-415, Brazil. FAU - Neto, Jandira AU - Neto J AD - Instituto de Arqueologia Brasileira, Estr. Cruz Vermelha, 45 - Vila Santa Teresa, Belford Roxo, Rio de Janeiro, RJ 26193-415, Brazil. FAU - Ribeiro da Silva, Laura da Piedade AU - Ribeiro da Silva LDP AD - Instituto de Arqueologia Brasileira, Estr. Cruz Vermelha, 45 - Vila Santa Teresa, Belford Roxo, Rio de Janeiro, RJ 26193-415, Brazil. FAU - Mendonça de Souza, Sheila M F AU - Mendonça de Souza SMF AD - Departamento de Endemias Samuel Pessoa, Escola Nacional de Saúde Pública Sérgio Arouca, Fundação Oswaldo Cruz, R. Leopoldo Bulhões, 1480 Bonsucesso, Rio de Janeiro, RJ 21041-210, Brazil. FAU - Iñiguez, Alena Mayo AU - Iñiguez AM AUID- ORCID: 0000-0002-9788-9533 AD - Laboratório de Biologia de Tripanosomatídeos (LABTRIP), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro, RJ 21040-900, Brazil. LA - eng PT - Historical Article PT - Journal Article DEP - 20181010 PL - United States TA - Biomed Res Int JT - BioMed research international JID - 101600173 SB - IM MH - Adolescent MH - Adult MH - Base Sequence MH - Brazil MH - Female MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Male MH - *Paleopathology MH - Syphilis/*genetics/*history/pathology MH - Treponema/genetics MH - Treponemal Infections/*genetics/*history/pathology MH - Young Adult PMC - PMC6199871 EDAT- 2018/11/09 06:00 MHDA- 2019/02/20 06:00 PMCR- 2018/10/10 CRDT- 2018/11/09 06:00 PHST- 2018/03/20 00:00 [received] PHST- 2018/05/25 00:00 [revised] PHST- 2018/09/12 00:00 [accepted] PHST- 2018/11/09 06:00 [entrez] PHST- 2018/11/09 06:00 [pubmed] PHST- 2019/02/20 06:00 [medline] PHST- 2018/10/10 00:00 [pmc-release] AID - 10.1155/2018/8304129 [doi] PST - epublish SO - Biomed Res Int. 2018 Oct 10;2018:8304129. doi: 10.1155/2018/8304129. eCollection 2018. PMID- 30249639 OWN - NLM STAT- MEDLINE DCOM- 20181115 LR - 20241114 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 115 IP - 41 DP - 2018 Oct 9 TI - Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia. PG - 10422-10427 LID - 10.1073/pnas.1807266115 [doi] AB - Louse-borne relapsing fever (LBRF) is known to have killed millions of people over the course of European history and remains a major cause of mortality in parts of the world. Its pathogen, Borrelia recurrentis, shares a common vector with global killers such as typhus and plague and is known for its involvement in devastating historical epidemics such as the Irish potato famine. Here, we describe a European and historical genome of Brecurrentis, recovered from a 15th century skeleton from Oslo. Our distinct European lineage has a discrete genomic makeup, displaying an ancestral oppA-1 gene and gene loss in antigenic variation sites. Our results illustrate the potential of ancient DNA research to elucidate dynamics of reductive evolution in a specialized human pathogen and to uncover aspects of human health usually invisible to the archaeological record. CI - Copyright © 2018 the Author(s). Published by PNAS. FAU - Guellil, Meriam AU - Guellil M AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; meriam.guellil@ibv.uio.no n.c.stenseth@ibv.uio.no barbara.bramanti@ibv.uio.no. FAU - Kersten, Oliver AU - Kersten O AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway. FAU - Namouchi, Amine AU - Namouchi A AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway. FAU - Bauer, Egil L AU - Bauer EL AD - Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway. FAU - Derrick, Michael AU - Derrick M AD - Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway. FAU - Jensen, Anne Ø AU - Jensen AØ AD - Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway. FAU - Stenseth, Nils C AU - Stenseth NC AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; meriam.guellil@ibv.uio.no n.c.stenseth@ibv.uio.no barbara.bramanti@ibv.uio.no. FAU - Bramanti, Barbara AU - Bramanti B AD - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; meriam.guellil@ibv.uio.no n.c.stenseth@ibv.uio.no barbara.bramanti@ibv.uio.no. AD - Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy and Prevention, University of Ferrara, 35-441221 Ferrara, Italy. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180924 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Proteins) SB - IM MH - Adult MH - Animals MH - Bacterial Proteins/*genetics MH - Borrelia/classification/*genetics/pathogenicity MH - Child MH - Female MH - *Genome, Bacterial MH - History, 15th Century MH - Humans MH - *Metagenomics MH - Phylogeny MH - Relapsing Fever/*genetics/history/microbiology MH - Scandinavian and Nordic Countries PMC - PMC6187149 OTO - NOTNLM OT - aDNA OT - ancient genomics OT - immune evasion OT - relapsing fever OT - vector-borne pathogen COIS- The authors declare no conflict of interest. EDAT- 2018/09/27 06:00 MHDA- 2018/11/16 06:00 PMCR- 2018/09/24 CRDT- 2018/09/26 06:00 PHST- 2018/09/27 06:00 [pubmed] PHST- 2018/11/16 06:00 [medline] PHST- 2018/09/26 06:00 [entrez] PHST- 2018/09/24 00:00 [pmc-release] AID - 1807266115 [pii] AID - 201807266 [pii] AID - 10.1073/pnas.1807266115 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):10422-10427. doi: 10.1073/pnas.1807266115. Epub 2018 Sep 24. PMID- 30291256 OWN - NLM STAT- MEDLINE DCOM- 20191125 LR - 20191125 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 8 IP - 1 DP - 2018 Oct 5 TI - A genomic Neolithic time transect of hunter-farmer admixture in central Poland. PG - 14879 LID - 10.1038/s41598-018-33067-w [doi] LID - 14879 AB - Ancient DNA genome-wide analyses of Neolithic individuals from central and southern Europe indicate an overall population turnover pattern in which migrating farmers from Anatolia and the Near East largely replaced autochthonous Mesolithic hunter-gatherers. However, the genetic history of the Neolithic transition in areas lying north of the European Neolithic core region involved different levels of admixture with hunter-gatherers. Here we analyse genome-wide data of 17 individuals spanning from the Middle Neolithic to the Early Bronze Age (4300-1900 BCE) in order to assess the Neolithic transition in north-central Poland, and the local impacts of hunter-farmer contacts and Late Neolithic steppe migrations. We evaluate the influence of these on local populations and assess if and how they change through time, reporting evidence of recurrent hunter-farmer admixture over three millennia, and the co-existence of unadmixed hunter-gatherers as late as 4300 BCE. During the Late Neolithic we report the appearance of steppe ancestry, but on a lesser scale than previously described for other central European regions, with evidence of stronger affinities to hunter-gatherers than to steppe pastoralists. These results help understand the Neolithic palaeogenomics of another central European area, Kuyavia, and highlight the complexity of population interactions during those times. FAU - Fernandes, D M AU - Fernandes DM AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. AD - School of Archaeology, and Earth Institute, University College Dublin, Dublin, Ireland. AD - CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. FAU - Strapagiel, D AU - Strapagiel D AUID- ORCID: 0000-0001-9752-4270 AD - Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland. dominik.strapagiel@biol.uni.lodz.pl. AD - BBMRI.pl Consortium, Wrocław, Poland. dominik.strapagiel@biol.uni.lodz.pl. FAU - Borówka, P AU - Borówka P AD - BBMRI.pl Consortium, Wrocław, Poland. AD - Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland. FAU - Marciniak, B AU - Marciniak B AD - Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland. AD - BBMRI.pl Consortium, Wrocław, Poland. FAU - Żądzińska, E AU - Żądzińska E AUID- ORCID: 0000-0003-1001-7319 AD - Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland. FAU - Sirak, K AU - Sirak K AD - School of Archaeology, and Earth Institute, University College Dublin, Dublin, Ireland. AD - Department of Anthropology, Emory University, Atlanta, United States of America. FAU - Siska, V AU - Siska V AD - Department of Zoology, University of Cambridge, Cambridge, United Kingdom. FAU - Grygiel, R AU - Grygiel R AD - Museum of Archaeology and Ethnography in Lodz, Lodz, Poland. FAU - Carlsson, J AU - Carlsson J AD - Area 52 Research Group, School of Biology and Environment Science/Earth Institute, University College Dublin, Dublin, Ireland. FAU - Manica, A AU - Manica A AUID- ORCID: 0000-0003-1895-450X AD - Department of Zoology, University of Cambridge, Cambridge, United Kingdom. FAU - Lorkiewicz, W AU - Lorkiewicz W AD - Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland. wieslaw.lorkiewicz@biol.uni.lodz.pl. FAU - Pinhasi, R AU - Pinhasi R AD - Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. ropinhasi@gmail.com. LA - eng GR - GOIPG/2013/36/Irish Research Council/International PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181005 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/history MH - Archaeology MH - Chromosomes, Human, Y/genetics MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/analysis/genetics MH - Europe MH - Farmers MH - Genetic Drift MH - Genetics, Population MH - Genome, Human MH - Genome-Wide Association Study MH - Genomics MH - History, Ancient MH - *Human Migration MH - Humans MH - Middle East MH - Poland PMC - PMC6173765 COIS- The authors declare no competing interests. EDAT- 2018/10/07 06:00 MHDA- 2019/11/26 06:00 PMCR- 2018/10/05 CRDT- 2018/10/07 06:00 PHST- 2018/06/06 00:00 [received] PHST- 2018/09/18 00:00 [accepted] PHST- 2018/10/07 06:00 [entrez] PHST- 2018/10/07 06:00 [pubmed] PHST- 2019/11/26 06:00 [medline] PHST- 2018/10/05 00:00 [pmc-release] AID - 10.1038/s41598-018-33067-w [pii] AID - 33067 [pii] AID - 10.1038/s41598-018-33067-w [doi] PST - epublish SO - Sci Rep. 2018 Oct 5;8(1):14879. doi: 10.1038/s41598-018-33067-w. PMID- 30282648 OWN - NLM STAT- MEDLINE DCOM- 20190814 LR - 20190814 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 285 IP - 1888 DP - 2018 Oct 3 TI - Molecular archaeoparasitology identifies cultural changes in the Medieval Hanseatic trading centre of Lübeck. LID - 10.1098/rspb.2018.0991 [doi] LID - 20180991 AB - Throughout history, humans have been afflicted by parasitic worms, and eggs are readily detected in archaeological deposits. This study integrated parasitological and ancient DNA methods with a large sample set dating between Neolithic and Early Modern periods to explore the utility of molecular archaeoparasitology as a new approach to study the past. Molecular analyses provided unequivocal species-level parasite identification and revealed location-specific epidemiological signatures. Faecal-oral transmitted nematodes (Ascaris lumbricoides and Trichuris trichiura) were ubiquitous across time and space. By contrast, high numbers of food-associated cestodes (Diphyllobothrium latum and Taenia saginata) were restricted to medieval Lübeck. The presence of these cestodes and changes in their prevalence at approximately 1300 CE indicate substantial alterations in diet or parasite availability. Trichuris trichiura ITS-1 sequences grouped into two clades; one ubiquitous and one restricted to medieval Lübeck and Bristol. The high sequence diversity of T.tITS-1 detected in Lübeck is consistent with its importance as a Hanseatic trading centre. Collectively, these results introduce molecular archaeoparasitology as an artefact-independent source of historical evidence. CI - © 2018 The Authors. FAU - Flammer, Patrik G AU - Flammer PG AUID- ORCID: 0000-0002-3153-3411 AD - Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK. AD - Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK. FAU - Dellicour, Simon AU - Dellicour S AD - Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK. AD - Rega Institute for Medical Research, Clinical and Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven-University of Leuven, 3000 Leuven, Belgium. FAU - Preston, Stephen G AU - Preston SG AD - Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK. FAU - Rieger, Dirk AU - Rieger D AD - Archäologie und Denkmalpflege der Hansestadt Lübeck, 23566 Lübeck, Germany. FAU - Warren, Sylvia AU - Warren S AD - Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK. FAU - Tan, Cedric K W AU - Tan CKW AD - Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK. FAU - Nicholson, Rebecca AU - Nicholson R AD - Oxford Archaeology Ltd., Janus House, Osney Mead, Oxford OX2 0ES, UK. FAU - Přichystalová, Renáta AU - Přichystalová R AD - Masaryk University Brno, 60177 Brno, Czech Republic. FAU - Bleicher, Niels AU - Bleicher N AD - Hochbauamt der Stadt Zürich, Abteilung Unterwasserarchäologie, 8008 Zürich, Switzerland. FAU - Wahl, Joachim AU - Wahl J AD - Universität Tübingen, 72070 Tübingen, Germany. AD - Regierungspräsidium Stuttgart, Landesamt für Denkmalpflege, 78467 Konstanz, Germany. FAU - Faria, Nuno R AU - Faria NR AD - Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK. FAU - Pybus, Oliver G AU - Pybus OG AUID- ORCID: 0000-0002-8797-2667 AD - Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK. FAU - Pollard, Mark AU - Pollard M AD - Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK. FAU - Smith, Adrian L AU - Smith AL AUID- ORCID: 0000-0002-7657-6191 AD - Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK adrian.smith@zoo.ox.ac.uk. LA - eng SI - figshare/10.6084/m9.figshare.c.4239758 GR - 204311/Z/16/Z/Wellcome Trust/United Kingdom GR - BB/K004468/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/K001388/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20181003 PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Ancient) MH - Animals MH - Archaeology MH - Cities/epidemiology MH - *Cultural Evolution MH - DNA, Ancient/analysis MH - Feces/*parasitology MH - Genetic Variation MH - Germany/epidemiology MH - Helminths/classification/*physiology MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, Ancient MH - History, Medieval MH - Humans MH - Parasite Egg Count MH - Parasitology MH - Trichuriasis/epidemiology/*history/parasitology MH - Trichuris/genetics/physiology PMC - PMC6191690 OTO - NOTNLM OT - ancient DNA OT - archaeology OT - diet OT - genetics OT - parasitology OT - trade COIS- The authors declare no competing interests. EDAT- 2018/10/05 06:00 MHDA- 2019/08/15 06:00 PMCR- 2018/10/03 CRDT- 2018/10/05 06:00 PHST- 2018/05/02 00:00 [received] PHST- 2018/09/07 00:00 [accepted] PHST- 2018/10/05 06:00 [entrez] PHST- 2018/10/05 06:00 [pubmed] PHST- 2019/08/15 06:00 [medline] PHST- 2018/10/03 00:00 [pmc-release] AID - rspb.2018.0991 [pii] AID - rspb20180991 [pii] AID - 10.1098/rspb.2018.0991 [doi] PST - epublish SO - Proc Biol Sci. 2018 Oct 3;285(1888):20180991. doi: 10.1098/rspb.2018.0991. PMID- 30224645 OWN - NLM STAT- MEDLINE DCOM- 20190426 LR - 20190903 IS - 1546-1718 (Electronic) IS - 1061-4036 (Print) IS - 1061-4036 (Linking) VI - 50 IP - 10 DP - 2018 Oct TI - Genomic history of the Sardinian population. PG - 1426-1434 LID - 10.1038/s41588-018-0215-8 [doi] AB - The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of complex disease traits and, based on ancient DNA studies of mainland Europe, Sardinia is hypothesized to be a unique refuge for early Neolithic ancestry. To provide new insights on the genetic history of this flagship population, we analyzed 3,514 whole-genome sequenced individuals from Sardinia. Sardinian samples show elevated levels of shared ancestry with Basque individuals, especially samples from the more historically isolated regions of Sardinia. Our analysis also uniquely illuminates how levels of genetic similarity with mainland ancient DNA samples varies subtly across the island. Together, our results indicate that within-island substructure and sex-biased processes have substantially impacted the genetic history of Sardinia. These results give new insight into the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations. FAU - Chiang, Charleston W K AU - Chiang CWK AUID- ORCID: 0000-0002-0668-7865 AD - Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. charleston.chiang@med.usc.edu. AD - Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Behavior, University of California, Los Angeles, Los Angeles, CA, USA. charleston.chiang@med.usc.edu. AD - Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA. charleston.chiang@med.usc.edu. FAU - Marcus, Joseph H AU - Marcus JH AUID- ORCID: 0000-0002-0923-9881 AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. FAU - Sidore, Carlo AU - Sidore C AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy. AD - Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA. FAU - Biddanda, Arjun AU - Biddanda A AUID- ORCID: 0000-0003-1861-1523 AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. FAU - Al-Asadi, Hussein AU - Al-Asadi H AD - Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA. FAU - Zoledziewska, Magdalena AU - Zoledziewska M AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy. FAU - Pitzalis, Maristella AU - Pitzalis M AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy. FAU - Busonero, Fabio AU - Busonero F AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy. AD - Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA. FAU - Maschio, Andrea AU - Maschio A AUID- ORCID: 0000-0002-4238-9144 AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy. FAU - Pistis, Giorgio AU - Pistis G AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy. AD - Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA. FAU - Steri, Maristella AU - Steri M AUID- ORCID: 0000-0001-5869-3872 AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy. FAU - Angius, Andrea AU - Angius A AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy. FAU - Lohmueller, Kirk E AU - Lohmueller KE AD - Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA. FAU - Abecasis, Goncalo R AU - Abecasis GR AD - Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA. FAU - Schlessinger, David AU - Schlessinger D AD - Laboratory of Genetics, National Institute on Aging, US National Institutes of Health, Baltimore, MD, USA. FAU - Cucca, Francesco AU - Cucca F AUID- ORCID: 0000-0002-7414-1995 AD - Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy. AD - Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy. FAU - Novembre, John AU - Novembre J AD - Department of Human Genetics, University of Chicago, Chicago, IL, USA. jnovembre@uchicago.edu. LA - eng GR - R01 GM108805/GM/NIGMS NIH HHS/United States GR - RC2 HG005552/HG/NHGRI NIH HHS/United States GR - U01 HG006513/HG/NHGRI NIH HHS/United States GR - T32 NS048004/NS/NINDS NIH HHS/United States GR - F32 GM106656/GM/NIGMS NIH HHS/United States GR - R01 HG007089/HG/NHGRI NIH HHS/United States GR - HHSN271201100005C/DA/NIDA NIH HHS/United States GR - N01 AG012109/AG/NIA NIH HHS/United States GR - T32 GM007197/GM/NIGMS NIH HHS/United States GR - R01 HG007022/HG/NHGRI NIH HHS/United States GR - U01 HL117626/HL/NHLBI NIH HHS/United States GR - R01 HL117626/HL/NHLBI NIH HHS/United States GR - RC2 HG005581/HG/NHGRI NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20180917 PL - United States TA - Nat Genet JT - Nature genetics JID - 9216904 SB - IM MH - Case-Control Studies MH - Demography MH - Female MH - Gene Frequency MH - *Genetic Variation MH - *Genetics, Population MH - Genome-Wide Association Study MH - History, Ancient MH - Human Migration/statistics & numerical data MH - Humans MH - Italy/epidemiology MH - Longitudinal Studies MH - Male MH - Mediterranean Region/epidemiology MH - *Phylogeny PMC - PMC6168346 MID - NIHMS1502262 COIS- COMPETING FINANCIAL INTEREST The authors declared no competing interests EDAT- 2018/09/19 06:00 MHDA- 2019/04/27 06:00 PMCR- 2019/03/17 CRDT- 2018/09/19 06:00 PHST- 2016/12/06 00:00 [received] PHST- 2018/07/30 00:00 [accepted] PHST- 2018/09/19 06:00 [pubmed] PHST- 2019/04/27 06:00 [medline] PHST- 2018/09/19 06:00 [entrez] PHST- 2019/03/17 00:00 [pmc-release] AID - 10.1038/s41588-018-0215-8 [pii] AID - 10.1038/s41588-018-0215-8 [doi] PST - ppublish SO - Nat Genet. 2018 Oct;50(10):1426-1434. doi: 10.1038/s41588-018-0215-8. Epub 2018 Sep 17. PMID- 30232341 OWN - NLM STAT- MEDLINE DCOM- 20191023 LR - 20191023 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 8 IP - 1 DP - 2018 Sep 19 TI - Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis. PG - 14075 LID - 10.1038/s41598-018-32083-0 [doi] LID - 14075 AB - In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio. FAU - Furtwängler, Anja AU - Furtwängler A AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. anja.furtwaengler@uni-tuebingen.de. FAU - Reiter, Ella AU - Reiter E AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Neumann, Gunnar U AU - Neumann GU AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Siebke, Inga AU - Siebke I AD - Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland. FAU - Steuri, Noah AU - Steuri N AD - Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland. FAU - Hafner, Albert AU - Hafner A AD - Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland. FAU - Lösch, Sandra AU - Lösch S AUID- ORCID: 0000-0003-3442-9764 AD - Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland. FAU - Anthes, Nils AU - Anthes N AUID- ORCID: 0000-0003-4189-7849 AD - Institute of Ecology and Evolution, Animal Evolutionary Ecology group University of Tübingen, Tübingen, Germany. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. krause@shh.mpg.de. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. krause@shh.mpg.de. AD - Max Planck Institute for the Science of Human History, Jena, Germany. krause@shh.mpg.de. LA - eng PT - Journal Article DEP - 20180919 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Bone and Bones/chemistry MH - Cell Nucleus/*genetics MH - DNA Contamination MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*analysis MH - Female MH - Haploidy MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Male MH - Sequence Analysis, DNA/methods MH - Sex Factors PMC - PMC6145933 COIS- The authors declare no competing interests. EDAT- 2018/09/21 06:00 MHDA- 2019/10/24 06:00 PMCR- 2018/09/19 CRDT- 2018/09/21 06:00 PHST- 2018/03/28 00:00 [received] PHST- 2018/08/29 00:00 [accepted] PHST- 2018/09/21 06:00 [entrez] PHST- 2018/09/21 06:00 [pubmed] PHST- 2019/10/24 06:00 [medline] PHST- 2018/09/19 00:00 [pmc-release] AID - 10.1038/s41598-018-32083-0 [pii] AID - 32083 [pii] AID - 10.1038/s41598-018-32083-0 [doi] PST - epublish SO - Sci Rep. 2018 Sep 19;8(1):14075. doi: 10.1038/s41598-018-32083-0. PMID- 30146150 OWN - NLM STAT- MEDLINE DCOM- 20191017 LR - 20191017 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 28 IP - 17 DP - 2018 Sep 10 TI - Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town. PG - 2730-2738.e10 LID - S0960-9822(18)30844-3 [pii] LID - 10.1016/j.cub.2018.06.053 [doi] AB - The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10(th) to 12(th) century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration. CI - Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Krzewińska, Maja AU - Krzewińska M AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden. Electronic address: maja.krzewinska@arklab.su.se. FAU - Kjellström, Anna AU - Kjellström A AD - Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden. Electronic address: anna.kjellstrom@ofl.su.se. FAU - Günther, Torsten AU - Günther T AD - Department of Organismal Biology, Evolutionary Biology Centre, Norbyvägen 18C, 752 36 Uppsala, Sweden. FAU - Hedenstierna-Jonson, Charlotte AU - Hedenstierna-Jonson C AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden. FAU - Zachrisson, Torun AU - Zachrisson T AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden. FAU - Omrak, Ayça AU - Omrak A AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden. FAU - Yaka, Reyhan AU - Yaka R AD - Department of Biological Sciences, Middle East Technical University, 06800 Tandogan, Ankara, Turkey. FAU - Kılınç, Gülşah Merve AU - Kılınç GM AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden. FAU - Somel, Mehmet AU - Somel M AD - Department of Biological Sciences, Middle East Technical University, 06800 Tandogan, Ankara, Turkey. FAU - Sobrado, Veronica AU - Sobrado V AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden. FAU - Evans, Jane AU - Evans J AD - NERC Isotope Geosciences Laboratory British Geological Survey, Keyworth, Nottingham NG12 5GG, UK. FAU - Knipper, Corina AU - Knipper C AD - Curt-Engelhorn-Zentrum Archäometrie, D6, 3, 68159 Mannheim, Germany. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Organismal Biology, Evolutionary Biology Centre, Norbyvägen 18C, 752 36 Uppsala, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden. FAU - Storå, Jan AU - Storå J AD - Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden. FAU - Götherström, Anders AU - Götherström A AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden. Electronic address: anders.gotherstrom@arklab.su.se. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180823 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (Strontium Isotopes) RN - 9007-49-2 (DNA) RN - YZS2RPE8LE (Strontium) SB - IM MH - Bone and Bones/chemistry MH - Cities MH - DNA/*genetics MH - *Emigration and Immigration/history MH - Female MH - *Genome-Wide Association Study MH - Genomics MH - History, Ancient MH - Humans MH - Male MH - Strontium/*chemistry MH - Strontium Isotopes MH - Sweden OTO - NOTNLM OT - Christian OT - Medieval OT - Sigtuna OT - Viking Age OT - ancient DNA OT - genome OT - migration OT - urbanization EDAT- 2018/08/28 06:00 MHDA- 2019/10/18 06:00 CRDT- 2018/08/28 06:00 PHST- 2018/03/05 00:00 [received] PHST- 2018/05/13 00:00 [revised] PHST- 2018/06/21 00:00 [accepted] PHST- 2018/08/28 06:00 [pubmed] PHST- 2019/10/18 06:00 [medline] PHST- 2018/08/28 06:00 [entrez] AID - S0960-9822(18)30844-3 [pii] AID - 10.1016/j.cub.2018.06.053 [doi] PST - ppublish SO - Curr Biol. 2018 Sep 10;28(17):2730-2738.e10. doi: 10.1016/j.cub.2018.06.053. Epub 2018 Aug 23. PMID- 30191172 OWN - NLM STAT- MEDLINE DCOM- 20191003 LR - 20191007 IS - 2375-2548 (Electronic) IS - 2375-2548 (Linking) VI - 4 IP - 9 DP - 2018 Sep TI - Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard. PG - eaao1262 LID - 10.1126/sciadv.aao1262 [doi] LID - eaao1262 AB - From historical and archeological records, it is posited that the European medieval household was a combination of close relatives and recruits. However, this kinship structure has not yet been directly tested at a genomic level on medieval burials. The early 7th century CE burial at Niederstotzingen, discovered in 1962, is the most complete and richest example of Alemannic funerary practice in Germany. Excavations found 13 individuals who were buried with an array of inscribed bridle gear, jewelry, armor, and swords. These artifacts support the view that the individuals had contact with France, northern Italy, and Byzantium. This study analyzed genome-wide sequences recovered from the remains, in tandem with analysis of the archeological context, to reconstruct kinship and the extent of outside contact. Eleven individuals had sufficient DNA preservation to genetically sex them as male and identify nine unique mitochondrial haplotypes and two distinct Y chromosome lineages. Genome-wide analyses were performed on eight individuals to estimate genetic affiliation to modern west Eurasians and genetic kinship at the burial. Five individuals were direct relatives. Three other individuals were not detectably related; two of these showed genomic affinity to southern Europeans. The genetic makeup of the individuals shares no observable pattern with their orientation in the burial or the cultural association of their grave goods, with the five related individuals buried with grave goods associated with three diverse cultural origins. These findings support the idea that not only were kinship and fellowship held in equal regard: Diverse cultural appropriation was practiced among closely related individuals as well. FAU - O'Sullivan, Niall AU - O'Sullivan N AUID- ORCID: 0000-0002-3840-4292 AD - Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy. AD - Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany. AD - School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin, Ireland. FAU - Posth, Cosimo AU - Posth C AD - Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany. FAU - Coia, Valentina AU - Coia V AD - Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany. AD - Senckenberg Center for Human Evolution and Paleoecology, Palaeoanthropology, University of Tübingen, 72070 Tübingen, Germany. FAU - Price, T Douglas AU - Price TD AD - Laboratory for Archaeological Chemistry, University of Wisconsin, 1180 Observatory Drive, Madison, WI 53706, USA. FAU - Wahl, Joachim AU - Wahl J AUID- ORCID: 0000-0002-5733-8905 AD - State Office for Cultural Heritage Management Baden-Württemberg, Osteology, D-78467 Konstanz, Germany. AD - Institute for Archaeological Sciences, Palaeoanthropology, University of Tübingen, 72070 Tübingen, Germany. FAU - Pinhasi, Ron AU - Pinhasi R AD - School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin, Ireland. AD - Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. FAU - Zink, Albert AU - Zink A AUID- ORCID: 0000-0002-1461-747X AD - Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany. FAU - Maixner, Frank AU - Maixner F AUID- ORCID: 0000-0003-2846-8994 AD - Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180905 PL - United States TA - Sci Adv JT - Science advances JID - 101653440 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - *Cemeteries MH - *DNA, Mitochondrial MH - Female MH - Genome-Wide Association Study/*methods MH - Germany MH - Haplotypes MH - History, Medieval MH - Humans MH - Male MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Sex Determination Analysis PMC - PMC6124919 EDAT- 2018/09/08 06:00 MHDA- 2019/10/08 06:00 PMCR- 2018/09/05 CRDT- 2018/09/08 06:00 PHST- 2017/06/17 00:00 [received] PHST- 2018/05/31 00:00 [accepted] PHST- 2018/09/08 06:00 [entrez] PHST- 2018/09/08 06:00 [pubmed] PHST- 2019/10/08 06:00 [medline] PHST- 2018/09/05 00:00 [pmc-release] AID - aao1262 [pii] AID - 10.1126/sciadv.aao1262 [doi] PST - epublish SO - Sci Adv. 2018 Sep 5;4(9):eaao1262. doi: 10.1126/sciadv.aao1262. eCollection 2018 Sep. PMID- 29900529 OWN - NLM STAT- MEDLINE DCOM- 20191014 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 167 IP - 1 DP - 2018 Sep TI - New genetic evidence of affinities and discontinuities between bronze age Siberian populations. PG - 97-107 LID - 10.1002/ajpa.23607 [doi] AB - OBJECTIVES: This work focuses on the populations of South Siberia during the Eneolithic and Bronze Age and specifically on the contribution of uniparental lineage and phenotypical data to the question of the genetic affinities and discontinuities between western and eastern populations. MATERIALS AND METHODS: We performed molecular analyses on the remains of 28 ancient humans (10 Afanasievo (3600-2500 BC) and 18 Okunevo (2500-1800 BC) individuals). For each sample, two uniparentally inherited systems (mitochondrial DNA and Y-chromosome DNA) were studied, in order to trace back maternal and paternal lineages. Phenotype-informative SNPs (Single Nucleotide Polymorphisms) were also analyzed, along with autosomal STRs (Short Tandem Repeats). RESULTS: Most of the Afanasievo men submitted to analysis belonged to a single sub-haplogroup, R1b1a1a, which reveals the predominance of this haplogroup in these early Bronze Age populations. Conversely, Okunevo individuals carried more diverse paternal lineages that mostly belonged to Asian/Siberian haplogroups. These differences are also apparent, although less strongly, in mitochondrial lineage composition and phenotype marker variant frequencies. DISCUSSION: This study provides new elements that contribute to our understanding of the genetic interactions between populations in Eneolithic and Bronze Age southern Siberia. Our results support the hypothesis of a genetic link between Afanasievo and Yamnaya (in western Eurasia), as suggested by previous studies of other markers. However, we found no Y-chromosome lineage evidence of a possible Afanasievo migration to the Tarim Basin. Moreover, the presence of Y-haplogroup Q in Okunevo individuals links them to Native American populations, as was suggested by whole-genome sequencing. CI - © 2018 Wiley Periodicals, Inc. FAU - Hollard, Clémence AU - Hollard C AUID- ORCID: 0000-0003-4464-912X AD - Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France. FAU - Zvénigorosky, Vincent AU - Zvénigorosky V AD - Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France. AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. FAU - Kovalev, Alexey AU - Kovalev A AD - Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia. FAU - Kiryushin, Yurii AU - Kiryushin Y AD - The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia. FAU - Tishkin, Alexey AU - Tishkin A AD - The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia. FAU - Lazaretov, Igor AU - Lazaretov I AD - Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia. FAU - Crubézy, Eric AU - Crubézy E AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. FAU - Ludes, Bertrand AU - Ludes B AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. AD - Institut Médico-légal de Paris, Paris, France. AD - Université Paris Descartes, Paris, France. FAU - Keyser, Christine AU - Keyser C AD - Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France. AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. LA - eng GR - French Ministry for Research and Education (MESR)/International GR - 14.Z50.31.0010/Altai State University/International PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180614 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - Asian People/*genetics MH - Chromosomes, Human, Y/*genetics MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/*genetics MH - Genetics, Population MH - History, Ancient MH - Human Migration MH - Humans MH - Male MH - Siberia OTO - NOTNLM OT - Afanasievo OT - Okunevo OT - R1b OT - Tarim Basin OT - ancient DNA EDAT- 2018/06/15 06:00 MHDA- 2019/10/15 06:00 CRDT- 2018/06/15 06:00 PHST- 2017/09/03 00:00 [received] PHST- 2018/04/10 00:00 [revised] PHST- 2018/04/26 00:00 [accepted] PHST- 2018/06/15 06:00 [pubmed] PHST- 2019/10/15 06:00 [medline] PHST- 2018/06/15 06:00 [entrez] AID - 10.1002/ajpa.23607 [doi] PST - ppublish SO - Am J Phys Anthropol. 2018 Sep;167(1):97-107. doi: 10.1002/ajpa.23607. Epub 2018 Jun 14. PMID- 29763671 OWN - NLM STAT- MEDLINE DCOM- 20190618 LR - 20190618 IS - 1567-7257 (Electronic) IS - 1567-1348 (Linking) VI - 63 DP - 2018 Sep TI - Searching for signals of recent natural selection in genes of the innate immune response - ancient DNA study. PG - 62-72 LID - S1567-1348(18)30263-6 [pii] LID - 10.1016/j.meegid.2018.05.008 [doi] AB - The last decade has seen sharp progress in the field of human evolutionary genetics and a great amount of genetic evidence of natural selection has been provided so far. Since host-pathogen co-evolution is difficult to trace due to the polygenic nature of human susceptibility to microbial diseases, of particular interest is any signal of natural selection in response to the strong selective pressure exerted by pathogens. Analysis of ancient DNA allows for the direct insight into changes of a gene pool content over time and enables monitoring allele frequency fluctuations. Among pathogenic agents, mycobacteria are proved to have remained in an intimate, long-lasting relation with humans, reflected by the current high level of host resistance. Therefore, we aimed to investigate the prevalence of several polymorphisms within innate immune response genes related to susceptibility to mycobacterial diseases (in SLC11A1, MBL2, TLR2, P2RX7, IL10, TNFA) in time series data from North and East Poland (1st-18th century AD, n = 207). The comparison of allele frequencies over time revealed a predominant role of genetic drift in shaping past gene pool of small, probably isolated groups, which was explained by the high level of population differentiation and limited gene flow. However, the trajectory of frequency fluctuations of two SNPs suggested the possibility of their non-neutral evolution and the results of applied forward simulations further strengthened the hypothesis of natural selection acting on those loci. However, we observed an unusual excess of homozygosity in the profile of several SNPs, which pinpoints to the necessity of further research on temporally and spatially diverse samples to support our inference on non-stochastic evolution, ideally employing pathway-based approaches. Nevertheless, our study confirms that time series data could help to decipher very recent human adaptation to life-threatening pathogens and assisting demographic events. CI - Copyright © 2018 Elsevier B.V. All rights reserved. FAU - Lewandowska, Magda AU - Lewandowska M AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Poland; Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel. Electronic address: magda.lewandowska@stud.umed.lodz.pl. FAU - Jędrychowska-Dańska, Krystyna AU - Jędrychowska-Dańska K AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Poland. FAU - Płoszaj, Tomasz AU - Płoszaj T AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Poland. FAU - Witas, Piotr AU - Witas P AD - Department of Medical Biotechnology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Poland. FAU - Zamerska, Alicja AU - Zamerska A AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Poland. FAU - Mańkowska-Pliszka, Hanna AU - Mańkowska-Pliszka H AD - Department of Descriptive and Clinical Anatomy, Medical University of Warsaw, Warsaw, Poland. FAU - Witas, Henryk W AU - Witas HW AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Poland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180512 PL - Netherlands TA - Infect Genet Evol JT - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JID - 101084138 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Archaeology MH - DNA/*genetics MH - DNA, Ancient/*isolation & purification MH - Evolution, Molecular MH - Genotype MH - Humans MH - Immunity, Innate/*genetics MH - Poland MH - Selection, Genetic/*genetics OTO - NOTNLM OT - Ancient DNA OT - Genetic drift OT - Innate immune response OT - Natural selection OT - Pathogens EDAT- 2018/05/16 06:00 MHDA- 2019/06/19 06:00 CRDT- 2018/05/16 06:00 PHST- 2017/12/02 00:00 [received] PHST- 2018/05/10 00:00 [revised] PHST- 2018/05/11 00:00 [accepted] PHST- 2018/05/16 06:00 [pubmed] PHST- 2019/06/19 06:00 [medline] PHST- 2018/05/16 06:00 [entrez] AID - S1567-1348(18)30263-6 [pii] AID - 10.1016/j.meegid.2018.05.008 [doi] PST - ppublish SO - Infect Genet Evol. 2018 Sep;63:62-72. doi: 10.1016/j.meegid.2018.05.008. Epub 2018 May 12. PMID- 29709204 OWN - NLM STAT- MEDLINE DCOM- 20190624 LR - 20190624 IS - 1545-293X (Electronic) IS - 1527-8204 (Linking) VI - 19 DP - 2018 Aug 31 TI - Ancient Genomics of Modern Humans: The First Decade. PG - 381-404 LID - 10.1146/annurev-genom-083117-021749 [doi] AB - The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent-in particular the effect of agricultural expansions in Africa, Europe, and Oceania-and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field. FAU - Skoglund, Pontus AU - Skoglund P AD - Francis Crick Institute, London NW1 1AT, United Kingdom; email: pontus.skoglund@crick.ac.uk. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA; email: mathi@upenn.edu. LA - eng PT - Journal Article PT - Review DEP - 20180425 PL - United States TA - Annu Rev Genomics Hum Genet JT - Annual review of genomics and human genetics JID - 100911346 SB - IM MH - Animals MH - Biological Evolution MH - *Genome, Human MH - Hominidae/*genetics MH - Human Migration MH - Humans OTO - NOTNLM OT - Holocene OT - adaptation OT - ancient DNA OT - human origins OT - migration OT - paleogenomics EDAT- 2018/05/02 06:00 MHDA- 2019/06/25 06:00 CRDT- 2018/05/01 06:00 PHST- 2018/05/02 06:00 [pubmed] PHST- 2019/06/25 06:00 [medline] PHST- 2018/05/01 06:00 [entrez] AID - 10.1146/annurev-genom-083117-021749 [doi] PST - ppublish SO - Annu Rev Genomics Hum Genet. 2018 Aug 31;19:381-404. doi: 10.1146/annurev-genom-083117-021749. Epub 2018 Apr 25. PMID- 30158639 OWN - NLM STAT- MEDLINE DCOM- 20191031 LR - 20240330 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 8 IP - 1 DP - 2018 Aug 29 TI - Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis. PG - 13003 LID - 10.1038/s41598-018-31123-z [doi] LID - 13003 AB - Genome-wide ancient DNA analysis of skeletons retrieved from archaeological excavations has provided a powerful new tool for the investigation of past populations and migrations. An important objective for the coming years is to properly integrate ancient genomics into archaeological research. This article aims to contribute to developing a better understanding and cooperation between the two disciplines and beyond. It focuses on the question of how best to name clusters encountered when analysing the genetic makeup of past human populations. Recent studies have frequently borrowed archaeological cultural designations to name these genetic groups, while neglecting the historically problematic nature of the concept of cultures in archaeology. After reviewing current practices in naming genetic clusters, we introduce three possible nomenclature systems ('numeric system', 'mixed system (a)', 'geographic-temporal system') along with their advantages and challenges. FAU - Eisenmann, Stefanie AU - Eisenmann S AD - Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, 07745, Germany. eisenmann@shh.mpg.de. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany & Cambridge, MA, USA. eisenmann@shh.mpg.de. FAU - Bánffy, Eszter AU - Bánffy E AD - Römisch-Germanische Kommission, Deutsches Archäologisches Institut, Frankfurt, a. M., 60325, Germany. FAU - van Dommelen, Peter AU - van Dommelen P AD - Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, RI, 02912, USA. FAU - Hofmann, Kerstin P AU - Hofmann KP AD - Römisch-Germanische Kommission, Deutsches Archäologisches Institut, Frankfurt, a. M., 60325, Germany. FAU - Maran, Joseph AU - Maran J AD - Institut für Ur- und Frühgeschichte und Vorderasiatische Archäologie, Ruprecht-Karls-Universität Heidelberg, Heidelberg, 69117, Germany. FAU - Lazaridis, Iosif AU - Lazaridis I AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany & Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. FAU - Mittnik, Alissa AU - Mittnik A AUID- ORCID: 0000-0002-6963-4824 AD - Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, 07745, Germany. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany & Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - McCormick, Michael AU - McCormick M AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany & Cambridge, MA, USA. AD - Department of History, Harvard University, Cambridge, MA, 02138, USA. AD - Initiative for the Science of the Human Past at Harvard, Harvard University, Cambridge, MA, USA. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, 07745, Germany. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany & Cambridge, MA, USA. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, 72074, Germany. FAU - Reich, David AU - Reich D AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany & Cambridge, MA, USA. AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. AD - Initiative for the Science of the Human Past at Harvard, Harvard University, Cambridge, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MD, 20815, USA. FAU - Stockhammer, Philipp W AU - Stockhammer PW AD - Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, 07745, Germany. philipp.stockhammer@lmu.de. AD - Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany & Cambridge, MA, USA. philipp.stockhammer@lmu.de. AD - Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich, 80799, Germany. philipp.stockhammer@lmu.de. LA - eng GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180829 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology/*methods MH - DNA, Ancient MH - *Fossils MH - Genomics/*methods MH - Humans MH - Skeleton MH - *Terminology as Topic PMC - PMC6115390 COIS- The authors declare no competing interests. EDAT- 2018/08/31 06:00 MHDA- 2019/11/02 06:00 PMCR- 2018/08/29 CRDT- 2018/08/31 06:00 PHST- 2018/02/23 00:00 [received] PHST- 2018/08/13 00:00 [accepted] PHST- 2018/08/31 06:00 [entrez] PHST- 2018/08/31 06:00 [pubmed] PHST- 2019/11/02 06:00 [medline] PHST- 2018/08/29 00:00 [pmc-release] AID - 10.1038/s41598-018-31123-z [pii] AID - 31123 [pii] AID - 10.1038/s41598-018-31123-z [doi] PST - epublish SO - Sci Rep. 2018 Aug 29;8(1):13003. doi: 10.1038/s41598-018-31123-z. PMID- 30139851 OWN - NLM STAT- MEDLINE DCOM- 20181026 LR - 20181026 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 361 IP - 6404 DP - 2018 Aug 24 TI - Ancient DNA reveals tryst between extinct human species. PG - 737 LID - 10.1126/science.361.6404.737 [doi] FAU - Vogel, Gretchen AU - Vogel G LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *Biological Evolution MH - Bone and Bones MH - *DNA, Ancient MH - *Extinction, Biological MH - Fathers/history MH - Female MH - History, Ancient MH - Humans MH - Mothers/history MH - Neanderthals/*genetics MH - Women/*history EDAT- 2018/08/25 06:00 MHDA- 2018/10/27 06:00 CRDT- 2018/08/25 06:00 PHST- 2018/08/25 06:00 [entrez] PHST- 2018/08/25 06:00 [pubmed] PHST- 2018/10/27 06:00 [medline] AID - 361/6404/737 [pii] AID - 10.1126/science.361.6404.737 [doi] PST - ppublish SO - Science. 2018 Aug 24;361(6404):737. doi: 10.1126/science.361.6404.737. PMID- 30127404 OWN - NLM STAT- MEDLINE DCOM- 20181217 LR - 20181217 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 9 IP - 1 DP - 2018 Aug 20 TI - Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation. PG - 3336 LID - 10.1038/s41467-018-05649-9 [doi] LID - 3336 AB - The material culture of the Late Chalcolithic period in the southern Levant (4500-3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi'in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi'in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi'in Cave. These results provide an example of how population movements propelled cultural changes in the deep past. FAU - Harney, Éadaoin AU - Harney É AD - Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. eadaoinharney@gmail.com. AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. eadaoinharney@gmail.com. AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA. eadaoinharney@gmail.com. FAU - May, Hila AU - May H AD - Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel. mayhila@post.tau.ac.il. AD - Shmunis Family Anthropology Institute, Dan David Center for Human Evolution and Biohistory Research, Sackler Faculty of Medicine, Steinhardt Natural History Museum, Tel Aviv University, Tel Aviv, 6997801, Israel. mayhila@post.tau.ac.il. FAU - Shalem, Dina AU - Shalem D AD - The Institute for Galilean Archaeology, Kinneret Academic College, Kinneret, 15132, Israel. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA. AD - Howard Hughes Medical Institute, Boston, MA, 02115, USA. FAU - Lazaridis, Iosif AU - Lazaridis I AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA. FAU - Sarig, Rachel AU - Sarig R AD - Shmunis Family Anthropology Institute, Dan David Center for Human Evolution and Biohistory Research, Sackler Faculty of Medicine, Steinhardt Natural History Museum, Tel Aviv University, Tel Aviv, 6997801, Israel. AD - The Maurice and Gabriela Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Boston, MA, 02115, USA. FAU - Nordenfelt, Susanne AU - Nordenfelt S AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - Howard Hughes Medical Institute, Boston, MA, 02115, USA. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA. AD - Howard Hughes Medical Institute, Boston, MA, 02115, USA. FAU - Hershkovitz, Israel AU - Hershkovitz I AD - Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel. AD - Shmunis Family Anthropology Institute, Dan David Center for Human Evolution and Biohistory Research, Sackler Faculty of Medicine, Steinhardt Natural History Museum, Tel Aviv University, Tel Aviv, 6997801, Israel. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. AD - The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA. AD - Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA. AD - Howard Hughes Medical Institute, Boston, MA, 02115, USA. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20180820 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) SB - IM EIN - Nat Commun. 2018 Sep 20;9(1):3913. doi: 10.1038/s41467-018-06484-8. PMID: 30237547 MH - Caves MH - *Culture MH - DNA, Ancient/*analysis MH - Genetic Heterogeneity MH - Genetic Variation MH - *Genetics, Population MH - *Geologic Sediments MH - Humans MH - Israel MH - Mutation/genetics PMC - PMC6102297 COIS- The authors declare no competing interests. EDAT- 2018/08/22 06:00 MHDA- 2018/12/18 06:00 PMCR- 2018/08/20 CRDT- 2018/08/22 06:00 PHST- 2017/11/24 00:00 [received] PHST- 2018/06/29 00:00 [accepted] PHST- 2018/08/22 06:00 [entrez] PHST- 2018/08/22 06:00 [pubmed] PHST- 2018/12/18 06:00 [medline] PHST- 2018/08/20 00:00 [pmc-release] AID - 10.1038/s41467-018-05649-9 [pii] AID - 5649 [pii] AID - 10.1038/s41467-018-05649-9 [doi] PST - epublish SO - Nat Commun. 2018 Aug 20;9(1):3336. doi: 10.1038/s41467-018-05649-9. PMID- 30065103 OWN - NLM STAT- MEDLINE DCOM- 20190218 LR - 20190219 IS - 1470-8752 (Electronic) IS - 0300-5127 (Linking) VI - 46 IP - 4 DP - 2018 Aug 20 TI - The biological relevance of a medieval king's DNA. PG - 1013-1020 LID - 10.1042/BST20170173 [doi] AB - The discovery of the presumably lost grave of the controversial English king Richard III in Leicester (U.K.) was one of the most important archaeological achievements of the last decennium. The skeleton was identified beyond reasonable doubt, mainly by the match of mitochondrial DNA to that of living maternal relatives, along with the specific archaeological context. Since the genetic genealogical analysis only involved the DNA sequences of a single 15th century individual and a few reference persons, biologists might consider this investigation a mere curiosity. This mini-review shows that the unique context of a historical king's DNA also has relevance for biological research per se - in addition to the more obvious historical, societal and educational value. In the first place, the historical identification appeared to be a renewed forensic case realising a conservative statement with statistical power based on genetic and non-genetic data, including discordant elements. Secondly, the observation of historical non-paternity events within Richard III's patrilineage has given rise to new research questions about potential factors influencing the extra-pair paternity rate in humans and the importance of biological relatedness for the legal recognition of a child in the past. Thirdly, the identification of a named and dated skeleton with the known historical context serves as a reference for bioarchaeological investigations and studies on the spatio-temporal distribution of particular genetic variance. Finally, the Richard III case revealed privacy issues for living relatives which appear to be inherent to any publication of genetic genealogical data. CI - © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society. FAU - Larmuseau, Maarten H D AU - Larmuseau MHD AD - Laboratory of Forensic Genetics and Molecular Archaeology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium maarten.larmuseau@kuleuven.be. AD - Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium. AD - Familiekunde Vlaanderen vzw, Merksem, Belgium. FAU - Bodner, Martin AU - Bodner M AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20180731 PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA, Mitochondrial/*genetics MH - Forensic Anthropology MH - Forensic Genetics MH - Humans MH - Pedigree MH - Privacy MH - United Kingdom OTO - NOTNLM OT - King Richard III OT - ancient DNA OT - celebrity genetics OT - forensic identification OT - genetic genealogy EDAT- 2018/08/02 06:00 MHDA- 2019/02/20 06:00 CRDT- 2018/08/02 06:00 PHST- 2017/11/25 00:00 [received] PHST- 2018/03/27 00:00 [revised] PHST- 2018/04/04 00:00 [accepted] PHST- 2018/08/02 06:00 [pubmed] PHST- 2019/02/20 06:00 [medline] PHST- 2018/08/02 06:00 [entrez] AID - BST20170173 [pii] AID - 10.1042/BST20170173 [doi] PST - ppublish SO - Biochem Soc Trans. 2018 Aug 20;46(4):1013-1020. doi: 10.1042/BST20170173. Epub 2018 Jul 31. PMID- 30107783 OWN - NLM STAT- MEDLINE DCOM- 20181025 LR - 20181114 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 19 IP - 1 DP - 2018 Aug 14 TI - In-solution Y-chromosome capture-enrichment on ancient DNA libraries. PG - 608 LID - 10.1186/s12864-018-4945-x [doi] LID - 608 AB - BACKGROUND: As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach-in-solution capture-enrichment-retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. RESULTS: The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1-1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12-9549 times more targeted unique Y-chromosome sequences after capture, where 0.0-6.2% (WGC + YCC) and 0.0-23.5% (YCC) of the sequence reads were on-target, compared to 0.0-0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries' initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. CONCLUSIONS: We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round. FAU - Cruz-Dávalos, Diana I AU - Cruz-Dávalos DI AD - Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. AD - International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico. AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. AD - Swiss Institute of Bioinformatics, Lausanne, Switzerland. FAU - Nieves-Colón, María A AU - Nieves-Colón MA AD - School of Human Evolution and Social Change, Arizona State University, Tempe, USA. FAU - Sockell, Alexandra AU - Sockell A AD - Department of Genetics, Stanford University, Stanford, USA. FAU - Poznik, G David AU - Poznik GD AD - 23andMe, Mountain View, USA. FAU - Schroeder, Hannes AU - Schroeder H AD - Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. AD - Faculty of Archaeology, Leiden University, Leiden, Netherlands. FAU - Stone, Anne C AU - Stone AC AD - School of Human Evolution and Social Change, Arizona State University, Tempe, USA. AD - Institute of Human Origins, Arizona State University, Tempe, USA. FAU - Bustamante, Carlos D AU - Bustamante CD AD - Department of Genetics, Stanford University, Stanford, USA. AD - Department of Biomedical Data Science, Stanford University, Stanford, USA. FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. annasapfo.malaspinas@unil.ch. AD - Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. annasapfo.malaspinas@unil.ch. AD - Swiss Institute of Bioinformatics, Lausanne, Switzerland. annasapfo.malaspinas@unil.ch. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AD - International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico. mavila@liigh.unam.mx. LA - eng GR - IA206817/Universidad Nacional Autónoma de México/ GR - FP7/2007-2013, grant no. 290344, EUROTAST/European Research Council/International PT - Historical Article PT - Journal Article DEP - 20180814 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (DNA, Ancient) SB - IM MH - *Chromosomes, Human, Y MH - DNA, Ancient/*analysis/*isolation & purification MH - *Gene Library MH - Genomics MH - History, Ancient MH - Humans MH - Sequence Analysis, DNA/*methods MH - Whole Genome Sequencing/*methods PMC - PMC6092841 OTO - NOTNLM OT - Ancient DNA OT - Capture-enrichment OT - Y chromosome COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: For STM1 and STM2, permission to sample and export remains was granted by the Sint Maarten Archaeological Center and the Department of Culture of the Government of Sint Maarten. For the Paso del Indio samples (PI174, PI383, PI435, PI437), permission to export remains and conduct genomic analysis was granted by the Consejo para la Protección del Patrimonio Arqueológico Terrestre de Puerto Rico. CONSENT FOR PUBLICATION: Not applicable COMPETING INTERESTS: The authors declare that they have no competing interests. PUBLISHER’S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EDAT- 2018/08/16 06:00 MHDA- 2018/10/26 06:00 PMCR- 2018/08/14 CRDT- 2018/08/16 06:00 PHST- 2017/11/22 00:00 [received] PHST- 2018/07/16 00:00 [accepted] PHST- 2018/08/16 06:00 [entrez] PHST- 2018/08/16 06:00 [pubmed] PHST- 2018/10/26 06:00 [medline] PHST- 2018/08/14 00:00 [pmc-release] AID - 10.1186/s12864-018-4945-x [pii] AID - 4945 [pii] AID - 10.1186/s12864-018-4945-x [doi] PST - epublish SO - BMC Genomics. 2018 Aug 14;19(1):608. doi: 10.1186/s12864-018-4945-x. PMID- 30033331 OWN - NLM STAT- MEDLINE DCOM- 20191018 LR - 20220129 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 28 IP - 15 DP - 2018 Aug 6 TI - Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia. PG - 2420-2428.e10 LID - S0960-9822(18)30694-8 [pii] LID - 10.1016/j.cub.2018.05.058 [doi] AB - Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia [1]. Paratyphi C is very rare in Europe and North America except for occasional travelers from South and East Asia or Africa, where the disease is more common [2, 3]. However, early 20(th)-century observations in Eastern Europe [3, 4] suggest that Paratyphi C enteric fever may once have had a wide-ranging impact on human societies. Here, we describe a draft Paratyphi C genome (Ragna) recovered from the 800-year-old skeleton (SK152) of a young woman in Trondheim, Norway. Paratyphi C sequences were recovered from her teeth and bones, suggesting that she died of enteric fever and demonstrating that these bacteria have long caused invasive salmonellosis in Europeans. Comparative analyses against modern Salmonella genome sequences revealed that Paratyphi C is a clade within the Para C lineage, which also includes serovars Choleraesuis, Typhisuis, and Lomita. Although Paratyphi C only infects humans, Choleraesuis causes septicemia in pigs and boar [5] (and occasionally humans), and Typhisuis causes epidemic swine salmonellosis (chronic paratyphoid) in domestic pigs [2, 3]. These different host specificities likely evolved in Europe over the last ∼4,000 years since the time of their most recent common ancestor (tMRCA) and are possibly associated with the differential acquisitions of two genomic islands, SPI-6 and SPI-7. The tMRCAs of these bacterial clades coincide with the timing of pig domestication in Europe [6]. CI - Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Zhou, Zhemin AU - Zhou Z AD - Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK. Electronic address: zhemin.zhou@warwick.ac.uk. FAU - Lundstrøm, Inge AU - Lundstrøm I AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. FAU - Tran-Dien, Alicia AU - Tran-Dien A AD - Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France. FAU - Duchêne, Sebastián AU - Duchêne S AD - Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia. FAU - Alikhan, Nabil-Fareed AU - Alikhan NF AD - Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK. FAU - Sergeant, Martin J AU - Sergeant MJ AD - Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK. FAU - Langridge, Gemma AU - Langridge G AD - Wellcome Trust Sanger Institute, Cambridge, UK. FAU - Fotakis, Anna K AU - Fotakis AK AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. FAU - Nair, Satheesh AU - Nair S AD - Wellcome Trust Sanger Institute, Cambridge, UK. FAU - Stenøien, Hans K AU - Stenøien HK AD - NTNU University Museum, N-7491 Trondheim, Norway. FAU - Hamre, Stian S AU - Hamre SS AD - Department of Archaeology, History, Cultural Studies and Religion, University of Bergen, Post Box 7805, 5020 Bergen, Norway. FAU - Casjens, Sherwood AU - Casjens S AD - Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA. FAU - Christophersen, Axel AU - Christophersen A AD - NTNU University Museum, N-7491 Trondheim, Norway. FAU - Quince, Christopher AU - Quince C AD - Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK. FAU - Thomson, Nicholas R AU - Thomson NR AD - Wellcome Trust Sanger Institute, Cambridge, UK. FAU - Weill, François-Xavier AU - Weill FX AD - Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France. FAU - Ho, Simon Y W AU - Ho SYW AD - School of Life and Environmental Sciences; University of Sydney, Sydney NSW 2006, Australia. FAU - Gilbert, M Thomas P AU - Gilbert MTP AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; NTNU University Museum, N-7491 Trondheim, Norway. Electronic address: tgilbert@snm.ku.dk. FAU - Achtman, Mark AU - Achtman M AD - Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK. Electronic address: m.achtman@warwick.ac.uk. LA - eng GR - BB/L027801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom GR - MR/M50161X/1/MRC_/Medical Research Council/United Kingdom GR - R01 GM114817/GM/NIGMS NIH HHS/United States GR - MR/L015080/1/MRC_/Medical Research Council/United Kingdom GR - 202792/Z/16/Z/WT_/Wellcome Trust/United Kingdom GR - WT_/Wellcome Trust/United Kingdom GR - BB/L020319/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180719 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Ancient/*analysis MH - DNA, Bacterial/*analysis MH - Female MH - *Genomic Instability MH - Genomic Islands MH - Humans MH - Norway MH - Salmonella enterica/*genetics MH - Typhoid Fever/*microbiology PMC - PMC6089836 OTO - NOTNLM OT - Ancient DNA OT - Salmonella enterica OT - enteric fever OT - genomic stability OT - historical infections OT - host jump OT - pan-genome OT - paratyphoid fever OT - population genomics OT - tMRCA of bacterial pathogens EDAT- 2018/07/24 06:00 MHDA- 2019/10/19 06:00 PMCR- 2018/08/06 CRDT- 2018/07/24 06:00 PHST- 2017/11/03 00:00 [received] PHST- 2018/02/09 00:00 [revised] PHST- 2018/05/18 00:00 [accepted] PHST- 2018/07/24 06:00 [pubmed] PHST- 2019/10/19 06:00 [medline] PHST- 2018/07/24 06:00 [entrez] PHST- 2018/08/06 00:00 [pmc-release] AID - S0960-9822(18)30694-8 [pii] AID - 10.1016/j.cub.2018.05.058 [doi] PST - ppublish SO - Curr Biol. 2018 Aug 6;28(15):2420-2428.e10. doi: 10.1016/j.cub.2018.05.058. Epub 2018 Jul 19. PMID- 29681138 OWN - NLM STAT- MEDLINE DCOM- 20181214 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 166 IP - 4 DP - 2018 Aug TI - The genome of an ancient Rouran individual reveals an important paternal lineage in the Donghu population. PG - 895-905 LID - 10.1002/ajpa.23491 [doi] AB - OBJECTIVES: Following the Xiongnu and Xianbei, the Rouran Khaganate (Rouran) was the third great nomadic tribe on the Mongolian Steppe. However, few human remains from this tribe are available for archaeologists and geneticists to study, as traces of the tombs of these nomadic people have rarely been found. In 2014, the IA-M1 remains (TL1) at the Khermen Tal site from the Rouran period were found by a Sino-Mongolian joint archaeological team in Mongolia, providing precious material for research into the genetic imprint of the Rouran. MATERIALS AND METHODS: The mtDNA hypervariable sequence I (HVS-I) and Y-chromosome SNPs were analyzed, and capture of the paternal non-recombining region of the Y chromosome (NRY) and whole-genome shotgun sequencing of TL1 were performed. The materials from three sites representing the three ancient nationalities (Donghu, Xianbei, and Shiwei) were selected for comparison with the TL1 individual. RESULTS: The mitochondrial haplotype of the TL1 individual was D4b1a2a1. The Y-chromosome haplotype was C2b1a1b/F3830 (ISOGG 2015), which was the same as that of the other two ancient male nomadic samples (ZHS5 and GG3) related to the Xianbei and Shiwei, which were also detected as F3889; this haplotype was reported to be downstream of F3830 by Wei et al. (). DISCUSSION: We conclude that F3889 downstream of F3830 is an important paternal lineage of the ancient Donghu nomads. The Donghu-Xianbei branch is expected to have made an important paternal genetic contribution to Rouran. This component of gene flow ultimately entered the gene pool of modern Mongolic- and Manchu-speaking populations. CI - © 2018 Wiley Periodicals, Inc. FAU - Li, Jiawei AU - Li J AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China. AD - College of Life Science, Jilin University, Changchun 130012, People's Republic of China. FAU - Zhang, Ye AU - Zhang Y AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China. FAU - Zhao, Yongbin AU - Zhao Y AD - Life Science College, Jilin Normal University, Siping 136000, People's Republic of China. FAU - Chen, Yongzhi AU - Chen Y AD - Director, Inner Mongolian Museum, Hohhot 010011, People's Republic of China. FAU - Ochir, A AU - Ochir A AD - Coordinator, International Institute for Study of Nomadic Civilization, 210620A, Ulaanbaatar 11, Mongolia. FAU - Sarenbilige AU - Sarenbilige AD - Editorial department, Cultural Relics and Archaeological Institute of Inner Mongolia, Hohhot 010010, People's Republic of China. FAU - Zhu, Hong AU - Zhu H AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China. FAU - Zhou, Hui AU - Zhou H AUID- ORCID: 0000-0001-5858-5636 AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China. AD - College of Life Science, Jilin University, Changchun 130012, People's Republic of China. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180421 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - Asian People/*genetics MH - Chromosomes, Human, Y/*genetics MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/genetics MH - Genetics, Population MH - Genome/*genetics MH - Haplotypes/genetics MH - Humans MH - Male MH - Mongolia MH - Phylogeny MH - Transients and Migrants OTO - NOTNLM OT - NRY capture OT - Rouran Khaganate OT - ancient DNA OT - nomadic population EDAT- 2018/04/24 06:00 MHDA- 2018/12/15 06:00 CRDT- 2018/04/23 06:00 PHST- 2017/11/05 00:00 [received] PHST- 2018/03/07 00:00 [revised] PHST- 2018/04/05 00:00 [accepted] PHST- 2018/04/24 06:00 [pubmed] PHST- 2018/12/15 06:00 [medline] PHST- 2018/04/23 06:00 [entrez] AID - 10.1002/ajpa.23491 [doi] PST - ppublish SO - Am J Phys Anthropol. 2018 Aug;166(4):895-905. doi: 10.1002/ajpa.23491. Epub 2018 Apr 21. PMID- 29607481 OWN - NLM STAT- MEDLINE DCOM- 20181214 LR - 20210202 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 166 IP - 4 DP - 2018 Aug TI - Ancient DNA reveals temporal population structure within the South-Central Andes area. PG - 851-860 LID - 10.1002/ajpa.23475 [doi] AB - OBJECTIVES: The main aim of this work was to contribute to the knowledge of pre-Hispanic genetic variation and population structure among the South-central Andes Area by studying individuals from Quebrada de Humahuaca, North-western (NW) Argentina. MATERIALS AND METHODS: We analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900-1430 AD). Compiling autosomal, mitochondrial, and Y-chromosome data, we evaluated population structure and differentiation among eight South-central Andean groups from the current territories of NW Argentina and Peru. RESULTS: Autosomal data revealed a structuring of the analyzed populations into two clusters which seemed to represent different temporalities in the Andean pre-Hispanic history: pre-Inca and Inca. All pre-Inca samples fell into the same cluster despite being from the two different territories of NW Argentina and Peru. Also, they were systematically differentiated from the Peruvian Inca group. These results were mostly confirmed by mitochondrial and Y-chromosome analyses. We mainly found a clearly different haplotype composition between clusters. DISCUSSION: Population structure in South America has been mostly studied on current native groups, mainly showing a west-to-east differentiation between the Andean and lowland regions. Here we demonstrated that genetic population differentiation preceded the European contact and might have been more complex than thought, being found within the South-central Andes Area. Moreover, divergence among temporally different populations might be reflecting socio-political changes occurred in the evermore complex pre-Hispanic Andean societies. CI - © 2018 Wiley Periodicals, Inc. FAU - Russo, M Gabriela AU - Russo MG AUID- ORCID: 0000-0002-5727-4956 AD - Universidad Maimónides, CONICET, Equipo de Antropología Biológica, Departamento de Cs. Naturales y Antropológicas, CEBBAD, Buenos Aires, C1405BCK, Argentina. FAU - Mendisco, Fanny AU - Mendisco F AD - Laboratory of Molecular Anthropology and Image Synthesis (AMIS), University Paul Sabatier (Toulouse III), Faculté de Médecine, CNRS, Toulouse, UMR 5288, France. FAU - Avena, Sergio A AU - Avena SA AD - Universidad Maimónides, CONICET, Equipo de Antropología Biológica, Departamento de Cs. Naturales y Antropológicas, CEBBAD, Buenos Aires, C1405BCK, Argentina. AD - UBA, Sección de Antropología Biológica, ICA, FFyL, Buenos Aires, C1406CQJ, Argentina. FAU - Crespo, Cristian M AU - Crespo CM AD - Universidad Maimónides, CONICET, Equipo de Antropología Biológica, Departamento de Cs. Naturales y Antropológicas, CEBBAD, Buenos Aires, C1405BCK, Argentina. FAU - Arencibia, Valeria AU - Arencibia V AD - Universidad Maimónides, Equipo de Antropología Biológica, Departamento de Cs. Naturales y Antropológicas, CEBBAD, Buenos Aires, C1405BCK, Argentina. FAU - Dejean, Cristina B AU - Dejean CB AD - UBA, Sección de Antropología Biológica, ICA, FFyL, Buenos Aires, C1406CQJ, Argentina. AD - Universidad Maimónides, Equipo de Antropología Biológica, Departamento de Cs. Naturales y Antropológicas, CEBBAD, Buenos Aires, C1405BCK, Argentina. FAU - Seldes, Verónica AU - Seldes V AD - UBA, CONICET, Instituto Interdisciplinario Tilcara, Centro Universitario Tilcara, FFyL, Tilcara, Jujuy, Y4624AFI, Argentina. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180401 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (Genetic Markers) SB - IM MH - Archaeology MH - DNA, Ancient/*analysis MH - Female MH - Genetic Markers/genetics MH - Genetics, Population MH - Humans MH - Indians, South American/*genetics MH - Male MH - Microsatellite Repeats/genetics MH - Peru MH - Sequence Analysis, DNA MH - Tooth/chemistry OTO - NOTNLM OT - Andean groups OT - NW Argentina OT - autosomal STRs OT - pre-Hispanic populations EDAT- 2018/04/03 06:00 MHDA- 2018/12/15 06:00 CRDT- 2018/04/03 06:00 PHST- 2017/09/30 00:00 [received] PHST- 2018/03/15 00:00 [revised] PHST- 2018/03/18 00:00 [accepted] PHST- 2018/04/03 06:00 [pubmed] PHST- 2018/12/15 06:00 [medline] PHST- 2018/04/03 06:00 [entrez] AID - 10.1002/ajpa.23475 [doi] PST - ppublish SO - Am J Phys Anthropol. 2018 Aug;166(4):851-860. doi: 10.1002/ajpa.23475. Epub 2018 Apr 1. PMID- 29603124 OWN - NLM STAT- MEDLINE DCOM- 20181214 LR - 20210202 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 166 IP - 4 DP - 2018 Aug TI - Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments. PG - 824-836 LID - 10.1002/ajpa.23472 [doi] AB - OBJECTIVES: The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi-tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12). MATERIALS AND METHODS: All samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step. RESULTS: No significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments. DISCUSSION: Both methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future. CI - © 2018 Wiley Periodicals, Inc. FAU - Nieves-Colón, Maria A AU - Nieves-Colón MA AUID- ORCID: 0000-0001-9035-6091 AD - School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287. FAU - Ozga, Andrew T AU - Ozga AT AD - School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287. AD - Institute of Human Origins, Arizona State University, Tempe, Arizona 85287. AD - Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287. FAU - Pestle, William J AU - Pestle WJ AD - Department of Anthropology, University of Miami, Coral Gables, Florida 33124. FAU - Cucina, Andrea AU - Cucina A AD - Facultad de Ciencias Antropológicas Universidad Autónoma de Yucatán, Mérida, Yucatán 97305, México. FAU - Tiesler, Vera AU - Tiesler V AD - Facultad de Ciencias Antropológicas Universidad Autónoma de Yucatán, Mérida, Yucatán 97305, México. FAU - Stanton, Travis W AU - Stanton TW AD - Department of Anthropology, University of California Riverside, Riverside, California 92521. FAU - Stone, Anne C AU - Stone AC AD - School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287. AD - Institute of Human Origins, Arizona State University, Tempe, Arizona 85287. AD - Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287. AD - Center for Bioarchaeological Research, Arizona State University, Tempe, Arizona 85287. LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180330 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) SB - IM MH - Anthropology, Physical MH - Base Composition/genetics MH - DNA Damage/genetics MH - DNA, Ancient/*analysis MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Mexico MH - Puerto Rico MH - Sequence Analysis, DNA/*methods MH - Tanzania MH - Tooth/chemistry MH - *Tropical Climate OTO - NOTNLM OT - DNA extraction OT - ancient DNA OT - next-generation sequencing OT - skeletal remains OT - tropics EDAT- 2018/04/01 06:00 MHDA- 2018/12/15 06:00 CRDT- 2018/04/01 06:00 PHST- 2017/09/02 00:00 [received] PHST- 2017/12/15 00:00 [revised] PHST- 2018/03/13 00:00 [accepted] PHST- 2018/04/01 06:00 [pubmed] PHST- 2018/12/15 06:00 [medline] PHST- 2018/04/01 06:00 [entrez] AID - 10.1002/ajpa.23472 [doi] PST - ppublish SO - Am J Phys Anthropol. 2018 Aug;166(4):824-836. doi: 10.1002/ajpa.23472. Epub 2018 Mar 30. PMID- 30017480 OWN - NLM STAT- MEDLINE DCOM- 20191029 LR - 20240922 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 28 IP - 14 DP - 2018 Jul 23 TI - The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals. PG - 2348-2355.e9 LID - S0960-9822(18)30703-6 [pii] LID - 10.1016/j.cub.2018.05.067 [doi] AB - The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual. CI - Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Maixner, Frank AU - Maixner F AD - Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy. Electronic address: frank.maixner@eurac.edu. FAU - Turaev, Dmitrij AU - Turaev D AD - CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. FAU - Cazenave-Gassiot, Amaury AU - Cazenave-Gassiot A AD - SLING, Life Sciences Institute, National University of Singapore, Singapore; Department of Biochemistry, National University of Singapore, Singapore. FAU - Janko, Marek AU - Janko M AD - Institute of Materials Science, Physics of Surfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 2, 64287 Darmstadt, Germany; Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 10, 64287 Darmstadt, Germany. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AD - Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany. FAU - Hoopmann, Michael R AU - Hoopmann MR AD - Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA. FAU - Kusebauch, Ulrike AU - Kusebauch U AD - Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA. FAU - Sartain, Mark AU - Sartain M AD - Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA. FAU - Guerriero, Gea AU - Guerriero G AD - Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg. FAU - O'Sullivan, Niall AU - O'Sullivan N AD - Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy. FAU - Teasdale, Matthew AU - Teasdale M AD - Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland. FAU - Cipollini, Giovanna AU - Cipollini G AD - Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy. FAU - Paladin, Alice AU - Paladin A AD - Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy. FAU - Mattiangeli, Valeria AU - Mattiangeli V AD - Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland. FAU - Samadelli, Marco AU - Samadelli M AD - Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy. FAU - Tecchiati, Umberto AU - Tecchiati U AD - Responsabile del Laboratorio di Archeozoologia della Soprintendenza Provinciale ai Beni culturali di Bolzano - Alto Adige, Ufficio Beni archeologica, 39100 Bolzano, Italy. FAU - Putzer, Andreas AU - Putzer A AD - South Tyrol Museum of Archaeology, Museumstrasse 43, 39100 Bolzano, Italy. FAU - Palazoglu, Mine AU - Palazoglu M AD - Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, Davis, CA, USA. FAU - Meissen, John AU - Meissen J AD - Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, Davis, CA, USA. FAU - Lösch, Sandra AU - Lösch S AD - Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland. FAU - Rausch, Philipp AU - Rausch P AD - Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306, Plön, Germany. FAU - Baines, John F AU - Baines JF AD - Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306, Plön, Germany. FAU - Kim, Bum Jin AU - Kim BJ AD - Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea. FAU - An, Hyun-Joo AU - An HJ AD - Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea. FAU - Gostner, Paul AU - Gostner P AD - Department of Radiodiagnostics, Central Hospital Bolzano, Bolzano, Italy. FAU - Egarter-Vigl, Eduard AU - Egarter-Vigl E AD - Scuola Superiore Sanitaria Provinciale "Claudiana," Via Lorenz Böhler 13, 39100 Bolzano, Italy. FAU - Malfertheiner, Peter AU - Malfertheiner P AD - Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University, Leipziger Strasse 44, 39120 Magdeburg, Germany. FAU - Keller, Andreas AU - Keller A AD - Chair for Clinical Bioinformatics, Saarland University, Medical Faculty, Saarbrücken, Germany. FAU - Stark, Robert W AU - Stark RW AD - Institute of Materials Science, Physics of Surfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 2, 64287 Darmstadt, Germany; Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 10, 64287 Darmstadt, Germany. FAU - Wenk, Markus AU - Wenk M AD - SLING, Life Sciences Institute, National University of Singapore, Singapore; Department of Biochemistry, National University of Singapore, Singapore. FAU - Bishop, David AU - Bishop D AD - Elemental Bio-imaging Facility, University of Technology Sydney, Broadway, New South Wales, 2007, Australia. FAU - Bradley, Daniel G AU - Bradley DG AD - Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland. FAU - Fiehn, Oliver AU - Fiehn O AD - Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, Davis, CA, USA. FAU - Engstrand, Lars AU - Engstrand L AD - Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 141 83 Stockholm, Sweden. FAU - Moritz, Robert L AU - Moritz RL AD - Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA. FAU - Doble, Philip AU - Doble P AD - Elemental Bio-imaging Facility, University of Technology Sydney, Broadway, New South Wales, 2007, Australia. FAU - Franke, Andre AU - Franke A AD - Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany. FAU - Nebel, Almut AU - Nebel A AD - Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany. FAU - Oeggl, Klaus AU - Oeggl K AD - Institute of Botany, Sternwartestrasse 15, University of Innsbruck, 6020 Innsbruck, Austria. FAU - Rattei, Thomas AU - Rattei T AD - CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. FAU - Grimm, Rudolf AU - Grimm R AD - Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA 95051, USA. FAU - Zink, Albert AU - Zink A AD - Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy. Electronic address: albert.zink@eurac.edu. LA - eng GR - P50 GM076547/GM/NIGMS NIH HHS/United States GR - R01 GM087221/GM/NIGMS NIH HHS/United States GR - S10 RR027584/RR/NCRR NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20180712 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (Dietary Fats) SB - IM MH - Archaeology MH - Austria MH - Diet/*history MH - Dietary Fats MH - Edible Grain MH - History, Ancient MH - Humans MH - Italy MH - Male MH - Meat MH - *Mummies PMC - PMC6065529 OTO - NOTNLM OT - European Copper Age mummy OT - Iceman OT - ancient DNA OT - diet OT - last meal OT - lipidomics OT - microscopy OT - multi-omics study OT - proteomics OT - stomach content EDAT- 2018/07/19 06:00 MHDA- 2019/10/30 06:00 PMCR- 2018/07/23 CRDT- 2018/07/19 06:00 PHST- 2018/04/05 00:00 [received] PHST- 2018/05/15 00:00 [revised] PHST- 2018/05/23 00:00 [accepted] PHST- 2018/07/19 06:00 [pubmed] PHST- 2019/10/30 06:00 [medline] PHST- 2018/07/19 06:00 [entrez] PHST- 2018/07/23 00:00 [pmc-release] AID - S0960-9822(18)30703-6 [pii] AID - 10.1016/j.cub.2018.05.067 [doi] PST - ppublish SO - Curr Biol. 2018 Jul 23;28(14):2348-2355.e9. doi: 10.1016/j.cub.2018.05.067. Epub 2018 Jul 12. PMID- 29967156 OWN - NLM STAT- MEDLINE DCOM- 20180911 LR - 20190118 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 115 IP - 29 DP - 2018 Jul 17 TI - Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans. PG - 7557-7562 LID - 10.1073/pnas.1804921115 [doi] AB - Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to ∼70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9-99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from ∼0.5 to ∼6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed ∼12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to ∼5.0-6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics. FAU - Mühlemann, Barbara AU - Mühlemann B AD - Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdom. FAU - Margaryan, Ashot AU - Margaryan A AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark. AD - Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia. FAU - Damgaard, Peter de Barros AU - Damgaard PB AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark. FAU - Allentoft, Morten E AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark. FAU - Vinner, Lasse AU - Vinner L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark. FAU - Hansen, Anders J AU - Hansen AJ AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark. FAU - Weber, Andrzej AU - Weber A AD - Department of Anthropology, University of Alberta, Edmonton, AB T6G 2H4, Canada. FAU - Bazaliiskii, Vladimir I AU - Bazaliiskii VI AD - Department of History, Irkutsk State University, 664003 Irkutsk, Russia. FAU - Molak, Martyna AU - Molak M AD - Museum and Institute of Zoology, Polish Academy of Sciences, 00-679 Warsaw, Poland. FAU - Arneborg, Jette AU - Arneborg J AD - The National Museum of Denmark, 1220 Copenhagen, Denmark. AD - School of GeoScience, University of Edinburgh, EH8 9XP Edinburgh, United Kingdom. FAU - Bogdanowicz, Wieslaw AU - Bogdanowicz W AD - Museum and Institute of Zoology, Polish Academy of Sciences, 00-679 Warsaw, Poland. FAU - Falys, Ceri AU - Falys C AD - Thames Valley Archaeological Services (TVAS), RG1 5NR Reading, United Kingdom. FAU - Sablin, Mikhail AU - Sablin M AD - Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, 199034 Saint Petersburg, Russia. FAU - Smrčka, Václav AU - Smrčka V AD - Institute for History of Medicine and Foreign Languages, First Faculty of Medicine, Charles University, 121 08 Prague, Czech Republic. FAU - Sten, Sabine AU - Sten S AD - Department of Archaeology and Ancient History, Uppsala University, 621 67 Visby, Sweden. FAU - Tashbaeva, Kadicha AU - Tashbaeva K AD - Institute of History and Cultural Heritage, National Academy of Sciences, 720001 Bishkek, Kyrgyzstan. FAU - Lynnerup, Niels AU - Lynnerup N AD - Department of Forensic Medicine, University of Copenhagen, Teilum, 2100 Copenhagen, Denmark. FAU - Sikora, Martin AU - Sikora M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark. FAU - Smith, Derek J AU - Smith DJ AD - Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdom. FAU - Fouchier, Ron A M AU - Fouchier RAM AD - Department of Viroscience, Erasmus Medical Centre, 3015 CN Rotterdam, The Netherlands. FAU - Drosten, Christian AU - Drosten C AD - Institute of Virology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany. FAU - Sjögren, Karl-Göran AU - Sjögren KG AD - Department of Historical Studies, University of Gothenburg, 412 61 Göteborg, Sweden. FAU - Kristiansen, Kristian AU - Kristiansen K AD - Department of Historical Studies, University of Gothenburg, 412 61 Göteborg, Sweden. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark; ewillerslev@snm.ku.dk tcj25@cam.ac.uk. AD - Cambridge GeoGenetics Group, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdom. AD - Human Genetics, Wellcome Trust Sanger Institute, CB10 1SA Hinxton, United Kingdom. FAU - Jones, Terry C AU - Jones TC AD - Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdom; ewillerslev@snm.ku.dk tcj25@cam.ac.uk. AD - Institute of Virology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20180702 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Erythema Infectiosum/*genetics/history MH - *Evolution, Molecular MH - *Genome, Viral MH - *Genotype MH - History, 19th Century MH - History, 20th Century MH - Humans MH - Parvovirus B19, Human/*genetics MH - *Phylogeny MH - *Sequence Analysis, DNA PMC - PMC6055166 OTO - NOTNLM OT - ancient DNA OT - paleo virology OT - parvovirus B19 OT - virology OT - virus evolution COIS- The authors declare no conflict of interest. EDAT- 2018/07/04 06:00 MHDA- 2018/09/12 06:00 PMCR- 2019/01/02 CRDT- 2018/07/04 06:00 PHST- 2018/07/04 06:00 [pubmed] PHST- 2018/09/12 06:00 [medline] PHST- 2018/07/04 06:00 [entrez] PHST- 2019/01/02 00:00 [pmc-release] AID - 1804921115 [pii] AID - 201804921 [pii] AID - 10.1073/pnas.1804921115 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2018 Jul 17;115(29):7557-7562. doi: 10.1073/pnas.1804921115. Epub 2018 Jul 2. PMID- 29773666 OWN - NLM STAT- MEDLINE DCOM- 20180803 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 361 IP - 6397 DP - 2018 Jul 6 TI - Ancient genomes document multiple waves of migration in Southeast Asian prehistory. PG - 92-95 LID - 10.1126/science.aat3188 [doi] AB - Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants. CI - Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. FAU - Lipson, Mark AU - Lipson M AUID- ORCID: 0000-0001-5346-9329 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. mlipson@genetics.med.harvard.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu. FAU - Cheronet, Olivia AU - Cheronet O AUID- ORCID: 0000-0001-6760-1204 AD - Department of Anthropology, University of Vienna, 1090 Vienna, Austria. AD - Earth Institute, University College Dublin, Dublin 4, Ireland. AD - School of Archaeology, University College Dublin, Dublin 4, Ireland. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Oxenham, Marc AU - Oxenham M AD - School of Archaeology and Anthropology, Australian National University, Canberra, ACT 0200, Australia. FAU - Pietrusewsky, Michael AU - Pietrusewsky M AD - Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA. FAU - Pryce, Thomas Oliver AU - Pryce TO AUID- ORCID: 0000-0002-7290-141X AD - Centre National de la Recherche Scientifique, 75016 Paris, France. AD - UMR 7055 Préhistoire et Technologie, Université Paris Nanterre, 92023 Nanterre, France. AD - CEA/CNRS UMR 3685 NIMBE, 91191 Gif-sur-Yvette, France. FAU - Willis, Anna AU - Willis A AUID- ORCID: 0000-0002-3265-862X AD - College of Arts, Society and Education, James Cook University, Townsville, Queensland 4811, Australia. FAU - Matsumura, Hirofumi AU - Matsumura H AD - School of Health Science, Sapporo Medical University, Sapporo 060-8556, Japan. FAU - Buckley, Hallie AU - Buckley H AD - Department of Anatomy, University of Otago, Dunedin 9054, New Zealand. FAU - Domett, Kate AU - Domett K AUID- ORCID: 0000-0001-5091-3105 AD - Division of Tropical Health and Medicine, College of Medicine and Dentistry, James Cook University, Townsville, Queensland 4811, Australia. FAU - Nguyen, Giang Hai AU - Nguyen GH AD - Department of Prehistoric Archaeology, Vietnam Institute of Archaeology, Hanoi, Vietnam. FAU - Trinh, Hoang Hiep AU - Trinh HH AD - Department of Prehistoric Archaeology, Vietnam Institute of Archaeology, Hanoi, Vietnam. FAU - Kyaw, Aung Aung AU - Kyaw AA AUID- ORCID: 0000-0001-7711-4100 AD - Department of Archaeology, Ministry of Religious Affairs and Culture, Mandalay, Myanmar. FAU - Win, Tin Tin AU - Win TT AD - Department of Archaeology, Ministry of Religious Affairs and Culture, Mandalay, Myanmar. FAU - Pradier, Baptiste AU - Pradier B AUID- ORCID: 0000-0002-0169-7589 AD - UMR 7055 Préhistoire et Technologie, Université Paris Nanterre, 92023 Nanterre, France. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Candilio, Francesca AU - Candilio F AUID- ORCID: 0000-0002-4668-1361 AD - Soprintendenza Archeologia Belle Arti e Paesaggio per la Città Metropolitana di Cagliari e per le Province di Oristano e Sud Sardegna, 09124 Cagliari, Italy. AD - Physical Anthropology Section, University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA. FAU - Changmai, Piya AU - Changmai P AUID- ORCID: 0000-0003-3307-0585 AD - Department of Biology and Ecology, Faculty of Science, University of Ostrava, 70103 Ostrava, Czech Republic. FAU - Fernandes, Daniel AU - Fernandes D AD - Department of Anthropology, University of Vienna, 1090 Vienna, Austria. AD - Earth Institute, University College Dublin, Dublin 4, Ireland. AD - CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal. FAU - Ferry, Matthew AU - Ferry M AUID- ORCID: 0000-0001-7319-0085 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Gamarra, Beatriz AU - Gamarra B AD - Earth Institute, University College Dublin, Dublin 4, Ireland. AD - School of Archaeology, University College Dublin, Dublin 4, Ireland. FAU - Harney, Eadaoin AU - Harney E AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Kampuansai, Jatupol AU - Kampuansai J AD - Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand. AD - Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand. FAU - Kutanan, Wibhu AU - Kutanan W AUID- ORCID: 0000-0001-7767-1644 AD - Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Novak, Mario AU - Novak M AD - Earth Institute, University College Dublin, Dublin 4, Ireland. AD - Institute for Anthropological Research, 10000 Zagreb, Croatia. FAU - Oppenheimer, Jonas AU - Oppenheimer J AUID- ORCID: 0000-0001-7973-6173 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Sirak, Kendra AU - Sirak K AD - Earth Institute, University College Dublin, Dublin 4, Ireland. AD - Department of Anthropology, Emory University, Atlanta, GA 30322, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Zhang, Zhao AU - Zhang Z AUID- ORCID: 0000-0002-7562-7559 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Flegontov, Pavel AU - Flegontov P AD - Department of Biology and Ecology, Faculty of Science, University of Ostrava, 70103 Ostrava, Czech Republic. AD - Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic. FAU - Pinhasi, Ron AU - Pinhasi R AUID- ORCID: 0000-0003-1629-8131 AD - Department of Anthropology, University of Vienna, 1090 Vienna, Austria. mlipson@genetics.med.harvard.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu. AD - Earth Institute, University College Dublin, Dublin 4, Ireland. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. mlipson@genetics.med.harvard.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu. AD - Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20180517 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM CIN - Science. 2018 Jul 6;361(6397):31-32. doi: 10.1126/science.aat8662. PMID: 29976814 MH - Agriculture/history MH - Asia, Southeastern MH - Asian People/genetics MH - DNA, Ancient MH - Genetic Variation MH - *Genome, Human MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Language/*history MH - Radiometric Dating PMC - PMC6476732 MID - NIHMS1018569 EDAT- 2018/05/19 06:00 MHDA- 2018/08/04 06:00 PMCR- 2019/04/22 CRDT- 2018/05/19 06:00 PHST- 2018/02/13 00:00 [received] PHST- 2018/05/03 00:00 [accepted] PHST- 2018/05/19 06:00 [pubmed] PHST- 2018/08/04 06:00 [medline] PHST- 2018/05/19 06:00 [entrez] PHST- 2019/04/22 00:00 [pmc-release] AID - science.aat3188 [pii] AID - 10.1126/science.aat3188 [doi] PST - ppublish SO - Science. 2018 Jul 6;361(6397):92-95. doi: 10.1126/science.aat3188. Epub 2018 May 17. PMID- 29744957 OWN - NLM STAT- MEDLINE DCOM- 20190926 LR - 20190926 IS - 1520-6300 (Electronic) IS - 1042-0533 (Linking) VI - 30 IP - 4 DP - 2018 Jul TI - Mitochondrial lineage A2ah found in a pre-Hispanic individual from the Andean region. PG - e23134 LID - 10.1002/ajhb.23134 [doi] AB - OBJECTIVES: The aim of this study was to contribute to the knowledge of pre-Hispanic Andean mitochondrial diversity by analyzing an individual from the archaeological site Pukara de La Cueva (North-western Argentina). The date of the discovery context (540 ± 60 BP) corresponds to the Regional Developments II period. METHODS: Two separate DNA extractions were performed from dentin powder of one tooth. HVR I was amplified by PCR from each extract in three overlapping fragments and the haplotype was determined by consensus among all obtained sequences. The procedures were carried out under strict protocols developed for working with ancient DNA. RESULTS: The individual belonged to the A2ah lineage due to the presence of the 16097C and 16098G transitions, which constitute its distinctive motif. This lineage is very rare in Native American populations and was described in four individuals from current groups inhabiting the Bolivian Llanos, two from South-eastern Brazil, and one from the Gran Chaco region. In addition, two other mutations (16260T and 16286T) were shared with one of the individuals from the Bolivian Llanos region. CONCLUSIONS: Considering that the origin of this lineage was postulated for the South American lowlands, the present pre-Hispanic discovery in the Andean area could be taken as a new evidence of gene flow between these regions. Also, it allows the questioning of the geographical origin of this mitochondrial lineage. CI - © 2018 Wiley Periodicals, Inc. FAU - Russo, M G AU - Russo MG AUID- ORCID: 0000-0002-5727-4956 AD - Universidad Maimónides, CONICET, CEBBAD, Equipo de Antropología Biológica, Buenos Aires, C1405BCK, Argentina. FAU - Dejean, C B AU - Dejean CB AD - UBA, Sección de Antropología Biológica, FFyL, Universidad Maimónides, CEBBAD, Equipo de Antropología Biológica, Buenos Aires C1406CQJ, Argentina. FAU - Avena, S A AU - Avena SA AD - Universidad Maimónides, CONICET, CEBBAD, Equipo de Antropología Biológica, Buenos Aires, C1405BCK, Argentina. AD - UBA, Sección de Antropología Biológica, FFyL, Universidad Maimónides, CEBBAD, Equipo de Antropología Biológica, Buenos Aires C1406CQJ, Argentina. FAU - Seldes, V AU - Seldes V AD - UBA, CONICET, Instituto Interdisciplinario de Tilcara, Tilcara, Jujuy, Y4624AFI, Argentina. FAU - Ramundo, P AU - Ramundo P AD - UCA, CONICET, Departamento de Historia, Facultad de Ciencias Sociales, Buenos Aires C1107AFD, Argentina. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180510 PL - United States TA - Am J Hum Biol JT - American journal of human biology : the official journal of the Human Biology Council JID - 8915029 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adolescent MH - Adult MH - Archaeology MH - Argentina MH - Child MH - Child, Preschool MH - DNA, Mitochondrial/analysis MH - Female MH - *Gene Flow MH - *Genetic Variation MH - *Haplotypes MH - Humans MH - Indians, South American/*genetics MH - Infant MH - Male MH - Middle Aged MH - Young Adult EDAT- 2018/05/11 06:00 MHDA- 2019/09/27 06:00 CRDT- 2018/05/11 06:00 PHST- 2017/12/27 00:00 [received] PHST- 2018/02/26 00:00 [revised] PHST- 2018/04/15 00:00 [accepted] PHST- 2018/05/11 06:00 [pubmed] PHST- 2019/09/27 06:00 [medline] PHST- 2018/05/11 06:00 [entrez] AID - 10.1002/ajhb.23134 [doi] PST - ppublish SO - Am J Hum Biol. 2018 Jul;30(4):e23134. doi: 10.1002/ajhb.23134. Epub 2018 May 10. PMID- 29895688 OWN - NLM STAT- MEDLINE DCOM- 20180907 LR - 20211204 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 115 IP - 26 DP - 2018 Jun 26 TI - Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. PG - 6774-6779 LID - 10.1073/pnas.1800851115 [doi] AB - The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals' genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb. FAU - Fregel, Rosa AU - Fregel R AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305; rfregel@ull.edu.es. FAU - Méndez, Fernando L AU - Méndez FL AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. FAU - Bokbot, Youssef AU - Bokbot Y AD - Institut National des Sciences de l'Archéologie et du Patrimoine, 6828 Rabat, Morocco. FAU - Martín-Socas, Dimas AU - Martín-Socas D AD - Departmento de Prehistoria, Universidad de La Laguna, 38320 San Cristóbal de La Laguna, Spain. FAU - Camalich-Massieu, María D AU - Camalich-Massieu MD AD - Departmento de Prehistoria, Universidad de La Laguna, 38320 San Cristóbal de La Laguna, Spain. FAU - Santana, Jonathan AU - Santana J AD - Department of Archaeology, Durham University, DH1 3LE Durham, United Kingdom. FAU - Morales, Jacob AU - Morales J AD - Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, 35003 Las Palmas de Gran Canaria, Spain. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. AD - International Laboratory for Human Genome Research, National Autonomous University of Mexico, 76230 Querétaro, Mexico. FAU - Underhill, Peter A AU - Underhill PA AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. FAU - Shapiro, Beth AU - Shapiro B AUID- ORCID: 0000-0002-2733-7776 AD - Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064. FAU - Wojcik, Genevieve AU - Wojcik G AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. FAU - Rasmussen, Morten AU - Rasmussen M AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. FAU - Soares, André E R AU - Soares AER AUID- ORCID: 0000-0002-7768-2199 AD - Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064. FAU - Kapp, Joshua AU - Kapp J AD - Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064. FAU - Sockell, Alexandra AU - Sockell A AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. FAU - Rodríguez-Santos, Francisco J AU - Rodríguez-Santos FJ AD - Instituto Internacional de Investigaciones Prehistóricas de Cantabria, 39005 Cantabria, Spain. FAU - Mikdad, Abdeslam AU - Mikdad A AD - Institut National des Sciences de l'Archéologie et du Patrimoine, 6828 Rabat, Morocco. FAU - Trujillo-Mederos, Aioze AU - Trujillo-Mederos A AD - Departmento de Prehistoria, Universidad de La Laguna, 38320 San Cristóbal de La Laguna, Spain. FAU - Bustamante, Carlos D AU - Bustamante CD AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. LA - eng PT - Comparative Study PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20180612 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM EIN - Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7231. doi: 10.1073/pnas.1811169115. PMID: 30012588 MH - Africa, Northern MH - Agriculture/history MH - Chromosomes, Human, Y/genetics MH - DNA, Mitochondrial/genetics MH - Ethnicity/*genetics/history MH - Europe MH - Gene Flow MH - Gene Library MH - Genetics, Population MH - *Genome, Human MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Middle East MH - Morocco MH - Sequence Analysis, DNA MH - Spain/ethnology PMC - PMC6042094 OTO - NOTNLM OT - Neolithic transition OT - North Africa OT - ancient DNA OT - paleogenomics COIS- The authors declare no conflict of interest. EDAT- 2018/06/14 06:00 MHDA- 2018/09/08 06:00 PMCR- 2018/12/12 CRDT- 2018/06/14 06:00 PHST- 2018/06/14 06:00 [pubmed] PHST- 2018/09/08 06:00 [medline] PHST- 2018/06/14 06:00 [entrez] PHST- 2018/12/12 00:00 [pmc-release] AID - 1800851115 [pii] AID - 201800851 [pii] AID - 10.1073/pnas.1800851115 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6774-6779. doi: 10.1073/pnas.1800851115. Epub 2018 Jun 12. PMID- 29924800 OWN - NLM STAT- MEDLINE DCOM- 20181127 LR - 20240327 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 13 IP - 6 DP - 2018 TI - Parasitic infections and resource economy of Danish Iron Age settlement through ancient DNA sequencing. PG - e0197399 LID - 10.1371/journal.pone.0197399 [doi] LID - e0197399 AB - In this study, we screen archaeological soil samples by microscopy and analyse the samples by next generation sequencing to obtain results with parasites at species level and untargeted findings of plant and animal DNA. Three separate sediment layers of an ancient man-made pond in Hoby, Denmark, ranging from 100 BC to 200 AD, were analysed by microscopy for presence of intestinal worm eggs and DNA analysis were performed to identify intestinal worms and dietary components. Ancient DNA of parasites, domestic animals and edible plants revealed a change in use of the pond over time reflecting the household practice in the adjacent Iron Age settlement. The most abundant parasite found belonged to the Ascaris genus, which was not possible to type at species level. For all sediment layers the presence of eggs of the human whipworm Trichuris trichiura and the beef tapeworm Taenia saginata suggests continuous disposal of human faeces in the pond. Moreover, the continuous findings of T. saginata further imply beef consumption and may suggest that cattle were living in the immediate surrounding of the site throughout the period. Findings of additional host-specific parasites suggest fluctuating presence of other domestic animals over time: Trichuris suis (pig), Parascaris univalens (horse), Taenia hydatigena (dog and sheep). Likewise, alternating occurrence of aDNA of edible plants may suggest changes in agricultural practices. Moreover, the composition of aDNA of parasites, plants and vertebrates suggests a significant change in the use of the ancient pond over a period of three centuries. FAU - Tams, Katrine Wegener AU - Tams KW AUID- ORCID: 0000-0002-8154-6122 AD - Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark. AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. FAU - Jensen Søe, Martin AU - Jensen Søe M AUID- ORCID: 0000-0002-0386-6294 AD - Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark. AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. FAU - Merkyte, Inga AU - Merkyte I AD - The Saxo Institute, University of Copenhagen, Copenhagen S, Denmark. FAU - Valeur Seersholm, Frederik AU - Valeur Seersholm F AD - Trace and Environmental DNA (TrEnD) Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia. FAU - Henriksen, Peter Steen AU - Henriksen PS AUID- ORCID: 0000-0003-0728-4029 AD - Environmental Archaeology and Material Science, National Museum of Denmark, Kongens Lyngby, Denmark. FAU - Klingenberg, Susanne AU - Klingenberg S AD - Ancient Cultures of Denmark and the Mediterranean, National Museum of Denmark, Kongens Lyngby, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. AD - Department of Zoology, University of Cambridge, Cambridge, United Kingdom. AD - Sanger Institute, Hinxton, Cambridge, United Kingdom. FAU - Kjær, Kurt H AU - Kjær KH AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. FAU - Hansen, Anders Johannes AU - Hansen AJ AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. FAU - Kapel, Christian Moliin Outzen AU - Kapel CMO AD - Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180620 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Archaeology MH - Cattle MH - DNA, Ancient/*analysis MH - Denmark MH - Feces/parasitology MH - Horses/parasitology MH - Humans MH - Parasites/*genetics/isolation & purification MH - Plants/genetics MH - *Sequence Analysis, DNA MH - Sheep/parasitology MH - Swine/parasitology MH - Trichuris/*genetics/isolation & purification/pathogenicity PMC - PMC6010210 COIS- The authors have declared that no competing interests exist. EDAT- 2018/06/21 06:00 MHDA- 2018/11/28 06:00 PMCR- 2018/06/20 CRDT- 2018/06/21 06:00 PHST- 2018/01/23 00:00 [received] PHST- 2018/05/01 00:00 [accepted] PHST- 2018/06/21 06:00 [entrez] PHST- 2018/06/21 06:00 [pubmed] PHST- 2018/11/28 06:00 [medline] PHST- 2018/06/20 00:00 [pmc-release] AID - PONE-D-18-02357 [pii] AID - 10.1371/journal.pone.0197399 [doi] PST - epublish SO - PLoS One. 2018 Jun 20;13(6):e0197399. doi: 10.1371/journal.pone.0197399. eCollection 2018. PMID- 29709200 OWN - NLM STAT- MEDLINE DCOM- 20190528 LR - 20190610 IS - 1545-4509 (Electronic) IS - 0066-4154 (Linking) VI - 87 DP - 2018 Jun 20 TI - Ancient Biomolecules and Evolutionary Inference. PG - 1029-1060 LID - 10.1146/annurev-biochem-062917-012002 [doi] AB - Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field. FAU - Cappellini, Enrico AU - Cappellini E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. FAU - Prohaska, Ana AU - Prohaska A AD - Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom. FAU - Racimo, Fernando AU - Racimo F AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. FAU - Welker, Frido AU - Welker F AD - Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Pedersen, Mikkel Winther AU - Pedersen MW AD - Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom. FAU - Allentoft, Morten E AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. FAU - de Barros Damgaard, Peter AU - de Barros Damgaard P AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. FAU - Gutenbrunner, Petra AU - Gutenbrunner P AD - Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. FAU - Dunne, Julie AU - Dunne J AD - Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; email: r.p.evershed@bristol.ac.uk. FAU - Hammann, Simon AU - Hammann S AD - Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; email: r.p.evershed@bristol.ac.uk. AD - Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, United Kingdom. FAU - Roffet-Salque, Mélanie AU - Roffet-Salque M AD - Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; email: r.p.evershed@bristol.ac.uk. FAU - Ilardo, Melissa AU - Ilardo M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. FAU - Moreno-Mayar, J Víctor AU - Moreno-Mayar JV AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. FAU - Wang, Yucheng AU - Wang Y AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. FAU - Sikora, Martin AU - Sikora M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. FAU - Vinner, Lasse AU - Vinner L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. FAU - Cox, Jürgen AU - Cox J AD - Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. FAU - Evershed, Richard P AU - Evershed RP AD - Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; email: r.p.evershed@bristol.ac.uk. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; email: ecappellini@snm.ku.dk , ewillerslev@snm.ku.dk. AD - Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom. AD - Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20180425 PL - United States TA - Annu Rev Biochem JT - Annual review of biochemistry JID - 2985150R RN - 0 (DNA, Ancient) RN - 0 (Lipids) RN - 0 (Proteins) SB - IM MH - Animals MH - Biological Evolution MH - *DNA, Ancient MH - *Evolution, Molecular MH - Extinction, Biological MH - Fossils MH - Genomics MH - Humans MH - Lipids/genetics MH - Paleontology MH - Phylogeny MH - Proteins/genetics MH - Proteomics OTO - NOTNLM OT - ancient DNA OT - ancient genomics OT - ancient lipids OT - ancient proteins OT - paleogenomics OT - paleoproteomics EDAT- 2018/05/02 06:00 MHDA- 2019/05/29 06:00 CRDT- 2018/05/01 06:00 PHST- 2018/05/02 06:00 [pubmed] PHST- 2019/05/29 06:00 [medline] PHST- 2018/05/01 06:00 [entrez] AID - 10.1146/annurev-biochem-062917-012002 [doi] PST - ppublish SO - Annu Rev Biochem. 2018 Jun 20;87:1029-1060. doi: 10.1146/annurev-biochem-062917-012002. Epub 2018 Apr 25. PMID- 30027753 OWN - NLM STAT- MEDLINE DCOM- 20190107 LR - 20190107 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 45 IP - 4 DP - 2018 Jun TI - Kinship analysis and allelic dropout: a forensic approach on an archaeological case. PG - 365-368 LID - 10.1080/03014460.2018.1484159 [doi] AB - BACKGROUND: This study relies on the discovery of two pit burials (LTA and LTB) of the Bronze Age Cogotas I archaeological culture (circa 3600-2950 BP) in Spain. LTA was a single burial and LTB contained three skeletal remains of two adults and a newborn or foetus at term. AIM: The central question posed by this find was whether the LTB tomb constituted a traditional nuclear family (father, mother and son or daughter). METHODS: Ancient and forensic DNA protocols were employed to obtain reliable results. Autosomal, X-STR markers and mitochondrial DNA were amplified. Subsequently, different kinship probabilities were estimated by means of LR values calculated using the Familias 3 software. Furthermore, an allelic dropout sensitivity test was developed in order to evaluate the influence of allelic dropout phenomena on the results. RESULTS: It was possible to determine the molecular sex of all individuals and to establish a maternal relationship between the perinatal individual and one of the adults. CONCLUSION: The remains in the LTB tomb were not a traditional nuclear family (father, mother and son/daughter) and it was probably a tomb where two women, one of them pregnant, were buried. FAU - Palomo-Díez, Sara AU - Palomo-Díez S AUID- ORCID: 0000-0003-1559-2291 AD - a Laboratory of Forensic and Population Genetics, Toxicology and Health Legislation Department , Medicine School, Complutense University of Madrid , Madrid , Spain. AD - b Department of Prehistory, Ancient History and Archaeology , University of Salamanca , Salamanca , Spain. FAU - Esparza Arroyo, Ángel AU - Esparza Arroyo Á AUID- ORCID: 0000-0002-9139-0774 AD - b Department of Prehistory, Ancient History and Archaeology , University of Salamanca , Salamanca , Spain. FAU - Tirado-Vizcaíno, Mirian AU - Tirado-Vizcaíno M AD - a Laboratory of Forensic and Population Genetics, Toxicology and Health Legislation Department , Medicine School, Complutense University of Madrid , Madrid , Spain. FAU - Velasco Vázquez, Javier AU - Velasco Vázquez J AD - c Department of Historical Sciences , University of Las Palmas de Gran Canaria , Las Palmas , Spain. FAU - López-Parra, Ana María AU - López-Parra AM AUID- ORCID: 0000-0001-8974-1005 AD - a Laboratory of Forensic and Population Genetics, Toxicology and Health Legislation Department , Medicine School, Complutense University of Madrid , Madrid , Spain. FAU - Gomes, Cláudia AU - Gomes C AUID- ORCID: 0000-0001-9748-9743 AD - a Laboratory of Forensic and Population Genetics, Toxicology and Health Legislation Department , Medicine School, Complutense University of Madrid , Madrid , Spain. FAU - Baeza-Richer, Carlos AU - Baeza-Richer C AUID- ORCID: 0000-0002-0009-7055 AD - a Laboratory of Forensic and Population Genetics, Toxicology and Health Legislation Department , Medicine School, Complutense University of Madrid , Madrid , Spain. FAU - Arroyo-Pardo, Eduardo AU - Arroyo-Pardo E AUID- ORCID: 0000-0003-1851-0589 AD - a Laboratory of Forensic and Population Genetics, Toxicology and Health Legislation Department , Medicine School, Complutense University of Madrid , Madrid , Spain. LA - eng PT - Journal Article DEP - 20180720 PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - Adolescent MH - Adult MH - Archaeology MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*analysis MH - Family MH - *Family Relations MH - Female MH - Fetus MH - Genetic Markers MH - Humans MH - Infant, Newborn MH - Male MH - Microsatellite Repeats/*genetics MH - Spain MH - Young Adult OTO - NOTNLM OT - Ancient DNA OT - Iberian Bronze Age OT - biological relationships OT - low template DNA OT - multiple burial EDAT- 2018/07/22 06:00 MHDA- 2019/01/08 06:00 CRDT- 2018/07/21 06:00 PHST- 2018/07/22 06:00 [pubmed] PHST- 2019/01/08 06:00 [medline] PHST- 2018/07/21 06:00 [entrez] AID - 10.1080/03014460.2018.1484159 [doi] PST - ppublish SO - Ann Hum Biol. 2018 Jun;45(4):365-368. doi: 10.1080/03014460.2018.1484159. Epub 2018 Jul 20. PMID- 29939091 OWN - NLM STAT- MEDLINE DCOM- 20190530 LR - 20190530 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 64 IP - 6 DP - 2018 Jun TI - A stainless-steel mortar, pestle and sleeve design for the efficient fragmentation of ancient bone. PG - 266-269 LID - 10.2144/btn-2018-0008 [doi] AB - Different types of milling equipment - such as oscillating ball mills, freezer mills, mortar and pestle - can be used to fragment ancient bone prior to DNA extraction. However, each of these tools is associated with practical drawbacks. Here, we present the design for a stainless-steel mortar and pestle, with a removable sleeve to contain bone material. The tool is easy to clean, practical and its simplicity allows university workshops equipped with a lathe, boring tools and a milling machine to make these components at local expense. This design allows for the efficient fragmentation of ancient bone and improves sample throughput. This design is recommended as a useful, economical addition to existing laboratory equipment for the handling of ancient bone. FAU - Gondek, Agata T AU - Gondek AT AD - Centre for Ecological & Evolutionary Synthesis (CEES), Department of Biosciences (IBV), University of Oslo (UIO), Blindern, NO-0316 Oslo, Norway. FAU - Boessenkool, Sanne AU - Boessenkool S AD - Centre for Ecological & Evolutionary Synthesis (CEES), Department of Biosciences (IBV), University of Oslo (UIO), Blindern, NO-0316 Oslo, Norway. FAU - Star, Bastiaan AU - Star B AD - Centre for Ecological & Evolutionary Synthesis (CEES), Department of Biosciences (IBV), University of Oslo (UIO), Blindern, NO-0316 Oslo, Norway. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Bone and Bones/*chemistry MH - DNA, Ancient/analysis/*isolation & purification MH - Equipment Design MH - Genetic Techniques/*instrumentation MH - Humans MH - Specimen Handling/*instrumentation OTO - NOTNLM OT - ancient DNA OT - bleach OT - bone OT - crushing OT - extraction OT - homogenize OT - pulverize OT - stainless steel EDAT- 2018/06/26 06:00 MHDA- 2019/05/31 06:00 CRDT- 2018/06/26 06:00 PHST- 2018/06/26 06:00 [entrez] PHST- 2018/06/26 06:00 [pubmed] PHST- 2019/05/31 06:00 [medline] AID - 10.2144/btn-2018-0008 [doi] PST - ppublish SO - Biotechniques. 2018 Jun;64(6):266-269. doi: 10.2144/btn-2018-0008. PMID- 29768437 OWN - NLM STAT- MEDLINE DCOM- 20180806 LR - 20181114 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 13 IP - 5 DP - 2018 TI - Oral health status in historic population: Macroscopic and metagenomic evidence. PG - e0196482 LID - 10.1371/journal.pone.0196482 [doi] LID - e0196482 AB - Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual. FAU - Willmann, Claire AU - Willmann C AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France. AD - Service d'odontologie de l'Hôtel-Dieu, Toulouse, France. FAU - Mata, Xavier AU - Mata X AUID- ORCID: 0000-0001-8484-2528 AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France. FAU - Hanghoej, Kristian AU - Hanghoej K AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France. AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. FAU - Tonasso, Laure AU - Tonasso L AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France. FAU - Tisseyre, Lenka AU - Tisseyre L AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France. FAU - Jeziorski, Céline AU - Jeziorski C AD - INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France. FAU - Cabot, Elodie AU - Cabot E AD - Institut National de Recherches Archéologiques Préventives, INRAP Grand Ouest, Cesson-Sévigné, France. AD - Anthropologie Bio-Culturelle, Droit, Ethique et Santé, Faculté de Médecine Site Nord (UMR 7268), Marseille, France. FAU - Chevet, Pierre AU - Chevet P AD - Institut National de Recherches Archéologiques Préventives, INRAP Grand Ouest, Cesson-Sévigné, France. FAU - Crubézy, Eric AU - Crubézy E AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France. FAU - Orlando, Ludovic AU - Orlando L AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France. AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. FAU - Esclassan, Rémi AU - Esclassan R AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France. AD - Service d'odontologie de l'Hôtel-Dieu, Toulouse, France. FAU - Thèves, Catherine AU - Thèves C AD - Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180516 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Ancient/isolation & purification MH - DNA, Bacterial/genetics/history/isolation & purification MH - Dental Caries/history/microbiology/pathology MH - Female MH - France MH - Health Status MH - History, 18th Century MH - Humans MH - Male MH - Metagenomics MH - Microbiota/genetics MH - Oral Health/*history MH - Paleodontology MH - Periodontitis/history/microbiology/pathology MH - Rural Population/history PMC - PMC5955521 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2018/05/17 06:00 MHDA- 2018/08/07 06:00 PMCR- 2018/05/16 CRDT- 2018/05/17 06:00 PHST- 2017/06/14 00:00 [received] PHST- 2018/04/13 00:00 [accepted] PHST- 2018/05/17 06:00 [entrez] PHST- 2018/05/17 06:00 [pubmed] PHST- 2018/08/07 06:00 [medline] PHST- 2018/05/16 00:00 [pmc-release] AID - PONE-D-17-22695 [pii] AID - 10.1371/journal.pone.0196482 [doi] PST - epublish SO - PLoS One. 2018 May 16;13(5):e0196482. doi: 10.1371/journal.pone.0196482. eCollection 2018. PMID- 29746563 OWN - NLM STAT- MEDLINE DCOM- 20180618 LR - 20181114 IS - 1553-7374 (Electronic) IS - 1553-7366 (Print) IS - 1553-7366 (Linking) VI - 14 IP - 5 DP - 2018 May TI - Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe. PG - e1006997 LID - 10.1371/journal.ppat.1006997 [doi] LID - e1006997 AB - Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide. FAU - Schuenemann, Verena J AU - Schuenemann VJ AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Avanzi, Charlotte AU - Avanzi C AUID- ORCID: 0000-0002-1062-4058 AD - Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AUID- ORCID: 0000-0001-9435-2872 AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Seitz, Alexander AU - Seitz A AUID- ORCID: 0000-0001-9626-2571 AD - Center for Bioinformatics, University of Tübingen, Tübingen, Germany. FAU - Herbig, Alexander AU - Herbig A AUID- ORCID: 0000-0003-1176-1166 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Inskip, Sarah AU - Inskip S AUID- ORCID: 0000-0001-7424-2094 AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom. FAU - Bonazzi, Marion AU - Bonazzi M AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Reiter, Ella AU - Reiter E AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Urban, Christian AU - Urban C AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Dangvard Pedersen, Dorthe AU - Dangvard Pedersen D AUID- ORCID: 0000-0002-4709-9170 AD - Unit of Anthropology (ADBOU), Department of Forensic Medicine, University of Southern Denmark, Odense S, Denmark. FAU - Taylor, G Michael AU - Taylor GM AD - Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom. FAU - Singh, Pushpendra AU - Singh P AUID- ORCID: 0000-0001-9453-8669 AD - Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. AD - Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, India. FAU - Stewart, Graham R AU - Stewart GR AUID- ORCID: 0000-0002-6867-6248 AD - Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom. FAU - Velemínský, Petr AU - Velemínský P AD - Department of Anthropology, National Museum, Prague, Czech Republic. FAU - Likovsky, Jakub AU - Likovsky J AD - Department of Archaeology of Landscape and Archaeobiology, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic. FAU - Marcsik, Antónia AU - Marcsik A AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Molnár, Erika AU - Molnár E AUID- ORCID: 0000-0001-6660-9239 AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Mariotti, Valentina AU - Mariotti V AUID- ORCID: 0000-0002-6956-781X AD - Department of Biological, Geological and Environmental Sciences, Bologna, Italy. AD - ADES AMU-CNRS- EFS: Anthropology and Health, Aix-Marseille Université, Marseille, France. FAU - Riga, Alessandro AU - Riga A AUID- ORCID: 0000-0002-7240-0009 AD - Department of Biology, University of Florence, Firenze, Italy. FAU - Belcastro, M Giovanna AU - Belcastro MG AUID- ORCID: 0000-0002-8932-8509 AD - Department of Biological, Geological and Environmental Sciences, Bologna, Italy. AD - ADES AMU-CNRS- EFS: Anthropology and Health, Aix-Marseille Université, Marseille, France. FAU - Boldsen, Jesper L AU - Boldsen JL AD - Unit of Anthropology (ADBOU), Department of Forensic Medicine, University of Southern Denmark, Odense S, Denmark. FAU - Nebel, Almut AU - Nebel A AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Mays, Simon AU - Mays S AD - Historic England, Portsmouth, United Kingdom. FAU - Donoghue, Helen D AU - Donoghue HD AUID- ORCID: 0000-0003-3918-5252 AD - Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom. FAU - Zakrzewski, Sonia AU - Zakrzewski S AUID- ORCID: 0000-0003-1796-065X AD - Department of Archaeology, University of Southampton, Southampton, United Kingdom. FAU - Benjak, Andrej AU - Benjak A AD - Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. FAU - Nieselt, Kay AU - Nieselt K AUID- ORCID: 0000-0002-1283-7065 AD - Center for Bioinformatics, University of Tübingen, Tübingen, Germany. FAU - Cole, Stewart T AU - Cole ST AUID- ORCID: 0000-0003-1400-5585 AD - Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. AD - Institut Pasteur, Paris, France. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180510 PL - United States TA - PLoS Pathog JT - PLoS pathogens JID - 101238921 RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Bacterial/genetics/history MH - Europe/epidemiology MH - Evolution, Molecular MH - Genetic Variation MH - Genome, Bacterial MH - History, Medieval MH - Host-Pathogen Interactions/genetics MH - Humans MH - Leprosy/epidemiology/*history/microbiology MH - Mycobacterium leprae/classification/*genetics/pathogenicity MH - Phylogeny MH - Phylogeography MH - Polymorphism, Single Nucleotide PMC - PMC5944922 COIS- The authors have declared that no competing interests exist. EDAT- 2018/05/11 06:00 MHDA- 2018/06/19 06:00 PMCR- 2018/05/10 CRDT- 2018/05/11 06:00 PHST- 2017/11/14 00:00 [received] PHST- 2018/03/28 00:00 [accepted] PHST- 2018/05/11 06:00 [entrez] PHST- 2018/05/11 06:00 [pubmed] PHST- 2018/06/19 06:00 [medline] PHST- 2018/05/10 00:00 [pmc-release] AID - PPATHOGENS-D-17-02430 [pii] AID - 10.1371/journal.ppat.1006997 [doi] PST - epublish SO - PLoS Pathog. 2018 May 10;14(5):e1006997. doi: 10.1371/journal.ppat.1006997. eCollection 2018 May. PMID- 29745896 OWN - NLM STAT- MEDLINE DCOM- 20190515 LR - 20190524 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 7 DP - 2018 May 10 TI - Neolithic and medieval virus genomes reveal complex evolution of hepatitis B. LID - 10.7554/eLife.36666 [doi] LID - e36666 AB - The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genome by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results demonstrated that HBV has circulated in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. The ancient viruses appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses. CI - © 2018, Krause-Kyora et al. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AUID- ORCID: 0000-0001-9435-2872 AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Susat, Julian AU - Susat J AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Key, Felix M AU - Key FM AUID- ORCID: 0000-0003-2812-6636 AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Kühnert, Denise AU - Kühnert D AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland. FAU - Bosse, Esther AU - Bosse E AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. AD - Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany. FAU - Immel, Alexander AU - Immel A AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Rinne, Christoph AU - Rinne C AD - Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany. FAU - Kornell, Sabin-Christin AU - Kornell SC AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Yepes, Diego AU - Yepes D AD - Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany. FAU - Franzenburg, Sören AU - Franzenburg S AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Heyne, Henrike O AU - Heyne HO AD - Stanley Center for Psychiatric Research, Broad Institute, Cambridge, United States. AD - Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, United States. AD - Program in Medical and Population Genetics, Broad Institute of MIT & Harvard, Cambridge, United States. FAU - Meier, Thomas AU - Meier T AD - Institute for Pre- and Protohistory and Near Eastern Archaeology, Heidelberg University, Heidelberg, Germany. AD - Heidelberg Center for the Environment, Heidelberg University, Heidelberg, Germany. FAU - Lösch, Sandra AU - Lösch S AD - Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland. FAU - Meller, Harald AU - Meller H AD - State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany. FAU - Friederich, Susanne AU - Friederich S AD - State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany. FAU - Nicklisch, Nicole AU - Nicklisch N AD - State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany. AD - Danube Private University, Krems, Austria. FAU - Alt, Kurt W AU - Alt KW AD - State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany. AD - Danube Private University, Krems, Austria. AD - Department of Biomedical Engineering, University Hospital Basel, University of Basel, Basel, Switzerland. AD - Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland. FAU - Schreiber, Stefan AU - Schreiber S AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. AD - Clinic for Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany. FAU - Tholey, Andreas AU - Tholey A AD - Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany. FAU - Herbig, Alexander AU - Herbig A AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Nebel, Almut AU - Nebel A AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Max Planck Institute for the Science of Human History, Jena, Germany. LA - eng GR - PMPDP3_171320/1/Swiss National Science Foundation/Switzerland GR - APGREID/European Research Council/International PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180510 PL - England TA - Elife JT - eLife JID - 101579614 RN - 0 (Proteome) RN - 0 (Viral Proteins) SB - IM MH - *Evolution, Molecular MH - Fossils/*virology MH - *Genome, Viral MH - Germany MH - Hepatitis B virus/classification/*genetics/isolation & purification MH - Humans MH - Phylogeny MH - Proteome/analysis MH - Sequence Analysis, DNA MH - Skeleton/chemistry/virology MH - Viral Proteins/analysis PMC - PMC6008052 OTO - NOTNLM OT - ancient DNA OT - ancient pathogens OT - genetics OT - genomics OT - hepatitis B OT - human evolution OT - infectious disease OT - microbiology OT - next generation sequencing OT - virus evolution COIS- BK, JS, FK, DK, EB, AI, CR, SK, DY, SF, HH, TM, SL, HM, SF, NN, KA, SS, AT, AH, AN, JK No competing interests declared EDAT- 2018/05/11 06:00 MHDA- 2019/05/16 06:00 PMCR- 2018/05/10 CRDT- 2018/05/11 06:00 PHST- 2018/03/14 00:00 [received] PHST- 2018/05/09 00:00 [accepted] PHST- 2018/05/11 06:00 [pubmed] PHST- 2019/05/16 06:00 [medline] PHST- 2018/05/11 06:00 [entrez] PHST- 2018/05/10 00:00 [pmc-release] AID - 36666 [pii] AID - 10.7554/eLife.36666 [doi] PST - epublish SO - Elife. 2018 May 10;7:e36666. doi: 10.7554/eLife.36666. PMID- 29738726 OWN - NLM STAT- MEDLINE DCOM- 20190911 LR - 20190911 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 28 IP - 9 DP - 2018 May 7 TI - Human Genetics: Busy Subway Networks in Remote Oceania? PG - R549-R551 LID - S0960-9822(18)30362-2 [pii] LID - 10.1016/j.cub.2018.03.033 [doi] AB - Ancient human DNA from the Oceanian islands of Vanuatu reveals a surprisingly complex history of human settlement, featuring almost complete replacement shortly after initial colonisation, followed by mixing and a puzzling disconnect between genetic ancestry and language. CI - Copyright © 2018 Elsevier Ltd. All rights reserved. FAU - Bergström, Anders AU - Bergström A AD - The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. Electronic address: ab34@sanger.ac.uk. FAU - Tyler-Smith, Chris AU - Tyler-Smith C AD - The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. LA - eng PT - Comment PT - Journal Article PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM CON - Nat Ecol Evol. 2018 Apr;2(4):731-740. doi: 10.1038/s41559-018-0498-2. PMID: 29487365 CON - Curr Biol. 2018 Apr 2;28(7):1157-1165.e7. doi: 10.1016/j.cub.2018.02.051. PMID: 29501328 MH - Animals MH - Humans MH - Islands MH - *Language MH - Oceania MH - Population Dynamics MH - *Railroads EDAT- 2018/05/09 06:00 MHDA- 2019/09/12 06:00 CRDT- 2018/05/09 06:00 PHST- 2018/05/09 06:00 [entrez] PHST- 2018/05/09 06:00 [pubmed] PHST- 2019/09/12 06:00 [medline] AID - S0960-9822(18)30362-2 [pii] AID - 10.1016/j.cub.2018.03.033 [doi] PST - ppublish SO - Curr Biol. 2018 May 7;28(9):R549-R551. doi: 10.1016/j.cub.2018.03.033. PMID- 29723195 OWN - NLM STAT- MEDLINE DCOM- 20180626 LR - 20201214 IS - 1553-7404 (Electronic) IS - 1553-7390 (Print) IS - 1553-7390 (Linking) VI - 14 IP - 5 DP - 2018 May TI - Human local adaptation of the TRPM8 cold receptor along a latitudinal cline. PG - e1007298 LID - 10.1371/journal.pgen.1007298 [doi] LID - e1007298 AB - Ambient temperature is a critical environmental factor for all living organisms. It was likely an important selective force as modern humans recently colonized temperate and cold Eurasian environments. Nevertheless, as of yet we have limited evidence of local adaptation to ambient temperature in populations from those environments. To shed light on this question, we exploit the fact that humans are a cosmopolitan species that inhabit territories under a wide range of temperatures. Focusing on cold perception-which is central to thermoregulation and survival in cold environments-we show evidence of recent local adaptation on TRPM8. This gene encodes for a cation channel that is, to date, the only temperature receptor known to mediate an endogenous response to moderate cold. The upstream variant rs10166942 shows extreme population differentiation, with frequencies that range from 5% in Nigeria to 88% in Finland (placing this SNP in the 0.02% tail of the FST empirical distribution). When all populations are jointly analyzed, allele frequencies correlate with latitude and temperature beyond what can be explained by shared ancestry and population substructure. Using a Bayesian approach, we infer that the allele originated and evolved neutrally in Africa, while positive selection raised its frequency to different degrees in Eurasian populations, resulting in allele frequencies that follow a latitudinal cline. We infer strong positive selection, in agreement with ancient DNA showing high frequency of the allele in Europe 3,000 to 8,000 years ago. rs10166942 is important phenotypically because its ancestral allele is protective of migraine. This debilitating disorder varies in prevalence across human populations, with highest prevalence in individuals of European descent-precisely the population with the highest frequency of rs10166942 derived allele. We thus hypothesize that local adaptation on previously neutral standing variation may have contributed to the genetic differences that exist in the prevalence of migraine among human populations today. FAU - Key, Felix M AU - Key FM AUID- ORCID: 0000-0003-2812-6636 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Abdul-Aziz, Muslihudeen A AU - Abdul-Aziz MA AUID- ORCID: 0000-0001-5600-0972 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Mundry, Roger AU - Mundry R AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Peter, Benjamin M AU - Peter BM AD - Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America. FAU - Sekar, Aarthi AU - Sekar A AD - Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, California, United States of America. FAU - D'Amato, Mauro AU - D'Amato M AD - BioDonostia Health Research Institute and IKERBASQUE, Basque Foundation for Science, San Sebastian, Spain. FAU - Dennis, Megan Y AU - Dennis MY AD - Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, California, United States of America. FAU - Schmidt, Joshua M AU - Schmidt JM AUID- ORCID: 0000-0002-5862-7389 AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Andrés, Aida M AU - Andrés AM AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom. LA - eng GR - R01 HG007089/NH/NIH HHS/United States GR - R00 NS083627/NS/NINDS NIH HHS/United States GR - R01 HG007089/HG/NHGRI NIH HHS/United States GR - T32 GM007377/GM/NIGMS NIH HHS/United States GR - R00NS083627/NH/NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20180503 PL - United States TA - PLoS Genet JT - PLoS genetics JID - 101239074 RN - 0 (TRPM Cation Channels) RN - 0 (TRPM8 protein, human) SB - IM MH - Adaptation, Physiological/*genetics MH - Africa MH - Asia MH - Bayes Theorem MH - *Cold Temperature MH - Europe MH - Gene Expression Profiling MH - Gene Frequency MH - Genetics, Population/statistics & numerical data MH - Genotype MH - Humans MH - Linkage Disequilibrium MH - *Polymorphism, Single Nucleotide MH - Selection, Genetic MH - TRPM Cation Channels/*genetics PMC - PMC5933706 COIS- The authors have declared that no competing interests exist. EDAT- 2018/05/04 06:00 MHDA- 2018/06/27 06:00 PMCR- 2018/05/03 CRDT- 2018/05/04 06:00 PHST- 2017/11/30 00:00 [received] PHST- 2018/03/07 00:00 [accepted] PHST- 2018/05/04 06:00 [entrez] PHST- 2018/05/04 06:00 [pubmed] PHST- 2018/06/27 06:00 [medline] PHST- 2018/05/03 00:00 [pmc-release] AID - PGENETICS-D-17-02331 [pii] AID - 10.1371/journal.pgen.1007298 [doi] PST - epublish SO - PLoS Genet. 2018 May 3;14(5):e1007298. doi: 10.1371/journal.pgen.1007298. eCollection 2018 May. PMID- 29706345 OWN - NLM STAT- MEDLINE DCOM- 20181211 LR - 20241109 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 102 IP - 5 DP - 2018 May 3 TI - Patterns of Genetic Coding Variation in a Native American Population before and after European Contact. PG - 806-815 LID - S0002-9297(18)30097-1 [pii] LID - 10.1016/j.ajhg.2018.03.008 [doi] AB - The effects of European colonization on the genomes of Native Americans may have produced excesses of potentially deleterious features, mainly due to the severe reductions in population size and corresponding losses of genetic diversity. This assumption, however, neither considers actual genomic patterns that existed before colonization nor does it adequately capture the effects of admixture. In this study, we analyze the whole-exome sequences of modern and ancient individuals from a Northwest Coast First Nation, with a demographic history similar to other indigenous populations from the Americas. We show that in approximately ten generations from initial European contact, the modern individuals exhibit reduced levels of novel and low-frequency variants, a lower proportion of potentially deleterious alleles, and decreased heterozygosity when compared to their ancestors. This pattern can be explained by a dramatic population decline, resulting in the loss of potentially damaging low-frequency variants, and subsequent admixture. We also find evidence that the indigenous population was on a steady decline in effective population size for several thousand years before contact, which emphasizes regional demography over the common conception of a uniform expansion after entry into the Americas. This study examines the genomic consequences of colonialism on an indigenous group and describes the continuing role of gene flow among modern populations. CI - Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. FAU - Lindo, John AU - Lindo J AD - Department of Anthropology, Emory University, Atlanta, GA 30322, USA. FAU - Rogers, Mary AU - Rogers M AD - Department of Anthropology, University of Illinois, Urbana, IL 61821, USA. FAU - Mallott, Elizabeth K AU - Mallott EK AD - Department of Anthropology, Northwestern University, Evanston, IL 60208, USA. FAU - Petzelt, Barbara AU - Petzelt B AD - Metlakatla Treaty Office, Prince Rupert, BC V8J 3P6, Canada. FAU - Mitchell, Joycelynn AU - Mitchell J AD - Metlakatla Treaty Office, Prince Rupert, BC V8J 3P6, Canada. FAU - Archer, David AU - Archer D AD - Department of Anthropology, Northwestern Community College, Prince Rupert, BC V8J 3P6, Canada. FAU - Cybulski, Jerome S AU - Cybulski JS AD - Research, Canadian Museum of History, Gatineau, QC K1A 0M8, Canada; Department of Anthropology, University of Western Ontario, London, ON N6A 3K7, Canada; Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada. FAU - Malhi, Ripan S AU - Malhi RS AD - Department of Anthropology, University of Illinois, Urbana, IL 61821, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61820, USA. Electronic address: malhi@illinois.edu. FAU - DeGiorgio, Michael AU - DeGiorgio M AD - Departments of Biology and Statistics, Pennsylvania State University, University Park, PA 16801, USA; Institute for CyberScience, Pennsylvania State University, University Park, PA 16801, USA. Electronic address: mxd60@psu.edu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20180426 PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 SB - IM MH - Base Pairing/genetics MH - Gene Frequency/genetics MH - Gene Pool MH - *Genetic Variation MH - Heterozygote MH - Humans MH - Indians, North American/*genetics MH - Polymorphism, Single Nucleotide/genetics MH - Time Factors MH - White People/*genetics PMC - PMC5986697 OTO - NOTNLM OT - First Nation OT - admixture OT - ancient DNA OT - collapse OT - colonialism OT - effective size EDAT- 2018/05/01 06:00 MHDA- 2018/12/12 06:00 PMCR- 2018/11/03 CRDT- 2018/05/01 06:00 PHST- 2017/11/27 00:00 [received] PHST- 2018/03/05 00:00 [accepted] PHST- 2018/05/01 06:00 [pubmed] PHST- 2018/12/12 06:00 [medline] PHST- 2018/05/01 06:00 [entrez] PHST- 2018/11/03 00:00 [pmc-release] AID - S0002-9297(18)30097-1 [pii] AID - 10.1016/j.ajhg.2018.03.008 [doi] PST - ppublish SO - Am J Hum Genet. 2018 May 3;102(5):806-815. doi: 10.1016/j.ajhg.2018.03.008. Epub 2018 Apr 26. PMID- 29717136 OWN - NLM STAT- MEDLINE DCOM- 20181211 LR - 20221207 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 9 IP - 1 DP - 2018 May 1 TI - Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans. PG - 1569 LID - 10.1038/s41467-018-03857-x [doi] LID - 1569 AB - Leprosy, a chronic infectious disease caused by Mycobacterium leprae (M. leprae), was very common in Europe till the 16th century. Here, we perform an ancient DNA study on medieval skeletons from Denmark that show lesions specific for lepromatous leprosy (LL). First, we test the remains for M. leprae DNA to confirm the infection status of the individuals and to assess the bacterial diversity. We assemble 10 complete M. leprae genomes that all differ from each other. Second, we evaluate whether the human leukocyte antigen allele DRB1*15:01, a strong LL susceptibility factor in modern populations, also predisposed medieval Europeans to the disease. The comparison of genotype data from 69 M. leprae DNA-positive LL cases with those from contemporary and medieval controls reveals a statistically significant association in both instances. In addition, we observe that DRB1*15:01 co-occurs with DQB1*06:02 on a haplotype that is a strong risk factor for inflammatory diseases today. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AUID- ORCID: 0000-0001-9435-2872 AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. b.krause-kyora@ikmb.uni-kiel.de. AD - Max Planck Institute for the Science of Human History, Jena, 07745, Germany. b.krause-kyora@ikmb.uni-kiel.de. FAU - Nutsua, Marcel AU - Nutsua M AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. FAU - Boehme, Lisa AU - Boehme L AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. FAU - Pierini, Federica AU - Pierini F AD - Department of Evolutionary Ecology, Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany. FAU - Pedersen, Dorthe Dangvard AU - Pedersen DD AUID- ORCID: 0000-0002-4709-9170 AD - Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark. FAU - Kornell, Sabin-Christin AU - Kornell SC AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. FAU - Drichel, Dmitriy AU - Drichel D AD - Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany. FAU - Bonazzi, Marion AU - Bonazzi M AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. FAU - Möbus, Lena AU - Möbus L AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. FAU - Tarp, Peter AU - Tarp P AD - Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark. FAU - Susat, Julian AU - Susat J AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. FAU - Bosse, Esther AU - Bosse E AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. FAU - Willburger, Beatrix AU - Willburger B AD - DKMS, Tübingen, 72072, Germany. FAU - Schmidt, Alexander H AU - Schmidt AH AD - DKMS, Tübingen, 72072, Germany. FAU - Sauter, Jürgen AU - Sauter J AD - DKMS, Tübingen, 72072, Germany. FAU - Franke, Andre AU - Franke A AUID- ORCID: 0000-0003-1530-5811 AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. FAU - Wittig, Michael AU - Wittig M AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. FAU - Caliebe, Amke AU - Caliebe A AD - Institute of Medical Informatics and Statistics, Kiel University, Kiel, 24105, Germany. FAU - Nothnagel, Michael AU - Nothnagel M AUID- ORCID: 0000-0001-8305-7114 AD - Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany. FAU - Schreiber, Stefan AU - Schreiber S AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. AD - Clinic for Internal Medicine, University Hospital of Schleswig-Holstein, Kiel, 24105, Germany. FAU - Boldsen, Jesper L AU - Boldsen JL AD - Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark. FAU - Lenz, Tobias L AU - Lenz TL AD - Department of Evolutionary Ecology, Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany. FAU - Nebel, Almut AU - Nebel A AD - Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180501 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) RN - 0 (HLA-DQ beta-Chains) RN - 0 (HLA-DQB1 antigen) RN - 0 (HLA-DRB1 Chains) SB - IM MH - *DNA, Ancient MH - DNA, Bacterial/genetics MH - Denmark MH - Fossils MH - *Genetic Predisposition to Disease MH - Genome, Bacterial MH - HLA-DQ beta-Chains/genetics MH - HLA-DRB1 Chains/genetics MH - High-Throughput Screening Assays MH - Humans MH - Leprosy/*genetics MH - Mycobacterium leprae/genetics MH - White People/*genetics PMC - PMC5931558 COIS- The authors declare no competing interests. EDAT- 2018/05/03 06:00 MHDA- 2018/12/12 06:00 PMCR- 2018/05/01 CRDT- 2018/05/03 06:00 PHST- 2017/07/14 00:00 [received] PHST- 2018/03/16 00:00 [accepted] PHST- 2018/05/03 06:00 [entrez] PHST- 2018/05/03 06:00 [pubmed] PHST- 2018/12/12 06:00 [medline] PHST- 2018/05/01 00:00 [pmc-release] AID - 10.1038/s41467-018-03857-x [pii] AID - 3857 [pii] AID - 10.1038/s41467-018-03857-x [doi] PST - epublish SO - Nat Commun. 2018 May 1;9(1):1569. doi: 10.1038/s41467-018-03857-x. PMID- 29609050 OWN - NLM STAT- MEDLINE DCOM- 20180524 LR - 20180524 IS - 1878-7487 (Electronic) IS - 1752-928X (Linking) VI - 56 DP - 2018 May TI - Poisoning histories in the Italian renaissance: The case of Pico Della Mirandola and Angelo Poliziano. PG - 83-89 LID - S1752-928X(18)30154-9 [pii] LID - 10.1016/j.jflm.2018.03.016 [doi] AB - Giovanni Pico della Mirandola and Angelo Poliziano were two of the most important humanists of the Italian Renaissance. They died suddenly in 1494 and their deaths have been for centuries a subject of debate. The exhumation of their remains offered the opportunity to study the cause of their death through a multidisciplinary research project. Anthropological analyses, together with documentary evidences, radiocarbon dating and ancient DNA analysis supported the identification of the remains attributed to Pico. Macroscopic examination did not reveal paleopathological lesions or signs related to syphilis. Heavy metals analysis, carried out on bones and mummified tissues, showed that in Pico's remains there were potentially lethal levels of arsenic, supporting the philosopher's poisoning theory reported by documentary sources. The arsenic concentrations obtained from analysis of Poliziano's remains, are probably more related to an As chronic exposure or diagenetic processes rather than poisoning. CI - Copyright © 2018 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved. FAU - Gallello, Gianni AU - Gallello G AD - Department of Archaeology, University of York, King's Manor, Exhibition Square, YO1 7EP, York, UK. Electronic address: gianni.gallello@york.ac.uk. FAU - Cilli, Elisabetta AU - Cilli E AD - Department of Cultural Heritage, Alma Mater Studiorum University of Bologna, 1 Ariani Street, 48121 Ravenna, Italy. FAU - Bartoli, Fulvio AU - Bartoli F AD - Department of Biology University of Pisa, 13 Luca Ghini Street, 56126 Pisa, Italy. FAU - Andretta, Massimo AU - Andretta M AD - School of Engineering and Architecture, Alma Mater Studiorum University of Bologna, CIRSA, 163 S. Alberto Street, 40123 Ravenna, Italy. FAU - Calcagnile, Lucio AU - Calcagnile L AD - Department of Mathematics and Physics "Ennio De Giorgi", University of Salento, Via per Arnesano Street, 73100 Lecce, Italy. FAU - Pastor, Agustin AU - Pastor A AD - Department of Analytical Chemistry University of Valencia, 50 Dr. Moliner Street, 46100 Burjassot, Valencia, Spain. FAU - de la Guardia, Miguel AU - de la Guardia M AD - Department of Analytical Chemistry University of Valencia, 50 Dr. Moliner Street, 46100 Burjassot, Valencia, Spain. FAU - Serventi, Patrizia AU - Serventi P AD - Department of Cultural Heritage, Alma Mater Studiorum University of Bologna, 1 Ariani Street, 48121 Ravenna, Italy; Department of Biological, Geological & Environmental Sciences, Alma Mater Studiorum University of Bologna, 3 Selmi Street, Bologna, Italy. FAU - Marino, Alberto AU - Marino A AD - Reparto Investigazioni Scientifiche (RIS), Arma dei Carabinieri, Parma, Italy. FAU - Benazzi, Stefano AU - Benazzi S AD - Department of Cultural Heritage, Alma Mater Studiorum University of Bologna, 1 Ariani Street, 48121 Ravenna, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Gruppioni, Giorgio AU - Gruppioni G AD - Department of Cultural Heritage, Alma Mater Studiorum University of Bologna, 1 Ariani Street, 48121 Ravenna, Italy. LA - eng PT - Historical Article PT - Journal Article DEP - 20180328 PL - England TA - J Forensic Leg Med JT - Journal of forensic and legal medicine JID - 101300022 RN - 0 (Carbon Radioisotopes) RN - 0 (DNA, Ancient) RN - N712M78A8G (Arsenic) SB - IM MH - Arsenic/*analysis MH - Arsenic Poisoning/*history MH - Bone and Bones/*chemistry MH - Carbon Radioisotopes MH - DNA, Ancient MH - Environmental Exposure/adverse effects MH - Forensic Toxicology MH - History, 15th Century MH - Humans MH - Italy MH - Male MH - Microscopy MH - Microscopy, Electron, Scanning MH - Mummies MH - Spectrum Analysis/methods OTO - NOTNLM OT - Ancient DNA OT - Angelo Poliziano OT - Arsenic poisoning OT - Girolamo benivieni OT - Pico della Mirandola OT - Radiocarbon dating EDAT- 2018/04/03 06:00 MHDA- 2018/05/25 06:00 CRDT- 2018/04/03 06:00 PHST- 2017/11/21 00:00 [received] PHST- 2018/03/10 00:00 [revised] PHST- 2018/03/27 00:00 [accepted] PHST- 2018/04/03 06:00 [pubmed] PHST- 2018/05/25 06:00 [medline] PHST- 2018/04/03 06:00 [entrez] AID - S1752-928X(18)30154-9 [pii] AID - 10.1016/j.jflm.2018.03.016 [doi] PST - ppublish SO - J Forensic Leg Med. 2018 May;56:83-89. doi: 10.1016/j.jflm.2018.03.016. Epub 2018 Mar 28. PMID- 29399779 OWN - NLM STAT- MEDLINE DCOM- 20181228 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 166 IP - 1 DP - 2018 May TI - Archaeogenetics of Late Iron Age Çemialo Sırtı, Batman: Investigating maternal genetic continuity in north Mesopotamia since the Neolithic. PG - 196-207 LID - 10.1002/ajpa.23423 [doi] AB - OBJECTIVES: North Mesopotamia has witnessed dramatic social change during the Holocene, but the impact of these events on its demographic history is poorly understood. Here, we study this question by analysing genetic data from the recently excavated Late Iron Age settlement of Çemialo Sırtı in Batman, southeast Turkey. Archaeological and radiocarbon evidence indicate that the site was inhabited during the second and first millennia BCE. Çemialo Sırtı reveals nomadic items of the Early Iron Age, as well as items associated with the Late Achaemenid and subsequent Hellenistic Periods. We compare Çemialo Sırtı mitochondrial DNA profiles with earlier and later populations from west Eurasia to describe genetic continuity patterns in the region. MATERIALS AND METHODS: A total of 16 Çemialo Sırtı individuals' remains were studied. PCR and Sanger sequencing were used to obtain mitochondrial DNA HVRI-HVRII sequences. We studied haplotype diversity and pairwise genetic distances using F(ST) , comparing the Çemialo Sırtı population with ancient and modern-day populations from west Eurasia. Coalescent simulations were carried out to test continuity for specific population comparisons. RESULTS: Mitochondrial DNA (mtDNA) haplotypes from 12 Çemialo Sırtı individuals reveal high haplotype diversity in this population, conspicuously higher than early Holocene west Eurasian populations, which supports the notion of increasing population admixture in west Eurasia through the Holocene. In its mtDNA composition, Çemialo Sırtı shows highest affinity to Neolithic north Syria and Neolithic Anatolia among ancient populations studied, and to modern-day southwest Asian populations. Based on population genetic simulations we cannot reject continuity between Neolithic and Iron Age, or between Iron Age and present-day populations of the region. DISCUSSION: Despite the region's complex sociopolitical history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian maternal genetic composition within the last 10,000 years. CI - © 2018 Wiley Periodicals, Inc. FAU - Yaka, Reyhan AU - Yaka R AUID- ORCID: 0000-0002-9359-4391 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Birand, Ayşegül AU - Birand A AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Yılmaz, Yasemin AU - Yılmaz Y AD - Department of Archaeology, Düzce University, Düzce, Turkey. FAU - Caner, Ceren AU - Caner C AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Açan, Sinan Can AU - Açan SC AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Gündüzalp, Sidar AU - Gündüzalp S AD - Department of Prehistory, İstanbul University, İstanbul, Turkey. FAU - Parvizi, Poorya AU - Parvizi P AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Erim Özdoğan, Aslı AU - Erim Özdoğan A AD - Department of Archaeology, Çanakkale Onsekiz Mart University, Çanakkale, Turkey. FAU - Togan, İnci AU - Togan İ AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. FAU - Somel, Mehmet AU - Somel M AUID- ORCID: 0000-0002-3138-1307 AD - Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180205 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Archaeology MH - Asian People/*genetics MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics MH - Female MH - Genetics, Population MH - History, Ancient MH - Humans MH - Male MH - Mesopotamia/ethnology MH - White People/genetics OTO - NOTNLM OT - Achaemenid Period OT - Lower Garzan Basin OT - Neolithic OT - ancient DNA OT - demographic history OT - mitochondrial DNA OT - north Mesopotamia OT - Çemialo Sırtı EDAT- 2018/02/06 06:00 MHDA- 2018/12/29 06:00 CRDT- 2018/02/06 06:00 PHST- 2017/08/18 00:00 [received] PHST- 2017/12/13 00:00 [revised] PHST- 2018/01/12 00:00 [accepted] PHST- 2018/02/06 06:00 [pubmed] PHST- 2018/12/29 06:00 [medline] PHST- 2018/02/06 06:00 [entrez] AID - 10.1002/ajpa.23423 [doi] PST - ppublish SO - Am J Phys Anthropol. 2018 May;166(1):196-207. doi: 10.1002/ajpa.23423. Epub 2018 Feb 5. PMID- 29694397 OWN - NLM STAT- MEDLINE DCOM- 20180730 LR - 20181114 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 13 IP - 4 DP - 2018 TI - Ancient DNA from latrines in Northern Europe and the Middle East (500 BC-1700 AD) reveals past parasites and diet. PG - e0195481 LID - 10.1371/journal.pone.0195481 [doi] LID - e0195481 AB - High-resolution insight into parasitic infections and diet of past populations in Northern Europe and the Middle East (500 BC- 1700 AD) was obtained by pre-concentration of parasite eggs from ancient latrines and deposits followed by shotgun sequencing of DNA. Complementary profiling of parasite, vertebrate and plant DNA proved highly informative in the study of ancient health, human-animal interactions as well as animal and plant dietary components. Most prominent were finding of soil-borne parasites transmitted directly between humans, but also meat-borne parasites that require consumption of raw or undercooked fish and pork. The detection of parasites for which sheep, horse, dog, pig, and rodents serves as definitive hosts are clear markers of domestic and synanthropic animals living in closer proximity of the respective sites. Finally, the reconstruction of full mitochondrial parasite genomes from whipworm (Ascaris lumbricoides) and roundworm species (Trichuris trichiura and Trichuris muris) and estimates of haplotype frequencies elucidates the genetic diversity and provides insights into epidemiology and parasite biology. FAU - Søe, Martin Jensen AU - Søe MJ AUID- ORCID: 0000-0002-0386-6294 AD - Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark. AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. FAU - Nejsum, Peter AU - Nejsum P AD - Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg, Denmark. FAU - Seersholm, Frederik Valeur AU - Seersholm FV AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. FAU - Fredensborg, Brian Lund AU - Fredensborg BL AD - Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark. FAU - Habraken, Ruben AU - Habraken R AD - BioArchaeological Research Bureau, Den Haag, The Netherlands. FAU - Haase, Kirstine AU - Haase K AD - Odense Bys Museer, Odense, Denmark. AD - Centre for Urban Network Evolutions, School of Culture and Society, Aarhus University, Højbjerg, Denmark. FAU - Hald, Mette Marie AU - Hald MM AD - Environmental Archaeology and Materials Science, National Museum of Denmark, Kgs. Lyngby, Denmark. FAU - Simonsen, Rikke AU - Simonsen R AD - Museum of Copenhagen, Copenhagen V, Denmark. FAU - Højlund, Flemming AU - Højlund F AD - Moesgaard Museum, Højbjerg, Denmark. FAU - Blanke, Louise AU - Blanke L AD - Department of Archaeology, School of Culture and Society, Aarhus University, Aarhus, Denmark. FAU - Merkyte, Inga AU - Merkyte I AD - The Saxo Institute, University of Copenhagen, Copenhagen S, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. AD - Department of Zoology, University of Cambridge, Downing St, Cambridge, United Kingdom. AD - Sanger Institute, Hinxton, Cambridge, United Kingdom. FAU - Kapel, Christian Moliin Outzen AU - Kapel CMO AD - Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180425 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - 0 (DNA, Plant) SB - IM MH - Agriculture MH - Animals MH - Archaeology/methods MH - Biodiversity MH - *DNA, Ancient MH - DNA, Mitochondrial MH - DNA, Plant MH - *Diet MH - Eggs MH - Europe MH - Feces/*chemistry/*parasitology MH - History, Ancient MH - Humans MH - Metagenome MH - Middle East MH - Parasites/genetics MH - Parasitic Diseases/epidemiology/history MH - Phylogeny MH - Sequence Analysis, DNA MH - *Toilet Facilities PMC - PMC5918799 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2018/04/26 06:00 MHDA- 2018/07/31 06:00 PMCR- 2018/04/25 CRDT- 2018/04/26 06:00 PHST- 2017/10/31 00:00 [received] PHST- 2018/03/24 00:00 [accepted] PHST- 2018/04/26 06:00 [entrez] PHST- 2018/04/26 06:00 [pubmed] PHST- 2018/07/31 06:00 [medline] PHST- 2018/04/25 00:00 [pmc-release] AID - PONE-D-17-38714 [pii] AID - 10.1371/journal.pone.0195481 [doi] PST - epublish SO - PLoS One. 2018 Apr 25;13(4):e0195481. doi: 10.1371/journal.pone.0195481. eCollection 2018. PMID- 29684051 OWN - NLM STAT- MEDLINE DCOM- 20180727 LR - 20240314 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 13 IP - 4 DP - 2018 TI - Estimating genetic kin relationships in prehistoric populations. PG - e0195491 LID - 10.1371/journal.pone.0195491 [doi] LID - e0195491 AB - Archaeogenomic research has proven to be a valuable tool to trace migrations of historic and prehistoric individuals and groups, whereas relationships within a group or burial site have not been investigated to a large extent. Knowing the genetic kinship of historic and prehistoric individuals would give important insights into social structures of ancient and historic cultures. Most archaeogenetic research concerning kinship has been restricted to uniparental markers, while studies using genome-wide information were mainly focused on comparisons between populations. Applications which infer the degree of relationship based on modern-day DNA information typically require diploid genotype data. Low concentration of endogenous DNA, fragmentation and other post-mortem damage to ancient DNA (aDNA) makes the application of such tools unfeasible for most archaeological samples. To infer family relationships for degraded samples, we developed the software READ (Relationship Estimation from Ancient DNA). We show that our heuristic approach can successfully infer up to second degree relationships with as little as 0.1x shotgun coverage per genome for pairs of individuals. We uncover previously unknown relationships among prehistoric individuals by applying READ to published aDNA data from several human remains excavated from different cultural contexts. In particular, we find a group of five closely related males from the same Corded Ware culture site in modern-day Germany, suggesting patrilocality, which highlights the possibility to uncover social structures of ancient populations by applying READ to genome-wide aDNA data. READ is publicly available from https://bitbucket.org/tguenther/read. FAU - Monroy Kuhn, Jose Manuel AU - Monroy Kuhn JM AD - Uppsala University, Evolutionary Biology Centre, Department of Organismal Biology, Norbyvägen 18C, SE-752 36 Uppsala, Sweden. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Uppsala University, Evolutionary Biology Centre, Department of Organismal Biology, Norbyvägen 18C, SE-752 36 Uppsala, Sweden. AD - Uppsala University, SciLifeLab, Norbyvägen 18C, SE-752 36 Uppsala, Sweden. FAU - Günther, Torsten AU - Günther T AUID- ORCID: 0000-0001-9460-390X AD - Uppsala University, Evolutionary Biology Centre, Department of Organismal Biology, Norbyvägen 18C, SE-752 36 Uppsala, Sweden. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180423 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Chromosomes, Human, Y MH - Computer Simulation MH - DNA Fragmentation MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial MH - *Family MH - Germany MH - Haplotypes MH - Humans MH - Male MH - Models, Genetic MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA/methods MH - Software PMC - PMC5912749 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2018/04/24 06:00 MHDA- 2018/07/28 06:00 PMCR- 2018/04/23 CRDT- 2018/04/24 06:00 PHST- 2017/02/01 00:00 [received] PHST- 2018/03/23 00:00 [accepted] PHST- 2018/04/24 06:00 [entrez] PHST- 2018/04/24 06:00 [pubmed] PHST- 2018/07/28 06:00 [medline] PHST- 2018/04/23 00:00 [pmc-release] AID - PONE-D-17-04198 [pii] AID - 10.1371/journal.pone.0195491 [doi] PST - epublish SO - PLoS One. 2018 Apr 23;13(4):e0195491. doi: 10.1371/journal.pone.0195491. eCollection 2018. PMID- 29674573 OWN - NLM STAT- MEDLINE DCOM- 20180625 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 360 IP - 6386 DP - 2018 Apr 20 TI - Ancient DNA untangles South Asian roots. PG - 252 LID - 10.1126/science.360.6386.252 [doi] FAU - Wade, Lizzie AU - Wade L AD - Austin. LA - eng PT - News DEP - 20180419 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Asia, Southeastern/ethnology MH - Asian People/*ethnology/*genetics MH - *Biological Evolution MH - *DNA, Ancient MH - Humans EDAT- 2018/04/21 06:00 MHDA- 2018/06/26 06:00 CRDT- 2018/04/21 06:00 PHST- 2018/04/21 06:00 [entrez] PHST- 2018/04/21 06:00 [pubmed] PHST- 2018/06/26 06:00 [medline] AID - 360/6386/252 [pii] AID - 10.1126/science.360.6386.252 [doi] PST - ppublish SO - Science. 2018 Apr 20;360(6386):252. doi: 10.1126/science.360.6386.252. Epub 2018 Apr 19. PMID- 29501328 OWN - NLM STAT- MEDLINE DCOM- 20190919 LR - 20250130 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 28 IP - 7 DP - 2018 Apr 2 TI - Population Turnover in Remote Oceania Shortly after Initial Settlement. PG - 1157-1165.e7 LID - S0960-9822(18)30236-7 [pii] LID - 10.1016/j.cub.2018.02.051 [doi] AB - Ancient DNA from Vanuatu and Tonga dating to about 2,900-2,600 years ago (before present, BP) has revealed that the "First Remote Oceanians" associated with the Lapita archaeological culture were directly descended from the population that, beginning around 5000 BP, spread Austronesian languages from Taiwan to the Philippines, western Melanesia, and eventually Remote Oceania. Thus, ancestors of the First Remote Oceanians must have passed by the Papuan-ancestry populations they encountered in New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture [1]. However, all present-day populations in Near and Remote Oceania harbor >25% Papuan ancestry, implying that additional eastward migration must have occurred. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu from 2900-150 BP, as well as 185 present-day individuals from 18 islands. We find that people of almost entirely Papuan ancestry arrived in Vanuatu by around 2300 BP, most likely reflecting migrations a few hundred years earlier at the end of the Lapita period, when there is also evidence of changes in skeletal morphology and cessation of long-distance trade between Near and Remote Oceania [2, 3]. Papuan ancestry was subsequently diluted through admixture but remains at least 80%-90% in most islands. Through a fine-grained analysis of ancestry profiles, we show that the Papuan ancestry in Vanuatu derives from the Bismarck Archipelago rather than the geographically closer Solomon Islands. However, the Papuan ancestry in Polynesia-the most remote Pacific islands-derives from different sources, documenting a third stream of migration from Near to Remote Oceania. CI - Copyright © 2018 Elsevier Ltd. All rights reserved. FAU - Lipson, Mark AU - Lipson M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: mlipson@genetics.med.harvard.edu. FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; The Francis Crick Institute, London NW1 1AT, UK. FAU - Spriggs, Matthew AU - Spriggs M AD - School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, ACT 2601, Australia; Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu. FAU - Valentin, Frederique AU - Valentin F AD - Maison de l'Archéologie et de l'Ethnologie, CNRS, UMR 7041, 92023 Nanterre, France. FAU - Bedford, Stuart AU - Bedford S AD - Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu; Department of Archaeology and Natural History, College of Asia-Pacific, The Australian National University, Canberra, ACT 2601, Australia. FAU - Shing, Richard AU - Shing R AD - Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu. FAU - Buckley, Hallie AU - Buckley H AD - Department of Anatomy, Otago Global Health Institute, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand. FAU - Phillip, Iarawai AU - Phillip I AD - Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu. FAU - Ward, Graeme K AU - Ward GK AD - Department of Archaeology and Natural History, College of Asia-Pacific, The Australian National University, Canberra, ACT 2601, Australia. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA. FAU - Cheronet, Olivia AU - Cheronet O AD - Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Earth Institute, University College Dublin, Dublin 4, Ireland. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA. FAU - Harper, Thomas K AU - Harper TK AD - Department of Anthropology and Institute for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA. FAU - Sirak, Kendra AU - Sirak K AD - Earth Institute, University College Dublin, Dublin 4, Ireland; Department of Anthropology, Emory University, Atlanta, GA, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA. FAU - Auckland, Kathryn AU - Auckland K AD - Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. FAU - Hill, Adrian V S AU - Hill AVS AD - Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. FAU - Maitland, Kathryn AU - Maitland K AD - Department of Paediatrics, Faculty of Medicine, Imperial College, St Mary's Hospital, Norfolk Place, Paddington, London W2 1PG, UK. FAU - Oppenheimer, Stephen J AU - Oppenheimer SJ AD - School of Anthropology and Museum Ethnography, University of Oxford, Oxford OX2 6PE, UK. FAU - Parks, Tom AU - Parks T AD - Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. FAU - Robson, Kathryn AU - Robson K AD - MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK. FAU - Williams, Thomas N AU - Williams TN AD - Department of Paediatrics, Faculty of Medicine, Imperial College, St Mary's Hospital, Norfolk Place, Paddington, London W2 1PG, UK. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology and Institute for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Mentzer, Alexander J AU - Mentzer AJ AD - Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Earth Institute, University College Dublin, Dublin 4, Ireland. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - 106289/Z/14/Z/WT_/Wellcome Trust/United Kingdom GR - PG/14/26/30509/BHF_/British Heart Foundation/United Kingdom GR - MRC_/Medical Research Council/United Kingdom GR - Wellcome Trust/United Kingdom GR - HHMI_/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20180228 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM CIN - Curr Biol. 2018 May 7;28(9):R549-R551. doi: 10.1016/j.cub.2018.03.033. PMID: 29738726 MH - Female MH - Humans MH - Male MH - *DNA, Ancient/analysis MH - *Genetics, Population MH - *Genome, Human MH - Genome-Wide Association Study MH - *Human Migration/statistics & numerical data MH - Oceania MH - Phylogeny MH - *Population Dynamics MH - Oceanians PMC - PMC5882562 MID - NIHMS947388 OTO - NOTNLM OT - Lapita OT - Near Oceania OT - Pacific Islanders OT - Remote Oceania OT - ancient DNA OT - migration COIS- Declaration of Interests: The authors declare no competing interests. EDAT- 2018/03/05 06:00 MHDA- 2019/09/20 06:00 PMCR- 2019/04/02 CRDT- 2018/03/05 06:00 PHST- 2018/02/12 00:00 [received] PHST- 2018/02/19 00:00 [revised] PHST- 2018/02/19 00:00 [accepted] PHST- 2018/03/05 06:00 [pubmed] PHST- 2019/09/20 06:00 [medline] PHST- 2018/03/05 06:00 [entrez] PHST- 2019/04/02 00:00 [pmc-release] AID - S0960-9822(18)30236-7 [pii] AID - 10.1016/j.cub.2018.02.051 [doi] PST - ppublish SO - Curr Biol. 2018 Apr 2;28(7):1157-1165.e7. doi: 10.1016/j.cub.2018.02.051. Epub 2018 Feb 28. PMID- 29557324 OWN - NLM STAT- MEDLINE DCOM- 20190503 LR - 20190503 IS - 1469-8161 (Electronic) IS - 0031-1820 (Linking) VI - 145 IP - 5 DP - 2018 Apr TI - DNA barcoding of ancient parasites. PG - 646-655 LID - 10.1017/S0031182018000380 [doi] AB - Ancient samples present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient samples can provide a number of unique scientific insights, for example: (1) into the parasite communities and health of prehistoric human populations; (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction; and (3) the ability to view in 'real-time' processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts. The application of DNA metabarcoding and high-throughput sequencing to ancient specimens has so far been limited, but in future promises great potential for gaining empirical data on poorly understood processes such as parasite co-extinction. FAU - Wood, Jamie R AU - Wood JR AD - Manaaki Whenua Landcare Research,PO Box 69040,Lincoln,Canterbury 7640,New Zealand. LA - eng PT - Journal Article PT - Review DEP - 20180320 PL - England TA - Parasitology JT - Parasitology JID - 0401121 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *DNA Barcoding, Taxonomic MH - DNA, Ancient/analysis/*isolation & purification MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Parasites/*genetics MH - Parasitic Diseases/parasitology OTO - NOTNLM OT - Holocene OT - Pleistocene OT - ancient DNA OT - archaeology OT - co-extinction OT - extinct species OT - fossils EDAT- 2018/03/21 06:00 MHDA- 2019/05/06 06:00 CRDT- 2018/03/21 06:00 PHST- 2018/03/21 06:00 [pubmed] PHST- 2019/05/06 06:00 [medline] PHST- 2018/03/21 06:00 [entrez] AID - S0031182018000380 [pii] AID - 10.1017/S0031182018000380 [doi] PST - ppublish SO - Parasitology. 2018 Apr;145(5):646-655. doi: 10.1017/S0031182018000380. Epub 2018 Mar 20. PMID- 29466330 OWN - NLM STAT- MEDLINE DCOM- 20180810 LR - 20220129 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 555 IP - 7695 DP - 2018 Mar 8 TI - The genomic history of southeastern Europe. PG - 197-203 LID - 10.1038/nature25778 [doi] AB - Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west-east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Alpaslan-Roodenberg, Songül AU - Alpaslan-Roodenberg S AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Posth, Cosimo AU - Posth C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AD - Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Olalde, Iñigo AU - Olalde I AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Candilio, Francesca AU - Candilio F AD - Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland. FAU - Cheronet, Olivia AU - Cheronet O AD - Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland. AD - Department of Anthropology, University of Vienna, 1090 Vienna, Austria. FAU - Fernandes, Daniel AU - Fernandes D AD - Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland. AD - CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Gamarra, Beatriz AU - Gamarra B AD - Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland. FAU - Fortes, Gloria González AU - Fortes GG AD - Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44100, Italy. FAU - Haak, Wolfgang AU - Haak W AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA-5005 Adelaide, South Australia, Australia. FAU - Harney, Eadaoin AU - Harney E AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Jones, Eppie AU - Jones E AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. AD - Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. FAU - Keating, Denise AU - Keating D AD - Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland. FAU - Krause-Kyora, Ben AU - Krause-Kyora B AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Kucukkalipci, Isil AU - Kucukkalipci I AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Mittnik, Alissa AU - Mittnik A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Nägele, Kathrin AU - Nägele K AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Novak, Mario AU - Novak M AD - Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland. AD - Institute for Anthropological Research, 10000 Zagreb, Croatia. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. FAU - Pfrengle, Saskia AU - Pfrengle S AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Sirak, Kendra AU - Sirak K AD - Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland. AD - Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Vai, Stefania AU - Vai S AD - Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy. FAU - Alexandrov, Stefan AU - Alexandrov S AD - National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria. FAU - Alt, Kurt W AU - Alt KW AD - Danube Private University, A-3500 Krems, Austria. AD - Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, CH-4123 Basel-Allschwil, Switzerland. AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, 06114 Halle, Germany. FAU - Andreescu, Radian AU - Andreescu R AD - National History Museum of Romania, 030026, Bucharest, Romania. FAU - Antonović, Dragana AU - Antonović D AD - Institute of Archaeology, Belgrade, Serbia. FAU - Ash, Abigail AU - Ash A AD - Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland. FAU - Atanassova, Nadezhda AU - Atanassova N AD - Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria. FAU - Bacvarov, Krum AU - Bacvarov K AD - National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria. FAU - Gusztáv, Mende Balázs AU - Gusztáv MB AD - Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary. FAU - Bocherens, Hervé AU - Bocherens H AD - Department of Geosciences, Biogeology, Universität Tübingen, 72074 Tübingen, Germany. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany. FAU - Bolus, Michael AU - Bolus M AD - ROCEEH Research Center, Heidelberg Academy of Sciences and Humanities, University of Tübingen, 72070 Tübingen, Germany. FAU - Boroneanţ, Adina AU - Boroneanţ A AD - Vasile Pârvan Institute of Archaeology, Romanian Academy, 010667 Bucharest, Romania. FAU - Boyadzhiev, Yavor AU - Boyadzhiev Y AD - National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria. FAU - Budnik, Alicja AU - Budnik A AD - Human Biology Department, Cardinal Stefan Wyszyński University, 01-938 Warsaw, Poland. FAU - Burmaz, Josip AU - Burmaz J AD - KADUCEJ d.o.o., 21000 Split, Croatia. FAU - Chohadzhiev, Stefan AU - Chohadzhiev S AD - St. Cyril and Methodius University, 5000 Veliko Turnovo, Bulgaria. FAU - Conard, Nicholas J AU - Conard NJ AD - Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany. AD - Department of Early Prehistory and Quaternary Ecology, University of Tübingen, 72070 Tübingen, Germany. FAU - Cottiaux, Richard AU - Cottiaux R AD - INRAP/UMR 8215 Trajectoires, 92023 Nanterre, France. FAU - Čuka, Maja AU - Čuka M AD - Archaeological Museum of Istria, 52100 Pula, Croatia. FAU - Cupillard, Christophe AU - Cupillard C AD - Service Régional de l'Archéologie de Bourgogne-Franche-Comté, 25043 Besançon Cedex, France. AD - Laboratoire Chronoenvironnement, UMR 6249 du CNRS, UFR des Sciences et Techniques, 25030 Besançon Cedex, France. FAU - Drucker, Dorothée G AU - Drucker DG AD - Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany. FAU - Elenski, Nedko AU - Elenski N AD - Regional Museum of History Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria. FAU - Francken, Michael AU - Francken M AD - Institute for Archaeological Sciences, Paleoanthropology, University of Tübingen, 72070 Tübingen, Germany. FAU - Galabova, Borislava AU - Galabova B AD - Laboratory for Human Bioarchaeology, 1202 Sofia, Bulgaria. FAU - Ganetsovski, Georgi AU - Ganetsovski G AD - Regional Museum of History, 3000 Vratsa, Bulgaria. FAU - Gély, Bernard AU - Gély B AD - DRAC Auvergne - Rhône Alpes, Ministère de la Culture, Lyon Cedex 01, France. FAU - Hajdu, Tamás AU - Hajdu T AD - Eötvös Loránd University, Faculty of Science, Institute of Biology, Department of Biological Anthropology, H-1117 Budapest, Hungary. FAU - Handzhyiska, Veneta AU - Handzhyiska V AD - Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria. FAU - Harvati, Katerina AU - Harvati K AD - Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany. AD - Institute for Archaeological Sciences, Paleoanthropology, University of Tübingen, 72070 Tübingen, Germany. FAU - Higham, Thomas AU - Higham T AD - Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, Oxford OX1 3QY, UK. FAU - Iliev, Stanislav AU - Iliev S AD - Regional Museum of History, 6300 Haskovo, Bulgaria. FAU - Janković, Ivor AU - Janković I AD - Institute for Anthropological Research, 10000 Zagreb, Croatia. AD - Department of Anthropology, University of Wyoming, Laramie, Wyoming 82071, USA. FAU - Karavanić, Ivor AU - Karavanić I AD - Department of Anthropology, University of Wyoming, Laramie, Wyoming 82071, USA. AD - Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, Pennsylvania 16802, USA. FAU - Komšo, Darko AU - Komšo D AD - Archaeological Museum of Istria, 52100 Pula, Croatia. FAU - Kozak, Alexandra AU - Kozak A AD - Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210 Kiev, Ukraine. FAU - Labuda, Damian AU - Labuda D AD - CHU Sainte-Justine Research Center, Pediatric Department, Université de Montréal, Montreal, Québec H3T 1C5, Canada. FAU - Lari, Martina AU - Lari M AD - Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy. FAU - Lazar, Catalin AU - Lazar C AD - National History Museum of Romania, 030026, Bucharest, Romania. AD - Department of Ancient History, Archaeology and History of Art, Faculty of History, University of Bucharest, 50107 Bucharest, Romania. FAU - Leppek, Maleen AU - Leppek M AD - Institute for Pre- and Protohistoric Archaeology and the Archaeology of the Roman Provinces, Ludwig-Maximilians-University, 80799 Munich, Germany. FAU - Leshtakov, Krassimir AU - Leshtakov K AD - Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria. FAU - Vetro, Domenico Lo AU - Vetro DL AD - Dipartimento SAGAS - Sezione di Archeologia e Antico Oriente, Università degli Studi di Firenze, 50122 Florence, Italy. AD - Museo e Istituto fiorentino di Preistoria, 50122 Florence, Italy. FAU - Los, Dženi AU - Los D AD - KADUCEJ d.o.o., 21000 Split, Croatia. FAU - Lozanov, Ivaylo AU - Lozanov I AD - Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria. FAU - Malina, Maria AU - Malina M AD - ROCEEH Research Center, Heidelberg Academy of Sciences and Humanities, University of Tübingen, 72070 Tübingen, Germany. FAU - Martini, Fabio AU - Martini F AD - Dipartimento SAGAS - Sezione di Archeologia e Antico Oriente, Università degli Studi di Firenze, 50122 Florence, Italy. AD - Museo e Istituto fiorentino di Preistoria, 50122 Florence, Italy. FAU - McSweeney, Kath AU - McSweeney K AD - School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK. FAU - Meller, Harald AU - Meller H AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, 06114 Halle, Germany. FAU - Menđušić, Marko AU - Menđušić M AD - Conservation Department in Šibenik, Ministry of Culture of the Republic of Croatia, 22000 Šibenik, Croatia. FAU - Mirea, Pavel AU - Mirea P AD - Teleorman County Museum, 140033 Alexandria, Romania. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia. FAU - Petrova, Vanya AU - Petrova V AD - Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria. FAU - Price, T Douglas AU - Price TD AD - Department of Anthropology, University of Wisconsin, Madison, Wisconsin 53706, USA. FAU - Simalcsik, Angela AU - Simalcsik A AD - Olga Necrasov Centre for Anthropological Research, Romanian Academy - Iaşi Branch, 700481 Iaşi, Romania. FAU - Sineo, Luca AU - Sineo L AD - Dipartimento di Scienze e tecnologie biologiche, chimiche e farmaceutiche, Lab. of Anthropology, Università degli studi di Palermo, 90133 Palermo, Italy. FAU - Šlaus, Mario AU - Šlaus M AD - Anthropological Center, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia. FAU - Slavchev, Vladimir AU - Slavchev V AD - Regional Historical Museum Varna, BG-9000 Varna, Bulgaria. FAU - Stanev, Petar AU - Stanev P AD - Regional Museum of History Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria. FAU - Starović, Andrej AU - Starović A AD - National Museum in Belgrade, Belgrade, Serbia. FAU - Szeniczey, Tamás AU - Szeniczey T AD - Eötvös Loránd University, Faculty of Science, Institute of Biology, Department of Biological Anthropology, H-1117 Budapest, Hungary. FAU - Talamo, Sahra AU - Talamo S AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Teschler-Nicola, Maria AU - Teschler-Nicola M AD - Department of Anthropology, University of Vienna, 1090 Vienna, Austria. AD - Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria. FAU - Thevenet, Corinne AU - Thevenet C AD - INRAP/UMR 8215 Trajectoires, 92023 Nanterre, France. FAU - Valchev, Ivan AU - Valchev I AD - Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria. FAU - Valentin, Frédérique AU - Valentin F AD - CNRS/UMR 7041 ArScAn MAE, 92023 Nanterre, France. FAU - Vasilyev, Sergey AU - Vasilyev S AD - Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119991, Russia. FAU - Veljanovska, Fanica AU - Veljanovska F AD - Archaeological Museum of Macedonia, 1000 Skopje, the former Yugoslav Republic of Macedonia. FAU - Venelinova, Svetlana AU - Venelinova S AD - Regional Museum of History, 9700 Shumen, Bulgaria. FAU - Veselovskaya, Elizaveta AU - Veselovskaya E AD - Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119991, Russia. FAU - Viola, Bence AU - Viola B AD - Department of Anthropology, University of Toronto, Toronto, Ontario, M5S 2S2, Canada. AD - Institute of Archaeology & Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia. FAU - Virag, Cristian AU - Virag C AD - Satu Mare County Museum Archaeology Department, 440026 Satu Mare, Romania. FAU - Zaninović, Joško AU - Zaninović J AD - Municipal Museum Drniš, 22320 Drniš, Croatia. FAU - Zäuner, Steve AU - Zäuner S AD - anthropol - Anthropologieservice, 72379 Hechingen, Germany. FAU - Stockhammer, Philipp W AU - Stockhammer PW AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Institute for Pre- and Protohistoric Archaeology and the Archaeology of the Roman Provinces, Ludwig-Maximilians-University, 80799 Munich, Germany. FAU - Catalano, Giulio AU - Catalano G AD - Dipartimento di Scienze e tecnologie biologiche, chimiche e farmaceutiche, Lab. of Anthropology, Università degli studi di Palermo, 90133 Palermo, Italy. FAU - Krauß, Raiko AU - Krauß R AD - Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany. FAU - Caramelli, David AU - Caramelli D AD - Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy. FAU - Zariņa, Gunita AU - Zariņa G AD - Institute of Latvian History, University of Latvia, Rı¯ga 1050, Latvia. FAU - Gaydarska, Bisserka AU - Gaydarska B AD - Department of Archaeology, Durham University, Durham DH1 3LE, UK. FAU - Lillie, Malcolm AU - Lillie M AD - School of Environmental Sciences, Geography, University of Hull, Hull HU6 7RX, UK. FAU - Nikitin, Alexey G AU - Nikitin AG AD - Department of Biology, Grand Valley State University, Allendale, Michigan 49401, USA. FAU - Potekhina, Inna AU - Potekhina I AD - Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210 Kiev, Ukraine. FAU - Papathanasiou, Anastasia AU - Papathanasiou A AD - Ephorate of Paleoanthropology and Speleology, 11636 Athens, Greece. FAU - Borić, Dušan AU - Borić D AD - The Italian Academy for Advanced Studies in America, Columbia University, New York, New York 10027, USA. FAU - Bonsall, Clive AU - Bonsall C AD - School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Pinhasi, Ron AU - Pinhasi R AD - Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland. AD - Department of Anthropology, University of Vienna, 1090 Vienna, Austria. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. LA - eng GR - HHMI_/Howard Hughes Medical Institute/United States GR - 263441/ERC_/European Research Council/International GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R01 HG006399/HG/NHGRI NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20180221 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - Agriculture/history MH - Asia/ethnology MH - DNA, Ancient MH - Europe MH - Farmers/*history MH - Female MH - Genetics, Population MH - Genome, Human/*genetics MH - *Genomics MH - Grassland MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Male MH - Sex Distribution PMC - PMC6091220 MID - NIHMS937437 EDAT- 2018/02/22 06:00 MHDA- 2018/08/11 06:00 PMCR- 2018/08/21 CRDT- 2018/02/22 06:00 PHST- 2017/05/06 00:00 [received] PHST- 2018/01/16 00:00 [accepted] PHST- 2018/02/22 06:00 [pubmed] PHST- 2018/08/11 06:00 [medline] PHST- 2018/02/22 06:00 [entrez] PHST- 2018/08/21 00:00 [pmc-release] AID - nature25778 [pii] AID - 10.1038/nature25778 [doi] PST - ppublish SO - Nature. 2018 Mar 8;555(7695):197-203. doi: 10.1038/nature25778. Epub 2018 Feb 21. PMID- 29515143 OWN - NLM STAT- MEDLINE DCOM- 20190918 LR - 20190918 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 8 IP - 1 DP - 2018 Mar 7 TI - A combined method for DNA analysis and radiocarbon dating from a single sample. PG - 4127 LID - 10.1038/s41598-018-22472-w [doi] LID - 4127 AB - Current protocols for ancient DNA and radiocarbon analysis of ancient bones and teeth call for multiple destructive samplings of a given specimen, thereby increasing the extent of undesirable damage to precious archaeological material. Here we present a method that makes it possible to obtain both ancient DNA sequences and radiocarbon dates from the same sample material. This is achieved by releasing DNA from the bone matrix through incubation with either EDTA or phosphate buffer prior to complete demineralization and collagen extraction utilizing the acid-base-acid-gelatinization and ultrafiltration procedure established in most radiocarbon dating laboratories. Using a set of 12 bones of different ages and preservation conditions we demonstrate that on average 89% of the DNA can be released from sample powder with minimal, or 38% without any, detectable collagen loss. We also detect no skews in radiocarbon dates compared to untreated samples. Given the different material demands for radiocarbon dating (500 mg of bone/dentine) and DNA analysis (10-100 mg), combined DNA and collagen extraction not only streamlines the sampling process but also drastically increases the amount of DNA that can be recovered from limited sample material. FAU - Korlević, Petra AU - Korlević P AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. petra_korlevic@eva.mpg.de. FAU - Talamo, Sahra AU - Talamo S AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. sahra.talamo@eva.mpg.de. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180307 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Archaeology/*methods MH - DNA, Ancient/*analysis MH - *Fossils MH - Humans MH - Radiometric Dating/*methods PMC - PMC5841407 COIS- The authors declare no competing interests. EDAT- 2018/03/09 06:00 MHDA- 2019/09/19 06:00 PMCR- 2018/03/07 CRDT- 2018/03/09 06:00 PHST- 2017/08/14 00:00 [received] PHST- 2018/02/21 00:00 [accepted] PHST- 2018/03/09 06:00 [entrez] PHST- 2018/03/09 06:00 [pubmed] PHST- 2019/09/19 06:00 [medline] PHST- 2018/03/07 00:00 [pmc-release] AID - 10.1038/s41598-018-22472-w [pii] AID - 22472 [pii] AID - 10.1038/s41598-018-22472-w [doi] PST - epublish SO - Sci Rep. 2018 Mar 7;8(1):4127. doi: 10.1038/s41598-018-22472-w. PMID- 29463742 OWN - NLM STAT- MEDLINE DCOM- 20180802 LR - 20221207 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 115 IP - 10 DP - 2018 Mar 6 TI - Origins and genetic legacies of the Caribbean Taino. PG - 2341-2346 LID - 10.1073/pnas.1716839115 [doi] AB - The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher's Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean. CI - Copyright © 2018 the Author(s). Published by PNAS. FAU - Schroeder, Hannes AU - Schroeder H AUID- ORCID: 0000-0002-6743-0270 AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; hschroeder@snm.ku.dk ewillerslev@snm.ku.dk. AD - Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands. FAU - Sikora, Martin AU - Sikora M AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Gopalakrishnan, Shyam AU - Gopalakrishnan S AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Cassidy, Lara M AU - Cassidy LM AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Maisano Delser, Pierpaolo AU - Maisano Delser P AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. AD - Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdom. FAU - Sandoval Velasco, Marcela AU - Sandoval Velasco M AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Schraiber, Joshua G AU - Schraiber JG AUID- ORCID: 0000-0002-7912-2195 AD - Department of Biology, Temple University, Philadelphia, PA 19122-6078. FAU - Rasmussen, Simon AU - Rasmussen S AD - DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark. FAU - Homburger, Julian R AU - Homburger JR AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AD - International Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla 76230, Santiago de Querétaro, Mexico. FAU - Allentoft, Morten E AU - Allentoft ME AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Moreno-Mayar, J Víctor AU - Moreno-Mayar JV AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Renaud, Gabriel AU - Renaud G AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Gómez-Carballa, Alberto AU - Gómez-Carballa A AD - Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain. AD - GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago, 15872 Galicia, Spain. FAU - Laffoon, Jason E AU - Laffoon JE AD - Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands. AD - Faculty of Sciences, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands. FAU - Hopkins, Rachel J A AU - Hopkins RJA AD - Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, OX1 3QY Oxford, United Kingdom. FAU - Higham, Thomas F G AU - Higham TFG AD - Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, OX1 3QY Oxford, United Kingdom. FAU - Carr, Robert S AU - Carr RS AD - Archaeological and Historical Conservancy Inc., Davie, FL 33341. FAU - Schaffer, William C AU - Schaffer WC AD - Liberal Arts Department, Phoenix College, Phoenix, AZ 85013. AD - Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281. FAU - Day, Jane S AU - Day JS AD - Research Atlantica Inc., Boca Raton, FL 33432. FAU - Hoogland, Menno AU - Hoogland M AD - Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands. FAU - Salas, Antonio AU - Salas A AD - Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain. AD - GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago, 15872 Galicia, Spain. FAU - Bustamante, Carlos D AU - Bustamante CD AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. FAU - Nielsen, Rasmus AU - Nielsen R AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. AD - Department of Integrative Biology, University of California, Berkeley, CA 94720. FAU - Bradley, Daniel G AU - Bradley DG AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Hofman, Corinne L AU - Hofman CL AD - Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands. FAU - Willerslev, Eske AU - Willerslev E AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; hschroeder@snm.ku.dk ewillerslev@snm.ku.dk. AD - Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdom. AD - Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom. LA - eng GR - R35 GM124745/GM/NIGMS NIH HHS/United States GR - T32 HG000044/HG/NHGRI NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20180220 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - American Indian or Alaska Native/*genetics MH - Archaeology MH - Bahamas MH - DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Female MH - Genetics, Population MH - Genome, Human/*genetics MH - Genomics MH - Hispanic or Latino/genetics MH - History, Ancient MH - Human Migration/history/*statistics & numerical data MH - Humans MH - Male MH - Paleontology MH - Phylogeny MH - Young Adult PMC - PMC5877975 OTO - NOTNLM OT - ancestry OT - ancient DNA OT - archaeology OT - migration OT - paleogenomics COIS- Conflict of interest statement: H.S. is on the scientific advisory board of Living DNA Ltd, J.R.H. is co-founder of Encompass Bioscience Inc, and C.D.B. is founder of IdentifyGenomics, LLC, and scientific advisor for Personalis Inc, Ancestry.com Inc, and Invitae Inc. This did not affect the design, execution, or interpretation of the experiments and results presented here. EDAT- 2018/02/22 06:00 MHDA- 2018/08/03 06:00 PMCR- 2018/02/20 CRDT- 2018/02/22 06:00 PHST- 2018/02/22 06:00 [pubmed] PHST- 2018/08/03 06:00 [medline] PHST- 2018/02/22 06:00 [entrez] PHST- 2018/02/20 00:00 [pmc-release] AID - 1716839115 [pii] AID - 201716839 [pii] AID - 10.1073/pnas.1716839115 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2341-2346. doi: 10.1073/pnas.1716839115. Epub 2018 Feb 20. PMID- 29395378 OWN - NLM STAT- MEDLINE DCOM- 20181217 LR - 20181217 IS - 0168-9525 (Print) IS - 0168-9525 (Linking) VI - 34 IP - 3 DP - 2018 Mar TI - Insights into Modern Human Prehistory Using Ancient Genomes. PG - 184-196 LID - S0168-9525(17)30210-X [pii] LID - 10.1016/j.tig.2017.11.008 [doi] AB - The genetic relationship of past modern humans to today's populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa. CI - Copyright © 2017 Elsevier Ltd. All rights reserved. FAU - Yang, Melinda A AU - Yang MA AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng GR - 55008731/HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20180125 PL - England TA - Trends Genet JT - Trends in genetics : TIG JID - 8507085 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA, Ancient/*analysis MH - Evolution, Molecular MH - Fossils MH - Gene Flow MH - *Genetic Variation MH - Genome, Human/*genetics MH - Hominidae/*genetics MH - Humans MH - Sequence Analysis, DNA OTO - NOTNLM OT - Upper Paleolithic OT - ancient DNA OT - archaic admixture OT - early Neolith OT - genetic prehistory OT - modern human EDAT- 2018/02/06 06:00 MHDA- 2018/12/18 06:00 CRDT- 2018/02/04 06:00 PHST- 2017/10/03 00:00 [received] PHST- 2017/11/26 00:00 [revised] PHST- 2017/11/29 00:00 [accepted] PHST- 2018/02/06 06:00 [pubmed] PHST- 2018/12/18 06:00 [medline] PHST- 2018/02/04 06:00 [entrez] AID - S0168-9525(17)30210-X [pii] AID - 10.1016/j.tig.2017.11.008 [doi] PST - ppublish SO - Trends Genet. 2018 Mar;34(3):184-196. doi: 10.1016/j.tig.2017.11.008. Epub 2018 Jan 25. PMID- 29345305 OWN - NLM STAT- MEDLINE DCOM- 20180730 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 165 IP - 3 DP - 2018 Mar TI - Detection of mitochondrial haplogroups in a small avar-slavic population from the eigth-ninth century AD. PG - 536-553 LID - 10.1002/ajpa.23380 [doi] AB - OBJECTIVES: In the sixth century AD, Avars came to Central Europe from middle Eurasian steppes and founded a strong Empire called the Avar Khagante (568-799/803 AD) in the Pannonian basin. During the existence of this empire, they undertook many military and pugnacious campaigns. In the seventh century, they conquered the northern territory inhabited by Slavs, who were further recruited in Avar military and were commissioned with obtaining food supplies. During almost 200 years of Avar domination, a significant influence by the Avar culture (especially on the burial rite) and assimilation with indigenous population (occurrence of "East Asian"cranial features) could be noticed in this mixed area, which is supported by achaeological and anthropologcal research. Therefore we expected higher incidence of east Eurasian haplogroups (introduced by Avars) than the frequencies detected in present-day central European populations. MATERIALS AND METHODS: Mitochondrial DNA from 62 human skeletal remains excavated from the Avar-Slavic burial site Cífer-Pác (Slovakia) dated to the eighth and ninth century was analyzed by the sequencing of hypervariable region I and selected parts of coding region. Obtained haplotypes were compared with other present-day and historical populations and genetic distances were calculated using standard statistical method. RESULTS AND DISCUSSION: In total, the detection of mitochondrial haplogroups was possible in 46 individuals. Our results prooved a higher frequency of east Eurasian haplogroups in our analyzed population (6.52%) than in present-day central European populations. However, it is almost three times lower than the frequency of east Eurasian haplogroups detected in other medieval Avar populations. The statistical analysis showed a greater similarity and the lowest genetic distances between the Avar-Slavic burial site Cifer-Pac and medieval European populations than the South Siberian, East and Central Asian populations. CONCLUSION: Our results indicate that the transfer of Avar genetic variation through their mtDNA was rather weak in the analyzed mixed population. CI - © 2018 Wiley Periodicals, Inc. FAU - Šebest, Lukáš AU - Šebest L AUID- ORCID: 0000-0003-2439-4385 AD - Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic. FAU - Baldovič, Marian AU - Baldovič M AD - Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic. FAU - Frtús, Adam AU - Frtús A AD - Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic. FAU - Bognár, Csaba AU - Bognár C AD - Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic. FAU - Kyselicová, Klaudia AU - Kyselicová K AD - Faculty of Medicine, Institute of Physiology, Comenius University, Sasinkova 2, Bratislava 813 72, Slovak Republic. AD - Department of Anthropology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic. FAU - Kádasi, Ľudevít AU - Kádasi Ľ AD - Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic. AD - Biomedical Research Center Slovak Academy of Sciences, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovak Republic. FAU - Beňuš, Radoslav AU - Beňuš R AD - Department of Anthropology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180118 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Adolescent MH - Adult MH - Anthropology, Physical MH - *Asian People/genetics/history/statistics & numerical data MH - Child MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/*genetics MH - Female MH - Genetics, Population MH - Haplotypes/*genetics MH - History, Medieval MH - Humans MH - Male MH - Polymorphism, Single Nucleotide/genetics MH - Slovakia MH - *White People/genetics/history/statistics & numerical data MH - Young Adult OTO - NOTNLM OT - PCA OT - SNP OT - ancient DNA OT - haplotype OT - medieval population EDAT- 2018/01/19 06:00 MHDA- 2018/07/31 06:00 CRDT- 2018/01/19 06:00 PHST- 2016/11/07 00:00 [received] PHST- 2017/10/31 00:00 [revised] PHST- 2017/12/09 00:00 [accepted] PHST- 2018/01/19 06:00 [pubmed] PHST- 2018/07/31 06:00 [medline] PHST- 2018/01/19 06:00 [entrez] AID - 10.1002/ajpa.23380 [doi] PST - ppublish SO - Am J Phys Anthropol. 2018 Mar;165(3):536-553. doi: 10.1002/ajpa.23380. Epub 2018 Jan 18. PMID- 29193490 OWN - NLM STAT- MEDLINE DCOM- 20190726 LR - 20190726 IS - 1520-6300 (Electronic) IS - 1042-0533 (Linking) VI - 30 IP - 2 DP - 2018 Mar TI - The Eastern side of the Westernmost Europeans: Insights from subclades within Y-chromosome haplogroup J-M304. LID - 10.1002/ajhb.23082 [doi] AB - OBJECTIVES: We examined internal lineages and haplotype diversity in Portuguese samples belonging to J-M304 to improve the spatial and temporal understanding of the introduction of this haplogroup in Iberia, using the available knowledge about the phylogeography of its main branches, J1-M267 and J2-M172. METHODS: A total of 110 males of Portuguese descent were analyzed for 17 Y-chromosome bi-allelic markers and seven Y-chromosome short tandem repeats (Y-STR) loci. RESULTS: Among J1-M267 individuals (n = 36), five different sub-haplogroups were identified, with the most common being J1a2b2-L147.1 (∼72%), which encompassed the majority of representatives of the J1a2b-P58 subclade. One sample belonged to the rare J1a1-M365.1 lineage and presented a core Y-STR haplotype consistent with the Iberian settlement during the fifth century by the Alans, a people of Iranian heritage. The analysis of J2-M172 Portuguese males (n = 74) enabled the detection of the two main subclades at very dissimilar frequencies, J2a-M410 (∼80%) and J2b-M12 (∼20%), among which the most common branches were J2a1(xJ2a1b,h)-L26 (22.9%), J2a1b(xJ2a1b1)-M67 (20.3%), J2a1h-L24 (27%), and J2b2-M241 (20.3%). CONCLUSIONS: While previous inferences based on modern haplogroup J Y-chromosomes implicated a main Neolithic dissemination, here we propose a later arrival of J lineages into Iberia using a combination of novel Portuguese Y-chromosomal data and recent evidence from ancient DNA. Our analysis suggests that a substantial tranche of J1-M267 lineages was likely carried into the Iberian Peninsula as a consequence of the trans-Mediterranean contacts during the first millennium BC, while most of the J2-M172 lineages may be associated with post-Neolithic population movements within Europe. CI - © 2017 Wiley Periodicals, Inc. FAU - Manco, Licínio AU - Manco L AUID- ORCID: 0000-0002-2636-0288 AD - Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal. AD - Department of Life Sciences, University of Coimbra, Coimbra, Portugal. FAU - Albuquerque, Joana AU - Albuquerque J AD - Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal. FAU - Sousa, Maria Francisca AU - Sousa MF AD - Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal. FAU - Martiniano, Rui AU - Martiniano R AD - The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambs CB10 1SA, United Kingdom. FAU - de Oliveira, Ricardo Costa AU - de Oliveira RC AD - Department of Sociology, Universidade Federal do Paraná, Curitiba, Brazil. FAU - Marques, Sofia AU - Marques S AD - Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal. AD - Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal. FAU - Gomes, Verónica AU - Gomes V AD - Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal. AD - Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal. FAU - Amorim, António AU - Amorim A AD - Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal. AD - Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal. AD - Department of Biology, Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal. FAU - Alvarez, Luís AU - Alvarez L AD - Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal. AD - Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal. FAU - Prata, Maria João AU - Prata MJ AD - Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal. AD - Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal. AD - Department of Biology, Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20171129 PL - United States TA - Am J Hum Biol JT - American journal of human biology : the official journal of the Human Biology Council JID - 8915029 RN - 0 (Genetic Markers) MH - Alleles MH - Chromosomes, Human, Y/*genetics MH - Genetic Markers/genetics MH - Haplotypes/*genetics MH - Humans MH - Male MH - *Microsatellite Repeats MH - Phylogeography MH - *Polymorphism, Single Nucleotide MH - Portugal OTO - NOTNLM OT - J1-M267 OT - J2-M172 OT - Portugal OT - Y-STR haplotypes OT - Y-chromosome haplogroup J EDAT- 2017/12/02 06:00 MHDA- 2019/07/28 06:00 CRDT- 2017/12/02 06:00 PHST- 2017/05/24 00:00 [received] PHST- 2017/09/22 00:00 [revised] PHST- 2017/11/05 00:00 [accepted] PHST- 2017/12/02 06:00 [pubmed] PHST- 2019/07/28 06:00 [medline] PHST- 2017/12/02 06:00 [entrez] AID - 10.1002/ajhb.23082 [doi] PST - ppublish SO - Am J Hum Biol. 2018 Mar;30(2). doi: 10.1002/ajhb.23082. Epub 2017 Nov 29. PMID- 29391530 OWN - NLM STAT- MEDLINE DCOM- 20190109 LR - 20190201 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 8 IP - 1 DP - 2018 Feb 1 TI - Inferring genetic origins and phenotypic traits of George Bähr, the architect of the Dresden Frauenkirche. PG - 2115 LID - 10.1038/s41598-018-20180-z [doi] LID - 2115 AB - For historic individuals, the outward appearance and other phenotypic characteristics remain often non-resolved. Unfortunately, images or detailed written sources are only scarcely available in many cases. Attempts to study historic individuals with genetic data so far focused on hypervariable regions of mitochondrial DNA and to some extent on complete mitochondrial genomes. To elucidate the potential of in-solution based genome-wide SNP capture methods - as now widely applied in population genetics - we extracted DNA from the 17th century remains of George Bähr, the architect of the Dresdner Frauenkirche. We were able to identify the remains to be of male origin, showing sufficient DNA damage, deriving from a single person and being thus likely authentic. Furthermore, we were able to show that George Bähr had light skin pigmentation and most likely brown eyes. His genomic DNA furthermore points to a Central European origin. We see this analysis as an example to demonstrate the prospects that new in-solution SNP capture methods can provide for historic cases of forensic interest, using methods well established in ancient DNA (aDNA) research and population genetics. FAU - Peltzer, Alexander AU - Peltzer A AUID- ORCID: 0000-0002-6503-2180 AD - Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany. FAU - Mittnik, Alissa AU - Mittnik A AUID- ORCID: 0000-0002-6963-4824 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, 72070, Germany. FAU - Wang, Chuan-Chao AU - Wang CC AUID- ORCID: 0000-0001-9628-0307 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany. AD - Department of Anthropology and Ethnology, Xiamen University, Xiamen, 361005, China. FAU - Begg, Tristan AU - Begg T AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany. FAU - Posth, Cosimo AU - Posth C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, 72070, Germany. FAU - Nieselt, Kay AU - Nieselt K AUID- ORCID: 0000-0002-1283-7065 AD - Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany. FAU - Krause, Johannes AU - Krause J AUID- ORCID: 0000-0001-9144-3920 AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany. krause@shh.mpg.de. AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, 72070, Germany. krause@shh.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180201 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA Damage MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics MH - *Eye Color MH - *Genetics, Population MH - *Genome, Mitochondrial MH - Humans MH - Male MH - Phenotype MH - *Polymorphism, Single Nucleotide MH - Skin Pigmentation/*genetics PMC - PMC5794802 COIS- The authors declare that they have no competing interests. EDAT- 2018/02/03 06:00 MHDA- 2019/01/10 06:00 PMCR- 2018/02/01 CRDT- 2018/02/03 06:00 PHST- 2017/09/06 00:00 [received] PHST- 2018/01/11 00:00 [accepted] PHST- 2018/02/03 06:00 [entrez] PHST- 2018/02/03 06:00 [pubmed] PHST- 2019/01/10 06:00 [medline] PHST- 2018/02/01 00:00 [pmc-release] AID - 10.1038/s41598-018-20180-z [pii] AID - 20180 [pii] AID - 10.1038/s41598-018-20180-z [doi] PST - epublish SO - Sci Rep. 2018 Feb 1;8(1):2115. doi: 10.1038/s41598-018-20180-z. PMID- 29382278 OWN - NLM STAT- MEDLINE DCOM- 20180808 LR - 20180808 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 45 IP - 1 DP - 2018 Feb TI - Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. PG - 20-33 LID - 10.1080/03014460.2017.1402956 [doi] AB - CONTEXT: Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE: For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS: A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS: Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS: There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility. FAU - Larmuseau, Maarten H D AU - Larmuseau MHD AD - a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium. AD - b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium. FAU - Ottoni, Claudio AU - Ottoni C AD - c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway. LA - eng PT - Journal Article PT - Review PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 SB - IM MH - Africa, Northern MH - Chromosomes, Human, Y/*genetics MH - *Demography MH - *Human Migration MH - Humans MH - Male MH - Mediterranean Region MH - Middle East OTO - NOTNLM OT - Mediterranean OT - Y-chromosome OT - extra-pair paternity OT - forensics OT - population genetics OT - surnames EDAT- 2018/02/01 06:00 MHDA- 2018/08/09 06:00 CRDT- 2018/02/01 06:00 PHST- 2018/02/01 06:00 [entrez] PHST- 2018/02/01 06:00 [pubmed] PHST- 2018/08/09 06:00 [medline] AID - 10.1080/03014460.2017.1402956 [doi] PST - ppublish SO - Ann Hum Biol. 2018 Feb;45(1):20-33. doi: 10.1080/03014460.2017.1402956. PMID- 29328350 OWN - NLM STAT- MEDLINE DCOM- 20180619 LR - 20201209 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 75 IP - 1 DP - 2018 Feb 1 TI - Helicobacter pylori DNA obtained from the stomach specimens of two 17(th) century Korean mummies. PG - 75-87 LID - 10.1127/anthranz/2018/0780 [doi] AB - Helicobacter pylori is a bacterium that grows in the stomach mucosal epithelium, and can induce gastric diseases. Although many studies on modern H. pylori genomes have been reported from all over the world, a comprehensive picture of H. pylori is still lacking. Therefore, there is a pressing need to obtain archaeological specimens and to subject the ancient DNA (aDNA) extracted therefrom to analysis. Considering the typically excellent state of preservation of Joseon mummies discovered in Korea, we thus tried to isolate ancient H. pylori DNA from their mummified stomach specimens. After screening Korean mummy stomachs containing remnant H. pylori DNA, vacA (s- and m-region) alleles were successfully identified in the stomach isolates of two samples. The H. pylori strains identified had vacA s1/m2 (Cheongdo mummy) and s1 (Dangjin mummy) alleles. This paper is significant in that it is the first report of presumptive ancient H. pylori DNA obtained from East Asian archaeological specimens. However, full characterization and exploitation of ancient H. pylori DNA remnant in Joseon mummy specimens will require subsequent investigations utilizing the most cutting-edge techniques established for the analysis of ancient intestinal-content samples, such as next-generation sequencing (NGS). FAU - Shin, Dong Hoon AU - Shin DH AD - Bioanthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea. AD - Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea. FAU - Oh, Chang Seok AU - Oh CS AD - Bioanthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea. FAU - Hong, Jong Ha AU - Hong JH AD - Bioanthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea. FAU - Lee, Hyejin AU - Lee H AD - Bioanthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea. AD - Ministry of National Defense Agency KIA Recovery & Identification, Seoul, South Korea. FAU - Lee, Soong Deok AU - Lee SD AD - Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea. AD - Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea. FAU - Lee, Eunju AU - Lee E AD - Department of Internal Medicine, Asan Medical Center, University of Ulsan, Seoul, South Korea. LA - eng PT - Historical Article PT - Journal Article DEP - 20180112 PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Bacterial/analysis/*isolation & purification MH - *Helicobacter Infections/ethnology/history/microbiology MH - *Helicobacter pylori/genetics/isolation & purification MH - History, 17th Century MH - Humans MH - *Mummies/history/microbiology MH - Republic of Korea/ethnology MH - Stomach/*microbiology EDAT- 2018/01/13 06:00 MHDA- 2018/06/21 06:00 CRDT- 2018/01/13 06:00 PHST- 2017/05/23 00:00 [received] PHST- 2017/09/08 00:00 [revised] PHST- 2017/09/08 00:00 [accepted] PHST- 2018/01/13 06:00 [pubmed] PHST- 2018/06/21 06:00 [medline] PHST- 2018/01/13 06:00 [entrez] AID - 10.1127/anthranz/2018/0780 [doi] PST - ppublish SO - Anthropol Anz. 2018 Feb 1;75(1):75-87. doi: 10.1127/anthranz/2018/0780. Epub 2018 Jan 12. PMID- 29216758 OWN - NLM STAT- MEDLINE DCOM- 20180808 LR - 20220408 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 45 IP - 1 DP - 2018 Feb TI - Iron Age Italic population genetics: the Piceni from Novilara (8th-7th century BC). PG - 34-43 LID - 10.1080/03014460.2017.1414876 [doi] AB - BACKGROUND: Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed. AIMS: To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis. SUBJECTS AND METHODS: In a first set of 10 individuals from Novilara, we performed deep sequencing of the HVS-I region of the mtDNA, combined with the genotyping of 22 SNPs in the coding region and the analysis of several autosomal markers. RESULTS: The results show a low nucleotide diversity for the inhabitants of Novilara and highlight a genetic affinity of this ancient population with the current inhabitants of central Italy. No family relationship was observed between the individuals analysed here. CONCLUSIONS: This study provides a preliminary characterisation of the mtDNA variability of the Piceni of Novilara, as well as a kinship assessment of two peculiar burials. FAU - Serventi, Patrizia AU - Serventi P AD - a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy. AD - b Department of Cultural Heritage , University of Bologna , Ravenna , Italy. FAU - Panicucci, Chiara AU - Panicucci C AD - b Department of Cultural Heritage , University of Bologna , Ravenna , Italy. FAU - Bodega, Roberta AU - Bodega R AD - a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy. FAU - De Fanti, Sara AU - De Fanti S AD - a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy. FAU - Sarno, Stefania AU - Sarno S AD - a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy. FAU - Fondevila Alvarez, Manuel AU - Fondevila Alvarez M AD - c Instituto de Ciencias Forenses 'Luis Concheiro' , University of Santiago de Compostela, Santiago de Compostela , Galicia , Spain. FAU - Brisighelli, Francesca AU - Brisighelli F AD - d Sezione di Medicina Legale-Istituto di Sanità Pubblica , Università Cattolica del Sacro Cuore , Roma , Italy. FAU - Trombetta, Beniamino AU - Trombetta B AD - e Department of Biology and Biotechnology 'Charles Darwin' , Sapienza University , Rome , Italy. FAU - Anagnostou, Paolo AU - Anagnostou P AUID- ORCID: 0000-0003-0768-4612 AD - f Department of Environmental Biology , University of Rome 'La Sapienza' , Rome , Italy. AD - g ISItA, Istituto Italiano di Antropologia , Rome , Italy. FAU - Ferri, Gianmarco AU - Ferri G AD - h Department of Diagnostic and Clinical Medicine and Public Health , University of Modena and Reggio Emilia , Modena , Italy. FAU - Vazzana, Antonino AU - Vazzana A AD - b Department of Cultural Heritage , University of Bologna , Ravenna , Italy. FAU - Delpino, Chiara AU - Delpino C AD - i Superintendence of Archaeological Heritage of Marche Region , Ancona , Italy. FAU - Gruppioni, Giorgio AU - Gruppioni G AD - b Department of Cultural Heritage , University of Bologna , Ravenna , Italy. FAU - Luiselli, Donata AU - Luiselli D AD - a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy. FAU - Cilli, Elisabetta AU - Cilli E AUID- ORCID: 0000-0003-0407-267X AD - b Department of Cultural Heritage , University of Bologna , Ravenna , Italy. LA - eng PT - Journal Article PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/*analysis MH - Female MH - *Genetic Variation MH - *Haplotypes MH - Humans MH - Italy MH - Male MH - *Polymorphism, Single Nucleotide OTO - NOTNLM OT - Ancient DNA OT - Italian population genetic OT - Mitochondrial DNA OT - Piceni OT - autosomal markers EDAT- 2017/12/09 06:00 MHDA- 2018/08/09 06:00 CRDT- 2017/12/09 06:00 PHST- 2017/12/09 06:00 [pubmed] PHST- 2018/08/09 06:00 [medline] PHST- 2017/12/09 06:00 [entrez] AID - 10.1080/03014460.2017.1414876 [doi] PST - ppublish SO - Ann Hum Biol. 2018 Feb;45(1):34-43. doi: 10.1080/03014460.2017.1414876. PMID- 29320542 OWN - NLM STAT- MEDLINE DCOM- 20180214 LR - 20211204 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 13 IP - 1 DP - 2018 TI - Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility. PG - e0190169 LID - 10.1371/journal.pone.0190169 [doi] LID - e0190169 AB - The Phoenicians emerged in the Northern Levant around 1800 BCE and by the 9th century BCE had spread their culture across the Mediterranean Basin, establishing trading posts, and settlements in various European Mediterranean and North African locations. Despite their widespread influence, what is known of the Phoenicians comes from what was written about them by the Greeks and Egyptians. In this study, we investigate the extent of Phoenician integration with the Sardinian communities they settled. We present 14 new ancient mitogenome sequences from pre-Phoenician (~1800 BCE) and Phoenician (~700-400 BCE) samples from Lebanon (n = 4) and Sardinia (n = 10) and compare these with 87 new complete mitogenomes from modern Lebanese and 21 recently published pre-Phoenician ancient mitogenomes from Sardinia to investigate the population dynamics of the Phoenician (Punic) site of Monte Sirai, in southern Sardinia. Our results indicate evidence of continuity of some lineages from pre-Phoenician populations suggesting integration of indigenous Sardinians in the Monte Sirai Phoenician community. We also find evidence of the arrival of new, unique mitochondrial lineages, indicating the movement of women from sites in the Near East or North Africa to Sardinia, but also possibly from non-Mediterranean populations and the likely movement of women from Europe to Phoenician sites in Lebanon. Combined, this evidence suggests female mobility and genetic diversity in Phoenician communities, reflecting the inclusive and multicultural nature of Phoenician society. FAU - Matisoo-Smith, E AU - Matisoo-Smith E AUID- ORCID: 0000-0002-3500-8307 AD - Department of Anatomy, University of Otago, Dunedin, New Zealand. FAU - Gosling, A L AU - Gosling AL AD - Department of Anatomy, University of Otago, Dunedin, New Zealand. FAU - Platt, D AU - Platt D AD - Department of Computational Genomics, IBM T. J. Watson Research Center, Yorktown Heights, New York, United States of America. FAU - Kardailsky, O AU - Kardailsky O AD - Department of Anatomy, University of Otago, Dunedin, New Zealand. FAU - Prost, S AU - Prost S AD - Department of Biology, Stanford University, Stanford, California, United States of America. AD - Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America. FAU - Cameron-Christie, S AU - Cameron-Christie S AD - Department of Anatomy, University of Otago, Dunedin, New Zealand. FAU - Collins, C J AU - Collins CJ AD - Department of Anatomy, University of Otago, Dunedin, New Zealand. FAU - Boocock, J AU - Boocock J AD - Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America. FAU - Kurumilian, Y AU - Kurumilian Y AD - School of Medicine, Lebanese American University, Byblos, Lebanon. FAU - Guirguis, M AU - Guirguis M AD - Department of Storia, Scienze dell'Uomo e della Formazione, University of Sassari, Sassari, Italy. FAU - Pla Orquín, R AU - Pla Orquín R AD - Department of Storia, Scienze dell'Uomo e della Formazione, University of Sassari, Sassari, Italy. FAU - Khalil, W AU - Khalil W AD - Department of Arts and Archeology, Lebanese University, Beirut, Lebanon. FAU - Genz, H AU - Genz H AD - Department of History and Archeology, American University of Beirut, Beirut, Lebanon. FAU - Abou Diwan, G AU - Abou Diwan G AD - Department of Arts and Archeology, Lebanese University, Beirut, Lebanon. FAU - Nassar, J AU - Nassar J AD - Department of Arts and Archeology, Lebanese University, Beirut, Lebanon. FAU - Zalloua, P AU - Zalloua P AD - School of Medicine, Lebanese American University, Byblos, Lebanon. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180110 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adolescent MH - Adult MH - Child MH - Culture MH - DNA, Mitochondrial/analysis/isolation & purification MH - *Demography MH - Ethnicity/genetics/*history MH - Female MH - Genetic Variation MH - *Genome, Mitochondrial MH - Haplotypes MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Italy MH - Lebanon/ethnology MH - Mediterranean Region MH - Phylogeny MH - Population Dynamics MH - Tooth MH - *Women PMC - PMC5761892 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2018/01/11 06:00 MHDA- 2018/02/15 06:00 PMCR- 2018/01/10 CRDT- 2018/01/11 06:00 PHST- 2017/06/27 00:00 [received] PHST- 2017/12/08 00:00 [accepted] PHST- 2018/01/11 06:00 [entrez] PHST- 2018/01/11 06:00 [pubmed] PHST- 2018/02/15 06:00 [medline] PHST- 2018/01/10 00:00 [pmc-release] AID - PONE-D-17-24250 [pii] AID - 10.1371/journal.pone.0190169 [doi] PST - epublish SO - PLoS One. 2018 Jan 10;13(1):e0190169. doi: 10.1371/journal.pone.0190169. eCollection 2018. PMID- 29310587 OWN - NLM STAT- MEDLINE DCOM- 20180810 LR - 20181113 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 19 IP - 1 DP - 2018 Jan 8 TI - Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing. PG - 30 LID - 10.1186/s12864-017-4428-5 [doi] LID - 30 AB - BACKGROUND: Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. Therefore, the limit-of-detection of an MPS assay is directly related to the degree of index cross-talk. RESULTS: Cross-talk rates up to 0.29% were observed when using standard, combinatorial adapters, resulting in 110,180 (0.1% cross-talk rate) or 1,121,074 (0.29% cross-talk rate) misassigned reads per lane in non-patterned and patterned Illumina flow cells, respectively. Here, we demonstrate that using unique, dual-matched indexed adapters dramatically reduces index cross-talk to ≤1 misassigned reads per flow cell lane. While the current study was performed using dual-matched indices, using unique, dual-unrelated indices would also be an effective alternative. CONCLUSIONS: For sensitive downstream analyses, the use of combinatorial indices for multiplexed hybrid capture and sequencing is inappropriate, as it results in an unacceptable number of misassigned reads. Cross-talk can be virtually eliminated using dual-matched indexed adapters. These results suggest that use of such adapters is critical to reduce false positive rates in assays that aim to identify low allele frequency events, and strongly indicate that dual-matched adapters be implemented for all sensitive MPS applications. FAU - MacConaill, Laura E AU - MacConaill LE AD - Center for Cancer Genome Discovery, DFCI, 450 Brookline Avenue, Dana840b, Boston, MA, 02215, USA. AD - Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA. FAU - Burns, Robert T AU - Burns RT AD - Center for Cancer Genome Discovery, DFCI, 450 Brookline Avenue, Dana840b, Boston, MA, 02215, USA. FAU - Nag, Anwesha AU - Nag A AD - Center for Cancer Genome Discovery, DFCI, 450 Brookline Avenue, Dana840b, Boston, MA, 02215, USA. FAU - Coleman, Haley A AU - Coleman HA AD - Center for Cancer Genome Discovery, DFCI, 450 Brookline Avenue, Dana840b, Boston, MA, 02215, USA. FAU - Slevin, Michael K AU - Slevin MK AD - Center for Cancer Genome Discovery, DFCI, 450 Brookline Avenue, Dana840b, Boston, MA, 02215, USA. FAU - Giorda, Kristina AU - Giorda K AD - Integrated DNA Technologies, Inc., Redwood City, CA, USA. FAU - Light, Madelyn AU - Light M AD - Integrated DNA Technologies, Inc., Redwood City, CA, USA. FAU - Lai, Kevin AU - Lai K AD - Integrated DNA Technologies, Inc., Redwood City, CA, USA. FAU - Jarosz, Mirna AU - Jarosz M AD - Integrated DNA Technologies, Inc., Redwood City, CA, USA. FAU - McNeill, Matthew S AU - McNeill MS AD - Integrated DNA Technologies, Inc., Coralville, IA, USA. FAU - Ducar, Matthew D AU - Ducar MD AD - Center for Cancer Genome Discovery, DFCI, 450 Brookline Avenue, Dana840b, Boston, MA, 02215, USA. FAU - Meyerson, Matthew AU - Meyerson M AD - Center for Cancer Genome Discovery, DFCI, 450 Brookline Avenue, Dana840b, Boston, MA, 02215, USA. AD - Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA. AD - Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA. AD - Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAU - Thorner, Aaron R AU - Thorner AR AD - Center for Cancer Genome Discovery, DFCI, 450 Brookline Avenue, Dana840b, Boston, MA, 02215, USA. Aaron_Thorner@dfci.harvard.edu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180108 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 SB - IM MH - Computational Biology/*methods MH - *High-Throughput Nucleotide Sequencing/methods/standards MH - Humans MH - Sensitivity and Specificity MH - *Sequence Analysis, DNA/methods/standards PMC - PMC5759201 OTO - NOTNLM OT - Adapter OT - Barcode cross-talk OT - Illumina OT - Index OT - Massively parallel sequencing OT - Molecular barcode OT - Multiplexing OT - Next generation sequencing OT - UMI COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Patient tumor sample collection and sequencing was performed with approval from the DFCI IRB (DFCI IRB protocol 11–104). Written informed consent was obtained from participants prior to inclusion. CONSENT FOR PUBLICATION: N/A COMPETING INTERESTS: The CCGD received dual-matched index sequencing adapter oligos at no cost from IDT for experimental testing. Matthew Meyerson is a founder and equity holder of Foundation Medicine, a for-profit company that provides next-generation sequencing diagnostic services. PUBLISHER’S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EDAT- 2018/01/10 06:00 MHDA- 2018/08/11 06:00 PMCR- 2018/01/08 CRDT- 2018/01/10 06:00 PHST- 2017/09/21 00:00 [received] PHST- 2017/12/29 00:00 [accepted] PHST- 2018/01/10 06:00 [entrez] PHST- 2018/01/10 06:00 [pubmed] PHST- 2018/08/11 06:00 [medline] PHST- 2018/01/08 00:00 [pmc-release] AID - 10.1186/s12864-017-4428-5 [pii] AID - 4428 [pii] AID - 10.1186/s12864-017-4428-5 [doi] PST - epublish SO - BMC Genomics. 2018 Jan 8;19(1):30. doi: 10.1186/s12864-017-4428-5. PMID- 29301990 OWN - NLM STAT- MEDLINE DCOM- 20180410 LR - 20180410 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 359 IP - 6371 DP - 2018 Jan 5 TI - Americas peopled in a single wave, ancient genome reveals. PG - 14 LID - 10.1126/science.359.6371.14 [doi] FAU - Price, Michael AU - Price M AD - Michael Price is a freelance writer in San Diego, California. LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Ancient) SB - IM MH - Alaska MH - Asia MH - *DNA, Ancient MH - *Genome, Human MH - *Human Migration MH - Humans MH - Infant EDAT- 2018/01/06 06:00 MHDA- 2018/04/11 06:00 CRDT- 2018/01/06 06:00 PHST- 2018/01/06 06:00 [entrez] PHST- 2018/01/06 06:00 [pubmed] PHST- 2018/04/11 06:00 [medline] AID - 359/6371/14 [pii] AID - 10.1126/science.359.6371.14 [doi] PST - ppublish SO - Science. 2018 Jan 5;359(6371):14. doi: 10.1126/science.359.6371.14. PMID- 29167200 OWN - NLM STAT- MEDLINE DCOM- 20181002 LR - 20181219 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 208 IP - 1 DP - 2018 Jan TI - Assessing the Relationship of Ancient and Modern Populations. PG - 383-398 LID - 10.1534/genetics.117.300448 [doi] AB - Genetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach, such as selecting a read at random for each site, to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population, while accounting for sequencing error and postmortem damage by analyzing raw reads from multiple ancient individuals simultaneously. We show that, when analyzing SNP data, it is better to sequence more ancient samples to low coverage: two samples sequenced to 0.5× coverage provide better resolution than a single sample sequenced to 2× coverage. We also examined the power to detect whether an ancient sample is directly ancestral to a modern population, finding that, with even a few high coverage individuals, even ancient samples that are very slightly diverged from the modern population can be detected with ease. When we applied our approach to European samples, we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth. CI - Copyright © 2018 Schraiber. FAU - Schraiber, Joshua G AU - Schraiber JG AUID- ORCID: 0000-0002-7912-2195 AD - Department of Biology, and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania 19122 joshua.schraiber@temple.edu. LA - eng GR - R35 GM124745/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20171122 PL - United States TA - Genetics JT - Genetics JID - 0374636 RN - 0 (DNA, Ancient) SB - IM MH - Algorithms MH - Alleles MH - *DNA, Ancient MH - *Genetics, Population MH - Humans MH - *Models, Genetic MH - Polymorphism, Single Nucleotide PMC - PMC5753871 OTO - NOTNLM OT - SNP data OT - ancient DNA OT - diffusion theory OT - population continuity EDAT- 2017/11/24 06:00 MHDA- 2018/10/03 06:00 PMCR- 2017/11/22 CRDT- 2017/11/24 06:00 PHST- 2017/07/24 00:00 [received] PHST- 2017/11/17 00:00 [accepted] PHST- 2017/11/24 06:00 [pubmed] PHST- 2018/10/03 06:00 [medline] PHST- 2017/11/24 06:00 [entrez] PHST- 2017/11/22 00:00 [pmc-release] AID - genetics.117.300448 [pii] AID - 300448 [pii] AID - 10.1534/genetics.117.300448 [doi] PST - ppublish SO - Genetics. 2018 Jan;208(1):383-398. doi: 10.1534/genetics.117.300448. Epub 2017 Nov 22. PMID- 29023628 OWN - NLM STAT- MEDLINE DCOM- 20180102 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 165 IP - 1 DP - 2018 Jan TI - Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data. PG - 139-148 LID - 10.1002/ajpa.23338 [doi] AB - OBJECTIVES: The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern-day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large-scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido. MATERIALS AND METHODS: Mitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup-defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations. RESULTS: Our findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan. DISCUSSION: Our results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual-structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people. CI - © 2017 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc. FAU - Adachi, Noboru AU - Adachi N AUID- ORCID: 0000-0002-5314-8047 AD - Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan. FAU - Kakuda, Tsuneo AU - Kakuda T AD - Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan. FAU - Takahashi, Ryohei AU - Takahashi R AD - Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan. FAU - Kanzawa-Kiriyama, Hideaki AU - Kanzawa-Kiriyama H AD - Department of Anthropology, National Museum of Nature and Science, Tokyo Tsukuba, Ibaraki 305-0005, Japan. FAU - Shinoda, Ken-Ichi AU - Shinoda KI AD - Department of Anthropology, National Museum of Nature and Science, Tokyo Tsukuba, Ibaraki 305-0005, Japan. LA - eng PT - Journal Article DEP - 20171011 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/*genetics MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/classification/*genetics MH - Ethnicity/*genetics MH - Genetics, Population MH - Haplotypes/genetics MH - Humans MH - Japan MH - Polymorphism, Single Nucleotide/genetics MH - Sequence Analysis, DNA MH - Siberia PMC - PMC5765509 OTO - NOTNLM OT - Jomon OT - Okhotsk culture OT - Satsumon OT - Siberia OT - ancient DNA EDAT- 2017/10/13 06:00 MHDA- 2018/01/03 06:00 PMCR- 2018/01/12 CRDT- 2017/10/13 06:00 PHST- 2017/03/21 00:00 [received] PHST- 2017/09/25 00:00 [revised] PHST- 2017/09/26 00:00 [accepted] PHST- 2017/10/13 06:00 [pubmed] PHST- 2018/01/03 06:00 [medline] PHST- 2017/10/13 06:00 [entrez] PHST- 2018/01/12 00:00 [pmc-release] AID - AJPA23338 [pii] AID - 10.1002/ajpa.23338 [doi] PST - ppublish SO - Am J Phys Anthropol. 2018 Jan;165(1):139-148. doi: 10.1002/ajpa.23338. Epub 2017 Oct 11. PMID- 28034339 OWN - NLM STAT- MEDLINE DCOM- 20180329 LR - 20221207 IS - 2470-1408 (Electronic) IS - 2470-1394 (Linking) VI - 29 IP - 1 DP - 2018 Jan TI - On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations. PG - 147-157 LID - 10.1080/24701394.2016.1258406 [doi] AB - The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000-11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000-10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations. The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean. FAU - Kefi, Rym AU - Kefi R AD - a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia. AD - b University Tunis El Manar , Tunis , Tunisia. FAU - Hechmi, Meriem AU - Hechmi M AD - a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia. FAU - Naouali, Chokri AU - Naouali C AD - a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia. AD - b University Tunis El Manar , Tunis , Tunisia. FAU - Jmel, Haifa AU - Jmel H AD - a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia. FAU - Hsouna, Sana AU - Hsouna S AD - a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia. AD - b University Tunis El Manar , Tunis , Tunisia. FAU - Bouzaid, Eric AU - Bouzaid E AD - c Institut National de Police Scientifique Laboratoire de Marseille , Marseille , France. FAU - Abdelhak, Sonia AU - Abdelhak S AD - a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia. AD - b University Tunis El Manar , Tunis , Tunisia. FAU - Beraud-Colomb, Eliane AU - Beraud-Colomb E AD - d 20 rue d'Endoume , Marseille 13007 , France. FAU - Stevanovitch, Alain AU - Stevanovitch A AD - c Institut National de Police Scientifique Laboratoire de Marseille , Marseille , France. LA - eng PT - Historical Article PT - Journal Article DEP - 20161230 PL - England TA - Mitochondrial DNA A DNA Mapp Seq Anal JT - Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis JID - 101679980 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Africa, Northern MH - *DNA, Ancient MH - *DNA, Mitochondrial MH - Gene Flow MH - Genetic Variation MH - Genetics, Population MH - Genome, Mitochondrial MH - History, Ancient MH - Humans MH - Mediterranean Region MH - *Phylogeny MH - Sequence Analysis, DNA MH - White People/*genetics OTO - NOTNLM OT - Epiplaeolithic OT - Genetic diversity OT - North Africa OT - ancient DNA OT - mitochondrial DNA EDAT- 2016/12/31 06:00 MHDA- 2018/03/30 06:00 CRDT- 2016/12/31 06:00 PHST- 2016/12/31 06:00 [pubmed] PHST- 2018/03/30 06:00 [medline] PHST- 2016/12/31 06:00 [entrez] AID - 10.1080/24701394.2016.1258406 [doi] PST - ppublish SO - Mitochondrial DNA A DNA Mapp Seq Anal. 2018 Jan;29(1):147-157. doi: 10.1080/24701394.2016.1258406. Epub 2016 Dec 30. PMID- 29273718 OWN - NLM STAT- MEDLINE DCOM- 20190726 LR - 20190726 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 7 IP - 1 DP - 2017 Dec 22 TI - Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico. PG - 18100 LID - 10.1038/s41598-017-18356-0 [doi] LID - 18100 AB - The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previous attempts to resolve these questions using conventional genetic techniques. We apply advanced in-solution mitogenome capture and high-throughput sequencing to fourteen dental samples obtained from the Greater Nicoya sites of Jícaro and La Cascabel in northwest Costa Rica (n = 9; A.D. 800-1250) and the Casas Grandes sites of Paquimé and Convento in northwest Mexico (n = 5; A.D. 1200-1450). Full mitogenome reconstruction was successful for three individuals from Jícaro and five individuals from Paquimé and Convento. The three Jícaro individuals belong to haplogroup B2d, a haplogroup found today only among Central American Chibchan-speakers. The five Paquimé and Convento individuals belong to haplogroups C1c1a, C1c5, B2f and B2a which, are found in contemporary populations in North America and Mesoamerica. We report the first successfully reconstructed ancient mitogenomes from Central America, and the first genetic evidence of ancestry affinity of the ancient inhabitants of Greater Nicoya and Casas Grandes with contemporary Isthmo-Columbian and Greater Southwest populations, respectively. FAU - Morales-Arce, Ana Y AU - Morales-Arce AY AUID- ORCID: 0000-0002-2934-3141 AD - Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada. aymorale@ucalgary.ca. FAU - Hofman, Courtney A AU - Hofman CA AUID- ORCID: 0000-0002-6808-3370 AD - Department of Anthropology, University of Oklahoma, Norman, Oklahoma, 73019, USA. FAU - Duggan, Ana T AU - Duggan AT AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, L8S 4L8, Canada. FAU - Benfer, Adam K AU - Benfer AK AD - Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada. FAU - Katzenberg, M Anne AU - Katzenberg MA AD - Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada. FAU - McCafferty, Geoffrey AU - McCafferty G AD - Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada. FAU - Warinner, Christina AU - Warinner C AD - Department of Anthropology, University of Oklahoma, Norman, Oklahoma, 73019, USA. warinner@shh.mpg.de. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07743, Germany. warinner@shh.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20171222 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) MH - Central America MH - *DNA, Ancient MH - Genetics, Population MH - *Genome, Mitochondrial MH - *Haplotypes MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Mexico PMC - PMC5741722 COIS- The authors declare that they have no competing interests. EDAT- 2017/12/24 06:00 MHDA- 2019/07/28 06:00 PMCR- 2017/12/22 CRDT- 2017/12/24 06:00 PHST- 2017/06/13 00:00 [received] PHST- 2017/12/11 00:00 [accepted] PHST- 2017/12/24 06:00 [entrez] PHST- 2017/12/24 06:00 [pubmed] PHST- 2019/07/28 06:00 [medline] PHST- 2017/12/22 00:00 [pmc-release] AID - 10.1038/s41598-017-18356-0 [pii] AID - 18356 [pii] AID - 10.1038/s41598-017-18356-0 [doi] PST - epublish SO - Sci Rep. 2017 Dec 22;7(1):18100. doi: 10.1038/s41598-017-18356-0. PMID- 29246100 OWN - NLM STAT- MEDLINE DCOM- 20180118 LR - 20221207 IS - 1471-2156 (Electronic) IS - 1471-2156 (Linking) VI - 18 IP - 1 DP - 2017 Dec 15 TI - Investigating population continuity with ancient DNA under a spatially explicit simulation framework. PG - 114 LID - 10.1186/s12863-017-0575-6 [doi] LID - 114 AB - BACKGROUND: Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory. Comparing samples taken in the same region but at different times, hereafter called "serial samples", may indicate whether there is continuity in the peopling history of that area or whether an immigration of a genetically different population has occurred between the two sampling times. However, the exploration of genetic relationships between serial samples generally ignores their geographical locations and the spatiotemporal dynamics of populations. Here, we present a new coalescent-based, spatially explicit modelling approach to investigate population continuity using aDNA, which includes two fundamental elements neglected in previous methods: population structure and migration. The approach also considers the extensive temporal and geographical variance that is commonly found in aDNA population samples. RESULTS: We first showed that our spatially explicit approach is more conservative than the previous (panmictic) approach and should be preferred to test for population continuity, especially when small and isolated populations are considered. We then applied our method to two mitochondrial datasets from Germany and France, both including modern and ancient lineages dating from the early Neolithic. The results clearly reject population continuity for the maternal line over the last 7500 years for the German dataset but not for the French dataset, suggesting regional heterogeneity in post-Neolithic migratory processes. CONCLUSIONS: Here, we demonstrate the benefits of using a spatially explicit method when investigating population continuity with aDNA. It constitutes an improvement over panmictic methods by considering the spatiotemporal dynamics of genetic lineages and the precise location of ancient samples. The method can be used to investigate population continuity between any pair of serial samples (ancient-ancient or ancient-modern) and to investigate more complex evolutionary scenarios. Although we based our study on mitochondrial DNA sequences, diploid molecular markers of different types (DNA, SNP, STR) can also be simulated with our approach. It thus constitutes a promising tool for the analysis of the numerous aDNA datasets being produced, including genome wide data, in humans but also in many other species. FAU - Silva, Nuno Miguel AU - Silva NM AD - AGP lab, Department of Genetics & Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland. FAU - Rio, Jeremy AU - Rio J AD - AGP lab, Department of Genetics & Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland. FAU - Currat, Mathias AU - Currat M AUID- ORCID: 0000-0001-5211-8922 AD - AGP lab, Department of Genetics & Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland. mathias.currat@unige.ch. AD - Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland. mathias.currat@unige.ch. LA - eng GR - grant 31003A_156853/Swiss NSF/ GR - Marie Curie initial training BEAN (GA 289966)/European Research Council/International PT - Journal Article DEP - 20171215 PL - England TA - BMC Genet JT - BMC genetics JID - 100966978 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - *Biological Evolution MH - *Computer Simulation MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Emigration and Immigration MH - Europe MH - Genetic Variation MH - Genetics, Population MH - Humans MH - White People/*genetics PMC - PMC5731203 OTO - NOTNLM OT - Ancient DNA OT - European Neolithic OT - Population continuity OT - Population genetics OT - Serial coalescent OT - Spatially-explicit simulations COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable. CONSENT FOR PUBLICATION: Not applicable. COMPETING INTERESTS: The authors declare that they have no competing interests. EDAT- 2017/12/17 06:00 MHDA- 2018/01/19 06:00 PMCR- 2017/12/15 CRDT- 2017/12/17 06:00 PHST- 2017/06/21 00:00 [received] PHST- 2017/11/29 00:00 [accepted] PHST- 2017/12/17 06:00 [entrez] PHST- 2017/12/17 06:00 [pubmed] PHST- 2018/01/19 06:00 [medline] PHST- 2017/12/15 00:00 [pmc-release] AID - 10.1186/s12863-017-0575-6 [pii] AID - 575 [pii] AID - 10.1186/s12863-017-0575-6 [doi] PST - epublish SO - BMC Genet. 2017 Dec 15;18(1):114. doi: 10.1186/s12863-017-0575-6. PMID- 29202706 OWN - NLM STAT- MEDLINE DCOM- 20180309 LR - 20221207 IS - 1471-2148 (Electronic) IS - 1471-2148 (Linking) VI - 17 IP - 1 DP - 2017 Dec 4 TI - Ancient DNA reveals genetic connections between early Di-Qiang and Han Chinese. PG - 239 LID - 10.1186/s12862-017-1082-0 [doi] LID - 239 AB - BACKGROUND: Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~4000 years old) and compared them to other ancient DNA across China, including an early Han-related site (Hengbei site dated ~3000 years old) to establish the underlying genetic relationship between the Di-Qiang and ancestors of Han Chinese. RESULTS: We found Mogou mtDNA haplogroups were highly diverse, comprising 14 haplogroups: A, B, C, D (D*, D4, D5), F, G, M7, M8, M10, M13, M25, N*, N9a, and Z. In contrast, Mogou males were all Y-DNA haplogroup O3a2/P201; specifically one male was further assigned to O3a2c1a/M117 using targeted unique regions on the non-recombining region of the Y-chromosome. We compared Mogou to 7 other ancient and 38 modern Chinese groups, in a total of 1793 individuals, and found that Mogou shared close genetic distances with Taojiazhai (a more recent Di-Qiang population), Hengbei, and Northern Han. We modeled their interactions using Approximate Bayesian Computation, and support was given to a potential admixture of ~13-18% between the Mogou and Northern Han around 3300-3800 years ago. CONCLUSIONS: Mogou harbors the earliest genetically identifiable Di-Qiang, ancestral to the Taojiazhai, and up to ~33% paternal and ~70% of its maternal haplogroups could be found in present-day Northern Han Chinese. FAU - Li, Jiawei AU - Li J AD - College of Life Science, Jilin University, Changchun, 130023, People's Republic of China. FAU - Zeng, Wen AU - Zeng W AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, People's Republic of China. FAU - Zhang, Ye AU - Zhang Y AD - College of Life Science, Jilin University, Changchun, 130023, People's Republic of China. FAU - Ko, Albert Min-Shan AU - Ko AM AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, 100044, People's Republic of China. FAU - Li, Chunxiang AU - Li C AD - College of Life Science, Jilin University, Changchun, 130023, People's Republic of China. FAU - Zhu, Hong AU - Zhu H AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, People's Republic of China. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, 100044, People's Republic of China. fuqiaomei@ivpp.ac.cn. FAU - Zhou, Hui AU - Zhou H AUID- ORCID: 0000-0001-5858-5636 AD - College of Life Science, Jilin University, Changchun, 130023, People's Republic of China. zhouhui@jlu.edu.cn. AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, People's Republic of China. zhouhui@jlu.edu.cn. LA - eng GR - 31371266/National Natural Science Foundation of China/International GR - 31200935/National Natural Science Foundation of China/International GR - 11&ZD182/National Social Science Foundation of China/International PT - Journal Article DEP - 20171204 PL - England TA - BMC Evol Biol JT - BMC evolutionary biology JID - 100966975 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/*genetics MH - Bayes Theorem MH - China MH - Chromosomes, Human, Y/genetics MH - Computer Simulation MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Ethnicity/*genetics MH - Genetics, Population MH - Geography MH - Haplotypes/genetics MH - Humans MH - Male MH - Models, Genetic MH - Phylogeny MH - Polymorphism, Single Nucleotide/genetics MH - Principal Component Analysis MH - Probability MH - Time Factors PMC - PMC5716020 OTO - NOTNLM OT - Ancient DNA OT - Di-Qiang population OT - Han Chinese population OT - Mitochondrial DNA OT - Non-recombining region of the Y-chromosome COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: No Ethics committee approval was required to conduct this research project. CONSENT FOR PUBLICATION: No living human subjects were part of the study, thus no consent to participate or to publish the data was required. COMPETING INTERESTS: The authors declare that they have no competing interests. PUBLISHER’S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EDAT- 2017/12/06 06:00 MHDA- 2018/03/10 06:00 PMCR- 2017/12/04 CRDT- 2017/12/06 06:00 PHST- 2017/03/25 00:00 [received] PHST- 2017/11/17 00:00 [accepted] PHST- 2017/12/06 06:00 [entrez] PHST- 2017/12/06 06:00 [pubmed] PHST- 2018/03/10 06:00 [medline] PHST- 2017/12/04 00:00 [pmc-release] AID - 10.1186/s12862-017-1082-0 [pii] AID - 1082 [pii] AID - 10.1186/s12862-017-1082-0 [doi] PST - epublish SO - BMC Evol Biol. 2017 Dec 4;17(1):239. doi: 10.1186/s12862-017-1082-0. PMID- 29174893 OWN - NLM STAT- MEDLINE DCOM- 20180806 LR - 20201209 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 27 IP - 23 DP - 2017 Dec 4 TI - The Stone Age Plague and Its Persistence in Eurasia. PG - 3683-3691.e8 LID - S0960-9822(17)31328-3 [pii] LID - 10.1016/j.cub.2017.10.025 [doi] AB - Yersinia pestis, the etiologic agent of plague, is a bacterium associated with wild rodents and their fleas. Historically it was responsible for three pandemics: the Plague of Justinian in the 6(th) century AD, which persisted until the 8(th) century [1]; the renowned Black Death of the 14(th) century [2, 3], with recurrent outbreaks until the 18(th) century [4]; and the most recent 19(th) century pandemic, in which Y. pestis spread worldwide [5] and became endemic in several regions [6]. The discovery of molecular signatures of Y. pestis in prehistoric Eurasian individuals and two genomes from Southern Siberia suggest that Y. pestis caused some form of disease in humans prior to the first historically documented pandemic [7]. Here, we present six new European Y. pestis genomes spanning the Late Neolithic to the Bronze Age (LNBA; 4,800 to 3,700 calibrated years before present). This time period is characterized by major transformative cultural and social changes that led to cross-European networks of contact and exchange [8, 9]. We show that all known LNBA strains form a single putatively extinct clade in the Y. pestis phylogeny. Interpreting our data within the context of recent ancient human genomic evidence that suggests an increase in human mobility during the LNBA, we propose a possible scenario for the early spread of Y. pestis: the pathogen may have entered Europe from Central Eurasia following an expansion of people from the steppe, persisted within Europe until the mid-Bronze Age, and moved back toward Central Eurasia in parallel with human populations. CI - Copyright © 2017 Elsevier Ltd. All rights reserved. FAU - Andrades Valtueña, Aida AU - Andrades Valtueña A AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Mittnik, Alissa AU - Mittnik A AD - Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Key, Felix M AU - Key FM AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Haak, Wolfgang AU - Haak W AD - Max Planck Institute for the Science of Human History, Jena, Germany; School of Biological Sciences, The University of Adelaide, Adelaide SA 5005, South Australia, Australia. FAU - Allmäe, Raili AU - Allmäe R AD - Archaeological Research Collection, Tallinn University, Tallinn, Estonia. FAU - Belinskij, Andrej AU - Belinskij A AD - "Nasledie" Cultural Heritage Unit, Stavropol, Russia. FAU - Daubaras, Mantas AU - Daubaras M AD - Department of Archaeology, Lithuanian Institute of History, Vilnius, Lithuania. FAU - Feldman, Michal AU - Feldman M AD - Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Jankauskas, Rimantas AU - Jankauskas R AD - Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius, Lithuania. FAU - Janković, Ivor AU - Janković I AD - Institute for Anthropological Research, Zagreb, Croatia; Department of Anthropology, University of Wyoming, Laramie, WY, USA. FAU - Massy, Ken AU - Massy K AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany; Heidelberg Academy of Sciences, Heidelberg, Germany. FAU - Novak, Mario AU - Novak M AD - Institute for Anthropological Research, Zagreb, Croatia. FAU - Pfrengle, Saskia AU - Pfrengle S AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Reinhold, Sabine AU - Reinhold S AD - Eurasia Department, German Archaeological Institute, Berlin, Germany. FAU - Šlaus, Mario AU - Šlaus M AD - Anthropological Center, Croatian Academy of Sciences and Arts, Zagreb, Croatia. FAU - Spyrou, Maria A AU - Spyrou MA AD - Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Tõrv, Mari AU - Tõrv M AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu, Estonia. FAU - Hansen, Svend AU - Hansen S AD - Eurasia Department, German Archaeological Institute, Berlin, Germany. FAU - Bos, Kirsten I AU - Bos KI AD - Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Stockhammer, Philipp W AU - Stockhammer PW AD - Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany. FAU - Herbig, Alexander AU - Herbig A AD - Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. Electronic address: herbig@shh.mpg.de. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. Electronic address: krause@shh.mpg.de. LA - eng PT - Journal Article DEP - 20171122 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - DNA, Ancient/*analysis MH - Europe MH - Genome, Bacterial/*genetics MH - Humans MH - Phylogeny MH - Plague/microbiology MH - Yersinia pestis/classification/*genetics OTO - NOTNLM OT - Bronze Age OT - Late Neolithic OT - Yersinia pestis OT - ancient DNA OT - archaeogenetics OT - comparative genomics OT - plague EDAT- 2017/11/28 06:00 MHDA- 2018/08/07 06:00 CRDT- 2017/11/28 06:00 PHST- 2017/05/16 00:00 [received] PHST- 2017/07/31 00:00 [revised] PHST- 2017/10/09 00:00 [accepted] PHST- 2017/11/28 06:00 [pubmed] PHST- 2018/08/07 06:00 [medline] PHST- 2017/11/28 06:00 [entrez] AID - S0960-9822(17)31328-3 [pii] AID - 10.1016/j.cub.2017.10.025 [doi] PST - ppublish SO - Curr Biol. 2017 Dec 4;27(23):3683-3691.e8. doi: 10.1016/j.cub.2017.10.025. Epub 2017 Nov 22. PMID- 29165562 OWN - NLM STAT- MEDLINE DCOM- 20180510 LR - 20181113 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 9 IP - 12 DP - 2017 Dec 1 TI - The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine. PG - 3225-3237 LID - 10.1093/gbe/evx237 [doi] AB - The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM)-an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its FST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, DREAM's autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies. CI - © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Elhaik, Eran AU - Elhaik E AD - Department of Animal and Plant Sciences, University of Sheffield, United Kingdom. FAU - Yusuf, Leeban AU - Yusuf L AD - Department of Animal and Plant Sciences, University of Sheffield, United Kingdom. FAU - Anderson, Ainan I J AU - Anderson AIJ AD - Independent researcher, Newick, United Kingdom. FAU - Pirooznia, Mehdi AU - Pirooznia M AD - Department of Psychiatry and Behavioral Sciences, Johns Hopkins University. FAU - Arnellos, Dimitrios AU - Arnellos D AD - Department of Animal and Plant Sciences, University of Sheffield, United Kingdom. AD - Department of Biology, Lund University, Sweden. FAU - Vilshansky, Gregory AU - Vilshansky G AD - National Geographic Society, Washington, District of Columbia. FAU - Ercal, Gunes AU - Ercal G AD - Department of Computer Science, Southern Illinois University Edwardsville. FAU - Lu, Yontao AU - Lu Y AD - Thermo Fisher Scientific, Santa Clara, California. FAU - Webster, Teresa AU - Webster T AD - Thermo Fisher Scientific, Santa Clara, California. FAU - Baird, Michael L AU - Baird ML AD - DNA Diagnostics Center, Fairfield, Ohio. FAU - Esposito, Umberto AU - Esposito U AD - Department of Animal and Plant Sciences, University of Sheffield, United Kingdom. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 RN - 0 (DNA, Ancient) RN - 0 (Genetic Markers) SB - IM MH - Anthropology/*methods MH - DNA Copy Number Variations MH - DNA, Ancient MH - Evolution, Molecular MH - Genetic Markers MH - Genetics, Population/*methods MH - *Genome, Human MH - Genotype MH - Humans MH - Microarray Analysis MH - Pedigree MH - Polymorphism, Single Nucleotide MH - Precision Medicine/*methods PMC - PMC5726468 OTO - NOTNLM OT - CNVs OT - ancient DNA OT - archaic DNA OT - biogeography OT - forensics OT - population genetics EDAT- 2017/11/23 06:00 MHDA- 2018/05/11 06:00 PMCR- 2017/11/20 CRDT- 2017/11/23 06:00 PHST- 2017/11/17 00:00 [accepted] PHST- 2017/11/23 06:00 [pubmed] PHST- 2018/05/11 06:00 [medline] PHST- 2017/11/23 06:00 [entrez] PHST- 2017/11/20 00:00 [pmc-release] AID - 4642844 [pii] AID - evx237 [pii] AID - 10.1093/gbe/evx237 [doi] PST - ppublish SO - Genome Biol Evol. 2017 Dec 1;9(12):3225-3237. doi: 10.1093/gbe/evx237. PMID- 28836000 OWN - NLM STAT- MEDLINE DCOM- 20171124 LR - 20181113 IS - 1617-4623 (Electronic) IS - 1617-4623 (Linking) VI - 292 IP - 6 DP - 2017 Dec TI - AntCaller: an accurate variant caller incorporating ancient DNA damage. PG - 1419-1430 LID - 10.1007/s00438-017-1358-5 [doi] AB - Ancient DNA obtained from ancient samples, such as sediments, bones, and teeth, is an important genetic resource that can be used to reconstruct an evolutional history of humans, animals, and plants. The application of high-throughput sequencing enables the research of ancient DNA to be conducted in a whole genome scale. However, post-mortem DNA damage mainly caused by deamination of cytosine to uracil (or methylated cytosine to thymine) may confound the variant calling and downstream analysis. In this article, we develop a Python program to implement a new variant caller, "AntCaller", which extracts the information on nucleotide substitutions from sequencing data and calculates the probability of each genotype based on a Bayesian rule. Through both simulation studies and real data analyses, it was shown that our method reduced the false discovery rate caused by nucleotide misincorporations and outperformed two mainstream variant callers (i.e., GATK and SAMtools) in terms of calling accuracy. In a real application with serious DNA damage, AntCaller still outperformed GATK and SAMtools combined with quality score recalling. FAU - Zhou, Boyan AU - Zhou B AD - State Key Laboratory of Genetic Engineering and Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China. FAU - Wen, Shaoqing AU - Wen S AD - State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, People's Republic of China. FAU - Wang, Lingxiang AU - Wang L AD - State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, People's Republic of China. FAU - Jin, Li AU - Jin L AD - State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, People's Republic of China. FAU - Li, Hui AU - Li H AD - State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, People's Republic of China. FAU - Zhang, Hong AU - Zhang H AD - State Key Laboratory of Genetic Engineering and Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China. zhanghfd@fudan.edu.cn. LA - eng PT - Journal Article DEP - 20170823 PL - Germany TA - Mol Genet Genomics JT - Molecular genetics and genomics : MGG JID - 101093320 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *DNA Damage MH - *DNA, Ancient MH - High-Throughput Nucleotide Sequencing/methods MH - Humans MH - Neanderthals MH - Ploidies MH - Postmortem Changes OTO - NOTNLM OT - Ancient DNA OT - Chemical damage OT - NGS OT - SNV/SNP calling EDAT- 2017/08/25 06:00 MHDA- 2017/11/29 06:00 CRDT- 2017/08/25 06:00 PHST- 2017/03/27 00:00 [received] PHST- 2017/08/16 00:00 [accepted] PHST- 2017/08/25 06:00 [pubmed] PHST- 2017/11/29 06:00 [medline] PHST- 2017/08/25 06:00 [entrez] AID - 10.1007/s00438-017-1358-5 [pii] AID - 10.1007/s00438-017-1358-5 [doi] PST - ppublish SO - Mol Genet Genomics. 2017 Dec;292(6):1419-1430. doi: 10.1007/s00438-017-1358-5. Epub 2017 Aug 23. PMID- 28799621 OWN - NLM STAT- MEDLINE DCOM- 20180409 LR - 20221207 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 74 IP - 4 DP - 2017 Dec 1 TI - Ancient DNA analysis might suggest external origin of individuals from chamber graves placed in medieval cemetery in Pień, Central Poland. PG - 319-337 LID - 10.1127/anthranz/2017/0727 [doi] AB - The participation of immigrants during early days in Poland of Piast's dynasty is a debated issue among archaeologists and anthropologists alike. Such hypotheses were formulated on the basis of, amongst others, the discovery of early medieval chamber graves characterized by construction features typical of the Scandinavian culture area. Archaeological and anthropological studies to date have not provided an unequivocal answer as to whether the individuals interred in those graves were autochthons who adopted a different burial rite, or perhaps immigrants from foreign lands. To characterize the gene pool of this population we analyzed the C/T allele of the nuclear gene LCT-13910 as well as fragments of the mitochondrial genome from individuals buried in very richly furnished chamber graves at the medieval cemetery in Pień. The obtained results for the nuclear allele and mtDNA do not corroborate the Scandinavian origin of the analyzed population. Moreover, we did not find haplogroup I, which is the one typical of populations that historically inhabited the north of Europe; and the frequency of the LCT-13910 T allele was similar to that of past and present Polish populations. On the other hand, we identified the atypical haplogroup C5c1, which suggests Asian origin of the studied individuals and confirms our previous reports concerning ancient human migrations from Asia to the territory of present-day Poland. While our findings do not conclusively disprove a Scandinavian lineage of the studied population, they certainly shed some new light on the origin of the individuals buried in chamber graves, which may be very different from the one initially proposed by archaeologists. FAU - Płoszaj, Tomasz AU - Płoszaj T AD - Department of Molecular Biology, Medical University of Lodz, Narutowicza 60, 90-136 Łódź, Poland. FAU - Jędrychowska-Dańska, Krystyna AU - Jędrychowska-Dańska K AD - Department of Molecular Biology, Medical University of Lodz, Narutowicza 60, 90-136 Łódź, Poland. FAU - Zamerska, Alicja AU - Zamerska A AD - Department of Molecular Biology, Medical University of Lodz, Narutowicza 60, 90-136 Łódź, Poland. FAU - Drozd-Lipińska, Alicja AU - Drozd-Lipińska A AD - Department of Anthropology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland. FAU - Poliński, Dariusz AU - Poliński D AD - Institute of Archaeology, Nicolaus Copernicus University, Szosa Bydgoska 44/48, 87-100 Toruń, Poland. FAU - Janowski, Andrzej AU - Janowski A AD - Center for Medieval Archaeology of the Baltic Region, Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kuśnierska 12/12a, 70-536 Szczecin, Poland. FAU - Witas, Henryk AU - Witas H AD - Department of Molecular Biology, Medical University of Lodz, Narutowicza 60, 90-136 Łódź, Poland. LA - eng PT - Historical Article PT - Journal Article DEP - 20170811 PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (DNA, Ancient) SB - IM MH - Adult MH - Archaeology MH - Cemeteries/*history MH - Child MH - DNA, Ancient/*analysis MH - Genetics, Population MH - Haplotypes/genetics MH - History, Medieval MH - Human Migration/*history MH - Humans MH - Poland MH - Scandinavian and Nordic Countries MH - White People/*genetics EDAT- 2017/08/12 06:00 MHDA- 2018/04/10 06:00 CRDT- 2017/08/12 06:00 PHST- 2016/12/03 00:00 [received] PHST- 2017/05/21 00:00 [revised] PHST- 2017/06/21 00:00 [accepted] PHST- 2017/08/12 06:00 [pubmed] PHST- 2018/04/10 06:00 [medline] PHST- 2017/08/12 06:00 [entrez] AID - 10.1127/anthranz/2017/0727 [doi] PST - ppublish SO - Anthropol Anz. 2017 Dec 1;74(4):319-337. doi: 10.1127/anthranz/2017/0727. Epub 2017 Aug 11. PMID- 28737475 OWN - NLM STAT- MEDLINE DCOM- 20190620 LR - 20190620 IS - 1937-2345 (Electronic) IS - 0022-3395 (Linking) VI - 103 IP - 6 DP - 2017 Dec TI - Ancient Ascaris DNA Sequences of Cytochrome B, Cytochrome C Oxidase Subunit 1, NADH Dehydrogenase Subunit 1, and Internal Transcribed Spacer 1 Genes from Korean Joseon Mummy Feces. PG - 795-800 LID - 10.1645/16-102 [doi] AB - We analyzed Ascaris ancient DNA of cytochrome b, cytochrome c oxidase subunit 1, NADH dehydrogenase subunit 1, and internal transcribed spacer 1 genes extracted from the feces or precipitates of 15- to 18th-century Korean mummies. After multiple Ascaris genes in ancient samples were successfully amplified by polymerase chain reaction (PCR), consensus sequences could be determined by the alignment of the sequences of cloned PCR products. The obtained sequences of each gene were highly similar to those of Ascaris spp. reported thus far but were genetically distinct from Baylisascaris, Parascaris, and Toxascaris spp. The current report establishes that the genetic characteristics of the Ascaris spp. infecting pre-modern Korean societies were not uniform but were diverse to some degree. FAU - Hong, Jong Ha AU - Hong JH AD - Bioanthropology and Paleopathology Lab, Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro (Yongon-dong), Jongno-gu, Seoul 03080, Republic of Korea. FAU - Oh, Chang Seok AU - Oh CS AD - Bioanthropology and Paleopathology Lab, Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro (Yongon-dong), Jongno-gu, Seoul 03080, Republic of Korea. FAU - Seo, Min AU - Seo M AD - Bioanthropology and Paleopathology Lab, Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro (Yongon-dong), Jongno-gu, Seoul 03080, Republic of Korea. FAU - Chai, Jong-Yil AU - Chai JY AD - Bioanthropology and Paleopathology Lab, Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro (Yongon-dong), Jongno-gu, Seoul 03080, Republic of Korea. FAU - Shin, Dong Hoon AU - Shin DH AD - Bioanthropology and Paleopathology Lab, Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro (Yongon-dong), Jongno-gu, Seoul 03080, Republic of Korea. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20170724 PL - United States TA - J Parasitol JT - The Journal of parasitology JID - 7803124 RN - 0 (DNA, Intergenic) RN - 9035-37-4 (Cytochromes b) RN - EC 1.6.99.3 (NADH Dehydrogenase) RN - EC 1.9.3.1 (Electron Transport Complex IV) SB - IM MH - Animals MH - Ascaris/classification/enzymology/*genetics MH - Base Sequence MH - Consensus Sequence MH - Cytochromes b/genetics/history MH - DNA, Intergenic/genetics/history MH - Electron Transport Complex IV/genetics/history MH - Feces/*parasitology MH - Female MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - Humans MH - Korea MH - Likelihood Functions MH - Male MH - Mummies/history/*parasitology MH - NADH Dehydrogenase/genetics/history MH - Pelvic Bones/parasitology MH - Phylogeny MH - Polymerase Chain Reaction MH - Sequence Alignment EDAT- 2017/07/25 06:00 MHDA- 2019/06/21 06:00 CRDT- 2017/07/25 06:00 PHST- 2017/07/25 06:00 [pubmed] PHST- 2019/06/21 06:00 [medline] PHST- 2017/07/25 06:00 [entrez] AID - 10.1645/16-102 [doi] PST - ppublish SO - J Parasitol. 2017 Dec;103(6):795-800. doi: 10.1645/16-102. Epub 2017 Jul 24. PMID- 29167366 OWN - NLM STAT- MEDLINE DCOM- 20180620 LR - 20190130 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 284 IP - 1867 DP - 2017 Nov 29 TI - Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean. LID - 10.1098/rspb.2017.2064 [doi] LID - 20172064 AB - The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter-gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe. CI - © 2017 The Author(s). FAU - Kılınç, Gülşah Merve AU - Kılınç GM AUID- ORCID: 0000-0002-2024-3910 AD - Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativaegen 7, Stockholm 114 18, Sweden gulsahhdal@gmail.com. FAU - Koptekin, Dilek AU - Koptekin D AD - Department of Health Informatics, Middle East Technical University, Ankara 06800, Turkey. FAU - Atakuman, Çiğdem AU - Atakuman Ç AD - Department of Settlement Archaeology, Middle East Technical University, Ankara 06800, Turkey. FAU - Sümer, Arev Pelin AU - Sümer AP AD - Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey. FAU - Dönertaş, Handan Melike AU - Dönertaş HM AD - European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, Hinxton CB10 1SD, UK. FAU - Yaka, Reyhan AU - Yaka R AD - Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey. FAU - Bilgin, Cemal Can AU - Bilgin CC AD - Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey. FAU - Büyükkarakaya, Ali Metin AU - Büyükkarakaya AM AD - Department of Anthropology, Hacettepe University, Ankara, Beytepe 06800, Turkey. FAU - Baird, Douglas AU - Baird D AD - Department of Archaeology, Classics, and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK. FAU - Altınışık, Ezgi AU - Altınışık E AUID- ORCID: 0000-0003-0653-4292 AD - Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic. FAU - Flegontov, Pavel AU - Flegontov P AD - Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic. AD - A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia. AD - Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic. FAU - Götherström, Anders AU - Götherström A AD - Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativaegen 7, Stockholm 114 18, Sweden anders.gotherstrom@arklab.su.se. FAU - Togan, İnci AU - Togan İ AD - Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey togan@metu.edu.tr. FAU - Somel, Mehmet AU - Somel M AD - Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey somel.mehmet@googlemail.com. LA - eng PT - Historical Article PT - Journal Article PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 SB - IM MH - Agriculture/*history MH - Archaeology MH - Farmers/history MH - *Gene Flow MH - *Genome, Human MH - Genomics MH - Greece MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Turkey PMC - PMC5719180 OTO - NOTNLM OT - Neolithic OT - acculturation OT - ancient DNA OT - archaeogenomics OT - migration OT - population genetics COIS- We declare we have no competing interests. EDAT- 2017/11/24 06:00 MHDA- 2018/06/21 06:00 PMCR- 2018/11/29 CRDT- 2017/11/24 06:00 PHST- 2017/09/14 00:00 [received] PHST- 2017/10/20 00:00 [accepted] PHST- 2017/11/24 06:00 [entrez] PHST- 2017/11/24 06:00 [pubmed] PHST- 2018/06/21 06:00 [medline] PHST- 2018/11/29 00:00 [pmc-release] AID - rspb.2017.2064 [pii] AID - rspb20172064 [pii] AID - 10.1098/rspb.2017.2064 [doi] PST - ppublish SO - Proc Biol Sci. 2017 Nov 29;284(1867):20172064. doi: 10.1098/rspb.2017.2064. PMID- 29167359 OWN - NLM STAT- MEDLINE DCOM- 20180620 LR - 20240327 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 284 IP - 1867 DP - 2017 Nov 29 TI - Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages. LID - 10.1098/rspb.2017.1540 [doi] LID - 20171540 AB - It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people. CI - © 2017 The Authors. FAU - Tassi, Francesca AU - Tassi F AD - Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy. FAU - Vai, Stefania AU - Vai S AD - Department of Biology, University of Firenze, Firenze, Italy. FAU - Ghirotto, Silvia AU - Ghirotto S AD - Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy. FAU - Lari, Martina AU - Lari M AD - Department of Biology, University of Firenze, Firenze, Italy. FAU - Modi, Alessandra AU - Modi A AD - Department of Biology, University of Firenze, Firenze, Italy. FAU - Pilli, Elena AU - Pilli E AD - Department of Biology, University of Firenze, Firenze, Italy. FAU - Brunelli, Andrea AU - Brunelli A AD - Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy. FAU - Susca, Roberta Rosa AU - Susca RR AD - Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy. FAU - Budnik, Alicja AU - Budnik A AD - Department of Human Biology, Cardinal Stefan Wyszyński University, Warsaw, Poland. FAU - Labuda, Damian AU - Labuda D AD - CHU Sainte-Justine Research Center, Department of Pediatrics, Université de Montréal, Montréal, PQ, Canada H3T 1C5. FAU - Alberti, Federica AU - Alberti F AD - Department of Evolutionary Biology, Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology, University Pompeu Fabra, Barcelona, Spain. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. FAU - Caramelli, David AU - Caramelli D AD - Department of Biology, University of Firenze, Firenze, Italy david.caramelli@unife.it. FAU - Barbujani, Guido AU - Barbujani G AUID- ORCID: 0000-0001-7854-6669 AD - Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy g.barbujani@unife.it. LA - eng GR - 295733/ERC_/European Research Council/International GR - R01 GM100233/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - Bayes Theorem MH - Cell Nucleus/genetics MH - DNA, Ancient/analysis MH - DNA, Mitochondrial/genetics MH - Europe MH - *Genetic Variation MH - *Genome, Human MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Language/*history PMC - PMC5719168 OTO - NOTNLM OT - Indo-European OT - Neolithic OT - ancient DNA OT - approximate Bayesian computation OT - migration OT - population genomics COIS- We declare we have no competing interests. EDAT- 2017/11/24 06:00 MHDA- 2018/06/21 06:00 PMCR- 2017/11/22 CRDT- 2017/11/24 06:00 PHST- 2017/07/12 00:00 [received] PHST- 2017/10/23 00:00 [accepted] PHST- 2017/11/24 06:00 [entrez] PHST- 2017/11/24 06:00 [pubmed] PHST- 2018/06/21 06:00 [medline] PHST- 2017/11/22 00:00 [pmc-release] AID - rspb.2017.1540 [pii] AID - rspb20171540 [pii] AID - 10.1098/rspb.2017.1540 [doi] PST - ppublish SO - Proc Biol Sci. 2017 Nov 29;284(1867):20171540. doi: 10.1098/rspb.2017.1540. PMID- 29144465 OWN - NLM STAT- MEDLINE DCOM- 20180410 LR - 20181113 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 551 IP - 7680 DP - 2017 Nov 16 TI - Parallel palaeogenomic transects reveal complex genetic history of early European farmers. PG - 368-372 LID - 10.1038/nature24476 [doi] AB - Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000-2900 bc, n = 100), Germany (5500-3000 bc, n = 42) and Spain (5500-2200 bc, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions. FAU - Lipson, Mark AU - Lipson M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. FAU - Pósa, Annamária AU - Pósa A AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Stégmár, Balázs AU - Stégmár B AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Keerl, Victoria AU - Keerl V AD - Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz 55128, Germany. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Oppenheimer, Jonas AU - Oppenheimer J AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Broomandkhoshbacht, Nasreen AU - Broomandkhoshbacht N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Harney, Eadaoin AU - Harney E AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Nordenfelt, Susanne AU - Nordenfelt S AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Gusztáv Mende, Balázs AU - Gusztáv Mende B AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Köhler, Kitti AU - Köhler K AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Oross, Krisztián AU - Oross K AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Bondár, Mária AU - Bondár M AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Marton, Tibor AU - Marton T AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Osztás, Anett AU - Osztás A AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Jakucs, János AU - Jakucs J AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Paluch, Tibor AU - Paluch T AD - Móra Ferenc Museum, Szeged 6720, Hungary. FAU - Horváth, Ferenc AU - Horváth F AD - Móra Ferenc Museum, Szeged 6720, Hungary. FAU - Csengeri, Piroska AU - Csengeri P AD - Herman Ottó Museum, Miskolc 3529, Hungary. FAU - Koós, Judit AU - Koós J AD - Herman Ottó Museum, Miskolc 3529, Hungary. FAU - Sebők, Katalin AU - Sebők K AD - Institute of Archaeological Sciences, Eötvös Loránd University, Budapest 1088, Hungary. FAU - Anders, Alexandra AU - Anders A AD - Institute of Archaeological Sciences, Eötvös Loránd University, Budapest 1088, Hungary. FAU - Raczky, Pál AU - Raczky P AD - Institute of Archaeological Sciences, Eötvös Loránd University, Budapest 1088, Hungary. FAU - Regenye, Judit AU - Regenye J AD - Laczkó Dezso˝ Museum, Veszprém 8200, Hungary. FAU - Barna, Judit P AU - Barna JP AD - Balaton Museum, Keszthely 8360, Hungary. FAU - Fábián, Szilvia AU - Fábián S AD - Department of Archaeological Excavations and Artefact Processing, Hungarian National Museum, Budapest 1088, Hungary. FAU - Serlegi, Gábor AU - Serlegi G AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. FAU - Toldi, Zoltán AU - Toldi Z AD - Jósa András Museum, Nyíregyháza 4400, Hungary. FAU - Gyöngyvér Nagy, Emese AU - Gyöngyvér Nagy E AD - Déri Museum, Debrecen 4026, Hungary. FAU - Dani, János AU - Dani J AD - Déri Museum, Debrecen 4026, Hungary. FAU - Molnár, Erika AU - Molnár E AD - Department of Biological Anthropology, Szeged University, Szeged 6726, Hungary. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, Szeged University, Szeged 6726, Hungary. FAU - Márk, László AU - Márk L AD - Department of Biochemistry and Medical Chemistry, University of Pécs, Pécs 7624, Hungary. AD - Imaging Center for Life and Material Sciences, University of Pécs, Pécs 7624, Hungary. AD - Szentágothai Research Center, University of Pécs, Pécs 7624, Hungary. AD - PTE-MTA Human Reproduction Research Group, Pécs 7624, Hungary. FAU - Melegh, Béla AU - Melegh B AD - Szentágothai Research Center, University of Pécs, Pécs 7624, Hungary. AD - Department of Medical Genetics and Szentágothai Research Center, University of Pécs, Pécs 7624, Hungary. FAU - Bánfai, Zsolt AU - Bánfai Z AD - Szentágothai Research Center, University of Pécs, Pécs 7624, Hungary. AD - Department of Medical Genetics and Szentágothai Research Center, University of Pécs, Pécs 7624, Hungary. FAU - Domboróczki, László AU - Domboróczki L AD - Dobó István Castle Museum, Eger 3300, Hungary. FAU - Fernández-Eraso, Javier AU - Fernández-Eraso J AD - Department of Geography, Prehistory, and Archaeology, University of the Basque Country, Investigation Group IT622-13, Vitoria-Gasteiz 01006, Spain. FAU - Antonio Mujika-Alustiza, José AU - Antonio Mujika-Alustiza J AD - Department of Geography, Prehistory, and Archaeology, University of the Basque Country, Investigation Group IT622-13, Vitoria-Gasteiz 01006, Spain. FAU - Alonso Fernández, Carmen AU - Alonso Fernández C AD - CRONOS SC, Burgos 09007, Spain. FAU - Jiménez Echevarría, Javier AU - Jiménez Echevarría J AD - CRONOS SC, Burgos 09007, Spain. FAU - Bollongino, Ruth AU - Bollongino R AD - Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz 55128, Germany. FAU - Orschiedt, Jörg AU - Orschiedt J AD - Department of Prehistoric Archaeology, Free University of Berlin, Berlin 14195, Germany. AD - Curt-Engelhorn-Centre Archaeometry gGmbH, Mannheim 68159, Germany. FAU - Schierhold, Kerstin AU - Schierhold K AD - Commission for Westphalian Antiquities, Westphalia-Lippe Regional Association, 48157 Münster, Germany. FAU - Meller, Harald AU - Meller H AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Heritage Museum, Halle 06114, Germany. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia. AD - Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Burger, Joachim AU - Burger J AD - Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz 55128, Germany. FAU - Bánffy, Eszter AU - Bánffy E AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary. AD - Romano-Germanic Commission, German Archaeological Institute, Frankfurt am Main 60325, Germany. FAU - Alt, Kurt W AU - Alt KW AD - Center of Natural and Cultural History of Man, Danube Private University, Krems-Stein 3500, Austria. AD - Department of Biomedical Engineering, University of Basel, Allschwil 4123, Switzerland. AD - Institute for Integrative Prehistory and Archaeological Science, University of Basel, Basel 4055, Switzerland. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology (CSIC-UPF), Barcelona 08003, Spain. FAU - Haak, Wolfgang AU - Haak W AD - Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia. AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20171108 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/analysis MH - Datasets as Topic MH - Farmers/*history MH - Female MH - Gene Flow/*genetics MH - *Genetic Variation MH - Germany MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Hungary MH - Male MH - Population Dynamics MH - Spain MH - Spatio-Temporal Analysis PMC - PMC5973800 MID - NIHMS911574 COIS- The authors declare no competing financial interests. EDAT- 2017/11/17 06:00 MHDA- 2018/04/11 06:00 PMCR- 2018/05/29 CRDT- 2017/11/17 06:00 PHST- 2017/03/01 00:00 [received] PHST- 2017/10/06 00:00 [accepted] PHST- 2017/11/17 06:00 [entrez] PHST- 2017/11/17 06:00 [pubmed] PHST- 2018/04/11 06:00 [medline] PHST- 2018/05/29 00:00 [pmc-release] AID - nature24476 [pii] AID - 10.1038/nature24476 [doi] PST - ppublish SO - Nature. 2017 Nov 16;551(7680):368-372. doi: 10.1038/nature24476. Epub 2017 Nov 8. PMID- 29142317 OWN - NLM STAT- MEDLINE DCOM- 20190703 LR - 20200306 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 7 IP - 1 DP - 2017 Nov 15 TI - The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age. PG - 15644 LID - 10.1038/s41598-017-15480-9 [doi] LID - 15644 AB - Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focus on the maternal genetic makeup of the Neolithic (~ 5500-3000 BCE), Chalcolithic (~ 3000-2200 BCE) and Early Bronze Age (~ 2200-1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AUID- ORCID: 0000-0003-2095-738X AD - Laboratory of Archaeogenetics in the Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary. szecsenyi-nagy.anna@btk.mta.hu. FAU - Roth, Christina AU - Roth C AD - Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany. FAU - Brandt, Guido AU - Brandt G AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Rihuete-Herrada, Cristina AU - Rihuete-Herrada C AUID- ORCID: 0000-0003-1535-0209 AD - Departamento de Prehistoria, Universitat Autònoma de Barcelona, Barcelona, Spain. FAU - Tejedor-Rodríguez, Cristina AU - Tejedor-Rodríguez C AD - Arcadia-General Foundation of Valladolid University, Valladolid, Spain. FAU - Held, Petra AU - Held P AD - Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany. FAU - García-Martínez-de-Lagrán, Íñigo AU - García-Martínez-de-Lagrán Í AD - Arcadia-General Foundation of Valladolid University, Valladolid, Spain. FAU - Arcusa Magallón, Héctor AU - Arcusa Magallón H AD - Arcadia-General Foundation of Valladolid University, Valladolid, Spain. FAU - Zesch, Stephanie AU - Zesch S AD - German Mummy Project, Reiss-Engelhorn-Museen, Mannheim, Germany. FAU - Knipper, Corina AU - Knipper C AD - Curt-Engelhorn-Zentrum Archäometrie gGmbH, Mannheim, Germany. FAU - Bánffy, Eszter AU - Bánffy E AD - Romano-Germanic Commission, German Archaeological Institute, Frankfurt am Main, Germany. FAU - Friederich, Susanne AU - Friederich S AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany. FAU - Meller, Harald AU - Meller H AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany. FAU - Bueno Ramírez, Primitiva AU - Bueno Ramírez P AD - Departamento de Historia y Filosofía, Universidad de Alcalá de Henares, Alcalá de Henares, Spain. FAU - Barroso Bermejo, Rosa AU - Barroso Bermejo R AD - Departamento de Historia y Filosofía, Universidad de Alcalá de Henares, Alcalá de Henares, Spain. FAU - de Balbín Behrmann, Rodrigo AU - de Balbín Behrmann R AD - Departamento de Historia y Filosofía, Universidad de Alcalá de Henares, Alcalá de Henares, Spain. FAU - Herrero-Corral, Ana M AU - Herrero-Corral AM AD - Departamento de Prehistoria, Universidad Complutense de Madrid, Madrid, Spain. FAU - Flores Fernández, Raúl AU - Flores Fernández R AD - Professional Archaeologist, Parla (Madrid), Spain. FAU - Alonso Fernández, Carmen AU - Alonso Fernández C AD - Cronos SC Arqueología y Patrimonio, Burgos, Spain. FAU - Jiménez Echevarria, Javier AU - Jiménez Echevarria J AD - Cronos SC Arqueología y Patrimonio, Burgos, Spain. FAU - Rindlisbacher, Laura AU - Rindlisbacher L AD - Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland. FAU - Oliart, Camila AU - Oliart C AD - Departamento de Prehistoria, Universitat Autònoma de Barcelona, Barcelona, Spain. FAU - Fregeiro, María-Inés AU - Fregeiro MI AD - Departamento de Prehistoria, Universitat Autònoma de Barcelona, Barcelona, Spain. FAU - Soriano, Ignacio AU - Soriano I AD - Departamento de Prehistoria, Universitat Autònoma de Barcelona, Barcelona, Spain. FAU - Vicente, Oriol AU - Vicente O AUID- ORCID: 0000-0003-2160-2492 AD - Departamento de Prehistoria, Universitat Autònoma de Barcelona, Barcelona, Spain. FAU - Micó, Rafael AU - Micó R AD - Departamento de Prehistoria, Universitat Autònoma de Barcelona, Barcelona, Spain. FAU - Lull, Vicente AU - Lull V AD - Departamento de Prehistoria, Universitat Autònoma de Barcelona, Barcelona, Spain. FAU - Soler Díaz, Jorge AU - Soler Díaz J AD - Museo Arqueológico de Alicante-MARQ, Alicante, Spain. FAU - López Padilla, Juan Antonio AU - López Padilla JA AD - Museo Arqueológico de Alicante-MARQ, Alicante, Spain. FAU - Roca de Togores Muñoz, Consuelo AU - Roca de Togores Muñoz C AD - Museo Arqueológico de Alicante-MARQ, Alicante, Spain. FAU - Hernández Pérez, Mauro S AU - Hernández Pérez MS AD - Departamento de Prehistoria, Arqueología, Historia Antigua, Filología Griega y Filología Latina, Universidad de Alicante, Alicante, Spain. FAU - Jover Maestre, Francisco Javier AU - Jover Maestre FJ AD - Departamento de Prehistoria, Arqueología, Historia Antigua, Filología Griega y Filología Latina, Universidad de Alicante, Alicante, Spain. FAU - Lomba Maurandi, Joaquín AU - Lomba Maurandi J AD - Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, Spain. FAU - Avilés Fernández, Azucena AU - Avilés Fernández A AD - Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, Spain. FAU - Lillios, Katina T AU - Lillios KT AD - Department of Anthropology, University of Iowa, Iowa City, Iowa, United States of America. FAU - Silva, Ana Maria AU - Silva AM AUID- ORCID: 0000-0002-1912-6581 AD - Laboratory of Prehistory, CIAS, Department of Anthropology, University of Coimbra, Coimbra, Portugal. AD - UNIARQ, University of Lisbon, Lisboa, Portugal. FAU - Magalhães Ramalho, Miguel AU - Magalhães Ramalho M AD - Laboratório Nacional de Energia e Geologia, I.P., Museu Geológico, Lisboa, Portugal. FAU - Oosterbeek, Luiz Miguel AU - Oosterbeek LM AD - Instituto Politécnico de Tomar, Instituto Terra e Memória, Geosciences Centre of Coimbra University, Tomar, Portugal. FAU - Cunha, Claudia AU - Cunha C AD - Programa de Capacitação Institucional MCTIC/MPEG, Museu Paraense Emílio Goeldi, Belém, Brazil. FAU - Waterman, Anna J AU - Waterman AJ AD - Department of Natural and Applied Sciences, Mount Mercy University, Cedar Rapids, Iowa, United States of America. FAU - Roig Buxó, Jordi AU - Roig Buxó J AD - Arrago Ltd, Barcelona, Spain. FAU - Martínez, Andrés AU - Martínez A AD - Museo Arquelógico de Lorca, Lorca, Spain. FAU - Ponce Martínez, Juana AU - Ponce Martínez J AD - Departamento de Prehistoria y Arqueología, Universidad de Sevilla, Sevilla, Spain. FAU - Hunt Ortiz, Mark AU - Hunt Ortiz M AD - Departamento de Prehistoria y Arqueología, Universidad de Sevilla, Sevilla, Spain. FAU - Mejías-García, Juan Carlos AU - Mejías-García JC AUID- ORCID: 0000-0002-9139-2825 AD - Departamento de Prehistoria y Arqueología, Universidad de Sevilla, Sevilla, Spain. FAU - Pecero Espín, Juan Carlos AU - Pecero Espín JC AD - Departamento de Prehistoria y Arqueología, Universidad de Sevilla, Sevilla, Spain. FAU - Cruz-Auñón Briones, Rosario AU - Cruz-Auñón Briones R AD - Departamento de Prehistoria y Arqueología, Universidad de Sevilla, Sevilla, Spain. FAU - Tomé, Tiago AU - Tomé T AD - Universidade Federal do Pará, Campus Universitário do Guamá, Belém, Brazil. FAU - Carmona Ballestero, Eduardo AU - Carmona Ballestero E AD - Servicio Territorial de Cultura de Valladolid, Valladolid, Spain. FAU - Cardoso, João Luís AU - Cardoso JL AD - Departamento de Ciencias Sociais e de Gestao, Universidade Aberta, Lisboa, Portugal. FAU - Araújo, Ana Cristina AU - Araújo AC AD - Research Centre in Biodiversity and Genetic Resources (CIBIO-InBIO) & Directorate-General for Cultural Heritage (DGPC), Lisboa, Portugal. FAU - Liesau von Lettow-Vorbeck, Corina AU - Liesau von Lettow-Vorbeck C AUID- ORCID: 0000-0001-5547-5415 AD - Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain. FAU - Blasco Bosqued, Concepción AU - Blasco Bosqued C AD - Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain. FAU - Ríos Mendoza, Patricia AU - Ríos Mendoza P AD - Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain. FAU - Pujante, Ana AU - Pujante A AD - Arqueología Estudios, Murcia, Spain. FAU - Royo-Guillén, José I AU - Royo-Guillén JI AD - Technical archaeologist, Gobierno de Aragón, Zaragoza, Spain. FAU - Esquembre Beviá, Marco Aurelio AU - Esquembre Beviá MA AD - Arpa Patrimonio Ltd, Alicante, Spain. FAU - Dos Santos Goncalves, Victor Manuel AU - Dos Santos Goncalves VM AD - Centro de Arqueologia da Universidade de Lisboa (Uniarq), Lisboa, Portugal. FAU - Parreira, Rui AU - Parreira R AD - Centro de Arqueologia da Universidade de Lisboa (Uniarq), Lisboa, Portugal. FAU - Morán Hernández, Elena AU - Morán Hernández E AD - Centro de Arqueologia da Universidade de Lisboa (Uniarq), Lisboa, Portugal. FAU - Méndez Izquierdo, Elena AU - Méndez Izquierdo E AD - Grupo de Investigación HUM-949 TELLUS, Prehistoria y Arqueología en el Sur de Iberia, Universidad de Sevilla, Sevilla, Spain. FAU - Vega Y Miguel, Jorge AU - Vega Y Miguel J AD - ARGEA Ltd., Madrid, Spain. FAU - Menduiña García, Roberto AU - Menduiña García R AD - ARGEA Ltd., Madrid, Spain. FAU - Martínez Calvo, Victoria AU - Martínez Calvo V AD - GIPSIA Ltd., Toledo, Spain. FAU - López Jiménez, Oscar AU - López Jiménez O AD - GIPSIA Ltd., Toledo, Spain. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Pichler, Sandra L AU - Pichler SL AUID- ORCID: 0000-0002-5557-1674 AD - Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland. FAU - Garrido-Pena, Rafael AU - Garrido-Pena R AD - Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain. FAU - Kunst, Michael AU - Kunst M AD - German Archaeological Institute Madrid, Madrid, Spain. FAU - Risch, Roberto AU - Risch R AD - Departamento de Prehistoria, Universitat Autònoma de Barcelona, Barcelona, Spain. FAU - Rojo-Guerra, Manuel A AU - Rojo-Guerra MA AD - Departamento de Prehistoria y Arqueología, Universidad de Valladolid, Valladolid, Spain. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - School of Biological Sciences, The University of Adelaide, Adelaide, Austria. FAU - Alt, Kurt W AU - Alt KW AD - Center for Natural and Cultural History of Man, Danube Private University, Krems, Austria. kurt.alt@unibas.ch. AD - Department of Biomedical Engineering and Department of Environmental Science, Basel University, Basel, Switzerland. kurt.alt@unibas.ch. LA - eng PT - Historical Article PT - Journal Article DEP - 20171115 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/history MH - *DNA, Ancient MH - DNA, Mitochondrial/*genetics/history MH - Europe MH - Genetic Variation/*genetics MH - *Genetics, Population MH - Haplotypes MH - History, Ancient MH - Humans PMC - PMC5688114 COIS- The authors declare that they have no competing interests. EDAT- 2017/11/17 06:00 MHDA- 2019/07/04 06:00 PMCR- 2017/11/15 CRDT- 2017/11/17 06:00 PHST- 2017/02/08 00:00 [received] PHST- 2017/10/27 00:00 [accepted] PHST- 2017/11/17 06:00 [entrez] PHST- 2017/11/17 06:00 [pubmed] PHST- 2019/07/04 06:00 [medline] PHST- 2017/11/15 00:00 [pmc-release] AID - 10.1038/s41598-017-15480-9 [pii] AID - 15480 [pii] AID - 10.1038/s41598-017-15480-9 [doi] PST - epublish SO - Sci Rep. 2017 Nov 15;7(1):15644. doi: 10.1038/s41598-017-15480-9. PMID- 29087301 OWN - NLM STAT- MEDLINE DCOM- 20180619 LR - 20181113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 114 IP - 46 DP - 2017 Nov 14 TI - Estimating mobility using sparse data: Application to human genetic variation. PG - 12213-12218 LID - 10.1073/pnas.1703642114 [doi] AB - Mobility is one of the most important processes shaping spatiotemporal patterns of variation in genetic, morphological, and cultural traits. However, current approaches for inferring past migration episodes in the fields of archaeology and population genetics lack either temporal resolution or formal quantification of the underlying mobility, are poorly suited to spatially and temporally sparsely sampled data, and permit only limited systematic comparison between different time periods or geographic regions. Here we present an estimator of past mobility that addresses these issues by explicitly linking trait differentiation in space and time. We demonstrate the efficacy of this estimator using spatiotemporally explicit simulations and apply it to a large set of ancient genomic data from Western Eurasia. We identify a sequence of changes in human mobility from the Late Pleistocene to the Iron Age. We find that mobility among European Holocene farmers was significantly higher than among European hunter-gatherers both pre- and postdating the Last Glacial Maximum. We also infer that this Holocene rise in mobility occurred in at least three distinct stages: the first centering on the well-known population expansion at the beginning of the Neolithic, and the second and third centering on the beginning of the Bronze Age and the late Iron Age, respectively. These findings suggest a strong link between technological change and human mobility in Holocene Western Eurasia and demonstrate the utility of this framework for exploring changes in mobility through space and time. CI - Copyright © 2017 the Author(s). Published by PNAS. FAU - Loog, Liisa AU - Loog L AD - Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; LiisaLoog@gmail.com m.thomas@ucl.ac.uk. AD - Research Laboratory for Archaeology & the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom. AD - Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom. AD - Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester M1 7DN, United Kingdom. FAU - Mirazón Lahr, Marta AU - Mirazón Lahr M AUID- ORCID: 0000-0001-5752-5770 AD - Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, United Kingdom. FAU - Kovacevic, Mirna AU - Kovacevic M AD - Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom. AD - Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1E 6BT, United Kingdom. FAU - Manica, Andrea AU - Manica A AD - Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom. FAU - Eriksson, Anders AU - Eriksson A AUID- ORCID: 0000-0003-3436-3726 AD - Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, United Kingdom. FAU - Thomas, Mark G AU - Thomas MG AUID- ORCID: 0000-0002-2452-981X AD - Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; LiisaLoog@gmail.com m.thomas@ucl.ac.uk. LA - eng GR - Wellcome Trust/United Kingdom GR - 100719/Z/12/Z/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20171030 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics MH - Europe MH - *Genetics, Population MH - History, Ancient MH - *Human Migration MH - Humans MH - *Models, Statistical MH - Sequence Analysis, DNA MH - Spatio-Temporal Analysis PMC - PMC5699029 OTO - NOTNLM OT - ancient DNA OT - cultural variation OT - mobility OT - morphological variation OT - time-series data COIS- The authors declare no conflict of interest. EDAT- 2017/11/01 06:00 MHDA- 2018/06/21 06:00 PMCR- 2017/10/30 CRDT- 2017/11/01 06:00 PHST- 2017/11/01 06:00 [pubmed] PHST- 2018/06/21 06:00 [medline] PHST- 2017/11/01 06:00 [entrez] PHST- 2017/10/30 00:00 [pmc-release] AID - 1703642114 [pii] AID - 201703642 [pii] AID - 10.1073/pnas.1703642114 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):12213-12218. doi: 10.1073/pnas.1703642114. Epub 2017 Oct 30. PMID- 29107554 OWN - NLM STAT- MEDLINE DCOM- 20180808 LR - 20211204 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 27 IP - 21 DP - 2017 Nov 6 TI - Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans. PG - 3396-3402.e5 LID - S0960-9822(17)31257-5 [pii] LID - 10.1016/j.cub.2017.09.059 [doi] AB - The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5(th) century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7(th)-11(th) centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria. CI - Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved. FAU - Rodríguez-Varela, Ricardo AU - Rodríguez-Varela R AD - Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain. Electronic address: ricardo.rodriguez.varela@arklab.su.se. FAU - Günther, Torsten AU - Günther T AD - Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden. FAU - Krzewińska, Maja AU - Krzewińska M AD - Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. FAU - Storå, Jan AU - Storå J AD - Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. FAU - Gillingwater, Thomas H AU - Gillingwater TH AD - Anatomy, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK. FAU - MacCallum, Malcolm AU - MacCallum M AD - Anatomy, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK. FAU - Arsuaga, Juan Luis AU - Arsuaga JL AD - Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain. FAU - Dobney, Keith AU - Dobney K AD - Department of Archaeology, School of Geosciences, University of Aberdeen, St. Mary's, Aberdeen AB24 3UF, UK; Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK; Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada. FAU - Valdiosera, Cristina AU - Valdiosera C AD - Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Department of Archaeology and History, La Trobe University, Melbourne, VIC 3086, Australia. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden. FAU - Götherström, Anders AU - Götherström A AD - Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. FAU - Girdland-Flink, Linus AU - Girdland-Flink L AD - Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Research Centre in Evolutionary Anthropology and Palaeoecology, School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK. Electronic address: linusflink@hotmail.com. LA - eng PT - Journal Article DEP - 20171026 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM EIN - Curr Biol. 2018 May 21;28(10):1677-1679. doi: 10.1016/j.cub.2018.04.083. PMID: 29787714 MH - Africa, Northern MH - Archaeology/methods MH - Body Remains MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration/*statistics & numerical data MH - Genetic Markers MH - Genetics, Population MH - Genome, Human/*genetics MH - Genome, Mitochondrial/*genetics MH - Humans MH - Polymorphism, Single Nucleotide/genetics MH - Racial Groups/*genetics MH - Spain MH - Tooth/anatomy & histology OTO - NOTNLM OT - Canary Islands OT - Guanche OT - aboriginal populations OT - admixture OT - ancient DNA OT - archaeogenomics OT - colonization OT - population genomics EDAT- 2017/11/07 06:00 MHDA- 2018/08/09 06:00 CRDT- 2017/11/07 06:00 PHST- 2017/07/28 00:00 [received] PHST- 2017/09/07 00:00 [revised] PHST- 2017/09/27 00:00 [accepted] PHST- 2017/11/07 06:00 [pubmed] PHST- 2018/08/09 06:00 [medline] PHST- 2017/11/07 06:00 [entrez] AID - S0960-9822(17)31257-5 [pii] AID - 10.1016/j.cub.2017.09.059 [doi] PST - ppublish SO - Curr Biol. 2017 Nov 6;27(21):3396-3402.e5. doi: 10.1016/j.cub.2017.09.059. Epub 2017 Oct 26. PMID- 28984227 OWN - NLM STAT- MEDLINE DCOM- 20171127 LR - 20191210 IS - 1473-5644 (Electronic) IS - 0022-2615 (Linking) VI - 66 IP - 11 DP - 2017 Nov TI - Leprosy in pre-Norman Suffolk, UK: biomolecular and geochemical analysis of the woman from Hoxne. PG - 1640-1649 LID - 10.1099/jmm.0.000606 [doi] AB - PURPOSE: A woman's skull, exhibiting features of lepromatous leprosy (LL), was recovered from a garden in Hoxne, Suffolk. The absence of post crania and lack of formal excavation meant that diagnosis and dating was uncertain. The aim of this research was to confirm the diagnosis using biomolecular means and second, to place it in context with other British leprosy cases using SNP genotyping and radiocarbon dating. METHODOLOGY: Bone from the skull was analysed by ancient DNA (aDNA) methods and subjected to radiocarbon dating. As a result, stable carbon and nitrogen isotope values were produced, both useful for assessing aspects of the woman's diet.Results/Key findings. aDNA confirmed the presence of mycobacterium leprae and genotyping demonstrated an ancestral variant of subtype 3I, the same lineage recently identified in living squirrels in the south of England. Radiocarbon dating revealed the woman lived approximately between 885-1015 AD, providing evidence for endurance of this subtype in East Anglia, having been previously identified as early as the fifth-sixth century (Great Chesterford) and as late as the thirteenth century (Ipswich). CONCLUSIONS: The confirmation of a new pre-Norman leprosy case in East Anglia is of interest as this is where a high proportion of cases are located. Possible factors for this may include preservation and excavation biases, population density, but also connection and trade, possibly of fur, with the continent. Future research on other British LL cases should focus on exploring these aspects to advance understanding of the disease's history, here and on the continent. FAU - Inskip, Sarah AU - Inskip S AD - McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, CB2 3ER, UK. FAU - Taylor, G Michael AU - Taylor GM AD - Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7TE, UK. FAU - Anderson, Sue AU - Anderson S AD - Spoilheap Archaeology, Norwich, NR2 4GZ, UK. FAU - Stewart, Graham AU - Stewart G AD - Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7TE, UK. LA - eng PT - Historical Article PT - Journal Article DEP - 20171006 PL - England TA - J Med Microbiol JT - Journal of medical microbiology JID - 0224131 SB - IM MH - Adult MH - Female MH - Genotype MH - History, Medieval MH - Humans MH - Leprosy, Lepromatous/diagnosis/*epidemiology/history/microbiology MH - Mycobacterium leprae/classification/*genetics/*isolation & purification MH - Osteology MH - Skull/microbiology MH - United Kingdom OTO - NOTNLM OT - East Anglia OT - PCR OT - SNP OT - archaeology OT - leprosy OT - medieval EDAT- 2017/10/07 06:00 MHDA- 2017/11/29 06:00 CRDT- 2017/10/07 06:00 PHST- 2017/10/07 06:00 [pubmed] PHST- 2017/11/29 06:00 [medline] PHST- 2017/10/07 06:00 [entrez] AID - 10.1099/jmm.0.000606 [doi] PST - ppublish SO - J Med Microbiol. 2017 Nov;66(11):1640-1649. doi: 10.1099/jmm.0.000606. Epub 2017 Oct 6. PMID- 28890534 OWN - NLM STAT- MEDLINE DCOM- 20171020 LR - 20240229 IS - 1471-0064 (Electronic) IS - 1471-0056 (Linking) VI - 18 IP - 11 DP - 2017 Nov TI - Harnessing ancient genomes to study the history of human adaptation. PG - 659-674 LID - 10.1038/nrg.2017.65 [doi] AB - The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone. FAU - Marciniak, Stephanie AU - Marciniak S AD - Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA. FAU - Perry, George H AU - Perry GH AD - Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA. AD - Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA. AD - Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA. LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review DEP - 20170911 PL - England TA - Nat Rev Genet JT - Nature reviews. Genetics JID - 100962779 SB - IM MH - Animals MH - *Adaptation, Physiological MH - *Biological Evolution MH - *Genome, Human MH - *Neanderthals/genetics MH - Humans EDAT- 2017/09/12 06:00 MHDA- 2017/10/20 06:00 CRDT- 2017/09/12 06:00 PHST- 2017/09/12 06:00 [pubmed] PHST- 2017/10/20 06:00 [medline] PHST- 2017/09/12 06:00 [entrez] AID - nrg.2017.65 [pii] AID - 10.1038/nrg.2017.65 [doi] PST - ppublish SO - Nat Rev Genet. 2017 Nov;18(11):659-674. doi: 10.1038/nrg.2017.65. Epub 2017 Sep 11. PMID- 29065293 OWN - NLM STAT- MEDLINE DCOM- 20190620 LR - 20190620 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 27 IP - 20 DP - 2017 Oct 23 TI - Genetics: Ancient DNA Clarifies Population Histories of the Northeastern Margin of North America. PG - R1116-R1118 LID - S0960-9822(17)31201-0 [pii] LID - 10.1016/j.cub.2017.09.036 [doi] AB - A new study of ancient mitochondrial DNA from Newfoundland and Labrador indicates that this region at the northeastern margin of North America was populated three times in succession by different indigenous groups. This research helps shed light on the movement of populations across the continent, following the initial peopling of the Americas. CI - Copyright © 2017 Elsevier Ltd. All rights reserved. FAU - Raff, Jennifer AU - Raff J AD - Department of Anthropology, University of Kansas, Lawrence, KS 66045, USA. Electronic address: jennifer.raff@ku.edu. LA - eng PT - Comment PT - Journal Article PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM CON - Curr Biol. 2017 Oct 23;27(20):3149-3156.e11. doi: 10.1016/j.cub.2017.08.053. PMID: 29033326 MH - Canada MH - *DNA, Ancient MH - DNA, Mitochondrial/genetics MH - Genetic Variation MH - Genetics, Population MH - Humans MH - Indians, North American/*genetics MH - Newfoundland and Labrador MH - North America EDAT- 2017/10/25 06:00 MHDA- 2019/06/21 06:00 CRDT- 2017/10/25 06:00 PHST- 2017/10/25 06:00 [entrez] PHST- 2017/10/25 06:00 [pubmed] PHST- 2019/06/21 06:00 [medline] AID - S0960-9822(17)31201-0 [pii] AID - 10.1016/j.cub.2017.09.036 [doi] PST - ppublish SO - Curr Biol. 2017 Oct 23;27(20):R1116-R1118. doi: 10.1016/j.cub.2017.09.036. PMID- 29033334 OWN - NLM STAT- MEDLINE DCOM- 20180730 LR - 20241205 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 27 IP - 20 DP - 2017 Oct 23 TI - Genetic Ancestry of Rapanui before and after European Contact. PG - 3209-3215.e6 LID - S0960-9822(17)31194-6 [pii] LID - 10.1016/j.cub.2017.09.029 [doi] AB - The origins and lifeways of the inhabitants of Rapa Nui (Easter Island), a remote island in the southeast Pacific Ocean, have been debated for generations. Archaeological evidence substantiates the widely accepted view that the island was first settled by people of Polynesian origin, as late as 1200 CE [1-4]. What remains controversial, however, is the nature of events in the island's population history prior to the first historic contact with Europeans in 1722 CE. Purported contact between Rapa Nui and South America is particularly contentious, and recent studies have reported genetic evidence for Native American admixture in present-day indigenous inhabitants of Rapa Nui [5-8]. Statistical modeling has suggested that this genetic contribution might have occurred prior to European contact [6]. Here we directly test the hypothesis that the Native American admixture of the current Rapa Nui population predates the arrival of Europeans with a paleogenomic analysis of five individual samples excavated from Ahu Nau Nau, Anakena, dating to pre- and post-European contact, respectively. Complete mitochondrial genomes and low-coverage autosomal genomes show that the analyzed individuals fall within the genetic diversity of present-day and ancient Polynesians, and we can reject the hypothesis that any of these individuals had substantial Native American ancestry. Our data thus suggest that the Native American ancestry in contemporary Easter Islanders was not present on the island prior to European contact and may thus be due to events in more recent history. CI - Copyright © 2017 Elsevier Ltd. All rights reserved. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AD - UCSC Paleogenomics Lab, Department of Anthropology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA. Electronic address: lfehrens@ucsc.edu. FAU - Jarman, Catrine L AU - Jarman CL AD - Department of Archaeology and Anthropology, University of Bristol, 43 Woodland Road, Bristol BS8 1UU, UK. FAU - Harkins, Kelly M AU - Harkins KM AD - UCSC Paleogenomics Lab, Department of Anthropology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA. FAU - Kayser, Manfred AU - Kayser M AD - Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands. FAU - Popp, Brian N AU - Popp BN AD - Department of Geology & Geophysics, University of Hawaii, 1680 East-West Road, Honolulu, HI 96822, USA. FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. LA - eng PT - Journal Article DEP - 20171012 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - Archaeology MH - Female MH - *Genetic Variation MH - *Genome, Human MH - Genome, Mitochondrial MH - *Human Migration MH - Humans MH - Indians, South American/*genetics MH - Male MH - Polynesia OTO - NOTNLM OT - Easter Island OT - Oceania OT - Rapa Nui OT - Rapanui OT - admixture OT - ancient DNA OT - population history EDAT- 2017/10/17 06:00 MHDA- 2018/07/31 06:00 CRDT- 2017/10/17 06:00 PHST- 2017/07/07 00:00 [received] PHST- 2017/08/21 00:00 [revised] PHST- 2017/09/13 00:00 [accepted] PHST- 2017/10/17 06:00 [pubmed] PHST- 2018/07/31 06:00 [medline] PHST- 2017/10/17 06:00 [entrez] AID - S0960-9822(17)31194-6 [pii] AID - 10.1016/j.cub.2017.09.029 [doi] PST - ppublish SO - Curr Biol. 2017 Oct 23;27(20):3209-3215.e6. doi: 10.1016/j.cub.2017.09.029. Epub 2017 Oct 12. PMID- 29033327 OWN - NLM STAT- MEDLINE DCOM- 20180730 LR - 20240717 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 27 IP - 20 DP - 2017 Oct 23 TI - 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia. PG - 3202-3208.e9 LID - S0960-9822(17)31195-8 [pii] LID - 10.1016/j.cub.2017.09.030 [doi] AB - By at least 45,000 years before present, anatomically modern humans had spread across Eurasia [1-3], but it is not well known how diverse these early populations were and whether they contributed substantially to later people or represent early modern human expansions into Eurasia that left no surviving descendants today. Analyses of genome-wide data from several ancient individuals from Western Eurasia and Siberia have shown that some of these individuals have relationships to present-day Europeans [4, 5] while others did not contribute to present-day Eurasian populations [3, 6]. As contributions from Upper Paleolithic populations in Eastern Eurasia to present-day humans and their relationship to other early Eurasians is not clear, we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China, [1, 7] to study his relationship to ancient and present-day humans. We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia [8] and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia. CI - Copyright © 2017 Elsevier Ltd. All rights reserved. FAU - Yang, Melinda A AU - Yang MA AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Laboratory on Molecular Paleontology of the Max Planck Institute for Evolutionary Anthropology and the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Gao, Xing AU - Gao X AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Laboratory on Molecular Paleontology of the Max Planck Institute for Evolutionary Anthropology and the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Theunert, Christoph AU - Theunert C AD - Department of Integrative Biology, University of California Berkeley, Berkeley, Berkeley, CA 94720, USA; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Tong, Haowen AU - Tong H AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Aximu-Petri, Ayinuer AU - Aximu-Petri A AD - Laboratory on Molecular Paleontology of the Max Planck Institute for Evolutionary Anthropology and the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Nickel, Birgit AU - Nickel B AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Slatkin, Montgomery AU - Slatkin M AD - Department of Integrative Biology, University of California Berkeley, Berkeley, Berkeley, CA 94720, USA. FAU - Meyer, Matthias AU - Meyer M AD - Laboratory on Molecular Paleontology of the Max Planck Institute for Evolutionary Anthropology and the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Pääbo, Svante AU - Pääbo S AD - Laboratory on Molecular Paleontology of the Max Planck Institute for Evolutionary Anthropology and the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Kelso, Janet AU - Kelso J AD - Laboratory on Molecular Paleontology of the Max Planck Institute for Evolutionary Anthropology and the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. Electronic address: kelso@eva.mpg.de. FAU - Fu, Qiaomei AU - Fu Q AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Laboratory on Molecular Paleontology of the Max Planck Institute for Evolutionary Anthropology and the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. Electronic address: fuqiaomei@ivpp.ac.cn. LA - eng GR - 694707/ERC_/European Research Council/International GR - R01 GM040282/GM/NIGMS NIH HHS/United States PT - Journal Article DEP - 20171012 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Biological Variation, Population MH - China MH - DNA, Ancient/*analysis MH - *Genome, Human MH - *Human Migration MH - Humans MH - Male MH - Phylogeny PMC - PMC6592271 MID - NIHMS1017243 OTO - NOTNLM OT - Tianyuan OT - Upper Paleolithic OT - ancient DNA OT - human prehistory OT - population structure EDAT- 2017/10/17 06:00 MHDA- 2018/07/31 06:00 PMCR- 2019/06/25 CRDT- 2017/10/17 06:00 PHST- 2017/06/14 00:00 [received] PHST- 2017/07/21 00:00 [revised] PHST- 2017/09/13 00:00 [accepted] PHST- 2017/10/17 06:00 [pubmed] PHST- 2018/07/31 06:00 [medline] PHST- 2017/10/17 06:00 [entrez] PHST- 2019/06/25 00:00 [pmc-release] AID - S0960-9822(17)31195-8 [pii] AID - 10.1016/j.cub.2017.09.030 [doi] PST - ppublish SO - Curr Biol. 2017 Oct 23;27(20):3202-3208.e9. doi: 10.1016/j.cub.2017.09.030. Epub 2017 Oct 12. PMID- 29033326 OWN - NLM STAT- MEDLINE DCOM- 20180730 LR - 20180730 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 27 IP - 20 DP - 2017 Oct 23 TI - Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada. PG - 3149-3156.e11 LID - S0960-9822(17)31091-6 [pii] LID - 10.1016/j.cub.2017.08.053 [doi] AB - Situated at the furthest northeastern edge of Canada, the island of Newfoundland (approximately 110,000 km(2)) and Labrador (approximately 295,000 km(2)) today constitute a province characterized by abundant natural resources but low population density. Both landmasses were covered by the Laurentide ice sheet during the Last Glacial Maximum (18,000 years before present [YBP]); after the glacier retreated, ice patches remained on the island until ca. 9,000 calibrated (cal) YBP [1]. Nevertheless, indigenous peoples, whose ancestors had trekked some 5,000 km from the west coast, arrived approximately 10,000 cal YBP in Labrador and ca. 6,000 cal YBP in Newfoundland [2, 3]. Differential features in material culture indicate at least three settlement episodes by distinct cultural groups, including the Maritime Archaic, Palaeoeskimo, and Beothuk. Newfoundland has remained home to indigenous peoples until present day with only one apparent hiatus (3,400-2,800 YBP). This record suggests abandonment, severe constriction, or local extinction followed by subsequent immigrations from single or multiple source populations, but the specific dynamics and the cultural and biological relationships, if any, among these successive peoples remain enigmatic [4]. By examining the mitochondrial genome diversity and isotopic ratios of 74 ancient remains in conjunction with the archaeological record, we have provided definitive evidence for the genetic discontinuity between the maternal lineages of these populations. This northeastern margin of North America appears to have been populated multiple times by distinct groups that did not share a recent common ancestry, but rather one much deeper in time at the entry point into the continent. CI - Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved. FAU - Duggan, Ana T AU - Duggan AT AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada. Electronic address: duggana@mcmaster.ca. FAU - Harris, Alison J T AU - Harris AJT AD - Department of Archaeology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada. FAU - Marciniak, Stephanie AU - Marciniak S AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada. FAU - Marshall, Ingeborg AU - Marshall I AD - Institute of Social and Economic Research, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada. FAU - Kuch, Melanie AU - Kuch M AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada. FAU - Kitchen, Andrew AU - Kitchen A AD - Department of Anthropology, University of Iowa, Iowa City, IA 52242, USA. FAU - Renaud, Gabriel AU - Renaud G AD - Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen, Denmark. FAU - Southon, John AU - Southon J AD - Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, Irvine, CA, USA. FAU - Fuller, Ben AU - Fuller B AD - Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, Irvine, CA, USA. FAU - Young, Janet AU - Young J AD - Canadian Museum of History, 100 Laurier Street, Gatineau, QC K1A 0M8, Canada. FAU - Fiedel, Stuart AU - Fiedel S AD - Louis Berger, 117 Kendrick Street No. 400, Needham, MA 02494, USA. FAU - Golding, G Brian AU - Golding GB AD - Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada. FAU - Grimes, Vaughan AU - Grimes V AD - Department of Archaeology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada; Department of Earth Sciences, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada. Electronic address: vgrimes@mun.ca. FAU - Poinar, Hendrik AU - Poinar H AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Humans & the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada. Electronic address: poinarh@mcmaster.ca. LA - eng PT - Journal Article DEP - 20171012 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM CIN - Curr Biol. 2017 Oct 23;27(20):R1116-R1118. doi: 10.1016/j.cub.2017.09.036. PMID: 29065293 MH - Adolescent MH - Adult MH - Aged MH - Aged, 80 and over MH - Archaeology MH - Child MH - Child, Preschool MH - DNA, Ancient/*analysis MH - Female MH - *Genetic Variation MH - *Genome, Human MH - *Genome, Mitochondrial MH - *Human Migration MH - Humans MH - Indians, North American MH - Infant MH - Infant, Newborn MH - Male MH - Middle Aged MH - Newfoundland and Labrador MH - Young Adult OTO - NOTNLM OT - Beothuk OT - Maritime Archaic OT - ancient DNA OT - mitochondrial genomes OT - population genetics OT - stable isotopes EDAT- 2017/10/17 06:00 MHDA- 2018/07/31 06:00 CRDT- 2017/10/17 06:00 PHST- 2017/07/19 00:00 [received] PHST- 2017/08/03 00:00 [revised] PHST- 2017/08/22 00:00 [accepted] PHST- 2017/10/17 06:00 [pubmed] PHST- 2018/07/31 06:00 [medline] PHST- 2017/10/17 06:00 [entrez] AID - S0960-9822(17)31091-6 [pii] AID - 10.1016/j.cub.2017.08.053 [doi] PST - ppublish SO - Curr Biol. 2017 Oct 23;27(20):3149-3156.e11. doi: 10.1016/j.cub.2017.08.053. Epub 2017 Oct 12. PMID- 29023552 OWN - NLM STAT- MEDLINE DCOM- 20171023 LR - 20181113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 12 IP - 10 DP - 2017 TI - The impact of male burials on the construction of Corded Ware identity: Reconstructing networks of information in the 3rd millennium BC. PG - e0185971 LID - 10.1371/journal.pone.0185971 [doi] LID - e0185971 AB - The emergence of Corded Ware Groups throughout Europe in the 3rd millennium BC is one of the most defining events in European history. From the Wolga to the Rhine communities start to speak Indo-European languages and bury their dead in an extremely similar fashion. Recent ancient DNA-analyses identify a massive migration from the Eurasian steppe as the prime cause for this event. However, there is a fundamental difference between expressing a Corded Ware identity-the sharing of world views and ideas-and having a specific DNA-profile. Therefore, we argue that investigating the exchange of cultural information on burial rites between these communities serves as a crucial complement to the exchange of biological information. By adopting a practice perspective to 1161 Corded Ware burials throughout north-western Europe, combined with similarity indexes and network representations, we demonstrate a high degree of information sharing on the burial ritual between different regions. Moreover, we show that male burials are much more international in character than female burials and as such can be considered as the vector along which cultural information and Corded Ware identity was transmitted. This finding highlights an underlying complex societal organization of Corded Ware burial rites in which gender roles had a significant impact on the composition and transmission of cultural information. Our findings corroborate recent studies that suggest the Corded Ware was a male focused society. FAU - Bourgeois, Quentin AU - Bourgeois Q AUID- ORCID: 0000-0001-7518-2142 AD - Faculty of Archaeology, Leiden University, Leiden, The Netherlands. FAU - Kroon, Erik AU - Kroon E AD - Faculty of Archaeology, Leiden University, Leiden, The Netherlands. LA - eng PT - Historical Article PT - Journal Article DEP - 20171012 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - Burial/*history MH - Culture MH - Europe MH - History, Ancient MH - Humans MH - Information Dissemination/*history MH - Male PMC - PMC5638321 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2017/10/13 06:00 MHDA- 2017/10/24 06:00 PMCR- 2017/10/12 CRDT- 2017/10/13 06:00 PHST- 2017/07/12 00:00 [received] PHST- 2017/09/24 00:00 [accepted] PHST- 2017/10/13 06:00 [entrez] PHST- 2017/10/13 06:00 [pubmed] PHST- 2017/10/24 06:00 [medline] PHST- 2017/10/12 00:00 [pmc-release] AID - PONE-D-17-26220 [pii] AID - 10.1371/journal.pone.0185971 [doi] PST - epublish SO - PLoS One. 2017 Oct 12;12(10):e0185971. doi: 10.1371/journal.pone.0185971. eCollection 2017. PMID- 28977014 OWN - NLM STAT- MEDLINE DCOM- 20171031 LR - 20181113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 12 IP - 10 DP - 2017 TI - Origin of the ornamented bâton percé from the Gołębiewo site 47 as a trigger of discussion on long-distance exchange among Early Mesolithic communities of Central Poland and Northern Europe. PG - e0184560 LID - 10.1371/journal.pone.0184560 [doi] LID - e0184560 AB - This article describes evidence for contact and exchange among Mesolithic communities in Poland and Scandinavia, based on the interdisciplinary analysis of an ornamented bâton percé from Gołębiewo site 47 (Central Poland). Typological and chronological-cultural analyses show the artefact to be most likely produced in the North European Plain, during the Boreal period. Carbon-14 dating confirms the antiquity of the artefact. Ancient DNA analysis shows the artefact to be of Rangifer tarandus antler. Following this species designation, a dispersion analysis of Early-Holocene reindeer remains in Europe was conducted, showing this species to exist only in northern Scandinavia and north-western Russia in this period. Therefore, the bâton from Gołębiewo constitutes the youngest reindeer remains in the European Plain and south-western Scandinavia known to date. An attempt was made to determine the biogeographic region from which the antler used to produce the artefact originates from. To this end, comprehensive δ18O, δ13C and δ15N isotope analyses were performed. North Karelia and South Lapland were determined as the most probable regions in terms of isotopic data, results which correspond to the known distribution range of Rangifer tarandus at this time. In light of these finds, the likelihood of contact between Scandinavia and Central Europe in Early Holocene is evaluated. The bâton percé from Gołębiewo is likely key evidence for long-distance exchange during the Boreal period. FAU - Osipowicz, Grzegorz AU - Osipowicz G AUID- ORCID: 0000-0002-4393-655X AD - Institute of Archaeology, Nicolaus Copernicus University, Toruń, Kuyavian-Pomeranian Voivodeship, Poland. FAU - Witas, Henryk AU - Witas H AD - Department of Molecular Biology, Medical University of Lodz, Łódź Voivodeship, Poland. FAU - Lisowska-Gaczorek, Aleksandra AU - Lisowska-Gaczorek A AD - Institute of Zoology, Jagiellonian University, Kraków, Lesser Poland Voivodeship, Poland. FAU - Reitsema, Laurie AU - Reitsema L AD - Bioarcheology and Biochemistry Laboratory, University of Georgia, Athens, Georgia, United States of America. FAU - Szostek, Krzysztof AU - Szostek K AD - Institute of Zoology, Jagiellonian University, Kraków, Lesser Poland Voivodeship, Poland. FAU - Płoszaj, Tomasz AU - Płoszaj T AD - Department of Molecular Biology, Medical University of Lodz, Łódź Voivodeship, Poland. FAU - Kuriga, Justyna AU - Kuriga J AD - Institute of Archaeology, Nicolaus Copernicus University, Toruń, Kuyavian-Pomeranian Voivodeship, Poland. FAU - Makowiecki, Daniel AU - Makowiecki D AD - Institute of Archaeology, Nicolaus Copernicus University, Toruń, Kuyavian-Pomeranian Voivodeship, Poland. FAU - Jędrychowska-Dańska, Krystyna AU - Jędrychowska-Dańska K AD - Department of Molecular Biology, Medical University of Lodz, Łódź Voivodeship, Poland. FAU - Cienkosz-Stepańczak, Beata AU - Cienkosz-Stepańczak B AD - Institute of Zoology, Jagiellonian University, Kraków, Lesser Poland Voivodeship, Poland. LA - eng PT - Journal Article DEP - 20171004 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 9007-49-2 (DNA) SB - IM MH - *Animal Migration MH - Animals MH - *Antlers MH - Artifacts MH - DNA/genetics MH - Europe MH - *Fossils MH - Humans MH - Paleontology MH - Poland MH - Polymorphism, Single Nucleotide MH - *Reindeer MH - Sequence Analysis, DNA PMC - PMC5627898 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2017/10/05 06:00 MHDA- 2017/11/01 06:00 PMCR- 2017/10/04 CRDT- 2017/10/05 06:00 PHST- 2017/06/01 00:00 [received] PHST- 2017/08/25 00:00 [accepted] PHST- 2017/10/05 06:00 [entrez] PHST- 2017/10/05 06:00 [pubmed] PHST- 2017/11/01 06:00 [medline] PHST- 2017/10/04 00:00 [pmc-release] AID - PONE-D-17-21035 [pii] AID - 10.1371/journal.pone.0184560 [doi] PST - epublish SO - PLoS One. 2017 Oct 4;12(10):e0184560. doi: 10.1371/journal.pone.0184560. eCollection 2017. PMID- 28957511 OWN - NLM STAT- MEDLINE DCOM- 20171129 LR - 20231112 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 34 IP - 10 DP - 2017 Oct 1 TI - Inferring Past Environments from Ancient Epigenomes. PG - 2429-2438 LID - 10.1093/molbev/msx211 [doi] AB - Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more. We demonstrate this approach by showing that hunger-related DNA methylation changes are found in ancient hunter-gatherers. The strategy we present here opens a window to reconstruct previously inaccessible aspects of the lives of past individuals. CI - © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Gokhman, David AU - Gokhman D AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel. FAU - Malul, Anat AU - Malul A AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel. FAU - Carmel, Liran AU - Carmel L AD - Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/genetics MH - DNA Methylation/genetics/physiology MH - DNA, Ancient/*analysis MH - Environment MH - Epigenesis, Genetic/genetics MH - Epigenomics/*methods MH - Hominidae/genetics MH - Humans PMC - PMC5850778 OTO - NOTNLM OT - DNA methylation OT - ancient DNA OT - ancient epigenetics OT - environmental epigenetics OT - environmental paleoepigenetics OT - paleoepigenetics EDAT- 2017/09/29 06:00 MHDA- 2017/12/01 06:00 PMCR- 2017/07/24 CRDT- 2017/09/29 06:00 PHST- 2017/09/29 06:00 [entrez] PHST- 2017/09/29 06:00 [pubmed] PHST- 2017/12/01 06:00 [medline] PHST- 2017/07/24 00:00 [pmc-release] AID - 4010936 [pii] AID - msx211 [pii] AID - 10.1093/molbev/msx211 [doi] PST - ppublish SO - Mol Biol Evol. 2017 Oct 1;34(10):2429-2438. doi: 10.1093/molbev/msx211. PMID- 28681914 OWN - NLM STAT- MEDLINE DCOM- 20171002 LR - 20180214 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 164 IP - 2 DP - 2017 Oct TI - 2,000 Year old β-thalassemia case in Sardinia suggests malaria was endemic by the Roman period. PG - 362-370 LID - 10.1002/ajpa.23278 [doi] AB - OBJECTIVES: The island of Sardinia has one of the highest incidence rates of β-thalassemia in Europe due to its long history of endemic malaria, which, according to historical records, was introduced around 2,600 years ago by the Punics and only became endemic around the Middle Ages. In particular, the cod39 mutation is responsible for more than 95% of all β-thalassemia cases observed on the island. Debates surround the origin of the mutation. Some argue that its presence in the Western Mediterranean reflects the migration of people away from Sardinia, others that it reflects the colonization of the island by the Punics who might have carried the disease allele. The aim of this study was to investigate β-globin mutations, including cod39, using ancient DNA (aDNA) analysis, to better understand the history and origin of β-thalassemia and malaria in Sardinia. MATERIALS AND METHODS: PCR analysis followed by sequencing were used to investigate the presence of β-thalassemia mutations in 19 individuals from three different Roman and Punic necropolises in Sardinia. RESULTS: The cod39 mutation was identified in one male individual buried in a necropolis from the Punic/Roman period. Further analyses have shown that his mitochondrial DNA (mtDNA) and Y-chromosome haplogroups were U5a and I2a1a1, respectively, indicating the individual was probably of Sardinian origin. CONCLUSIONS: This is the earliest documented case of β-thalassemia in Sardinia to date. The presence of such a pathogenic mutation and its persistence until present day indicates that malaria was likely endemic on the island by the Roman period, earlier than the historical sources suggest. CI - © 2017 Wiley Periodicals, Inc. FAU - Viganó, Claudia AU - Viganó C AUID- ORCID: 0000-0002-7353-9053 AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, 8057, Switzerland. FAU - Haas, Cordula AU - Haas C AD - Zurich Institute of Forensic Medicine, University of Zurich, Zurich, 8057, Switzerland. FAU - Rühli, Frank J AU - Rühli FJ AUID- ORCID: 0000-0001-7937-001X AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, 8057, Switzerland. FAU - Bouwman, Abigail AU - Bouwman A AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, 8057, Switzerland. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20170706 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) RN - 0 (beta-Globins) SB - IM MH - Anthropology, Physical MH - Chromosomes, Human, Y/genetics MH - DNA, Mitochondrial/analysis/genetics MH - Endemic Diseases/history MH - Female MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Italy MH - Malaria/history MH - Male MH - Mutation/genetics MH - beta-Globins/*genetics MH - beta-Thalassemia/*genetics/*history OTO - NOTNLM OT - Sardinia OT - aDNA OT - beta-globin OT - cod39 mutation OT - malaria adaptation EDAT- 2017/07/07 06:00 MHDA- 2017/10/03 06:00 CRDT- 2017/07/07 06:00 PHST- 2017/02/03 00:00 [received] PHST- 2017/06/15 00:00 [revised] PHST- 2017/06/23 00:00 [accepted] PHST- 2017/07/07 06:00 [pubmed] PHST- 2017/10/03 06:00 [medline] PHST- 2017/07/07 06:00 [entrez] AID - 10.1002/ajpa.23278 [doi] PST - ppublish SO - Am J Phys Anthropol. 2017 Oct;164(2):362-370. doi: 10.1002/ajpa.23278. Epub 2017 Jul 6. PMID- 27859602 OWN - NLM STAT- MEDLINE DCOM- 20180104 LR - 20181202 IS - 1523-1739 (Electronic) IS - 0888-8892 (Linking) VI - 31 IP - 5 DP - 2017 Oct TI - Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska. PG - 1163-1172 LID - 10.1111/cobi.12865 [doi] AB - The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human-mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation. CI - © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology. FAU - West, Catherine AU - West C AD - Department of Archaeology, Boston University, 675 Commonwealth Avenue, Boston, MA, 02215, U.S.A. FAU - Hofman, Courtney A AU - Hofman CA AD - Department of Anthropology, University of Oklahoma, Norman, OK, 73019, U.S.A. AD - Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, P.O. Box 37012, MRC 5513, Washington, D.C., 20013-7012, U.S.A. FAU - Ebbert, Steve AU - Ebbert S AD - Alaska Maritime National Wildlife Refuge, U.S. Fish and Wildlife Service, 95 Sterling Hwy #1, Homer, AK, 99603, U.S.A. FAU - Martin, John AU - Martin J AD - Alaska Region, U.S. Fish and Wildlife Service, 1011 East Tudor Road, MS 211, Anchorage, AK, 99503, U.S.A. FAU - Shirazi, Sabrina AU - Shirazi S AD - Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, P.O. Box 37012, MRC 5513, Washington, D.C., 20013-7012, U.S.A. FAU - Dunning, Samantha AU - Dunning S AD - Department of Anthropology, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK, 99508, U.S.A. FAU - Maldonado, Jesus E AU - Maldonado JE AD - Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, P.O. Box 37012, MRC 5513, Washington, D.C., 20013-7012, U.S.A. LA - eng PT - Journal Article DEP - 20170515 PL - United States TA - Conserv Biol JT - Conservation biology : the journal of the Society for Conservation Biology JID - 9882301 RN - 0 (DNA, Ancient) SB - IM MH - Alaska MH - Animals MH - Archaeology MH - *Conservation of Natural Resources MH - *DNA, Ancient MH - Humans MH - *Introduced Species MH - Islands MH - *Sciuridae OTO - NOTNLM OT - Urocitellus parryii OT - ancient translocation OT - ardilla terrestre OT - ground squirrel OT - invasive species management OT - manejo de especies invasoras OT - translocación antigua OT - zooarchaeology OT - zooarqueología EDAT- 2016/11/20 06:00 MHDA- 2018/01/05 06:00 CRDT- 2016/11/19 06:00 PHST- 2016/07/31 00:00 [received] PHST- 2016/10/29 00:00 [revised] PHST- 2016/11/12 00:00 [accepted] PHST- 2016/11/20 06:00 [pubmed] PHST- 2018/01/05 06:00 [medline] PHST- 2016/11/19 06:00 [entrez] AID - 10.1111/cobi.12865 [doi] PST - ppublish SO - Conserv Biol. 2017 Oct;31(5):1163-1172. doi: 10.1111/cobi.12865. Epub 2017 May 15. PMID- 28938123 OWN - NLM STAT- MEDLINE DCOM- 20171010 LR - 20240610 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 171 IP - 1 DP - 2017 Sep 21 TI - Reconstructing Prehistoric African Population Structure. PG - 59-71.e21 LID - S0092-8674(17)31008-5 [pii] LID - 10.1016/j.cell.2017.08.049 [doi] AB - We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP. CI - Copyright © 2017 Elsevier Inc. All rights reserved. FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: skoglund@genetics.med.harvard.edu. FAU - Thompson, Jessica C AU - Thompson JC AD - Department of Anthropology, Emory University, Atlanta, GA 30322, USA. FAU - Prendergast, Mary E AU - Prendergast ME AD - Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA. FAU - Mittnik, Alissa AU - Mittnik A AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archeological Sciences, Eberhard-Karls-University, Tuebingen 72070, Germany. FAU - Sirak, Kendra AU - Sirak K AD - Department of Anthropology, Emory University, Atlanta, GA 30322, USA; School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland. FAU - Hajdinjak, Mateja AU - Hajdinjak M AD - Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Salie, Tasneem AU - Salie T AD - Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. FAU - Peltzer, Alexander AU - Peltzer A AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany; Integrative Transcriptomics, Centre for Bioinformatics, University of Tuebingen, Tuebingen 72076, Germany. FAU - Heinze, Anja AU - Heinze A AD - Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Olalde, Iñigo AU - Olalde I AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. FAU - Ferry, Matthew AU - Ferry M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Harney, Eadaoin AU - Harney E AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Michel, Megan AU - Michel M AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Cerezo-Román, Jessica I AU - Cerezo-Román JI AD - Department of Geography and Anthropology, California State Polytechnic University, Pomona, Pomona, CA 91768, USA. FAU - Chiumia, Chrissy AU - Chiumia C AD - Malawi Department of Museums and Monuments, Lilongwe 3, Malawi. FAU - Crowther, Alison AU - Crowther A AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany; School of Social Science, The University of Queensland, Brisbane, Queensland 4072, Australia. FAU - Gomani-Chindebvu, Elizabeth AU - Gomani-Chindebvu E AD - Malawi Department of Museums and Monuments, Lilongwe 3, Malawi. FAU - Gidna, Agness O AU - Gidna AO AD - National Museums of Tanzania, Dar es Salaam, Tanzania. FAU - Grillo, Katherine M AU - Grillo KM AD - Department of Archaeology and Anthropology, University of Wisconsin - La Crosse, La Crosse, WI 54601, USA. FAU - Helenius, I Taneli AU - Helenius IT AD - Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. FAU - Hellenthal, Garrett AU - Hellenthal G AD - Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. FAU - Helm, Richard AU - Helm R AD - Canterbury Archaeological Trust, Canterbury CT1 2LU, UK. FAU - Horton, Mark AU - Horton M AD - Department Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK. FAU - López, Saioa AU - López S AD - Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. FAU - Mabulla, Audax Z P AU - Mabulla AZP AD - National Museums of Tanzania, Dar es Salaam, Tanzania. FAU - Parkington, John AU - Parkington J AD - Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa. FAU - Shipton, Ceri AU - Shipton C AD - McDonald Institute for Archaeological Research, Cambridge CB2 3ER, UK; British Institute in Eastern Africa, Nairobi 30710, Kenya. FAU - Thomas, Mark G AU - Thomas MG AD - Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. FAU - Tibesasa, Ruth AU - Tibesasa R AD - Department of Anthropology and Archaeology, University of Pretoria, Pretoria 0083, South Africa. FAU - Welling, Menno AU - Welling M AD - African Studies Centre Leiden, Leiden University, Leiden 2300 RB, Netherlands; African Heritage Ltd, Zomba, Malawi. FAU - Hayes, Vanessa M AU - Hayes VM AD - Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia; School of Health Systems and Public Health, University of Pretoria, Gezina 0031, South Africa. FAU - Kennett, Douglas J AU - Kennett DJ AD - Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA. FAU - Ramesar, Raj AU - Ramesar R AD - Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa. FAU - Meyer, Matthias AU - Meyer M AD - Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Pääbo, Svante AU - Pääbo S AD - Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Patterson, Nick AU - Patterson N AD - Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. FAU - Morris, Alan G AU - Morris AG AD - Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa. FAU - Boivin, Nicole AU - Boivin N AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany. FAU - Pinhasi, Ron AU - Pinhasi R AD - School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland; Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archeological Sciences, Eberhard-Karls-University, Tuebingen 72070, Germany. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 263441/ERC_/European Research Council/International GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R01 HG006399/HG/NHGRI NIH HHS/United States PT - Journal Article PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Ancient) SB - IM MH - Africa MH - Black People/*genetics MH - Bone and Bones/chemistry MH - DNA, Ancient/analysis MH - Female MH - Fossils MH - Genetics, Medical MH - Genetics, Population MH - *Genome, Human MH - Genome-Wide Association Study MH - Humans MH - Life Style MH - Male PMC - PMC5679310 MID - NIHMS903612 OTO - NOTNLM OT - Africa OT - adaptation OT - ancient DNA OT - hunter-gatherers OT - natural selection OT - population genetics OT - population history EDAT- 2017/09/25 06:00 MHDA- 2017/10/11 06:00 PMCR- 2018/09/21 CRDT- 2017/09/23 06:00 PHST- 2016/12/12 00:00 [received] PHST- 2017/07/01 00:00 [revised] PHST- 2017/08/29 00:00 [accepted] PHST- 2017/09/23 06:00 [entrez] PHST- 2017/09/25 06:00 [pubmed] PHST- 2017/10/11 06:00 [medline] PHST- 2018/09/21 00:00 [pmc-release] AID - S0092-8674(17)31008-5 [pii] AID - 10.1016/j.cell.2017.08.049 [doi] PST - ppublish SO - Cell. 2017 Sep 21;171(1):59-71.e21. doi: 10.1016/j.cell.2017.08.049. PMID- 28935946 OWN - NLM STAT- MEDLINE DCOM- 20190702 LR - 20190702 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 7 IP - 1 DP - 2017 Sep 21 TI - Population resequencing of European mitochondrial genomes highlights sex-bias in Bronze Age demographic expansions. PG - 12086 LID - 10.1038/s41598-017-11307-9 [doi] LID - 12086 AB - Interpretations of genetic data concerning the prehistory of Europe have long been a subject of great debate, but increasing amounts of ancient and modern DNA data are now providing new and more informative evidence. Y-chromosome resequencing studies in Europe have highlighted the prevalence of recent expansions of male lineages, and focused interest on the Bronze Age as a period of cultural and demographic change. These findings contrast with phylogeographic studies based on mitochondrial DNA (mtDNA), which have been interpreted as supporting expansions from glacial refugia. Here we have undertaken a population-based resequencing of complete mitochondrial genomes in Europe and the Middle East, in 340 samples from 17 populations for which Y-chromosome sequence data are also available. Demographic reconstructions show no signal of Bronze Age expansion, but evidence of Paleolithic expansions in all populations except the Saami, and with an absence of detectable geographical pattern. In agreement with previous inference from modern and ancient DNA data, the unbiased comparison between the mtDNA and Y-chromosome population datasets emphasizes the sex-biased nature of recent demographic transitions in Europe. FAU - Batini, Chiara AU - Batini C AUID- ORCID: 0000-0002-7140-2985 AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. cb334@le.ac.uk. AD - Department of Health Sciences, University of Leicester, Leicester, UK. cb334@le.ac.uk. FAU - Hallast, Pille AU - Hallast P AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia. FAU - Vågene, Åshild J AU - Vågene ÅJ AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Zadik, Daniel AU - Zadik D AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. AD - Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, UK. FAU - Eriksen, Heidi A AU - Eriksen HA AD - Centre of Arctic Medicine, Thule Institute, University of Oulu, Oulu, Finland. AD - Utsjoki Health Care Centre, Utsjoki, Finland. FAU - Pamjav, Horolma AU - Pamjav H AD - Hungarian Institute of Forensic Sciences, Institute of Forensic Genetics, Budapest, Hungary. FAU - Sajantila, Antti AU - Sajantila A AD - Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki, Finland. AD - Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA. FAU - Wetton, Jon H AU - Wetton JH AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. FAU - Jobling, Mark A AU - Jobling MA AD - Department of Genetics & Genome Biology, University of Leicester, Leicester, UK. maj4@le.ac.uk. LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20170921 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Chromosomes, Human, Y/genetics MH - DNA, Ancient/*analysis/chemistry MH - DNA, Mitochondrial/chemistry/*genetics MH - Europe MH - Female MH - Genetics, Population MH - Genome, Mitochondrial/*genetics MH - Haplotypes MH - Humans MH - Male MH - Middle East MH - Mitochondria/genetics MH - Phylogeography MH - Sequence Analysis, DNA/*methods PMC - PMC5608872 COIS- The authors declare that they have no competing interests. EDAT- 2017/09/25 06:00 MHDA- 2019/07/03 06:00 PMCR- 2017/09/21 CRDT- 2017/09/23 06:00 PHST- 2017/01/10 00:00 [received] PHST- 2017/08/22 00:00 [accepted] PHST- 2017/09/23 06:00 [entrez] PHST- 2017/09/25 06:00 [pubmed] PHST- 2019/07/03 06:00 [medline] PHST- 2017/09/21 00:00 [pmc-release] AID - 10.1038/s41598-017-11307-9 [pii] AID - 11307 [pii] AID - 10.1038/s41598-017-11307-9 [doi] PST - epublish SO - Sci Rep. 2017 Sep 21;7(1):12086. doi: 10.1038/s41598-017-11307-9. PMID- 28874531 OWN - NLM STAT- MEDLINE DCOM- 20180605 LR - 20181113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 114 IP - 38 DP - 2017 Sep 19 TI - Female exogamy and gene pool diversification at the transition from the Final Neolithic to the Early Bronze Age in central Europe. PG - 10083-10088 LID - 10.1073/pnas.1706355114 [doi] AB - Human mobility has been vigorously debated as a key factor for the spread of bronze technology and profound changes in burial practices as well as material culture in central Europe at the transition from the Neolithic to the Bronze Age. However, the relevance of individual residential changes and their importance among specific age and sex groups are still poorly understood. Here, we present ancient DNA analysis, stable isotope data of oxygen, and radiogenic isotope ratios of strontium for 84 radiocarbon-dated skeletons from seven archaeological sites of the Late Neolithic Bell Beaker Complex and the Early Bronze Age from the Lech River valley in southern Bavaria, Germany. Complete mitochondrial genomes documented a diversification of maternal lineages over time. The isotope ratios disclosed the majority of the females to be nonlocal, while this is the case for only a few males and subadults. Most nonlocal females arrived in the study area as adults, but we do not detect their offspring among the sampled individuals. The striking patterns of patrilocality and female exogamy prevailed over at least 800 y between about 2500 and 1700 BC. The persisting residential rules and even a direct kinship relation across the transition from the Neolithic to the Bronze Age add to the archaeological evidence of continuing traditions from the Bell Beaker Complex to the Early Bronze Age. The results also attest to female mobility as a driving force for regional and supraregional communication and exchange at the dawn of the European metal ages. FAU - Knipper, Corina AU - Knipper C AUID- ORCID: 0000-0002-4274-4636 AD - Curt Engelhorn Center for Archaeometry gGmbH, 68159 Mannheim, Germany; corina.knipper@cez-archaeometrie.de krause@shh.mpg.de philipp.stockhammer@lmu.de. FAU - Mittnik, Alissa AU - Mittnik A AD - Institute for Archaeological Sciences, Eberhardt Karls University Tübingen, 72070 Tübingen, Germany. AD - Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Massy, Ken AU - Massy K AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians University Munich, 80799 Munich, Germany. FAU - Kociumaka, Catharina AU - Kociumaka C AD - Private address, 86672 Thierhaupten, Germany. FAU - Kucukkalipci, Isil AU - Kucukkalipci I AD - Institute for Archaeological Sciences, Eberhardt Karls University Tübingen, 72070 Tübingen, Germany. FAU - Maus, Michael AU - Maus M AD - Applied and Analytical Paleontology, Institute of Geosciences, Johannes Gutenberg University Mainz, 55128 Mainz, Germany. FAU - Wittenborn, Fabian AU - Wittenborn F AD - Heidelberg Academy of Sciences, 69117 Heidelberg, Germany. FAU - Metz, Stephanie E AU - Metz SE AD - Heidelberg Academy of Sciences, 69117 Heidelberg, Germany. FAU - Staskiewicz, Anja AU - Staskiewicz A AD - Private address, 81247 München, Germany. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, 07745 Jena, Germany; corina.knipper@cez-archaeometrie.de krause@shh.mpg.de philipp.stockhammer@lmu.de. FAU - Stockhammer, Philipp W AU - Stockhammer PW AD - Max Planck Institute for the Science of Human History, 07745 Jena, Germany; corina.knipper@cez-archaeometrie.de krause@shh.mpg.de philipp.stockhammer@lmu.de. AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians University Munich, 80799 Munich, Germany. LA - eng SI - GENBANK/MF498658 SI - GENBANK/MF498737 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20170905 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - *Anthropology, Cultural MH - Europe MH - Female MH - *Gene Pool MH - *Genome, Mitochondrial MH - History, Ancient MH - Humans MH - Male PMC - PMC5617280 OTO - NOTNLM OT - human mobility OT - kinship OT - mtDNA OT - oxygen OT - strontium COIS- The authors declare no conflict of interest. EDAT- 2017/09/07 06:00 MHDA- 2018/06/06 06:00 PMCR- 2018/03/19 CRDT- 2017/09/07 06:00 PHST- 2017/09/07 06:00 [pubmed] PHST- 2018/06/06 06:00 [medline] PHST- 2017/09/07 06:00 [entrez] PHST- 2018/03/19 00:00 [pmc-release] AID - 1706355114 [pii] AID - 201706355 [pii] AID - 10.1073/pnas.1706355114 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10083-10088. doi: 10.1073/pnas.1706355114. Epub 2017 Sep 5. PMID- 29114402 OWN - NLM STAT- MEDLINE DCOM- 20190426 LR - 20190611 IS - 2057-5858 (Electronic) IS - 2057-5858 (Linking) VI - 3 IP - 9 DP - 2017 Sep TI - Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. PG - e000123 LID - 10.1099/mgen.0.000123 [doi] LID - e000123 AB - Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Y. pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements. It has recently been shown that comparative scaffolding approaches can improve the assembly of ancient Y. pestis genomes at a chromosome level. In the present work, we address the last step of genome assembly, the gap-filling stage. We describe an optimization-based method AGapEs (ancestral gap estimation) to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads. We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and comparative signal. We applied our method to two Y. pestis data sets from the London and Marseilles outbreaks, for which we obtained highly improved genome assemblies for both genomes, comprised of, respectively, five and six scaffolds with 95 % of the assemblies supported by ancient reads. We analysed the genome evolution between both ancient genomes in terms of genome rearrangements, and observed a high level of synteny conservation between these strains. FAU - Luhmann, Nina AU - Luhmann N AD - 2Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany. AD - 1International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes", Bielefeld University, Bielefeld, Germany. FAU - Doerr, Daniel AU - Doerr D AD - 2Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany. AD - 3School of Computer and Communication Sciences, EPFL, 1015 Lausanne, Switzerland. FAU - Chauve, Cedric AU - Chauve C AD - 4Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada. LA - eng PT - Comparative Study PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20170708 PL - England TA - Microb Genom JT - Microbial genomics JID - 101671820 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM MH - Contig Mapping/*methods MH - *DNA, Ancient MH - DNA, Bacterial MH - Evolution, Molecular MH - France/epidemiology MH - *Genome, Bacterial MH - History, 18th Century MH - History, Medieval MH - Humans MH - London/epidemiology MH - Pandemics/history MH - Phylogeny MH - Plague/epidemiology/history/*microbiology MH - Yersinia pestis/*genetics PMC - PMC5643016 OTO - NOTNLM OT - Yersinia pestis OT - ancestral reconstruction OT - assembly OT - comparative genomics EDAT- 2017/11/09 06:00 MHDA- 2019/04/27 06:00 PMCR- 2017/07/08 CRDT- 2017/11/09 06:00 PHST- 2017/03/01 00:00 [received] PHST- 2017/06/07 00:00 [accepted] PHST- 2017/11/09 06:00 [entrez] PHST- 2017/11/09 06:00 [pubmed] PHST- 2019/04/27 06:00 [medline] PHST- 2017/07/08 00:00 [pmc-release] AID - mgen000123 [pii] AID - 10.1099/mgen.0.000123 [doi] PST - epublish SO - Microb Genom. 2017 Jul 8;3(9):e000123. doi: 10.1099/mgen.0.000123. eCollection 2017 Sep. PMID- 29027332 OWN - NLM STAT- MEDLINE DCOM- 20171019 LR - 20171019 IS - 1520-6505 (Electronic) IS - 1060-1538 (Linking) VI - 26 IP - 5 DP - 2017 Sep TI - Demic and cultural diffusion in prehistoric Europe in the age of ancient genomes. PG - 228-241 LID - 10.1002/evan.21545 [doi] AB - Ancient genomes can help us detect prehistoric migrations, population contractions, and admixture among populations. Knowing the dynamics of demography is invaluable for understanding culture change in prehistory, particularly the roles played by demic and cultural diffusion in transformations of material cultures. Prehistoric Europe is a region where ancient genome analyses can help illuminate the interplay between demography and culture change. In Europe, there is more archeological evidence, in terms of detailed studies, radiometric dates, and explanatory hypotheses that can be evaluated, than in any other region of the world. Here I show some important ways that ancient genomes have given us insights into population movements in European prehistory. I also propose that studies might be increasingly focused on specific questions of culture change, for example in evaluating the makers of "transitional" industries as well as the origins of the Gravettian and spread of the Magdalenian. I also discuss genomic evidence supporting the large role that demic expansion has played in the Neolithization of Europe and the formation of the European population during the Bronze Age. CI - © 2017 Wiley Periodicals, Inc. FAU - Harris, Eugene E AU - Harris EE AD - Department of Biological Sciences and Geology, Queensborough Community College, City University of New York, Medical Arts Building, M-213, 222-05, 56th Avenue Bayside, NY, 1136411364. AD - Affiliated Researcher, Center for the Study of Human Origins, New York University. LA - eng PT - Journal Article PL - United States TA - Evol Anthropol JT - Evolutionary anthropology JID - 9306331 RN - 0 (DNA, Ancient) SB - IM MH - Anthropology, Physical MH - Biological Evolution MH - *Cultural Evolution MH - DNA, Ancient MH - Europe MH - Genome, Human/*genetics MH - *Human Migration MH - Humans MH - Metagenomics MH - *Population Dynamics OTO - NOTNLM OT - Neolithic transition OT - Upper Paleolithic OT - ancient genomes OT - demic and cultural diffusion EDAT- 2017/10/14 06:00 MHDA- 2017/10/20 06:00 CRDT- 2017/10/14 06:00 PHST- 2017/08/23 00:00 [accepted] PHST- 2017/10/14 06:00 [entrez] PHST- 2017/10/14 06:00 [pubmed] PHST- 2017/10/20 06:00 [medline] AID - 10.1002/evan.21545 [doi] PST - ppublish SO - Evol Anthropol. 2017 Sep;26(5):228-241. doi: 10.1002/evan.21545. PMID- 28715914 OWN - NLM STAT- MEDLINE DCOM- 20180514 LR - 20180514 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 44 IP - 6 DP - 2017 Sep TI - Leprosy in a Lombard-Avar cemetery in central Italy (Campochiaro, Molise, 6th-8th century AD): ancient DNA evidence and demography. PG - 510-521 LID - 10.1080/03014460.2017.1346709 [doi] AB - BACKGROUND: The study of past infectious diseases increases knowledge of the presence, impact and spread of pathogens within ancient populations. AIM: Polymerase chain reaction (PCR) was used to examine bones for the presence of Mycobacterium leprae ancient DNA (aDNA) as, even when leprosy is present, bony changes are not always pathognomonic of the disease. This study also examined the demographic profile of this population and compared it with two other populations to investigate any changes in mortality trends between different infectious diseases and between the pre-antibiotic and antibiotic eras. SUBJECTS AND METHODS: The individuals were from a site in Central Italy (6th-8th CE) and were examined for the presence of Mycobacterium leprae aDNA. In addition, an abridged life mortality table was constructed. RESULTS: Two individuals had typical leprosy palaeopathology, and one was positive for Mycobacterium leprae aDNA. However, the demographic profile shows a mortality curve similar to that of the standard, in contrast to a population that had been subjected to bubonic plague. CONCLUSIONS: This study shows that, in the historical population with leprosy, the risk factors for health seem to be constant and distributed across all age classes, similar to what is found today in the antibiotic era. There were no peaks of mortality equivalent to those found in fatal diseases such as the plague, probably due to the long clinical course of leprosy. FAU - Rubini, Mauro AU - Rubini M AD - a Department of Archaeology , Foggia University , Foggia , Italy. AD - b Anthropological Service of S.A.L.E.M. , Ministry of Culture Italy , Rome , Italy. FAU - Zaio, Paola AU - Zaio P AD - b Anthropological Service of S.A.L.E.M. , Ministry of Culture Italy , Rome , Italy. FAU - Spigelman, Mark AU - Spigelman M AD - c The Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, The Hebrew University , Jerusalem , Israel. AD - d Department of Anatomy and Anthropology Sackler Medical School , Tel Aviv University , Tel Aviv , Israel. FAU - Donoghue, Helen D AU - Donoghue HD AD - e Centre for Clinical Microbiology , Division of Infection and Immunity , UCL , London , UK. LA - eng PT - Historical Article PT - Journal Article DEP - 20170717 PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Ancient) SB - IM MH - Cemeteries MH - DNA, Ancient/*analysis/isolation & purification MH - Demography MH - History, Medieval MH - Humans MH - Italy MH - Leprosy/*history/microbiology MH - Mycobacterium leprae/genetics/*isolation & purification MH - Paleopathology OTO - NOTNLM OT - aDNA OT - demography OT - infectious diseases OT - leprosy OT - mortality curves EDAT- 2017/07/19 06:00 MHDA- 2018/05/15 06:00 CRDT- 2017/07/19 06:00 PHST- 2017/07/19 06:00 [pubmed] PHST- 2018/05/15 06:00 [medline] PHST- 2017/07/19 06:00 [entrez] AID - 10.1080/03014460.2017.1346709 [doi] PST - ppublish SO - Ann Hum Biol. 2017 Sep;44(6):510-521. doi: 10.1080/03014460.2017.1346709. Epub 2017 Jul 17. PMID- 27246811 OWN - NLM STAT- MEDLINE DCOM- 20170919 LR - 20221207 IS - 2470-1408 (Electronic) IS - 2470-1394 (Linking) VI - 28 IP - 5 DP - 2017 Sep TI - Investigation on maternal lineage of a Neolithic group from northern Shaanxi based on ancient DNA. PG - 732-739 LID - 10.1080/24701394.2016.1177039 [doi] AB - A magnetic bead purification method was successfully used to extract ancient DNA from the skeletal remains of 10 specimens excavated from Wuzhuangguoliang (Wzhgl) site, which was located in northern Shaanxi. The multidimensional scaling (MDS) and analysis of molecular variance approach (AMOVA) revealed that ancient Wzhgl people bored a very high similarity to southern Han Chinese. By constructing the MJ-network of various modern people including Han Chinese and Japanese, the phylogenetic analysis indicated that the Wzhgl population had close maternal distance with ancient Shandong and Xinjiang people. These findings indicated that Wzhgl contributed to the gene pool of Han Chinese and modern Japanese. In addition, population migration and interflow between Wzhgl people and ancient Shandong or Xinjiang probably occurred in Neolithic period. FAU - Zhao, Jing AU - Zhao J AD - a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China. FAU - Liu, Fang-E AU - Liu FE AD - b The Center of Basic Medicine Teaching Experiments , School of Basic Medicine, Fourth Military Medicine University (FMMU) , Xi'an , PR China. FAU - Lin, Song AU - Lin S AD - a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China. FAU - Liu, Zhi-Zhen AU - Liu ZZ AD - a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China. FAU - Sun, Zhou-Yong AU - Sun ZY AD - c Shaanxi Provincial Institute of Archaeology , Xi'an , Shaanxi Province , PR China. FAU - Wu, Xiao-Ming AU - Wu XM AD - a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China. FAU - Zhang, Hu-Qin AU - Zhang HQ AD - a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China. LA - eng PT - Journal Article DEP - 20160601 PL - England TA - Mitochondrial DNA A DNA Mapp Seq Anal JT - Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis JID - 101679980 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/ethnology/*genetics MH - China/ethnology MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*analysis MH - Gene Pool MH - Humans MH - Japan/ethnology MH - Phylogeny MH - Principal Component Analysis MH - Sequence Analysis, DNA/*methods OTO - NOTNLM OT - Ancient DNA OT - Neolithic period OT - Wuzhuangguoliang site OT - maternal lineage OT - phylogenetic analysis EDAT- 2016/06/02 06:00 MHDA- 2017/09/20 06:00 CRDT- 2016/06/02 06:00 PHST- 2016/06/02 06:00 [pubmed] PHST- 2017/09/20 06:00 [medline] PHST- 2016/06/02 06:00 [entrez] AID - 10.1080/24701394.2016.1177039 [doi] PST - ppublish SO - Mitochondrial DNA A DNA Mapp Seq Anal. 2017 Sep;28(5):732-739. doi: 10.1080/24701394.2016.1177039. Epub 2016 Jun 1. PMID- 28859116 OWN - NLM STAT- MEDLINE DCOM- 20171013 LR - 20181113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 12 IP - 8 DP - 2017 TI - The Sommersdorf mummies-An interdisciplinary investigation on human remains from a 17th-19th century aristocratic crypt in southern Germany. PG - e0183588 LID - 10.1371/journal.pone.0183588 [doi] LID - e0183588 AB - Sommersdorf Castle (Bavaria, Germany) is a medieval castle complex which has been inhabited by the aristocratic family von Crailsheim. The deceased were entombed in a crypt located in the parapets underneath the castle's church, resulting in mummification of the bodies. Based on the family chronicle and oral history, identities have been ascribed to the mummies. The aim of the study is therefore to test the accuracy of the historical records in comparison to archaeological, anthropological and genetic data. Today, the crypt houses eleven wooden coffins from the 17th to 19th century AD. In ten of these, mummified and scattered human remains were found. Archive records were studied in order to identify names, ancestry, titles, occupation, date of birth and death, and place of interment of the individuals. The coffins were visually inspected and dated by typo-chronology, and the mummified and scattered skeletal remains were subjected to a physical anthropological examination. In total, the crypt contains the remains of a minimum number of nine individuals, among them three adult males, five adult females and one infant. A detailed scientific examination, including prior conservation, ancient DNA analyses, and computed tomography (CT), was performed on five mummies. By means of the CT data age at death, sex, body height, pathologies, and anatomical variants were investigated. CT analysis further showed that the bodies were naturally mummified. Mitochondrial DNA analyses revealed that the tested individuals are not maternally related. In addition, health, living conditions and circumstances of death of the entombed individuals could be highlighted. Being confronted with the strengths, weaknesses and limitations of each methodological approach, probable identification was achieved in two cases. FAU - Alterauge, Amelie AU - Alterauge A AUID- ORCID: 0000-0001-6838-271X AD - Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland. AD - Institute of Pre- and Protohistory and Near Eastern Archaeology, University of Heidelberg, Heidelberg, Germany. FAU - Kellinghaus, Manuel AU - Kellinghaus M AD - Institute of Forensic Medicine, University of Bern, Bern, Switzerland. FAU - Jackowski, Christian AU - Jackowski C AD - Institute of Forensic Medicine, University of Bern, Bern, Switzerland. FAU - Shved, Natallia AU - Shved N AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Rühli, Frank AU - Rühli F AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummy Studies, Eurac Research, Bolzano, Italy. FAU - Zink, Albert AU - Zink A AD - Institute for Mummy Studies, Eurac Research, Bolzano, Italy. FAU - Rosendahl, Wilfried AU - Rosendahl W AD - German Mummy Project, Reiss-Engelhorn-Museen, Mannheim, Germany. FAU - Lösch, Sandra AU - Lösch S AD - Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland. LA - eng PT - Journal Article DEP - 20170831 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology MH - Archaeology MH - DNA, Ancient/*analysis/isolation & purification MH - DNA, Mitochondrial/*analysis/genetics MH - *Fossils MH - Germany MH - Humans MH - *Mummies PMC - PMC5578507 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2017/09/01 06:00 MHDA- 2017/10/14 06:00 PMCR- 2017/08/31 CRDT- 2017/09/01 06:00 PHST- 2017/03/03 00:00 [received] PHST- 2017/08/06 00:00 [accepted] PHST- 2017/09/01 06:00 [entrez] PHST- 2017/09/01 06:00 [pubmed] PHST- 2017/10/14 06:00 [medline] PHST- 2017/08/31 00:00 [pmc-release] AID - PONE-D-17-08545 [pii] AID - 10.1371/journal.pone.0183588 [doi] PST - epublish SO - PLoS One. 2017 Aug 31;12(8):e0183588. doi: 10.1371/journal.pone.0183588. eCollection 2017. PMID- 28460196 OWN - NLM STAT- MEDLINE DCOM- 20171018 LR - 20231112 IS - 1545-293X (Electronic) IS - 1527-8204 (Print) IS - 1527-8204 (Linking) VI - 18 DP - 2017 Aug 31 TI - A Robust Framework for Microbial Archaeology. PG - 321-356 LID - 10.1146/annurev-genom-091416-035526 [doi] AB - Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field. FAU - Warinner, Christina AU - Warinner C AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; email: warinner@shh.mpg.de. AD - Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019. FAU - Herbig, Alexander AU - Herbig A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; email: warinner@shh.mpg.de. FAU - Mann, Allison AU - Mann A AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; email: warinner@shh.mpg.de. AD - Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019. FAU - Fellows Yates, James A AU - Fellows Yates JA AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; email: warinner@shh.mpg.de. FAU - Weiß, Clemens L AU - Weiß CL AD - Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany. FAU - Burbano, Hernán A AU - Burbano HA AD - Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen K, Denmark. AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Toulouse III - Paul Sabatier, Toulouse 31000, France. FAU - Krause, Johannes AU - Krause J AD - Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; email: warinner@shh.mpg.de. LA - eng GR - R01 GM089886/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review DEP - 20170426 PL - United States TA - Annu Rev Genomics Hum Genet JT - Annual review of genomics and human genetics JID - 100911346 RN - 0 (DNA, Ancient) SB - IM MH - Archaea/genetics/*isolation & purification MH - Archaeology/methods MH - Bacteria/genetics/*isolation & purification MH - DNA, Ancient/*analysis MH - Genome, Archaeal MH - Genome, Bacterial MH - Humans MH - Metagenomics/*methods MH - Microbiota/*genetics MH - Sequence Analysis, DNA/*methods PMC - PMC5581243 MID - NIHMS878214 OTO - NOTNLM OT - ancient DNA OT - bacteria OT - high-throughput sequencing OT - metagenomics OT - microbiology OT - microbiome OT - pathogens EDAT- 2017/05/02 06:00 MHDA- 2017/10/19 06:00 PMCR- 2018/02/28 CRDT- 2017/05/02 06:00 PHST- 2017/05/02 06:00 [pubmed] PHST- 2017/10/19 06:00 [medline] PHST- 2017/05/02 06:00 [entrez] PHST- 2018/02/28 00:00 [pmc-release] AID - 10.1146/annurev-genom-091416-035526 [doi] PST - ppublish SO - Annu Rev Genomics Hum Genet. 2017 Aug 31;18:321-356. doi: 10.1146/annurev-genom-091416-035526. Epub 2017 Apr 26. PMID- 28796208 OWN - NLM STAT- MEDLINE DCOM- 20171212 LR - 20181202 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 548 IP - 7666 DP - 2017 Aug 9 TI - Palaeobiology: Ensure equal access to ancient DNA. PG - 158 LID - 10.1038/548158a [doi] FAU - Makarewicz, Cheryl AU - Makarewicz C AD - Christian-Albrechts University, Kiel, Germany. FAU - Marom, Nimrod AU - Marom N AD - University of Haifa, Israel. FAU - Bar-Oz, Guy AU - Bar-Oz G AD - University of Haifa, Israel. LA - eng PT - Comment PT - Letter PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM CON - PLoS One. 2015 Jun 18;10(6):e0129102. doi: 10.1371/journal.pone.0129102. PMID: 26086078 MH - *DNA MH - *DNA, Ancient MH - Fossils MH - Humans MH - Sequence Analysis, DNA EDAT- 2017/08/11 06:00 MHDA- 2017/12/13 06:00 CRDT- 2017/08/11 06:00 PHST- 2017/08/11 06:00 [entrez] PHST- 2017/08/11 06:00 [pubmed] PHST- 2017/12/13 06:00 [medline] AID - 548158a [pii] AID - 10.1038/548158a [doi] PST - ppublish SO - Nature. 2017 Aug 9;548(7666):158. doi: 10.1038/548158a. PMID- 28778150 OWN - NLM STAT- MEDLINE DCOM- 20171204 LR - 20181202 IS - 1471-2148 (Electronic) IS - 1471-2148 (Linking) VI - 17 IP - 1 DP - 2017 Aug 4 TI - Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans. PG - 179 LID - 10.1186/s12862-017-1018-8 [doi] LID - 179 AB - BACKGROUND: Small insertions and deletions occur in humans at a lower rate compared to nucleotide changes, but evolve under more constraint than nucleotide changes. While the evolution of insertions and deletions have been investigated using ape outgroups, the now available genome of a Neandertal can shed light on the evolution of indels in more recent times. RESULTS: We used the Neandertal genome together with several primate outgroup genomes to differentiate between human insertion/deletion changes that likely occurred before the split from Neandertals and those that likely arose later. Changes that pre-date the split from Neandertals show a smaller proportion of deletions than those that occurred later. The presence of a Neandertal-shared allele in Europeans or Asians but the absence in Africans was used to detect putatively introgressed indels in Europeans and Asians. A larger proportion of these variants reside in intergenic regions compared to other modern human variants, and some variants are linked to SNPs that have been associated with traits in modern humans. CONCLUSIONS: Our results are in agreement with earlier results that suggested that deletions evolve under more constraint than insertions. When considering Neandertal introgressed variants, we find some evidence that negative selection affected these variants more than other variants segregating in modern humans. Among introgressed variants we also identify indels that may influence the phenotype of their carriers. In particular an introgressed deletion associated with a decrease in the time to menarche may constitute an example of a former Neandertal-specific trait contributing to modern human phenotypic diversity. FAU - Chintalapati, Manjusha AU - Chintalapati M AD - Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. FAU - Dannemann, Michael AU - Dannemann M AD - Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. FAU - Prüfer, Kay AU - Prüfer K AUID- ORCID: 0000-0001-6242-3058 AD - Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. pruefer@eva.mpg.de. LA - eng PT - Journal Article DEP - 20170804 PL - England TA - BMC Evol Biol JT - BMC evolutionary biology JID - 100966975 SB - IM MH - Animals MH - *Evolution, Molecular MH - Gene Frequency/genetics MH - Gene Ontology MH - *Genome MH - Genome-Wide Association Study MH - Humans MH - INDEL Mutation/*genetics MH - Neanderthals/*genetics MH - Phenotype MH - Phylogeny MH - Polymorphism, Single Nucleotide/genetics MH - Primates/genetics PMC - PMC5543596 OTO - NOTNLM OT - Ancient DNA OT - Indel evolution OT - Neandertal COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable. CONSENT FOR PUBLICATION: Not applicable. COMPETING INTERESTS: The authors declare that they have no competing interests. PUBLISHER’S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EDAT- 2017/08/06 06:00 MHDA- 2017/12/05 06:00 PMCR- 2017/08/04 CRDT- 2017/08/06 06:00 PHST- 2017/05/03 00:00 [received] PHST- 2017/07/19 00:00 [accepted] PHST- 2017/08/06 06:00 [entrez] PHST- 2017/08/06 06:00 [pubmed] PHST- 2017/12/05 06:00 [medline] PHST- 2017/08/04 00:00 [pmc-release] AID - 10.1186/s12862-017-1018-8 [pii] AID - 1018 [pii] AID - 10.1186/s12862-017-1018-8 [doi] PST - epublish SO - BMC Evol Biol. 2017 Aug 4;17(1):179. doi: 10.1186/s12862-017-1018-8. PMID- 28543951 OWN - NLM STAT- MEDLINE DCOM- 20180205 LR - 20200225 IS - 1365-294X (Electronic) IS - 0962-1083 (Print) IS - 0962-1083 (Linking) VI - 26 IP - 16 DP - 2017 Aug TI - Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations. PG - 4145-4157 LID - 10.1111/mec.14188 [doi] AB - We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present-day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available. CI - © 2017 John Wiley & Sons Ltd. FAU - Martin, Michael D AU - Martin MD AUID- ORCID: 0000-0002-2010-5139 AD - Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway. AD - Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA. FAU - Jay, Flora AU - Jay F AD - Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA. AD - Laboratoire de Recherche en Informatique, CNRS UMR 8623, Université Paris-Sud, Paris-Saclay, France. FAU - Castellano, Sergi AU - Castellano S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Slatkin, Montgomery AU - Slatkin M AD - Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA. LA - eng GR - R01 GM040282/GM/NIGMS NIH HHS/United States PT - Journal Article DEP - 20170707 PL - England TA - Mol Ecol JT - Molecular ecology JID - 9214478 SB - IM MH - *Computer Simulation MH - *Genome, Human MH - Genotype MH - Humans MH - *Models, Genetic MH - *Pedigree MH - Polymorphism, Single Nucleotide MH - Software PMC - PMC6485253 MID - NIHMS1017238 OTO - NOTNLM OT - DNA OT - ancient DNA OT - computer simulation OT - genetics OT - genome OT - genomics OT - humans OT - pedigree OT - polymorphism OT - relatedness OT - single nucleotide EDAT- 2017/05/26 06:00 MHDA- 2018/02/06 06:00 PMCR- 2019/04/26 CRDT- 2017/05/26 06:00 PHST- 2015/11/10 00:00 [received] PHST- 2017/05/05 00:00 [accepted] PHST- 2017/05/26 06:00 [pubmed] PHST- 2018/02/06 06:00 [medline] PHST- 2017/05/26 06:00 [entrez] PHST- 2019/04/26 00:00 [pmc-release] AID - 10.1111/mec.14188 [doi] PST - ppublish SO - Mol Ecol. 2017 Aug;26(16):4145-4157. doi: 10.1111/mec.14188. Epub 2017 Jul 7. PMID- 28511559 OWN - NLM STAT- MEDLINE DCOM- 20180406 LR - 20180406 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 44 IP - 5 DP - 2017 Aug TI - Migrating microbes: what pathogens can tell us about population movements and human evolution. PG - 397-407 LID - 10.1080/03014460.2017.1325515 [doi] AB - BACKGROUND: The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases. METHODS: This study explores which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts. RESULTS: Three stories are then presented of germs on a journey. The first is the story of HIV's spread on the back of colonialism and the railway networks over the last 150 years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2. CONCLUSIONS: Evidence from modern African pathogen genomes can provide data on human behaviour and migration in deep time and contribute to the improvement of human quality-of-life and longevity. FAU - Houldcroft, Charlotte J AU - Houldcroft CJ AUID- ORCID: 0000-0002-1833-5285 AD - a Department of Archaeology and Anthropology, Division of Biological Anthropology , University of Cambridge , Cambridge , UK. AD - b McDonald Institute of Archaeological Research, University of Cambridge , Cambridge , UK. FAU - Ramond, Jean-Baptiste AU - Ramond JB AUID- ORCID: 0000-0003-4790-6232 AD - c Department of Genetics , Centre for Microbial Ecology and Genomics, Genomic Research Institute, University of Pretoria , Hatfield , South Africa. FAU - Rifkin, Riaan F AU - Rifkin RF AUID- ORCID: 0000-0003-1791-3706 AD - c Department of Genetics , Centre for Microbial Ecology and Genomics, Genomic Research Institute, University of Pretoria , Hatfield , South Africa. FAU - Underdown, Simon J AU - Underdown SJ AUID- ORCID: 0000-0001-6056-2353 AD - d Department of Anthropology & Geography, Human Origins and Palaeoenvironmental Research Group (HOPE) , Oxford Brookes University , Oxford , UK. AD - e Leverhulme Centre for Human Evolutionary Studies , Henry Wellcome Building , Cambridge , UK. LA - eng PT - Journal Article PT - Review DEP - 20170516 PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 SB - IM MH - Africa South of the Sahara MH - Animal Distribution MH - Animals MH - *Archaeology MH - *Biological Evolution MH - Communicable Diseases/epidemiology MH - *Human Migration MH - Humans OTO - NOTNLM OT - Archaeology OT - ancient DNA OT - human evolution, sub Saharan Africa OT - microbial archaeology OT - migration OT - pathogens EDAT- 2017/05/18 06:00 MHDA- 2018/04/07 06:00 CRDT- 2017/05/18 06:00 PHST- 2017/05/18 06:00 [pubmed] PHST- 2018/04/07 06:00 [medline] PHST- 2017/05/18 06:00 [entrez] AID - 10.1080/03014460.2017.1325515 [doi] PST - ppublish SO - Ann Hum Biol. 2017 Aug;44(5):397-407. doi: 10.1080/03014460.2017.1325515. Epub 2017 May 16. PMID- 28409264 OWN - NLM STAT- MEDLINE DCOM- 20170803 LR - 20211204 IS - 1617-4623 (Electronic) IS - 1617-4623 (Linking) VI - 292 IP - 4 DP - 2017 Aug TI - A study of the Bodrogköz population in north-eastern Hungary by Y chromosomal haplotypes and haplogroups. PG - 883-894 LID - 10.1007/s00438-017-1319-z [doi] AB - We have determined the distribution of Y chromosomal haplotypes and haplogroups in population samples from one of the most important areas in north-eastern Hungary from many villages in the Bodrogköz. The Bodrogköz region was chosen due to its isolated nature, because this area was a moorland encircled by the Tisza, Bodrog, and Latorca Rivers and inhabitants of this part of Hungary escaped from both Tatar and Ottoman invasions, which decimated the post-Hungarian Conquest populations in many parts of the country. Furthermore, in the first half of the tenth century, this region served as the Palatial Centre and burial grounds of the Hungarian tribes. It has thus been assumed that the present population in this area is likely to be more similar to the population that lived in the Conquest period. We analysed male-specific markers, 23 Y-STRs and more than 30 Y-SNPs, that reflect the past and recent genetic history. We found that the general haplogroup distribution of the samples showed high genetic similarity to non-Bodrogköz Hungarians and neighbouring populations, despite its sheltered location and historical record. We were able to classify the Y-chromosomal haplogroups into four large groups based on STR mutation events: pre-Roman/Roman ancient lineage, Finno-Ugric speakers arriving into the Carpathian Basin, Migration period admixture, and post-Hungarian Conquest admixture. It is clear that a significantly larger database with deep haplogroup resolution, including ancient DNA data, is required to strengthen this research. FAU - Pamjav, Horolma AU - Pamjav H AD - National Centre of Forensic Experts and Research, Budapest, Hungary. phorolma@hotmail.com. FAU - Fóthi, Á AU - Fóthi Á AD - Department of Genetics, Faculty of Sciences, Eötvös Loránd University, Budapest, Hungary. AD - Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary. FAU - Fehér, T AU - Fehér T AD - The Hungarian Magyar Family Tree DNA Project, Budapest, Hungary. FAU - Fóthi, Erzsébet AU - Fóthi E AD - Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary. fothi.erzsebet@nhmus.hu. LA - eng PT - Journal Article DEP - 20170413 PL - Germany TA - Mol Genet Genomics JT - Molecular genetics and genomics : MGG JID - 101093320 SB - IM MH - Chromosomes, Human, Y/*genetics MH - Ethnicity/*genetics MH - Genetics, Population MH - Haplotypes/*genetics MH - Humans MH - Hungary MH - Male MH - Microsatellite Repeats/genetics MH - Phylogeny MH - Polymorphism, Single Nucleotide/*genetics MH - Rural Population OTO - NOTNLM OT - Hungarian ancient history OT - Phylogenetic study OT - Recent Bodrogköz Hungarian population OT - Y haplogroup and Y haplotype analysis EDAT- 2017/04/15 06:00 MHDA- 2017/08/05 06:00 CRDT- 2017/04/15 06:00 PHST- 2017/01/23 00:00 [received] PHST- 2017/04/09 00:00 [accepted] PHST- 2017/04/15 06:00 [pubmed] PHST- 2017/08/05 06:00 [medline] PHST- 2017/04/15 06:00 [entrez] AID - 10.1007/s00438-017-1319-z [pii] AID - 10.1007/s00438-017-1319-z [doi] PST - ppublish SO - Mol Genet Genomics. 2017 Aug;292(4):883-894. doi: 10.1007/s00438-017-1319-z. Epub 2017 Apr 13. PMID- 28747476 OWN - NLM STAT- MEDLINE DCOM- 20180202 LR - 20231112 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 284 IP - 1859 DP - 2017 Jul 26 TI - Ancient DNA and morphometric analysis reveal extinction and replacement of New Zealand's unique black swans. LID - 10.1098/rspb.2017.0876 [doi] LID - 20170876 AB - Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans (Cygnus atratus) including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage (C. sumnerensis, Poūwa), divergent from modern (Australian) C. atratus Morphological analyses indicate C. sumnerensis exhibited classic signs of the 'island rule' effect, being larger, and likely flight-reduced compared to C. atratus Our research reveals sudden extinction and replacement events within this anatid species complex, coinciding with recent human colonization of New Zealand. This research highlights the role of anthropogenic processes in rapidly reshaping island ecosystems and raises new questions for avian conservation, ecosystem re-wilding, and de-extinction. CI - © 2017 The Author(s). FAU - Rawlence, Nicolas J AU - Rawlence NJ AUID- ORCID: 0000-0001-6968-6643 AD - Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand nic.rawlence@otago.ac.nz. AD - Canterbury Museum, Christchurch, New Zealand. FAU - Kardamaki, Afroditi AU - Kardamaki A AD - Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand. FAU - Easton, Luke J AU - Easton LJ AD - Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand. FAU - Tennyson, Alan J D AU - Tennyson AJD AD - Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand. FAU - Scofield, R Paul AU - Scofield RP AUID- ORCID: 0000-0002-7510-6980 AD - Canterbury Museum, Christchurch, New Zealand. FAU - Waters, Jonathan M AU - Waters JM AUID- ORCID: 0000-0002-1514-7916 AD - Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand. LA - eng PT - Journal Article PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Anseriformes/*classification MH - Australia MH - *DNA, Ancient MH - *Extinction, Biological MH - Humans MH - Islands MH - New Zealand PMC - PMC5543223 OTO - NOTNLM OT - New Zealand OT - ancient DNA OT - black swan OT - extinction OT - island rule OT - recolonization COIS- The authors have no competing interests EDAT- 2017/07/28 06:00 MHDA- 2018/02/03 06:00 PMCR- 2018/07/26 CRDT- 2017/07/28 06:00 PHST- 2017/04/24 00:00 [received] PHST- 2017/06/20 00:00 [accepted] PHST- 2017/07/28 06:00 [entrez] PHST- 2017/07/28 06:00 [pubmed] PHST- 2018/02/03 06:00 [medline] PHST- 2018/07/26 00:00 [pmc-release] AID - rspb.2017.0876 [pii] AID - rspb20170876 [pii] AID - 10.1098/rspb.2017.0876 [doi] PST - ppublish SO - Proc Biol Sci. 2017 Jul 26;284(1859):20170876. doi: 10.1098/rspb.2017.0876. PMID- 28712569 OWN - NLM STAT- MEDLINE DCOM- 20180719 LR - 20180719 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 27 IP - 14 DP - 2017 Jul 24 TI - Extensive Farming in Estonia Started through a Sex-Biased Migration from the Steppe. PG - 2185-2193.e6 LID - S0960-9822(17)30724-8 [pii] LID - 10.1016/j.cub.2017.06.022 [doi] AB - The transition from hunting and gathering to farming in Europe was brought upon by arrival of new people carrying novel material culture and genetic ancestry. The exact nature and scale of the transition-both material and genetic-varied in different parts of Europe [1-7]. Farming-based economies appear relatively late in Northeast Europe, and the extent to which they involve change in genetic ancestry is not fully understood due to the lack of relevant ancient DNA data. Here we present the results from new low-coverage whole-genome shotgun sequence data from five hunter-gatherers and five first farmers of Estonia whose remains date to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X chromosome, and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic culture are closest to Eastern hunter-gatherers, which is in contrast to earlier hunter-gatherers from the Baltics, who are close to Western hunter-gatherers [8, 9]. The Estonian first farmers of Corded Ware culture show high similarity in their autosomes with European hunter-gatherers, Steppe Eneolithic and Bronze Age populations, and European Late Neolithic/Bronze Age populations, while their X chromosomes are in addition equally closely related to European and Anatolian and Levantine early farmers. These findings suggest that the shift to intensive cultivation and animal husbandry in Estonia was triggered by the arrival of new people with predominantly Steppe ancestry but whose ancestors had undergone sex-specific admixture with early farmers with Anatolian ancestry. CI - Copyright © 2017 Elsevier Ltd. All rights reserved. FAU - Saag, Lehti AU - Saag L AD - Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia; Estonian Biocentre, Tartu 51010, Estonia. Electronic address: lehtis@ut.ee. FAU - Varul, Liivi AU - Varul L AD - School of Humanities, Tallinn University, Tallinn 10120, Estonia. FAU - Scheib, Christiana Lyn AU - Scheib CL AD - Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 3QG, UK. FAU - Stenderup, Jesper AU - Stenderup J AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark. FAU - Allentoft, Morten E AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark. FAU - Saag, Lauri AU - Saag L AD - Estonian Biocentre, Tartu 51010, Estonia. FAU - Pagani, Luca AU - Pagani L AD - Estonian Biocentre, Tartu 51010, Estonia. FAU - Reidla, Maere AU - Reidla M AD - Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia; Estonian Biocentre, Tartu 51010, Estonia. FAU - Tambets, Kristiina AU - Tambets K AD - Estonian Biocentre, Tartu 51010, Estonia. FAU - Metspalu, Ene AU - Metspalu E AD - Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia; Estonian Biocentre, Tartu 51010, Estonia. FAU - Kriiska, Aivar AU - Kriiska A AD - Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark. FAU - Kivisild, Toomas AU - Kivisild T AD - Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia; Estonian Biocentre, Tartu 51010, Estonia; Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 3QG, UK. FAU - Metspalu, Mait AU - Metspalu M AD - Estonian Biocentre, Tartu 51010, Estonia. Electronic address: mait@ebc.ee. LA - eng PT - Historical Article PT - Journal Article DEP - 20170714 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/*history MH - Chromosomes, Human, X/genetics MH - Chromosomes, Human, Y/genetics MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/chemistry MH - Estonia MH - Genome, Human/*genetics MH - History, Ancient MH - *Human Migration MH - Humans OTO - NOTNLM OT - Comb Ceramic culture OT - Corded Ware culture OT - Neolithic OT - aDNA OT - ancient DNA OT - farming OT - hunter-gatherers OT - migration OT - population genetics OT - shotgun sequencing EDAT- 2017/07/18 06:00 MHDA- 2018/07/20 06:00 CRDT- 2017/07/18 06:00 PHST- 2017/03/20 00:00 [received] PHST- 2017/05/26 00:00 [revised] PHST- 2017/06/08 00:00 [accepted] PHST- 2017/07/18 06:00 [pubmed] PHST- 2018/07/20 06:00 [medline] PHST- 2017/07/18 06:00 [entrez] AID - S0960-9822(17)30724-8 [pii] AID - 10.1016/j.cub.2017.06.022 [doi] PST - ppublish SO - Curr Biol. 2017 Jul 24;27(14):2185-2193.e6. doi: 10.1016/j.cub.2017.06.022. Epub 2017 Jul 14. PMID- 28669760 OWN - NLM STAT- MEDLINE DCOM- 20180731 LR - 20180731 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 27 IP - 13 DP - 2017 Jul 10 TI - Eight Millennia of Matrilineal Genetic Continuity in the South Caucasus. PG - 2023-2028.e7 LID - S0960-9822(17)30695-4 [pii] LID - 10.1016/j.cub.2017.05.087 [doi] AB - The South Caucasus, situated between the Black and Caspian Seas, geographically links Europe with the Near East and has served as a crossroad for human migrations for many millennia [1-7]. Despite a vast archaeological record showing distinct cultural turnovers, the demographic events that shaped the human populations of this region is not known [8, 9]. To shed light on the maternal genetic history of the region, we analyzed the complete mitochondrial genomes of 52 ancient skeletons from present-day Armenia and Artsakh spanning 7,800 years and combined this dataset with 206 mitochondrial genomes of modern Armenians. We also included previously published data of seven neighboring populations (n = 482). Coalescence-based analyses suggest that the population size in this region rapidly increased after the Last Glacial Maximum ca. 18 kya. We find that the lowest genetic distance in this dataset is between modern Armenians and the ancient individuals, as also reflected in both network analyses and discriminant analysis of principal components. We used approximate Bayesian computation to test five different demographic scenarios explaining the formation of the modern Armenian gene pool. Despite well documented cultural shifts in the South Caucasus across this time period, our results strongly favor a genetic continuity model in the maternal gene pool. This has implications for interpreting prehistoric migration dynamics and cultural shifts in this part of the world. CI - Copyright © 2017 Elsevier Ltd. All rights reserved. FAU - Margaryan, Ashot AU - Margaryan A AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Institute of Molecular Biology, National Academy of Sciences, 7 Hasratian Street, 0014 Yerevan, Armenia. Electronic address: ashot.margaryan@snm.ku.dk. FAU - Derenko, Miroslava AU - Derenko M AD - Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, 18 Portovaya Street, 685000 Magadan, Russia. FAU - Hovhannisyan, Hrant AU - Hovhannisyan H AD - Institute of Molecular Biology, National Academy of Sciences, 7 Hasratian Street, 0014 Yerevan, Armenia; Russian-Armenian University, H. Emin 123, 0051 Yerevan, Armenia. FAU - Malyarchuk, Boris AU - Malyarchuk B AD - Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, 18 Portovaya Street, 685000 Magadan, Russia. FAU - Heller, Rasmus AU - Heller R AD - Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark. FAU - Khachatryan, Zaruhi AU - Khachatryan Z AD - Institute of Molecular Biology, National Academy of Sciences, 7 Hasratian Street, 0014 Yerevan, Armenia. FAU - Avetisyan, Pavel AU - Avetisyan P AD - Institute of Archaeology and Ethnography, National Academy of Sciences, 15 Charents Street, 0025 Yerevan, Armenia. FAU - Badalyan, Ruben AU - Badalyan R AD - Institute of Archaeology and Ethnography, National Academy of Sciences, 15 Charents Street, 0025 Yerevan, Armenia. FAU - Bobokhyan, Arsen AU - Bobokhyan A AD - Institute of Archaeology and Ethnography, National Academy of Sciences, 15 Charents Street, 0025 Yerevan, Armenia. FAU - Melikyan, Varduhi AU - Melikyan V AD - Institute of Archaeology and Ethnography, National Academy of Sciences, 15 Charents Street, 0025 Yerevan, Armenia. FAU - Sargsyan, Gagik AU - Sargsyan G AD - Institute of Archaeology and Ethnography, National Academy of Sciences, 15 Charents Street, 0025 Yerevan, Armenia. FAU - Piliposyan, Ashot AU - Piliposyan A AD - Armenian State Pedagogical University, 13 Alek Manukyan Street, 0070 Yerevan, Armenia. FAU - Simonyan, Hakob AU - Simonyan H AD - Scientific Research Center of the Historical and Cultural Heritage, Ministry of Culture, 1/3 Pavstos Buzandi Street, 0010 Yerevan, Armenia. FAU - Mkrtchyan, Ruzan AU - Mkrtchyan R AD - Yerevan State University, 1 Alek Manukyan Street, 0025 Yerevan, Armenia. FAU - Denisova, Galina AU - Denisova G AD - Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, 18 Portovaya Street, 685000 Magadan, Russia. FAU - Yepiskoposyan, Levon AU - Yepiskoposyan L AD - Institute of Molecular Biology, National Academy of Sciences, 7 Hasratian Street, 0014 Yerevan, Armenia. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. FAU - Allentoft, Morten E AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Electronic address: meallentoft@snm.ku.dk. LA - eng PT - Journal Article DEP - 20170629 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology MH - Armenia MH - Azerbaijan MH - Bayes Theorem MH - DNA, Ancient/analysis MH - *Gene Pool MH - *Genetic Variation MH - *Genome, Human MH - *Genome, Mitochondrial MH - Human Migration MH - Humans OTO - NOTNLM OT - Armenia OT - South Caucasus OT - ancient DNA OT - genetic continuity OT - mitogenomes OT - mtDNA OT - population genetics EDAT- 2017/07/04 06:00 MHDA- 2018/08/01 06:00 CRDT- 2017/07/04 06:00 PHST- 2017/03/04 00:00 [received] PHST- 2017/04/25 00:00 [revised] PHST- 2017/05/26 00:00 [accepted] PHST- 2017/07/04 06:00 [pubmed] PHST- 2018/08/01 06:00 [medline] PHST- 2017/07/04 06:00 [entrez] AID - S0960-9822(17)30695-4 [pii] AID - 10.1016/j.cub.2017.05.087 [doi] PST - ppublish SO - Curr Biol. 2017 Jul 10;27(13):2023-2028.e7. doi: 10.1016/j.cub.2017.05.087. Epub 2017 Jun 29. PMID- 28678860 OWN - NLM STAT- MEDLINE DCOM- 20170922 LR - 20190113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 12 IP - 7 DP - 2017 TI - Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice. PG - e0179742 LID - 10.1371/journal.pone.0179742 [doi] LID - e0179742 AB - In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in "non-conventional" positions (deposited in the pits without any particular treatment). If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace). At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses) permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i) the occidental origin of the Michelsberg groups and (ii) the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution. FAU - Beau, Alice AU - Beau A AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France. FAU - Rivollat, Maïté AU - Rivollat M AUID- ORCID: 0000-0002-4011-2862 AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France. FAU - Réveillas, Hélène AU - Réveillas H AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France. AD - Centre d'Archéologie Préventive de Bordeaux Métropole, Direction des Bâtiments et Moyens, Esplanade Charles-de-Gaulle, Bordeaux cedex, France. AD - Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d'Altkirch, Strasbourg, France. FAU - Pemonge, Marie-Hélène AU - Pemonge MH AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France. FAU - Mendisco, Fanny AU - Mendisco F AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France. FAU - Thomas, Yohann AU - Thomas Y AD - Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d'Altkirch, Strasbourg, France. FAU - Lefranc, Philippe AU - Lefranc P AD - Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d'Altkirch, Strasbourg, France. AD - Archéologie et Histoire Ancienne: Méditerranée/Europe-UMR 7044, Université de Strasbourg, Maison Interuniversitaire des Sciences de l'Homme d'Alsace, 5 Allée du Général Rouvillois, CS, Strasbourg cedex, France. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France. LA - eng PT - Journal Article DEP - 20170705 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Burial MH - *Ceremonial Behavior MH - Chromosomes, Human, Y/genetics MH - DNA, Ancient/*isolation & purification MH - DNA, Mitochondrial/genetics/isolation & purification MH - Farmers MH - Female MH - France MH - Human Migration MH - Humans MH - Male MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA PMC - PMC5497962 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2017/07/06 06:00 MHDA- 2017/09/25 06:00 PMCR- 2017/07/05 CRDT- 2017/07/06 06:00 PHST- 2017/02/25 00:00 [received] PHST- 2017/06/02 00:00 [accepted] PHST- 2017/07/06 06:00 [entrez] PHST- 2017/07/06 06:00 [pubmed] PHST- 2017/09/25 06:00 [medline] PHST- 2017/07/05 00:00 [pmc-release] AID - PONE-D-17-07664 [pii] AID - 10.1371/journal.pone.0179742 [doi] PST - epublish SO - PLoS One. 2017 Jul 5;12(7):e0179742. doi: 10.1371/journal.pone.0179742. eCollection 2017. PMID- 28675384 OWN - NLM STAT- MEDLINE DCOM- 20181219 LR - 20221207 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 8 DP - 2017 Jul 4 TI - Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals. PG - 16046 LID - 10.1038/ncomms16046 [doi] LID - 16046 AB - Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein-Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods. FAU - Posth, Cosimo AU - Posth C AD - Institute for Archaeological Sciences, University of Tübingen, Rümelin Strasse 23, Tübingen 72070, Germany. AD - Max Planck Institute for the Science of Human History, Khalaische Strasse 10, Jena 07745, Germany. FAU - Wißing, Christoph AU - Wißing C AD - Department of Geosciences, Biogeology, University of Tübingen, Hölderlin Strasse 12, Tübingen 72074, Germany. FAU - Kitagawa, Keiko AU - Kitagawa K AD - Institute for Archaeological Sciences, University of Tübingen, Rümelin Strasse 23, Tübingen 72070, Germany. AD - Department of Prehistory, National Museum of Natural History, UMR 7194 CNRS, 1 rue René Panhard, Paris 75013, France. FAU - Pagani, Luca AU - Pagani L AD - Estonian Biocentre, Riia 23b, Tartu 51010, Estonia. AD - Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova 35121, Italy. FAU - van Holstein, Laura AU - van Holstein L AD - Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK. FAU - Racimo, Fernando AU - Racimo F AD - New York Genome Center, 101 Avenue of the Americas, New York, New York 10013, USA. FAU - Wehrberger, Kurt AU - Wehrberger K AD - Ulmer Museum, Marktplatz 9, Ulm 89073, Germany. FAU - Conard, Nicholas J AU - Conard NJ AD - Institute for Archaeological Sciences, University of Tübingen, Rümelin Strasse 23, Tübingen 72070, Germany. AD - Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Schloss Hohentübingen, Tübingen 72070, Germany. FAU - Kind, Claus Joachim AU - Kind CJ AD - State Office for Cultural Heritage Baden-Württemberg, Berliner Strasse 12, Esslingen 73728, Germany. FAU - Bocherens, Hervé AU - Bocherens H AD - Department of Geosciences, Biogeology, University of Tübingen, Hölderlin Strasse 12, Tübingen 72074, Germany. AD - Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Hölderlin Strasse 12, Tübingen 72074, Germany. FAU - Krause, Johannes AU - Krause J AD - Institute for Archaeological Sciences, University of Tübingen, Rümelin Strasse 23, Tübingen 72070, Germany. AD - Max Planck Institute for the Science of Human History, Khalaische Strasse 10, Jena 07745, Germany. LA - eng PT - Journal Article DEP - 20170704 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Black People/*genetics MH - DNA, Mitochondrial/*genetics MH - *Evolution, Molecular MH - Femur MH - *Gene Flow MH - Genome, Human/genetics MH - *Genome, Mitochondrial MH - Germany MH - Hominidae/*genetics MH - Humans MH - Neanderthals/*genetics MH - Time Factors PMC - PMC5500885 COIS- The authors declare no competing financial interests. EDAT- 2017/07/05 06:00 MHDA- 2018/12/20 06:00 PMCR- 2017/07/04 CRDT- 2017/07/05 06:00 PHST- 2016/10/28 00:00 [received] PHST- 2017/05/23 00:00 [accepted] PHST- 2017/07/05 06:00 [entrez] PHST- 2017/07/05 06:00 [pubmed] PHST- 2018/12/20 06:00 [medline] PHST- 2017/07/04 00:00 [pmc-release] AID - ncomms16046 [pii] AID - 10.1038/ncomms16046 [doi] PST - epublish SO - Nat Commun. 2017 Jul 4;8:16046. doi: 10.1038/ncomms16046. PMID- 29745246 OWN - NLM STAT- MEDLINE DCOM- 20181029 LR - 20200306 IS - 1534-6617 (Electronic) IS - 0018-7143 (Print) IS - 0018-7143 (Linking) VI - 89 IP - 3 DP - 2017 Jul TI - Chaco Canyon Dig Unearths Ethical Concerns. PG - 177-180 AB - The field of paleogenomics (the study of ancient genomes) is rapidly advancing, with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to as ancestors, are used in research. We highlight a 2017 article by Kennett et al., "Archaeogenomic evidence reveals prehistoric matrilineal dynasty," that brings to light several ethical issues that should be addressed in paleogenomics research. The study helps elucidate the matrilineal relationships in ancient Chacoan society through ancient DNA analysis. However, we, as Indigenous researchers and allies, raise ethical concerns with the study's scientific conclusions that can be problematic for Native American communities: (1) the lack of tribal consultation, (2) the use of culturally insensitive descriptions, and (3) the potential impact on marginalized groups. Further, we explore the limitations of the Native American Graves Protection and Repatriation Act, which addresses repatriation but not research, because clear ethical guidelines have not been established for research involving Native American ancestors, especially those deemed "culturally unaffiliated." Multiple studies of "culturally unaffiliated" remains have been initiated recently, so it is imperative that researchers consider the ethical ramifications of paleogenomics research. Past research indiscretions have created a history of mistrust and exploitation in many Native American communities. To promote ethical engagement of Native American communities in research, we therefore suggest careful attention to ethical considerations, strong tribal consultation requirements, and greater collaborations among museums, federal agencies, researchers, scientific journals, and granting agencies. FAU - Claw, Katrina G AU - Claw KG AD - 1 Department of Pharmaceutics, University of Washington, Seattle, Washington, USA. FAU - Lippert, Dorothy AU - Lippert D AD - 2 Repatriation Program, National Museum of Natural History, Washington, DC, USA. FAU - Bardill, Jessica AU - Bardill J AD - 3 Department of English, Concordia University, Montreal, Quebec, Canada. FAU - Cordova, Anna AU - Cordova A AD - 4 Department of Anthropology, University of Colorado, Colorado Springs, Colorado, USA. FAU - Fox, Keolu AU - Fox K AD - 5 Department of Endocrinology and Metabolic Disease, University of California, San Diego, California, USA. FAU - Yracheta, Joseph M AU - Yracheta JM AD - 6 Missouri Breaks Industries Research, Inc., Cheyenne River Sioux Nation, Eagle Butte, South Dakota, USA. FAU - Bader, Alyssa C AU - Bader AC AD - 7 Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. FAU - Bolnick, Deborah A AU - Bolnick DA AD - 8 Department of Anthropology and Population Research Center, University of Texas at Austin, Austin, Texas, USA. FAU - Malhi, Ripan S AU - Malhi RS AD - 9 Departments of Anthropology and Animal Biology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana- Champaign, Urbana, Illinois, USA. FAU - TallBear, Kimberly AU - TallBear K AD - 10 Faculty of Native Studies, University of Alberta, Edmonton, Alberta, Canada. FAU - Garrison, Nanibaa' A AU - Garrison NA AD - 11 Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, Washington, USA. AD - 12 Department of Pediatrics, Division of Bioethics, University of Washington, Seattle, Washington, USA. LA - eng GR - F32 GM119237/GM/NIGMS NIH HHS/United States GR - R25 HG007158/HG/NHGRI NIH HHS/United States PT - Journal Article PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Ancient) SB - IM CON - Hum Biol. MH - Communication MH - DNA, Ancient MH - Genomics/*ethics MH - Humans MH - Indians, North American/ethnology/*genetics MH - New Mexico/ethnology MH - Paleontology/*ethics MH - Researcher-Subject Relations/ethics PMC - PMC5951383 MID - NIHMS961557 OTO - NOTNLM OT - ANCIENT DNA OT - ETHICS OT - NATIVE AMERICANS OT - PALEOGENOMICS EDAT- 2018/05/11 06:00 MHDA- 2018/10/30 06:00 PMCR- 2018/05/14 CRDT- 2018/05/11 06:00 PHST- 2018/05/11 06:00 [entrez] PHST- 2018/05/11 06:00 [pubmed] PHST- 2018/10/30 06:00 [medline] PHST- 2018/05/14 00:00 [pmc-release] AID - 10.13110/humanbiology.89.3.01 [pii] AID - 10.13110/humanbiology.89.3.01 [doi] PST - ppublish SO - Hum Biol. 2017 Jul;89(3):177-180. doi: 10.13110/humanbiology.89.3.01. PMID- 28609785 OWN - NLM STAT- MEDLINE DCOM- 20180523 LR - 20240325 IS - 2047-217X (Electronic) IS - 2047-217X (Linking) VI - 6 IP - 7 DP - 2017 Jul 1 TI - Comprehensive analysis of microorganisms accompanying human archaeological remains. PG - 1-13 LID - 10.1093/gigascience/gix044 [doi] AB - Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently. CI - © The Authors 2017. Published by Oxford University Press. FAU - Philips, Anna AU - Philips A AD - European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland. FAU - Stolarek, Ireneusz AU - Stolarek I AD - European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland. FAU - Kuczkowska, Bogna AU - Kuczkowska B AD - European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland. FAU - Juras, Anna AU - Juras A AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland. FAU - Handschuh, Luiza AU - Handschuh L AD - European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland. AD - Department of Hematology and Bone Marrow Transplantation, University of Medical Sciences, Poznan, 60-569, Poland. AD - Institute of Technology and Chemical Engineering, Poznan University of Technology, Poznan, 60-965, Poland. FAU - Piontek, Janusz AU - Piontek J AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland. FAU - Kozlowski, Piotr AU - Kozlowski P AD - European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland. AD - Institute of Technology and Chemical Engineering, Poznan University of Technology, Poznan, 60-965, Poland. FAU - Figlerowicz, Marek AU - Figlerowicz M AD - European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland. AD - Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Gigascience JT - GigaScience JID - 101596872 RN - 0 (DNA, Ancient) SB - IM MH - Archaeology/*methods MH - Bone and Bones/microbiology MH - *DNA, Ancient MH - Fossils/microbiology MH - Humans MH - Metagenome MH - *Microbiota MH - Sequence Analysis, DNA/methods PMC - PMC5965364 OTO - NOTNLM OT - NGS OT - ancient DNA OT - metagenomics OT - microbiome EDAT- 2017/06/14 06:00 MHDA- 2018/05/24 06:00 PMCR- 2017/06/13 CRDT- 2017/06/14 06:00 PHST- 2017/03/14 00:00 [received] PHST- 2017/06/11 00:00 [accepted] PHST- 2017/06/14 06:00 [pubmed] PHST- 2018/05/24 06:00 [medline] PHST- 2017/06/14 06:00 [entrez] PHST- 2017/06/13 00:00 [pmc-release] AID - 3867068 [pii] AID - gix044 [pii] AID - 10.1093/gigascience/gix044 [doi] PST - ppublish SO - Gigascience. 2017 Jul 1;6(7):1-13. doi: 10.1093/gigascience/gix044. PMID- 28382719 OWN - NLM STAT- MEDLINE DCOM- 20170821 LR - 20180214 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 163 IP - 3 DP - 2017 Jul TI - Ancient mitochondrial DNA and ancestry of Paquimé inhabitants, Casas Grandes (A.D. 1200-1450). PG - 616-626 LID - 10.1002/ajpa.23223 [doi] AB - OBJECTIVES: The Casas Grandes (Paquimé) culture, located in the Northwest of Chihuahua, Mexico reached its apogee during the Medio Period (A.D. 1200-1450). Paquimé was abandoned by the end of the Medio Period (A.D. 1450), and the ancestry of its inhabitants remains unsolved. Some authors suggest that waves of Mesoamerican immigrants, possibly merchants, stimulated Paquimé's development during the Medio Period. Archaeological evidence suggests possible ties to groups that inhabited the Southwestern US cultures. This study uses ancient DNA analysis from fourteen samples to estimate genetic affinities of ancient Paquimé inhabitants. MATERIALS AND METHODS: DNA was extracted from 14 dental ancient samples from Paquimé. PCR and Sanger sequencing were used to obtain mitochondrial control region sequences. Networks, PCoA, and Nei genetic distances were estimated to compare Paquimé haplotypes against available past haplotypes data from Southwestern and Mesoamerican groups. RESULTS: Haplogroups were characterized for 11 of the samples, and the results revealed the presence of four distinct Amerindian mitochondrial lineages: B (n = 5; 45%), A (n = 3; 27%), C (n = 2; 18%) and D (n = 1; 10%). Statistical analysis of the haplotypes, haplogroup frequencies, and Nei genetic distances showed close affinity of Paquimé with Mimbres. DISCUSSION: Although our results provide strong evidence of genetic affinities between Paquimé and Mimbres, with the majority of haplotypes shared or derived from ancient Southwest populations, the causes of cultural development at Paquimé still remain a question. These preliminary results provide evidence in support of other bioarchaeological studies, which have shown close biological affinities between Paquimé and Mimbres, a Puebloan culture, in the Southwestern US. CI - © 2017 Wiley Periodicals, Inc. FAU - Morales-Arce, Ana Y AU - Morales-Arce AY AUID- ORCID: 0000-0002-2934-3141 AD - Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada, T2N 1N4. FAU - Snow, Meradeth H AU - Snow MH AD - Anthropology, College of Humanities and Sciences, University of Montana, Missoula, Montana, 59812. FAU - Kelley, Jane H AU - Kelley JH AD - Department of Archaeology, University of Calgary (deceased), Calgary, Alberta, Canada, T2N 1N4. FAU - Anne Katzenberg, M AU - Anne Katzenberg M AD - Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada, T2N 1N4. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20170406 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - *DNA, Ancient/analysis/isolation & purification MH - *DNA, Mitochondrial/analysis/genetics/isolation & purification MH - Human Migration MH - Humans MH - Indians, Central American/*genetics MH - Mexico MH - Tooth/chemistry OTO - NOTNLM OT - Medio Period OT - Mesoamerica OT - Southwest US OT - migration OT - paleogenetics EDAT- 2017/04/07 06:00 MHDA- 2017/08/22 06:00 CRDT- 2017/04/07 06:00 PHST- 2016/10/02 00:00 [received] PHST- 2017/01/05 00:00 [revised] PHST- 2017/03/18 00:00 [accepted] PHST- 2017/04/07 06:00 [pubmed] PHST- 2017/08/22 06:00 [medline] PHST- 2017/04/07 06:00 [entrez] AID - 10.1002/ajpa.23223 [doi] PST - ppublish SO - Am J Phys Anthropol. 2017 Jul;163(3):616-626. doi: 10.1002/ajpa.23223. Epub 2017 Apr 6. PMID- 28486705 OWN - NLM STAT- MEDLINE DCOM- 20171128 LR - 20240318 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 45 IP - 11 DP - 2017 Jun 20 TI - A new model for ancient DNA decay based on paleogenomic meta-analysis. PG - 6310-6320 LID - 10.1093/nar/gkx361 [doi] AB - The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics. CI - © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. FAU - Kistler, Logan AU - Kistler L AD - School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK. AD - Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA. FAU - Ware, Roselyn AU - Ware R AD - School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK. FAU - Smith, Oliver AU - Smith O AD - School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK. AD - Section for Evolutionary Genomics, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1307 Copenhagen K, Denmark. FAU - Collins, Matthew AU - Collins M AD - Section for Evolutionary Genomics, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1307 Copenhagen K, Denmark. AD - Department of Archaeology, University of York, PO Box 373, York, UK. FAU - Allaby, Robin G AU - Allaby RG AD - School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK. LA - eng GR - R21 DC020560/DC/NIDCD NIH HHS/United States PT - Journal Article PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - 0 (DNA, Plant) SB - IM MH - Base Composition MH - Base Sequence MH - DNA Fragmentation MH - DNA, Ancient/analysis/*chemistry MH - DNA, Mitochondrial/analysis/chemistry/genetics MH - DNA, Plant/genetics MH - Deamination MH - Genome, Human MH - Genome, Mitochondrial MH - Humans MH - Meta-Analysis as Topic MH - Models, Chemical MH - Paleontology/methods MH - Sequence Analysis, DNA MH - Thermodynamics PMC - PMC5499742 EDAT- 2017/05/10 06:00 MHDA- 2017/11/29 06:00 PMCR- 2017/05/09 CRDT- 2017/05/10 06:00 PHST- 2017/03/21 00:00 [received] PHST- 2017/04/20 00:00 [accepted] PHST- 2017/05/10 06:00 [pubmed] PHST- 2017/11/29 06:00 [medline] PHST- 2017/05/10 06:00 [entrez] PHST- 2017/05/09 00:00 [pmc-release] AID - 3806656 [pii] AID - gkx361 [pii] AID - 10.1093/nar/gkx361 [doi] PST - ppublish SO - Nucleic Acids Res. 2017 Jun 20;45(11):6310-6320. doi: 10.1093/nar/gkx361. PMID- 28552360 OWN - NLM STAT- MEDLINE DCOM- 20180730 LR - 20240601 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 27 IP - 12 DP - 2017 Jun 19 TI - Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin. PG - 1801-1810.e10 LID - S0960-9822(17)30559-6 [pii] LID - 10.1016/j.cub.2017.05.023 [doi] AB - The transition from hunting and gathering to farming involved profound cultural and technological changes. In Western and Central Europe, these changes occurred rapidly and synchronously after the arrival of early farmers of Anatolian origin [1-3], who largely replaced the local Mesolithic hunter-gatherers [1, 4-6]. Further east, in the Baltic region, the transition was gradual, with little or no genetic input from incoming farmers [7]. Here we use ancient DNA to investigate the relationship between hunter-gatherers and farmers in the Lower Danube basin, a geographically intermediate area that is characterized by a rapid Neolithic transition but also by the presence of archaeological evidence that points to cultural exchange, and thus possible admixture, between hunter-gatherers and farmers. We recovered four human paleogenomes (1.1× to 4.1× coverage) from Romania spanning a time transect between 8.8 thousand years ago (kya) and 5.4 kya and supplemented them with two Mesolithic genomes (1.7× and 5.3×) from Spain to provide further context on the genetic background of Mesolithic Europe. Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. Dietary stable-isotope analysis of this sample suggests a mixed terrestrial/aquatic diet. Our results provide support for complex interactions among hunter-gatherers and farmers in the Danube basin, demonstrating that in some regions, demic and cultural diffusion were not mutually exclusive, but merely the ends of a continuum for the process of Neolithization. CI - Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - González-Fortes, Gloria AU - González-Fortes G AD - Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara 44100, Italy; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam OT Golm, Germany. Electronic address: gnzgrm@unife.it. FAU - Jones, Eppie R AU - Jones ER AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. Electronic address: erj35@cam.ac.uk. FAU - Lightfoot, Emma AU - Lightfoot E AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK. FAU - Bonsall, Clive AU - Bonsall C AD - School of History, Classics and Archaeology, University of Edinburgh, William Robertson Wing, Old Medical School, Teviot Place, Edinburgh EH8 9AG, UK. FAU - Lazar, Catalin AU - Lazar C AD - National History Museum of Romania, Bucharest 030026, Romania. FAU - Grandal-d'Anglade, Aurora AU - Grandal-d'Anglade A AD - Instituto Universitario de Xeoloxía, Universidade da Coruña, A Coruña 15081, Spain. FAU - Garralda, María Dolores AU - Garralda MD AD - Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid 28040, Spain. FAU - Drak, Labib AU - Drak L AD - Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid 28040, Spain. FAU - Siska, Veronika AU - Siska V AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. FAU - Simalcsik, Angela AU - Simalcsik A AD - "Olga Necrasov" Centre for Anthropological Research of the Romanian Academy, Iaşi Branch, Theodor Codrescu Strada 2, 700481 Iaşi, Romania. FAU - Boroneanţ, Adina AU - Boroneanţ A AD - "Vasile Pârvan" Institute of Archaeology, Romanian Academy, Henri Coandă Strada 11, Bucharest 010667, Romania. FAU - Vidal Romaní, Juan Ramón AU - Vidal Romaní JR AD - Instituto Universitario de Xeoloxía, Universidade da Coruña, A Coruña 15081, Spain. FAU - Vaqueiro Rodríguez, Marcos AU - Vaqueiro Rodríguez M AD - Instituto Universitario de Xeoloxía, Universidade da Coruña, A Coruña 15081, Spain. FAU - Arias, Pablo AU - Arias P AD - International Institute of Prehistorical Research, University of Cantabria-Government of Cantabria-Bank of Santander, Santander 39005, Spain. FAU - Pinhasi, Ron AU - Pinhasi R AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland; Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. Electronic address: ron.pinhasi@ucd.ie. FAU - Manica, Andrea AU - Manica A AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. Electronic address: am315@cam.ac.uk. FAU - Hofreiter, Michael AU - Hofreiter M AD - Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam OT Golm, Germany. Electronic address: michi@palaeo.eu. LA - eng GR - 263441/ERC_/European Research Council/International PT - Journal Article DEP - 20170525 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - *Archaeology MH - Cultural Evolution MH - DNA, Ancient/*analysis MH - *Diet MH - Farmers MH - *Genome, Human MH - *Human Migration MH - Humans MH - Life Style MH - Romania PMC - PMC5483232 OTO - NOTNLM OT - Eneolithic OT - Iron Gates OT - Mesolithic OT - Neolithic transition OT - Romania OT - ancient DNA EDAT- 2017/05/30 06:00 MHDA- 2018/07/31 06:00 PMCR- 2017/06/19 CRDT- 2017/05/30 06:00 PHST- 2017/02/28 00:00 [received] PHST- 2017/04/21 00:00 [revised] PHST- 2017/05/04 00:00 [accepted] PHST- 2017/05/30 06:00 [pubmed] PHST- 2018/07/31 06:00 [medline] PHST- 2017/05/30 06:00 [entrez] PHST- 2017/06/19 00:00 [pmc-release] AID - S0960-9822(17)30559-6 [pii] AID - 10.1016/j.cub.2017.05.023 [doi] PST - ppublish SO - Curr Biol. 2017 Jun 19;27(12):1801-1810.e10. doi: 10.1016/j.cub.2017.05.023. Epub 2017 May 25. PMID- 28615043 OWN - NLM STAT- MEDLINE DCOM- 20180315 LR - 20211204 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 18 IP - 1 DP - 2017 Jun 14 TI - "Like sugar in milk": reconstructing the genetic history of the Parsi population. PG - 110 LID - 10.1186/s13059-017-1244-9 [doi] LID - 110 AB - BACKGROUND: The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India. RESULTS: Among present-day populations, the Parsis are genetically closest to Iranian and the Caucasus populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ~1,200 years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement. Finally, we show that Parsis are genetically closer to Neolithic Iranians than to modern Iranians, who have witnessed a more recent wave of admixture from the Near East. CONCLUSIONS: Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7th century and in agreement with their assimilation into the Indian sub-continent's population and cultural milieu "like sugar in milk". Moreover, in a wider context our results support a major demographic transition in West Asia due to the Islamic conquest. FAU - Chaubey, Gyaneshwer AU - Chaubey G AUID- ORCID: 0000-0003-2899-3852 AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. gyanc@ebc.ee. FAU - Ayub, Qasim AU - Ayub Q AD - The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. qa1@sanger.ac.uk. FAU - Rai, Niraj AU - Rai N AD - CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India. AD - Present address: Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India. FAU - Prakash, Satya AU - Prakash S AD - CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India. FAU - Mushrif-Tripathy, Veena AU - Mushrif-Tripathy V AD - Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune, Maharashtra, 411006, India. FAU - Mezzavilla, Massimo AU - Mezzavilla M AD - The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. FAU - Pathak, Ajai Kumar AU - Pathak AK AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. AD - Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia. FAU - Tamang, Rakesh AU - Tamang R AD - Department of Zoology, University of Calcutta, Kolkata, 700073, India. FAU - Firasat, Sadaf AU - Firasat S AD - Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation, Karachi, 74200, Pakistan. FAU - Reidla, Maere AU - Reidla M AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. AD - Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia. FAU - Karmin, Monika AU - Karmin M AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. AD - Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia. AD - Department of Psychology, University of Auckland, Auckland, 1142, New Zealand. FAU - Rani, Deepa Selvi AU - Rani DS AD - CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India. FAU - Reddy, Alla G AU - Reddy AG AD - CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India. FAU - Parik, Jüri AU - Parik J AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. AD - Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia. FAU - Metspalu, Ene AU - Metspalu E AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. AD - Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia. FAU - Rootsi, Siiri AU - Rootsi S AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. FAU - Dalal, Kurush AU - Dalal K AD - Centre for Archaeology (CfA), Centre for Extra Mural Studies (CEMS) University of Mumbai (Kalina Campus) Vidyanagri, Santacruz E Mumbai, 400098, India. FAU - Khaliq, Shagufta AU - Khaliq S AD - Department of Human Genetics & Molecular Biology, University of Health Sciences, Lahore, 54000, Pakistan. FAU - Mehdi, Syed Qasim AU - Mehdi SQ AD - Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation, Karachi, 74200, Pakistan. FAU - Singh, Lalji AU - Singh L AD - Genome foundation, C/o Prasad Hospital, Nacharam, Hyderabad, 500076, India. FAU - Metspalu, Mait AU - Metspalu M AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. FAU - Kivisild, Toomas AU - Kivisild T AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. AD - Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK. FAU - Tyler-Smith, Chris AU - Tyler-Smith C AD - The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. FAU - Villems, Richard AU - Villems R AD - Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia. AD - Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia. FAU - Thangaraj, Kumarasamy AU - Thangaraj K AD - CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India. thangs@ccmb.res.in. LA - eng GR - Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article DEP - 20170614 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (DNA, Mitochondrial) SB - IM MH - Chromosomes, Human, Y/*genetics MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration MH - Ethnicity/*genetics/history MH - Female MH - *Genetics, Population MH - Geography MH - Haplotypes MH - History, Ancient MH - Humans MH - India MH - Iran MH - Pakistan MH - Phylogeny PMC - PMC5470188 OTO - NOTNLM OT - Parsi OT - Y chromosome OT - Zoroastrian OT - ancient DNA OT - autosomes OT - mtDNA EDAT- 2017/06/16 06:00 MHDA- 2018/03/16 06:00 PMCR- 2017/06/14 CRDT- 2017/06/16 06:00 PHST- 2017/02/01 00:00 [received] PHST- 2017/05/23 00:00 [accepted] PHST- 2017/06/16 06:00 [entrez] PHST- 2017/06/16 06:00 [pubmed] PHST- 2018/03/16 06:00 [medline] PHST- 2017/06/14 00:00 [pmc-release] AID - 10.1186/s13059-017-1244-9 [pii] AID - 1244 [pii] AID - 10.1186/s13059-017-1244-9 [doi] PST - epublish SO - Genome Biol. 2017 Jun 14;18(1):110. doi: 10.1186/s13059-017-1244-9. PMID- 28613039 OWN - NLM STAT- MEDLINE DCOM- 20170904 LR - 20190609 IS - 1332-8166 (Electronic) IS - 0353-9504 (Print) IS - 0353-9504 (Linking) VI - 58 IP - 3 DP - 2017 Jun 14 TI - Sex estimation standards for medieval and contemporary Croats. PG - 222-230 AB - AIM: To develop discriminant functions for sex estimation on medieval Croatian population and test their application on contemporary Croatian population. METHODS: From a total of 519 skeletons, we chose 84 adult excellently preserved skeletons free of antemortem or postmortem changes and took all standard measurements. Sex was estimated/determined using standard anthropological procedures and ancient DNA (amelogenin analysis) where pelvis was insufficiently preserved or where sex morphological indicators were not consistent. We explored which measurements showed sexual dimorphism and used them for developing univariate and multivariate discriminant functions for sex estimation. We included only those functions that reached accuracy rate ≥80%. We tested the applicability of developed functions on modern Croatian sample (n=37). RESULTS: From 69 standard skeletal measurements used in this study, 56 of them showed statistically significant sexual dimorphism (74.7%). We developed five univariate discriminant functions with classification rate 80.6%-85.2% and seven multivariate discriminant functions with an accuracy rate of 81.8%-93.0%. When tested on the modern population functions showed classification rates 74.1%-100%, and ten of them reached aimed accuracy rate. Females showed higher classified in the mediaeval populations, whereas males were better classification rates in the modern populations. CONCLUSION: Developed discriminant functions are sufficiently accurate for reliable sex estimation in both medieval Croatian population and modern Croatian samples and may be used in forensic settings. The methodological issues that emerged regarding the importance of considering external factors in development and application of discriminant functions for sex estimation should be further explored. FAU - Bašić, Željana AU - Bašić Ž AD - Željana Bašić, University Department of Forensic Sciences, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia, zeljana.basic@unist.hr. FAU - Kružić, Ivana AU - Kružić I FAU - Jerković, Ivan AU - Jerković I FAU - Anđelinović, Deny AU - Anđelinović D FAU - Anđelinović, Šimun AU - Anđelinović Š LA - eng PT - Journal Article PL - Croatia TA - Croat Med J JT - Croatian medical journal JID - 9424324 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Croatia MH - DNA/*analysis MH - DNA, Ancient/analysis MH - Discriminant Analysis MH - Female MH - Forensic Anthropology MH - Humans MH - Male MH - Sex Characteristics MH - Sex Determination by Skeleton/methods/*standards PMC - PMC5470124 EDAT- 2017/06/15 06:00 MHDA- 2017/09/05 06:00 PMCR- 2017/06/01 CRDT- 2017/06/15 06:00 PHST- 2017/06/15 06:00 [entrez] PHST- 2017/06/15 06:00 [pubmed] PHST- 2017/09/05 06:00 [medline] PHST- 2017/06/01 00:00 [pmc-release] AID - CroatMedJ_58_0222 [pii] AID - 10.3325/cmj.2017.58.222 [doi] PST - ppublish SO - Croat Med J. 2017 Jun 14;58(3):222-230. doi: 10.3325/cmj.2017.58.222. PMID- 28119419 OWN - NLM STAT- MEDLINE DCOM- 20170912 LR - 20181113 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 45 IP - 10 DP - 2017 Jun 2 TI - Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. PG - e79 LID - 10.1093/nar/gkx033 [doi] AB - DNA library preparation for high-throughput sequencing of genomic DNA usually involves ligation of adapters to double-stranded DNA fragments. However, for highly degraded DNA, especially ancient DNA, library preparation has been found to be more efficient if each of the two DNA strands are converted into library molecules separately. We present a new method for single-stranded library preparation, ssDNA2.0, which is based on single-stranded DNA ligation with T4 DNA ligase utilizing a splinter oligonucleotide with a stretch of random bases hybridized to a 3΄ biotinylated donor oligonucleotide. A thorough evaluation of this ligation scheme shows that single-stranded DNA can be ligated to adapter oligonucleotides in higher concentration than with CircLigase (an RNA ligase that was previously chosen for end-to-end ligation in single-stranded library preparation) and that biases in ligation can be minimized when choosing splinters with 7 or 8 random nucleotides. We show that ssDNA2.0 tolerates higher quantities of input DNA than CircLigase-based library preparation, is less costly and better compatible with automation. We also provide an in-depth comparison of library preparation methods on degraded DNA from various sources. Most strikingly, we find that single-stranded library preparation increases library yields from tissues stored in formalin for many years by several orders of magnitude. CI - © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. FAU - Gansauge, Marie-Theres AU - Gansauge MT AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Gerber, Tobias AU - Gerber T AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Glocke, Isabelle AU - Glocke I AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Korlevic, Petra AU - Korlevic P AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Lippik, Laurin AU - Lippik L AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Nagel, Sarah AU - Nagel S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Riehl, Lara Maria AU - Riehl LM AD - Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, 89075 Ulm, Germany. FAU - Schmidt, Anna AU - Schmidt A AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. LA - eng PT - Journal Article PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA Primers) RN - 0 (DNA, Single-Stranded) RN - 0 (Oligonucleotides) RN - 9007-49-2 (DNA) RN - EC 6.5.1.- (DNA Ligases) SB - IM MH - Animals MH - Bone and Bones/chemistry MH - DNA/genetics/metabolism MH - DNA Ligases/*genetics/metabolism MH - DNA Primers/chemistry/metabolism MH - DNA, Single-Stranded/*genetics/metabolism MH - Fossils MH - *Gene Library MH - High-Throughput Nucleotide Sequencing MH - Horses MH - Humans MH - Liver/chemistry MH - Nucleic Acid Hybridization MH - Oligonucleotides/genetics/metabolism MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA MH - Swine PMC - PMC5449542 EDAT- 2017/01/26 06:00 MHDA- 2017/09/13 06:00 PMCR- 2017/01/24 CRDT- 2017/01/26 06:00 PHST- 2016/09/08 00:00 [received] PHST- 2017/01/13 00:00 [accepted] PHST- 2017/01/26 06:00 [pubmed] PHST- 2017/09/13 06:00 [medline] PHST- 2017/01/26 06:00 [entrez] PHST- 2017/01/24 00:00 [pmc-release] AID - gkx033 [pii] AID - 10.1093/nar/gkx033 [doi] PST - ppublish SO - Nucleic Acids Res. 2017 Jun 2;45(10):e79. doi: 10.1093/nar/gkx033. PMID- 28625158 OWN - NLM STAT- MEDLINE DCOM- 20180315 LR - 20181107 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 62 IP - 6 DP - 2017 Jun 1 TI - A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis. PG - 283-289 LID - 10.2144/000114558 [doi] AB - Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base. Here, we describe a novel cranial base drilling method (CBDM) for accessing the osseous labyrinth from the cranial base that prevents damaging the surrounding cranial features, making it highly complementary to morphological analyses. We assessed this method by comparing the aDNA results from one petrous bone processed using our novel method to its pair, which was processed using established protocols for sampling disarticulated petrous bones. We show a decrease in endogenous DNA and molecular copy numbers when the drilling method is used; however, we also show that this method produces more endogenous DNA and higher copy numbers than any postcranial bone. Our results demonstrate that this minimally-invasive method reduces the loss of genetic data associated with the use of other skeletal elements and enables the combined craniometric and genetic study of individuals with archeological, cultural, and evolutionary value. FAU - Sirak, Kendra A AU - Sirak KA AD - Department of Anthropology, Emory University, Atlanta, GA, USA. AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Ireland. FAU - Fernandes, Daniel M AU - Fernandes DM AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Ireland. AD - CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. FAU - Cheronet, Olivia AU - Cheronet O AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Ireland. FAU - Novak, Mario AU - Novak M AD - Institute for Anthropological Research, Zagreb, Croatia. FAU - Gamarra, Beatriz AU - Gamarra B AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Ireland. FAU - Balassa, Tímea AU - Balassa T AD - Biomedical Centrum Ltd., Pomáz, Hungary. FAU - Bernert, Zsolt AU - Bernert Z AD - Hungarian Natural History Museum, Department of Anthropology, Budapest, Hungary. FAU - Cséki, Andrea AU - Cséki A AD - Archeodata 1998 Ltd., Polgár, Hungary. FAU - Dani, János AU - Dani J AD - Déri Museum, Debrecen, Hungary. FAU - Gallina, József Zsolt AU - Gallina JZ AD - Ásatárs Ltd., Kecskemét, Hungary. FAU - Kocsis-Buruzs, Gábor AU - Kocsis-Buruzs G AD - Salisbury Ltd., Budaörs, Hungary. FAU - Kővári, Ivett AU - Kővári I AD - Defense POW/MIA Accounting Agency (DPAA), HI, USA. FAU - László, Orsolya AU - László O AD - Hungarian National Museum, Analytical Laboratory, Budapest, Hungary. FAU - Pap, Ildikó AU - Pap I AD - Hungarian Natural History Museum, Department of Anthropology, Budapest, Hungary. FAU - Patay, Róbert AU - Patay R AD - Ferenczy Museum Center, Department of Archaeology, Szentendre, Hungary. FAU - Petkes, Zsolt AU - Petkes Z AD - Hungarian Academy of Sciences, Research Centre for the Humanities, Institute of History, Budapest, Hungary. FAU - Szenthe, Gergely AU - Szenthe G AD - Hungarian National Museum, Department of Archaeology, Budapest, Hungary. FAU - Szeniczey, Tamás AU - Szeniczey T AD - Eötvös Loránd University, Institute of Biology, Department of Biological Anthropology, Budapest, Hungary. FAU - Hajdu, Tamás AU - Hajdu T AD - Eötvös Loránd University, Institute of Biology, Department of Biological Anthropology, Budapest, Hungary. FAU - Pinhasi, Ron AU - Pinhasi R AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Ireland. AD - Department of Anthropology, University of Vienna, Vienna, Austria. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20170601 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Ancient) SB - IM MH - Anthropology/methods MH - DNA, Ancient/*analysis MH - Gene Library MH - Humans MH - Minimally Invasive Surgical Procedures/methods MH - Orthopedic Procedures/methods MH - Petrous Bone/anatomy & histology/*chemistry/surgery MH - Sequence Analysis, DNA/methods MH - Skull/anatomy & histology/surgery MH - Specimen Handling/methods OTO - NOTNLM OT - ancient DNA OT - cranial base drilling method OT - petrous bone OT - preservation of skeletal remains EDAT- 2017/06/20 06:00 MHDA- 2018/03/16 06:00 CRDT- 2017/06/20 06:00 PHST- 2017/01/11 00:00 [received] PHST- 2017/04/17 00:00 [accepted] PHST- 2017/06/20 06:00 [entrez] PHST- 2017/06/20 06:00 [pubmed] PHST- 2018/03/16 06:00 [medline] AID - 000114558 [pii] AID - 10.2144/000114558 [doi] PST - epublish SO - Biotechniques. 2017 Jun 1;62(6):283-289. doi: 10.2144/000114558. PMID- 28526291 OWN - NLM STAT- MEDLINE DCOM- 20180404 LR - 20211205 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 107 DP - 2017 Jun TI - Direct radiocarbon dating and DNA analysis of the Darra-i-Kur (Afghanistan) human temporal bone. PG - 86-93 LID - S0047-2484(17)30113-6 [pii] LID - 10.1016/j.jhevol.2017.03.003 [doi] AB - The temporal bone discovered in the 1960s from the Darra-i-Kur cave in Afghanistan is often cited as one of the very few Pleistocene human fossils from Central Asia. Here we report the first direct radiocarbon date for the specimen and the genetic analyses of DNA extracted and sequenced from two areas of the bone. The new radiocarbon determination places the find to ∼4500 cal BP (∼2500 BCE) contradicting an assumed Palaeolithic age of ∼30,000 years, as originally suggested. The DNA retrieved from the specimen originates from a male individual who carried mitochondrial DNA of the modern human type. The petrous part yielded more endogenous ancient DNA molecules than the squamous part of the same bone. Molecular dating of the Darra-i-Kur mitochondrial DNA sequence corroborates the radiocarbon date and suggests that the specimen is younger than previously thought. Taken together, the results consolidate the fact that the human bone is not associated with the Pleistocene-age deposits of Darra-i-Kur; instead it is intrusive, possibly re-deposited from upper levels dating to much later periods (Neolithic). Despite its Holocene age, the Darra-i-Kur specimen is, so far, the first and only ancient human from Afghanistan whose DNA has been sequenced. CI - Copyright © 2017 Elsevier Ltd. All rights reserved. FAU - Douka, Katerina AU - Douka K AD - Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, United Kingdom. Electronic address: katerina.douka@rlaha.ox.ac.uk. FAU - Slon, Viviane AU - Slon V AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Stringer, Chris AU - Stringer C AD - The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom. FAU - Potts, Richard AU - Potts R AD - Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA. FAU - Hübner, Alexander AU - Hübner A AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Spoor, Fred AU - Spoor F AD - Research Department of Cell and Developmental Biology, University College London, London, UK; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Pääbo, Svante AU - Pääbo S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Higham, Tom AU - Higham T AD - Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, United Kingdom. LA - eng GR - 324139/ERC_/European Research Council/International PT - Journal Article DEP - 20170504 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 SB - IM MH - Afghanistan MH - *Fossils MH - Humans MH - Male MH - Radiometric Dating/*methods MH - *Temporal Bone OTO - NOTNLM OT - Ancient DNA OT - Central Asia OT - Darra-i-Kur OT - Middle Palaeolithic OT - Neanderthals OT - Radiocarbon dating EDAT- 2017/05/21 06:00 MHDA- 2018/04/05 06:00 CRDT- 2017/05/21 06:00 PHST- 2016/08/09 00:00 [received] PHST- 2017/03/13 00:00 [revised] PHST- 2017/03/14 00:00 [accepted] PHST- 2017/05/21 06:00 [entrez] PHST- 2017/05/21 06:00 [pubmed] PHST- 2018/04/05 06:00 [medline] AID - S0047-2484(17)30113-6 [pii] AID - 10.1016/j.jhevol.2017.03.003 [doi] PST - ppublish SO - J Hum Evol. 2017 Jun;107:86-93. doi: 10.1016/j.jhevol.2017.03.003. Epub 2017 May 4. PMID- 28396504 OWN - NLM STAT- MEDLINE DCOM- 20170711 LR - 20181113 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 206 IP - 2 DP - 2017 Jun TI - Joint Estimation of Relatedness Coefficients and Allele Frequencies from Ancient Samples. PG - 1025-1035 LID - 10.1534/genetics.117.200600 [doi] AB - Here, we develop and test a method to address whether DNA samples sequenced from a group of fossil hominin bone or tooth fragments originate from the same individual or from closely related individuals. Our method assumes low amounts of retrievable DNA, significant levels of sequencing error, and contamination from one or more present-day humans. We develop and implement a maximum likelihood method that estimates levels of contamination, sequencing error rates, and pairwise relatedness coefficients in a set of individuals. We assume that there is no reference panel for the ancient population to provide allele and haplotype frequencies. Our approach makes use of single nucleotide polymorphisms (SNPs) and does not make assumptions about the underlying demographic model. By artificially mating genomes from the 1000 Genomes Project, we determine the numbers of individuals at a given genomic coverage that are required to detect different levels of genetic relatedness with confidence. CI - Copyright © 2017 by the Genetics Society of America. FAU - Theunert, Christoph AU - Theunert C AD - Department of Integrative Biology, University of California, Berkeley, California 94720 christoph_theunert@eva.mpg.de. AD - Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany, and. FAU - Racimo, Fernando AU - Racimo F AUID- ORCID: 0000-0002-5025-2607 AD - New York Genome Center, New York, New York 10013. FAU - Slatkin, Montgomery AU - Slatkin M AD - Department of Integrative Biology, University of California, Berkeley, California 94720. LA - eng GR - R01 GM040282/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20170410 PL - United States TA - Genetics JT - Genetics JID - 0374636 SB - IM MH - Bone and Bones MH - *Fossils MH - Gene Frequency/*genetics MH - Genome, Human/*genetics MH - Humans MH - Likelihood Functions MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA/*methods PMC - PMC5499161 OTO - NOTNLM OT - ancient DNA OT - population genetics OT - relatedness EDAT- 2017/04/12 06:00 MHDA- 2017/07/14 06:00 PMCR- 2018/06/01 CRDT- 2017/04/12 06:00 PHST- 2017/01/27 00:00 [received] PHST- 2017/04/03 00:00 [accepted] PHST- 2017/04/12 06:00 [pubmed] PHST- 2017/07/14 06:00 [medline] PHST- 2017/04/12 06:00 [entrez] PHST- 2018/06/01 00:00 [pmc-release] AID - genetics.117.200600 [pii] AID - 200600 [pii] AID - 10.1534/genetics.117.200600 [doi] PST - ppublish SO - Genetics. 2017 Jun;206(2):1025-1035. doi: 10.1534/genetics.117.200600. Epub 2017 Apr 10. PMID- 28455625 OWN - NLM STAT- MEDLINE DCOM- 20170731 LR - 20210109 IS - 1432-1203 (Electronic) IS - 0340-6717 (Linking) VI - 136 IP - 5 DP - 2017 May TI - Toward a consensus on SNP and STR mutation rates on the human Y-chromosome. PG - 575-590 LID - 10.1007/s00439-017-1805-8 [doi] AB - The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate. The current estimate of the "envelope rate" is 0.75-0.89 substitutions per billion base pairs per year. The available Y-SNP mutation rates can be applied to high-coverage data from the entire X-degenerate region, but other datasets may demand recalibrated rates. While a consensus on Y-SNP rates is approaching, the debate on Y-STR rates has continued for two decades, because multiple genealogical rates were consistent with each other but three times faster than the single evolutionary estimate. Applying Y-SNP and Y-STR rates to the same haplogroups recently helped to clarify the issue. Genealogical and evolutionary STR rates typically provide lower and upper bounds of the "true" (SNP-based) age. The genealogical rate often-but not always-works well for haplogroups less than 7000 years old. The evolutionary rate, although calibrated using recent events, inflates ages of young haplogroups and deflates the age of the entire Y-chromosomal tree, but often provides reasonable estimates for intermediate ages (old haplogroups). Future rate estimates and accumulating case studies should further clarify the Y-SNP rates. FAU - Balanovsky, O AU - Balanovsky O AUID- ORCID: 0000-0003-4218-6889 AD - Vavilov Institute of General Genetics, Moscow, Russia. balanovsky@inbox.ru. AD - Research Centre for Medical Genetics, Moscow, Russia. balanovsky@inbox.ru. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20170428 PL - Germany TA - Hum Genet JT - Human genetics JID - 7613873 SB - IM MH - Chromosomes, Human, Y/*genetics MH - Genetics, Population MH - Haplotypes MH - Humans MH - Male MH - *Microsatellite Repeats MH - *Mutation MH - *Mutation Rate MH - Pedigree MH - Phylogeny MH - *Polymorphism, Single Nucleotide EDAT- 2017/04/30 06:00 MHDA- 2017/08/02 06:00 CRDT- 2017/04/30 06:00 PHST- 2017/01/25 00:00 [received] PHST- 2017/04/20 00:00 [accepted] PHST- 2017/04/30 06:00 [pubmed] PHST- 2017/08/02 06:00 [medline] PHST- 2017/04/30 06:00 [entrez] AID - 10.1007/s00439-017-1805-8 [pii] AID - 10.1007/s00439-017-1805-8 [doi] PST - ppublish SO - Hum Genet. 2017 May;136(5):575-590. doi: 10.1007/s00439-017-1805-8. Epub 2017 Apr 28. PMID- 28402470 OWN - NLM STAT- MEDLINE DCOM- 20171226 LR - 20181202 IS - 1574-6941 (Electronic) IS - 0168-6496 (Linking) VI - 93 IP - 5 DP - 2017 May 1 TI - Proper authentication of ancient DNA is essential, yes; but so are undogmatic approaches. LID - 10.1093/femsec/fix043 [doi] FAU - Toranzos, Gary A AU - Toranzos GA AD - Environmental Microbiology Laboratory, Department of Biology, University of Puerto Rico, San Juan 00932, Puerto Rico. FAU - Santiago-Rodriguez, Tasha M AU - Santiago-Rodriguez TM AD - Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA. AD - Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA. AD - Institute for Life Science Entrepreneurship, Union, NJ 07083, USA. FAU - Cano, Raul J AU - Cano RJ AD - Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA. AD - Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA. AD - Institute for Life Science Entrepreneurship, Union, NJ 07083, USA. FAU - Fornaciari, Gino AU - Fornaciari G AD - Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa 56126, Italy. AD - Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy. LA - eng PT - Comment PT - Letter PL - England TA - FEMS Microbiol Ecol JT - FEMS microbiology ecology JID - 8901229 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM CON - FEMS Microbiol Ecol. 2016 Nov;92(11):fiw182. doi: 10.1093/femsec/fiw182. PMID: 27559027 CON - FEMS Microbiol Ecol. 2017 May 1;93(5). doi: 10.1093/femsec/fix042. PMID: 28369385 MH - DNA/*genetics MH - *DNA, Ancient MH - Humans EDAT- 2017/04/13 06:00 MHDA- 2017/12/27 06:00 CRDT- 2017/04/13 06:00 PHST- 2017/03/09 00:00 [received] PHST- 2017/03/20 00:00 [accepted] PHST- 2017/04/13 06:00 [pubmed] PHST- 2017/12/27 06:00 [medline] PHST- 2017/04/13 06:00 [entrez] AID - 3586619 [pii] AID - 10.1093/femsec/fix043 [doi] PST - ppublish SO - FEMS Microbiol Ecol. 2017 May 1;93(5). doi: 10.1093/femsec/fix043. PMID- 28369385 OWN - NLM STAT- MEDLINE DCOM- 20171226 LR - 20181202 IS - 1574-6941 (Electronic) IS - 0168-6496 (Linking) VI - 93 IP - 5 DP - 2017 May 1 TI - Reply to Santiago-Rodriguez et al.: proper authentication of ancient DNA is essential. LID - 10.1093/femsec/fix042 [doi] FAU - Eisenhofer, Raphael AU - Eisenhofer R FAU - Cooper, Alan AU - Cooper A FAU - Weyrich, Laura S AU - Weyrich LS LA - eng PT - Comment PT - Letter PL - England TA - FEMS Microbiol Ecol JT - FEMS microbiology ecology JID - 8901229 RN - 0 (DNA, Ancient) SB - IM CON - FEMS Microbiol Ecol. 2016 Nov;92(11):fiw182. doi: 10.1093/femsec/fiw182. PMID: 27559027 CIN - FEMS Microbiol Ecol. 2017 May 1;93(5). doi: 10.1093/femsec/fix043. PMID: 28402470 MH - *DNA, Ancient MH - Humans EDAT- 2017/04/04 06:00 MHDA- 2017/12/27 06:00 CRDT- 2017/04/04 06:00 PHST- 2017/02/22 00:00 [received] PHST- 2017/03/20 00:00 [accepted] PHST- 2017/04/04 06:00 [pubmed] PHST- 2017/12/27 06:00 [medline] PHST- 2017/04/04 06:00 [entrez] AID - 3089752 [pii] AID - 10.1093/femsec/fix042 [doi] PST - ppublish SO - FEMS Microbiol Ecol. 2017 May 1;93(5). doi: 10.1093/femsec/fix042. PMID- 28279935 OWN - NLM STAT- MEDLINE DCOM- 20170707 LR - 20191210 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 28 DP - 2017 May TI - Evaluation of the Illumina ForenSeq™ DNA Signature Prep Kit - MPS forensic application for the MiSeq FGx™ benchtop sequencer. PG - 188-194 LID - S1872-4973(17)30047-9 [pii] LID - 10.1016/j.fsigen.2017.02.018 [doi] AB - Massively Parallel (Next Generation) Sequencing (MPS) technologies have recently been proven useful and successful in typing various markers relevant in forensic genetics, such as STRs, SNPs and mitochondrial genomes. Early studies investigated self-developed DNA libraries, commercially supplied kits are currently being made available to allow a smoother and gradual implementation of such technologies in forensic laboratories. The ForenSeq™ DNA Signature Prep Kit (Illumina, CA) is the first commercially available STR kit that can be used on the MiSeq FGx™ (Illumina, CA) benchtop high-throughput sequencer. This kit allows the simultaneous typing of 59 STRs and up to 172 SNPs in a single reaction and presents a short library preparation protocol adapted to contemporary forensic requirements. In this study, we evaluated the beta version of the ForenSeq DNA Signature Prep Kit MiSeq FGx system by investigating reproducibility, sensitivity, mixtures, concordance, casework-type and aDNA samples and found it to perform successfully, proving to be a robust method for future forensic applications. MPS brings the possibility of complex multiplexing, high sensitivity and sequencing resolution to forensics; however, the need for consensual directions on databasing, data storage and nomenclature must be taken into consideration. CI - Copyright © 2017 Elsevier B.V. All rights reserved. FAU - Xavier, Catarina AU - Xavier C AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria. FAU - Parson, Walther AU - Parson W AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA. Electronic address: walther.parson@i-med.ac.at. LA - eng PT - Evaluation Study PT - Journal Article DEP - 20170301 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 SB - IM MH - Chromosomes, Human, X MH - Chromosomes, Human, Y MH - *DNA Fingerprinting MH - Female MH - Forensic Genetics MH - High-Throughput Nucleotide Sequencing/*instrumentation MH - Humans MH - Male MH - *Microsatellite Repeats MH - *Polymorphism, Single Nucleotide MH - Reproducibility of Results OTO - NOTNLM OT - Ancient DNA OT - Forensic science OT - Massiv parallel sequencing OT - Short tandem repeats OT - Single nucleotide polymorphisms EDAT- 2017/03/11 06:00 MHDA- 2017/07/08 06:00 CRDT- 2017/03/11 06:00 PHST- 2016/11/14 00:00 [received] PHST- 2017/02/22 00:00 [revised] PHST- 2017/02/28 00:00 [accepted] PHST- 2017/03/11 06:00 [pubmed] PHST- 2017/07/08 06:00 [medline] PHST- 2017/03/11 06:00 [entrez] AID - S1872-4973(17)30047-9 [pii] AID - 10.1016/j.fsigen.2017.02.018 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2017 May;28:188-194. doi: 10.1016/j.fsigen.2017.02.018. Epub 2017 Mar 1. PMID- 28260210 OWN - NLM STAT- MEDLINE DCOM- 20170731 LR - 20240330 IS - 1432-1203 (Electronic) IS - 0340-6717 (Print) IS - 0340-6717 (Linking) VI - 136 IP - 5 DP - 2017 May TI - The study of human Y chromosome variation through ancient DNA. PG - 529-546 LID - 10.1007/s00439-017-1773-z [doi] AB - High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World. FAU - Kivisild, Toomas AU - Kivisild T AUID- ORCID: 0000-0002-6297-7808 AD - Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 1QH, UK. tk331@cam.ac.uk. AD - Estonian Biocentre, 51010, Tartu, Estonia. tk331@cam.ac.uk. LA - eng PT - Journal Article PT - Review DEP - 20170304 PL - Germany TA - Hum Genet JT - Human genetics JID - 7613873 RN - 0 (DNA, Ancient) SB - IM EIN - Hum Genet. 2018 Oct;137(10):863. doi: 10.1007/s00439-018-1937-5. PMID: 30232557 MH - Chromosomes, Human, Y/*genetics MH - *DNA, Ancient MH - Humans MH - Male MH - Phylogeography MH - *Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA PMC - PMC5418327 COIS- I declare no conflict of interests. EDAT- 2017/03/06 06:00 MHDA- 2017/08/02 06:00 PMCR- 2017/03/04 CRDT- 2017/03/06 06:00 PHST- 2017/01/12 00:00 [received] PHST- 2017/02/24 00:00 [accepted] PHST- 2017/03/06 06:00 [pubmed] PHST- 2017/08/02 06:00 [medline] PHST- 2017/03/06 06:00 [entrez] PHST- 2017/03/04 00:00 [pmc-release] AID - 10.1007/s00439-017-1773-z [pii] AID - 1773 [pii] AID - 10.1007/s00439-017-1773-z [doi] PST - ppublish SO - Hum Genet. 2017 May;136(5):529-546. doi: 10.1007/s00439-017-1773-z. Epub 2017 Mar 4. PMID- 28273061 OWN - NLM STAT- MEDLINE DCOM- 20170706 LR - 20201209 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 544 IP - 7650 DP - 2017 Apr 20 TI - Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. PG - 357-361 LID - 10.1038/nature21674 [doi] AB - Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution. FAU - Weyrich, Laura S AU - Weyrich LS AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. FAU - Duchene, Sebastian AU - Duchene S AD - Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, Australia. FAU - Soubrier, Julien AU - Soubrier J AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. FAU - Arriola, Luis AU - Arriola L AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. FAU - Breen, James AU - Breen J AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. FAU - Morris, Alan G AU - Morris AG AD - Department of Human Biology, University of Cape Town, Cape Town, South Africa. FAU - Alt, Kurt W AU - Alt KW AD - Danube Private University, Krems, Austria. AD - State Office for Heritage Management and Archaeology, Saxony-Anhalt, Germany. AD - Heritage Museum, Halle, Germany. AD - Institute for Prehistory and Archaeological Science, Basel University, Switzerland. FAU - Caramelli, David AU - Caramelli D AD - Department of Biology, University of Florence, Florence, Italy. FAU - Dresely, Veit AU - Dresely V AD - State Office for Heritage Management and Archaeology, Saxony-Anhalt, Germany. AD - Heritage Museum, Halle, Germany. FAU - Farrell, Milly AU - Farrell M AD - Human Origins and Palaeo Environments Group, Oxford Brookes University, Oxford, UK. FAU - Farrer, Andrew G AU - Farrer AG AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. FAU - Francken, Michael AU - Francken M AD - Paleoanthropology, Senckenberg Centre for Human Evolution and Paleoenvironments, Eberhard Karls University of Tübingen, Tübingen, Germany. FAU - Gully, Neville AU - Gully N AD - School of Dentistry, The University of Adelaide, Adelaide, Australia. FAU - Haak, Wolfgang AU - Haak W AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. FAU - Hardy, Karen AU - Hardy K AD - Catalan Institution for Research and Advanced Studies (ICREA), Pg Lluís Companys 23, 08010 Barcelona, Catalonia, Spain. AD - Departament de Prehistòria, Facultat de Filosofia i Lletres, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain. FAU - Harvati, Katerina AU - Harvati K AD - Paleoanthropology, Senckenberg Centre for Human Evolution and Paleoenvironments, Eberhard Karls University of Tübingen, Tübingen, Germany. FAU - Held, Petra AU - Held P AD - Institute of Anthropology, University of Mainz, Mainz, Germany. FAU - Holmes, Edward C AU - Holmes EC AD - Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, Australia. FAU - Kaidonis, John AU - Kaidonis J AD - School of Dentistry, The University of Adelaide, Adelaide, Australia. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain. FAU - de la Rasilla, Marco AU - de la Rasilla M AD - Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, Oviedo, Spain. FAU - Rosas, Antonio AU - Rosas A AD - Paleoanthropology Group, Department of Paleobiology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain. FAU - Semal, Patrick AU - Semal P AD - Scientific Service Heritage, Royal Belgian Institute of Natural Sciences, Brussels, Belgium. FAU - Soltysiak, Arkadiusz AU - Soltysiak A AD - Department of Bioarchaeology, Institute of Archaeology, University of Warsaw, Warsaw, Poland. FAU - Townsend, Grant AU - Townsend G AD - School of Dentistry, The University of Adelaide, Adelaide, Australia. FAU - Usai, Donatella AU - Usai D AD - Istituto Italiano per l'Africa e l'Oriente (IsIAO), Rome, Italy. FAU - Wahl, Joachim AU - Wahl J AD - State Office for Cultural Heritage Management Baden-Württemberg, Esslingen, Germany. FAU - Huson, Daniel H AU - Huson DH AD - Department of Algorithms in Bioinformatics, University of Tübingen, Tübingen, Germany. FAU - Dobney, Keith AU - Dobney K AD - Department of Archaeology, Classics and Egyptology, School of Histories, Languages and Cultures, University of Liverpool, Liverpool, UK. AD - Department of Archaeology, University of Aberdeen, Aberdeen, UK. AD - Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20170308 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) SB - IM CIN - Nature. 2017 Mar 8;543(7644):163. doi: 10.1038/543163a. PMID: 28277523 MH - Animals MH - Belgium MH - Carnivory MH - Caves MH - DNA, Ancient/*analysis MH - Dental Calculus/*chemistry MH - Diet/*history MH - Enterocytozoon/genetics/isolation & purification MH - *Food Preferences MH - Genome, Bacterial/genetics MH - Health/*history MH - History, Ancient MH - Humans MH - Intestines/microbiology MH - Meat/history MH - Methanobrevibacter/genetics/isolation & purification MH - Mouth/microbiology MH - Neanderthals/*microbiology/*psychology MH - Pan troglodytes/microbiology MH - Penicillium/chemistry MH - Perissodactyla MH - Sheep MH - Spain MH - Stomach/microbiology MH - Symbiosis MH - Time Factors MH - Vegetarians/history EDAT- 2017/03/09 06:00 MHDA- 2017/07/07 06:00 CRDT- 2017/03/09 06:00 PHST- 2016/08/02 00:00 [received] PHST- 2017/01/30 00:00 [accepted] PHST- 2017/03/09 06:00 [pubmed] PHST- 2017/07/07 06:00 [medline] PHST- 2017/03/09 06:00 [entrez] AID - nature21674 [pii] AID - 10.1038/nature21674 [doi] PST - ppublish SO - Nature. 2017 Apr 20;544(7650):357-361. doi: 10.1038/nature21674. Epub 2017 Mar 8. PMID- 28422985 OWN - NLM STAT- MEDLINE DCOM- 20170427 LR - 20190208 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 12 IP - 4 DP - 2017 TI - Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing. PG - e0174886 LID - 10.1371/journal.pone.0174886 [doi] LID - e0174886 AB - As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination. FAU - Neparáczki, Endre AU - Neparáczki E AD - Department of Genetics, University of Szeged, Szeged, Hungary. AD - Department of Biological Anthropology University of Szeged, Szeged, Hungary. FAU - Kocsy, Klaudia AU - Kocsy K AD - Department of Genetics, University of Szeged, Szeged, Hungary. FAU - Tóth, Gábor Endre AU - Tóth GE AD - Department of Genetics, University of Szeged, Szeged, Hungary. FAU - Maróti, Zoltán AU - Maróti Z AD - Department of Pediatrics and Pediatric Health Center, University of Szeged, Faculty of Medicine, Szeged, Hungary. FAU - Kalmár, Tibor AU - Kalmár T AD - Department of Pediatrics and Pediatric Health Center, University of Szeged, Faculty of Medicine, Szeged, Hungary. FAU - Bihari, Péter AU - Bihari P AD - SeqOmics Biotechnology Ltd., Mórahalom, Hungary. FAU - Nagy, István AU - Nagy I AD - SeqOmics Biotechnology Ltd., Mórahalom, Hungary. AD - Institute of Biochemistry, Biological Research Centre, Szeged, Hungary. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology University of Szeged, Szeged, Hungary. FAU - Molnár, Erika AU - Molnár E AD - Department of Biological Anthropology University of Szeged, Szeged, Hungary. FAU - Raskó, István AU - Raskó I AD - Institute of Genetics, Biological Research Centre, Szeged, Hungary. FAU - Török, Tibor AU - Török T AUID- ORCID: 0000-0002-2128-1126 AD - Department of Genetics, University of Szeged, Szeged, Hungary. LA - eng PT - Historical Article PT - Journal Article DEP - 20170419 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Bone and Bones/chemistry MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics/history MH - Fossils MH - *Haplotypes MH - High-Throughput Nucleotide Sequencing/*methods MH - History, Medieval MH - Humans MH - Hungary MH - Molecular Typing/*methods MH - *Paleontology MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA PMC - PMC5396865 COIS- Competing Interests: Dr. Bihari and Dr. Nagy had consulting positions at SeqOmics Biotechnology Ltd. at the time the study was conceived. SeqOmics Biotechnology Ltd. was not directly involved in the design and execution of the experiments or in the writing of the manuscript. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. EDAT- 2017/04/20 06:00 MHDA- 2017/04/28 06:00 PMCR- 2017/04/19 CRDT- 2017/04/20 06:00 PHST- 2016/12/13 00:00 [received] PHST- 2017/03/16 00:00 [accepted] PHST- 2017/04/20 06:00 [entrez] PHST- 2017/04/20 06:00 [pubmed] PHST- 2017/04/28 06:00 [medline] PHST- 2017/04/19 00:00 [pmc-release] AID - PONE-D-16-49179 [pii] AID - 10.1371/journal.pone.0174886 [doi] PST - epublish SO - PLoS One. 2017 Apr 19;12(4):e0174886. doi: 10.1371/journal.pone.0174886. eCollection 2017. PMID- 28377518 OWN - NLM STAT- MEDLINE DCOM- 20180529 LR - 20181113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 114 IP - 16 DP - 2017 Apr 18 TI - Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity. PG - 4093-4098 LID - 10.1073/pnas.1620410114 [doi] AB - Recent genomic studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific Northwest Coast proves an intriguing focus for these studies because of its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here, we report the low-coverage genome sequence of an ancient individual known as "Shuká Káa" ("Man Ahead of Us") recovered from the On Your Knees Cave (OYKC) in southeastern Alaska (archaeological site 49-PET-408). The human remains date to ∼10,300 calendar (cal) y B.P. We also analyze low-coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from ∼6,075 to 1,750 cal y B.P. From the resulting time series of genetic data, we show that the Pacific Northwest Coast exhibits genetic continuity for at least the past 10,300 cal y B.P. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared with other North American individuals from the late Pleistocene or early Holocene (i.e., Anzick-1 and Kennewick Man). Despite regional shifts in mtDNA haplogroups, we conclude from individuals sampled through time that people of the northern Northwest Coast belong to an early genetic lineage that may stem from a late Pleistocene coastal migration into the Americas. FAU - Lindo, John AU - Lindo J AD - Department of Human Genetics, University of Chicago, Chicago, IL 60637. FAU - Achilli, Alessandro AU - Achilli A AD - Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, 27100 Pavia, Italy. FAU - Perego, Ugo A AU - Perego UA AD - Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, 27100 Pavia, Italy. FAU - Archer, David AU - Archer D AD - Department of Anthropology, Northwestern Community College, Prince Rupert, BC, Canada V8J 3P6. FAU - Valdiosera, Cristina AU - Valdiosera C AD - Department of Archaeology and History, La Trobe University, Melbourne, VIC 3086, Australia. AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark. FAU - Petzelt, Barbara AU - Petzelt B AD - Metlakatla Treaty Office, Metlakatla First Nation, Prince Rupert, BC, Canada V8J 3P6. FAU - Mitchell, Joycelynn AU - Mitchell J AD - Metlakatla Treaty Office, Metlakatla First Nation, Prince Rupert, BC, Canada V8J 3P6. FAU - Worl, Rosita AU - Worl R AD - Sealaska Heritage Institute, Juneau, AK 99801. FAU - Dixon, E James AU - Dixon EJ AD - Maxwell Museum of Anthropology, University of New Mexico, Albuquerque, NM 87131. AD - Department of Anthropology, University of New Mexico, Albuquerque, NM 87131. FAU - Fifield, Terence E AU - Fifield TE AD - Sociology and Anthropology Department, University of Alaska Southeast, Ketchikan, AK 99901. AD - Tongass National Forest, US Department of Agriculture Forest Service, Ketchikan, AK 99901. FAU - Rasmussen, Morten AU - Rasmussen M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark. AD - Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark. AD - Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom. AD - Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom. FAU - Cybulski, Jerome S AU - Cybulski JS AD - Research, Canadian Museum of History, Gatineau, QC, Canada K1A 0M8. AD - Department of Anthropology, University of Western Ontario, London, ON, Canada N6A 3K7. AD - Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada V5A 1S6. FAU - Kemp, Brian M AU - Kemp BM AD - Department of Anthropology, University of Oklahoma, Norman, OK 73019; bmkemp@ou.edu mxd60@psu.edu malhi@illinois.edu. FAU - DeGiorgio, Michael AU - DeGiorgio M AD - Department of Biology, Pennsylvania State University, University Park, PA 16802; bmkemp@ou.edu mxd60@psu.edu malhi@illinois.edu. AD - Institute for CyberScience, Pennsylvania State University, University Park, PA 16802. FAU - Malhi, Ripan S AU - Malhi RS AD - Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61820; bmkemp@ou.edu mxd60@psu.edu malhi@illinois.edu. AD - Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20170404 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration MH - *Evolution, Molecular MH - Female MH - *Genetic Variation MH - *Genetics, Population MH - *Genome, Mitochondrial MH - Genomics/*methods MH - Humans MH - Indians, North American/*genetics MH - Male MH - Phylogeny PMC - PMC5402414 OTO - NOTNLM OT - Native American OT - ancient DNA OT - indigenous OT - paleogenomics OT - peopling COIS- The authors declare no conflict of interest. EDAT- 2017/04/06 06:00 MHDA- 2018/05/31 06:00 PMCR- 2017/10/18 CRDT- 2017/04/06 06:00 PHST- 2017/04/06 06:00 [pubmed] PHST- 2018/05/31 06:00 [medline] PHST- 2017/04/06 06:00 [entrez] PHST- 2017/10/18 00:00 [pmc-release] AID - 1620410114 [pii] AID - 201620410 [pii] AID - 10.1073/pnas.1620410114 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4093-4098. doi: 10.1073/pnas.1620410114. Epub 2017 Apr 4. PMID- 28376731 OWN - NLM STAT- MEDLINE DCOM- 20170823 LR - 20181202 IS - 1471-2105 (Electronic) IS - 1471-2105 (Linking) VI - 18 IP - 1 DP - 2017 Apr 4 TI - AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data. PG - 203 LID - 10.1186/s12859-017-1613-0 [doi] LID - 203 AB - BACKGROUND: Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA. RESULTS: We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87-91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Finally, we demonstrate that AD-LIBS is more effective than HAPMIX at inferring ancestry when preexisting phased reference data are unavailable and genomes are sequenced to low coverage. CONCLUSIONS: AD-LIBS is an effective tool for ancestry inference that can be used even when few individuals are available for comparison or when genomes are sequenced to low coverage. AD-LIBS is therefore likely to be useful in studies of non-model or ancient organisms that lack large amounts of genomic DNA. AD-LIBS can therefore expand the range of studies in which admixture mapping is a viable tool. FAU - Schaefer, Nathan K AU - Schaefer NK AD - Department of Biomolecular Engineering, University of California, Santa Cruz, USA. nkschaefer@soe.ucsc.edu. AD - UCSC Genomics Institute, University of California, Santa Cruz, USA. nkschaefer@soe.ucsc.edu. FAU - Shapiro, Beth AU - Shapiro B AD - Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA. AD - UCSC Genomics Institute, University of California, Santa Cruz, USA. FAU - Green, Richard E AU - Green RE AD - Department of Biomolecular Engineering, University of California, Santa Cruz, USA. AD - UCSC Genomics Institute, University of California, Santa Cruz, USA. LA - eng GR - T32 HG008345/HG/NHGRI NIH HHS/United States PT - Journal Article DEP - 20170404 PL - England TA - BMC Bioinformatics JT - BMC bioinformatics JID - 100965194 SB - IM MH - Animals MH - Genetic Speciation MH - *Genome MH - Humans MH - *Hybridization, Genetic MH - Markov Chains MH - Polymorphism, Single Nucleotide MH - *Software MH - Ursidae/*genetics PMC - PMC5381037 OTO - NOTNLM OT - Admixture OT - Ancestry OT - Bears OT - Hybridization OT - Speciation EDAT- 2017/04/06 06:00 MHDA- 2017/08/24 06:00 PMCR- 2017/04/04 CRDT- 2017/04/06 06:00 PHST- 2016/11/08 00:00 [received] PHST- 2017/03/24 00:00 [accepted] PHST- 2017/04/06 06:00 [entrez] PHST- 2017/04/06 06:00 [pubmed] PHST- 2017/08/24 06:00 [medline] PHST- 2017/04/04 00:00 [pmc-release] AID - 10.1186/s12859-017-1613-0 [pii] AID - 1613 [pii] AID - 10.1186/s12859-017-1613-0 [doi] PST - epublish SO - BMC Bioinformatics. 2017 Apr 4;18(1):203. doi: 10.1186/s12859-017-1613-0. PMID- 29299966 OWN - NLM STAT- MEDLINE DCOM- 20181015 LR - 20221207 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 89 IP - 2 DP - 2017 Apr TI - Ancient DNA Investigation of a Medieval German Cemetery Confirms Long-Term Stability of CCR5-Δ32 Allele Frequencies in Central Europe. PG - 119-124 AB - The CCR5-Δ32 mutation present in European populations is among the most prominently debated cases of recent positive selection in humans. This allele, a 32-bp deletion that renders the T-cell CCR5 receptor nonfunctional, has important epidemiological and public health significance, as homozygous carriers are resistant to several HIV strains. However, although the function of this allele in preventing HIV infection is now well described, its human evolutionary origin is poorly understood. Initial attempts to determine the emergence of the CCR5-Δ32 allele pointed to selection during the 14th-century Black Death pandemic; however, subsequent analyses suggest that the allele rose in frequency more than 5,000 years ago, possibly through drift. Recently, three studies have identified populations predating the 14th century CE that are positive for the CCR5-Δ32 allele, supporting the claim for a more ancient origin. However, these studies also suggest poorly understood regional differences in the recent evolutionary history of the CCR5-Δ32 allele. Here a new hydrolysis-probe-based real-time PCR assay was designed to ascertain CCR5 allele frequency in 53 individuals from a 10th- to 12th-century CE church and convent complex in central Germany that predates outbreaks of the Black Death pandemic. High-confidence genotypes were obtained for 32 individuals, and results show that CCR5-Δ32 allele frequency has remained unchanged in this region of Central Europe over the last millennium, suggesting that there has been no strong positive selective pressure over this time period and confirming a more ancient origin for the allele. FAU - Bouwman, Abigail AU - Bouwman A AD - 1 Institute of Evolutionary Medicine, University of Zürich, Zürich, CH-8057, Switzerland. FAU - Shved, Natallia AU - Shved N AD - 1 Institute of Evolutionary Medicine, University of Zürich, Zürich, CH-8057, Switzerland. FAU - Akgül, Gülfirde AU - Akgül G AD - 1 Institute of Evolutionary Medicine, University of Zürich, Zürich, CH-8057, Switzerland. FAU - Rühli, Frank AU - Rühli F AD - 1 Institute of Evolutionary Medicine, University of Zürich, Zürich, CH-8057, Switzerland. FAU - Warinner, Christina AU - Warinner C AD - 1 Institute of Evolutionary Medicine, University of Zürich, Zürich, CH-8057, Switzerland. AD - 2 Department of Anthropology, University of Oklahoma, Norman, Oklahoma, USA. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (CCR5 protein, human) RN - 0 (DNA, Ancient) RN - 0 (Receptors, CCR5) SB - IM MH - Cemeteries MH - DNA, Ancient/*analysis MH - Disease Outbreaks MH - Ethnicity/genetics MH - Gene Frequency/*genetics MH - Genotype MH - Germany/ethnology MH - History, Medieval MH - Homozygote MH - Humans MH - Plague/epidemiology MH - Receptors, CCR5/*genetics MH - Sequence Deletion/genetics MH - White People/*genetics OTO - NOTNLM OT - ancient dna OT - ccr5 OT - medieval EDAT- 2018/01/05 06:00 MHDA- 2018/10/16 06:00 CRDT- 2018/01/05 06:00 PHST- 2018/01/05 06:00 [entrez] PHST- 2018/01/05 06:00 [pubmed] PHST- 2018/10/16 06:00 [medline] AID - 10.13110/humanbiology.89.2.02 [pii] AID - 10.13110/humanbiology.89.2.02 [doi] PST - ppublish SO - Hum Biol. 2017 Apr;89(2):119-124. doi: 10.13110/humanbiology.89.2.02. PMID- 29299965 OWN - NLM STAT- MEDLINE DCOM- 20181015 LR - 20211204 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 89 IP - 2 DP - 2017 Apr TI - The Multiple Histories of Western Asia: Perspectives from Ancient and Modern Genomes. PG - 107-117 AB - Western Asia lies at the heart of the Old World, in the midst of Africa, Asia, and Europe. As such, this region has been populated and repopulated by myriad peoples, starting with the first migrants from Africa. All evidence points to Western Asia for the beginnings of sedentary life, and indeed, first the villages and later the cities of this land remain as archaeological wonders, revealing complex histories of multiple peoples and their interactions. With the wondrous breakthroughs in genomic studies, we now have the power to look at these histories with a truly quantitative lens. Here, we review the recent anthropological genomics literature pertaining to this region, with an outlook for the future challenges and exciting possibilities for the field. FAU - Taskent, Recep Ozgur AU - Taskent RO AD - 1 Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA. FAU - Gokcumen, Omer AU - Gokcumen O AD - 1 Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA. LA - eng PT - Historical Article PT - Journal Article PT - Review PL - United States TA - Hum Biol JT - Human biology JID - 0116717 SB - IM MH - Africa/ethnology MH - Anthropology/history MH - Archaeology/history MH - Asia/ethnology MH - Asia, Western/ethnology MH - Europe/ethnology MH - Genetic Variation/*genetics MH - Genomics/*history/trends MH - History, 20th Century MH - History, 21st Century MH - History, Ancient MH - Human Migration/history MH - Humans MH - Racial Groups/*genetics MH - Sedentary Behavior/ethnology OTO - NOTNLM OT - anatolia OT - ancient dna OT - genomics OT - levant OT - middle east OT - molecular anthropology OT - near east OT - turkey EDAT- 2018/01/05 06:00 MHDA- 2018/10/16 06:00 CRDT- 2018/01/05 06:00 PHST- 2018/01/05 06:00 [entrez] PHST- 2018/01/05 06:00 [pubmed] PHST- 2018/10/16 06:00 [medline] AID - 10.13110/humanbiology.89.2.01 [pii] AID - 10.13110/humanbiology.89.2.01 [doi] PST - ppublish SO - Hum Biol. 2017 Apr;89(2):107-117. doi: 10.13110/humanbiology.89.2.01. PMID- 28384042 OWN - NLM STAT- MEDLINE DCOM- 20170518 LR - 20170518 IS - 1945-0257 (Electronic) IS - 1945-0257 (Linking) VI - 21 IP - 4 DP - 2017 Apr TI - Comparison of Suitability of the Most Common Ancient DNA Quantification Methods. PG - 265-271 LID - 10.1089/gtmb.2016.0197 [doi] AB - AIMS: Ancient DNA (aDNA) extracted from historical bones is damaged and fragmented into short segments, present in low quantity, and usually copurified with microbial DNA. A wide range of DNA quantification methods are available. The aim of this study was to compare the five most common DNA quantification methods for aDNA. MATERIALS AND METHODS: Quantification methods were tested on DNA extracted from skeletal material originating from an early medieval burial site. The tested methods included ultraviolet (UV) absorbance, real-time quantitative polymerase chain reaction (qPCR) based on SYBR(®) green detection, real-time qPCR based on a forensic kit, quantification via fluorescent dyes bonded to DNA, and fragmentary analysis. Differences between groups were tested using a paired t-test. RESULTS: Methods that measure total DNA present in the sample (NanoDrop(™) UV spectrophotometer and Qubit(®) fluorometer) showed the highest concentrations. Methods based on real-time qPCR underestimated the quantity of aDNA. The most accurate method of aDNA quantification was fragmentary analysis, which also allows DNA quantification of the desired length and is not affected by PCR inhibitors. CONCLUSIONS: Methods based on the quantification of the total amount of DNA in samples are unsuitable for ancient samples as they overestimate the amount of DNA presumably due to the presence of microbial DNA. Real-time qPCR methods give undervalued results due to DNA damage and the presence of PCR inhibitors. DNA quantification methods based on fragment analysis show not only the quantity of DNA but also fragment length. FAU - Brzobohatá, Kristýna AU - Brzobohatá K AD - 1 Laboratory of Biological and Molecular Anthropology, Institute of Experimental Biology, Faculty of Science, Masaryk University , Brno, Czech Republic . FAU - Drozdová, Eva AU - Drozdová E AD - 1 Laboratory of Biological and Molecular Anthropology, Institute of Experimental Biology, Faculty of Science, Masaryk University , Brno, Czech Republic . FAU - Smutný, Jiří AU - Smutný J AD - 2 Biovendor, Laboratory Medicine , Brno, Czech Republic . FAU - Zeman, Tomáš AU - Zeman T AD - 3 Department of Anthropology, Faculty of Natural Sciences, Comenius University , Bratislava, Slovak Republic . FAU - Beňuš, Radoslav AU - Beňuš R AD - 3 Department of Anthropology, Faculty of Natural Sciences, Comenius University , Bratislava, Slovak Republic . LA - eng PT - Comparative Study PT - Journal Article DEP - 20170221 PL - United States TA - Genet Test Mol Biomarkers JT - Genetic testing and molecular biomarkers JID - 101494210 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - DNA/genetics MH - DNA, Ancient/*analysis/*isolation & purification MH - Humans MH - Polymerase Chain Reaction/methods MH - Real-Time Polymerase Chain Reaction/*methods OTO - NOTNLM OT - aDNA fragmentation OT - aDNA quantification OT - ancient DNA OT - real-time qPCR EDAT- 2017/04/07 06:00 MHDA- 2017/05/19 06:00 CRDT- 2017/04/07 06:00 PHST- 2017/04/07 06:00 [entrez] PHST- 2017/04/07 06:00 [pubmed] PHST- 2017/05/19 06:00 [medline] AID - 10.1089/gtmb.2016.0197 [doi] PST - ppublish SO - Genet Test Mol Biomarkers. 2017 Apr;21(4):265-271. doi: 10.1089/gtmb.2016.0197. Epub 2017 Feb 21. PMID- 28330913 OWN - NLM STAT- MEDLINE DCOM- 20180129 LR - 20221207 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 284 IP - 1851 DP - 2017 Mar 29 TI - Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe. LID - 10.1098/rspb.2016.1976 [doi] LID - 20161976 AB - Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe. CI - © 2017 The Author(s). FAU - Pereira, Joana B AU - Pereira JB AUID- ORCID: 0000-0002-4409-514X AD - Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. AD - Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal. AD - Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal. FAU - Costa, Marta D AU - Costa MD AD - Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. AD - Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal. AD - Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. AD - ICVS/3Bs-PT Government Associate Laboratory, Braga/Guimarães, Portugal. FAU - Vieira, Daniel AU - Vieira D AD - Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal. FAU - Pala, Maria AU - Pala M AD - Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK. FAU - Bamford, Lisa AU - Bamford L AD - Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. FAU - Harich, Nourdin AU - Harich N AD - Laboratoire d'Anthropogenetique, Department de Biologie, Universite Chouaib Doukkali, El Jadida 24000, Morocco. FAU - Cherni, Lotfi AU - Cherni L AD - Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis 2092, Tunisia. AD - Tunis and High Institute of Biotechnology, University of Monastir, 5000 Monastir, Tunisia. FAU - Alshamali, Farida AU - Alshamali F AD - General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates. FAU - Hatina, Jiři AU - Hatina J AD - Medical Faculty in Pilsen, Institute of Biology, Charles University, Pilsen, Czech Republic. FAU - Rychkov, Sergey AU - Rychkov S AD - Vavilov Institute of General Genetics, Moscow, Russia. FAU - Stefanescu, Gheorghe AU - Stefanescu G AD - Institutul de Cercetari Biologice, Iasi, Romania. FAU - King, Turi AU - King T AD - Department of Genetics, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK. FAU - Torroni, Antonio AU - Torroni A AD - Dipartimento di Biologia e Biotecnologie 'L. Spallanzani', Università di Pavia, Pavia, Italy. FAU - Soares, Pedro AU - Soares P AD - Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal. AD - Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal. FAU - Pereira, Luísa AU - Pereira L AD - Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal. AD - Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal. AD - Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal. FAU - Richards, Martin B AU - Richards MB AUID- ORCID: 0000-0003-3118-0967 AD - Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK m.b.richards@hud.ac.uk. AD - Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK. LA - eng PT - Journal Article PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*analysis MH - Ethnicity MH - Europe MH - Founder Effect MH - *Genetic Variation MH - *Genome, Human MH - Haplotypes MH - Humans MH - Mediterranean Region MH - Middle East MH - White People PMC - PMC5378072 OTO - NOTNLM OT - European origins OT - Late Glacial OT - Neolithic OT - haplogroups OT - mitogenomes OT - phylogeography EDAT- 2017/03/24 06:00 MHDA- 2018/01/30 06:00 PMCR- 2018/03/29 CRDT- 2017/03/24 06:00 PHST- 2016/09/07 00:00 [received] PHST- 2017/02/14 00:00 [accepted] PHST- 2017/03/24 06:00 [entrez] PHST- 2017/03/24 06:00 [pubmed] PHST- 2018/01/30 06:00 [medline] PHST- 2018/03/29 00:00 [pmc-release] AID - rspb.2016.1976 [pii] AID - rspb20161976 [pii] AID - 10.1098/rspb.2016.1976 [doi] PST - ppublish SO - Proc Biol Sci. 2017 Mar 29;284(1851):20161976. doi: 10.1098/rspb.2016.1976. PMID- 28302068 OWN - NLM STAT- MEDLINE DCOM- 20170626 LR - 20221207 IS - 1471-2148 (Electronic) IS - 1471-2148 (Linking) VI - 17 IP - 1 DP - 2017 Mar 16 TI - Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5(th) millennium BC. PG - 80 LID - 10.1186/s12862-017-0924-0 [doi] LID - 80 AB - BACKGROUND: Recent aDNA studies are progressively focusing on various Neolithic and Hunter - Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities. RESULTS: Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK. CONCLUSIONS: We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities. FAU - Chyleński, Maciej AU - Chyleński M AD - Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614, Poznań, Poland. maciej.ch@amu.edu.pl. FAU - Juras, Anna AU - Juras A AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland. FAU - Ehler, Edvard AU - Ehler E AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland. AD - Department of Biology and Environmental Studies, Faculty of Education, Charles University in Prague, Magdalény Rettigové 4, 116 39, Prague, Czech Republic. FAU - Malmström, Helena AU - Malmström H AD - Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden. FAU - Piontek, Janusz AU - Piontek J AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden. FAU - Marciniak, Arkadiusz AU - Marciniak A AD - Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614, Poznań, Poland. FAU - Dabert, Miroslawa AU - Dabert M AD - Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland. LA - eng PT - Journal Article DEP - 20170316 PL - England TA - BMC Evol Biol JT - BMC evolutionary biology JID - 100966975 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - Europe MH - Genetics, Medical MH - Genome, Mitochondrial MH - Haplotypes MH - *Human Migration MH - Humans MH - Poland MH - White People/genetics PMC - PMC5356262 OTO - NOTNLM OT - Ancient DNA OT - Danubian Neolithic OT - Mitochondrial DNA OT - Neolithic transition OT - U5 haplogroup EDAT- 2017/03/18 06:00 MHDA- 2017/06/27 06:00 PMCR- 2017/03/16 CRDT- 2017/03/18 06:00 PHST- 2016/11/15 00:00 [received] PHST- 2017/02/23 00:00 [accepted] PHST- 2017/03/18 06:00 [entrez] PHST- 2017/03/18 06:00 [pubmed] PHST- 2017/06/27 06:00 [medline] PHST- 2017/03/16 00:00 [pmc-release] AID - 10.1186/s12862-017-0924-0 [pii] AID - 924 [pii] AID - 10.1186/s12862-017-0924-0 [doi] PST - epublish SO - BMC Evol Biol. 2017 Mar 16;17(1):80. doi: 10.1186/s12862-017-0924-0. PMID- 28266657 OWN - NLM STAT- MEDLINE DCOM- 20181114 LR - 20211204 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 7 DP - 2017 Mar 7 TI - Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians. PG - 43950 LID - 10.1038/srep43950 [doi] LID - 43950 AB - Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians. FAU - Juras, Anna AU - Juras A AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland. FAU - Krzewińska, Maja AU - Krzewińska M AD - Department of Archaeology and Classical Studies, Stockholm University Wallenberglaboratoriet, SE-106 91 Stockholm, Sweden. FAU - Nikitin, Alexey G AU - Nikitin AG AD - Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States of America. FAU - Ehler, Edvard AU - Ehler E AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland. AD - Department of Biology and Environmental Studies, Faculty of Education, Charles University in Prague, Magdalény Rettigové 4, 116 39, Prague, Czech Republic. FAU - Chyleński, Maciej AU - Chyleński M AD - Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614 Poznan, Poland. FAU - Łukasik, Sylwia AU - Łukasik S AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland. FAU - Krenz-Niedbała, Marta AU - Krenz-Niedbała M AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland. FAU - Sinika, Vitaly AU - Sinika V AD - Taras Shevchenko University in Tiraspol, Taras Shevchenko University in Tiraspol, October Street 25, 33-00 Tiraspol, Moldova. FAU - Piontek, Janusz AU - Piontek J AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland. FAU - Ivanova, Svetlana AU - Ivanova S AD - Institute of Archaeology, National Academy of Sciences of Ukraine, Lanzheronivska Street, 65026, Odessa, Ukraine. FAU - Dabert, Miroslawa AU - Dabert M AD - Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland. FAU - Götherström, Anders AU - Götherström A AD - Department of Archaeology and Classical Studies, Stockholm University Wallenberglaboratoriet, SE-106 91 Stockholm, Sweden. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20170307 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Asia MH - Black Sea MH - DNA, Ancient/*chemistry MH - DNA, Mitochondrial/chemistry/*genetics MH - *Ethnicity MH - Europe MH - *Genetic Variation MH - *Genetics, Population MH - Humans MH - Phylogeography MH - *Racial Groups MH - *Sequence Analysis, DNA PMC - PMC5339713 COIS- The authors declare no competing financial interests. EDAT- 2017/03/08 06:00 MHDA- 2018/11/15 06:00 PMCR- 2017/03/07 CRDT- 2017/03/08 06:00 PHST- 2016/10/31 00:00 [received] PHST- 2017/01/31 00:00 [accepted] PHST- 2017/03/08 06:00 [entrez] PHST- 2017/03/08 06:00 [pubmed] PHST- 2018/11/15 06:00 [medline] PHST- 2017/03/07 00:00 [pmc-release] AID - srep43950 [pii] AID - 10.1038/srep43950 [doi] PST - epublish SO - Sci Rep. 2017 Mar 7;7:43950. doi: 10.1038/srep43950. PMID- 28389681 OWN - NLM STAT- MEDLINE DCOM- 20181211 LR - 20200306 IS - 1420-9144 (Electronic) IS - 0036-6978 (Linking) VI - 25 IP - 1 DP - 2017 Mar TI - [aDNA Research From a Historical Perspective]. PG - 99-142 LID - 10.1007/s00048-017-0168-5 [doi] AB - aDNA studies are a cooperative field of research with a broad range of applications including evolutionary biology, genetics, anthropology and archaeology. Scientists are using ancient molecules as source material for historical questions. Colleagues from the humanities are observing this with both interest and concern because aDNA research is affecting academic identities and both concepts of history and historiography. aDNA research developed in a way that can be described as a Hype Cycle (Chackie Fenn). Technological triggers such as Sanger Sequencing and the Polymerase Chain Reaction kicked off a multitude of experiments with ancient DNA during the 1980s and 1990s. Geneticists, microbiologists, anthropologists and many more euphorically joined a "molecule hunt". aDNA was promoted as a time machine. Media attention was enormous. As experiments and implementations began to fail and contamination was discovered to be a tremendous problem, media interest waned and many labs lost their interest. Some turned their disillusionment into systematic research into methodology and painstakingly established lab routines. The authenticity problem was first addressed by control oriented measures but later approached from a more cognitive theoretical perspective as the pitfalls and limits of aDNA became clearer. By the end of the 2000s the field reached its current plateau of productivity. Cross-disciplinary debates, conflicts and collaborations are increasing critical reflection among all participants. Historians should consider joining the field in a kind of critical friendship to both make the most of its possibilities and give an input from a constructivist perspective. FAU - Bösl, Elsbeth AU - Bösl E AD - Professur für Wirtschafts-, Sozial- und Technikgeschichte, Historisches Seminar, Universität der Bundeswehr München, Werner-Heisenberg-Weg 39, 85577, Neubiberg, Deutschland. elsbeth.boesl@unibw.de. LA - ger PT - Journal Article TT - Zur Wissenschaftsgeschichte der aDNA-Forschung. PL - Switzerland TA - NTM JT - NTM JID - 0347631 RN - 0 (DNA, Ancient) MH - *Archaeology MH - DNA, Ancient/*analysis MH - Fossils MH - *Genetics MH - Historiography MH - *History MH - Humans MH - Interdisciplinary Communication MH - Polymerase Chain Reaction MH - *Research MH - Sequence Analysis, DNA OTO - NOTNLM OT - Archaeology OT - Genetics OT - Interdisciplinary research OT - aDNA EDAT- 2017/04/09 06:00 MHDA- 2018/12/12 06:00 CRDT- 2017/04/09 06:00 PHST- 2017/04/09 06:00 [pubmed] PHST- 2018/12/12 06:00 [medline] PHST- 2017/04/09 06:00 [entrez] AID - 10.1007/s00048-017-0168-5 [pii] AID - 10.1007/s00048-017-0168-5 [doi] PST - ppublish SO - NTM. 2017 Mar;25(1):99-142. doi: 10.1007/s00048-017-0168-5. PMID- 27915106 OWN - NLM STAT- MEDLINE DCOM- 20170828 LR - 20181202 IS - 1878-3511 (Electronic) IS - 1201-9712 (Linking) VI - 56 DP - 2017 Mar TI - Insights gained from ancient biomolecules into past and present tuberculosis-a personal perspective. PG - 176-180 LID - S1201-9712(16)31631-9 [pii] LID - 10.1016/j.ijid.2016.11.413 [doi] AB - Ancient and historical tuberculosis (TB) can be recognized by its typical paleopathology in human remains. Using paleomicrobiology, it is possible to detect many more individuals infected with TB but with no visible lesions. Due to advances in molecular analysis over the past two decades, it is clear that TB was widespread in humans from the Neolithic period and has remained so until the present day. Past human populations were associated with different lineages of the Mycobacterium tuberculosis complex, thereby elucidating early human migrations. Using paleomicrobiology, it is possible to detect individuals infected with TB who are also co-infected with other bacteria or parasites. TB is also found in hosts with co-morbidities such as neoplasms, or metabolic disorders such as rickets and scurvy. In well-preserved human skeletal or mummified tissue, whole genome sequencing has detected individuals with multiple infections of different M. tuberculosis strains. Such studies put modern findings into context and emphasize the importance of human population density in such circumstances. CI - Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centre for Clinical Microbiology, Division of Infection and Immunity, Royal Free Campus, University College London, London NW3 2PF, UK. Electronic address: h.donoghue@ucl.ac.uk. LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20161130 PL - Canada TA - Int J Infect Dis JT - International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases JID - 9610933 RN - 0 (DNA, Bacterial) SB - IM MH - Coinfection/genetics/immunology MH - DNA, Bacterial/genetics MH - Evolution, Molecular MH - History, Ancient MH - Humans MH - Morbidity MH - Mycobacterium tuberculosis/*genetics MH - *Paleopathology MH - Tuberculosis/*history/immunology/*microbiology OTO - NOTNLM OT - Ancient DNA (aDNA) OT - Bacterial cell wall lipids OT - Evolution OT - Human migration OT - Mycobacterium tuberculosis OT - Paleomicrobiology EDAT- 2016/12/05 06:00 MHDA- 2017/08/29 06:00 CRDT- 2016/12/05 06:00 PHST- 2016/10/06 00:00 [received] PHST- 2016/11/17 00:00 [revised] PHST- 2016/11/20 00:00 [accepted] PHST- 2016/12/05 06:00 [pubmed] PHST- 2017/08/29 06:00 [medline] PHST- 2016/12/05 06:00 [entrez] AID - S1201-9712(16)31631-9 [pii] AID - 10.1016/j.ijid.2016.11.413 [doi] PST - ppublish SO - Int J Infect Dis. 2017 Mar;56:176-180. doi: 10.1016/j.ijid.2016.11.413. Epub 2016 Nov 30. PMID- 27907810 OWN - NLM STAT- MEDLINE DCOM- 20170614 LR - 20180129 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 27 DP - 2017 Mar TI - Prediction of autosomal STR typing success in ancient and Second World War bone samples. PG - 17-26 LID - S1872-4973(16)30214-9 [pii] LID - 10.1016/j.fsigen.2016.11.004 [doi] AB - Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded. Therefore the new commercial qPCR kits able to assess the degree of degradation are potentially able to predict the success of downstream short tandem repeat (STR) typing. The goal of this study was to verify the quantification step using the PowerQuant kit with regard to its suitability as a screening method for autosomal STR typing success on ancient and Second World War (WWII) skeletal remains. We analysed 60 skeletons excavated from five archaeological sites and four WWII mass graves from Slovenia. The bones were cleaned, surface contamination was removed and the bones ground to a powder. Genomic DNA was obtained from 0.5g of bone powder after total demineralization. The DNA was purified using a Biorobot EZ1 device. Following PowerQuant quantification, DNA samples were subjected to autosomal STR amplification using the NGM kit. Up to 2.51ng DNA/g of powder were extracted. No inhibition was detected in any of bones analysed. 82% of the WWII bones gave full profiles while 73% of the ancient bones gave profiles not suitable for interpretation. Four bone extracts yielded no detectable amplification or zero quantification results and no profiles were obtained from any of them. Full or useful partial profiles were produced only from bone extracts where short autosomal (Auto) and long degradation (Deg) PowerQuant targets were detected. It is concluded that STR typing of old bones after quantification with the PowerQuant should be performed only when both Auto and Deg targets are detected simultaneously with no respect to [Auto]/[Deg] ratio. Prediction of STR typing success could be made according to successful amplification of Deg fragment. The PowerQuant kit is capable of identifying bone DNA samples that will not yield useful STR profiles using the NGM kit, and it can be used as a predictor of autosomal STR typing success of bone extracts obtained from ancient and WWII skeletal remains. CI - Copyright © 2016 Elsevier Ireland Ltd. All rights reserved. FAU - Zupanič Pajnič, Irena AU - Zupanič Pajnič I AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia. Electronic address: irena.zupanic@mf.uni-lj.si. FAU - Zupanc, Tomaž AU - Zupanc T AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia. FAU - Balažic, Jože AU - Balažic J AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia. FAU - Geršak, Živa Miriam AU - Geršak ŽM AD - Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia. FAU - Stojković, Oliver AU - Stojković O AD - Institute for Legal Medicine, Faculty of Medicine, University of Belgrade, Deligradska 31, 11000 Belgrade, Serbia. FAU - Skadrić, Ivan AU - Skadrić I AD - Institute for Legal Medicine, Faculty of Medicine, University of Belgrade, Deligradska 31, 11000 Belgrade, Serbia. FAU - Črešnar, Matija AU - Črešnar M AD - University of Ljubljana, Faculty of Arts, Department of Archaeology, Aškerčeva 2, 1000 Ljubljana, Slovenia; Institute for the Protection of Cultural Heritage, Centre for Preventive Archaeology, Poljanska 40, 1000 Ljubljana, Slovenia. LA - eng PT - Journal Article DEP - 20161119 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Bone and Bones/*chemistry MH - DNA/*genetics MH - DNA Degradation, Necrotic MH - DNA Fingerprinting/*methods MH - *DNA, Ancient MH - Humans MH - Male MH - *Microsatellite Repeats MH - Multiplex Polymerase Chain Reaction MH - Slovenia MH - World War II OTO - NOTNLM OT - Ancient DNA OT - Autosomal STR typing OT - PowerQuant OT - Second World War OT - Skeletal remains OT - qPCR EDAT- 2016/12/03 06:00 MHDA- 2017/06/15 06:00 CRDT- 2016/12/02 06:00 PHST- 2016/06/06 00:00 [received] PHST- 2016/10/08 00:00 [revised] PHST- 2016/11/18 00:00 [accepted] PHST- 2016/12/03 06:00 [pubmed] PHST- 2017/06/15 06:00 [medline] PHST- 2016/12/02 06:00 [entrez] AID - S1872-4973(16)30214-9 [pii] AID - 10.1016/j.fsigen.2016.11.004 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2017 Mar;27:17-26. doi: 10.1016/j.fsigen.2016.11.004. Epub 2016 Nov 19. PMID- 28162894 OWN - NLM STAT- MEDLINE DCOM- 20180713 LR - 20221207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 27 IP - 4 DP - 2017 Feb 20 TI - The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers. PG - 576-582 LID - S0960-9822(16)31542-1 [pii] LID - 10.1016/j.cub.2016.12.060 [doi] AB - The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the Neolithic transition across Europe, we analyzed eight ancient genomes: six samples (four to ∼1- to 4-fold coverage) from a 3,500 year temporal transect (∼8,300-4,800 calibrated years before present) through the Baltic region dating from the Mesolithic to the Late Neolithic and two samples spanning the Mesolithic-Neolithic boundary from the Dnieper Rapids region of Ukraine. We find evidence that some hunter-gatherer ancestry persisted across the Neolithic transition in both regions. However, we also find signals consistent with influxes of non-local people, most likely from northern Eurasia and the Pontic Steppe. During the Late Neolithic, this Steppe-related impact coincides with the proposed emergence of Indo-European languages in the Baltic region [3, 4]. These influences are distinct from the early farmer admixture that transformed the genetic landscape of central Europe, suggesting that changes associated with the Neolithic package in the Baltic were not driven by the same Anatolian-sourced genetic exchange. CI - Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Jones, Eppie R AU - Jones ER AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. Electronic address: erj35@cam.ac.uk. FAU - Zarina, Gunita AU - Zarina G AD - Institute of Latvian History, University of Latvia, Kalpaka Bulvāris 4, Rīga 1050, Latvia. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia. FAU - Lightfoot, Emma AU - Lightfoot E AD - McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK. FAU - Nigst, Philip R AU - Nigst PR AD - Division of Archaeology, Department of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK. FAU - Manica, Andrea AU - Manica A AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. Electronic address: am315@cam.ac.uk. FAU - Pinhasi, Ron AU - Pinhasi R AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. Electronic address: ron.pinhasi@ucd.ie. FAU - Bradley, Daniel G AU - Bradley DG AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. Electronic address: dbradley@tcd.ie. LA - eng GR - 263441/ERC_/European Research Council/International PT - Historical Article PT - Journal Article DEP - 20170202 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Ancient) SB - IM MH - Agriculture/*history MH - Archaeology MH - *Cultural Evolution MH - DNA, Ancient/analysis MH - *Farmers MH - Genome, Human/*genetics MH - History, Ancient MH - Human Migration MH - Humans MH - Latvia MH - Ukraine MH - White People/genetics PMC - PMC5321670 OTO - NOTNLM OT - Baltic OT - Neolithic transition OT - Ukraine OT - ancient DNA OT - genomics OT - population genetics EDAT- 2017/02/07 06:00 MHDA- 2018/07/14 06:00 PMCR- 2017/02/20 CRDT- 2017/02/07 06:00 PHST- 2016/10/30 00:00 [received] PHST- 2016/11/10 00:00 [revised] PHST- 2016/12/29 00:00 [accepted] PHST- 2017/02/07 06:00 [pubmed] PHST- 2018/07/14 06:00 [medline] PHST- 2017/02/07 06:00 [entrez] PHST- 2017/02/20 00:00 [pmc-release] AID - S0960-9822(16)31542-1 [pii] AID - 10.1016/j.cub.2016.12.060 [doi] PST - ppublish SO - Curr Biol. 2017 Feb 20;27(4):576-582. doi: 10.1016/j.cub.2016.12.060. Epub 2017 Feb 2. PMID- 27794556 OWN - NLM STAT- MEDLINE DCOM- 20171018 LR - 20200306 IS - 1367-4811 (Electronic) IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 33 IP - 4 DP - 2017 Feb 15 TI - gargammel: a sequence simulator for ancient DNA. PG - 577-579 LID - 10.1093/bioinformatics/btw670 [doi] AB - SUMMARY: Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico , we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets. AVAILABILITY AND IMPLEMENTATION: The package is publicly available on github: https://grenaud.github.io/gargammel/ and released under the GPL. CONTACT: gabriel.renaud@snm.ku.dk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CI - © The Author 2016. Published by Oxford University Press. FAU - Renaud, Gabriel AU - Renaud G AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark. FAU - Hanghøj, Kristian AU - Hanghøj K AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark. AD - Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, Toulouse, France. FAU - Willerslev, Eske AU - Willerslev E AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark. AD - Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK. AD - Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. FAU - Orlando, Ludovic AU - Orlando L AD - Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark. AD - Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, Toulouse, France. LA - eng PT - Journal Article PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *Computer Simulation MH - DNA Contamination MH - *DNA Damage MH - DNA, Ancient/*chemistry MH - Humans MH - *Postmortem Changes MH - Sequence Analysis, DNA/methods MH - *Software PMC - PMC5408798 EDAT- 2016/11/01 06:00 MHDA- 2017/10/19 06:00 PMCR- 2016/11/21 CRDT- 2016/11/01 06:00 PHST- 2016/08/19 00:00 [received] PHST- 2016/10/20 00:00 [accepted] PHST- 2016/11/01 06:00 [pubmed] PHST- 2017/10/19 06:00 [medline] PHST- 2016/11/01 06:00 [entrez] PHST- 2016/11/21 00:00 [pmc-release] AID - btw670 [pii] AID - 10.1093/bioinformatics/btw670 [doi] PST - ppublish SO - Bioinformatics. 2017 Feb 15;33(4):577-579. doi: 10.1093/bioinformatics/btw670. PMID- 27994125 OWN - NLM STAT- MEDLINE DCOM- 20171130 LR - 20190129 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 372 IP - 1713 DP - 2017 Feb 5 TI - Human evolution: a tale from ancient genomes. LID - 20150484 AB - The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. CI - © 2016 The Author(s). FAU - Llamas, Bastien AU - Llamas B AUID- ORCID: 0000-0002-5550-9176 AD - Australian Centre for ADNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Willerslev, Eske AU - Willerslev E AUID- ORCID: 0000-0002-7081-6748 AD - Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark. AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. AD - Wellcome Genome Campus Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK. FAU - Orlando, Ludovic AU - Orlando L AUID- ORCID: 0000-0003-3936-1850 AD - Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark lorlando@snm.ku.dk. AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, CNRS UMR 5288, 31000 Toulouse, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA, Ancient/*analysis MH - *Evolution, Molecular MH - *Genome, Human MH - Hominidae/*genetics MH - Humans PMC - PMC5182416 OTO - NOTNLM OT - Archaic hominins OT - ancient DNA OT - anthropology OT - human evolution EDAT- 2016/12/21 06:00 MHDA- 2017/12/01 06:00 PMCR- 2018/02/05 CRDT- 2016/12/21 06:00 PHST- 2016/09/05 00:00 [accepted] PHST- 2016/12/21 06:00 [entrez] PHST- 2016/12/21 06:00 [pubmed] PHST- 2017/12/01 06:00 [medline] PHST- 2018/02/05 00:00 [pmc-release] AID - rstb.2015.0484 [pii] AID - rstb20150484 [pii] AID - 10.1098/rstb.2015.0484 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2017 Feb 5;372(1713):20150484. doi: 10.1098/rstb.2015.0484. PMID- 28029148 OWN - NLM STAT- MEDLINE DCOM- 20170807 LR - 20221207 IS - 1476-5438 (Electronic) IS - 1018-4813 (Print) IS - 1018-4813 (Linking) VI - 25 IP - 3 DP - 2017 Feb TI - Investigating mitochondrial DNA relationships in Neolithic Western Europe through serial coalescent simulations. PG - 388-392 LID - 10.1038/ejhg.2016.180 [doi] AB - Recent ancient DNA studies on European Neolithic human populations have provided persuasive evidence of a major migration of farmers originating from the Aegean, accompanied by sporadic hunter-gatherer admixture into early Neolithic populations, but increasing toward the Late Neolithic. In this context, ancient mitochondrial DNA data collected from the Neolithic necropolis of Gurgy (Paris Basin, France), the largest mitochondrial DNA sample obtained from a single archeological site for the Early/Middle Neolithic period, indicate little differentiation from farmers associated to both the Danubian and Mediterranean Neolithic migration routes, as well as from Western European hunter-gatherers. To test whether this pattern of differentiation could arise in a single unstructured population by genetic drift alone, we used serial coalescent simulations. We explore female effective population size parameter combinations at the time of the colonization of Europe 45000 years ago and the most recent of the Neolithic samples analyzed in this study 5900 years ago, and identify conditions under which population panmixia between hunter-gatherers/Early-Middle Neolithic farmers and Gurgy cannot be rejected. In relation to other studies on the current debate of the origins of Europeans, these results suggest increasing hunter-gatherer admixture into farmers' group migrating farther west in Europe. FAU - Rivollat, Maïté AU - Rivollat M AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Bordeaux, France. FAU - Rottier, Stéphane AU - Rottier S AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Bordeaux, France. FAU - Couture, Christine AU - Couture C AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Bordeaux, France. FAU - Pemonge, Marie-Hélène AU - Pemonge MH AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Bordeaux, France. FAU - Mendisco, Fanny AU - Mendisco F AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Bordeaux, France. FAU - Thomas, Mark G AU - Thomas MG AD - UCL Research Department of Genetics, Evolution and Environment, London, UK. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie-UMR 5199, CNRS, Université de Bordeaux, Bordeaux, France. FAU - Gerbault, Pascale AU - Gerbault P AD - UCL Research Department of Genetics, Evolution and Environment, London, UK. AD - UCL Department of Anthropology, London, UK. AD - Department of Life Sciences, University of Westminster, London, UK. LA - eng PT - Journal Article DEP - 20161228 PL - England TA - Eur J Hum Genet JT - European journal of human genetics : EJHG JID - 9302235 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - Europe MH - *Evolution, Molecular MH - Female MH - Genetic Drift MH - Human Migration MH - Humans MH - Male MH - *Models, Genetic MH - Pedigree MH - White People/genetics PMC - PMC5315516 COIS- The authors declare no conflict of interest. EDAT- 2016/12/29 06:00 MHDA- 2017/08/08 06:00 PMCR- 2018/03/01 CRDT- 2016/12/29 06:00 PHST- 2016/01/28 00:00 [received] PHST- 2016/11/18 00:00 [revised] PHST- 2016/11/24 00:00 [accepted] PHST- 2016/12/29 06:00 [pubmed] PHST- 2017/08/08 06:00 [medline] PHST- 2016/12/29 06:00 [entrez] PHST- 2018/03/01 00:00 [pmc-release] AID - ejhg2016180 [pii] AID - 10.1038/ejhg.2016.180 [doi] PST - ppublish SO - Eur J Hum Genet. 2017 Feb;25(3):388-392. doi: 10.1038/ejhg.2016.180. Epub 2016 Dec 28. PMID- 27803981 OWN - NLM STAT- MEDLINE DCOM- 20170208 LR - 20221207 IS - 1617-4623 (Electronic) IS - 1617-4623 (Linking) VI - 292 IP - 1 DP - 2017 Feb TI - Genetic structure of the early Hungarian conquerors inferred from mtDNA haplotypes and Y-chromosome haplogroups in a small cemetery. PG - 201-214 LID - 10.1007/s00438-016-1267-z [doi] AB - We applied ancient DNA methods to shed light on the origin of ancient Hungarians and their relation to modern populations. Hungarians moved into the Carpathian Basin from the Eurasian Pontic steppes in the year 895 AD as a confederation of seven tribes, but their further origin remains obscure. Here, we present 17 mtDNA haplotypes and four Y-chromosome haplogroups, which portray the genetic composition of an entire small cemetery of the first generation Hungarians. Using novel algorithms to compare these mitochondrial DNA haplogroups with other ancient and modern Eurasian data, we revealed that a significant portion of the Hungarians probably originated from a long ago consolidated gene pool in Central Asia-South Siberia, which still persists in modern Hungarians. Another genetic layer of the early Hungarians was obtained during their westward migrations by admixing with various populations of European origin, and an important component of these was derived from the Caucasus region. Most of the modern populations, which are genetically closest relatives of ancient Hungarians, today speak non-Indo-European languages. Our results contribute to our understanding of the peopling of Europe by providing ancient DNA data from a still genetically poorly studied period of medieval human migrations. FAU - Neparáczki, Endre AU - Neparáczki E AD - Department of Genetics, University of Szeged, Szeged, Hungary. FAU - Juhász, Zoltán AU - Juhász Z AD - Hungarian Academy of Sciences, Centre for Energy Research, Budapest, Hungary. FAU - Pamjav, Horolma AU - Pamjav H AD - DNA Laboratory, Network of Forensic Science Institutes, Ministry of Justice, Budapest, Hungary. FAU - Fehér, Tibor AU - Fehér T AD - DNA Laboratory, Network of Forensic Science Institutes, Ministry of Justice, Budapest, Hungary. FAU - Csányi, Bernadett AU - Csányi B AD - Department of Forensic Medicine, University of Szeged, Szeged, Hungary. FAU - Zink, Albert AU - Zink A AD - Institute for Mummies and the Iceman EURAC, Bolzano, Italy. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummies and the Iceman EURAC, Bolzano, Italy. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Molnár, Erika AU - Molnár E AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Pap, Ildikó AU - Pap I AD - Department of Anthropology, Hungarian Natural History Museum Budapest, Budapest, Hungary. FAU - Kustár, Ágnes AU - Kustár Á AD - Department of Anthropology, Hungarian Natural History Museum Budapest, Budapest, Hungary. FAU - Révész, László AU - Révész L AD - Department of Archaeology, University of Szeged, Szeged, Hungary. FAU - Raskó, István AU - Raskó I AD - Institute of Genetics, Biological Research Centre, Szeged, Hungary. FAU - Török, Tibor AU - Török T AUID- ORCID: 0000-0002-2128-1126 AD - Department of Genetics, University of Szeged, Szeged, Hungary. torokt@bio.u-szeged.hu. LA - eng PT - Journal Article DEP - 20161101 PL - Germany TA - Mol Genet Genomics JT - Molecular genetics and genomics : MGG JID - 101093320 RN - 0 (DNA, Mitochondrial) SB - IM MH - Algorithms MH - Archaeology MH - Cemeteries MH - Chromosomes, Human, Y/*genetics MH - DNA, Mitochondrial/*genetics MH - Female MH - Genetics, Medical/methods MH - Genetics, Population MH - Genome, Human MH - *Haplotypes MH - Human Migration MH - Humans MH - Hungary MH - Male MH - Phylogeny MH - White People/*genetics OTO - NOTNLM OT - Ancient DNA OT - Early Hungarian OT - Iterative rank correlation OT - MDS mapping OT - Self-organizing cloud algorithm EDAT- 2016/11/03 06:00 MHDA- 2017/02/09 06:00 CRDT- 2016/11/03 06:00 PHST- 2016/07/15 00:00 [received] PHST- 2016/10/25 00:00 [accepted] PHST- 2016/11/03 06:00 [pubmed] PHST- 2017/02/09 06:00 [medline] PHST- 2016/11/03 06:00 [entrez] AID - 10.1007/s00438-016-1267-z [pii] AID - 10.1007/s00438-016-1267-z [doi] PST - ppublish SO - Mol Genet Genomics. 2017 Feb;292(1):201-214. doi: 10.1007/s00438-016-1267-z. Epub 2016 Nov 1. PMID- 27756828 OWN - NLM STAT- MEDLINE DCOM- 20170608 LR - 20250110 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 34 IP - 2 DP - 2017 Feb 1 TI - Signatures of Archaic Adaptive Introgression in Present-Day Human Populations. PG - 296-317 LID - 10.1093/molbev/msw216 [doi] AB - Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process-adaptive introgression-may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions. CI - © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Racimo, Fernando AU - Racimo F AD - Department of Integrative Biology, University of California Berkeley, Berkeley, CA. FAU - Marnetto, Davide AU - Marnetto D AD - Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy. FAU - Huerta-Sánchez, Emilia AU - Huerta-Sánchez E AD - School of Natural Sciences, University of California Merced, Merced, CA. LA - eng GR - R01 HG003229/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) SB - IM MH - Adaptation, Biological/*genetics MH - Alleles MH - Animals MH - Biological Evolution MH - Computer Simulation MH - DNA, Ancient/*analysis MH - Databases, Nucleic Acid MH - Evolution, Molecular MH - Gene Frequency MH - Genetics, Population MH - Haplotypes MH - Humans MH - Neanderthals MH - Phylogeny MH - Selection, Genetic MH - Sequence Analysis, DNA/*methods PMC - PMC5400396 OTO - NOTNLM OT - adaptive introgression OT - ancient DNA OT - denisova OT - neanderthal EDAT- 2016/10/21 06:00 MHDA- 2017/06/09 06:00 PMCR- 2016/08/18 CRDT- 2016/10/21 06:00 PHST- 2016/10/21 06:00 [pubmed] PHST- 2017/06/09 06:00 [medline] PHST- 2016/10/21 06:00 [entrez] PHST- 2016/08/18 00:00 [pmc-release] AID - msw216 [pii] AID - 10.1093/molbev/msw216 [doi] PST - ppublish SO - Mol Biol Evol. 2017 Feb 1;34(2):296-317. doi: 10.1093/molbev/msw216. PMID- 27432000 OWN - NLM STAT- MEDLINE DCOM- 20171213 LR - 20181202 IS - 1531-5320 (Electronic) IS - 1069-9384 (Print) IS - 1069-9384 (Linking) VI - 24 IP - 1 DP - 2017 Feb TI - Evolution of language: Lessons from the genome. PG - 34-40 LID - 10.3758/s13423-016-1112-8 [doi] AB - The post-genomic era is an exciting time for researchers interested in the biology of speech and language. Substantive advances in molecular methodologies have opened up entire vistas of investigation that were not previously possible, or in some cases even imagined. Speculations concerning the origins of human cognitive traits are being transformed into empirically addressable questions, generating specific hypotheses that can be explicitly tested using data collected from both the natural world and experimental settings. In this article, I discuss a number of promising lines of research in this area. For example, the field has begun to identify genes implicated in speech and language skills, including not just disorders but also the normal range of abilities. Such genes provide powerful entry points for gaining insights into neural bases and evolutionary origins, using sophisticated experimental tools from molecular neuroscience and developmental neurobiology. At the same time, sequencing of ancient hominin genomes is giving us an unprecedented view of the molecular genetic changes that have occurred during the evolution of our species. Synthesis of data from these complementary sources offers an opportunity to robustly evaluate alternative accounts of language evolution. Of course, this endeavour remains challenging on many fronts, as I also highlight in the article. Nonetheless, such an integrated approach holds great potential for untangling the complexities of the capacities that make us human. FAU - Fisher, Simon E AU - Fisher SE AD - Language and Genetics Department, Max Planck Institute for Psycholinguistics, Wundtlaan 1, 6525 XD, Nijmegen, The Netherlands. simon.fisher@mpi.nl. AD - Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 EN, Nijmegen, The Netherlands. simon.fisher@mpi.nl. LA - eng PT - Journal Article PL - United States TA - Psychon Bull Rev JT - Psychonomic bulletin & review JID - 9502924 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Biological Evolution MH - *DNA, Ancient MH - Evolution, Molecular MH - *Genome MH - Hominidae/*genetics MH - Humans MH - *Language MH - Neural Pathways MH - *Speech PMC - PMC5325862 OTO - NOTNLM OT - Ancient DNA OT - Evolution OT - Genetics and genomics OT - Model systems OT - Speech and language EDAT- 2016/07/20 06:00 MHDA- 2017/12/14 06:00 PMCR- 2016/07/18 CRDT- 2016/07/20 06:00 PHST- 2016/07/20 06:00 [pubmed] PHST- 2017/12/14 06:00 [medline] PHST- 2016/07/20 06:00 [entrez] PHST- 2016/07/18 00:00 [pmc-release] AID - 10.3758/s13423-016-1112-8 [pii] AID - 1112 [pii] AID - 10.3758/s13423-016-1112-8 [doi] PST - ppublish SO - Psychon Bull Rev. 2017 Feb;24(1):34-40. doi: 10.3758/s13423-016-1112-8. PMID- 26856190 OWN - NLM STAT- MEDLINE DCOM- 20170116 LR - 20170116 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 44 IP - 1 DP - 2017 Feb TI - Analysis of medieval mtDNA from Napole cemetery provides new insights into the early history of Polish state. PG - 91-94 LID - 10.3109/03014460.2016.1151550 [doi] AB - Contemporary historical anthropology and classical archaeology are concerned not only with such fundamental issues as the origins of ancient human populations and migration routes, but also with the formation and development of inter-population relations and the mixing of gene pools as a result of inter-breeding between individuals representing different cultural units. The contribution of immigrants to the analysed autochthonous population and their effect on the gene pool of that population has proven difficult to evaluate with classical morphological methods. The burial of one individual in the studied Napole cemetery located in central Poland had the form of a chamber grave, which is typical of Scandinavian culture from that period. However, this fact cannot be interpreted as absolute proof that the individual (in the biological sense) was allochtonous. This gives rise to the question as to who was actually buried in that cemetery. The ancient DNA results indicate that one of the individuals had an mtDNA haplotype typical of Iron Age northern Europe, which suggests that he could have arrived from that area at a later period. This seems to indirectly confirm the claims of many anthropologists that the development of the early medieval Polish state was significantly and directly influenced by the Scandinavians. FAU - Płoszaj, Tomasz AU - Płoszaj T AD - a Department of Molecular Biology , Medical University of Łódź , Łódź , Poland. FAU - Jędrychowska-Dańska, Krystyna AU - Jędrychowska-Dańska K AD - a Department of Molecular Biology , Medical University of Łódź , Łódź , Poland. FAU - Masłowska, Alicja AU - Masłowska A AD - a Department of Molecular Biology , Medical University of Łódź , Łódź , Poland. FAU - Kozłowski, Tomasz AU - Kozłowski T AD - b Department of Anthropology , Nicolaus Copernicus University , Toruń , Poland. FAU - Chudziak, Wojciech AU - Chudziak W AD - c Institute of Archaeology, Nicolaus Copernicus University , Toruń , Poland. FAU - Bojarski, Jacek AU - Bojarski J AD - c Institute of Archaeology, Nicolaus Copernicus University , Toruń , Poland. FAU - Robaszkiewicz, Agnieszka AU - Robaszkiewicz A AD - d Department of Environmental Pollution Biophysics , University of Łódź , Łódź , Poland. FAU - Witas, Henryk W AU - Witas HW AD - a Department of Molecular Biology , Medical University of Łódź , Łódź , Poland. LA - eng PT - Historical Article PT - Journal Article DEP - 20160311 PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Cemeteries/*history MH - DNA, Mitochondrial/*genetics MH - History, Medieval MH - Humans MH - Male MH - Poland OTO - NOTNLM OT - Haplogroup OT - ancient DNA OT - chamber grave EDAT- 2016/02/10 06:00 MHDA- 2017/01/17 06:00 CRDT- 2016/02/10 06:00 PHST- 2016/02/10 06:00 [pubmed] PHST- 2017/01/17 06:00 [medline] PHST- 2016/02/10 06:00 [entrez] AID - 10.3109/03014460.2016.1151550 [doi] PST - ppublish SO - Ann Hum Biol. 2017 Feb;44(1):91-94. doi: 10.3109/03014460.2016.1151550. Epub 2016 Mar 11. PMID- 28129388 OWN - NLM STAT- MEDLINE DCOM- 20170808 LR - 20181113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 12 IP - 1 DP - 2017 TI - Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum. PG - e0170940 LID - 10.1371/journal.pone.0170940 [doi] LID - e0170940 AB - Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively) than parietal skull bone (average of 2.2%). Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001). This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (<10% endogenous DNA). In the remaining skeletons there is no systematic difference between the two substrates. A crude preservation (good/bad) applied to each sample prior to DNA-extraction predicted the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, we observe signficantly higher levels of cytosine to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons of sampling the different elements. FAU - Hansen, Henrik B AU - Hansen HB AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. FAU - Damgaard, Peter B AU - Damgaard PB AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. FAU - Margaryan, Ashot AU - Margaryan A AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. FAU - Stenderup, Jesper AU - Stenderup J AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. FAU - Lynnerup, Niels AU - Lynnerup N AD - Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. AD - Department of Zoology, University of Cambridge, Cambridge, United Kingdom. AD - Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom. FAU - Allentoft, Morten E AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. LA - eng PT - Journal Article DEP - 20170127 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Ancient/*chemistry/isolation & purification MH - DNA, Mitochondrial/*chemistry/genetics MH - Dental Cementum/*chemistry MH - Humans MH - Petrous Bone/*chemistry MH - Tooth/chemistry PMC - PMC5271384 COIS- The authors have declared that no competing interests exist. EDAT- 2017/01/28 06:00 MHDA- 2017/08/09 06:00 PMCR- 2017/01/27 CRDT- 2017/01/28 06:00 PHST- 2016/10/20 00:00 [received] PHST- 2017/01/12 00:00 [accepted] PHST- 2017/01/28 06:00 [entrez] PHST- 2017/01/28 06:00 [pubmed] PHST- 2017/08/09 06:00 [medline] PHST- 2017/01/27 00:00 [pmc-release] AID - PONE-D-16-41933 [pii] AID - 10.1371/journal.pone.0170940 [doi] PST - epublish SO - PLoS One. 2017 Jan 27;12(1):e0170940. doi: 10.1371/journal.pone.0170940. eCollection 2017. PMID- 28072390 OWN - NLM STAT- MEDLINE DCOM- 20180207 LR - 20190109 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 6 DP - 2017 Jan 10 TI - A molecular portrait of maternal sepsis from Byzantine Troy. LID - e20983 [pii] LID - 10.7554/eLife.20983 [doi] AB - Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman's remains. Scanning electron microscopy of the tissue revealed 'ghost cells', resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed that G. vaginalis Troy fell within contemporary genetic diversity, whereas S. saprophyticus Troy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology of S. saprophyticus infection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. These results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections. FAU - Devault, Alison M AU - Devault AM AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada. AD - MYcroarray, Ann Arbor, United States. FAU - Mortimer, Tatum D AU - Mortimer TD AUID- ORCID: 0000-0001-6255-690X AD - Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States. AD - Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, United States. FAU - Kitchen, Andrew AU - Kitchen A AD - Department of Anthropology, University of Iowa, Iowa City, United States. FAU - Kiesewetter, Henrike AU - Kiesewetter H AD - Project Troia, Institute of Prehistory, Early History, and Medieval Archaeology, Tübingen University, Tübingen, Germany. FAU - Enk, Jacob M AU - Enk JM AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada. AD - MYcroarray, Ann Arbor, United States. FAU - Golding, G Brian AU - Golding GB AD - Department of Biology, McMaster University, Hamilton, Canada. FAU - Southon, John AU - Southon J AD - Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, United States. FAU - Kuch, Melanie AU - Kuch M AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada. FAU - Duggan, Ana T AU - Duggan AT AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada. FAU - Aylward, William AU - Aylward W AD - Molecular Archaeology Laboratory, Biotechnology Center, University of Wisconsin-Madison, Madison, United States. AD - Department of Classics and Ancient Near Eastern Studies, University of Wisconsin-Madison, Madison, United States. FAU - Gardner, Shea N AU - Gardner SN AD - Lawrence Livermore National Laboratory, Livermore, United States. FAU - Allen, Jonathan E AU - Allen JE AD - Lawrence Livermore National Laboratory, Livermore, United States. FAU - King, Andrew M AU - King AM AD - Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. FAU - Wright, Gerard AU - Wright G AD - Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. FAU - Kuroda, Makoto AU - Kuroda M AD - Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan. FAU - Kato, Kengo AU - Kato K AD - Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan. FAU - Briggs, Derek Eg AU - Briggs DE AD - Department of Geology and Geophysics, Yale University, New Haven, United States. FAU - Fornaciari, Gino AU - Fornaciari G AD - Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy. FAU - Holmes, Edward C AU - Holmes EC AUID- ORCID: 0000-0001-9596-3552 AD - Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia. FAU - Poinar, Hendrik N AU - Poinar HN AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada. AD - Department of Biology, McMaster University, Hamilton, Canada. AD - Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. AD - Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada. FAU - Pepperell, Caitlin S AU - Pepperell CS AUID- ORCID: 0000-0002-6324-1333 AD - Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States. AD - Molecular Archaeology Laboratory, Biotechnology Center, University of Wisconsin-Madison, Madison, United States. AD - Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States. LA - eng GR - R01 AI113287/AI/NIAID NIH HHS/United States GR - T32 GM007215/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20170110 PL - England TA - Elife JT - eLife JID - 101579614 RN - 0 (DNA, Bacterial) SB - IM MH - Abscess/microbiology/*pathology MH - DNA, Bacterial/genetics/isolation & purification MH - Female MH - *Fossils MH - Gardnerella vaginalis/classification/genetics MH - Gram-Positive Bacterial Infections/microbiology/*pathology MH - Humans MH - Microscopy, Electron, Scanning MH - Pregnancy MH - Pregnancy Complications, Infectious/*pathology MH - Staphylococcus saprophyticus/classification/genetics PMC - PMC5224923 OTO - NOTNLM OT - Ancient DNA OT - Gardnerella vaginalis OT - Staphylococcus saprophyticus OT - chorioamnionitis OT - evolution OT - evolutionary biology OT - genomics OT - human OT - infectious disease OT - microbiology COIS- The authors declare that no competing interests exist. EDAT- 2017/01/11 06:00 MHDA- 2018/02/08 06:00 PMCR- 2017/01/11 CRDT- 2017/01/11 06:00 PHST- 2016/08/25 00:00 [received] PHST- 2016/11/24 00:00 [accepted] PHST- 2017/01/11 06:00 [entrez] PHST- 2017/01/11 06:00 [pubmed] PHST- 2018/02/08 06:00 [medline] PHST- 2017/01/11 00:00 [pmc-release] AID - e20983 [pii] AID - 20983 [pii] AID - 10.7554/eLife.20983 [doi] PST - epublish SO - Elife. 2017 Jan 10;6:e20983. doi: 10.7554/eLife.20983. PMID- 29285971 OWN - NLM STAT- MEDLINE DCOM- 20181109 LR - 20191113 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 89 IP - 1 DP - 2017 Jan TI - Leveraging Multiple Populations across Time Helps Define Accurate Models of Human Evolution: A Reanalysis of the Lactase Persistence Adaptation. PG - 81-97 AB - Access to a geographically diverse set of modern human samples from the present time and from ancient remains, combined with archaic hominin samples, provides an unprecedented level of resolution to study both human history and adaptation. The amount and quality of ancient human data continue to improve and enable tracking the trajectory of genetic variation over time. These data have the potential to help us redefine or generate new hypotheses of how human evolution occurred and to revise previous conjectures. In this article, we argue that leveraging all these data will help us better detail adaptive histories in humans. As a case in point, we focus on one of the most celebrated examples of human adaptation: the evolution of lactase persistence. We briefly review this dietary adaptation and argue that, effectively, the evolutionary history of lactase persistence is still not fully resolved. We propose that, by leveraging data from multiple populations across time and space, we will find evidence of a more nuanced history than just a simple selective sweep. We support our hypotheses with simulation results and make some cautionary notes regarding the use of haplotype-based summary statistics to estimate evolutionary parameters. FAU - Antelope, Chenling Xu AU - Antelope CX AD - 1 Computational Biology, University of California, Berkeley, Berkeley, California, USA. FAU - Marnetto, Davide AU - Marnetto D AD - 2 Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy. FAU - Casey, Fergal AU - Casey F AD - 3 School of Natural Sciences, University of California, Merced, Merced, California, USA. FAU - Huerta-Sanchez, Emilia AU - Huerta-Sanchez E AD - 3 School of Natural Sciences, University of California, Merced, Merced, California, USA. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA Primers) RN - EC 3.2.1.108 (Lactase) SB - IM MH - Adaptation, Physiological/*genetics MH - Animals MH - DNA Primers MH - Diet MH - *Evolution, Molecular MH - Gene Frequency/*genetics MH - Genetic Drift MH - Genetics, Population MH - Haplotypes/genetics MH - History, Ancient MH - *Hominidae MH - Humans MH - Lactase/*genetics/metabolism MH - Lactose Tolerance Test MH - Microsatellite Repeats/*genetics MH - Milk MH - Selection, Genetic OTO - NOTNLM OT - adaptation OT - ancient dna OT - positive selection EDAT- 2017/12/30 06:00 MHDA- 2018/11/10 06:00 CRDT- 2017/12/30 06:00 PHST- 2017/12/30 06:00 [entrez] PHST- 2017/12/30 06:00 [pubmed] PHST- 2018/11/10 06:00 [medline] AID - 10.13110/humanbiology.89.1.05 [pii] AID - 10.13110/humanbiology.89.1.05 [doi] PST - ppublish SO - Hum Biol. 2017 Jan;89(1):81-97. doi: 10.13110/humanbiology.89.1.05. PMID- 29285967 OWN - NLM STAT- MEDLINE DCOM- 20181109 LR - 20191113 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 89 IP - 1 DP - 2017 Jan TI - The Genomic Health of Ancient Hominins. PG - 7-19 AB - The genomes of ancient humans, Neandertals, and Denisovans contain many alleles that influence disease risks. Using genotypes at 3,180 disease-associated loci, we estimated the disease burden of 147 ancient genomes. After correcting for missing data, genetic risk scores (GRS) were generated for nine disease categories and the set of all combined diseases. We used these genetic risk scores to examine the effects of different types of subsistence, geography, and sample age on the number of risk alleles in each ancient genome. On a broad scale, hereditary disease risks are similar for ancient hominins and modern-day humans, and the GRS percentiles of ancient individuals span the full range of what is observed in present-day individuals. In addition, there is evidence that ancient pastoralists may have had healthier genomes than hunter-gatherers and agriculturalists. We also observed a temporal trend whereby genomes from the recent past are more likely to be healthier than genomes from the deep past. This calls into question the idea that modern lifestyles have caused genetic load to increase over time. Focusing on individual genomes, we found that the overall genomic health of the Altai Neandertal is worse than 97% of present-day humans and that Ötzi, the Tyrolean Iceman, had a genetic predisposition for gastrointestinal and cardiovascular diseases. As demonstrated by this work, ancient genomes afford us new opportunities to diagnose past human health, which has previously been limited by the quality and completeness of remains. FAU - Berens, Ali J AU - Berens AJ AD - 1 School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA. FAU - Cooper, Taylor L AU - Cooper TL AD - 1 School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA. FAU - Lachance, Joseph AU - Lachance J AD - 1 School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - DNA Primers MH - DNA, Mitochondrial/classification/genetics MH - Evolution, Molecular MH - Gene Library MH - Genetic Association Studies MH - Genetic Predisposition to Disease/classification/*genetics/history MH - Genetic Variation/*genetics MH - Genomics MH - Geography/classification/history MH - History, Ancient MH - Hominidae/*genetics MH - Humans MH - Neanderthals/genetics MH - Phylogeny OTO - NOTNLM OT - ancient dna OT - genetic disease risks OT - human evolution OT - population genetics OT - predictive health EDAT- 2017/12/30 06:00 MHDA- 2018/11/10 06:00 CRDT- 2017/12/30 06:00 PHST- 2017/12/30 06:00 [entrez] PHST- 2017/12/30 06:00 [pubmed] PHST- 2018/11/10 06:00 [medline] AID - 10.13110/humanbiology.89.1.01 [pii] AID - 10.13110/humanbiology.89.1.01 [doi] PST - ppublish SO - Hum Biol. 2017 Jan;89(1):7-19. doi: 10.13110/humanbiology.89.1.01. PMID- 27847329 OWN - NLM STAT- MEDLINE DCOM- 20171002 LR - 20171219 IS - 1567-7257 (Electronic) IS - 1567-1348 (Linking) VI - 47 DP - 2017 Jan TI - The genetic profile of susceptibility to infectious diseases in Roman-Period populations from Central Poland. PG - 1-8 LID - S1567-1348(16)30485-3 [pii] LID - 10.1016/j.meegid.2016.11.011 [doi] AB - For thousands of years human beings have resisted life-threatening pathogens. This ongoing battle is considered to be the major force shaping our gene pool as every micro-evolutionary process provokes specific shifts in the genome, both that of the host and the pathogen. Past populations were more susceptible to changes in allele frequencies not only due to selection pressure, but also as a result of genetic drift, migration and inbreeding. In the present study we have investigated the frequency of five polymorphisms within innate immune-response genes (SLC11A1 D543N, MBL2 G161A, P2RX7 A1513C, IL10 A-1082G, TLR2 -196 to -174 ins/del) related to susceptibility to infections in humans. The DNA of individuals from two early Roman-Period populations of Linowo and Rogowo was analysed. The distribution of three mutations varied significantly when compared to the modern Polish population. The TAFT analysis suggests that the decreased frequency of SLC11A1 D543N in modern Poles as compared to 2nd century Linowo samples is the result of non-stochastic mechanisms, such as purifying or balancing selection. The disparity in frequency of other mutations is most likely the result of genetic drift, an evolutionary force which is remarkably amplified in low-size groups. Together with the F(ST) analysis, mtDNA haplotypes' distribution and deviation from the Hardy-Weinberg equilibrium, we suggest that the two populations were not interbreeding (despite the close proximity between them), but rather inbreeding, the results of which are particularly pronounced among Rogowo habitants. CI - Copyright © 2016 Elsevier B.V. All rights reserved. FAU - Lewandowska, Magda AU - Lewandowska M AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Lodz, 90-136, Poland. Electronic address: magda.lewandowska@stud.umed.lodz.pl. FAU - Jędrychowska-Dańska, Krystyna AU - Jędrychowska-Dańska K AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Lodz, 90-136, Poland. FAU - Zamerska, Alicja AU - Zamerska A AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Lodz, 90-136, Poland. FAU - Płoszaj, Tomasz AU - Płoszaj T AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Lodz, 90-136, Poland. FAU - Witas, Henryk W AU - Witas HW AD - Department of Molecular Biology, Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Lodz, Lodz, 90-136, Poland. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20161112 PL - Netherlands TA - Infect Genet Evol JT - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JID - 101084138 RN - 0 (Cation Transport Proteins) RN - 0 (DNA, Ancient) RN - 0 (natural resistance-associated macrophage protein 1) SB - IM MH - Cation Transport Proteins/genetics MH - Communicable Diseases/*genetics MH - DNA, Ancient/*analysis MH - Genetic Drift MH - Genetic Predisposition to Disease/*genetics MH - History, Ancient MH - Humans MH - Immunity, Innate/genetics MH - Poland MH - Polymorphism, Single Nucleotide/genetics MH - Roman World OTO - NOTNLM OT - Ancient DNA OT - Genetic drift OT - Innate immune response OT - Natural selection EDAT- 2016/11/17 06:00 MHDA- 2017/10/03 06:00 CRDT- 2016/11/17 06:00 PHST- 2016/08/04 00:00 [received] PHST- 2016/10/13 00:00 [revised] PHST- 2016/11/11 00:00 [accepted] PHST- 2016/11/17 06:00 [pubmed] PHST- 2017/10/03 06:00 [medline] PHST- 2016/11/17 06:00 [entrez] AID - S1567-1348(16)30485-3 [pii] AID - 10.1016/j.meegid.2016.11.011 [doi] PST - ppublish SO - Infect Genet Evol. 2017 Jan;47:1-8. doi: 10.1016/j.meegid.2016.11.011. Epub 2016 Nov 12. PMID- 27821432 OWN - NLM STAT- MEDLINE DCOM- 20170613 LR - 20181113 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 205 IP - 1 DP - 2017 Jan TI - Inferring Heterozygosity from Ancient and Low Coverage Genomes. PG - 317-332 LID - 10.1534/genetics.116.189985 [doi] AB - While genetic diversity can be quantified accurately from high coverage sequencing data, it is often desirable to obtain such estimates from data with low coverage, either to save costs or because of low DNA quality, as is observed for ancient samples. Here, we introduce a method to accurately infer heterozygosity probabilistically from sequences with average coverage [Formula: see text] of a single individual. The method relaxes the infinite sites assumption of previous methods, does not require a reference sequence, except for the initial alignment of the sequencing data, and takes into account both variable sequencing errors and potential postmortem damage. It is thus also applicable to nonmodel organisms and ancient genomes. Since error rates as reported by sequencing machines are generally distorted and require recalibration, we also introduce a method to accurately infer recalibration parameters in the presence of postmortem damage. This method does not require knowledge about the underlying genome sequence, but instead works with haploid data (e.g., from the X-chromosome from mammalian males) and integrates over the unknown genotypes. Using extensive simulations we show that a few megabasepairs of haploid data are sufficient for accurate recalibration, even at average coverages as low as [Formula: see text] At similar coverages, our method also produces very accurate estimates of heterozygosity down to [Formula: see text] within windows of about 1 Mbp. We further illustrate the usefulness of our approach by inferring genome-wide patterns of diversity for several ancient human samples, and we found that 3000-5000-year-old samples showed diversity patterns comparable to those of modern humans. In contrast, two European hunter-gatherer samples exhibited not only considerably lower levels of diversity than modern samples, but also highly distinct distributions of diversity along their genomes. Interestingly, these distributions were also very different between the two samples, supporting earlier conclusions of a highly diverse and structured population in Europe prior to the arrival of farming. CI - Copyright © 2017 by the Genetics Society of America. FAU - Kousathanas, Athanasios AU - Kousathanas A AD - Department of Biology and Biochemistry, University of Fribourg, 1700, Switzerland. AD - Statistical and Computational Evolutionary Biology Group, Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland. FAU - Leuenberger, Christoph AU - Leuenberger C AD - Department of Mathematics, University of Fribourg, 1200, Switzerland. FAU - Link, Vivian AU - Link V AD - Department of Biology and Biochemistry, University of Fribourg, 1700, Switzerland. AD - Statistical and Computational Evolutionary Biology Group, Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland. FAU - Sell, Christian AU - Sell C AD - Paleogenetics Group, University of Mainz, 55122, Germany. FAU - Burger, Joachim AU - Burger J AD - Paleogenetics Group, University of Mainz, 55122, Germany. FAU - Wegmann, Daniel AU - Wegmann D AD - Department of Biology and Biochemistry, University of Fribourg, 1700, Switzerland daniel.wegmann@unifr.ch. AD - Statistical and Computational Evolutionary Biology Group, Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20161107 PL - United States TA - Genetics JT - Genetics JID - 0374636 RN - 0 (DNA, Ancient) SB - IM MH - Base Sequence MH - Chromosome Mapping/methods MH - DNA, Ancient/*analysis MH - Genetic Carrier Screening/*methods MH - Genetic Variation MH - Genetics, Population/methods MH - Genome, Human MH - Heterozygote MH - Humans MH - Male MH - Sequence Analysis, DNA/*methods MH - Software PMC - PMC5223511 OTO - NOTNLM OT - ancient DNA OT - base recalibration OT - heterozygosity OT - low coverage OT - postmortem damage EDAT- 2016/11/09 06:00 MHDA- 2017/06/14 06:00 PMCR- 2016/11/07 CRDT- 2016/11/09 06:00 PHST- 2016/04/01 00:00 [received] PHST- 2016/10/19 00:00 [accepted] PHST- 2016/11/09 06:00 [pubmed] PHST- 2017/06/14 06:00 [medline] PHST- 2016/11/09 06:00 [entrez] PHST- 2016/11/07 00:00 [pmc-release] AID - genetics.116.189985 [pii] AID - 189985 [pii] AID - 10.1534/genetics.116.189985 [doi] PST - ppublish SO - Genetics. 2017 Jan;205(1):317-332. doi: 10.1534/genetics.116.189985. Epub 2016 Nov 7. PMID- 27771467 OWN - NLM STAT- MEDLINE DCOM- 20170614 LR - 20180129 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 26 DP - 2017 Jan TI - Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA. PG - 30-39 LID - S1872-4973(16)30193-4 [pii] LID - 10.1016/j.fsigen.2016.10.008 [doi] AB - We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq™ Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS (14)C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used. We found distinct mitochondrial genomes belonging to haplogroups U5b2a1a, K1c and H3d in the first grave cluster, and excluded maternal kin patterns among the three analyzed individuals. In the second grave cluster one individual belonged to K1a4. However, we could not affiliate the second individual to a certain haplogroup due to the fragmented state of the mitochondrial genome. Although the individuals from the second grave cluster differ at position 6643, we believe that more data is needed to fully resolve this issue. We retrieved between 26 and 77 autosomal SNPs from three of the individuals. Based on kinship estimations, taking into account the allelic dropout distribution, we could not exclude first degree kin relation between the two individuals from the second grave cluster. We could, however, exclude a first degree kinship between these two individuals and an individual from the first grave cluster. Presumably, not only biological kinship, but also social relations played an important role in the funerary practice during this time period. We further conclude that the HID-Ion AmpliSeq™ Identity Panel may prove useful for first degree kin relation studies for samples with good DNA preservation, and that mitochondrial genome capture enrichment is a powerful tool for excluding direct maternal relationship in ancient individuals. CI - Copyright © 2016 Elsevier Ireland Ltd. All rights reserved. FAU - Juras, Anna AU - Juras A AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland. Electronic address: annaj@amu.edu.pl. FAU - Chyleński, Maciej AU - Chyleński M AD - Institute of Prehistory, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland. Electronic address: maciej.ch@amu.edu.pl. FAU - Krenz-Niedbała, Marta AU - Krenz-Niedbała M AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland. Electronic address: martak@amu.edu.pl. FAU - Malmström, Helena AU - Malmström H AD - Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden. Electronic address: helena.malmstrom@ebc.uu.se. FAU - Ehler, Edvard AU - Ehler E AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland. Electronic address: eda.ehler@seznam.cz. FAU - Pospieszny, Łukasz AU - Pospieszny Ł AD - Institute of Archaeology and Ethnology of the Polish Academy of Sciences, Rubiez 46, 61-612 Poznań, Poland. Electronic address: lukasz.pospieszny@iaepan.poznan.pl. FAU - Łukasik, Sylwia AU - Łukasik S AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland. Electronic address: lukasik@amu.edu.pl. FAU - Bednarczyk, Józef AU - Bednarczyk J AD - Institute of Prehistory, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland. Electronic address: jotbe@amu.edu.pl. FAU - Piontek, Janusz AU - Piontek J AD - Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland. Electronic address: piontek@amu.edu.pl. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden. Electronic address: mattias.jakobsson@ebc.uu.se. FAU - Dabert, Miroslawa AU - Dabert M AD - Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland. Electronic address: mirkad@amu.edu.pl. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20161014 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (Carbon Isotopes) RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - 0 (Nitrogen Isotopes) SB - IM MH - Bone and Bones/chemistry MH - Carbon Isotopes MH - *DNA, Ancient MH - DNA, Mitochondrial/*genetics MH - Female MH - Genotype MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Male MH - Nitrogen Isotopes MH - *Pedigree MH - Poland MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Sex Determination Analysis MH - Tooth/chemistry OTO - NOTNLM OT - Ancient DNA OT - HID-Ion AmpliSeq™ OT - Identity panel OT - Kinship OT - Lengyel culture OT - Mitochondrial capture OT - Radiocarbon dating EDAT- 2016/10/25 06:00 MHDA- 2017/06/15 06:00 CRDT- 2016/11/07 06:00 PHST- 2016/06/24 00:00 [received] PHST- 2016/09/15 00:00 [revised] PHST- 2016/10/13 00:00 [accepted] PHST- 2016/10/25 06:00 [pubmed] PHST- 2017/06/15 06:00 [medline] PHST- 2016/11/07 06:00 [entrez] AID - S1872-4973(16)30193-4 [pii] AID - 10.1016/j.fsigen.2016.10.008 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2017 Jan;26:30-39. doi: 10.1016/j.fsigen.2016.10.008. Epub 2016 Oct 14. PMID- 27423248 OWN - NLM STAT- MEDLINE DCOM- 20170807 LR - 20171108 IS - 1465-7333 (Electronic) IS - 0022-1503 (Linking) VI - 108 IP - 1 DP - 2017 Jan TI - Chromosome-Specific Centromere Sequences Provide an Estimate of the Ancestral Chromosome 2 Fusion Event in Hominin Genomes. PG - 45-52 AB - Human chromosome 2 is a product of a telomere fusion of two ancestral chromosomes and loss/degeneration of one of the two original centromeres. Genomic signatures of this event are limited to inverted telomeric repeats at the precise site of chromosomal fusion and to the small amount of relic centromeric sequences that remain on 2q21.2. Unlike the site of fusion, which is enriched for sequences that are shared elsewhere in the human genome, the region of the nonfunctioning and degenerate ancestral centromere appears to share limited similarity with other sites in the human genome, thereby providing an opportunity to study this genomic arrangement in short, fragmented ancient DNA genomic datasets. Here, chromosome-assigned satellite DNAs are used to study shared centromere sequence organization in Denisovan and Neandertal genomes. By doing so, one is able to provide evidence for the presence of both active and degenerate centromeric satellite profiles on chromosome 2 in these archaic genomes, supporting the hypothesis that the chromosomal fusion event took place prior to our last common ancestor with Denisovan and Neandertal hominins and presenting a genomic reference for predicting karyotype in ancient genomic datasets. CI - © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. FAU - Miga, Karen H AU - Miga KH AD - From the Center for Biomolecular Science and Engineering, University of California, 501 Engineering 2 Building, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064. khmiga@soe.ucsc.edu. LA - eng PT - Journal Article DEP - 20160716 PL - United States TA - J Hered JT - The Journal of heredity JID - 0375373 RN - 0 (DNA, Satellite) SB - IM MH - Animals MH - *Centromere MH - Chromosomes, Human, Pair 2 MH - *Chromosomes, Mammalian MH - DNA, Satellite MH - *Evolution, Molecular MH - *Genome MH - Genomics/methods MH - Hominidae/*genetics MH - Humans MH - Pan troglodytes/genetics OTO - NOTNLM OT - centromere OT - chromosome fusion OT - hominin OT - repeats OT - satellite DNA EDAT- 2016/07/18 06:00 MHDA- 2017/08/08 06:00 CRDT- 2016/07/18 06:00 PHST- 2016/03/02 00:00 [received] PHST- 2016/06/20 00:00 [accepted] PHST- 2016/07/18 06:00 [pubmed] PHST- 2017/08/08 06:00 [medline] PHST- 2016/07/18 06:00 [entrez] AID - esw039 [pii] AID - 10.1093/jhered/esw039 [doi] PST - ppublish SO - J Hered. 2017 Jan;108(1):45-52. doi: 10.1093/jhered/esw039. Epub 2016 Jul 16. PMID- 27939314 OWN - NLM STAT- MEDLINE DCOM- 20180122 LR - 20190116 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 26 IP - 24 DP - 2016 Dec 19 TI - 17(th) Century Variola Virus Reveals the Recent History of Smallpox. PG - 3407-3412 LID - S0960-9822(16)31324-0 [pii] LID - 10.1016/j.cub.2016.10.061 [doi] AB - Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1-4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4-9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4-6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20(th) century VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18(th) and 19(th) centuries, concomitant with the development of modern vaccination. CI - Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Duggan, Ana T AU - Duggan AT AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada. Electronic address: duggana@mcmaster.ca. FAU - Perdomo, Maria F AU - Perdomo MF AD - Department of Virology, University of Helsinki, Helsinki 00014, Finland. FAU - Piombino-Mascali, Dario AU - Piombino-Mascali D AD - Department of Anatomy, Histology, and Anthropology, Faculty of Medicine, Vilnius University, Vilnius 03101, Lithuania. FAU - Marciniak, Stephanie AU - Marciniak S AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada. FAU - Poinar, Debi AU - Poinar D AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada. FAU - Emery, Matthew V AU - Emery MV AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada. FAU - Buchmann, Jan P AU - Buchmann JP AD - Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2145, Australia. FAU - Duchêne, Sebastian AU - Duchêne S AD - Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2145, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia. FAU - Jankauskas, Rimantas AU - Jankauskas R AD - Department of Anatomy, Histology, and Anthropology, Faculty of Medicine, Vilnius University, Vilnius 03101, Lithuania. FAU - Humphreys, Margaret AU - Humphreys M AD - Department of History, Duke University, Durham, NC 27708-0719, USA. FAU - Golding, G Brian AU - Golding GB AD - Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada. FAU - Southon, John AU - Southon J AD - Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, CA 92697-3100, USA. FAU - Devault, Alison AU - Devault A AD - MYcroarray, Ann Arbor, MI 48105, USA. FAU - Rouillard, Jean-Marie AU - Rouillard JM AD - MYcroarray, Ann Arbor, MI 48105, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2136, USA. FAU - Sahl, Jason W AU - Sahl JW AD - Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA. FAU - Dutour, Olivier AU - Dutour O AD - Laboratoire d'Anthropologie Biologique Paul Broca, Ecole Pratique des Hautes Etudes, PSL Research University, Paris 75014, France; PACEA, CNRS, Université de Bordeaux, Pessac 33615, France. FAU - Hedman, Klaus AU - Hedman K AD - Department of Virology, University of Helsinki, Helsinki 00014, Finland; Helsinki University Hospital, Helsinki 00029, Finland. FAU - Sajantila, Antti AU - Sajantila A AD - Department of Forensic Medicine, University of Helsinki, Helsinki 00014, Finland. FAU - Smith, Geoffrey L AU - Smith GL AD - Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK. FAU - Holmes, Edward C AU - Holmes EC AD - Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2145, Australia. Electronic address: edward.holmes@sydney.edu.au. FAU - Poinar, Hendrik N AU - Poinar HN AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada. Electronic address: poinarh@mcmaster.ca. LA - eng GR - Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20161208 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Viral) RN - 0 (Smallpox Vaccine) SB - IM MH - Child, Preschool MH - DNA, Viral/*genetics/isolation & purification MH - *Evolution, Molecular MH - Genome, Viral MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, 20th Century MH - History, 21st Century MH - Humans MH - Mummies/history/virology MH - Phylogeny MH - Smallpox/*history/virology MH - Smallpox Vaccine/history MH - Vaccination/history MH - Variola virus/*genetics PMC - PMC5196022 OTO - NOTNLM OT - Lithuanian Mummy Project OT - ancient DNA OT - evolution OT - molecular clock OT - phylogeny OT - smallpox OT - variola virus EDAT- 2016/12/13 06:00 MHDA- 2018/01/23 06:00 PMCR- 2016/12/19 CRDT- 2016/12/13 06:00 PHST- 2016/09/26 00:00 [received] PHST- 2016/10/20 00:00 [revised] PHST- 2016/10/31 00:00 [accepted] PHST- 2016/12/13 06:00 [pubmed] PHST- 2018/01/23 06:00 [medline] PHST- 2016/12/13 06:00 [entrez] PHST- 2016/12/19 00:00 [pmc-release] AID - S0960-9822(16)31324-0 [pii] AID - 10.1016/j.cub.2016.10.061 [doi] PST - ppublish SO - Curr Biol. 2016 Dec 19;26(24):3407-3412. doi: 10.1016/j.cub.2016.10.061. Epub 2016 Dec 8. PMID- 27923126 OWN - NLM STAT- MEDLINE DCOM- 20180125 LR - 20181024 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 26 IP - 23 DP - 2016 Dec 5 TI - Plasmodium falciparum malaria in 1(st)-2(nd) century CE southern Italy. PG - R1220-R1222 LID - S0960-9822(16)31201-5 [pii] LID - 10.1016/j.cub.2016.10.016 [doi] AB - The historical record attests to the devastation malaria exacted on ancient civilizations, particularly the Roman Empire [1]. However, evidence for the presence of malaria during the Imperial period in Italy (1st-5th century CE) is based on indirect sources, such as historical, epigraphic, or skeletal evidence. Although these sources are crucial for revealing the context of this disease, they cannot establish the causative species of Plasmodium. Importantly, definitive evidence for the presence of malaria is now possible through the implementation of ancient DNA technology. As malaria is presumed to have been at its zenith during the Imperial period [1], we selected first or second molars from 58 adults from three cemeteries from this time: Isola Sacra (associated with Portus Romae, 1st-3rd century CE), Velia (1st-2nd century CE), and Vagnari (1st-4th century CE). We performed hybridization capture using baits designed from the mitochondrial (mtDNA) genomes of Plasmodium spp. on a prioritized subset of 11 adults (informed by metagenomic sequencing). The mtDNA sequences generated provided compelling phylogenetic evidence for the presence of P. falciparum in two individuals. This is the first genomic data directly implicating P. falciparum in Imperial period southern Italy in adults. CI - Copyright © 2016 Elsevier Ltd. All rights reserved. FAU - Marciniak, Stephanie AU - Marciniak S AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada. Electronic address: marcis@mcmaster.ca. FAU - Prowse, Tracy L AU - Prowse TL AD - Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada. FAU - Herring, D Ann AU - Herring DA AD - Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada. FAU - Klunk, Jennifer AU - Klunk J AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, Ontario L8S 4L9, Canada. FAU - Kuch, Melanie AU - Kuch M AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada. FAU - Duggan, Ana T AU - Duggan AT AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada. FAU - Bondioli, Luca AU - Bondioli L AD - Museo delle Civiltà, Museo Nazionale Preistorico Etnografico 'Luigi Pigorini', Sezione di Bioarcheologia, P. le G. Marconi 14, 00144, Rome, Italy. FAU - Holmes, Edward C AU - Holmes EC AD - Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia. FAU - Poinar, Hendrik N AU - Poinar HN AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, Ontario L8S 4L9, Canada; DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L9, Canada; Humans & the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada. Electronic address: poinarh@mcmaster.ca. LA - eng PT - Historical Article PT - Letter PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) RN - 0 (DNA, Protozoan) SB - IM MH - Cadaver MH - DNA, Mitochondrial/genetics MH - DNA, Protozoan/genetics MH - History, Ancient MH - Humans MH - Italy/epidemiology MH - Malaria, Falciparum/epidemiology/*history MH - Molar/chemistry MH - Plasmodium falciparum/genetics/*isolation & purification MH - Roman World/history EDAT- 2016/12/07 06:00 MHDA- 2018/01/26 06:00 CRDT- 2016/12/07 06:00 PHST- 2016/12/07 06:00 [entrez] PHST- 2016/12/07 06:00 [pubmed] PHST- 2018/01/26 06:00 [medline] AID - S0960-9822(16)31201-5 [pii] AID - 10.1016/j.cub.2016.10.016 [doi] PST - ppublish SO - Curr Biol. 2016 Dec 5;26(23):R1220-R1222. doi: 10.1016/j.cub.2016.10.016. PMID- 27662060 OWN - NLM STAT- MEDLINE DCOM- 20171205 LR - 20190109 IS - 1879-0380 (Electronic) IS - 0959-437X (Print) IS - 0959-437X (Linking) VI - 41 DP - 2016 Dec TI - Recent advances in the study of fine-scale population structure in humans. PG - 98-105 LID - S0959-437X(16)30111-3 [pii] LID - 10.1016/j.gde.2016.08.007 [doi] AB - Empowered by modern genotyping and large samples, population structure can be accurately described and quantified even when it only explains a fraction of a percent of total genetic variance. This is especially relevant and interesting for humans, where fine-scale population structure can both confound disease-mapping studies and reveal the history of migration and divergence that shaped our species' diversity. Here we review notable recent advances in the detection, use, and understanding of population structure. Our work addresses multiple areas where substantial progress is being made: improved statistics and models for better capturing differentiation, admixture, and the spatial distribution of variation; computational speed-ups that allow methods to scale to modern data; and advances in haplotypic modeling that have wide ranging consequences for the analysis of population structure. We conclude by outlining four important open challenges: the limitations of discrete population models, uncertainty in individual origins, the incorporation of both fine-scale structure and ancient DNA in parametric models, and the development of efficient computational tools, particularly for haplotype-based methods. CI - Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved. FAU - Novembre, John AU - Novembre J AD - Department of Human Genetics, University of Chicago, IL 60636, United States; Department of Ecology and Evolutionary Biology, University of Chicago, IL 60636, United States. FAU - Peter, Benjamin M AU - Peter BM AD - Department of Human Genetics, University of Chicago, IL 60636, United States. LA - eng GR - R01 GM108805/GM/NIGMS NIH HHS/United States GR - R01 HG007089/HG/NHGRI NIH HHS/United States GR - U01 CA198933/CA/NCI NIH HHS/United States PT - Historical Article PT - Journal Article PT - Review DEP - 20160920 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/genetics MH - *Genetic Variation MH - *Genetics, Population MH - Genotype MH - History, Ancient MH - Human Migration/*history MH - Humans PMC - PMC5291306 MID - NIHMS818319 EDAT- 2016/09/24 06:00 MHDA- 2017/12/06 06:00 PMCR- 2017/12/01 CRDT- 2016/09/24 06:00 PHST- 2016/07/06 00:00 [received] PHST- 2016/08/18 00:00 [revised] PHST- 2016/08/24 00:00 [accepted] PHST- 2016/09/24 06:00 [pubmed] PHST- 2017/12/06 06:00 [medline] PHST- 2016/09/24 06:00 [entrez] PHST- 2017/12/01 00:00 [pmc-release] AID - S0959-437X(16)30111-3 [pii] AID - 10.1016/j.gde.2016.08.007 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2016 Dec;41:98-105. doi: 10.1016/j.gde.2016.08.007. Epub 2016 Sep 20. PMID- 27624717 OWN - NLM STAT- MEDLINE DCOM- 20170627 LR - 20181113 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 33 IP - 12 DP - 2016 Dec TI - Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX. PG - 3284-3298 AB - The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts. CI - © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Hanghøj, Kristian AU - Hanghøj K AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, Toulouse, France. FAU - Seguin-Orlando, Andaine AU - Seguin-Orlando A AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. AD - Danish National High-Throughput DNA Sequencing Center, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Schubert, Mikkel AU - Schubert M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Madsen, Tobias AU - Madsen T AD - Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark. AD - Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark. FAU - Pedersen, Jakob Skou AU - Pedersen JS AD - Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark. AD - Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. AD - Department of Zoology, University of Cambridge, Cambridge, United Kingdom. AD - Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark lorlando@snm.ku.dk. AD - Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, Toulouse, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160913 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) RN - 0 (Nucleosomes) RN - 8J337D1HZY (Cytosine) RN - 9007-49-2 (DNA) SB - IM MH - Chromatin Assembly and Disassembly MH - Computer Simulation MH - Cytosine/metabolism MH - DNA/genetics MH - *DNA Methylation MH - DNA, Ancient/*analysis MH - Epigenesis, Genetic MH - Genome MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Nucleosomes/*genetics MH - Sequence Analysis, DNA/*methods MH - Software PMC - PMC5100044 OTO - NOTNLM OT - DNA methylation OT - ancient DNA OT - epigenome OT - nucleosome. EDAT- 2016/09/15 06:00 MHDA- 2017/06/28 06:00 PMCR- 2016/09/13 CRDT- 2016/09/15 06:00 PHST- 2016/09/15 06:00 [pubmed] PHST- 2017/06/28 06:00 [medline] PHST- 2016/09/15 06:00 [entrez] PHST- 2016/09/13 00:00 [pmc-release] AID - msw184 [pii] AID - 10.1093/molbev/msw184 [doi] PST - ppublish SO - Mol Biol Evol. 2016 Dec;33(12):3284-3298. doi: 10.1093/molbev/msw184. Epub 2016 Sep 13. PMID- 27618404 OWN - NLM STAT- MEDLINE DCOM- 20170612 LR - 20180321 IS - 1878-4380 (Electronic) IS - 0966-842X (Linking) VI - 24 IP - 12 DP - 2016 Dec TI - Microbial Genomics of Ancient Plagues and Outbreaks. PG - 978-990 LID - S0966-842X(16)30113-5 [pii] LID - 10.1016/j.tim.2016.08.004 [doi] AB - The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illustrate how microbial genomics has provided new insights into the nature and etiology of infectious diseases of historical importance, such as plague, tuberculosis, and leprosy. Sequenced isolates collected from archaeological remains also provide evidence for the timing of historical evolutionary events as well as geographic spread of these pathogens. Elucidating the genomic basis of virulence in historical diseases can provide relevant information on how we can effectively understand the emergence and re-emergence of infectious diseases today and in the future. CI - Copyright © 2016 Elsevier Ltd. All rights reserved. FAU - Andam, Cheryl P AU - Andam CP AD - Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA; University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH 03824, USA. Electronic address: cheryl.andam@unh.edu. FAU - Worby, Colin J AU - Worby CJ AD - Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA. FAU - Chang, Qiuzhi AU - Chang Q AD - Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA. FAU - Campana, Michael G AU - Campana MG AD - Smithsonian Conservation Biology Institute, Center for Conservation Genomics, 3001 Connecticut Avenue NW, Washington, DC 20008, USA. Electronic address: campanam@si.edu. LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20160908 PL - England TA - Trends Microbiol JT - Trends in microbiology JID - 9310916 RN - 0 (DNA, Ancient) SB - IM MH - Communicable Diseases/*epidemiology/etiology/history MH - DNA, Ancient MH - *Disease Outbreaks/history MH - Epidemics/history MH - Genome, Bacterial MH - *Genomics MH - High-Throughput Nucleotide Sequencing/methods MH - History, 19th Century MH - History, Ancient MH - Humans MH - Phylogeny MH - Plague/*epidemiology/history/microbiology MH - Virulence MH - Yersinia pestis/*genetics/pathogenicity OTO - NOTNLM OT - ancient DNA OT - epidemic OT - genome OT - genomics OT - pathogen OT - plague EDAT- 2016/09/13 06:00 MHDA- 2017/06/13 06:00 CRDT- 2016/09/13 06:00 PHST- 2016/05/28 00:00 [received] PHST- 2016/07/29 00:00 [revised] PHST- 2016/08/16 00:00 [accepted] PHST- 2016/09/13 06:00 [pubmed] PHST- 2017/06/13 06:00 [medline] PHST- 2016/09/13 06:00 [entrez] AID - S0966-842X(16)30113-5 [pii] AID - 10.1016/j.tim.2016.08.004 [doi] PST - ppublish SO - Trends Microbiol. 2016 Dec;24(12):978-990. doi: 10.1016/j.tim.2016.08.004. Epub 2016 Sep 8. PMID- 27606907 OWN - NLM STAT- MEDLINE DCOM- 20171205 LR - 20181113 IS - 1879-0380 (Electronic) IS - 0959-437X (Print) IS - 0959-437X (Linking) VI - 41 DP - 2016 Dec TI - Statistical methods for analyzing ancient DNA from hominins. PG - 72-76 LID - S0959-437X(16)30108-3 [pii] LID - 10.1016/j.gde.2016.08.004 [doi] AB - In the past few years, the number of autosomal DNA sequences from human fossils has grown explosively and numerous partial or complete sequences are available from our closest relatives, Neanderthal and Denisovans. I review commonly used statistical methods applied to these sequences. These methods fall into three broad classes: methods for estimating levels of contamination, descriptive methods, and methods based on population genetic models. The latter two classes are largely methods developed for the analysis of present-day genomic data. When they are applied to ancient DNA (aDNA), they usually ignore the time dimension. A few methods, particularly those concerned with inferring something about selection or ancestor-descendant relationships, take explicit account of the ages of aDNA samples. CI - Copyright © 2016 Elsevier Ltd. All rights reserved. FAU - Slatkin, Montgomery AU - Slatkin M AD - Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA. Electronic address: slatkin@berkeley.edu. LA - eng GR - R01 GM040282/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Review DEP - 20160905 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics MH - Fossils MH - Genetics, Population/*statistics & numerical data MH - Genome/genetics MH - Hominidae/*genetics MH - Humans MH - Neanderthals/genetics PMC - PMC5161690 MID - NIHMS812038 EDAT- 2016/09/09 06:00 MHDA- 2017/12/06 06:00 PMCR- 2017/12/01 CRDT- 2016/09/09 06:00 PHST- 2016/03/03 00:00 [received] PHST- 2016/06/22 00:00 [revised] PHST- 2016/08/02 00:00 [accepted] PHST- 2016/09/09 06:00 [pubmed] PHST- 2017/12/06 06:00 [medline] PHST- 2016/09/09 06:00 [entrez] PHST- 2017/12/01 00:00 [pmc-release] AID - S0959-437X(16)30108-3 [pii] AID - 10.1016/j.gde.2016.08.004 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2016 Dec;41:72-76. doi: 10.1016/j.gde.2016.08.004. Epub 2016 Sep 5. PMID- 27507099 OWN - NLM STAT- MEDLINE DCOM- 20171205 LR - 20240603 IS - 1879-0380 (Electronic) IS - 0959-437X (Print) IS - 0959-437X (Linking) VI - 41 DP - 2016 Dec TI - A genomic view of the peopling of the Americas. PG - 27-35 LID - S0959-437X(16)30091-0 [pii] LID - 10.1016/j.gde.2016.06.016 [doi] AB - Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ∼4500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research. CI - Copyright © 2016 Elsevier Ltd. All rights reserved. FAU - Skoglund, Pontus AU - Skoglund P AD - Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Archaeology and Classical History, Stockholm, Sweden. Electronic address: pontus.skoglund@gmail.com. FAU - Reich, David AU - Reich D AD - Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Review DEP - 20160806 PL - England TA - Curr Opin Genet Dev JT - Current opinion in genetics & development JID - 9111375 SB - IM MH - Americas MH - Arctic Regions MH - Asia MH - *Genome, Human MH - *Genomics MH - History, Ancient MH - *Human Migration MH - Humans MH - Indians, North American/*genetics/history MH - North America PMC - PMC5161672 MID - NIHMS806927 EDAT- 2016/08/11 06:00 MHDA- 2017/12/06 06:00 PMCR- 2017/12/01 CRDT- 2016/08/11 06:00 PHST- 2016/06/14 00:00 [received] PHST- 2016/06/23 00:00 [revised] PHST- 2016/06/25 00:00 [accepted] PHST- 2016/08/11 06:00 [pubmed] PHST- 2017/12/06 06:00 [medline] PHST- 2016/08/11 06:00 [entrez] PHST- 2017/12/01 00:00 [pmc-release] AID - S0959-437X(16)30091-0 [pii] AID - 10.1016/j.gde.2016.06.016 [doi] PST - ppublish SO - Curr Opin Genet Dev. 2016 Dec;41:27-35. doi: 10.1016/j.gde.2016.06.016. Epub 2016 Aug 6. PMID- 27848937 OWN - NLM STAT- MEDLINE DCOM- 20180423 LR - 20211204 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 6 DP - 2016 Nov 16 TI - Reconstructing Druze population history. PG - 35837 LID - 10.1038/srep35837 [doi] LID - 35837 AB - The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. We investigated the genetic relationships between Israeli Druze and both modern and ancient populations. We evaluated our findings in light of three hypotheses purporting to explain Druze history that posit Arabian, Persian or mixed Near Eastern-Levantine roots. The biogeographical analysis localised proto-Druze to the mountainous regions of southeastern Turkey, northern Iraq and southeast Syria and their descendants clustered along a trajectory between these two regions. The mixed Near Eastern-Middle Eastern localisation of the Druze, shown using both modern and ancient DNA data, is distinct from that of neighbouring Syrians, Palestinians and most of the Lebanese, who exhibit a high affinity to the Levant. Druze biogeographic affinity, migration patterns, time of emergence and genetic similarity to Near Eastern populations are highly suggestive of Armenian-Turkish ancestries for the proto-Druze. FAU - Marshall, Scarlett AU - Marshall S AD - Independent Researcher, Oxford, UK. FAU - Das, Ranajit AU - Das R AD - Manipal Centre for Natural Sciences (MCNS), Manipal University, Manipal, Karnataka, India. FAU - Pirooznia, Mehdi AU - Pirooznia M AD - Johns Hopkins University, Department of Psychiatry and Behavioral Sciences, Baltimore, MD 21205, USA. FAU - Elhaik, Eran AU - Elhaik E AD - University of Sheffield, Department of Animal and Plant Sciences, Sheffield S10 2TN, UK. LA - eng GR - MC_PC_14115/MRC_/Medical Research Council/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20161116 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM MH - Anthropology, Cultural MH - Emigration and Immigration/*history MH - Ethnicity/*genetics/*history MH - Female MH - History, Ancient MH - Humans MH - Israel MH - Lebanon MH - Male MH - Phylogeography MH - Syria PMC - PMC5111078 COIS- E.E. is a consultant to DNA Diagnostic Centre. S.M., R.D. and M.P. declare no competing financial interests. EDAT- 2016/11/17 06:00 MHDA- 2018/04/24 06:00 PMCR- 2016/11/16 CRDT- 2016/11/17 06:00 PHST- 2016/04/27 00:00 [received] PHST- 2016/10/05 00:00 [accepted] PHST- 2016/11/17 06:00 [entrez] PHST- 2016/11/17 06:00 [pubmed] PHST- 2018/04/24 06:00 [medline] PHST- 2016/11/16 00:00 [pmc-release] AID - srep35837 [pii] AID - 10.1038/srep35837 [doi] PST - epublish SO - Sci Rep. 2016 Nov 16;6:35837. doi: 10.1038/srep35837. PMID- 27824339 OWN - NLM STAT- MEDLINE DCOM- 20180827 LR - 20221207 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 7 DP - 2016 Nov 8 TI - DNA evidence of bowhead whale exploitation by Greenlandic Paleo-Inuit 4,000 years ago. PG - 13389 LID - 10.1038/ncomms13389 [doi] LID - 13389 AB - The demographic history of Greenland is characterized by recurrent migrations and extinctions since the first humans arrived 4,500 years ago. Our current understanding of these extinct cultures relies primarily on preserved fossils found in their archaeological deposits, which hold valuable information on past subsistence practices. However, some exploited taxa, though economically important, comprise only a small fraction of these sub-fossil assemblages. Here we reconstruct a comprehensive record of past subsistence economies in Greenland by sequencing ancient DNA from four well-described midden deposits. Our results confirm that the species found in the fossil record, like harp seal and ringed seal, were a vital part of Inuit subsistence, but also add a new dimension with evidence that caribou, walrus and whale species played a more prominent role for the survival of Paleo-Inuit cultures than previously reported. Most notably, we report evidence of bowhead whale exploitation by the Saqqaq culture 4,000 years ago. FAU - Seersholm, Frederik Valeur AU - Seersholm FV AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. AD - Trace and Environmental DNA(TrEnD) Laboratory, Department of the Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. FAU - Pedersen, Mikkel Winther AU - Pedersen MW AUID- ORCID: 0000-0002-7291-8887 AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Søe, Martin Jensen AU - Søe MJ AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. AD - Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark. FAU - Shokry, Hussein AU - Shokry H AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Mak, Sarah Siu Tze AU - Mak SS AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Ruter, Anthony AU - Ruter A AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Raghavan, Maanasa AU - Raghavan M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. AD - Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. FAU - Fitzhugh, William AU - Fitzhugh W AD - Smithsonian Institution, Washington, D.C. 20013-7012, USA. FAU - Kjær, Kurt H AU - Kjær KH AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. AD - Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. FAU - Meldgaard, Morten AU - Meldgaard M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. AD - University of Greenland, Manutooq 1, Nuussuaq 3905, Greenland. FAU - Kapel, Christian M O AU - Kapel CM AD - Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark. FAU - Hansen, Anders Johannes AU - Hansen AJ AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20161108 PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (DNA, Plant) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Archaeology MH - Biodiversity MH - Bowhead Whale/*genetics MH - DNA/*genetics MH - DNA Damage MH - DNA, Plant/genetics MH - Fossils MH - Geography MH - Geologic Sediments MH - Greenland MH - Helminths/classification MH - Humans MH - *Inuit MH - Sequence Analysis, DNA MH - Time Factors PMC - PMC5105157 EDAT- 2016/11/09 06:00 MHDA- 2018/08/28 06:00 PMCR- 2016/11/08 CRDT- 2016/11/09 06:00 PHST- 2016/05/31 00:00 [received] PHST- 2016/09/29 00:00 [accepted] PHST- 2016/11/09 06:00 [entrez] PHST- 2016/11/09 06:00 [pubmed] PHST- 2018/08/28 06:00 [medline] PHST- 2016/11/08 00:00 [pmc-release] AID - ncomms13389 [pii] AID - 10.1038/ncomms13389 [doi] PST - epublish SO - Nat Commun. 2016 Nov 8;7:13389. doi: 10.1038/ncomms13389. PMID- 27821149 OWN - NLM STAT- MEDLINE DCOM- 20170621 LR - 20231111 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 17 IP - 1 DP - 2016 Nov 7 TI - Understanding rare and common diseases in the context of human evolution. PG - 225 LID - 225 AB - The wealth of available genetic information is allowing the reconstruction of human demographic and adaptive history. Demography and purifying selection affect the purge of rare, deleterious mutations from the human population, whereas positive and balancing selection can increase the frequency of advantageous variants, improving survival and reproduction in specific environmental conditions. In this review, I discuss how theoretical and empirical population genetics studies, using both modern and ancient DNA data, are a powerful tool for obtaining new insight into the genetic basis of severe disorders and complex disease phenotypes, rare and common, focusing particularly on infectious disease risk. FAU - Quintana-Murci, Lluis AU - Quintana-Murci L AD - Human Evolutionary Genetics Unit, Department of Genomes & Genetics, Institut Pasteur, Paris, 75015, France. quintana@pasteur.fr. AD - Centre National de la Recherche Scientifique, URA3012, Paris, 75015, France. quintana@pasteur.fr. AD - Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, 75015, France. quintana@pasteur.fr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20161107 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 SB - IM MH - Demography MH - Disease/*genetics MH - *Evolution, Molecular MH - *Genetics, Population MH - Humans MH - Models, Genetic MH - Mutation MH - Polymorphism, Genetic MH - *Selection, Genetic PMC - PMC5098287 EDAT- 2016/11/09 06:00 MHDA- 2017/06/22 06:00 PMCR- 2016/11/07 CRDT- 2016/11/09 06:00 PHST- 2016/11/09 06:00 [entrez] PHST- 2016/11/09 06:00 [pubmed] PHST- 2017/06/22 06:00 [medline] PHST- 2016/11/07 00:00 [pmc-release] AID - 10.1186/s13059-016-1093-y [pii] AID - 1093 [pii] AID - 10.1186/s13059-016-1093-y [doi] PST - epublish SO - Genome Biol. 2016 Nov 7;17(1):225. doi: 10.1186/s13059-016-1093-y. PMID- 27613970 OWN - NLM STAT- MEDLINE DCOM- 20170614 LR - 20180108 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 25 DP - 2016 Nov TI - TriXY-Homogeneous genetic sexing of highly degraded forensic samples including hair shafts. PG - 166-174 LID - S1872-4973(16)30164-8 [pii] LID - 10.1016/j.fsigen.2016.09.001 [doi] AB - Sexing of biological evidence is an important aspect in forensic investigations. A routinely used molecular-genetic approach to this endeavour is the amelogenin sex test, which is integrated in most commercially available polymerase chain reaction (PCR) kits for human identification. However, this assay is not entirely effective in respect to highly degraded DNA samples. This study presents a homogeneous PCR assay for robust sex diagnosis, especially for the analysis of severely fragmented DNA. The introduced triplex for the X and Y chromosome (TriXY) is based on real-time PCR amplification of short intergenic sequences (<50bp) on both gonosomes. Subsequent PCR product examination and molecular-genetic sex-assignment rely on high-resolution melting (HRM) curve analysis. TriXY was optimized using commercially available multi-donor human DNA preparations of either male or female origin and successfully evaluated on challenging samples, including 46 ancient DNA specimens from archaeological excavations and a total of 16 DNA samples extracted from different segments of eight hair shafts of male and female donors. Additionally, sensitivity and cross-species amplification were examined to further test the assay's utility in forensic investigations. TriXY's closed-tube format avoids post-PCR sample manipulations and, therefore, distinctly reduces the risk of PCR product carry-over contamination and sample mix-up, while reducing labour and financial expenses at the same time. The method is sensitive down to the DNA content of approximately two diploid cells and has proven highly useful on severely fragmented and low quantity ancient DNA samples. Furthermore, it even allowed for sexing of proximal hair shafts with very good results. In summary, TriXY facilitates highly sensitive, rapid, and costeffective genetic sex-determination. It outperforms existing sexing methods both in terms of sensitivity and minimum required template molecule lengths. Therefore, we feel confident that TriXY will prove to be a reliable addition to the toolbox currently used for sex-typing in forensic genetics and other fields of research. CI - Copyright © 2016 Elsevier Ireland Ltd. All rights reserved. FAU - Madel, Maria-Bernadette AU - Madel MB AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria. FAU - Niederstätter, Harald AU - Niederstätter H AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria. FAU - Parson, Walther AU - Parson W AD - Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA. Electronic address: walther.parson@i-med.ac.at. LA - eng PT - Journal Article DEP - 20160903 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Intergenic) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Chromosomes, Human, X MH - *Chromosomes, Human, Y MH - DNA/*genetics MH - DNA Degradation, Necrotic MH - *DNA, Intergenic MH - Female MH - Hair/chemistry MH - Humans MH - Male MH - *Real-Time Polymerase Chain Reaction MH - Sex Determination Analysis/*methods MH - Species Specificity OTO - NOTNLM OT - Ancient DNA OT - Degraded DNA OT - Forensic science OT - High-resolution melting OT - Real-time PCR OT - Sex determination EDAT- 2016/10/23 06:00 MHDA- 2017/06/15 06:00 CRDT- 2016/09/11 06:00 PHST- 2016/08/05 00:00 [received] PHST- 2016/09/01 00:00 [accepted] PHST- 2016/10/23 06:00 [pubmed] PHST- 2017/06/15 06:00 [medline] PHST- 2016/09/11 06:00 [entrez] AID - S1872-4973(16)30164-8 [pii] AID - 10.1016/j.fsigen.2016.09.001 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2016 Nov;25:166-174. doi: 10.1016/j.fsigen.2016.09.001. Epub 2016 Sep 3. PMID- 27578768 OWN - NLM STAT- MEDLINE DCOM- 20170621 LR - 20240531 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 33 IP - 11 DP - 2016 Nov TI - A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim. PG - 2911-2923 LID - 10.1093/molbev/msw170 [doi] AB - The Justinianic Plague, which started in the sixth century and lasted to the mid eighth century, is thought to be the first of three historically documented plague pandemics causing massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany. CI - © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Feldman, Michal AU - Feldman M AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Harbeck, Michaela AU - Harbeck M AD - SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany. FAU - Keller, Marcel AU - Keller M AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany. FAU - Spyrou, Maria A AU - Spyrou MA AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Rott, Andreas AU - Rott A AD - SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany. FAU - Trautmann, Bernd AU - Trautmann B AD - SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany. FAU - Scholz, Holger C AU - Scholz HC AD - Bundeswehr Institute of Microbiology, Munich, Germany. AD - German Center for Infection Research (DZIF), Munich, Germany. FAU - Päffgen, Bernd AU - Päffgen B AD - Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilian University Munich, Germany. FAU - Peters, Joris AU - Peters J AD - SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany. AD - Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University of Munich, Germany. FAU - McCormick, Michael AU - McCormick M AD - Department of History, Harvard University, Initiative for the Science of the Human Past. FAU - Bos, Kirsten AU - Bos K AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Herbig, Alexander AU - Herbig A AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena, Germany. AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. LA - eng PT - Journal Article DEP - 20160830 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Ancient) RN - 0 (DNA, Bacterial) SB - IM CIN - Mol Biol Evol. 2016 Nov;33(11):3028-3029. doi: 10.1093/molbev/msw203. PMID: 27738270 MH - Base Sequence MH - DNA, Ancient/*analysis MH - DNA, Bacterial/genetics MH - Genetic Variation MH - Genome, Bacterial MH - High-Throughput Nucleotide Sequencing/methods MH - Humans MH - Pandemics MH - Plague/*microbiology MH - Virulence/genetics MH - Yersinia pestis/*genetics PMC - PMC5062324 OTO - NOTNLM OT - Yersinia pestis OT - ancient DNA OT - justinianic plague OT - reconstruction OT - whole genome EDAT- 2016/09/01 06:00 MHDA- 2017/06/22 06:00 PMCR- 2016/08/30 CRDT- 2016/09/01 06:00 PHST- 2016/09/01 06:00 [pubmed] PHST- 2017/06/22 06:00 [medline] PHST- 2016/09/01 06:00 [entrez] PHST- 2016/08/30 00:00 [pmc-release] AID - msw170 [pii] AID - 10.1093/molbev/msw170 [doi] PST - ppublish SO - Mol Biol Evol. 2016 Nov;33(11):2911-2923. doi: 10.1093/molbev/msw170. Epub 2016 Aug 30. PMID- 27500649 OWN - NLM STAT- MEDLINE DCOM- 20170614 LR - 20211204 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 25 DP - 2016 Nov TI - The genetics of kinship in remote human groups. PG - 52-62 LID - S1872-4973(16)30138-7 [pii] LID - 10.1016/j.fsigen.2016.07.018 [doi] AB - For fifteen years, part of the work of our research team has been focused on the study of parental links between individuals living hundreds or thousands of years ago, whose remains have been found in single graves or large funerary complexes. These studies have been undertaken using methods developed by forensic genetics to identify individuals, mainly based on the genotyping of autosomal STR (Short Tandem Repeats). Issues arose from this work, namely the limits of studying small numbers of subjects, originating from groups of finite sizes where kinships cannot be inferred a priori and for which reference allelic frequencies do not exist. Although ideal human populations are rare when undertaking such studies, the Yakuts of Eastern Siberia constitute a very advantageous model, with large numbers of small pastoral communities and well-preserved archaeological material. The study of kinship in the ancient Yakuts allowed us to highlight the difficulties in analysing genetic data from small ancient human groups and to develop a strategy to improve the accuracy of statistical computations. This work describes this strategy and possible solutions to the study of populations outside of the frame of reference of global meta-populations, due either to isolation, remoteness or antiquity. CI - Copyright © 2016. Published by Elsevier Ireland Ltd. FAU - Zvénigorosky, Vincent AU - Zvénigorosky V AD - Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France; Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. Electronic address: zvenigorosky@unistra.fr. FAU - Crubézy, Eric AU - Crubézy E AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. FAU - Gibert, Morgane AU - Gibert M AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. FAU - Thèves, Catherine AU - Thèves C AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. FAU - Hollard, Clémence AU - Hollard C AD - Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France. FAU - Gonzalez, Angéla AU - Gonzalez A AD - Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France. FAU - Fedorova, Sardana A AU - Fedorova SA AD - Laboratory of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Yakutsk, Sakha Republic, Russia; Laboratory of Molecular Biology, North-Eastern Federal University, Sakha Republic, Russia. FAU - Alexeev, Anatoly N AU - Alexeev AN AD - Institut des sciences humaines et des problèmes des peuples minoritaires du Nord, Branche Sibérienne de l'Académie des sciences de Russie (Yakoutsk), Russia. FAU - Bravina, Rozalia I AU - Bravina RI AD - Institut des sciences humaines et des problèmes des peuples minoritaires du Nord, Branche Sibérienne de l'Académie des sciences de Russie (Yakoutsk), Russia. FAU - Ludes, Bertrand AU - Ludes B AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France; Institut Médico-Légal, Université Paris Descartes, Paris, France. FAU - Keyser, Christine AU - Keyser C AD - Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France; Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. LA - eng PT - Journal Article DEP - 20160728 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Ancient) SB - IM MH - Chromosomes, Human, Y MH - *DNA Fingerprinting MH - *DNA, Ancient MH - Ethnicity/*genetics MH - Female MH - Gene Frequency MH - Genetics, Population MH - Genotype MH - Humans MH - Male MH - *Microsatellite Repeats MH - *Pedigree MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Russia OTO - NOTNLM OT - Ancient DNA OT - Genetic kinship OT - Population genetics OT - Short tandem repeats OT - Yakutia EDAT- 2016/10/23 06:00 MHDA- 2017/06/15 06:00 CRDT- 2016/08/09 06:00 PHST- 2016/02/29 00:00 [received] PHST- 2016/07/05 00:00 [revised] PHST- 2016/07/27 00:00 [accepted] PHST- 2016/10/23 06:00 [pubmed] PHST- 2017/06/15 06:00 [medline] PHST- 2016/08/09 06:00 [entrez] AID - S1872-4973(16)30138-7 [pii] AID - 10.1016/j.fsigen.2016.07.018 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2016 Nov;25:52-62. doi: 10.1016/j.fsigen.2016.07.018. Epub 2016 Jul 28. PMID- 27498082 OWN - NLM STAT- MEDLINE DCOM- 20170223 LR - 20170223 IS - 1469-0691 (Electronic) IS - 1198-743X (Linking) VI - 22 IP - 11 DP - 2016 Nov TI - Tools for opening new chapters in the book of Treponema pallidum evolutionary history. PG - 916-921 LID - S1198-743X(16)30265-8 [pii] LID - 10.1016/j.cmi.2016.07.027 [doi] AB - Treponema pallidum infections causing yaws disease and venereal syphilis are globally widespread in human populations, infecting hundreds of thousands and millions annually respectively; endemic syphilis is much less common, and pinta has not been observed in decades. We discuss controversy surrounding the origin, evolution and history of these pathogens in light of available molecular and anthropological evidence. These bacteria (or close relatives) seem to affect many wild African nonhuman primate (NHP) species, though to date only a single NHP Treponema pallidum genome has been published, hindering detection of spillover events and our understanding of potential wildlife reservoirs. Similarly, only ten genomes of Treponema pallidum infecting humans have been published, impeding a full understanding of their diversity and evolutionary history. Research efforts have been hampered by the difficulty of culturing and propagating Treponema pallidum. Here we highlight avenues of research recently opened by the coupling of hybridization capture and next-generation sequencing. We present data generated with such an approach suggesting that asymptomatic bones from NHP occasionally contain enough treponemal DNA to recover large fractions of their genomes. We expect that these methods, which naturally can be applied to modern biopsy samples and ancient human bones, will soon considerably improve our understanding of these enigmatic pathogens and lay rest to old yet unresolved controversies. CI - Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved. FAU - Gogarten, J F AU - Gogarten JF AD - Epidemiology of Highly Pathogenic Microorganisms, Germany; Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Department of Biology, McGill University, Montreal, Quebec, Canada. FAU - Düx, A AU - Düx A AD - Epidemiology of Highly Pathogenic Microorganisms, Germany; Viral Evolution, Robert Koch Institute, Berlin, Germany. FAU - Schuenemann, V J AU - Schuenemann VJ AD - Institute for Archeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Nowak, K AU - Nowak K AD - Epidemiology of Highly Pathogenic Microorganisms, Germany. FAU - Boesch, C AU - Boesch C AD - Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Wittig, R M AU - Wittig RM AD - Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Taï Chimpanzee Project, CSRS, Abidjan, Cote d'Ivoire. FAU - Krause, J AU - Krause J AD - Institute for Archeological Sciences, University of Tübingen, Tübingen, Germany; Max Planck Institute for the Science of Human History, Jena, Germany. FAU - Calvignac-Spencer, S AU - Calvignac-Spencer S AD - Epidemiology of Highly Pathogenic Microorganisms, Germany; Viral Evolution, Robert Koch Institute, Berlin, Germany. Electronic address: CalvignacS@rki.de. FAU - Leendertz, F H AU - Leendertz FH AD - Epidemiology of Highly Pathogenic Microorganisms, Germany. Electronic address: LeendertzF@rki.de. LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20160804 PL - England TA - Clin Microbiol Infect JT - Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases JID - 9516420 SB - IM MH - Bone and Bones/*microbiology MH - Evolution, Molecular MH - High-Throughput Nucleotide Sequencing/methods MH - History, 15th Century MH - Humans MH - Phylogeny MH - Sequence Analysis, DNA/methods MH - Syphilis/*history/microbiology MH - Treponema pallidum/classification/*genetics/isolation & purification MH - Yaws/*history/microbiology OTO - NOTNLM OT - *Ancient DNA OT - *Nonhuman primate reservoirs OT - *Syphilis OT - *Treponema pallidum OT - *Yaws EDAT- 2016/08/09 06:00 MHDA- 2017/02/24 06:00 CRDT- 2016/08/08 06:00 PHST- 2016/05/09 00:00 [received] PHST- 2016/07/04 00:00 [revised] PHST- 2016/07/25 00:00 [accepted] PHST- 2016/08/09 06:00 [pubmed] PHST- 2017/02/24 06:00 [medline] PHST- 2016/08/08 06:00 [entrez] AID - S1198-743X(16)30265-8 [pii] AID - 10.1016/j.cmi.2016.07.027 [doi] PST - ppublish SO - Clin Microbiol Infect. 2016 Nov;22(11):916-921. doi: 10.1016/j.cmi.2016.07.027. Epub 2016 Aug 4. PMID- 27447353 OWN - NLM STAT- MEDLINE DCOM- 20170615 LR - 20180213 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 161 IP - 3 DP - 2016 Nov TI - Ancient mitochondrial DNA from the middle neolithic necropolis of Obernai extends the genetic influence of the LBK to west of the Rhine. PG - 522-529 LID - 10.1002/ajpa.23055 [doi] AB - OBJECTIVES: The arrival of Neolithic farmers in Europe was the source of major cultural and genetic transitions. Neolithic settlers brought a new set of maternal lineages (mitochondrial DNA), recently well-characterized on the continental road, from the Balkans to West Germany (Rhine River). In the present study, the first mitochondrial DNA data from groups associated with this continental expansion wave located west of the Rhine River has been provided and their genetic affinities with contemporary groups have been discussed. MATERIAL AND METHODS: The mitochondrial DNA analysis of 27 human remains originating from Obernai (5,000-4,400 cal. BC), a necropolis located in French Alsace Region and attributed to Grossgartach, Planig-Friedberg, and Roessen cultures was conducted. RESULTS AND DISCUSSION: Among the 27 individuals studied, 15 HVR-I sequences and 17 mitochondrial haplogroups could be determined. The analysis of the Obernai gene pool clearly confirmed the genetic homogeneity of Linearbandkeramik (LBK) groups on both sides of the Rhine River. Notably, one N1a sequence found in Obernai is shared with LBK farmers from Central Europe, including one individual from the Flomborn site located approximately 200 km north-east of Obernai. On the whole, data gathered so far showed major genetic influence of the Danubian wave from Transdanubia to Atlantic French Coast, going by Alsace Region. However, the genetic influence of descendants from the Mediterranean Neolithic expansion and the significant hunter-gatherer admixture detected further west in the Paris Basin were not perceived in the Obernai necropolis. CONCLUSIONS: Genetic homogeneity and continuity within LBK groups can be proposed on both sides of the Rhine River for the middle Neolithic groups. Nevertheless, mitochondrial data gathered so far for Neolithic groups from the entire extant French Territory clearly point out the complexity and the variability of Neolithic communities interactions that is worthy of further investigation. CI - © 2016 Wiley Periodicals, Inc. FAU - Rivollat, Maïté AU - Rivollat M AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France. Maite.Rivollat@u-bordeaux.Fr, maite87@live.Fr. FAU - Réveillas, Hélène AU - Réveillas H AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France. AD - Centre d'Archéologie Préventive de Bordeaux Métropole, direction des Bâtiments et Moyens, Esplanade Charles-de-Gaulle, Bordeaux Cedex, 33 076, France. AD - Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d'Altkirch, Strasbourg, 67000, France. FAU - Mendisco, Fanny AU - Mendisco F AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France. FAU - Pemonge, Marie-Hélène AU - Pemonge MH AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France. FAU - Justeau, Pierre AU - Justeau P AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France. FAU - Couture, Christine AU - Couture C AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France. FAU - Lefranc, Philippe AU - Lefranc P AD - Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d'Altkirch, Strasbourg, 67000, France. AD - Archéologie et Histoire Ancienne: Méditerranée/Europe - UMR 7044, Université de Strasbourg, Maison Interuniversitaire des Sciences de l'Homme d'Alsace, 5 allée du Général Rouvillois, CS 50008, Strasbourg Cedex, 67083, France. FAU - Féliu, Clément AU - Féliu C AD - Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d'Altkirch, Strasbourg, 67000, France. AD - Archéologie et Histoire Ancienne: Méditerranée/Europe - UMR 7044, Université de Strasbourg, Maison Interuniversitaire des Sciences de l'Homme d'Alsace, 5 allée du Général Rouvillois, CS 50008, Strasbourg Cedex, 67083, France. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160722 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture MH - Anthropology, Physical MH - DNA, Ancient/*analysis MH - DNA, Mitochondrial/*genetics/*history MH - France MH - Haplotypes/genetics MH - History, Ancient MH - Humans OTO - NOTNLM OT - 5,000-4,400 cal. BC OT - Rhine region OT - Western Europe OT - farmers OT - paleogenetics EDAT- 2016/10/23 06:00 MHDA- 2017/06/16 06:00 CRDT- 2016/07/23 06:00 PHST- 2016/01/10 00:00 [received] PHST- 2016/07/04 00:00 [revised] PHST- 2016/07/06 00:00 [accepted] PHST- 2016/10/23 06:00 [pubmed] PHST- 2017/06/16 06:00 [medline] PHST- 2016/07/23 06:00 [entrez] AID - 10.1002/ajpa.23055 [doi] PST - ppublish SO - Am J Phys Anthropol. 2016 Nov;161(3):522-529. doi: 10.1002/ajpa.23055. Epub 2016 Jul 22. PMID- 27698418 OWN - NLM STAT- MEDLINE DCOM- 20170321 LR - 20250130 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 538 IP - 7626 DP - 2016 Oct 27 TI - Genomic insights into the peopling of the Southwest Pacific. PG - 510-513 LID - 10.1038/nature19844 [doi] AB - The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100-2,700 years before present) and one from Tonga (about 2,700-2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceania. However, our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands. FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. FAU - Posth, Cosimo AU - Posth C AD - Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany. AD - Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Sirak, Kendra AU - Sirak K AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Dublin, Ireland. AD - Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA. FAU - Spriggs, Matthew AU - Spriggs M AD - School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, Australian Capital Territory 2601, Australia. AD - Vanuatu National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu. FAU - Valentin, Frederique AU - Valentin F AD - Maison de l'Archéologie et de l'Ethnologie, CNRS, UMR 7041, 92023 Nanterre, France. FAU - Bedford, Stuart AU - Bedford S AD - Vanuatu National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu. AD - Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory 2601, Australia. FAU - Clark, Geoffrey R AU - Clark GR AD - Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory 2601, Australia. FAU - Reepmeyer, Christian AU - Reepmeyer C AD - College of Arts, Society and Education, James Cook University, Queensland 4870, Australia. FAU - Petchey, Fiona AU - Petchey F AD - Radiocarbon Dating Laboratory, University of Waikato, Hamilton 3240, New Zealand. FAU - Fernandes, Daniel AU - Fernandes D AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Dublin, Ireland. AD - CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal. FAU - Fu, Qiaomei AU - Fu Q AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China. AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. FAU - Harney, Eadaoin AU - Harney E AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. FAU - Lipson, Mark AU - Lipson M AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. FAU - Novak, Mario AU - Novak M AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Dublin, Ireland. AD - Institute for Anthropological Research, 10000 Zagreb, Croatia. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Abdullah, Syafiq AU - Abdullah S AD - RIPAS Hospital, Bandar Seri Begawan, Brunei Darussalam. FAU - Cox, Murray P AU - Cox MP AD - Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand. FAU - Friedlaender, Françoise R AU - Friedlaender FR AD - Independent Scientist, Sharon, Connecticut 06069, USA. FAU - Friedlaender, Jonathan S AU - Friedlaender JS AD - Department of Anthropology, Temple University, Gladfelter Hall, Philadelphia, Pennsylvania 19122, USA. FAU - Kivisild, Toomas AU - Kivisild T AD - Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia. AD - Division of Archaeology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK. FAU - Koki, George AU - Koki G AD - Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands Province 441, Papua New Guinea. FAU - Kusuma, Pradiptajati AU - Kusuma P AD - Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia. FAU - Merriwether, D Andrew AU - Merriwether DA AD - Department of Anthropology, Binghamton University, Binghamton, New York 13902, USA. FAU - Ricaut, Francois-X AU - Ricaut FX AD - Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université de Toulouse, Toulouse 31073, France. FAU - Wee, Joseph T S AU - Wee JT AD - National Cancer Centre Singapore, Singapore 169610, Singapore. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, 07745 Jena, Germany. FAU - Pinhasi, Ron AU - Pinhasi R AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Dublin, Ireland. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. LA - eng GR - HHMI/HHMI/ GR - 261213/ERC_/European Research Council/International GR - GM100233/National Institute of Health/International GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - 263441/ERC_/European Research Council/International PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20161003 PL - England TA - Nature JT - Nature JID - 0410462 SB - IM MH - Female MH - Humans MH - Male MH - Asian People/genetics MH - Genetics, Population MH - *Genome, Human/genetics MH - *Genomics MH - History, Ancient MH - *Human Migration/history MH - New Guinea/ethnology MH - *Phylogeny MH - Polynesia/ethnology MH - Tonga MH - Vanuatu MH - *Pacific Island People/genetics PMC - PMC5515717 MID - NIHMS862743 COIS- The authors declare no competing financial interests. Readers are welcome to comment on the online version of the paper EDAT- 2016/10/28 06:00 MHDA- 2017/03/23 06:00 PMCR- 2017/07/18 CRDT- 2016/10/05 06:00 PHST- 2016/04/20 00:00 [received] PHST- 2016/09/13 00:00 [accepted] PHST- 2016/10/28 06:00 [pubmed] PHST- 2017/03/23 06:00 [medline] PHST- 2016/10/05 06:00 [entrez] PHST- 2017/07/18 00:00 [pmc-release] AID - nature19844 [pii] AID - 10.1038/nature19844 [doi] PST - ppublish SO - Nature. 2016 Oct 27;538(7626):510-513. doi: 10.1038/nature19844. Epub 2016 Oct 3. PMID- 27741281 OWN - NLM STAT- MEDLINE DCOM- 20170531 LR - 20181113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 11 IP - 10 DP - 2016 TI - High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice. PG - e0164659 LID - 10.1371/journal.pone.0164659 [doi] LID - e0164659 AB - The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A. FAU - Amanzougaghene, Nadia AU - Amanzougaghene N AD - Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille cedex 05, France. FAU - Mumcuoglu, Kosta Y AU - Mumcuoglu KY AD - Parasitology Unit, Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hadassah Medical School, The Hebrew University, Jerusalem, Israel. FAU - Fenollar, Florence AU - Fenollar F AD - Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille cedex 05, France. AD - Campus International UCAD-IRD, Dakar, Senegal. FAU - Alfi, Shir AU - Alfi S AD - Parasitology Unit, Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hadassah Medical School, The Hebrew University, Jerusalem, Israel. FAU - Yesilyurt, Gonca AU - Yesilyurt G AD - Parasitology Unit, Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hadassah Medical School, The Hebrew University, Jerusalem, Israel. FAU - Raoult, Didier AU - Raoult D AD - Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille cedex 05, France. AD - Campus International UCAD-IRD, Dakar, Senegal. FAU - Mediannikov, Oleg AU - Mediannikov O AD - Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille cedex 05, France. AD - Campus International UCAD-IRD, Dakar, Senegal. LA - eng PT - Historical Article PT - Journal Article DEP - 20161014 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (RNA, Ribosomal) RN - 0 (RNA, ribosomal, 12S) RN - 9007-49-2 (DNA) RN - 9035-37-4 (Cytochromes b) SB - IM MH - Animals MH - Base Sequence MH - Cytochromes b/genetics MH - DNA/history/isolation & purification/metabolism MH - *Genetic Variation MH - Haplotypes MH - History, Ancient MH - Humans MH - Israel MH - Likelihood Functions MH - Molecular Sequence Data MH - Ovum/metabolism MH - Pediculus/classification/*genetics/growth & development MH - Phylogeny MH - RNA, Ribosomal/chemistry/genetics/metabolism MH - Real-Time Polymerase Chain Reaction MH - Sequence Alignment PMC - PMC5065229 COIS- The authors have declared that no competing interests exist. EDAT- 2016/10/16 06:00 MHDA- 2017/06/01 06:00 PMCR- 2016/10/14 CRDT- 2016/10/15 06:00 PHST- 2016/07/08 00:00 [received] PHST- 2016/09/28 00:00 [accepted] PHST- 2016/10/15 06:00 [entrez] PHST- 2016/10/16 06:00 [pubmed] PHST- 2017/06/01 06:00 [medline] PHST- 2016/10/14 00:00 [pmc-release] AID - PONE-D-16-27393 [pii] AID - 10.1371/journal.pone.0164659 [doi] PST - epublish SO - PLoS One. 2016 Oct 14;11(10):e0164659. doi: 10.1371/journal.pone.0164659. eCollection 2016. PMID- 27498567 OWN - NLM STAT- MEDLINE DCOM- 20171226 LR - 20181113 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 26 IP - 19 DP - 2016 Oct 10 TI - The Demographic Development of the First Farmers in Anatolia. PG - 2659-2666 LID - S0960-9822(16)30850-8 [pii] LID - 10.1016/j.cub.2016.07.057 [doi] AB - The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [1-3]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [4]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur. CI - Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved. FAU - Kılınç, Gülşah Merve AU - Kılınç GM AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey; Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden. FAU - Omrak, Ayça AU - Omrak A AD - Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativaegen 7, 114 18 Stockholm, Sweden. FAU - Özer, Füsun AU - Özer F AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Günther, Torsten AU - Günther T AD - Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden. FAU - Büyükkarakaya, Ali Metin AU - Büyükkarakaya AM AD - Department of Anthropology, Hacettepe University, Beytepe, 06800 Ankara, Turkey. FAU - Bıçakçı, Erhan AU - Bıçakçı E AD - Department of Prehistory, Istanbul University, Laleli, 34134 Istanbul, Turkey. FAU - Baird, Douglas AU - Baird D AD - Department of Archaeology, Classics, and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK. FAU - Dönertaş, Handan Melike AU - Dönertaş HM AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Ghalichi, Ayshin AU - Ghalichi A AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Yaka, Reyhan AU - Yaka R AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Koptekin, Dilek AU - Koptekin D AD - Department of Health Informatics, Middle East Technical University, 06800 Ankara, Turkey. FAU - Açan, Sinan Can AU - Açan SC AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Parvizi, Poorya AU - Parvizi P AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Krzewińska, Maja AU - Krzewińska M AD - Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden. FAU - Daskalaki, Evangelia A AU - Daskalaki EA AD - Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativaegen 7, 114 18 Stockholm, Sweden. FAU - Yüncü, Eren AU - Yüncü E AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Dağtaş, Nihan Dilşad AU - Dağtaş ND AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. FAU - Fairbairn, Andrew AU - Fairbairn A AD - School of Social Science, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia. FAU - Pearson, Jessica AU - Pearson J AD - Department of Archaeology, Classics, and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK. FAU - Mustafaoğlu, Gökhan AU - Mustafaoğlu G AD - Department of Archaeology, Bülent Ecevit University, 67100 İncivez, Zonguldak, Turkey. FAU - Erdal, Yılmaz Selim AU - Erdal YS AD - Department of Anthropology, Hacettepe University, Beytepe, 06800 Ankara, Turkey. FAU - Çakan, Yasin Gökhan AU - Çakan YG AD - Department of Prehistory, Istanbul University, Laleli, 34134 Istanbul, Turkey. FAU - Togan, İnci AU - Togan İ AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. Electronic address: togan@metu.edu.tr. FAU - Somel, Mehmet AU - Somel M AD - Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey. Electronic address: msomel@metu.edu.tr. FAU - Storå, Jan AU - Storå J AD - Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden. Electronic address: jan.stora@ofl.su.se. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativaegen 7, 114 18 Stockholm, Sweden. Electronic address: mattias.jakobsson@ebc.uu.se. FAU - Götherström, Anders AU - Götherström A AD - Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden. Electronic address: anders.gotherstrom@arklab.su.se. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160804 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM MH - *Agriculture MH - *Archaeology MH - *Farmers MH - *Genetic Variation MH - Humans MH - Turkey PMC - PMC5069350 OTO - NOTNLM OT - Anatolia OT - Neolithic OT - ancient DNA OT - archaeogenomics OT - genetic diversity OT - population genetics EDAT- 2016/08/09 06:00 MHDA- 2017/12/27 06:00 PMCR- 2016/10/10 CRDT- 2016/08/09 06:00 PHST- 2016/07/03 00:00 [received] PHST- 2016/07/18 00:00 [revised] PHST- 2016/07/20 00:00 [accepted] PHST- 2016/08/09 06:00 [pubmed] PHST- 2017/12/27 06:00 [medline] PHST- 2016/08/09 06:00 [entrez] PHST- 2016/10/10 00:00 [pmc-release] AID - S0960-9822(16)30850-8 [pii] AID - 10.1016/j.cub.2016.07.057 [doi] PST - ppublish SO - Curr Biol. 2016 Oct 10;26(19):2659-2666. doi: 10.1016/j.cub.2016.07.057. Epub 2016 Aug 4. PMID- 27846491 OWN - NLM STAT- MEDLINE DCOM- 20170323 LR - 20181113 IS - 1095-9203 (Electronic) IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 354 IP - 6308 DP - 2016 Oct 7 TI - Going global by adapting local: A review of recent human adaptation. PG - 54-59 AB - The spread of modern humans across the globe has led to genetic adaptations to diverse local environments. Recent developments in genomic technologies, statistical analyses, and expanded sampled populations have led to improved identification and fine-mapping of genetic variants associated with adaptations to regional living conditions and dietary practices. Ongoing efforts in sequencing genomes of indigenous populations, accompanied by the growing availability of "-omics" and ancient DNA data, promises a new era in our understanding of recent human evolution and the origins of variable traits and disease risks. CI - Copyright © 2016, American Association for the Advancement of Science. FAU - Fan, Shaohua AU - Fan S AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Hansen, Matthew E B AU - Hansen ME AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Lo, Yancy AU - Lo Y AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. AD - Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Tishkoff, Sarah A AU - Tishkoff SA AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. tishkoff@mail.med.upenn.edu. AD - Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA. LA - eng GR - R01 DK104339/DK/NIDDK NIH HHS/United States GR - P30 ES013508/ES/NIEHS NIH HHS/United States GR - R01 LM010098/LM/NLM NIH HHS/United States GR - R01 LM009012/LM/NLM NIH HHS/United States GR - T32 ES019851/ES/NIEHS NIH HHS/United States GR - R01 GM113657/GM/NIGMS NIH HHS/United States GR - DP1 ES022577/ES/NIEHS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 SB - IM MH - Acclimatization/genetics MH - Adaptation, Physiological/*genetics MH - Altitude MH - Dairy Products MH - Environment MH - *Gene-Environment Interaction MH - Humans MH - Radiation Exposure MH - Rainforest MH - Selection, Genetic MH - Tropical Climate PMC - PMC5154245 MID - NIHMS834016 EDAT- 2016/11/16 06:00 MHDA- 2017/03/24 06:00 PMCR- 2017/04/07 CRDT- 2016/11/16 06:00 PHST- 2016/11/16 06:00 [entrez] PHST- 2016/11/16 06:00 [pubmed] PHST- 2017/03/24 06:00 [medline] PHST- 2017/04/07 00:00 [pmc-release] AID - 354/6308/54 [pii] AID - 10.1126/science.aaf5098 [doi] PST - ppublish SO - Science. 2016 Oct 7;354(6308):54-59. doi: 10.1126/science.aaf5098. PMID- 27706187 OWN - NLM STAT- MEDLINE DCOM- 20170620 LR - 20190212 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 11 IP - 10 DP - 2016 TI - A Molecular Approach to the Sexing of the Triple Burial at the Upper Paleolithic Site of Dolní Věstonice. PG - e0163019 LID - 10.1371/journal.pone.0163019 [doi] LID - e0163019 AB - In the past decades ancient DNA research has brought numerous insights to archaeological research where traditional approaches were limited. The determination of sex in human skeletal remains is often challenging for physical anthropologists when dealing with incomplete, juvenile or pathological specimens. Molecular approaches allow sexing on the basis of sex-specific markers or by calculating the ratio of DNA derived from different chromosomes. Here we propose a novel approach that relies on the ratio of X chromosome-derived shotgun sequencing data to the autosomal coverage, thus establishing the probability of an XX or XY karyotype. Applying this approach to the individuals of the Upper Paleolithic triple burial of Dolní Věstonice reveals that all three skeletons, including the individual DV 15, whose sex has long been debated due to a pathological condition, were male. FAU - Mittnik, Alissa AU - Mittnik A AD - Max Planck Institute for the Science of Human History, D-07745, Jena, Germany. AD - Institute for Archeological Sciences, University of Tübingen, D-72070, Tübingen, Germany. FAU - Wang, Chuan-Chao AU - Wang CC AD - Institute for Archeological Sciences, University of Tübingen, D-72070, Tübingen, Germany. AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, United States of America. FAU - Svoboda, Jiří AU - Svoboda J AD - Department of Anthropology, Faculty of Science, Masaryk University, Kotlářská, 61137, Brno, Czech Republic. AD - Institute of Archaeology, Academy of Science of the Czech Republic, 69129, Dolní Věstonice, Czech Republic. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, D-07745, Jena, Germany. AD - Institute for Archeological Sciences, University of Tübingen, D-72070, Tübingen, Germany. LA - eng PT - Journal Article DEP - 20161005 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 9007-49-2 (DNA) SB - IM MH - Archaeology MH - Bone and Bones/*metabolism MH - Chromosomes, Human, X/*genetics MH - DNA/chemistry/isolation & purification/metabolism MH - Female MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Karyotype MH - Male MH - Sequence Analysis, DNA MH - Sex PMC - PMC5051676 COIS- The authors have declared that no competing interests exist. EDAT- 2016/10/06 06:00 MHDA- 2017/06/21 06:00 PMCR- 2016/10/05 CRDT- 2016/10/06 06:00 PHST- 2015/12/08 00:00 [received] PHST- 2016/09/01 00:00 [accepted] PHST- 2016/10/06 06:00 [entrez] PHST- 2016/10/06 06:00 [pubmed] PHST- 2017/06/21 06:00 [medline] PHST- 2016/10/05 00:00 [pmc-release] AID - PONE-D-15-53244 [pii] AID - 10.1371/journal.pone.0163019 [doi] PST - epublish SO - PLoS One. 2016 Oct 5;11(10):e0163019. doi: 10.1371/journal.pone.0163019. eCollection 2016. PMID- 27378746 OWN - NLM STAT- MEDLINE DCOM- 20180417 LR - 20181202 IS - 1096-0325 (Electronic) IS - 0040-5809 (Linking) VI - 111 DP - 2016 Oct TI - Genetic demographic networks: Mathematical model and applications. PG - 75-86 LID - S0040-5809(16)30025-9 [pii] LID - 10.1016/j.tpb.2016.06.004 [doi] AB - Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans. CI - Copyright © 2016 Elsevier Inc. All rights reserved. FAU - Kimmel, Marek AU - Kimmel M AD - Department of Statistics, Rice University, 6100 Main Street, Houston, TX 77005, USA; Systems Engineering Group, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland. Electronic address: kimmel@rice.edu. FAU - Wojdyła, Tomasz AU - Wojdyła T AD - Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland. Electronic address: tomasz.wojdyla@gmail.com. LA - eng PT - Journal Article DEP - 20160701 PL - United States TA - Theor Popul Biol JT - Theoretical population biology JID - 0256422 SB - IM MH - *Demography MH - Genetic Variation MH - *Genetics, Population MH - Humans MH - *Markov Chains MH - *Models, Theoretical OTO - NOTNLM OT - Allele joint distributions OT - Cro-Magnoids and Neanderthals OT - Demographic networks OT - Farming expansion OT - Finns–Balts–Slavs history OT - Gene genealogies EDAT- 2016/07/06 06:00 MHDA- 2018/04/18 06:00 CRDT- 2016/07/06 06:00 PHST- 2015/06/07 00:00 [received] PHST- 2016/06/21 00:00 [revised] PHST- 2016/06/24 00:00 [accepted] PHST- 2016/07/06 06:00 [entrez] PHST- 2016/07/06 06:00 [pubmed] PHST- 2018/04/18 06:00 [medline] AID - S0040-5809(16)30025-9 [pii] AID - 10.1016/j.tpb.2016.06.004 [doi] PST - ppublish SO - Theor Popul Biol. 2016 Oct;111:75-86. doi: 10.1016/j.tpb.2016.06.004. Epub 2016 Jul 1. PMID- 27869396 OWN - NLM STAT- MEDLINE DCOM- 20180326 LR - 20181202 IS - 2590-7379 (Electronic) IS - 0120-4157 (Linking) VI - 36 IP - 3 DP - 2016 Sep 1 TI - [Real-time quantification to analyze historical Colombian samples detecting a short fragment of hypervariable region II of mitochondrial DNA]. PG - 475-482 LID - 10.7705/biomedica.v36i3.3098 [doi] AB - Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples. Materials and methods: The proposed method is based on the use of mini-primers for the specific amplification of short fragments of mitochondrial DNA. The subsequent purification of these amplified fragments allows a standard curve to be constructed with concentrations in accordance to the state of degradation of the samples. Results: The proposed method successfully detected DNA from ancient samples including bone remains and mummified tissue. DNA inhibitory substances were also detected. Conclusion: The proposed method represents a simpler and cost-effective way to detect low amounts of aDNA, and a tool to differentiate DNA-free samples from samples with inhibitory substances. FAU - Pérez, Luz Adriana AU - Pérez LA AD - Laboratorio de ADN, Universidad de los Andes, Bogotá, D.C., Colombia. la.perez58@uniandes.edu.co. FAU - Rodríguez, Freddy AU - Rodríguez F FAU - Langebaek, Carl Henrik AU - Langebaek CH FAU - Groot, Helena AU - Groot H LA - spa PT - Journal Article DEP - 20160901 PL - Colombia TA - Biomedica JT - Biomedica : revista del Instituto Nacional de Salud JID - 8205605 RN - 0 (DNA, Mitochondrial) SB - IM MH - Colombia MH - *DNA, Mitochondrial MH - Humans MH - *Real-Time Polymerase Chain Reaction OTO - NOTNLM OT - DNA OT - DNA, mitocondrial OT - polymerase chain reaction EDAT- 2016/11/22 06:00 MHDA- 2018/03/27 06:00 CRDT- 2016/11/22 06:00 PHST- 2015/10/16 00:00 [received] PHST- 2016/03/17 00:00 [revised] PHST- 2016/11/22 06:00 [entrez] PHST- 2016/11/22 06:00 [pubmed] PHST- 2018/03/27 06:00 [medline] AID - 10.7705/biomedica.v36i3.3098 [doi] PST - epublish SO - Biomedica. 2016 Sep 1;36(3):475-482. doi: 10.7705/biomedica.v36i3.3098. PMID- 27509860 OWN - NLM STAT- MEDLINE DCOM- 20170303 LR - 20181202 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 537 IP - 7618 DP - 2016 Sep 1 TI - Ancient DNA: Muddy messages about American migration. PG - 43-44 LID - 10.1038/nature19421 [doi] FAU - McGowan, Suzanne AU - McGowan S AD - School of Geography, University of Nottingham, Nottingham NG7 2RD, UK. LA - eng PT - Comment PT - Journal Article DEP - 20160810 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM CON - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130383. doi: 10.1098/rstb.2013.0383. PMID: 25487334 CON - New Phytol. 2016 Jan;209(2):499-506. doi: 10.1111/nph.13657. PMID: 26402315 CON - Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):8057-63. doi: 10.1073/pnas.1601077113. PMID: 27274051 CON - Nature. 2016 Sep 1;537(7618):45-49. doi: 10.1038/nature19085. PMID: 27509852 MH - DNA MH - *DNA, Ancient MH - DNA, Mitochondrial MH - *Fossils MH - Humans MH - Sequence Analysis, DNA EDAT- 2016/08/12 06:00 MHDA- 2017/03/04 06:00 CRDT- 2016/08/12 06:00 PHST- 2016/08/12 06:00 [pubmed] PHST- 2017/03/04 06:00 [medline] PHST- 2016/08/12 06:00 [entrez] AID - nature19421 [pii] AID - 10.1038/nature19421 [doi] PST - ppublish SO - Nature. 2016 Sep 1;537(7618):43-44. doi: 10.1038/nature19421. Epub 2016 Aug 10. PMID- 27362779 OWN - NLM STAT- MEDLINE DCOM- 20180309 LR - 20181202 IS - 1556-4029 (Electronic) IS - 0022-1198 (Linking) VI - 61 IP - 5 DP - 2016 Sep TI - Forensic Analysis Reveals Acute Decompensation of Chronic Heart Failure in a 3500-Year-Old Egyptian Dignitary. PG - 1378-81 LID - 10.1111/1556-4029.13138 [doi] AB - Naturally preserved and embalmed bodies from archeological contexts represent a powerful source of information for forensic investigators. They allow one to ascertain pathology, cause of death, to enhance diagnostic methodology, and to improve the analysis of altered remains. We investigated the complete head and lung remnants of a 3,500-year-old Egyptian dignitary by radiological, microscopic, and genetic approaches. The individual, a middle-aged male, suffered from severe periodontitis, mild atherosclerosis, and experienced cardiogenic pulmonary insufficiency with recurrent mini-bleeds and pulmonary edema. Histology and ancient DNA analyses excluded the presence of Mycobacterium tuberculosis or of any other pathogenic species. Based on our collection of evidence, we propose that acute decompensation complicating chronic cardiac insufficiency was the likely cause of death. The underlying causes for this failure remain unknown although chronic hypertension appears to be the most likely candidate. Our finding represents the earliest reported case of chronic heart failure in ancient mummies. CI - © 2016 American Academy of Forensic Sciences. FAU - Bianucci, Raffaella AU - Bianucci R AUID- ORCID: 0000-0003-2740-4112 AD - Legal Medicine Section, Department of Public Health and Paediatric Sciences, University of Turin, Corso Galileo Galilei, 22, 10126, Turin, Italy. raffaella.bianucci@unito.it, raffaella.bianucci@gmail.com. AD - UMR 7268, Laboratoire d'Anthropologie bio-culturelle, Droit, Etique & Santé (Adés), Faculté de Médecine de Marseille, Bd Pierre Dramard, BAT A CS, 80011, 13444, Marseilles- Cedex 15- France. raffaella.bianucci@unito.it, raffaella.bianucci@gmail.com. FAU - Loynes, Robert D AU - Loynes RD AD - KNH Centre for Biomedical Egyptology, University of Manchester, 3.5 Stopford Building, Oxford Road, Manchester, M13 9PT, U.K. FAU - Sutherland, M Linda AU - Sutherland ML AD - Newport Diagnostic Center, 1605 Avocado Avenue, Newport Beach, CA 92660. FAU - Lallo, Rudy AU - Lallo R AD - Clinica Pinna Pintor, Via Amerigo Vespucci 61, 10129, Turin, Italy. FAU - Kay, Gemma L AU - Kay GL AD - Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Medical School Building, Coventry, West Midlands CV4, United Kingdom. FAU - Froesch, Philippe AU - Froesch P AD - Section of Medical and Forensic Anthropology (UVSQ & Paris 5 University EA 4569), 2 Avenue de la source de la Bièvre, Montigny-le-Bretonneux, 78180, France. FAU - Pallen, Mark J AU - Pallen MJ AD - Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Medical School Building, Coventry, West Midlands CV4, United Kingdom. FAU - Charlier, Philippe AU - Charlier P AD - Section of Medical and Forensic Anthropology (UVSQ & Paris 5 University EA 4569), 2 Avenue de la source de la Bièvre, Montigny-le-Bretonneux, 78180, France. FAU - Nerlich, Andreas G AU - Nerlich AG AD - Institute of Pathology, Klinikum München-Bogenhausen, Englschalkinger Str. 77, 81925, Munich, Germany. LA - eng PT - Case Reports PT - Journal Article DEP - 20160630 PL - United States TA - J Forensic Sci JT - Journal of forensic sciences JID - 0375370 SB - IM MH - *Atherosclerosis MH - Egypt MH - Forensic Anthropology MH - *Heart Failure MH - Humans MH - Lung MH - Male MH - *Mummies OTO - NOTNLM OT - forensic science OT - histology OT - mummified remains OT - pulmonary bleeding OT - pulmonary edema OT - shotgun metagenomics EDAT- 2016/07/01 06:00 MHDA- 2018/03/10 06:00 CRDT- 2016/07/01 06:00 PHST- 2015/09/09 00:00 [received] PHST- 2015/12/19 00:00 [revised] PHST- 2016/01/02 00:00 [accepted] PHST- 2016/07/01 06:00 [entrez] PHST- 2016/07/01 06:00 [pubmed] PHST- 2018/03/10 06:00 [medline] AID - 10.1111/1556-4029.13138 [doi] PST - ppublish SO - J Forensic Sci. 2016 Sep;61(5):1378-81. doi: 10.1111/1556-4029.13138. Epub 2016 Jun 30. PMID- 27292545 OWN - NLM STAT- MEDLINE DCOM- 20170105 LR - 20170106 IS - 1090-2449 (Electronic) IS - 0014-4894 (Linking) VI - 168 DP - 2016 Sep TI - Recovery of Toxoplasma gondii DNA in experimentally mummified skin and bones: Prospects for paleoparasitological studies to unveil the origin of toxoplasmosis. PG - 51-5 LID - S0014-4894(16)30115-1 [pii] LID - 10.1016/j.exppara.2016.06.003 [doi] AB - Paleoparasitology studies parasite infections by finding the parasites' remains in preserved organic remains such as natural or artificial mummy tissues, skeletons, teeth, and coprolites, among others. However, some currently important infections like toxoplasmosis have not been studied by paleoparasitology. The reasons include this parasite's complex life cycle, the resulting difficulties in locating this protozoan in the intermediate host tissues, and the limitation of coprolite studies to felines, the protozoan's definitive host. The current study thus aimed to produce an experimental model for molecular diagnosis of toxoplasmosis, prioritizing its study in bones and skin, the most abundant materials in archeological collections and sites. The study demonstrated the feasibility of recovering Toxoplasma gondii DNA from desiccated material, including bones and skin, in experimental models both with circulating tachyzoites (RH strain), characteristic of acute infection, and with cysts (ME49 cystogenic strain), characteristic of chronic infection. At present, most individuals with T. gondii infection are in the chronic phase, and the same was probably true in the past. The current study thus expands the odds of finding the parasite in archeological material, enhanced by the nature of the material in which the diagnosis was made. Finding the parasite may help answer questions that are widely debated in the literature on this protozoan's origin (Old World versus New World). In addition, when conditions do not allow ideal storage of samples for molecular tests, the methodology creates the possibility of testing oven-dried samples transported at room temperature. CI - Copyright © 2016 Elsevier Inc. All rights reserved. FAU - Leles, Daniela AU - Leles D AD - Laboratory of Parasite Molecular Biology, Department of Microbiology and Parasitology, Fluminense Federal University, Niterói, RJ, Brazil. Electronic address: dleles@id.uff.br. FAU - Lobo, Amanda AU - Lobo A AD - Laboratory of Paleoparasitology, Escola Nacional de Saúde Pública/Fiocruz, Rio de Janeiro, RJ, Brazil. FAU - Rhodes, Taís AU - Rhodes T AD - Laboratory of Parasite Molecular Biology, Department of Microbiology and Parasitology, Fluminense Federal University, Niterói, RJ, Brazil. FAU - Millar, Patrícia Riddell AU - Millar PR AD - Laboratory of Parasite Molecular Biology, Department of Microbiology and Parasitology, Fluminense Federal University, Niterói, RJ, Brazil. FAU - Amendoeira, Maria Regina Reis AU - Amendoeira MR AD - Laboratory of Toxoplasmosis and Other Protozoan Infections, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, RJ, Brazil. FAU - Araújo, Adauto AU - Araújo A AD - Laboratory of Paleoparasitology, Escola Nacional de Saúde Pública/Fiocruz, Rio de Janeiro, RJ, Brazil. LA - eng PT - Historical Article PT - Journal Article DEP - 20160610 PL - United States TA - Exp Parasitol JT - Experimental parasitology JID - 0370713 RN - 0 (DNA, Protozoan) SB - IM MH - Animals MH - Bone and Bones/parasitology MH - DNA, Protozoan/*isolation & purification MH - History, Ancient MH - Humans MH - Mice MH - Models, Animal MH - Mummies/*parasitology MH - Skin/parasitology MH - Toxoplasma/*genetics/isolation & purification MH - Toxoplasmosis/*history OTO - NOTNLM OT - Ancient DNA OT - Bones OT - Diagnosis OT - Mummies OT - Toxoplasmosis EDAT- 2016/06/14 06:00 MHDA- 2017/01/06 06:00 CRDT- 2016/06/14 06:00 PHST- 2015/12/21 00:00 [received] PHST- 2016/06/06 00:00 [revised] PHST- 2016/06/08 00:00 [accepted] PHST- 2016/06/14 06:00 [entrez] PHST- 2016/06/14 06:00 [pubmed] PHST- 2017/01/06 06:00 [medline] AID - S0014-4894(16)30115-1 [pii] AID - 10.1016/j.exppara.2016.06.003 [doi] PST - ppublish SO - Exp Parasitol. 2016 Sep;168:51-5. doi: 10.1016/j.exppara.2016.06.003. Epub 2016 Jun 10. PMID- 27289479 OWN - NLM STAT- MEDLINE DCOM- 20180201 LR - 20181113 IS - 1432-1440 (Electronic) IS - 0946-2716 (Linking) VI - 94 IP - 9 DP - 2016 Sep TI - Archaeogenetics in evolutionary medicine. PG - 971-7 LID - 10.1007/s00109-016-1438-8 [doi] AB - Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming. FAU - Bouwman, Abigail AU - Bouwman A AD - Universitat Zurich, Zürich, Switzerland. abigail.bouwman@iem.uzh.ch. FAU - Rühli, Frank AU - Rühli F AD - Universitat Zurich, Zürich, Switzerland. LA - eng PT - Journal Article PT - Review DEP - 20160611 PL - Germany TA - J Mol Med (Berl) JT - Journal of molecular medicine (Berlin, Germany) JID - 9504370 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Archaeology/methods MH - DNA/genetics MH - Environment MH - *Evolution, Molecular MH - Gene-Environment Interaction MH - *Genetic Association Studies/methods MH - *Genetic Predisposition to Disease MH - Genetics, Population MH - Genomics/methods MH - Host-Pathogen Interactions/*genetics MH - Humans OTO - NOTNLM OT - Adaptive changes OT - Evolution of health OT - Immunity OT - Pathogen EDAT- 2016/06/13 06:00 MHDA- 2018/02/02 06:00 CRDT- 2016/06/13 06:00 PHST- 2015/12/24 00:00 [received] PHST- 2016/06/03 00:00 [accepted] PHST- 2016/05/22 00:00 [revised] PHST- 2016/06/13 06:00 [entrez] PHST- 2016/06/13 06:00 [pubmed] PHST- 2018/02/02 06:00 [medline] AID - 10.1007/s00109-016-1438-8 [pii] AID - 10.1007/s00109-016-1438-8 [doi] PST - ppublish SO - J Mol Med (Berl). 2016 Sep;94(9):971-7. doi: 10.1007/s00109-016-1438-8. Epub 2016 Jun 11. PMID- 27459054 OWN - NLM STAT- MEDLINE DCOM- 20160927 LR - 20220129 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 536 IP - 7617 DP - 2016 Aug 25 TI - Genomic insights into the origin of farming in the ancient Near East. PG - 419-24 AB - We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia. FAU - Lazaridis, Iosif AU - Lazaridis I FAU - Nadel, Dani AU - Nadel D FAU - Rollefson, Gary AU - Rollefson G FAU - Merrett, Deborah C AU - Merrett DC FAU - Rohland, Nadin AU - Rohland N FAU - Mallick, Swapan AU - Mallick S FAU - Fernandes, Daniel AU - Fernandes D FAU - Novak, Mario AU - Novak M FAU - Gamarra, Beatriz AU - Gamarra B FAU - Sirak, Kendra AU - Sirak K FAU - Connell, Sarah AU - Connell S FAU - Stewardson, Kristin AU - Stewardson K FAU - Harney, Eadaoin AU - Harney E FAU - Fu, Qiaomei AU - Fu Q FAU - Gonzalez-Fortes, Gloria AU - Gonzalez-Fortes G FAU - Jones, Eppie R AU - Jones ER FAU - Roodenberg, Songül Alpaslan AU - Roodenberg SA FAU - Lengyel, György AU - Lengyel G FAU - Bocquentin, Fanny AU - Bocquentin F FAU - Gasparian, Boris AU - Gasparian B FAU - Monge, Janet M AU - Monge JM FAU - Gregg, Michael AU - Gregg M FAU - Eshed, Vered AU - Eshed V FAU - Mizrahi, Ahuva-Sivan AU - Mizrahi AS FAU - Meiklejohn, Christopher AU - Meiklejohn C FAU - Gerritsen, Fokke AU - Gerritsen F FAU - Bejenaru, Luminita AU - Bejenaru L FAU - Blüher, Matthias AU - Blüher M FAU - Campbell, Archie AU - Campbell A FAU - Cavalleri, Gianpiero AU - Cavalleri G FAU - Comas, David AU - Comas D FAU - Froguel, Philippe AU - Froguel P FAU - Gilbert, Edmund AU - Gilbert E FAU - Kerr, Shona M AU - Kerr SM FAU - Kovacs, Peter AU - Kovacs P FAU - Krause, Johannes AU - Krause J FAU - McGettigan, Darren AU - McGettigan D FAU - Merrigan, Michael AU - Merrigan M FAU - Merriwether, D Andrew AU - Merriwether DA FAU - O'Reilly, Seamus AU - O'Reilly S FAU - Richards, Martin B AU - Richards MB FAU - Semino, Ornella AU - Semino O FAU - Shamoon-Pour, Michel AU - Shamoon-Pour M FAU - Stefanescu, Gheorghe AU - Stefanescu G FAU - Stumvoll, Michael AU - Stumvoll M FAU - Tönjes, Anke AU - Tönjes A FAU - Torroni, Antonio AU - Torroni A FAU - Wilson, James F AU - Wilson JF FAU - Yengo, Loic AU - Yengo L FAU - Hovhannisyan, Nelli A AU - Hovhannisyan NA FAU - Patterson, Nick AU - Patterson N FAU - Pinhasi, Ron AU - Pinhasi R FAU - Reich, David AU - Reich D LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - CZD/16/6/Chief Scientist Office/United Kingdom GR - HHMI/Howard Hughes Medical Institute/United States GR - CZD/16/6/4/CSO_/Chief Scientist Office/United Kingdom GR - 263441/ERC_/European Research Council/International GR - MC_PC_U127561128/MRC_/Medical Research Council/United Kingdom GR - GM100233/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20160725 PL - England TA - Nature JT - Nature JID - 0410462 RN - 9007-49-2 (DNA) SB - IM MH - Africa, Eastern MH - Agriculture/*history MH - Animals MH - Armenia MH - Asia MH - DNA/analysis MH - Europe MH - *Genomics MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Hybridization, Genetic/genetics MH - Iran MH - Israel MH - Jordan MH - Neanderthals/genetics MH - *Phylogeny MH - Phylogeography MH - Racial Groups/*genetics MH - Turkey PMC - PMC5003663 MID - NIHMS804247 EDAT- 2016/07/28 06:00 MHDA- 2016/09/28 06:00 PMCR- 2017/02/25 CRDT- 2016/07/27 06:00 PHST- 2016/03/08 00:00 [received] PHST- 2016/07/18 00:00 [accepted] PHST- 2017/02/25 00:00 [pmc-release] PHST- 2016/07/27 06:00 [entrez] PHST- 2016/07/28 06:00 [pubmed] PHST- 2016/09/28 06:00 [medline] AID - nature19310 [pii] AID - 10.1038/nature19310 [doi] PST - ppublish SO - Nature. 2016 Aug 25;536(7617):419-24. doi: 10.1038/nature19310. Epub 2016 Jul 25. PMID- 27534956 OWN - NLM STAT- MEDLINE DCOM- 20171211 LR - 20210109 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 283 IP - 1836 DP - 2016 Aug 17 TI - How old are bacterial pathogens? LID - 10.1098/rspb.2016.0990 [doi] LID - 20160990 AB - Only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. The global genetic diversity of Helicobacter pylori, which infects human stomachs, parallels that of its human host. The time to the most recent common ancestor (tMRCA) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence within H. pylori against major ancient human migrations. Similarly, genomic reconstructions of Mycobacterium tuberculosis, the cause of tuberculosis, from ancient skeletons in South America and mummies in Hungary support estimates of less than 6000 years for the tMRCA of M. tuberculosis Finally, modern global patterns of genetic diversity and ancient DNA studies indicate that during the last 5000 years plague caused by Yersinia pestis has spread globally on multiple occasions from China and Central Asia. Such tMRCA estimates provide only lower bounds on the ages of bacterial pathogens, and additional studies are needed for realistic upper bounds on how long humans and animals have suffered from bacterial diseases. CI - © 2016 The Author(s). FAU - Achtman, Mark AU - Achtman M AUID- ORCID: 0000-0001-6815-0070 AD - Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK m.achtman@warwick.ac.uk. LA - eng GR - BB/L020319/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Review PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Bacterial) SB - IM MH - Animals MH - *Biological Evolution MH - DNA, Bacterial/analysis MH - *Genome, Bacterial MH - Helicobacter pylori/*genetics MH - Humans MH - Mycobacterium tuberculosis/*genetics MH - Yersinia pestis/*genetics PMC - PMC5013766 OTO - NOTNLM OT - ancient DNA OT - comparative genomics OT - gastritis OT - history of disease OT - plague OT - tuberculosis EDAT- 2016/08/19 06:00 MHDA- 2017/12/12 06:00 PMCR- 2016/08/17 CRDT- 2016/08/19 06:00 PHST- 2016/05/05 00:00 [received] PHST- 2016/07/21 00:00 [accepted] PHST- 2016/08/19 06:00 [entrez] PHST- 2016/08/19 06:00 [pubmed] PHST- 2017/12/12 06:00 [medline] PHST- 2016/08/17 00:00 [pmc-release] AID - rspb.2016.0990 [pii] AID - rspb20160990 [pii] AID - 10.1098/rspb.2016.0990 [doi] PST - ppublish SO - Proc Biol Sci. 2016 Aug 17;283(1836):20160990. doi: 10.1098/rspb.2016.0990. PMID- 27726782 OWN - NLM STAT- MEDLINE DCOM- 20170705 LR - 20200108 IS - 2165-0497 (Electronic) IS - 2165-0497 (Linking) VI - 4 IP - 4 DP - 2016 Aug TI - Paleomicrobiology of Human Tuberculosis. LID - 10.1128/microbiolspec.PoH-0003-2014 [doi] AB - Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections. These can be recognized in historical and archaeological material, along with nonspecific paleopathology such as new bone formation (periostitis), especially on ribs. Based on such lesions, tuberculosis has been found in ancient Egypt, pre-Columbian America, and Neolithic Europe. The detection of M. tuberculosis ancient DNA (aDNA) by using PCR led to the development of the new field of paleomicrobiology. As a result, a large number of tuberculosis cases were recognized in mummified tissue and bones with nonspecific or no lesions. In parallel with these developments, M. tuberculosis cell wall lipid biomarkers have detected tuberculosis suggested by paleopathology and confirmed aDNA findings. In well-preserved cases, molecular typing has identified M. tuberculosis lineages and genotypes. The current interest in targeted enrichment, shotgun sequencing, and metagenomic analysis reveals ancient mixed infections with different M. tuberculosis strains and other pathogens. Identification of M. tuberculosis lineages from samples of known age enables the date of the emergence of strains and lineages to be calculated directly rather than by making assumptions on the rate of evolutionary change. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, United Kingdom. LA - eng PT - Historical Article PT - Journal Article PT - Review PL - United States TA - Microbiol Spectr JT - Microbiology spectrum JID - 101634614 RN - 0 (DNA, Bacterial) SB - IM MH - Americas MH - Animals MH - DNA, Bacterial/genetics/isolation & purification MH - Egypt MH - Europe MH - Fossils/*microbiology MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, 20th Century MH - History, 21st Century MH - History, Ancient MH - History, Medieval MH - Humans MH - Microbiological Techniques/*methods MH - Mycobacterium tuberculosis/classification/genetics/*isolation & purification MH - Paleopathology/*methods MH - Phylogeny MH - Polymerase Chain Reaction MH - Tuberculosis/*epidemiology/history/*microbiology EDAT- 2016/10/12 06:00 MHDA- 2017/07/06 06:00 CRDT- 2016/10/12 06:00 PHST- 2016/10/12 06:00 [entrez] PHST- 2016/10/12 06:00 [pubmed] PHST- 2017/07/06 06:00 [medline] AID - 10.1128/microbiolspec.PoH-0003-2014 [doi] PST - ppublish SO - Microbiol Spectr. 2016 Aug;4(4). doi: 10.1128/microbiolspec.PoH-0003-2014. PMID- 27726770 OWN - NLM STAT- MEDLINE DCOM- 20170705 LR - 20240324 IS - 2165-0497 (Electronic) IS - 2165-0497 (Linking) VI - 4 IP - 4 DP - 2016 Aug TI - Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology. LID - 10.1128/microbiolspec.EMF-0006-2015 [doi] AB - Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses. FAU - Rivera-Perez, Jessica I AU - Rivera-Perez JI AD - University of Puerto Rico, San Juan, Puerto Rico 00933. FAU - Santiago-Rodriguez, Tasha M AU - Santiago-Rodriguez TM AD - California Polytechnic State University, San Luis Obispo, CA 93407. FAU - Toranzos, Gary A AU - Toranzos GA AD - University of Puerto Rico, San Juan, Puerto Rico 00933. LA - eng GR - R25 GM061151/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Review PL - United States TA - Microbiol Spectr JT - Microbiology spectrum JID - 101634614 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/genetics/isolation & purification MH - Forensic Medicine/*methods MH - Fossils/*microbiology MH - Humans MH - Microbiological Techniques/*methods MH - Paleopathology/*methods PMC - PMC5287379 MID - NIHMS845536 EDAT- 2016/10/12 06:00 MHDA- 2017/07/06 06:00 PMCR- 2017/08/01 CRDT- 2016/10/12 06:00 PHST- 2016/10/12 06:00 [entrez] PHST- 2016/10/12 06:00 [pubmed] PHST- 2017/07/06 06:00 [medline] PHST- 2017/08/01 00:00 [pmc-release] AID - 10.1128/microbiolspec.EMF-0006-2015 [doi] PST - ppublish SO - Microbiol Spectr. 2016 Aug;4(4):10.1128/microbiolspec.EMF-0006-2015. doi: 10.1128/microbiolspec.EMF-0006-2015. PMID- 27517578 OWN - NLM STAT- MEDLINE DCOM- 20170526 LR - 20181113 IS - 1432-1432 (Electronic) IS - 0022-2844 (Linking) VI - 83 IP - 1-2 DP - 2016 Aug TI - Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept. PG - 78-87 LID - 10.1007/s00239-016-9755-7 [doi] AB - A number of recent articles have appeared on the Denisova fossil remains and attempts to produce DNA sequences from them. One of these recently appeared in Science by Vernot et al. (Science 352:235-239, 2016). We would like to advance an alternative interpretation of the data presented. One concerns the problem of contamination/degradation of the determined DNA sequenced. Just as the publication of the first Neandertal sequence included an interpretation that argued that Neandertals had not contributed any genes to modern humans, the Denisovan interpretation has considerable influence on ideas regarding human evolution. The new papers, however, confuse established ideas concerning the nature of species, as well as the use of terms like premodern, Archaic Homo, and Homo heidelbergensis. Examination of these problems presents a solution by means of reinterpreting the results. Given the claims for gene transfer among a number of Mid Pleistocene hominids, it may be time to reexamine the idea of anagenesis in hominid evolution. FAU - Caldararo, Niccolo AU - Caldararo N AD - Department of Anthropology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA, 94132, USA. cald@sfsu.edu. LA - eng PT - Letter DEP - 20160812 PL - Germany TA - J Mol Evol JT - Journal of molecular evolution JID - 0360051 RN - 0 (DNA, Ancient) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Biological Evolution MH - DNA/genetics MH - DNA, Ancient/*analysis MH - Fossils MH - Hominidae/genetics MH - Humans MH - Neanderthals/*genetics MH - Sequence Alignment/methods MH - Sequence Analysis, DNA/methods OTO - NOTNLM OT - Anagenesis OT - Ancient DNA OT - Denisovans OT - Evolution OT - Neandertals OT - Premoderns OT - Sima de los Huesos OT - Speciation EDAT- 2016/08/16 06:00 MHDA- 2017/05/27 06:00 CRDT- 2016/08/13 06:00 PHST- 2016/06/02 00:00 [received] PHST- 2016/07/30 00:00 [accepted] PHST- 2016/08/13 06:00 [entrez] PHST- 2016/08/16 06:00 [pubmed] PHST- 2017/05/27 06:00 [medline] AID - 10.1007/s00239-016-9755-7 [pii] AID - 10.1007/s00239-016-9755-7 [doi] PST - ppublish SO - J Mol Evol. 2016 Aug;83(1-2):78-87. doi: 10.1007/s00239-016-9755-7. Epub 2016 Aug 12. PMID- 27436340 OWN - NLM STAT- MEDLINE DCOM- 20170118 LR - 20210109 IS - 1756-1663 (Electronic) IS - 1340-2838 (Print) IS - 1340-2838 (Linking) VI - 23 IP - 4 DP - 2016 Aug TI - Toward high-resolution population genomics using archaeological samples. PG - 295-310 LID - 10.1093/dnares/dsw029 [doi] AB - The term 'ancient DNA' (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of 'molecular paleontology'. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research. CI - © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. FAU - Morozova, Irina AU - Morozova I AD - Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland tatiana.tatarinova@usc.edu irina.morozova@iem.uzh.ch. FAU - Flegontov, Pavel AU - Flegontov P AD - Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation. FAU - Mikheyev, Alexander S AU - Mikheyev AS AD - Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan. FAU - Bruskin, Sergey AU - Bruskin S AD - Vavilov Institute of General Genetics RAS, Moscow, Russia. FAU - Asgharian, Hosseinali AU - Asgharian H AD - Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA. FAU - Ponomarenko, Petr AU - Ponomarenko P AD - Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA. FAU - Klyuchnikov, Vladimir AU - Klyuchnikov V AD - Donskaya Archeologia, Rostov, Russia. FAU - ArunKumar, GaneshPrasad AU - ArunKumar G AD - School of Chemical and Biotechnology, SASTRA University, Tanjore, India. FAU - Prokhortchouk, Egor AU - Prokhortchouk E AD - Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia. FAU - Gankin, Yuriy AU - Gankin Y AD - EPAM Systems, Newtown, PA, USA. FAU - Rogaev, Evgeny AU - Rogaev E AD - Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA. FAU - Nikolsky, Yuri AU - Nikolsky Y AD - Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA. FAU - Baranova, Ancha AU - Baranova A AD - School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia. FAU - Elhaik, Eran AU - Elhaik E AD - Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK. FAU - Tatarinova, Tatiana V AU - Tatarinova TV AD - Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA tatiana.tatarinova@usc.edu irina.morozova@iem.uzh.ch. LA - eng GR - MC_PC_14115/MRC_/Medical Research Council/United Kingdom PT - Journal Article PT - Review DEP - 20160719 PL - England TA - DNA Res JT - DNA research : an international journal for rapid publication of reports on genes and genomes JID - 9423827 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - *DNA, Ancient MH - *Evolution, Molecular MH - Genetics, Population/*methods MH - *Genome, Human MH - Genomics/*methods MH - Humans MH - Sequence Analysis, DNA/*methods PMC - PMC4991838 OTO - NOTNLM OT - ancient DNA OT - bioinformatics OT - epigenetics OT - next-generation sequencing OT - population genetics EDAT- 2016/07/21 06:00 MHDA- 2017/01/19 06:00 PMCR- 2016/07/19 CRDT- 2016/07/21 06:00 PHST- 2015/11/22 00:00 [received] PHST- 2016/05/22 00:00 [accepted] PHST- 2016/07/21 06:00 [entrez] PHST- 2016/07/21 06:00 [pubmed] PHST- 2017/01/19 06:00 [medline] PHST- 2016/07/19 00:00 [pmc-release] AID - dsw029 [pii] AID - 10.1093/dnares/dsw029 [doi] PST - ppublish SO - DNA Res. 2016 Aug;23(4):295-310. doi: 10.1093/dnares/dsw029. Epub 2016 Jul 19. PMID- 26619959 OWN - NLM STAT- MEDLINE DCOM- 20170612 LR - 20211204 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 160 IP - 4 DP - 2016 Aug TI - The apportionment of human diversity revisited. PG - 561-9 LID - 10.1002/ajpa.22899 [doi] AB - OBJECTIVES: Studies of the apportionment of human genetic diversity have found that local populations harbor nearly as much diversity as the species as a whole. These studies have been a valuable cornerstone in rejecting race as a biological framework in anthropology. The current study presents new analyses that use updated statistical methods based on bifurcating trees to assess the structure of human genetic diversity and its implications for the existence of canonical biological races. MATERIALS AND METHODS: We examine patterns of both goodness-of-fit and lack-of-fit of two bifurcating trees to patterns of diversity determined from autosomal short tandem repeat genotypes in 1,037 people representing 52 populations with worldwide distribution. RESULTS: From goodness-of-fit, we infer a root for the tree within Africa, and we recapitulate a pattern of decreasing genetic diversity with increasing geographic distance from Africa. From lack-of-fit, we present tentative evidence for admixture events with archaic hominins. We do not find evidence that long-range migration or local gene flow have contributed appreciably to the lack of fit at a global scale. CONCLUSION: This is the first study to find a root for a tree of human populations without comparison to a nonhuman out-group, and it is one of the first studies to identify a signature of admixture with archaic hominins without reference to ancient DNA. Our findings complement previous studies of the apportionment of human diversity and provide a more solid evolutionary foundation for the rejection of biological race. Am J Phys Anthropol 160:561-569, 2016. © 2015 Wiley Periodicals, Inc. CI - © 2015 Wiley Periodicals, Inc. FAU - Hunley, Keith L AU - Hunley KL AD - Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131. FAU - Cabana, Graciela S AU - Cabana GS AD - Department of Anthropology, University of Tennessee, Knoxville, TN, 37996. FAU - Long, Jeffrey C AU - Long JC AD - Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131. LA - eng PT - Journal Article DEP - 20151201 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 SB - IM MH - Anthropology, Physical/*methods MH - Gene Flow/genetics MH - Genetic Variation/*genetics MH - *Genetics, Population MH - Humans MH - Microsatellite Repeats MH - *Models, Statistical MH - Racial Groups/genetics/statistics & numerical data OTO - NOTNLM OT - F-statistics OT - admixture OT - gene flow OT - generalized hierarchical modeling OT - genetic structure EDAT- 2015/12/02 06:00 MHDA- 2017/06/13 06:00 CRDT- 2015/12/02 06:00 PHST- 2015/06/11 00:00 [received] PHST- 2015/11/06 00:00 [revised] PHST- 2015/11/06 00:00 [accepted] PHST- 2015/12/02 06:00 [entrez] PHST- 2015/12/02 06:00 [pubmed] PHST- 2017/06/13 06:00 [medline] AID - 10.1002/ajpa.22899 [doi] PST - ppublish SO - Am J Phys Anthropol. 2016 Aug;160(4):561-9. doi: 10.1002/ajpa.22899. Epub 2015 Dec 1. PMID- 27418483 OWN - NLM STAT- MEDLINE DCOM- 20161014 LR - 20161230 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 353 IP - 6296 DP - 2016 Jul 15 TI - ANCIENT DNA. First farmers' motley roots. PG - 207-8 LID - 10.1126/science.353.6296.207 [doi] FAU - Gibbons, Ann AU - Gibbons A LA - eng PT - Historical Article PT - News DEP - 20160714 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 9007-49-2 (DNA) SB - IM MH - Agriculture/*history MH - Cell Nucleus/genetics MH - DNA/analysis/genetics/*history MH - Farmers/*history MH - History, Ancient MH - Humans MH - Iran MH - Tooth/chemistry EDAT- 2016/07/16 06:00 MHDA- 2016/10/16 06:00 CRDT- 2016/07/16 06:00 PHST- 2016/07/16 06:00 [entrez] PHST- 2016/07/16 06:00 [pubmed] PHST- 2016/10/16 06:00 [medline] AID - 353/6296/207 [pii] AID - 10.1126/science.353.6296.207 [doi] PST - ppublish SO - Science. 2016 Jul 15;353(6296):207-8. doi: 10.1126/science.353.6296.207. Epub 2016 Jul 14. PMID- 27060406 OWN - NLM STAT- MEDLINE DCOM- 20170103 LR - 20221207 IS - 1879-0038 (Electronic) IS - 0378-1119 (Linking) VI - 586 IP - 1 DP - 2016 Jul 15 TI - The genetic history of Peninsular Malaysia. PG - 129-35 LID - S0378-1119(16)30256-6 [pii] LID - 10.1016/j.gene.2016.04.008 [doi] AB - This article explores the genetic history of the various sub-populations currently living in Peninsular Malaysia. This region has received multiple waves of migrants like the Orang Asli in prehistoric times and the Chinese, Indians, Europeans and Arabs during historic times. There are three highly distinct lineages that make up the Orang Asli; Semang, Senoi and Proto-Malays. The Semang, who have 'Negrito' characteristics, represent the first human settlers in Peninsular Malaysia arriving from about 50,000ya. The Senoi later migrated from Indochina and are a mix between an Asian Neolithic population and the Semang. These Asian genomes probably came in before Austroasiatic languages arrived between 5000 and 4000years ago. Semang and Senoi both now speak Austro-Asiatic languages indicative of cultural diffusion from Senoi to Semang. In contrast, the Proto-Malays who came last to the southern part of this region speak Austronesian language and are Austronesians with some Negrito admixture. It is from this group that the contemporary Malays emerged. Here we provide an overview of the best available genetic evidences (single nucleotide polymorphisms, mitochondrial DNA, Y-chromosome, blood groups, human platelet antigen, human leukocyte antigen, human neutrophil antigen and killer-cell immunoglobulin-like receptor) supporting the complex genetic history of Peninsular Malaysia. Large scale sampling and high throughput genetic screening programmes such as those using genome-wide single nucleotide polymorphism analyses have provided insights into various ancestral and admixture genetic fractions in this region. Given the now extensive admixture present in the contemporary descendants of ancient sub-populations in Peninsular Malaysia, improved reconstruction of human migration history in this region will require new evidence from ancient DNA in well-preserved skeletons. All other aspects of the highly diverse and complex genetic makeup in Peninsular Malaysia should be considered carefully for genetic mapping of disease loci and policy formation by health authorities. CI - Copyright © 2016 Elsevier B.V. All rights reserved. FAU - Norhalifah, Hanim Kamis AU - Norhalifah HK AD - Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia. FAU - Syaza, Fatnin Hisham AU - Syaza FH AD - Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia. FAU - Chambers, Geoffrey Keith AU - Chambers GK AD - School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand. FAU - Edinur, Hisham Atan AU - Edinur HA AD - Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia. Electronic address: edinur@usm.my. LA - eng PT - Journal Article PT - Review DEP - 20160407 PL - Netherlands TA - Gene JT - Gene JID - 7706761 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/genetics MH - Australia MH - DNA, Mitochondrial MH - Ethnicity/*genetics MH - *Human Migration MH - Humans MH - Malaysia/ethnology MH - Polymorphism, Single Nucleotide MH - White People/genetics OTO - NOTNLM OT - Austronesians OT - Genetics OT - Malays OT - Orang Asli OT - Peninsular Malaysia EDAT- 2016/04/10 06:00 MHDA- 2017/01/04 06:00 CRDT- 2016/04/10 06:00 PHST- 2015/08/25 00:00 [received] PHST- 2016/03/17 00:00 [revised] PHST- 2016/04/05 00:00 [accepted] PHST- 2016/04/10 06:00 [entrez] PHST- 2016/04/10 06:00 [pubmed] PHST- 2017/01/04 06:00 [medline] AID - S0378-1119(16)30256-6 [pii] AID - 10.1016/j.gene.2016.04.008 [doi] PST - ppublish SO - Gene. 2016 Jul 15;586(1):129-35. doi: 10.1016/j.gene.2016.04.008. Epub 2016 Apr 7. PMID- 27389305 OWN - NLM STAT- MEDLINE DCOM- 20180625 LR - 20181113 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 6 DP - 2016 Jul 8 TI - Direct radiocarbon dating and genetic analyses on the purported Neanderthal mandible from the Monti Lessini (Italy). PG - 29144 LID - 10.1038/srep29144 [doi] LID - 29144 AB - Anatomically modern humans replaced Neanderthals in Europe around 40,000 years ago. The demise of the Neanderthals and the nature of the possible relationship with anatomically modern humans has captured our imagination and stimulated research for more than a century now. Recent chronological studies suggest a possible overlap between Neanderthals and anatomically modern humans of more than 5,000 years. Analyses of ancient genome sequences from both groups have shown that they interbred multiple times, including in Europe. A potential place of interbreeding is the notable Palaeolithic site of Riparo Mezzena in Northern Italy. In order to improve our understanding of prehistoric occupation at Mezzena, we analysed the human mandible and several cranial fragments from the site using radiocarbon dating, ancient DNA, ZooMS and isotope analyses. We also performed a more detailed investigation of the lithic assemblage of layer I. Surprisingly we found that the Riparo Mezzena mandible is not from a Neanderthal but belonged to an anatomically modern human. Furthermore, we found no evidence for the presence of Neanderthal remains among 11 of the 13 cranial and post-cranial fragments re-investigated in this study. FAU - Talamo, Sahra AU - Talamo S AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. FAU - Hajdinjak, Mateja AU - Hajdinjak M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. FAU - Mannino, Marcello A AU - Mannino MA AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. AD - Department of Archaeology, School of Culture and Society, Aarhus University, Moesgård Allé 20, 8270 Højbjerg, Denmark. FAU - Fasani, Leone AU - Fasani L AD - Università degli Studi di Milano-Bicocca, Piazza dell'Ateneo Nuovo 1, 20126 Milano, Italy. FAU - Welker, Frido AU - Welker F AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. AD - BioArCh, University of York, York, YO10 5DD, United Kingdom. FAU - Martini, Fabio AU - Martini F AD - Università degli Studi di Firenze, Dipartimento di Storia, Archeologia, Geografia, Arte e Spettacolo. Cattedra di Paletnologia (Prehistory), Via S. Egidio 21, 50122 Firenze, Italy. FAU - Romagnoli, Francesca AU - Romagnoli F AD - Università degli Studi di Firenze, Dipartimento di Storia, Archeologia, Geografia, Arte e Spettacolo. Cattedra di Paletnologia (Prehistory), Via S. Egidio 21, 50122 Firenze, Italy. AD - Institut Català de Paleoecologia Humana i Evolució Social (IPHES) Zona Educacional 4-Campus Sescelades URV (Edifici W3) 43007 Tarragona, Spain. AD - Area de Prehistoria, Universitat Rovira i Virgili (URV), Avinguda de Catalunya 35, 43002 Tarragona, Spain. FAU - Zorzin, Roberto AU - Zorzin R AD - Museo Civico di Storia Naturale di Verona, Sezione di Geologia e Paleontologia, Lungadige Porta Vittoria 9, 37129 Verona, Italy. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. FAU - Hublin, Jean-Jacques AU - Hublin JJ AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160708 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA, Ancient/*isolation & purification MH - *Fossils MH - Genetic Testing MH - Humans MH - Italy MH - Mandible/chemistry MH - Neanderthals/*genetics MH - *Radiometric Dating MH - Skull/chemistry PMC - PMC4937366 EDAT- 2016/07/09 06:00 MHDA- 2018/06/26 06:00 PMCR- 2016/07/08 CRDT- 2016/07/09 06:00 PHST- 2016/04/07 00:00 [received] PHST- 2016/06/13 00:00 [accepted] PHST- 2016/07/09 06:00 [entrez] PHST- 2016/07/09 06:00 [pubmed] PHST- 2018/06/26 06:00 [medline] PHST- 2016/07/08 00:00 [pmc-release] AID - srep29144 [pii] AID - 10.1038/srep29144 [doi] PST - epublish SO - Sci Rep. 2016 Jul 8;6:29144. doi: 10.1038/srep29144. PMID- 27325755 OWN - NLM STAT- MEDLINE DCOM- 20170724 LR - 20181113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 113 IP - 27 DP - 2016 Jul 5 TI - Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc. PG - 7485-90 LID - 10.1073/pnas.1520844113 [doi] AB - The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04×-7.25×, mean 2.16×) and mitochondrial genomes (20.8×-1,311.0×, mean 482.1×) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations. FAU - Jeong, Choongwon AU - Jeong C AD - Department of Human Genetics, University of Chicago, Chicago, IL 60637; FAU - Ozga, Andrew T AU - Ozga AT AD - Department of Anthropology, University of Oklahoma, Norman, OK 73019; FAU - Witonsky, David B AU - Witonsky DB AD - Department of Human Genetics, University of Chicago, Chicago, IL 60637; FAU - Malmström, Helena AU - Malmström H AD - Department of Organismal Biology, Uppsala University, Uppsala SE-752 36, Sweden; FAU - Edlund, Hanna AU - Edlund H AD - Department of Organismal Biology, Uppsala University, Uppsala SE-752 36, Sweden; FAU - Hofman, Courtney A AU - Hofman CA AD - Department of Anthropology, University of Oklahoma, Norman, OK 73019; FAU - Hagan, Richard W AU - Hagan RW AD - Department of Anthropology, University of Oklahoma, Norman, OK 73019; FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Organismal Biology, Uppsala University, Uppsala SE-752 36, Sweden; FAU - Lewis, Cecil M AU - Lewis CM AD - Department of Anthropology, University of Oklahoma, Norman, OK 73019; FAU - Aldenderfer, Mark S AU - Aldenderfer MS AD - School of Social Sciences, Humanities, and Arts, University of California, Merced, CA 95343; christina.warinner@ou.edu maldenderfer@ucmerced.edu dirienzo@bsd.uchicago.edu. FAU - Di Rienzo, Anna AU - Di Rienzo A AD - Department of Human Genetics, University of Chicago, Chicago, IL 60637; christina.warinner@ou.edu maldenderfer@ucmerced.edu dirienzo@bsd.uchicago.edu. FAU - Warinner, Christina AU - Warinner C AUID- ORCID: 0000-0002-4528-5877 AD - Department of Anthropology, University of Oklahoma, Norman, OK 73019; Institute of Evolutionary Medicine, University of Zurich, Zurich CH-8057, Switzerland christina.warinner@ou.edu maldenderfer@ucmerced.edu dirienzo@bsd.uchicago.edu. LA - eng GR - P30 CA014599/CA/NCI NIH HHS/United States GR - R01 HL119577/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160620 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Altitude MH - *Gene Flow MH - *Genome, Human MH - Humans MH - Nepal MH - Paleodontology MH - Phylogeography MH - Sequence Analysis, DNA MH - Tibet PMC - PMC4941446 OTO - NOTNLM OT - Ancient DNA OT - EGLN1 OT - EPAS1 OT - high altitude OT - population genetics COIS- The authors declare no conflict of interest. EDAT- 2016/06/22 06:00 MHDA- 2017/07/25 06:00 PMCR- 2016/06/20 CRDT- 2016/06/22 06:00 PHST- 2016/06/22 06:00 [entrez] PHST- 2016/06/22 06:00 [pubmed] PHST- 2017/07/25 06:00 [medline] PHST- 2016/06/20 00:00 [pmc-release] AID - 1520844113 [pii] AID - 201520844 [pii] AID - 10.1073/pnas.1520844113 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7485-90. doi: 10.1073/pnas.1520844113. Epub 2016 Jun 20. PMID- 27346733 OWN - NLM STAT- MEDLINE DCOM- 20170526 LR - 20180620 IS - 1469-1809 (Electronic) IS - 0003-4800 (Linking) VI - 80 IP - 4 DP - 2016 Jul TI - Pre-Hispanic Mortuary Practices in Quebrada de Humahuaca (North-Western Argentina): Genetic Relatedness among Individuals Buried in the Same Grave. PG - 210-20 LID - 10.1111/ahg.12159 [doi] AB - Almost all pre-Hispanic societies from Quebrada de Humahuaca (north-western Argentina) buried their defuncts in domestic areas, demonstrating the importance of death and its daily presence among the living. Presumably, the collective graves contained related individuals, a hypothesis that can be tested through the study of ancient DNA. This study analyzes autosomal and uniparental genetic markers in individuals from two archaeological sites in Quebrada de Humahuaca occupied during the Late Formative (1450-1050 BP) and Regional Developments I (1050-700 BP) periods. Mitochondrial and Y-chromosome haplotypes were compared in order to establish possible maternal and paternal relatedness. Genotypes for 15 autosomal STRs were used to calculate pairwise relatedness coefficients and pedigree probabilities. High kinship levels among individuals buried in the same graves were found in both sites. Although only two particular cases were analyzed, these results represent an important contribution to the study of mortuary practices in the region by means of ancient DNA. CI - © 2016 John Wiley & Sons Ltd/University College London. FAU - Russo, M Gabriela AU - Russo MG AD - Universidad Maimónides, CONICET, CEBBAD, Equipo de Antropología Biológica, Fundación Azara, Hidalgo 775, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina. FAU - Mendisco, Fanny AU - Mendisco F AD - University Paul Sabatier, AMIS, CNRS, UMR 5288, F-31073, Toulouse, France. FAU - Avena, Sergio A AU - Avena SA AD - Universidad Maimónides, CONICET, CEBBAD, Equipo de Antropología Biológica, Fundación Azara, Hidalgo 775, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina. AD - Sección de Antropología Biológica, ICA, FFyL, UBA, Puán 480, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina. FAU - Dejean, Cristina B AU - Dejean CB AD - Sección de Antropología Biológica, ICA, FFyL, UBA, Puán 480, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina. AD - Universidad Maimónides, CEBBAD, Equipo de Antropología Biológica, Fundación Azara, Hidalgo 775, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina. FAU - Seldes, Verónica AU - Seldes V AD - UBA, CONICET, Instituto Interdisciplinario Tilcara, FFyL, Belgrano 445, CP 4624, Tilcara, Jujuy, Argentina. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Ann Hum Genet JT - Annals of human genetics JID - 0416661 RN - 0 (DNA, Mitochondrial) SB - IM MH - Argentina MH - *Cemeteries MH - DNA, Mitochondrial/genetics MH - Female MH - Humans MH - Indians, South American/*genetics MH - Male MH - Pedigree MH - Sequence Analysis, DNA OTO - NOTNLM OT - Ancient DNA OT - burial practices OT - kinship relationships OT - north-western Argentina EDAT- 2016/06/28 06:00 MHDA- 2017/05/27 06:00 CRDT- 2016/06/28 06:00 PHST- 2016/02/25 00:00 [received] PHST- 2016/04/25 00:00 [revised] PHST- 2016/05/12 00:00 [accepted] PHST- 2016/06/28 06:00 [entrez] PHST- 2016/06/28 06:00 [pubmed] PHST- 2017/05/27 06:00 [medline] AID - 10.1111/ahg.12159 [doi] PST - ppublish SO - Ann Hum Genet. 2016 Jul;80(4):210-20. doi: 10.1111/ahg.12159. PMID- 27274055 OWN - NLM STAT- MEDLINE DCOM- 20170711 LR - 20240325 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 113 IP - 25 DP - 2016 Jun 21 TI - Ancient mtDNA sequences from the First Australians revisited. PG - 6892-7 LID - 10.1073/pnas.1521066113 [doi] AB - The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains. FAU - Heupink, Tim H AU - Heupink TH AUID- ORCID: 0000-0001-6237-3898 AD - Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia; FAU - Subramanian, Sankar AU - Subramanian S AD - Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia; FAU - Wright, Joanne L AU - Wright JL AD - Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia; FAU - Endicott, Phillip AU - Endicott P AD - Department of Zoology, Oxford University, Oxford OX1 2JD, United Kingdom; FAU - Westaway, Michael Carrington AU - Westaway MC AD - Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia; FAU - Huynen, Leon AU - Huynen L AD - Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia; FAU - Parson, Walther AU - Parson W AD - Institute of Legal Medicine, Innsbruck Medical University, 6020 Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA 16801; FAU - Millar, Craig D AU - Millar CD AD - Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand; FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, University of Copenhagen, 1017 Copenhagen, Denmark ewillerslev@snm.ku.dk d.lambert@griffith.edu.au. FAU - Lambert, David M AU - Lambert DM AD - Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia; ewillerslev@snm.ku.dk d.lambert@griffith.edu.au. LA - eng SI - GENBANK/KU659023 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160606 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM MH - Australia MH - DNA, Mitochondrial/*genetics MH - Humans MH - Likelihood Functions MH - Phylogeny PMC - PMC4922152 OTO - NOTNLM OT - Aboriginal Australians OT - ancient DNA OT - anthropology OT - biological sciences OT - mitogenomics COIS- The authors declare no conflict of interest. EDAT- 2016/06/09 06:00 MHDA- 2017/07/14 06:00 PMCR- 2016/06/06 CRDT- 2016/06/09 06:00 PHST- 2016/06/09 06:00 [entrez] PHST- 2016/06/09 06:00 [pubmed] PHST- 2017/07/14 06:00 [medline] PHST- 2016/06/06 00:00 [pmc-release] AID - 1521066113 [pii] AID - 201521066 [pii] AID - 10.1073/pnas.1521066113 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2016 Jun 21;113(25):6892-7. doi: 10.1073/pnas.1521066113. Epub 2016 Jun 6. PMID- 27274049 OWN - NLM STAT- MEDLINE DCOM- 20170711 LR - 20230723 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 113 IP - 25 DP - 2016 Jun 21 TI - Early farmers from across Europe directly descended from Neolithic Aegeans. PG - 6886-91 LID - 10.1073/pnas.1523951113 [doi] AB - Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia. FAU - Hofmanová, Zuzana AU - Hofmanová Z AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; FAU - Kreutzer, Susanne AU - Kreutzer S AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; FAU - Hellenthal, Garrett AU - Hellenthal G AD - Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom; FAU - Sell, Christian AU - Sell C AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; FAU - Diekmann, Yoan AU - Diekmann Y AD - Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom; FAU - Díez-Del-Molino, David AU - Díez-Del-Molino D AD - Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom; FAU - van Dorp, Lucy AU - van Dorp L AD - Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom; FAU - López, Saioa AU - López S AD - Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom; FAU - Kousathanas, Athanasios AU - Kousathanas A AD - Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; FAU - Link, Vivian AU - Link V AD - Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; FAU - Kirsanow, Karola AU - Kirsanow K AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; FAU - Cassidy, Lara M AU - Cassidy LM AD - Molecular Population Genetics, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland; FAU - Martiniano, Rui AU - Martiniano R AD - Molecular Population Genetics, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland; FAU - Strobel, Melanie AU - Strobel M AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; FAU - Scheu, Amelie AU - Scheu A AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; Molecular Population Genetics, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland; FAU - Kotsakis, Kostas AU - Kotsakis K AD - Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; FAU - Halstead, Paul AU - Halstead P AD - Department of Archaeology, University of Sheffield, Sheffield S1 4ET, United Kingdom; FAU - Triantaphyllou, Sevi AU - Triantaphyllou S AD - Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; FAU - Kyparissi-Apostolika, Nina AU - Kyparissi-Apostolika N AD - Honorary Ephor of Antiquities, Hellenic Ministry of Culture & Sports, 106 82 Athens, Greece; FAU - Urem-Kotsou, Dushka AU - Urem-Kotsou D AUID- ORCID: 0000-0002-9534-6340 AD - Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece; FAU - Ziota, Christina AU - Ziota C AD - Ephorate of Antiquities of Florina, Hellenic Ministry of Culture & Sports, 106 82 Athens, Greece; FAU - Adaktylou, Fotini AU - Adaktylou F AD - Ephorate of Antiquities of Chalkidiki and Mount Athos, Hellenic Ministry of Culture & Sports, 106 82 Athens, Greece; FAU - Gopalan, Shyamalika AU - Gopalan S AD - Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245; FAU - Bobo, Dean M AU - Bobo DM AD - Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245; FAU - Winkelbach, Laura AU - Winkelbach L AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; FAU - Blöcher, Jens AU - Blöcher J AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; FAU - Unterländer, Martina AU - Unterländer M AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; FAU - Leuenberger, Christoph AU - Leuenberger C AD - Department of Mathematics, University of Fribourg, 1700 Fribourg, Switzerland; FAU - Çilingiroğlu, Çiler AU - Çilingiroğlu Ç AD - Department of Protohistory and Near Eastern Archeology, Faculty of Letters, Ege University, 35100 Bornova, Izmir, Turkey; FAU - Horejs, Barbara AU - Horejs B AD - Institute of Oriental and European Archaeology, Austrian Academy of Sciences, 1010 Vienna, Austria; FAU - Gerritsen, Fokke AU - Gerritsen F AD - Netherlands Institute in Turkey, Beyoglu 34433, Istanbul, Turkey; FAU - Shennan, Stephen J AU - Shennan SJ AD - Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom; FAU - Bradley, Daniel G AU - Bradley DG AD - Molecular Population Genetics, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland; FAU - Currat, Mathias AU - Currat M AD - Anthropology Unit, Department of Genetics & Evolution, University of Geneva, 1211 Geneva, Switzerland; FAU - Veeramah, Krishna R AU - Veeramah KR AD - Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245; FAU - Wegmann, Daniel AU - Wegmann D AUID- ORCID: 0000-0003-2866-6739 AD - Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; FAU - Thomas, Mark G AU - Thomas MG AD - Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom; FAU - Papageorgopoulou, Christina AU - Papageorgopoulou C AD - Laboratory of Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece cpapage@he.duth.gr jburger@uni-mainz.de. FAU - Burger, Joachim AU - Burger J AD - Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; cpapage@he.duth.gr jburger@uni-mainz.de. LA - eng SI - GENBANK/KU171094 SI - GENBANK/KU171100 GR - WT_/Wellcome Trust/United Kingdom GR - Y 528/FWF_/Austrian Science Fund FWF/Austria PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160606 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - *Agriculture MH - *Anthropology MH - Europe MH - Genetics, Population MH - Humans MH - Mediterranean Region MH - Principal Component Analysis PMC - PMC4922144 OTO - NOTNLM OT - Anatolia OT - Greece OT - Mesolithic OT - Neolithic OT - paleogenomics COIS- The authors declare no conflict of interest. EDAT- 2016/06/09 06:00 MHDA- 2017/07/14 06:00 PMCR- 2016/06/06 CRDT- 2016/06/09 06:00 PHST- 2016/06/09 06:00 [entrez] PHST- 2016/06/09 06:00 [pubmed] PHST- 2017/07/14 06:00 [medline] PHST- 2016/06/06 00:00 [pmc-release] AID - 1523951113 [pii] AID - 201523951 [pii] AID - 10.1073/pnas.1523951113 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2016 Jun 21;113(25):6886-91. doi: 10.1073/pnas.1523951113. Epub 2016 Jun 6. PMID- 27313020 OWN - NLM STAT- MEDLINE DCOM- 20160626 LR - 20160617 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 352 IP - 6292 DP - 2016 Jun 17 TI - Ancient DNA divide. PG - 1384-7 LID - 10.1126/science.352.6292.1384 [doi] FAU - Gibbons, Ann AU - Gibbons A LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Bacterial) SB - IM MH - Anthropology/*economics MH - DNA, Bacterial/*genetics/isolation & purification MH - Dairying/history MH - Dental Plaque/microbiology MH - Fossils MH - Germany MH - History, Ancient MH - Humans MH - Oklahoma MH - Research Personnel/*economics MH - *Research Support as Topic MH - Tooth EDAT- 2016/06/18 06:00 MHDA- 2016/06/28 06:00 CRDT- 2016/06/18 06:00 PHST- 2016/06/18 06:00 [entrez] PHST- 2016/06/18 06:00 [pubmed] PHST- 2016/06/28 06:00 [medline] AID - 352/6292/1384 [pii] AID - 10.1126/science.352.6292.1384 [doi] PST - ppublish SO - Science. 2016 Jun 17;352(6292):1384-7. doi: 10.1126/science.352.6292.1384. PMID- 27281573 OWN - NLM STAT- MEDLINE DCOM- 20170921 LR - 20201209 IS - 1934-6069 (Electronic) IS - 1931-3128 (Linking) VI - 19 IP - 6 DP - 2016 Jun 8 TI - Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics. PG - 874-81 LID - S1931-3128(16)30208-6 [pii] LID - 10.1016/j.chom.2016.05.012 [doi] AB - Ancient DNA analysis has revealed an involvement of the bacterial pathogen Yersinia pestis in several historical pandemics, including the second plague pandemic (Europe, mid-14(th) century Black Death until the mid-18(th) century AD). Here we present reconstructed Y. pestis genomes from plague victims of the Black Death and two subsequent historical outbreaks spanning Europe and its vicinity, namely Barcelona, Spain (1300-1420 cal AD), Bolgar City, Russia (1362-1400 AD), and Ellwangen, Germany (1485-1627 cal AD). Our results provide support for (1) a single entry of Y. pestis in Europe during the Black Death, (2) a wave of plague that traveled toward Asia to later become the source population for contemporary worldwide epidemics, and (3) the presence of an historical European plague focus involved in post-Black Death outbreaks that is now likely extinct. CI - Copyright © 2016 Elsevier Inc. All rights reserved. FAU - Spyrou, Maria A AU - Spyrou MA AD - Max Planck Institute for the Science of Human History, Jena 07743, Germany. FAU - Tukhbatova, Rezeda I AU - Tukhbatova RI AD - Laboratory of Paleoanthropology & Paleogenetics, Kazan Federal University, Kazan 420008, Russian Federation; Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan 420012, Russian Federation. FAU - Feldman, Michal AU - Feldman M AD - Max Planck Institute for the Science of Human History, Jena 07743, Germany. FAU - Drath, Joanna AU - Drath J AD - Department of Archeological Sciences, University of Tuebingen, Tuebingen 72070, Germany. FAU - Kacki, Sacha AU - Kacki S AD - PACEA, CNRS Institute, Université de Bordeaux, Pessac 33615, France. FAU - Beltrán de Heredia, Julia AU - Beltrán de Heredia J AD - Museu de Historia de Barcelona, Barcelona 08002, Spain. FAU - Arnold, Susanne AU - Arnold S AD - State Office for Cultural Heritage Management Baden-Württemberg, Esslingen 73728, Germany. FAU - Sitdikov, Airat G AU - Sitdikov AG AD - Laboratory of Paleoanthropology & Paleogenetics, Kazan Federal University, Kazan 420008, Russian Federation; Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan 420012, Russian Federation. FAU - Castex, Dominique AU - Castex D AD - PACEA, CNRS Institute, Université de Bordeaux, Pessac 33615, France. FAU - Wahl, Joachim AU - Wahl J AD - Department of Archeological Sciences, University of Tuebingen, Tuebingen 72070, Germany; State Office for Cultural Heritage Management Baden-Württemberg, Osteology, Konstanz 78467, Germany. FAU - Gazimzyanov, Ilgizar R AU - Gazimzyanov IR AD - Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan 420012, Russian Federation. FAU - Nurgaliev, Danis K AU - Nurgaliev DK AD - Institute of Geology and Petroleum Technologies, Kazan Federal University, Kazan 420008, Russian Federation. FAU - Herbig, Alexander AU - Herbig A AD - Max Planck Institute for the Science of Human History, Jena 07743, Germany. Electronic address: herbig@shh.mpg.de. FAU - Bos, Kirsten I AU - Bos KI AD - Max Planck Institute for the Science of Human History, Jena 07743, Germany. Electronic address: bos@shh.mpg.de. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, Jena 07743, Germany; Department of Archeological Sciences, University of Tuebingen, Tuebingen 72070, Germany. Electronic address: krause@shh.mpg.de. LA - eng PT - Historical Article PT - Journal Article PL - United States TA - Cell Host Microbe JT - Cell host & microbe JID - 101302316 RN - 0 (DNA, Bacterial) SB - IM MH - Asia/epidemiology MH - Bone and Bones/microbiology MH - DNA, Bacterial/genetics MH - Disease Reservoirs MH - Europe/epidemiology MH - Genome, Bacterial MH - Genotype MH - High-Throughput Nucleotide Sequencing MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, Medieval MH - Humans MH - Molecular Epidemiology MH - Pandemics/*history MH - Phylogeny MH - Plague/epidemiology/*history/*microbiology MH - Tooth/microbiology MH - Yersinia pestis/*genetics/isolation & purification EDAT- 2016/06/10 06:00 MHDA- 2017/09/22 06:00 CRDT- 2016/06/10 06:00 PHST- 2016/03/04 00:00 [received] PHST- 2016/04/23 00:00 [revised] PHST- 2016/05/13 00:00 [accepted] PHST- 2016/06/10 06:00 [entrez] PHST- 2016/06/10 06:00 [pubmed] PHST- 2017/09/22 06:00 [medline] AID - S1931-3128(16)30208-6 [pii] AID - 10.1016/j.chom.2016.05.012 [doi] PST - ppublish SO - Cell Host Microbe. 2016 Jun 8;19(6):874-81. doi: 10.1016/j.chom.2016.05.012. PMID- 27274046 OWN - NLM STAT- MEDLINE DCOM- 20170127 LR - 20220330 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 113 IP - 23 DP - 2016 Jun 7 TI - Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions. PG - 6388-96 LID - 10.1073/pnas.1525200113 [doi] AB - The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity-the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences. FAU - Boivin, Nicole L AU - Boivin NL AD - School of Archaeology, University of Oxford, Oxford OX1 2PG, United Kingdom; Max Planck Institute for the Science of Human History, Jena D-07743, Germany; boivin@shh.mpg.de. FAU - Zeder, Melinda A AU - Zeder MA AD - Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013; External Faculty, Santa Fe Institute, Santa Fe, NM 87501; FAU - Fuller, Dorian Q AU - Fuller DQ AD - Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom; FAU - Crowther, Alison AU - Crowther A AD - School of Social Science, The University of Queensland, Brisbane, QLD 4072, Australia; FAU - Larson, Greger AU - Larson G AD - Palaeogenomics & Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3QY, United Kingdom; FAU - Erlandson, Jon M AU - Erlandson JM AD - Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403-1224; FAU - Denham, Tim AU - Denham T AD - School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra, ACT 0200, Australia. FAU - Petraglia, Michael D AU - Petraglia MD AD - School of Archaeology, University of Oxford, Oxford OX1 2PG, United Kingdom; LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM CIN - Proc Natl Acad Sci U S A. 2016 Aug 2;113(31):E4436. doi: 10.1073/pnas.1609425113. PMID: 27432994 CIN - Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):E4757-8. doi: 10.1073/pnas.1609950113. PMID: 27462114 MH - Agriculture MH - Animals MH - *Demography MH - *Ecosystem MH - Human Activities MH - Humans MH - Islands MH - Urbanization PMC - PMC4988612 OTO - NOTNLM OT - Anthropocene OT - biodiversity OT - extinctions OT - invasive species OT - novel ecosystems COIS- The authors declare no conflict of interest. EDAT- 2016/06/09 06:00 MHDA- 2017/01/28 06:00 PMCR- 2016/06/06 CRDT- 2016/06/09 06:00 PHST- 2016/06/09 06:00 [entrez] PHST- 2016/06/09 06:00 [pubmed] PHST- 2017/01/28 06:00 [medline] PHST- 2016/06/06 00:00 [pmc-release] AID - 1525200113 [pii] AID - 201525200 [pii] AID - 10.1073/pnas.1525200113 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):6388-96. doi: 10.1073/pnas.1525200113. PMID- 27274045 OWN - NLM STAT- MEDLINE DCOM- 20170127 LR - 20240529 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 113 IP - 23 DP - 2016 Jun 7 TI - Ancient DNA and human history. PG - 6380-7 LID - 10.1073/pnas.1524306113 [doi] AB - We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history. FAU - Slatkin, Montgomery AU - Slatkin M AD - Department of Integrative Biology, University of California, Berkeley, CA 94720-3140 slatkin@berkeley.edu. FAU - Racimo, Fernando AU - Racimo F AD - Department of Integrative Biology, University of California, Berkeley, CA 94720-3140. LA - eng GR - R01 GM040282/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20160606 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - DNA Contamination MH - *DNA, Ancient MH - Fossils MH - Genome MH - Hominidae/*genetics MH - Humans PMC - PMC4988579 OTO - NOTNLM OT - Denisovan OT - Neanderthal OT - ancient DNA OT - demography OT - human history COIS- The authors declare no conflict of interest. EDAT- 2016/06/09 06:00 MHDA- 2017/01/28 06:00 PMCR- 2016/06/06 CRDT- 2016/06/09 06:00 PHST- 2016/06/09 06:00 [entrez] PHST- 2016/06/09 06:00 [pubmed] PHST- 2017/01/28 06:00 [medline] PHST- 2016/06/06 00:00 [pmc-release] AID - 1524306113 [pii] AID - 201524306 [pii] AID - 10.1073/pnas.1524306113 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):6380-7. doi: 10.1073/pnas.1524306113. Epub 2016 Jun 6. PMID- 27016326 OWN - NLM STAT- MEDLINE DCOM- 20170509 LR - 20170509 IS - 1618-1301 (Electronic) IS - 0018-442X (Linking) VI - 67 IP - 3 DP - 2016 Jun TI - All different, all equal: Evidence of a heterogeneous Neolithic population at the Bom Santo Cave necropolis (Portugal). PG - 203-15 LID - S0018-442X(16)30003-8 [pii] LID - 10.1016/j.jchb.2015.12.004 [doi] AB - The objective of this paper was to contribute to the discussion regarding the socio-political organization of south-western Iberian Middle Neolithic populations. To that end, the preservation and distribution of human remains and the dispersion of grave goods within two rooms of the Bom Santo Cave (Rooms A and B) were investigated and combined with genetic and isotopic data previously published. Grave goods distribution and skeletal analyses highlighted an important diversity in terms of funerary practices thus corroborating data from ancient DNA and Sr/O isotopic analyses that suggested a great genetic and geographic diversity. Grave goods presented an uneven spatial distribution and were made of raw materials from different sources and using different pottery manufacturing styles albeit typologically homogeneous. The preservation and distribution of human remains suggested that Room A was mainly used for secondary depositions while Room B was used for both primary and secondary depositions. No link between the two rooms was found since remains from the same individuals were apparently exclusive of one room or another. The results suggest that this society presented substantial inner genetic, social and geographical heterogeneity. Most probably, this was due to the presence of distinct but coeval groups in the cave that shared a larger-scale social identity (as in "segmentary societies") or, less likely, to the presence of one single, but internally heterogeneous society (as in fully sedentary societies) that assimilated foreigners. CI - Copyright © 2016 Elsevier GmbH. All rights reserved. FAU - Gonçalves, D AU - Gonçalves D AD - Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; Laboratório de Arqueociências, Direcção Geral do Património Cultural and LARC/CIBIO/InBIO, Rua da Bica do Marquês 2, 1300-087 Lisboa, Portugal. Electronic address: davidmiguelgoncalves@gmail.com. FAU - Granja, R AU - Granja R AD - Universidade do Algarve, Campus de Gambelas, 8000-117 Faro, Portugal. FAU - Alves-Cardoso, F AU - Alves-Cardoso F AD - Centro em Rede de Investigação em Antropologia (CRIA), FCSH, Universidade NOVA de Lisboa, Av. Berna, 26-C, 1069-061 Lisboa, Portugal. FAU - Carvalho, A F AU - Carvalho AF AD - Universidade do Algarve, Campus de Gambelas, 8000-117 Faro, Portugal. LA - eng PT - Historical Article PT - Journal Article DEP - 20160314 PL - Germany TA - Homo JT - Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen JID - 0374655 SB - IM MH - Anthropology, Physical MH - Cemeteries/history MH - Female MH - Fossils/anatomy & histology/*history MH - Genetics, Population MH - History, Ancient MH - Humans MH - Male MH - Portugal EDAT- 2016/03/27 06:00 MHDA- 2017/05/10 06:00 CRDT- 2016/03/27 06:00 PHST- 2015/02/20 00:00 [received] PHST- 2015/12/02 00:00 [accepted] PHST- 2016/03/27 06:00 [entrez] PHST- 2016/03/27 06:00 [pubmed] PHST- 2017/05/10 06:00 [medline] AID - S0018-442X(16)30003-8 [pii] AID - 10.1016/j.jchb.2015.12.004 [doi] PST - ppublish SO - Homo. 2016 Jun;67(3):203-15. doi: 10.1016/j.jchb.2015.12.004. Epub 2016 Mar 14. PMID- 26989998 OWN - NLM STAT- MEDLINE DCOM- 20170612 LR - 20240325 IS - 1096-8644 (Electronic) IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 160 IP - 2 DP - 2016 Jun TI - Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. PG - 220-8 LID - 10.1002/ajpa.22960 [doi] AB - OBJECTIVES: Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. MATERIALS AND METHODS: Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. RESULTS: Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. DISCUSSION: Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc. CI - © 2016 Wiley Periodicals, Inc. FAU - Ozga, Andrew T AU - Ozga AT AD - Department of Anthropology, University of Oklahoma, Norman, OK, 73019. FAU - Nieves-Colón, Maria A AU - Nieves-Colón MA AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287. FAU - Honap, Tanvi P AU - Honap TP AD - School of Life Sciences, Arizona State University, Tempe, AZ, 85287. FAU - Sankaranarayanan, Krithivasan AU - Sankaranarayanan K AD - Department of Anthropology, University of Oklahoma, Norman, OK, 73019. FAU - Hofman, Courtney A AU - Hofman CA AD - Department of Anthropology, University of Oklahoma, Norman, OK, 73019. FAU - Milner, George R AU - Milner GR AD - Department of Anthropology, Pennsylvania State University, University Park, PA, 16802. FAU - Lewis, Cecil M Jr AU - Lewis CM Jr AD - Department of Anthropology, University of Oklahoma, Norman, OK, 73019. FAU - Stone, Anne C AU - Stone AC AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287. AD - Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, 85287. AD - Institute of Human Origins, Arizona State University, Tempe, AZ, 85287. FAU - Warinner, Christina AU - Warinner C AD - Department of Anthropology, University of Oklahoma, Norman, OK, 73019. AD - Institute of Evolutionary Medicine, University of Zurich, 8057 Zurich, Switzerland. LA - eng GR - R01 GM089886/GM/NIGMS NIH HHS/United States GR - UL1 TR001863/TR/NCATS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20160316 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - Archaeology MH - DNA, Mitochondrial/*analysis/genetics/isolation & purification MH - Dental Calculus/*genetics MH - Genome, Mitochondrial/*genetics MH - History, 15th Century MH - Humans MH - Sequence Analysis, DNA/*methods PMC - PMC4866892 MID - NIHMS755821 OTO - NOTNLM OT - Mississippian culture OT - NAGPRA OT - ancient DNA OT - dental calculus OT - ethics OT - in-solution capture enrichment OT - mitochondrial genome OT - mitogenome OT - next-generation sequencing EDAT- 2016/03/19 06:00 MHDA- 2017/06/13 06:00 PMCR- 2016/09/13 CRDT- 2016/03/19 06:00 PHST- 2015/09/07 00:00 [received] PHST- 2016/01/05 00:00 [revised] PHST- 2016/01/25 00:00 [accepted] PHST- 2016/03/19 06:00 [entrez] PHST- 2016/03/19 06:00 [pubmed] PHST- 2017/06/13 06:00 [medline] PHST- 2016/09/13 00:00 [pmc-release] AID - AJPA22960 [pii] AID - 10.1002/ajpa.22960 [doi] PST - ppublish SO - Am J Phys Anthropol. 2016 Jun;160(2):220-8. doi: 10.1002/ajpa.22960. Epub 2016 Mar 16. PMID- 26826668 OWN - NLM STAT- MEDLINE DCOM- 20170504 LR - 20231111 IS - 1365-294X (Electronic) IS - 0962-1083 (Print) IS - 0962-1083 (Linking) VI - 25 IP - 11 DP - 2016 Jun TI - Detecting hybridization using ancient DNA. PG - 2398-412 LID - 10.1111/mec.13556 [doi] AB - It is well established that related species hybridize and that this can have varied but significant effects on speciation and environmental adaptation. It should therefore come as no surprise that hybridization is not limited to species that are alive today. In the last several decades, advances in technologies for recovering and sequencing DNA from fossil remains have enabled the assembly of high-coverage genome sequences for a growing diversity of organisms, including many that are extinct. Thanks to the development of new statistical approaches for detecting and quantifying admixture from genomic data, genomes from extinct populations have proven useful both in revealing previously unknown hybridization events and informing the study of hybridization between living organisms. Here, we review some of the key recent statistical innovations for detecting ancient hybridization using genomewide sequence data and discuss how these innovations have revised our understanding of human evolutionary history. CI - © 2016 John Wiley & Sons Ltd. FAU - Schaefer, Nathan K AU - Schaefer NK AD - Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA. AD - UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA. FAU - Shapiro, Beth AU - Shapiro B AD - UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA. AD - Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA. FAU - Green, Richard E AU - Green RE AD - Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA. AD - UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA. LA - eng GR - T32 HG008345/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Review DEP - 20160323 PL - England TA - Mol Ecol JT - Molecular ecology JID - 9214478 RN - 0 (DNA, Ancient) SB - IM MH - Animals MH - Biological Evolution MH - *DNA, Ancient MH - Fossils MH - Gene Flow MH - Genomics/*methods MH - Hominidae/genetics MH - Human Migration MH - Humans MH - *Hybridization, Genetic MH - Models, Genetic MH - Models, Statistical MH - Neanderthals/genetics MH - Sequence Analysis, DNA PMC - PMC5063030 MID - NIHMS773906 OTO - NOTNLM OT - D-statistics OT - admixture OT - ancient DNA OT - f-statistics OT - hybridization OT - palaeogenomics EDAT- 2016/01/31 06:00 MHDA- 2017/05/05 06:00 PMCR- 2017/06/01 CRDT- 2016/01/31 06:00 PHST- 2015/10/12 00:00 [received] PHST- 2016/01/06 00:00 [accepted] PHST- 2016/01/31 06:00 [entrez] PHST- 2016/01/31 06:00 [pubmed] PHST- 2017/05/05 06:00 [medline] PHST- 2017/06/01 00:00 [pmc-release] AID - 10.1111/mec.13556 [doi] PST - ppublish SO - Mol Ecol. 2016 Jun;25(11):2398-412. doi: 10.1111/mec.13556. Epub 2016 Mar 23. PMID- 27224451 OWN - NLM STAT- MEDLINE DCOM- 20170706 LR - 20240327 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 11 IP - 5 DP - 2016 TI - A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa. PG - e0155046 LID - 10.1371/journal.pone.0155046 [doi] LID - e0155046 AB - While Phoenician culture and trade networks had a significant impact on Western civilizations, we know little about the Phoenicians themselves. In 1994, a Punic burial crypt was discovered on Byrsa Hill, near the entry to the National Museum of Carthage in Tunisia. Inside this crypt were the remains of a young man along with a range of burial goods, all dating to the late 6th century BCE. Here we describe the complete mitochondrial genome recovered from the Young Man of Byrsa and identify that he carried a rare European haplogroup, likely linking his maternal ancestry to Phoenician influenced locations somewhere on the North Mediterranean coast, the islands of the Mediterranean or the Iberian Peninsula. This result not only provides the first direct ancient DNA evidence of a Phoenician individual but the earliest evidence of a European mitochondrial haplogroup, U5b2c1, in North Africa. FAU - Matisoo-Smith, Elizabeth A AU - Matisoo-Smith EA AD - Department of Anatomy and Allan Wilson Centre, University of Otago, Dunedin, New Zealand. FAU - Gosling, Anna L AU - Gosling AL AD - Department of Anatomy and Allan Wilson Centre, University of Otago, Dunedin, New Zealand. AD - Department of Biochemistry, University of Otago, Dunedin, New Zealand. FAU - Boocock, James AU - Boocock J AD - Department of Biochemistry, University of Otago, Dunedin, New Zealand. FAU - Kardailsky, Olga AU - Kardailsky O AD - Department of Anatomy and Allan Wilson Centre, University of Otago, Dunedin, New Zealand. FAU - Kurumilian, Yara AU - Kurumilian Y AD - School of Medicine, Lebanese American University, Byblos, Lebanon. FAU - Roudesli-Chebbi, Sihem AU - Roudesli-Chebbi S AD - National Heritage Institute, Tunis, Tunisia. FAU - Badre, Leila AU - Badre L AD - Archaeological Museum, American University of Beirut, Beirut, Lebanon. FAU - Morel, Jean-Paul AU - Morel JP AD - Université d'Aix-Marseille, Centre Camille Jullian, Aix-en-Provence, France. FAU - Sebaï, Leïla Ladjimi AU - Sebaï LL AD - National Heritage Institute, Tunis, Tunisia. FAU - Zalloua, Pierre A AU - Zalloua PA AD - School of Medicine, Lebanese American University, Byblos, Lebanon. LA - eng PT - Historical Article PT - Journal Article DEP - 20160525 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - *Haplotypes MH - History, Ancient MH - Humans MH - Male MH - Tunisia MH - White People/*genetics PMC - PMC4880306 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2016/05/26 06:00 MHDA- 2017/07/07 06:00 PMCR- 2016/05/25 CRDT- 2016/05/26 06:00 PHST- 2016/01/19 00:00 [received] PHST- 2016/04/22 00:00 [accepted] PHST- 2016/05/26 06:00 [entrez] PHST- 2016/05/26 06:00 [pubmed] PHST- 2017/07/07 06:00 [medline] PHST- 2016/05/25 00:00 [pmc-release] AID - PONE-D-16-02583 [pii] AID - 10.1371/journal.pone.0155046 [doi] PST - epublish SO - PLoS One. 2016 May 25;11(5):e0155046. doi: 10.1371/journal.pone.0155046. eCollection 2016. PMID- 27140627 OWN - NLM STAT- MEDLINE DCOM- 20161213 LR - 20190111 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 113 IP - 20 DP - 2016 May 17 TI - A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. PG - 5652-7 LID - 10.1073/pnas.1514696113 [doi] AB - The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen's age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and (14)C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the (14)C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26-30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier. FAU - Moorjani, Priya AU - Moorjani P AD - Department of Biological Sciences, Columbia University, New York, NY 10027; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142; pm2730@columbia.edu reich@genetics.med.harvard.edu. FAU - Sankararaman, Sriram AU - Sankararaman S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Computer Science, University of California, Los Angeles, CA 90095; Department of Human Genetics, University of California, Los Angeles, CA 90095; FAU - Fu, Qiaomei AU - Fu Q AD - Department of Genetics, Harvard Medical School, Boston, MA 02115; Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; FAU - Przeworski, Molly AU - Przeworski M AD - Department of Biological Sciences, Columbia University, New York, NY 10027; Department of Systems Biology, Columbia University, New York, NY 10027; FAU - Patterson, Nick AU - Patterson N AD - Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142; FAU - Reich, David AU - Reich D AD - Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142; Department of Genetics, Harvard Medical School, Boston, MA 02115; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 pm2730@columbia.edu reich@genetics.med.harvard.edu. LA - eng GR - F32 GM115006/GM/NIGMS NIH HHS/United States GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - K99 GM111744/GM/NIGMS NIH HHS/United States GR - R00 GM111744/GM/NIGMS NIH HHS/United States GR - R01 GM083098/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20160502 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Animals MH - *Biological Evolution MH - *Genetic Techniques MH - *Genome, Human MH - Humans MH - Neanderthals/*genetics MH - Polymorphism, Single Nucleotide MH - Radiometric Dating/*methods PMC - PMC4878468 OTO - NOTNLM OT - ancient DNA OT - branch shortening OT - generation interval OT - molecular clock COIS- The authors declare no conflict of interest. EDAT- 2016/05/04 06:00 MHDA- 2016/12/15 06:00 PMCR- 2016/11/17 CRDT- 2016/05/04 06:00 PHST- 2016/05/04 06:00 [entrez] PHST- 2016/05/04 06:00 [pubmed] PHST- 2016/12/15 06:00 [medline] PHST- 2016/11/17 00:00 [pmc-release] AID - 1514696113 [pii] AID - 201514696 [pii] AID - 10.1073/pnas.1514696113 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2016 May 17;113(20):5652-7. doi: 10.1073/pnas.1514696113. Epub 2016 May 2. PMID- 27173330 OWN - NLM STAT- MEDLINE DCOM- 20170206 LR - 20170206 IS - 1676-5680 (Electronic) IS - 1676-5680 (Linking) VI - 15 IP - 2 DP - 2016 May 6 TI - Ancient DNA in historical parchments - identifying a procedure for extraction and amplification of genetic material. LID - 10.4238/gmr.15028661 [doi] AB - Historical parchments in the form of documents, manuscripts, books, or letters, make up a large portion of cultural heritage collections. Their priceless historical value is associated with not only their content, but also the information hidden in the DNA deposited on them. Analyses of ancient DNA (aDNA) retrieved from parchments can be used in various investigations, including, but not limited to, studying their authentication, tracing the development of the culture, diplomacy, and technology, as well as obtaining information on the usage and domestication of animals. This article proposes and verifies a procedure for aDNA recovery from historical parchments and its appropriate preparation for further analyses. This study involved experimental selection of an aDNA extraction method with the highest efficiency and quality of extracted genetic material, from among the multi-stage phenol-chloroform extraction methods, and the modern, column-based techniques that use selective DNA-binding membranes. Moreover, current techniques to amplify entire genetic material were questioned, and the possibility of using mitochondrial DNA for species identification was analyzed. The usefulness of the proposed procedure was successfully confirmed in identification tests of historical parchments dating back to the 13-16th century AD. FAU - Lech, T AU - Lech T AD - Department of Microbiology, Faculty of Commodity Science, Cracow University of Economics, Rakowicka, Krakow, Poland. LA - eng PT - Journal Article DEP - 20160506 PL - Brazil TA - Genet Mol Res JT - Genetics and molecular research : GMR JID - 101169387 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - DNA, Ancient/*chemistry/isolation & purification MH - DNA, Mitochondrial/*chemistry/isolation & purification MH - Humans MH - Manuscripts as Topic EDAT- 2016/05/14 06:00 MHDA- 2017/02/07 06:00 CRDT- 2016/05/14 06:00 PHST- 2016/05/14 06:00 [entrez] PHST- 2016/05/14 06:00 [pubmed] PHST- 2017/02/07 06:00 [medline] AID - gmr8661 [pii] AID - 10.4238/gmr.15028661 [doi] PST - epublish SO - Genet Mol Res. 2016 May 6;15(2). doi: 10.4238/gmr.15028661. PMID- 27183562 OWN - NLM STAT- MEDLINE DCOM- 20170223 LR - 20181113 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 203 IP - 1 DP - 2016 May TI - Genetic Time Travel. PG - 9-12 LID - 10.1534/genetics.116.187856 [doi] AB - At its core, genetics is a historical discipline. Mutations are passed on from generation to generation and accumulate as a result of chance as well as of selection within and between populations and species. However, until recently, geneticists were confined to the study of present-day genetic variation and could only indirectly make inferences about the historical processes that resulted in the variation in present-day gene pools. This "time trap" has now been overcome thanks to the ability to analyze DNA extracted from ancient remains, and this is about to revolutionize several aspects of genetics. CI - Copyright © 2016 by the Genetics Society of America. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, D-07745 Jena, Germany krause@shh.mpg.de. FAU - Pääbo, Svante AU - Pääbo S AD - Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany krause@shh.mpg.de. LA - eng PT - Letter PL - United States TA - Genetics JT - Genetics JID - 0374636 SB - IM MH - Animals MH - *Evolution, Molecular MH - Extinction, Biological MH - Genetic Variation MH - Genetics, Population MH - Genome-Wide Association Study MH - Host-Pathogen Interactions/genetics MH - Humans PMC - PMC4858805 OTO - NOTNLM OT - *ancient DNA OT - *evolution EDAT- 2016/05/18 06:00 MHDA- 2017/02/24 06:00 PMCR- 2017/05/01 CRDT- 2016/05/17 06:00 PHST- 2016/02/02 00:00 [received] PHST- 2016/02/10 00:00 [accepted] PHST- 2016/05/17 06:00 [entrez] PHST- 2016/05/18 06:00 [pubmed] PHST- 2017/02/24 06:00 [medline] PHST- 2017/05/01 00:00 [pmc-release] AID - 203/1/9 [pii] AID - 187856 [pii] AID - 10.1534/genetics.116.187856 [doi] PST - ppublish SO - Genetics. 2016 May;203(1):9-12. doi: 10.1534/genetics.116.187856. PMID- 26968017 OWN - NLM STAT- MEDLINE DCOM- 20170202 LR - 20170202 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 262 DP - 2016 May TI - About 42% of 154 remains from the "Battle of Le Mans", France (1793) belong to women and children: Morphological and genetic evidence. PG - 30-6 LID - S0379-0738(16)30051-2 [pii] LID - 10.1016/j.forsciint.2016.02.029 [doi] AB - Mass graves were discovered in Le Mans and 154 skeletons were exhumed, representing a remarkable historical series of human remains from western France. We aimed to characterise the age-class and sex of these subjects, and to determine whether their profile fits with that of the Catholic and Royal Army of Vendée, who fought against the Republican Army during the Battle of Le Mans (12th-13th December, 1793). This atypical army was composed of male soldiers, but also of civilian people who followed the troops, including the elderly, children and women. In total 154 skeletons from nine mass graves were exhumed from 2009 to 2010. Two morphological methods were used to determine the sex of the subjects: the Probabilist Sexual Diagnosis (DSP) and Secondary Sexual Diagnosis (DSS) methods. Samples were handled cautiously to avoid any pre-laboratory contamination. Molecular genetic sex-typing using a recently developed assay was used to maximise sex-diagnosis of the ancient DNA samples, and 97 successful profiles including immatures were generated. Using morphological and genetic data combined, we successfully determined the sex of 93% of the subjects; 62% were male and 31% female. About 87% of subjects could be considered adults (>18 years old), 6% adolescents (15-19 years old) and 7% infants (<15 years old). Our results of an unexpected population profile for an armed conflict (42% were women and children), in addition to traumatological and historical elements, tend to confirm that these subjects were involved in the Battle of Le Mans, either actively (Republican Army, the Catholic and Royal Army) or passively (collateral victims from the civilian population of Le Mans). They represent 5-6% of the estimated 2500-3000 victims. CI - Copyright © 2016 Elsevier Ireland Ltd. All rights reserved. FAU - Thèves, Catherine AU - Thèves C AD - Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR5288 Université de Toulouse-CNRS, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France. FAU - Cabot, Elodie AU - Cabot E AD - Institut National de Recherches Archéologiques Préventives, INRAP Grand Ouest, 37 rue du Bignon, 35577 Cesson-Sévigné, France; Anthropologie Bio-culturelle, Droit, Ethique et Santé, Faculté de Médecine Site Nord (UMR 7268), 51 Boulevard Pierre Dramard, 13344 Marseille Cedex 15, France. FAU - Bouakaze, Caroline AU - Bouakaze C AD - Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR5288 Université de Toulouse-CNRS, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France. FAU - Chevet, Pierre AU - Chevet P AD - Institut National de Recherches Archéologiques Préventives, INRAP Grand Ouest, 37 rue du Bignon, 35577 Cesson-Sévigné, France. FAU - Crubézy, Éric AU - Crubézy É AD - Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR5288 Université de Toulouse-CNRS, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France. FAU - Balaresque, Patricia AU - Balaresque P AD - Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR5288 Université de Toulouse-CNRS, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France. Electronic address: patricia.balaresque@univ-tlse3.fr. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160223 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (DNA, Ancient) SB - IM MH - Adolescent MH - Adult MH - Armed Conflicts/history MH - *Body Remains MH - Burial MH - Child MH - Child, Preschool MH - DNA, Ancient MH - *Exhumation MH - Female MH - Forensic Anthropology MH - France MH - History, 18th Century MH - Humans MH - Infant MH - Male MH - Sex Determination Analysis MH - Sex Determination by Skeleton MH - Young Adult OTO - NOTNLM OT - Ancient DNA OT - Battle of Le Mans OT - Forensic archeology OT - Molecular genetic sex-typing OT - Morphological sex diagnosis OT - SRY-UTY-UTX OT - mtDNA EDAT- 2016/03/12 06:00 MHDA- 2017/02/06 06:00 CRDT- 2016/03/12 06:00 PHST- 2015/05/10 00:00 [received] PHST- 2016/02/15 00:00 [revised] PHST- 2016/02/16 00:00 [accepted] PHST- 2016/03/12 06:00 [entrez] PHST- 2016/03/12 06:00 [pubmed] PHST- 2017/02/06 06:00 [medline] AID - S0379-0738(16)30051-2 [pii] AID - 10.1016/j.forsciint.2016.02.029 [doi] PST - ppublish SO - Forensic Sci Int. 2016 May;262:30-6. doi: 10.1016/j.forsciint.2016.02.029. Epub 2016 Feb 23. PMID- 27126014 OWN - NLM STAT- MEDLINE DCOM- 20160509 LR - 20160429 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 352 IP - 6285 DP - 2016 Apr 29 TI - ANCIENT DNA. How Europe exported the Black Death. PG - 501-2 LID - 10.1126/science.352.6285.501 [doi] FAU - Lawler, Andrew AU - Lawler A LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Bacterial) SB - IM MH - China/epidemiology MH - DNA, Bacterial/*genetics MH - Disease Outbreaks/*history MH - Europe/epidemiology MH - History, Medieval MH - Humans MH - Plague/epidemiology/*history/microbiology MH - Yersinia pestis/*classification/genetics/pathogenicity EDAT- 2016/04/30 06:00 MHDA- 2016/05/10 06:00 CRDT- 2016/04/30 06:00 PHST- 2016/04/30 06:00 [entrez] PHST- 2016/04/30 06:00 [pubmed] PHST- 2016/05/10 06:00 [medline] AID - 352/6285/501 [pii] AID - 10.1126/science.352.6285.501 [doi] PST - ppublish SO - Science. 2016 Apr 29;352(6285):501-2. doi: 10.1126/science.352.6285.501. PMID- 27049965 OWN - NLM STAT- MEDLINE DCOM- 20160816 LR - 20201215 IS - 1553-7404 (Electronic) IS - 1553-7390 (Print) IS - 1553-7390 (Linking) VI - 12 IP - 4 DP - 2016 Apr TI - Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans. PG - e1005972 LID - 10.1371/journal.pgen.1005972 [doi] LID - e1005972 AB - When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters-including drift times and admixture rates-for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called 'Demographic Inference with Contamination and Error' (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%. FAU - Racimo, Fernando AU - Racimo F AD - Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America. FAU - Renaud, Gabriel AU - Renaud G AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Slatkin, Montgomery AU - Slatkin M AD - Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America. LA - eng GR - R01 GM040282/GM/NIGMS NIH HHS/United States GR - R01-GM40282/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20160406 PL - United States TA - PLoS Genet JT - PLoS genetics JID - 101239074 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM EIN - PLoS Genet. 2016 Nov 8;12(11):e1006444. doi: 10.1371/journal.pgen.1006444. PMID: 27824857 MH - Algorithms MH - Animals MH - Base Sequence MH - Computer Simulation MH - DNA/*genetics MH - *DNA Contamination MH - DNA, Mitochondrial/genetics MH - Fossils MH - *Genetic Drift MH - Genetics, Population MH - Humans MH - Markov Chains MH - Monte Carlo Method MH - Neanderthals/*genetics MH - Sequence Analysis, DNA MH - Software PMC - PMC4822957 COIS- The authors have declared that no competing interests exist. EDAT- 2016/04/07 06:00 MHDA- 2016/08/17 06:00 PMCR- 2016/04/06 CRDT- 2016/04/07 06:00 PHST- 2015/08/19 00:00 [received] PHST- 2016/03/11 00:00 [accepted] PHST- 2016/04/07 06:00 [entrez] PHST- 2016/04/07 06:00 [pubmed] PHST- 2016/08/17 06:00 [medline] PHST- 2016/04/06 00:00 [pmc-release] AID - PGENETICS-D-15-02092 [pii] AID - 10.1371/journal.pgen.1005972 [doi] PST - epublish SO - PLoS Genet. 2016 Apr 6;12(4):e1005972. doi: 10.1371/journal.pgen.1005972. eCollection 2016 Apr. PMID- 28162001 OWN - NLM STAT- MEDLINE DCOM- 20170522 LR - 20191113 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 88 IP - 2 DP - 2016 Apr TI - Genetic Affiliation of Pre-Hispanic and Contemporary Mayas Through Maternal Linage. PG - 136-167 AB - Maya civilization developed in Mesoamerica and encompassed the Yucatan Peninsula, Guatemala, Belize, part of the Mexican states of Tabasco and Chiapas, and the western parts of Honduras and El Salvador. This civilization persisted approximately 3,000 years and was one of the most advanced of its time, possessing the only known full writing system at the time, as well as art, sophisticated architecture, and mathematical and astronomical systems. This civilization reached the apex of its power and influence during the Preclassic period, from 2000 BCE to 250 CE. Genetic variation in the pre-Hispanic Mayas from archaeological sites in the Mexican states of Yucatan, Chiapas, Quintana Roo, and Tabasco and their relationship with the contemporary communities in these regions have not been previously studied. Consequently, the principal aim of this study was to determine mitochondrial DNA (mtDNA) variation in the pre-Hispanic Maya population and to assess the relationship of these individuals with contemporary Mesoamerican Maya and populations from Asia, Beringia, and North, Central, and South America. Our results revealed interactions and gene flow between populations in the different archaeological sites assessed in this study. The mtDNA haplogroup frequency in the pre-Hispanic Maya population (60.53%, 34.21%, and 5.26% for haplogroups A, C, and D, respectively) was similar to that of most Mexican and Guatemalan Maya populations, with haplogroup A exhibiting the highest frequency. Haplogroup B most likely arrived independently and mixed with populations carrying haplogroups A and C based on its absence in the pre-Hispanic Mexican Maya populations and low frequencies in most Mexican and Guatemalan Maya populations, although this also may be due to drift. Maya and Ciboneys sharing haplotype H10 belonged to haplogroup C1 and haplotype H4 of haplogroup D, suggesting shared regional haplotypes. This may indicate a shared genetic ancestry, suggesting more regional interaction between populations in the circum-Caribbean region than previously demonstrated. Haplotype sharing between the pre-Hispanic Maya and the indigenous populations from Asia, the Aleutian Islands, and North, Central, and South America provides evidence for gene flow from the ancestral Amerindian population of the pre-Hispanic Maya to Central and South America. FAU - Ochoa-Lugo, Mirna Isabel AU - Ochoa-Lugo MI AD - 1 Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico. FAU - Muñoz, María de Lourdes AU - Muñoz ML AD - 1 Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico. AD - 2 Laboratory of Biological Anthropology, University of Kansas, Lawrence, Kansas. FAU - Pérez-Ramírez, Gerardo AU - Pérez-Ramírez G AD - 1 Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico. FAU - Beaty, Kristine G AU - Beaty KG AD - 2 Laboratory of Biological Anthropology, University of Kansas, Lawrence, Kansas. FAU - López-Armenta, Mauro AU - López-Armenta M AD - 3 Laboratorio de Genética del Instituto de Ciencias Forenses del Tribunal Superior de Justicia del Distrito Federal, Mexico City, Mexico. FAU - Cervini-Silva, Javiera AU - Cervini-Silva J AD - 4 Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California. AD - 5 Universidad Autónoma Metropolitana Unidad Cuajimalpa, Mexico City, Mexico. FAU - Moreno-Galeana, Miguel AU - Moreno-Galeana M AD - 1 Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico. FAU - Meza, Adrián Martínez AU - Meza AM AD - 6 Department of Physical Anthropology, Instituto Nacional de Antropología e Historia, Mexico City, Mexico. FAU - Ramos, Eduardo AU - Ramos E AD - 6 Department of Physical Anthropology, Instituto Nacional de Antropología e Historia, Mexico City, Mexico. FAU - Crawford, Michael H AU - Crawford MH AD - 2 Laboratory of Biological Anthropology, University of Kansas, Lawrence, Kansas. FAU - Romano-Pacheco, Arturo AU - Romano-Pacheco A AD - 6 Department of Physical Anthropology, Instituto Nacional de Antropología e Historia, Mexico City, Mexico. AD - 7 Universidad del Claustro de Sor Juana, Mexico City, Mexico. LA - eng PT - Journal Article PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA, Mitochondrial/*genetics MH - Evolution, Molecular MH - Gene Flow MH - *Genetic Variation MH - Genetics, Population MH - Haplotypes MH - Humans MH - Indians, Central American/*genetics MH - Phylogeography OTO - NOTNLM OT - america OT - ancient dna OT - indigenous people OT - mesoamerica OT - migration OT - mitochondrial dna OT - pre-hispanic populations EDAT- 2017/02/07 06:00 MHDA- 2017/05/23 06:00 CRDT- 2017/02/07 06:00 PHST- 2017/02/07 06:00 [entrez] PHST- 2017/02/07 06:00 [pubmed] PHST- 2017/05/23 06:00 [medline] AID - 10.13110/humanbiology.88.2.0136 [pii] AID - 10.13110/humanbiology.88.2.0136 [doi] PST - ppublish SO - Hum Biol. 2016 Apr;88(2):136-167. doi: 10.13110/humanbiology.88.2.0136. PMID- 27051878 OWN - NLM STAT- MEDLINE DCOM- 20161220 LR - 20181113 IS - 2375-2548 (Electronic) IS - 2375-2548 (Linking) VI - 2 IP - 4 DP - 2016 Apr TI - Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. PG - e1501385 LID - 10.1126/sciadv.1501385 [doi] LID - e1501385 AB - The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages. FAU - Llamas, Bastien AU - Llamas B AUID- ORCID: 0000-0002-5550-9176 AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AUID- ORCID: 0000-0001-5510-1114 AD - Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. FAU - Valverde, Guido AU - Valverde G AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Soubrier, Julien AU - Soubrier J AUID- ORCID: 0000-0001-9350-7369 AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Mallick, Swapan AU - Mallick S AUID- ORCID: 0000-0002-4531-4439 AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.; Howard Hughes Medical Institute, Boston, MA 20815, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.; Howard Hughes Medical Institute, Boston, MA 20815, USA. FAU - Nordenfelt, Susanne AU - Nordenfelt S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.; Howard Hughes Medical Institute, Boston, MA 20815, USA. FAU - Valdiosera, Cristina AU - Valdiosera C AUID- ORCID: 0000-0003-4948-2226 AD - Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia. FAU - Richards, Stephen M AU - Richards SM AUID- ORCID: 0000-0002-0202-9654 AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Rohrlach, Adam AU - Rohrlach A AD - School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Romero, Maria Inés Barreto AU - Romero MI AD - Museo de Sitio Huaca Pucllana, Miraflores, Lima 18, Peru. FAU - Espinoza, Isabel Flores AU - Espinoza IF AD - Museo de Sitio Huaca Pucllana, Miraflores, Lima 18, Peru. FAU - Cagigao, Elsa Tomasto AU - Cagigao ET AUID- ORCID: 0000-0002-5326-8102 AD - Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru. FAU - Jiménez, Lucía Watson AU - Jiménez LW AD - Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru.; Centro de Investigaciones Arqueológicas del Museo de Sitio de Ancón, Lima 38, Peru. FAU - Makowski, Krzysztof AU - Makowski K AUID- ORCID: 0000-0002-1523-1624 AD - Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru. FAU - Reyna, Ilán Santiago Leboreiro AU - Reyna IS AD - Instituto Nacional de Antropología e Historia, Ciudad de Mexico, Mexico City 6500, Mexico. FAU - Lory, Josefina Mansilla AU - Lory JM AD - Instituto Nacional de Antropología e Historia, Ciudad de Mexico, Mexico City 6500, Mexico. FAU - Torrez, Julio Alejandro Ballivián AU - Torrez JA AUID- ORCID: 0000-0002-0432-530X AD - Unidad de Arqueología y Museos, Ministerio de Culturas y Turismo de Bolivia, La Paz 3165, Bolivia. FAU - Rivera, Mario A AU - Rivera MA AD - Universidad de Magallanes, Punta Arenas 6210427, Chile. FAU - Burger, Richard L AU - Burger RL AD - Peabody Museum of Archaeology and Ethnology at Harvard University, Boston, MA 02138, USA. FAU - Ceruti, Maria Constanza AU - Ceruti MC AD - Instituto de Investigaciones de Alta Montaña, Universidad Católica de Salta, Salta 4400, Argentina.; Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Cdad. Autónoma de Buenos Aires, Argentina. FAU - Reinhard, Johan AU - Reinhard J AUID- ORCID: 0000-0002-1142-0479 AD - National Geographic Society, Washington, DC 20036, USA. FAU - Wells, R Spencer AU - Wells RS AUID- ORCID: 0000-0002-8171-1204 AD - National Geographic Society, Washington, DC 20036, USA. FAU - Politis, Gustavo AU - Politis G AUID- ORCID: 0000-0003-4161-9873 AD - Instituto de Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina. FAU - Santoro, Calogero M AU - Santoro CM AD - Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile. FAU - Standen, Vivien G AU - Standen VG AD - Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile. FAU - Smith, Colin AU - Smith C AUID- ORCID: 0000-0001-5901-8780 AD - Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.; Howard Hughes Medical Institute, Boston, MA 20815, USA. FAU - Ho, Simon Y W AU - Ho SY AUID- ORCID: 0000-0002-0361-2307 AD - School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Haak, Wolfgang AU - Haak W AUID- ORCID: 0000-0003-2475-2007 AD - Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia. LA - eng GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - GM100233/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20160401 PL - United States TA - Sci Adv JT - Science advances JID - 101653440 RN - 0 (DNA, Ancient) RN - 0 (DNA, Mitochondrial) SB - IM MH - Americas MH - Archaeology MH - Bayes Theorem MH - Chile MH - DNA, Ancient MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration MH - *Genetic Variation MH - *Genetics, Population MH - Genome, Mitochondrial/genetics MH - Haplotypes/genetics MH - Humans MH - Indians, North American/genetics MH - *Phylogeny MH - South America PMC - PMC4820370 OTO - NOTNLM OT - Ancient DNA OT - Beringia OT - Native America OT - colonization EDAT- 2016/04/07 06:00 MHDA- 2016/12/21 06:00 PMCR- 2016/04/01 CRDT- 2016/04/07 06:00 PHST- 2015/10/05 00:00 [received] PHST- 2016/03/21 00:00 [accepted] PHST- 2016/04/07 06:00 [entrez] PHST- 2016/04/07 06:00 [pubmed] PHST- 2016/12/21 06:00 [medline] PHST- 2016/04/01 00:00 [pmc-release] AID - 1501385 [pii] AID - 10.1126/sciadv.1501385 [doi] PST - epublish SO - Sci Adv. 2016 Apr 1;2(4):e1501385. doi: 10.1126/sciadv.1501385. eCollection 2016 Apr. PMID- 26667772 OWN - NLM STAT- MEDLINE DCOM- 20161213 LR - 20191210 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 159 IP - 4 DP - 2016 Apr TI - Inferring chronological age from DNA methylation patterns of human teeth. PG - 585-95 LID - 10.1002/ajpa.22921 [doi] AB - OBJECTIVE: Current methods to determine chronological age from modern and ancient remains rely on both morphological and molecular approaches. However, low accuracy and the lack of standardized protocols make the development of alternative methods for the estimation of individual's age even more urgent for several research fields, such as biological anthropology, biodemography, forensics, evolutionary genetics, and ancient DNA studies. Therefore, the aim of this study is to identify genomic regions whose DNA methylation level correlates with age in modern teeth. METHODS: We used MALDI-TOF mass spectrometry to analyze DNA methylation levels of specific CpGs located in the ELOVL2, FHL2, and PENK genes. We considered methylation data from cementum, dentin and pulp of 21 modern teeth (from 17 to 77 years old) to construct a mathematical model able to exploit DNA methylation values to predict age of the individuals. RESULTS: The median difference between the real age and that estimated using DNA methylation values is 1.20 years (SD = 1.9) if DNA is recovered from both cementum and pulp of the same modern teeth, 2.25 years (SD = 2.5) if DNA is recovered from dental pulp, 2.45 years (SD = 3.3) if DNA is extracted from cementum and 7.07 years (SD = 7.0) when DNA is recovered from dentin only. DISCUSSION: We propose for the first time the evaluation of DNA methylation at ELOVL2, FHL2, and PENK genes as a powerful tool to predict age in modern teeth for anthropological applications. Future studies are needed to apply this method also to historical and relatively ancient human teeth. CI - © 2015 Wiley Periodicals, Inc. FAU - Giuliani, Cristina AU - Giuliani C AD - Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy. FAU - Cilli, Elisabetta AU - Cilli E AD - Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy. FAU - Bacalini, Maria Giulia AU - Bacalini MG AD - Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy. AD - Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy. FAU - Pirazzini, Chiara AU - Pirazzini C AD - Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy. AD - Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy. FAU - Sazzini, Marco AU - Sazzini M AD - Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy. FAU - Gruppioni, Giorgio AU - Gruppioni G AD - Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy. FAU - Franceschi, Claudio AU - Franceschi C AD - Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy. AD - Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy. AD - IRCCS Institute of Neurological Sciences, Bologna, 40139, Italy. FAU - Garagnani, Paolo AU - Garagnani P AD - Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy. AD - Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy. AD - Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy. FAU - Luiselli, Donata AU - Luiselli D AD - Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20151215 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (ELOVL2 protein, human) RN - 9007-49-2 (DNA) RN - EC 2.3.1.- (Acetyltransferases) RN - EC 2.3.1.- (Fatty Acid Elongases) SB - IM MH - Acetyltransferases/genetics MH - Adolescent MH - Adult MH - Age Determination by Teeth/*methods MH - Aged MH - Anthropology, Physical MH - DNA/analysis/*chemistry/*genetics/isolation & purification MH - DNA Methylation/*genetics MH - Fatty Acid Elongases MH - Humans MH - Middle Aged MH - Tooth/*chemistry MH - Young Adult OTO - NOTNLM OT - DNA methylation OT - ELOVL2 OT - age-estimation OT - teeth EDAT- 2015/12/17 06:00 MHDA- 2016/12/15 06:00 CRDT- 2015/12/16 06:00 PHST- 2015/03/18 00:00 [received] PHST- 2015/11/16 00:00 [revised] PHST- 2015/11/23 00:00 [accepted] PHST- 2015/12/16 06:00 [entrez] PHST- 2015/12/17 06:00 [pubmed] PHST- 2016/12/15 06:00 [medline] AID - 10.1002/ajpa.22921 [doi] PST - ppublish SO - Am J Phys Anthropol. 2016 Apr;159(4):585-95. doi: 10.1002/ajpa.22921. Epub 2015 Dec 15. PMID- 26641720 OWN - NLM STAT- MEDLINE DCOM- 20170428 LR - 20170428 IS - 1937-2345 (Electronic) IS - 0022-3395 (Linking) VI - 102 IP - 2 DP - 2016 Apr TI - Evidence of Helminth Infection in Guanche Mummies: Integrating Paleoparasitological and Paleogenetic Investigations. PG - 222-8 LID - 10.1645/15-866 [doi] AB - The Guanches, ancient inhabitants of the Canary Islands, Spain, practiced mummification of their dead. A paleoparasitological and paleogenetic analysis was conducted on mummified bodies (n = 6) (AD 1200, Cal BP 750) belonging to the Guanche culture from Gran Canaria Island. Coprolite and sediment samples (n = 19) were removed from below the abdominal region or sacral foramina. The samples were rehydrated in 0.5% trisodium phosphate solution for 72 hr at 4 C, and the paleoparasitological investigation was conducted by spontaneous sedimentation method and microscopic examination. The results revealed the presence of well-preserved eggs of Ascaris sp., Trichuris trichiura , Enterobius vermicularis , and hookworms. Ancient DNA was extracted from sediment samples to elucidate the ancestry of the mummies and for molecular detection of Ascaris sp. infection. Results of paleogenetic analysis demonstrated Ascaris sp. infection using 2 molecular targets, cytb and nad1. The mtDNA haplotypes U6b, U6b1, and HV were identified, which confirmed records of Guanche ancestry. The excellent preservation of Guanche mummies facilitated the paleoparasitological and paleogenetic study, the results of which contribute to our knowledge of Guanche culture and their health status. FAU - Jaeger, Lauren Hubert AU - Jaeger LH AD - LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil. FAU - Gijón-Botella, Herminia AU - Gijón-Botella H AD - LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil. FAU - Del Carmen Del Arco-Aguilar, María AU - Del Carmen Del Arco-Aguilar M AD - LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil. FAU - Martín-Oval, Mercedes AU - Martín-Oval M AD - LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil. FAU - Rodríguez-Maffiotte, Conrado AU - Rodríguez-Maffiotte C AD - LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil. FAU - Del Arco-Aguilar, Mercedes AU - Del Arco-Aguilar M AD - LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil. FAU - Araújo, Adauto AU - Araújo A AD - LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil. FAU - Iñiguez, Alena Mayo AU - Iñiguez AM AD - LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil. LA - eng PT - Historical Article PT - Journal Article DEP - 20151207 PL - United States TA - J Parasitol JT - The Journal of parasitology JID - 7803124 SB - IM MH - Helminthiasis/genetics/*history MH - History, Medieval MH - Humans MH - Mummies/history/*parasitology MH - *Paleopathology MH - Spain EDAT- 2015/12/08 06:00 MHDA- 2017/04/30 06:00 CRDT- 2015/12/08 06:00 PHST- 2015/12/08 06:00 [entrez] PHST- 2015/12/08 06:00 [pubmed] PHST- 2017/04/30 06:00 [medline] AID - 10.1645/15-866 [doi] PST - ppublish SO - J Parasitol. 2016 Apr;102(2):222-8. doi: 10.1645/15-866. Epub 2015 Dec 7. PMID- 26592162 OWN - NLM STAT- MEDLINE DCOM- 20161213 LR - 20241003 IS - 1096-0325 (Electronic) IS - 0040-5809 (Print) IS - 0040-5809 (Linking) VI - 108 DP - 2016 Apr TI - Isolation-by-distance-and-time in a stepping-stone model. PG - 24-35 LID - S0040-5809(15)00112-4 [pii] LID - 10.1016/j.tpb.2015.11.003 [doi] AB - With the great advances in ancient DNA extraction, genetic data are now obtained from geographically separated individuals from both present and past. However, population genetics theory about the joint effect of space and time has not been thoroughly studied. Based on the classical stepping-stone model, we develop the theory of Isolation by distance and time. We derive the correlation of allele frequencies between demes in the case where ancient samples are present, and investigate the impact of edge effects with forward-in-time simulations. We also derive results about coalescent times in circular and toroidal models. As one of the most common ways to investigate population structure is principal components analysis (PCA), we evaluate the impact of our theory on PCA plots. Our results demonstrate that time between samples is an important factor. Ancient samples tend to be drawn to the center of a PCA plot. CI - Published by Elsevier Inc. FAU - Duforet-Frebourg, Nicolas AU - Duforet-Frebourg N AD - Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, United States. Electronic address: duforetn@berkeley.edu. FAU - Slatkin, Montgomery AU - Slatkin M AD - Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, United States. LA - eng GR - R01 GM040282/GM/NIGMS NIH HHS/United States GR - R01-GM40282/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20151121 PL - United States TA - Theor Popul Biol JT - Theoretical population biology JID - 0256422 SB - IM MH - Gene Flow MH - Gene Frequency MH - *Genetics, Population MH - Humans MH - *Models, Genetic MH - Principal Component Analysis PMC - PMC4779737 MID - NIHMS738601 OTO - NOTNLM OT - Ancient DNA OT - Coalescence times OT - Isolation-by-distance OT - Principal component analysis EDAT- 2015/11/26 06:00 MHDA- 2016/12/15 06:00 PMCR- 2017/04/01 CRDT- 2015/11/24 06:00 PHST- 2015/08/07 00:00 [received] PHST- 2015/10/26 00:00 [revised] PHST- 2015/11/03 00:00 [accepted] PHST- 2015/11/24 06:00 [entrez] PHST- 2015/11/26 06:00 [pubmed] PHST- 2016/12/15 06:00 [medline] PHST- 2017/04/01 00:00 [pmc-release] AID - S0040-5809(15)00112-4 [pii] AID - 10.1016/j.tpb.2015.11.003 [doi] PST - ppublish SO - Theor Popul Biol. 2016 Apr;108:24-35. doi: 10.1016/j.tpb.2015.11.003. Epub 2015 Nov 21. PMID- 26996763 OWN - NLM STAT- MEDLINE DCOM- 20170110 LR - 20190110 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 6 DP - 2016 Mar 21 TI - Ancient DNA reveals selection acting on genes associated with hypoxia response in pre-Columbian Peruvian Highlanders in the last 8500 years. PG - 23485 LID - 10.1038/srep23485 [doi] LID - 23485 AB - Archaeological evidence shows that humans began living in the high altitude Andes approximately 12,000 years ago. Andean highlanders are known to have developed the most complex societies of pre-Columbian South America despite challenges to their health and reproductive success resulting from chronic exposure to hypoxia. While the physiological adaptations to this environmental stressor are well studied in contemporary Andean highlanders, the molecular evolutionary processes associated with such adaptations remain unclear. We aim to better understand how humans managed to demographically establish in this harsh environment by addressing a central question: did exposure to hypoxia drive adaptation via natural selection within Andean populations or did an existing phenotype--characterized by reduced susceptibility to hypoxic stress--enable human settlement of the Andes? We genotyped three variable loci within the NOS3 and EGLN1 genes previously associated with adaptation to high altitude in 150 ancient human DNA samples from Peruvian high altitude and coastal low altitude sites in a time frame between ~8500-560 BP. We compare the data of 109 successful samples to forward simulations of genetic drift with natural selection and find that selection, rather than drift, explains the gradual frequency changes observed in the highland populations for two of the three SNPs. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AD - UCSC Human Paleogenomics Lab, Department of Anthropology, University of California, Santa Cruz, Santa Cruz, Ca 95064, USA. FAU - Georges, Lea AU - Georges L AD - UCSC Human Paleogenomics Lab, Department of Anthropology, University of California, Santa Cruz, Santa Cruz, Ca 95064, USA. AD - Historical Anthropology and Human Ecology, University Goettingen, Goettingen, D-37073, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160321 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Ancient) RN - EC 1.14.11.2 (EGLN1 protein, human) RN - EC 1.14.11.29 (Hypoxia-Inducible Factor-Proline Dioxygenases) RN - EC 1.14.13.39 (NOS3 protein, human) RN - EC 1.14.13.39 (Nitric Oxide Synthase Type III) SB - IM MH - *Acclimatization MH - Archaeology MH - DNA, Ancient/*analysis MH - *Evolution, Molecular MH - Genetic Drift MH - Genotype MH - Humans MH - Hypoxia/*genetics MH - Hypoxia-Inducible Factor-Proline Dioxygenases/genetics MH - Nitric Oxide Synthase Type III/genetics MH - Peru MH - *Selection, Genetic PMC - PMC4800713 EDAT- 2016/03/22 06:00 MHDA- 2017/01/11 06:00 PMCR- 2016/03/21 CRDT- 2016/03/22 06:00 PHST- 2015/10/14 00:00 [received] PHST- 2016/03/07 00:00 [accepted] PHST- 2016/03/22 06:00 [entrez] PHST- 2016/03/22 06:00 [pubmed] PHST- 2017/01/11 06:00 [medline] PHST- 2016/03/21 00:00 [pmc-release] AID - srep23485 [pii] AID - 10.1038/srep23485 [doi] PST - epublish SO - Sci Rep. 2016 Mar 21;6:23485. doi: 10.1038/srep23485. PMID- 26983523 OWN - NLM STAT- MEDLINE DCOM- 20160412 LR - 20160317 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 531 IP - 7594 DP - 2016 Mar 17 TI - Oldest ancient-human DNA details dawn of Neanderthals. PG - 286 LID - 10.1038/531286a [doi] FAU - Callaway, Ewen AU - Callaway E LA - eng PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Cell Nucleus/genetics MH - DNA/*analysis/genetics MH - DNA, Mitochondrial/analysis/genetics MH - Evolution, Molecular MH - Humans MH - Neanderthals/*genetics MH - *Phylogeny MH - Sequence Analysis, DNA MH - Time Factors EDAT- 2016/03/18 06:00 MHDA- 2016/04/14 06:00 CRDT- 2016/03/18 06:00 PHST- 2016/03/18 06:00 [entrez] PHST- 2016/03/18 06:00 [pubmed] PHST- 2016/04/14 06:00 [medline] AID - 531286a [pii] AID - 10.1038/531286a [doi] PST - ppublish SO - Nature. 2016 Mar 17;531(7594):286. doi: 10.1038/531286a. PMID- 26888264 OWN - NLM STAT- MEDLINE DCOM- 20161213 LR - 20221207 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 26 IP - 3 DP - 2016 Mar TI - Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies. PG - 291-300 LID - 10.1101/gr.196634.115 [doi] AB - Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr. CI - © 2016 Hsieh et al.; Published by Cold Spring Harbor Laboratory Press. FAU - Hsieh, PingHsun AU - Hsieh P AD - Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; FAU - Woerner, August E AU - Woerner AE AD - Graduate Interdisciplinary Program in Genetics, University of Arizona, Tucson, Arizona 85721, USA; Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA; FAU - Wall, Jeffrey D AU - Wall JD AD - Institute for Human Genetics, University of California, San Francisco, California 94143, USA; FAU - Lachance, Joseph AU - Lachance J AD - Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Department of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; FAU - Tishkoff, Sarah A AU - Tishkoff SA AD - Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; FAU - Gutenkunst, Ryan N AU - Gutenkunst RN AD - Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA. FAU - Hammer, Michael F AU - Hammer MF AD - Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA; LA - eng GR - 8DP1ES022577-04/DP/NCCDPHP CDC HHS/United States GR - R01 HG005226/HG/NHGRI NIH HHS/United States GR - 1R01GM113657-01/GM/NIGMS NIH HHS/United States GR - F32HG006648/HG/NHGRI NIH HHS/United States GR - R01 GM113657/GM/NIGMS NIH HHS/United States GR - F32 HG006648/HG/NHGRI NIH HHS/United States GR - DP1 ES022577/ES/NIEHS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20160217 PL - United States TA - Genome Res JT - Genome research JID - 9518021 SB - IM EIN - Genome Res. 2016 May;26(5):717.1. doi: 10.1101/gr.206524.116. PMID: 27197244 MH - Animals MH - Black People/*genetics MH - *Evolution, Molecular MH - Gene Flow MH - Gene Frequency MH - Genetic Loci MH - *Genetics, Population MH - *Genome MH - *Genome, Human MH - *Genomics MH - Haplotypes MH - Humans MH - Linkage Disequilibrium MH - Pan paniscus/*genetics MH - Polymorphism, Single Nucleotide PMC - PMC4772012 EDAT- 2016/02/19 06:00 MHDA- 2016/12/15 06:00 PMCR- 2016/09/01 CRDT- 2016/02/19 06:00 PHST- 2015/07/07 00:00 [received] PHST- 2016/01/19 00:00 [accepted] PHST- 2016/02/19 06:00 [entrez] PHST- 2016/02/19 06:00 [pubmed] PHST- 2016/12/15 06:00 [medline] PHST- 2016/09/01 00:00 [pmc-release] AID - gr.196634.115 [pii] AID - 10.1101/gr.196634.115 [doi] PST - ppublish SO - Genome Res. 2016 Mar;26(3):291-300. doi: 10.1101/gr.196634.115. Epub 2016 Feb 17. PMID- 26545921 OWN - NLM STAT- MEDLINE DCOM- 20161104 LR - 20181113 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 33 IP - 3 DP - 2016 Mar TI - Estimating the Ages of Selection Signals from Different Epochs in Human History. PG - 657-69 LID - 10.1093/molbev/msv256 [doi] AB - Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs. CI - © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. FAU - Nakagome, Shigeki AU - Nakagome S AD - Department of Human Genetics, University of Chicago. FAU - Alkorta-Aranburu, Gorka AU - Alkorta-Aranburu G AD - Department of Human Genetics, University of Chicago. FAU - Amato, Roberto AU - Amato R AD - Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom. FAU - Howie, Bryan AU - Howie B AD - Department of Human Genetics, University of Chicago. FAU - Peter, Benjamin M AU - Peter BM AD - Department of Human Genetics, University of Chicago. FAU - Hudson, Richard R AU - Hudson RR AD - Department of Human Genetics, University of Chicago Department of Ecology and Evolution, University of Chicago dirienzo@bsd.uchicago.edu rr-hudson@uchicago.edu. FAU - Di Rienzo, Anna AU - Di Rienzo A AD - Department of Human Genetics, University of Chicago dirienzo@bsd.uchicago.edu rr-hudson@uchicago.edu. LA - eng GR - R01 GM101682/GM/NIGMS NIH HHS/United States GR - P30 CA14599/CA/NCI NIH HHS/United States GR - P30 CA014599/CA/NCI NIH HHS/United States GR - R01 HL119577/HL/NHLBI NIH HHS/United States GR - R01GM10168/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20151105 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 SB - IM MH - Alleles MH - Bayes Theorem MH - Computational Biology/methods MH - Computer Simulation MH - Evolution, Molecular MH - Gene Frequency MH - Genetic Variation MH - *Genetics, Population MH - Humans MH - *Models, Genetic MH - Polymorphism, Single Nucleotide MH - *Selection, Genetic MH - Sequence Analysis, DNA PMC - PMC5009997 OTO - NOTNLM OT - approximate Bayesian computation OT - autoimmune disease OT - onset of selection OT - selective pressures EDAT- 2015/11/08 06:00 MHDA- 2016/11/05 06:00 PMCR- 2017/03/01 CRDT- 2015/11/08 06:00 PHST- 2017/03/01 00:00 [pmc-release] PHST- 2015/11/08 06:00 [entrez] PHST- 2015/11/08 06:00 [pubmed] PHST- 2016/11/05 06:00 [medline] AID - msv256 [pii] AID - 10.1093/molbev/msv256 [doi] PST - ppublish SO - Mol Biol Evol. 2016 Mar;33(3):657-69. doi: 10.1093/molbev/msv256. Epub 2015 Nov 5. PMID- 26375610 OWN - NLM STAT- MEDLINE DCOM- 20170118 LR - 20170614 IS - 1556-4029 (Electronic) IS - 0022-1198 (Linking) VI - 61 IP - 2 DP - 2016 Mar TI - Effectiveness of Coupled Application of AmpFℓSTR Yfiler Kit and Reduced Size Y-chromosomal Short Tandem Repeat Analysis for Archeological Human Bones. PG - 430-438 LID - 10.1111/1556-4029.12950 [doi] AB - The AmpFℓSTR Yfiler PCR Amplification (Yfiler) kit continues to be improved for a better analytical efficiency in cases of highly degraded DNA. The authors endeavored to determine whether coupling of the Yfiler kit with supplemental multiplex amplification of some Y-STR loci is a more efficient analytical mode for poorly preserved human femurs (n = 15) discovered at Korean archeological sites. To reveal locus profiles not easily obtained by Yfiler analysis, custom-designed primers were adopted for the DYS390, DYS391, DYS392, DYS438, DYS439, and DYS635 loci. The success rate for 16 Y-STR locus profiles obtained from the 15 femurs was improved from 18.33% (in the use of Yfiler kit only) to 49.17% (the coupled use of Yfiler and custom-designed primers). In this study, the authors established that the custom-designed primers offer a markedly improved success rate for obtainment of Y-STR profiles from degraded aDNA not easily identified by sole use of the Yfiler assay. CI - © 2015 American Academy of Forensic Sciences. FAU - Oh, Chang Seok AU - Oh CS AD - Institute of Forensic Science, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-Gu, Seoul, 110-799, South Korea. AD - Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-Gu, Seoul, 110-799, South Korea. FAU - Lee, Soong Deok AU - Lee SD AD - Institute of Forensic Science, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-Gu, Seoul, 110-799, South Korea. AD - Department of Forensic Medicine, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-Gu, Seoul, 110-799, South Korea. FAU - Shin, Kyoung-Jin AU - Shin KJ AD - Department of Forensic Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-Gu, Seoul, 120-752, South Korea. FAU - Shin, Dong Hoon AU - Shin DH AD - Institute of Forensic Science, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-Gu, Seoul, 110-799, South Korea. AD - Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-Gu, Seoul, 110-799, South Korea. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150916 PL - United States TA - J Forensic Sci JT - Journal of forensic sciences JID - 0375370 RN - 0 (DNA Primers) SB - IM MH - *Chromosomes, Human, Y MH - *DNA Degradation, Necrotic MH - DNA Fingerprinting/*methods MH - DNA Primers MH - Femur/*chemistry MH - Humans MH - Male MH - *Microsatellite Repeats MH - *Polymerase Chain Reaction OTO - NOTNLM OT - AmpFℓSTR Yfiler PCR amplification kit OT - Joseon OT - Korea OT - Y-chromosomal short tandem repeat OT - Y-miniplex primer OT - ancient DNA OT - forensic science EDAT- 2015/09/17 06:00 MHDA- 2017/01/19 06:00 CRDT- 2015/09/17 06:00 PHST- 2014/04/28 00:00 [received] PHST- 2015/03/13 00:00 [revised] PHST- 2015/03/22 00:00 [accepted] PHST- 2015/09/17 06:00 [entrez] PHST- 2015/09/17 06:00 [pubmed] PHST- 2017/01/19 06:00 [medline] AID - 10.1111/1556-4029.12950 [doi] PST - ppublish SO - J Forensic Sci. 2016 Mar;61(2):430-438. doi: 10.1111/1556-4029.12950. Epub 2015 Sep 16. PMID- 27572991 OWN - NLM STAT- MEDLINE DCOM- 20190521 LR - 20190521 IS - 2365-0869 (Print) IS - 2364-8961 (Linking) VI - 374 IP - 1 DP - 2016 Feb TI - DNA Sequencing in Cultural Heritage. PG - 8 LID - 10.1007/s41061-015-0009-8 [doi] AB - During the last three decades, DNA analysis on degraded samples revealed itself as an important research tool in anthropology, archaeozoology, molecular evolution, and population genetics. Application on topics such as determination of species origin of prehistoric and historic objects, individual identification of famous personalities, characterization of particular samples important for historical, archeological, or evolutionary reconstructions, confers to the paleogenetics an important role also for the enhancement of cultural heritage. A really fast improvement in methodologies in recent years led to a revolution that permitted recovering even complete genomes from highly degraded samples with the possibility to go back in time 400,000 years for samples from temperate regions and 700,000 years for permafrozen remains and to analyze even more recent material that has been subjected to hard biochemical treatments. Here we propose a review on the different methodological approaches used so far for the molecular analysis of degraded samples and their application on some case studies. FAU - Vai, Stefania AU - Vai S AD - Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy. stefania.vai@unifi.it. FAU - Lari, Martina AU - Lari M AD - Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy. FAU - Caramelli, David AU - Caramelli D AD - Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy. LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20160112 PL - Switzerland TA - Top Curr Chem (Cham) JT - Topics in current chemistry (Cham) JID - 101691301 RN - 0 (DNA, Ancient) SB - IM MH - DNA, Ancient/*chemistry/isolation & purification MH - Gene Library MH - Genetics, Population MH - High-Throughput Nucleotide Sequencing MH - History, Ancient MH - Humans MH - Paleontology MH - *Sequence Analysis, DNA OTO - NOTNLM OT - Ancient DNA OT - Cultural heritage OT - New generation sequencing OT - Paleogenetics EDAT- 2016/08/31 06:00 MHDA- 2019/05/22 06:00 CRDT- 2016/08/31 06:00 PHST- 2015/09/30 00:00 [received] PHST- 2015/12/31 00:00 [accepted] PHST- 2016/08/31 06:00 [entrez] PHST- 2016/08/31 06:00 [pubmed] PHST- 2019/05/22 06:00 [medline] AID - 10.1007/s41061-015-0009-8 [pii] AID - 10.1007/s41061-015-0009-8 [doi] PST - ppublish SO - Top Curr Chem (Cham). 2016 Feb;374(1):8. doi: 10.1007/s41061-015-0009-8. Epub 2016 Jan 12. PMID- 26458007 OWN - NLM STAT- MEDLINE DCOM- 20160823 LR - 20181202 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 159 IP - 2 DP - 2016 Feb TI - The early colonial atlantic world: New insights on the African Diaspora from isotopic and ancient DNA analyses of a multiethnic 15th-17th century burial population from the Canary Islands, Spain. PG - 300-12 LID - 10.1002/ajpa.22879 [doi] AB - OBJECTIVES: The Canary Islands are considered one of the first places where Atlantic slave plantations with labourers of African origin were established, during the 15th century AD. In Gran Canaria (Canary Islands, Spain), a unique cemetery dated to the 15th and 17th centuries was discovered adjacent to an ancient sugar plantation with funerary practices that could be related to enslaved people. In this article, we investigate the origin and possible birthplace of each individual buried in this cemetery, as well as the identity and social status of these people. MATERIALS AND METHODS: The sample consists of 14 individuals radiocarbon dated to the 15th and 17th centuries AD. We have employed several methods, including the analysis of ancient human DNA, stable isotopes, and skeletal markers of physical activity. RESULTS: 1) the funerary practices indicate a set of rituals not previously recorded in the Canary Islands; 2) genetic data show that some people buried in the cemetery could have North-African and sub-Saharan African lineages; 3) isotopic results suggest that some individuals were born outside Gran Canaria; and 4) markers of physical activity show a pattern of labour involving high levels of effort. DISCUSSION: This set of evidence, along with information from historical sources, suggests that Finca Clavijo was a cemetery for a multiethnic marginalized population that had being likely enslaved. Results also indicate that this population kept practicing non-Christian rituals well into the 17th century. We propose that this was possible because the location of the Canaries, far from mainland Spain and the control of the Spanish Crown, allowed the emergence of a new society with multicultural origins that was more tolerant to foreign rituals and syncretism. CI - © 2015 Wiley Periodicals, Inc. FAU - Santana, Jonathan AU - Santana J AD - State University of Peninsula de Santa Elena, La Libertad, Ecuador. AD - G.I. Tarha. Deparment of Historical Sciences, Las Palmas de Gran Canaria, Spain. FAU - Fregel, Rosa AU - Fregel R AD - Department of Genetics, Stanford University, Stanford, United States of America. FAU - Lightfoot, Emma AU - Lightfoot E AD - University of Cambridge, Cambridge, United Kingdom. FAU - Morales, Jacob AU - Morales J AD - University of the Basque Country, Vitoria, Spain. FAU - Alamón, Martha AU - Alamón M AD - Tibicena, Las Palmas de Gran Canaria, Spain. FAU - Guillén, José AU - Guillén J AD - Tibicena, Las Palmas de Gran Canaria, Spain. FAU - Moreno, Marco AU - Moreno M AD - Tibicena, Las Palmas de Gran Canaria, Spain. FAU - Rodríguez, Amelia AU - Rodríguez A AD - G.I. Tarha. Deparment of Historical Sciences, Las Palmas de Gran Canaria, Spain. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20151012 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Carbon Isotopes) RN - 0 (Oxygen Isotopes) RN - 9007-49-2 (DNA) SB - IM MH - Adolescent MH - Adult MH - Africa MH - Anthropology, Physical MH - Carbon Isotopes/analysis MH - Cemeteries/history MH - Child MH - DNA/*genetics MH - Enslavement/*history MH - Female MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - Humans MH - Male MH - Middle Aged MH - Oxygen Isotopes/analysis MH - Radiometric Dating MH - Spain MH - Tooth/chemistry MH - Young Adult OTO - NOTNLM OT - African Diaspora OT - Canary Islands OT - ancient DNA OT - skeletal markers of physical activity OT - stable isotopes EDAT- 2015/10/13 06:00 MHDA- 2016/08/24 06:00 CRDT- 2015/10/13 06:00 PHST- 2015/02/16 00:00 [received] PHST- 2015/09/09 00:00 [revised] PHST- 2015/09/21 00:00 [accepted] PHST- 2015/10/13 06:00 [entrez] PHST- 2015/10/13 06:00 [pubmed] PHST- 2016/08/24 06:00 [medline] AID - 10.1002/ajpa.22879 [doi] PST - ppublish SO - Am J Phys Anthropol. 2016 Feb;159(2):300-12. doi: 10.1002/ajpa.22879. Epub 2015 Oct 12. PMID- 26826871 OWN - NLM STAT- MEDLINE DCOM- 20161012 LR - 20161230 IS - 1424-3997 (Electronic) IS - 0036-7672 (Linking) VI - 146 DP - 2016 TI - Tuberculosis in early medieval Switzerland--osteological and molecular evidence. PG - w14269 LID - 10.4414/smw.2016.14269 [doi] AB - Lesions consistent with skeletal tuberculosis were found in 13 individuals from an early medieval skeletal sample from Courroux (Switzerland). One case of Pott's disease as well as lytic lesions in vertebrae and joints, rib lesions and endocranial new bone formation were identified. Three individuals with lesions and one without were tested for the presence of Myobacterium tuberculosis complex (MTBC) ancient DNA (aDNA), and in two cases, evidence for MTBC aDNA was detected. Our results suggest the presence of tuberculosis in the analysed material, which is in accordance with other osteological and biomolecular research that reported a high prevalence of tuberculosis in medieval skeletons. FAU - Cooper, Christine AU - Cooper C AD - Department of Physical Anthropology, Institute of Forensic Medicine, Bern University, Switzerland. FAU - Fellner, Robert AU - Fellner R AD - Office de la Culture, Section d'archéologie et paléontologie, Porrentruy, Switzerland. FAU - Heubi, Olivier AU - Heubi O AD - Office de la Culture, Section d'archéologie et paléontologie, Porrentruy, Switzerland. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummies and the Iceman, EURAC Research, Bolzano, Italy. FAU - Zink, Albert AU - Zink A AD - Institute for Mummies and the Iceman, EURAC Research, Bolzano, Italy. FAU - Lösch, Sandra AU - Lösch S AD - Department of Physical Anthropology, Institute of Forensic Medicine, Bern University, Switzerland. LA - eng PT - Historical Article PT - Journal Article DEP - 20160131 PL - Switzerland TA - Swiss Med Wkly JT - Swiss medical weekly JID - 100970884 RN - 0 (DNA, Bacterial) SB - IM MH - Adult MH - Aged MH - Aged, 80 and over MH - Child MH - Child, Preschool MH - DNA, Bacterial/*genetics MH - Female MH - History, Medieval MH - Humans MH - Male MH - Middle Aged MH - Mycobacterium tuberculosis/*genetics MH - Osteolysis/*diagnosis/metabolism MH - Paleopathology MH - Polymerase Chain Reaction MH - Ribs MH - Switzerland MH - Tuberculosis/diagnosis/metabolism MH - Tuberculosis, Osteoarticular/diagnosis/metabolism MH - Tuberculosis, Spinal/*diagnosis/metabolism MH - Young Adult EDAT- 2016/02/02 06:00 MHDA- 2016/10/13 06:00 CRDT- 2016/02/01 06:00 PHST- 2016/02/01 06:00 [entrez] PHST- 2016/02/02 06:00 [pubmed] PHST- 2016/10/13 06:00 [medline] AID - smw-14269 [pii] AID - 10.4414/smw.2016.14269 [doi] PST - epublish SO - Swiss Med Wkly. 2016 Jan 31;146:w14269. doi: 10.4414/smw.2016.14269. eCollection 2016. PMID- 26748850 OWN - NLM STAT- MEDLINE DCOM- 20161213 LR - 20221207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 26 IP - 2 DP - 2016 Jan 25 TI - Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool. PG - 270-275 LID - S0960-9822(15)01516-X [pii] LID - 10.1016/j.cub.2015.12.019 [doi] AB - Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [1-5]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [6-9]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [10]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia's central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic. CI - Copyright © 2016 Elsevier Ltd. All rights reserved. FAU - Omrak, Ayça AU - Omrak A AD - Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 114 18, Stockholm, Sweden. Electronic address: ayca.omrak@arklab.su.se. FAU - Günther, Torsten AU - Günther T AD - Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden. FAU - Valdiosera, Cristina AU - Valdiosera C AD - Department of Archaeology, Environment and Community Planning, La Trobe University, VIC 3086, Melbourne, Australia; Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden. FAU - Svensson, Emma M AU - Svensson EM AD - Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Ullsväg 26, 75007, Uppsala, Sweden. FAU - Malmström, Helena AU - Malmström H AD - Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden. FAU - Kiesewetter, Henrike AU - Kiesewetter H AD - Project Troia, Institute of Prehistory, Early History, and Medieval Archaeology, Tübingen University, Schloss-Burgsteige 11, 72070, Tuebingen, Germany. FAU - Aylward, William AU - Aylward W AD - Biotechnology Center and Department of Classics and Ancient Near Eastern Studies, University of Wisconsin-Madison, 1220 Linden Drive, Madison, WI 53706, USA. FAU - Storå, Jan AU - Storå J AD - Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 114 18, Stockholm, Sweden. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden. FAU - Götherström, Anders AU - Götherström A AD - Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 114 18, Stockholm, Sweden. Electronic address: anders.gotherstrom@arklab.su.se. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20151231 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - *Gene Pool MH - Genetics, Population/methods MH - *Genome MH - Genomics MH - Humans MH - Middle East MH - White People/*genetics EDAT- 2016/01/11 06:00 MHDA- 2016/12/15 06:00 CRDT- 2016/01/11 06:00 PHST- 2015/11/20 00:00 [received] PHST- 2015/12/07 00:00 [revised] PHST- 2015/12/09 00:00 [accepted] PHST- 2016/01/11 06:00 [entrez] PHST- 2016/01/11 06:00 [pubmed] PHST- 2016/12/15 06:00 [medline] AID - S0960-9822(15)01516-X [pii] AID - 10.1016/j.cub.2015.12.019 [doi] PST - ppublish SO - Curr Biol. 2016 Jan 25;26(2):270-275. doi: 10.1016/j.cub.2015.12.019. Epub 2015 Dec 31. PMID- 26760973 OWN - NLM STAT- MEDLINE DCOM- 20160702 LR - 20190222 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 11 IP - 1 DP - 2016 TI - Genotyping Yersinia pestis in Historical Plague: Evidence for Long-Term Persistence of Y. pestis in Europe from the 14th to the 17th Century. PG - e0145194 LID - 10.1371/journal.pone.0145194 [doi] LID - e0145194 AB - Ancient DNA (aDNA) recovered from plague victims of the second plague pandemic (14th to 17th century), excavated from two different burial sites in Germany, and spanning a time period of more than 300 years, was characterized using single nucleotide polymorphism (SNP) analysis. Of 30 tested skeletons 8 were positive for Yersinia pestis-specific nucleic acid, as determined by qPCR targeting the pla gene. In one individual (MP-19-II), the pla copy number in DNA extracted from tooth pulp was as high as 700 gene copies/μl, indicating severe generalized infection. All positive individuals were identical in all 16 SNP positions, separating phylogenetic branches within nodes N07_N10 (14 SNPs), N07_N08 (SNP s19) and N06_N07 (s545), and were highly similar to previously investigated plague victims from other European countries. Thus, beside the assumed continuous reintroduction of Y. pestis from central Asia in multiple waves during the second pandemic, long-term persistence of Y. pestis in Europe in a yet unknown reservoir host has also to be considered. FAU - Seifert, Lisa AU - Seifert L AD - Ludwig Maximilian University of Munich, Munich, Germany. FAU - Wiechmann, Ingrid AU - Wiechmann I AD - Ludwig Maximilian University of Munich, Munich, Germany. FAU - Harbeck, Michaela AU - Harbeck M AD - State Collection for Anthropology and Palaeoanatomy, Munich, Germany. FAU - Thomas, Astrid AU - Thomas A AD - Bundeswehr Institute of Microbiology, Munich, Germany. FAU - Grupe, Gisela AU - Grupe G AD - Ludwig Maximilian University of Munich, Munich, Germany. FAU - Projahn, Michaela AU - Projahn M AD - Bundeswehr Institute of Microbiology, Munich, Germany. FAU - Scholz, Holger C AU - Scholz HC AD - Bundeswehr Institute of Microbiology, Munich, Germany. FAU - Riehm, Julia M AU - Riehm JM AD - Bundeswehr Institute of Microbiology, Munich, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20160113 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - Europe MH - *Genotyping Techniques MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, Medieval MH - Humans MH - Male MH - Phylogeny MH - Plague/genetics/*history/microbiology MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide/genetics MH - Yersinia pestis/*genetics PMC - PMC4712009 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2016/01/14 06:00 MHDA- 2016/07/03 06:00 PMCR- 2016/01/13 CRDT- 2016/01/14 06:00 PHST- 2015/10/10 00:00 [received] PHST- 2015/12/01 00:00 [accepted] PHST- 2016/01/14 06:00 [entrez] PHST- 2016/01/14 06:00 [pubmed] PHST- 2016/07/03 06:00 [medline] PHST- 2016/01/13 00:00 [pmc-release] AID - PONE-D-15-43573 [pii] AID - 10.1371/journal.pone.0145194 [doi] PST - epublish SO - PLoS One. 2016 Jan 13;11(1):e0145194. doi: 10.1371/journal.pone.0145194. eCollection 2016. PMID- 26712024 OWN - NLM STAT- MEDLINE DCOM- 20160614 LR - 20220311 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 113 IP - 2 DP - 2016 Jan 12 TI - Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. PG - 368-73 LID - 10.1073/pnas.1518445113 [doi] AB - The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343-3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter-gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026-1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago. FAU - Cassidy, Lara M AU - Cassidy LM AD - Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland; FAU - Martiniano, Rui AU - Martiniano R AD - Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland; FAU - Murphy, Eileen M AU - Murphy EM AD - School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland. FAU - Teasdale, Matthew D AU - Teasdale MD AD - Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland; FAU - Mallory, James AU - Mallory J AD - School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland. FAU - Hartwell, Barrie AU - Hartwell B AD - School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland. FAU - Bradley, Daniel G AU - Bradley DG AD - Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland; dbradley@tcd.ie. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20151228 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 9007-49-2 (DNA) SB - IM MH - Atlantic Ocean MH - DNA/genetics/isolation & purification MH - Gene Pool MH - *Genome, Human MH - Haplotypes/genetics MH - Homozygote MH - *Human Migration MH - Humans MH - Ireland MH - Phenotype MH - Principal Component Analysis MH - Sequence Analysis, DNA MH - Time Factors PMC - PMC4720318 OTO - NOTNLM OT - ancient DNA OT - genomics OT - population genetics COIS- The authors declare no conflict of interest. EDAT- 2015/12/30 06:00 MHDA- 2016/06/15 06:00 PMCR- 2015/12/28 CRDT- 2015/12/30 06:00 PHST- 2015/12/30 06:00 [entrez] PHST- 2015/12/30 06:00 [pubmed] PHST- 2016/06/15 06:00 [medline] PHST- 2015/12/28 00:00 [pmc-release] AID - 1518445113 [pii] AID - 201518445 [pii] AID - 10.1073/pnas.1518445113 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):368-73. doi: 10.1073/pnas.1518445113. Epub 2015 Dec 28. PMID- 26753840 OWN - NLM STAT- MEDLINE DCOM- 20161006 LR - 20220318 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 17 DP - 2016 Jan 11 TI - Ancient DNA and the rewriting of human history: be sparing with Occam's razor. PG - 1 LID - 10.1186/s13059-015-0866-z [doi] LID - 1 AB - Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. FAU - Haber, Marc AU - Haber M AD - The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. FAU - Mezzavilla, Massimo AU - Mezzavilla M AD - The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. AD - Institute for Maternal and Child Health, IRCCS BurloGarofolo, University of Trieste, 34137, Trieste, Italy. FAU - Xue, Yali AU - Xue Y AD - The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. FAU - Tyler-Smith, Chris AU - Tyler-Smith C AD - The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. cts@sanger.ac.uk. LA - eng GR - 098051/WT_/Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20160111 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 9007-49-2 (DNA) SB - IM MH - DNA/*genetics/history MH - *History, Ancient MH - Human Migration/history MH - Humans MH - Selection, Genetic/*genetics PMC - PMC4707776 EDAT- 2016/01/13 06:00 MHDA- 2016/10/08 06:00 PMCR- 2016/01/11 CRDT- 2016/01/13 06:00 PHST- 2016/01/13 06:00 [entrez] PHST- 2016/01/13 06:00 [pubmed] PHST- 2016/10/08 06:00 [medline] PHST- 2016/01/11 00:00 [pmc-release] AID - 10.1186/s13059-015-0866-z [pii] AID - 866 [pii] AID - 10.1186/s13059-015-0866-z [doi] PST - epublish SO - Genome Biol. 2016 Jan 11;17:1. doi: 10.1186/s13059-015-0866-z. PMID- 26832369 OWN - NLM STAT- MEDLINE DCOM- 20161031 LR - 20161230 IS - 1873-4162 (Electronic) IS - 1344-6223 (Linking) VI - 18 DP - 2016 Jan TI - Modified DOP-PCR for improved STR typing of degraded DNA from human skeletal remains and bloodstains. PG - 7-12 LID - S1344-6223(15)30040-7 [pii] LID - 10.1016/j.legalmed.2015.10.013 [doi] AB - Forensic and ancient DNA samples often are damaged and in limited quantity as a result of exposure to harsh environments and the passage of time. Several strategies have been proposed to address the challenges posed by degraded and low copy templates, including a PCR based whole genome amplification method called degenerate oligonucleotide-primed PCR (DOP-PCR). This study assessed the efficacy of four modified versions of the original DOP-PCR primer that retain at least a portion of the 5' defined sequence and alter the number of bases on the 3' end. The use of each of the four modified primers resulted in improved STR profiles from environmentally-damaged bloodstains, contemporary human skeletal remains, American Civil War era bone samples, and skeletal remains of WWII soldiers over those obtained by previously described DOP-PCR methods and routine STR typing. Additionally, the modified DOP-PCR procedure allows for a larger volume of DNA extract to be used, reducing the need to concentrate the sample and thus mitigating the effects of concurrent concentration of inhibitors. CI - Published by Elsevier Ireland Ltd. FAU - Ambers, Angie AU - Ambers A AD - Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA; Department of Biological Sciences, University of North Texas, 1511 W. Sycamore, Denton, TX, USA. Electronic address: angie.ambers@unt.edu. FAU - Turnbough, Meredith AU - Turnbough M AD - Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA. FAU - Benjamin, Robert AU - Benjamin R AD - Department of Biological Sciences, University of North Texas, 1511 W. Sycamore, Denton, TX, USA. FAU - Gill-King, Harrell AU - Gill-King H AD - Department of Biological Sciences, University of North Texas, 1511 W. Sycamore, Denton, TX, USA; Laboratory of Forensic Anthropology, Center for Human Identification, University of North Texas, Department of Biological Sciences, 1511 W. Sycamore, Denton, TX, USA. FAU - King, Jonathan AU - King J AD - Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA. FAU - Sajantila, Antti AU - Sajantila A AD - Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA; Department of Forensic Medicine, University of Helsinki, Helsinki, Finland. FAU - Budowle, Bruce AU - Budowle B AD - Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia. LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20151111 PL - Ireland TA - Leg Med (Tokyo) JT - Legal medicine (Tokyo, Japan) JID - 100889186 RN - 0 (DNA Primers) SB - IM MH - *Blood Stains MH - *Bone and Bones MH - Cell Line MH - DNA Primers/*analysis/genetics MH - Female MH - Forensic Anthropology/*methods MH - Humans MH - Male MH - Polymerase Chain Reaction/*methods OTO - NOTNLM OT - Bloodstains OT - DOP-PCR OT - Degraded DNA OT - Human skeletal remains OT - Whole genome amplification EDAT- 2016/02/03 06:00 MHDA- 2016/11/01 06:00 CRDT- 2016/02/03 06:00 PHST- 2015/04/09 00:00 [received] PHST- 2015/08/28 00:00 [revised] PHST- 2015/10/30 00:00 [accepted] PHST- 2016/02/03 06:00 [entrez] PHST- 2016/02/03 06:00 [pubmed] PHST- 2016/11/01 06:00 [medline] AID - S1344-6223(15)30040-7 [pii] AID - 10.1016/j.legalmed.2015.10.013 [doi] PST - ppublish SO - Leg Med (Tokyo). 2016 Jan;18:7-12. doi: 10.1016/j.legalmed.2015.10.013. Epub 2015 Nov 11. PMID- 26808107 OWN - NLM STAT- MEDLINE DCOM- 20161011 LR - 20161230 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 159 IP - Suppl 61 DP - 2016 Jan TI - Identifications of ancient Egyptian royal mummies from the 18th Dynasty reconsidered. PG - S216-31 LID - 10.1002/ajpa.22909 [doi] AB - For centuries, ancient Egyptian Royal mummies have drawn the attention both of the general public and scientists. Many royal mummies from the New Kingdom have survived. The discoveries of the bodies of these ancient rulers have always sparked much attention, yet not all identifications are clear even nowadays. This study presents a meta-analysis to demonstrate the difficulties in identifying ancient Egyptian royal mummies. Various methods and pitfalls in the identification of the Pharaohs are reassessed since new scientific methods can be used, such as ancient DNA-profiling and CT-scanning. While the ancestors of Tutankhamun have been identified, some identities are still highly controversial (e.g., the mystery of the KV-55 skeleton, recently most likely identified as the genetic father of Tutankhamun). The meta-analysis confirms the suggested identity of some mummies (e.g., Amenhotep III, Thutmosis IV, and Queen Tjye). CI - © 2016 Wiley Periodicals, Inc. FAU - Habicht, M E AU - Habicht ME AD - Institute for Evolutionary Medicine, University of Zurich, CH, 8057, Switzerland. FAU - Bouwman, A S AU - Bouwman AS AD - Institute for Evolutionary Medicine, University of Zurich, CH, 8057, Switzerland. FAU - Rühli, F J AU - Rühli FJ AD - Institute for Evolutionary Medicine, University of Zurich, CH, 8057, Switzerland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 SB - IM MH - Adolescent MH - Adult MH - Egypt MH - Female MH - Humans MH - Male MH - Middle Aged MH - *Mummies MH - Young Adult OTO - NOTNLM OT - Akhenaton OT - Amenhotep II OT - Amenhotep III OT - Ay OT - CT-scan OT - DB 320 OT - KV 21 OT - KV 35 OT - KV 55 OT - KV 62 OT - Nefertiti OT - Thutmosis I-III OT - Thutmosis IV OT - Thuya OT - Tije OT - Tutankhamun OT - X-ray OT - Yuya OT - aDNA OT - ancient OT - identification OT - methods OT - molecular genetics OT - mummy OT - pharaoh OT - skeleton EDAT- 2016/01/26 06:00 MHDA- 2016/10/12 06:00 CRDT- 2016/01/26 06:00 PHST- 2016/01/26 06:00 [entrez] PHST- 2016/01/26 06:00 [pubmed] PHST- 2016/10/12 06:00 [medline] AID - 10.1002/ajpa.22909 [doi] PST - ppublish SO - Am J Phys Anthropol. 2016 Jan;159(Suppl 61):S216-31. doi: 10.1002/ajpa.22909. PMID- 26791510 OWN - NLM STAT- MEDLINE DCOM- 20161014 LR - 20161230 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1399 DP - 2016 TI - Analysis of Ancient DNA in Microbial Ecology. PG - 289-315 LID - 10.1007/978-1-4939-3369-3_17 [doi] AB - The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota. FAU - Gorgé, Olivier AU - Gorgé O AD - Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France. gorge@ijm.univ-paris-diderot.fr. FAU - Bennett, E Andrew AU - Bennett EA AD - Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France. FAU - Massilani, Diyendo AU - Massilani D AD - Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France. FAU - Daligault, Julien AU - Daligault J AD - Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France. FAU - Pruvost, Melanie AU - Pruvost M AD - Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France. FAU - Geigl, Eva-Maria AU - Geigl EM AD - Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France. FAU - Grange, Thierry AU - Grange T AD - Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (DNA, Bacterial) SB - IM MH - Animals MH - DNA, Bacterial/*genetics/isolation & purification MH - Fossils MH - Genome, Microbial/*genetics MH - Genomics/methods MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Paleontology/*methods MH - Soil Microbiology OTO - NOTNLM OT - Ancient DNA OT - Contamination OT - Double-stranded library OT - Illumina OT - IonTorrent OT - NGS OT - Single-stranded library EDAT- 2016/01/23 06:00 MHDA- 2016/10/16 06:00 CRDT- 2016/01/22 06:00 PHST- 2016/01/22 06:00 [entrez] PHST- 2016/01/23 06:00 [pubmed] PHST- 2016/10/16 06:00 [medline] AID - 10.1007/978-1-4939-3369-3_17 [doi] PST - ppublish SO - Methods Mol Biol. 2016;1399:289-315. doi: 10.1007/978-1-4939-3369-3_17. PMID- 26613371 OWN - NLM STAT- MEDLINE DCOM- 20160505 LR - 20160109 IS - 1365-294X (Electronic) IS - 0962-1083 (Linking) VI - 25 IP - 1 DP - 2016 Jan TI - Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective. PG - 24-41 LID - 10.1111/mec.13492 [doi] AB - With hundreds of ancient genomes becoming available this year, ancient DNA research has now entered the genomics era. Utilizing the temporal aspect of these new data, we can now address fundamental evolutionary questions such as the characterization of selection processes shaping the genomes. The temporal dimension in the data has spurred the development in the last 10 years of new methods allowing the detection of loci evolving non-neutrally but also the inference of selection coefficients across genomes capitalizing on these time serial data. To guide empirically oriented researchers towards the statistical approach most appropriate for their data, this article reviews several of those methods, discussing their underlying assumptions and the parameter ranges for which they have been developed. While I discuss some methods developed for experimental evolution, the main focus is ancient DNA. CI - © 2015 John Wiley & Sons Ltd. FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland. AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Mol Ecol JT - Molecular ecology JID - 9214478 SB - IM MH - Animals MH - *Evolution, Molecular MH - Genetic Loci MH - *Genetics, Population MH - Genomics/*methods MH - Horses/genetics MH - Humans MH - Models, Genetic MH - Population Density MH - *Selection, Genetic MH - Sequence Analysis, DNA MH - Spatio-Temporal Analysis MH - Zea mays/genetics OTO - NOTNLM OT - adaptation OT - genomics/proteomics OT - population genetics - empirical OT - population genetics - theoretical EDAT- 2015/11/28 06:00 MHDA- 2016/05/06 06:00 CRDT- 2015/11/28 06:00 PHST- 2015/06/01 00:00 [received] PHST- 2015/11/08 00:00 [revised] PHST- 2015/11/10 00:00 [accepted] PHST- 2015/11/28 06:00 [entrez] PHST- 2015/11/28 06:00 [pubmed] PHST- 2016/05/06 06:00 [medline] AID - 10.1111/mec.13492 [doi] PST - ppublish SO - Mol Ecol. 2016 Jan;25(1):24-41. doi: 10.1111/mec.13492. PMID- 26595274 OWN - NLM STAT- MEDLINE DCOM- 20160201 LR - 20220311 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 528 IP - 7583 DP - 2015 Dec 24 TI - Genome-wide patterns of selection in 230 ancient Eurasians. PG - 499-503 LID - 10.1038/nature16152 [doi] AB - Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. FAU - Mathieson, Iain AU - Mathieson I AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Lazaridis, Iosif AU - Lazaridis I AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. FAU - Roodenberg, Songül Alpaslan AU - Roodenberg SA AD - Independent researcher, Santpoort-Noord, The Netherlands. FAU - Harney, Eadaoin AU - Harney E AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Fernandes, Daniel AU - Fernandes D AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. FAU - Novak, Mario AU - Novak M AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. AD - Institute for Anthropological Research, Zagreb 10000, Croatia. FAU - Sirak, Kendra AU - Sirak K AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. AD - Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA. FAU - Gamba, Cristina AU - Gamba C AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Jones, Eppie R AU - Jones ER AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Biological Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Dryomov, Stanislav AU - Dryomov S AD - Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. AD - Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. FAU - Pickrell, Joseph AU - Pickrell J AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Arsuaga, Juan Luís AU - Arsuaga JL AD - Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, 28040 Madrid, Spain. AD - Departamento de Paleontología, Facultad Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain. FAU - de Castro, José María Bermúdez AU - de Castro JM AD - Centro Nacional de Investigacíon sobre Evolución Humana (CENIEH), 09002 Burgos, Spain. FAU - Carbonell, Eudald AU - Carbonell E AD - IPHES. Institut Català de Paleoecologia Humana i Evolució Social, Campus Sescelades-URV, 43007 Tarragona, Spain. AD - Area de Prehistoria, Universitat Rovira i Virgili (URV), 43002 Tarragona, Spain. FAU - Gerritsen, Fokke AU - Gerritsen F AD - Netherlands Institute in Turkey, Istiklal Caddesi, Nur-i Ziya Sokak 5, Beyog˘ lu 34433, Istanbul, Turkey. FAU - Khokhlov, Aleksandr AU - Khokhlov A AD - Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia. FAU - Kuznetsov, Pavel AU - Kuznetsov P AD - Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia. FAU - Lozano, Marina AU - Lozano M AD - IPHES. Institut Català de Paleoecologia Humana i Evolució Social, Campus Sescelades-URV, 43007 Tarragona, Spain. AD - Area de Prehistoria, Universitat Rovira i Virgili (URV), 43002 Tarragona, Spain. FAU - Meller, Harald AU - Meller H AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany. FAU - Mochalov, Oleg AU - Mochalov O AD - Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg 199034, Russia. FAU - Guerra, Manuel A Rojo AU - Guerra MA AD - Department of Prehistory and Archaeology, University of Valladolid, 47002 Valladolid, Spain. FAU - Roodenberg, Jacob AU - Roodenberg J AD - The Netherlands Institute for the Near East, Leiden RA-2300, the Netherlands. FAU - Vergès, Josep Maria AU - Vergès JM AD - IPHES. Institut Català de Paleoecologia Humana i Evolució Social, Campus Sescelades-URV, 43007 Tarragona, Spain. AD - Area de Prehistoria, Universitat Rovira i Virgili (URV), 43002 Tarragona, Spain. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for the Science of Human History, D-07745 Jena, Germany. AD - Institute for Archaeological Sciences, University of Tübingen, D-72070 Tübingen, Germany. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, School of Biological Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Alt, Kurt W AU - Alt KW AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany. AD - Danube Private University, A-3500 Krems, Austria. AD - Institute for Prehistory and Archaeological Science, University of Basel, CH-4003 Basel, Switzerland. FAU - Brown, Dorcas AU - Brown D AD - Anthropology Department, Hartwick College, Oneonta, New York 13820, USA. FAU - Anthony, David AU - Anthony D AD - Anthropology Department, Hartwick College, Oneonta, New York 13820, USA. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain. FAU - Haak, Wolfgang AU - Haak W AD - Australian Centre for Ancient DNA, School of Biological Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia. AD - Max Planck Institute for the Science of Human History, D-07745 Jena, Germany. FAU - Pinhasi, Ron AU - Pinhasi R AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. AD - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. LA - eng GR - 263441/ERC_/European Research Council/International GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - GM100233/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20151123 PL - England TA - Nature JT - Nature JID - 0410462 RN - 9007-49-2 (DNA) SB - IM MH - Agriculture/history MH - Asia/ethnology MH - Body Height/genetics MH - Bone and Bones MH - DNA/genetics/isolation & purification MH - Diet/history MH - Europe/ethnology MH - Genetics, Population MH - Genome, Human/*genetics MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Immunity/genetics MH - Male MH - Multifactorial Inheritance/genetics MH - Pigmentation/genetics MH - Selection, Genetic/*genetics MH - Sequence Analysis, DNA PMC - PMC4918750 MID - NIHMS734926 COIS- The authors declare no competing financial interests. EDAT- 2015/11/26 06:00 MHDA- 2016/02/02 06:00 PMCR- 2016/06/24 CRDT- 2015/11/24 06:00 PHST- 2015/03/12 00:00 [received] PHST- 2015/10/30 00:00 [accepted] PHST- 2015/11/24 06:00 [entrez] PHST- 2015/11/26 06:00 [pubmed] PHST- 2016/02/02 06:00 [medline] PHST- 2016/06/24 00:00 [pmc-release] AID - nature16152 [pii] AID - 10.1038/nature16152 [doi] PST - ppublish SO - Nature. 2015 Dec 24;528(7583):499-503. doi: 10.1038/nature16152. Epub 2015 Nov 23. PMID- 26660678 OWN - NLM STAT- MEDLINE DCOM- 20160706 LR - 20201215 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 12 DP - 2015 TI - Retroviral DNA Sequences as a Means for Determining Ancient Diets. PG - e0144951 LID - 10.1371/journal.pone.0144951 [doi] LID - e0144951 AB - For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeological specimens from various regions of the world; however the complex dynamics represented in those microbial communities still remain unclear. Theoretically, similar to eukaryote DNA the presence of genes from key microbes or enzymes, as well as the presence of DNA from viruses specific to key organisms, may suggest the ingestion of specific diet components. In this study we demonstrate that ancient virus DNA obtained from coprolites also provides information reconstructing the host's diet, as inferred from sequences obtained from pre-Columbian coprolites. This depicts a novel and reliable approach to determine new components as well as validate the previously suggested diets of extinct cultures and animals. Furthermore, to our knowledge this represents the first description of the eukaryotic viral diversity found in paleofaeces belonging to pre-Columbian cultures. FAU - Rivera-Perez, Jessica I AU - Rivera-Perez JI AD - Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico. FAU - Cano, Raul J AU - Cano RJ AD - Center for Applications in Biotechnology, Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, United States of America. FAU - Narganes-Storde, Yvonne AU - Narganes-Storde Y AD - Center for Archaeological Research, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico. FAU - Chanlatte-Baik, Luis AU - Chanlatte-Baik L AD - Center for Archaeological Research, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico. FAU - Toranzos, Gary A AU - Toranzos GA AD - Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico. LA - eng GR - R25 GM061151/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20151214 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Viral) SB - IM MH - Animals MH - DNA, Viral/*chemistry MH - *Diet MH - Feces/virology MH - Fossils MH - Humans MH - Metagenomics MH - Retroviridae/*genetics MH - Sequence Analysis, DNA PMC - PMC4682816 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/12/15 06:00 MHDA- 2016/07/07 06:00 PMCR- 2015/12/14 CRDT- 2015/12/15 06:00 PHST- 2015/04/30 00:00 [received] PHST- 2015/11/25 00:00 [accepted] PHST- 2015/12/15 06:00 [entrez] PHST- 2015/12/15 06:00 [pubmed] PHST- 2016/07/07 06:00 [medline] PHST- 2015/12/14 00:00 [pmc-release] AID - PONE-D-15-18486 [pii] AID - 10.1371/journal.pone.0144951 [doi] PST - epublish SO - PLoS One. 2015 Dec 14;10(12):e0144951. doi: 10.1371/journal.pone.0144951. eCollection 2015. PMID- 26213269 OWN - NLM STAT- MEDLINE DCOM- 20161014 LR - 20161230 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 158 IP - 4 DP - 2015 Dec TI - Ancient marine hunter-gatherers from Patagonia and Tierra Del Fuego: Diversity and differentiation using uniparentally inherited genetic markers. PG - 719-29 LID - 10.1002/ajpa.22815 [doi] AB - OBJECTIVES: The human population history from Patagonia and Tierra del Fuego has been of great interest in the context of the American peopling. Different sources of evidence have contributed to the characterization of the local populations, but some main questions about their history remain unsolved. Among the native populations, two marine hunter-gatherers groups inhabited the Patagonian channels below the 478S: Kawéskar and Yámana. Regardless of their geographical proximity and cultural resemblance, their languages were mutually unintelligible. In this study we aim to evaluate the genetic diversity of uniparental genetic markers in both groups and to test if there is a high genetic differentiation between them, mirroring their linguistic differences. MATERIAL AND METHODS: Ancient DNA was extracted from 37 samples from both populations. We compared their genetic variability of their mitochondrial lineages and Y-STR as well as with other modern native populations from the area and further north. RESULTS AND DISCUSSION: We observed an important differentiation in their maternal lineages: while Kawéskar shows a high frequency of D (80%), Yámana shows a high frequency of C (90%). The analysis of paternal lineages reveals the presence of only Q1a2a1a1 and little variation was found between individuals. Both groups show very low levels of genetic diversity compared with modern populations. We also notice shared and unique mitochondrial DNA variants between modern and ancient samples of Kawéskar and Yámana. CI - © 2015 Wiley Periodicals, Inc. FAU - de la Fuente, Constanza AU - de la Fuente C AD - Human Genetic Program, ICBM, Faculty of Medicine, University of Chile, Santiago, 8380453, Chile. FAU - Galimany, Jacqueline AU - Galimany J AD - Human Genetic Program, ICBM, Faculty of Medicine, University of Chile, Santiago, 8380453, Chile. FAU - Kemp, Brian M AU - Kemp BM AD - Human Genetic Program, ICBM, Faculty of Medicine, University of Chile, Santiago, 8380453, Chile. FAU - Judd, Kathleen AU - Judd K AD - Human Genetic Program, ICBM, Faculty of Medicine, University of Chile, Santiago, 8380453, Chile. FAU - Reyes, Omar AU - Reyes O AD - Human Genetic Program, ICBM, Faculty of Medicine, University of Chile, Santiago, 8380453, Chile. FAU - Moraga, Mauricio AU - Moraga M AD - Human Genetic Program, ICBM, Faculty of Medicine, University of Chile, Santiago, 8380453, Chile. LA - eng PT - Journal Article DEP - 20150724 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Genetic Markers) SB - IM MH - Anthropology, Physical MH - Archaeology MH - Argentina MH - Chile MH - Female MH - Genetic Markers/*genetics MH - Haplotypes MH - Humans MH - Indians, South American/*genetics MH - Male OTO - NOTNLM OT - Patagonia OT - ancient DNA OT - marine hunter-gatherers EDAT- 2015/07/28 06:00 MHDA- 2016/10/16 06:00 CRDT- 2015/07/28 06:00 PHST- 2015/03/13 00:00 [received] PHST- 2015/06/18 00:00 [revised] PHST- 2015/07/03 00:00 [accepted] PHST- 2015/07/28 06:00 [entrez] PHST- 2015/07/28 06:00 [pubmed] PHST- 2016/10/16 06:00 [medline] AID - 10.1002/ajpa.22815 [doi] PST - ppublish SO - Am J Phys Anthropol. 2015 Dec;158(4):719-29. doi: 10.1002/ajpa.22815. Epub 2015 Jul 24. PMID- 26563586 OWN - NLM STAT- MEDLINE DCOM- 20161014 LR - 20190109 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 5 DP - 2015 Nov 13 TI - Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. PG - 16498 LID - 10.1038/srep16498 [doi] LID - 16498 AB - To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions. FAU - Ziesemer, Kirsten A AU - Ziesemer KA AD - Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands. FAU - Mann, Allison E AU - Mann AE AD - Department of Anthropology, University of Oklahoma, Norman, OK, USA. FAU - Sankaranarayanan, Krithivasan AU - Sankaranarayanan K AD - Department of Anthropology, University of Oklahoma, Norman, OK, USA. FAU - Schroeder, Hannes AU - Schroeder H AD - Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands. AD - Center for Geogenetics, University of Copenhagen, Denmark. FAU - Ozga, Andrew T AU - Ozga AT AD - Department of Anthropology, University of Oklahoma, Norman, OK, USA. FAU - Brandt, Bernd W AU - Brandt BW AD - Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands. FAU - Zaura, Egija AU - Zaura E AD - Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands. FAU - Waters-Rist, Andrea AU - Waters-Rist A AD - Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands. FAU - Hoogland, Menno AU - Hoogland M AD - Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands. FAU - Salazar-García, Domingo C AU - Salazar-García DC AD - Department of Anthropology, University of Cape Town, South Africa. AD - Departament de Prehistòria i Arqueologia, Universitat de València, Spain. AD - Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Aldenderfer, Mark AU - Aldenderfer M AD - School of Social Sciences, Humanities, and Arts, University of California, Merced, USA. FAU - Speller, Camilla AU - Speller C AD - Department of Archaeology, University of York, York, UK. FAU - Hendy, Jessica AU - Hendy J AD - Department of Archaeology, University of York, York, UK. FAU - Weston, Darlene A AU - Weston DA AD - Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands. AD - Department of Anthropology, University of British Columbia, Vancouver, Canada. FAU - MacDonald, Sandy J AU - MacDonald SJ AD - Department of Biology, University of York, York, UK. FAU - Thomas, Gavin H AU - Thomas GH AD - Department of Biology, University of York, York, UK. FAU - Collins, Matthew J AU - Collins MJ AD - Department of Archaeology, University of York, York, UK. FAU - Lewis, Cecil M AU - Lewis CM AD - Department of Anthropology, University of Oklahoma, Norman, OK, USA. FAU - Hofman, Corinne AU - Hofman C AD - Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands. FAU - Warinner, Christina AU - Warinner C AD - Department of Anthropology, University of Oklahoma, Norman, OK, USA. LA - eng SI - SRA/PRJNA278036 GR - Wellcome Trust/United Kingdom GR - R01 GM089886/GM/NIGMS NIH HHS/United States GR - 097829/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20151113 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (RNA, Ribosomal, 16S) SB - IM EIN - Sci Rep. 2016 Jun 02;6:27163. doi: 10.1038/srep27163. PMID: 27254246 MH - Archaeology MH - Bacteria/classification/genetics MH - Dental Calculus/microbiology MH - Female MH - Gastrointestinal Microbiome/genetics MH - *Gene Amplification MH - High-Throughput Nucleotide Sequencing/methods MH - Humans MH - Male MH - Metagenome/*genetics MH - Metagenomics/*methods MH - Methanobrevibacter/classification/genetics MH - Microbiota/*genetics MH - Nucleic Acid Conformation MH - Phylogeny MH - RNA, Ribosomal, 16S/chemistry/*genetics PMC - PMC4643231 EDAT- 2015/11/14 06:00 MHDA- 2016/10/16 06:00 PMCR- 2015/11/13 CRDT- 2015/11/14 06:00 PHST- 2015/04/10 00:00 [received] PHST- 2015/10/14 00:00 [accepted] PHST- 2015/11/14 06:00 [entrez] PHST- 2015/11/14 06:00 [pubmed] PHST- 2016/10/16 06:00 [medline] PHST- 2015/11/13 00:00 [pmc-release] AID - srep16498 [pii] AID - 10.1038/srep16498 [doi] PST - epublish SO - Sci Rep. 2015 Nov 13;5:16498. doi: 10.1038/srep16498. PMID- 26449472 OWN - NLM STAT- MEDLINE DCOM- 20151214 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 350 IP - 6262 DP - 2015 Nov 13 TI - Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. PG - 820-2 LID - 10.1126/science.aad2879 [doi] AB - Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5× coverage ancient genome of an Ethiopian male ("Mota") who lived approximately 4500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West, and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6 to 7% Eurasian ancestry. CI - Copyright © 2015, American Association for the Advancement of Science. FAU - Gallego Llorente, M AU - Gallego Llorente M AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. mg632@cam.ac.uk joneser@tcd.ie ron.pinhasi@ucd.ie am315@cam.ac.uk. FAU - Jones, E R AU - Jones ER AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. mg632@cam.ac.uk joneser@tcd.ie ron.pinhasi@ucd.ie am315@cam.ac.uk. FAU - Eriksson, A AU - Eriksson A AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. Integrative Systems Biology Laboratory, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia. FAU - Siska, V AU - Siska V AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. FAU - Arthur, K W AU - Arthur KW AD - Department of Society, Culture, and Language, University of South Florida St. Petersburg, 140 7th Avenue South, St. Petersburg, FL 33701, USA. FAU - Arthur, J W AU - Arthur JW AD - Department of Society, Culture, and Language, University of South Florida St. Petersburg, 140 7th Avenue South, St. Petersburg, FL 33701, USA. FAU - Curtis, M C AU - Curtis MC AD - Department of Anthropology, Ventura College, 4667 Telegraph Road, Ventura, CA 93003, USA. Humanities and Social Sciences Program, UCLA Extension, University of California Los Angeles, 10995 Le Conte Avenue, Los Angeles, CA 90095, USA. FAU - Stock, J T AU - Stock JT AD - Department of Archaeology and Anthropology, University of Cambridge, Pembroke Street, Cambridge CB2 3QG, UK. FAU - Coltorti, M AU - Coltorti M AD - Department of Physical Sciences, Earth and Environment, University of Siena, Via di Laterina, 8-53100 Siena, Italy. FAU - Pieruccini, P AU - Pieruccini P AD - Department of Physical Sciences, Earth and Environment, University of Siena, Via di Laterina, 8-53100 Siena, Italy. FAU - Stretton, S AU - Stretton S AD - Department of Anthropology, University of Illinois at Urbana-Champaign, Public Service Archaeology and Architecture Program, 109 Davenport Hall, 607 South Mathews Avenue, Urbana, IL 61801, USA. FAU - Brock, F AU - Brock F AD - Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK. Cranfield Forensic Institute, Cranfield University, Defence Academy of the United Kingdom, Shrivenham, Oxon SN6 8LA, UK. FAU - Higham, T AU - Higham T AD - Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK. FAU - Park, Y AU - Park Y AD - Theragen BiO Institute, 2nd Floor B-dong, AICT bldg, Iui-dong, Youngtong-gu, Suwon 443-270, Republic of Korea. FAU - Hofreiter, M AU - Hofreiter M AD - Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknechtstraße 24-25, 14476 Potsdam Golm, Germany. Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK. FAU - Bradley, D G AU - Bradley DG AD - Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. FAU - Bhak, J AU - Bhak J AD - The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea. FAU - Pinhasi, R AU - Pinhasi R AD - School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland. mg632@cam.ac.uk joneser@tcd.ie ron.pinhasi@ucd.ie am315@cam.ac.uk. FAU - Manica, A AU - Manica A AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. mg632@cam.ac.uk joneser@tcd.ie ron.pinhasi@ucd.ie am315@cam.ac.uk. LA - eng GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20151008 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 SB - IM EIN - Science. 2016 Feb 19;351(6275):aaf3945. doi: 10.1126/science.aaf3945. PMID: 26912899 MH - Asia MH - Biological Evolution MH - Black People/*genetics MH - Ethiopia MH - Europe MH - Genetic Variation MH - *Genome, Human MH - *Human Migration MH - Humans MH - Male EDAT- 2015/10/10 06:00 MHDA- 2015/12/15 06:00 CRDT- 2015/10/10 06:00 PHST- 2015/08/25 00:00 [received] PHST- 2015/09/28 00:00 [accepted] PHST- 2015/10/10 06:00 [entrez] PHST- 2015/10/10 06:00 [pubmed] PHST- 2015/12/15 06:00 [medline] AID - science.aad2879 [pii] AID - 10.1126/science.aad2879 [doi] PST - ppublish SO - Science. 2015 Nov 13;350(6262):820-2. doi: 10.1126/science.aad2879. Epub 2015 Oct 8. PMID- 26561991 OWN - NLM STAT- MEDLINE DCOM- 20161014 LR - 20181113 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 5 DP - 2015 Nov 12 TI - The complete mitogenome of a 500-year-old Inca child mummy. PG - 16462 LID - 10.1038/srep16462 [doi] LID - 16462 AB - In 1985, a frozen mummy was found in Cerro Aconcagua (Argentina). Archaeological studies identified the mummy as a seven-year-old Inca sacrifice victim who lived >500 years ago, at the time of the expansion of the Inca Empire towards the southern cone. The sequence of its entire mitogenome was obtained. After querying a large worldwide database of mitogenomes (>28,000) we found that the Inca haplotype belonged to a branch of haplogroup C1b (C1bi) that has not yet been identified in modern Native Americans. The expansion of C1b into the Americas, as estimated using 203 C1b mitogenomes, dates to the initial Paleoindian settlements (~18.3 thousand years ago [kya]); however, its internal variation differs between Mesoamerica and South America. By querying large databases of control region haplotypes (>150,000), we found only a few C1bi members in Peru and Bolivia (e.g. Aymaras), including one haplotype retrieved from ancient DNA of an individual belonging to the Wari Empire (Peruvian Andes). Overall, the results suggest that the profile of the mummy represents a very rare sub-clade that arose 14.3 (5-23.6) kya and could have been more frequent in the past. A Peruvian Inca origin for present-day C1bi haplotypes would satisfy both the genetic and paleo-anthropological findings. FAU - Gómez-Carballa, Alberto AU - Gómez-Carballa A AD - Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872, Galicia, Spain. AD - Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain. FAU - Catelli, Laura AU - Catelli L AD - Equipo Argentino de Antropología Forense, Independencia 644-3A, Edif. EME1, Córdoba, Argentina. FAU - Pardo-Seco, Jacobo AU - Pardo-Seco J AD - Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872, Galicia, Spain. AD - Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain. FAU - Martinón-Torres, Federico AU - Martinón-Torres F AD - Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain. AD - Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain. FAU - Roewer, Lutz AU - Roewer L AD - Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Germany. FAU - Vullo, Carlos AU - Vullo C AD - Equipo Argentino de Antropología Forense, Independencia 644-3A, Edif. EME1, Córdoba, Argentina. FAU - Salas, Antonio AU - Salas A AD - Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872, Galicia, Spain. AD - Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20151112 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) SB - IM MH - Argentina MH - Child MH - DNA, Mitochondrial/chemistry/classification/*genetics MH - Genome, Mitochondrial/*genetics MH - Haplotypes MH - Humans MH - *Indians, South American MH - *Mummies MH - Phylogeny MH - Religion MH - Sequence Analysis, DNA PMC - PMC4642457 EDAT- 2015/11/13 06:00 MHDA- 2016/10/16 06:00 PMCR- 2015/11/12 CRDT- 2015/11/13 06:00 PHST- 2015/06/17 00:00 [received] PHST- 2015/10/16 00:00 [accepted] PHST- 2015/11/13 06:00 [entrez] PHST- 2015/11/13 06:00 [pubmed] PHST- 2016/10/16 06:00 [medline] PHST- 2015/11/12 00:00 [pmc-release] AID - srep16462 [pii] AID - 10.1038/srep16462 [doi] PST - epublish SO - Sci Rep. 2015 Nov 12;5:16462. doi: 10.1038/srep16462. PMID- 26504230 OWN - NLM STAT- MEDLINE DCOM- 20160226 LR - 20181113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 112 IP - 45 DP - 2015 Nov 10 TI - Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia. PG - 13833-8 LID - 10.1073/pnas.1511903112 [doi] AB - Pleistocene residential sites with multiple contemporaneous human burials are extremely rare in the Americas. We report mitochondrial genomic variation in the first multiple mitochondrial genomes from a single prehistoric population: two infant burials (USR1 and USR2) from a common interment at the Upward Sun River Site in central Alaska dating to ∼11,500 cal B.P. Using a targeted capture method and next-generation sequencing, we determined that the USR1 infant possessed variants that define mitochondrial lineage C1b, whereas the USR2 genome falls at the root of lineage B2, allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model. FAU - Tackney, Justin C AU - Tackney JC AD - Department of Anthropology, University of Utah, Salt Lake City, UT 84112; justin.tackney@anthro.utah.edu. FAU - Potter, Ben A AU - Potter BA AD - Department of Anthropology, University of Alaska, Fairbanks, AK 99775; FAU - Raff, Jennifer AU - Raff J AD - Department of Anthropology, University of Kansas, Lawrence, KS 66045; FAU - Powers, Michael AU - Powers M AD - DNA Sequencing Core, University of Utah, Salt Lake City, UT 84112; FAU - Watkins, W Scott AU - Watkins WS AD - Department of Human Genetics, University of Utah, Salt Lake City, UT 84112; FAU - Warner, Derek AU - Warner D AD - DNA Sequencing Core, University of Utah, Salt Lake City, UT 84112; FAU - Reuther, Joshua D AU - Reuther JD AD - Department of Anthropology, University of Alaska, Fairbanks, AK 99775; Archaeology Department, University of Alaska Museum of the North, Fairbanks, AK 99775; FAU - Irish, Joel D AU - Irish JD AD - Research Centre in Evolutionary Anthropology and Paleoecology, Liverpool John Moores University, Liverpool L33AF, United Kingdom. FAU - O'Rourke, Dennis H AU - O'Rourke DH AD - Department of Anthropology, University of Utah, Salt Lake City, UT 84112; LA - eng SI - GENBANK/KT891989 SI - GENBANK/KT891990 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20151026 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) RN - 0 (Oligonucleotides) SB - IM MH - Alaska MH - Archaeology/methods MH - Base Sequence MH - Bayes Theorem MH - Burial/history MH - DNA, Mitochondrial/*genetics MH - Evolution, Molecular MH - *Genetic Variation MH - Geography MH - Haplotypes/*genetics MH - High-Throughput Nucleotide Sequencing MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Infant MH - Likelihood Functions MH - Models, Genetic MH - *Models, Theoretical MH - Molecular Sequence Data MH - Oligonucleotides/genetics MH - *Phylogeny PMC - PMC4653186 OTO - NOTNLM OT - Americas OT - Pleistocene burials OT - ancient mitochondrial DNA OT - paleogenomics OT - peopling COIS- The authors declare no conflict of interest. EDAT- 2015/10/28 06:00 MHDA- 2016/02/27 06:00 PMCR- 2016/05/10 CRDT- 2015/10/28 06:00 PHST- 2015/10/28 06:00 [entrez] PHST- 2015/10/28 06:00 [pubmed] PHST- 2016/02/27 06:00 [medline] PHST- 2016/05/10 00:00 [pmc-release] AID - 1511903112 [pii] AID - 201511903 [pii] AID - 10.1073/pnas.1511903112 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13833-8. doi: 10.1073/pnas.1511903112. Epub 2015 Oct 26. PMID- 26344900 OWN - NLM STAT- MEDLINE DCOM- 20160718 LR - 20170910 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 19 DP - 2015 Nov TI - Molecular genetic analysis on the remains of the Dark Countess: Revisiting the French Royal family. PG - 252-254 LID - S1872-4973(15)30061-2 [pii] LID - 10.1016/j.fsigen.2015.08.006 [doi] AB - The "Dark Counts" were a mysterious couple that appeared in the Thuringian village Eishausen in 1807. After living in self imposed solitude for 30 years the woman died and was buried under the name Sophia Botta. Her companion, who presented himself as Vavel de Versay, died in 1845 and was later identified as Leonardus Cornelius van der Valck, secretary of the Dutch embassy in Paris. Their lifestyle led to speculations that she was the true princess Marie Thérèse Charlotte of France, daughter of Louis XVI and Marie Antoinette. According to these speculations she was substituted by another young woman on a voyage from Paris to Vienna. Molecular genetic analyses were set out to test the remains attributed to the Dark Countess. Mitochondrial DNA testing brought concordant results determined in two forensic laboratories (Innsbruck, Austria and Freiburg, Germany) on parallel samples of the remains. The results were in exclusion to both, the mitochondrial lineage earlier reported for the French Royal family and the mitochondrial haplotype observed in a living descendant of the Royal family. CI - Copyright © 2015 Elsevier Ireland Ltd. All rights reserved. FAU - Parson, Walther AU - Parson W AD - Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, A-6020 Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, 107 Whitmore Lab, 16802 University Park, PA, USA. Electronic address: walther.parson@gmail.com. FAU - Berger, Cordula AU - Berger C AD - Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, A-6020 Innsbruck, Austria. FAU - Sänger, Timo AU - Sänger T AD - Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany. FAU - Lutz-Bonengel, Sabine AU - Lutz-Bonengel S AD - Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany. LA - eng PT - Case Reports PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150824 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - DNA/genetics MH - DNA, Mitochondrial/*genetics MH - Female MH - *Forensic Anthropology MH - France MH - History, 19th Century MH - Humans MH - Male MH - Pedigree MH - Real-Time Polymerase Chain Reaction OTO - NOTNLM OT - Ancient DNA OT - EMPOP OT - Genetic identification OT - Mitochondrial DNA EDAT- 2015/09/08 06:00 MHDA- 2016/07/19 06:00 CRDT- 2015/09/08 06:00 PHST- 2015/05/15 00:00 [received] PHST- 2015/08/06 00:00 [revised] PHST- 2015/08/18 00:00 [accepted] PHST- 2015/09/08 06:00 [entrez] PHST- 2015/09/08 06:00 [pubmed] PHST- 2016/07/19 06:00 [medline] AID - S1872-4973(15)30061-2 [pii] AID - 10.1016/j.fsigen.2015.08.006 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2015 Nov;19:252-254. doi: 10.1016/j.fsigen.2015.08.006. Epub 2015 Aug 24. PMID- 26509686 OWN - NLM STAT- MEDLINE DCOM- 20160616 LR - 20221207 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 10 DP - 2015 TI - A South American Prehistoric Mitogenome: Context, Continuity, and the Origin of Haplogroup C1d. PG - e0141808 LID - 10.1371/journal.pone.0141808 [doi] LID - e0141808 AB - Based on mitochondrial DNA (mtDNA), it has been estimated that at least 15 founder haplogroups peopled the Americas. Subhaplogroup C1d3 was defined based on the mitogenome of a living individual from Uruguay that carried a lineage previously identified in hypervariable region I sequences from ancient and modern Uruguayan individuals. When complete mitogenomes were studied, additional substitutions were found in the coding region of the mitochondrial genome. Using a complete ancient mitogenome and three modern mitogenomes, we aim to clarify the ancestral state of subhaplogroup C1d3 and to better understand the peopling of the region of the Río de la Plata basin, as well as of the builders of the mounds from which the ancient individuals were recovered. The ancient mitogenome, belonging to a female dated to 1,610±46 years before present, was identical to the mitogenome of one of the modern individuals. All individuals share the mutations defining subhaplogroup C1d3. We estimated an age of 8,974 (5,748-12,261) years for the most recent common ancestor of C1d3, in agreement with the initial peopling of the geographic region. No individuals belonging to the defined lineage were found outside of Uruguay, which raises questions regarding the mobility of the prehistoric inhabitants of the country. Moreover, the present study shows the continuity of Native lineages over at least 6,000 years. FAU - Sans, Mónica AU - Sans M AD - Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay. FAU - Figueiro, Gonzalo AU - Figueiro G AD - Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay. FAU - Hughes, Cris E AU - Hughes CE AD - Department of Anthropology, University of Illinois, Urbana, Illinois, United States of America. FAU - Lindo, John AU - Lindo J AD - Department of Anthropology, University of Illinois, Urbana, Illinois, United States of America. FAU - Hidalgo, Pedro C AU - Hidalgo PC AD - Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay. FAU - Malhi, Ripan S AU - Malhi RS AD - Department of Anthropology, University of Illinois, Urbana, Illinois, United States of America; Carl R Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20151028 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (C1D protein, human) RN - 0 (Co-Repressor Proteins) RN - 0 (DNA, Mitochondrial) SB - IM MH - American Indian or Alaska Native/*genetics MH - Archaeology MH - Brazil MH - Co-Repressor Proteins/genetics MH - DNA, Mitochondrial MH - Evolution, Molecular MH - *Genetics, Population MH - *Genome, Mitochondrial MH - *Genomics/methods MH - Haplotypes MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Sequence Analysis, DNA PMC - PMC4625051 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/10/29 06:00 MHDA- 2016/06/17 06:00 PMCR- 2015/10/28 CRDT- 2015/10/29 06:00 PHST- 2015/03/24 00:00 [received] PHST- 2015/10/13 00:00 [accepted] PHST- 2015/10/29 06:00 [entrez] PHST- 2015/10/29 06:00 [pubmed] PHST- 2016/06/17 06:00 [medline] PHST- 2015/10/28 00:00 [pmc-release] AID - PONE-D-15-11168 [pii] AID - 10.1371/journal.pone.0141808 [doi] PST - epublish SO - PLoS One. 2015 Oct 28;10(10):e0141808. doi: 10.1371/journal.pone.0141808. eCollection 2015. PMID- 26496604 OWN - NLM STAT- MEDLINE DCOM- 20160201 LR - 20181113 IS - 1097-4172 (Electronic) IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 163 IP - 3 DP - 2015 Oct 22 TI - Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. PG - 571-82 LID - S0092-8674(15)01322-7 [pii] LID - 10.1016/j.cell.2015.10.009 [doi] AB - The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics. CI - Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Rasmussen, Simon AU - Rasmussen S AD - Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark. FAU - Allentoft, Morten Erik AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. FAU - Nielsen, Kasper AU - Nielsen K AD - Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. FAU - Sikora, Martin AU - Sikora M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. FAU - Sjögren, Karl-Göran AU - Sjögren KG AD - Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. FAU - Pedersen, Anders Gorm AU - Pedersen AG AD - Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark. FAU - Schubert, Mikkel AU - Schubert M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. FAU - Van Dam, Alex AU - Van Dam A AD - Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark. FAU - Kapel, Christian Moliin Outzen AU - Kapel CM AD - Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark. FAU - Nielsen, Henrik Bjørn AU - Nielsen HB AD - Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark. FAU - Brunak, Søren AU - Brunak S AD - Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark. FAU - Avetisyan, Pavel AU - Avetisyan P AD - Division of Armenology and Social Sciences, Institute of Archaeology and Ethnography, National Academy of Sciences, 0025 Yerevan, Republic of Armenia. FAU - Epimakhov, Andrey AU - Epimakhov A AD - Institute of History and Archaeology RAS (South Ural Department), South Ural State University, 454080 Chelyabinsk, Russia. FAU - Khalyapin, Mikhail Viktorovich AU - Khalyapin MV AD - Orenburg Museum of Fine Arts, 460000 Orenburg, Russia. FAU - Gnuni, Artak AU - Gnuni A AD - Department of Archaeology and Ethnography, Yerevan State University, 0025 Yerevan, Republic of Armenia. FAU - Kriiska, Aivar AU - Kriiska A AD - Department of Archaeology, University of Tartu, 51003 Tartu, Estonia. FAU - Lasak, Irena AU - Lasak I AD - Institute of Archaeology, University of Wrocław, 50-139 Wrocław, Poland. FAU - Metspalu, Mait AU - Metspalu M AD - Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia. FAU - Gromov, Andrei AU - Gromov A AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia. FAU - Pokutta, Dalia AU - Pokutta D AD - Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. FAU - Saag, Lehti AU - Saag L AD - Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia. FAU - Varul, Liivi AU - Varul L AD - Department of Archaeology, University of Tartu, 51003 Tartu, Estonia. FAU - Yepiskoposyan, Levon AU - Yepiskoposyan L AD - Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia. FAU - Sicheritz-Pontén, Thomas AU - Sicheritz-Pontén T AD - Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark. FAU - Foley, Robert A AU - Foley RA AD - Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK. FAU - Lahr, Marta Mirazón AU - Lahr MM AD - Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK. FAU - Nielsen, Rasmus AU - Nielsen R AD - Center for Theoretical Evolutionary Genetics, University of California, Berkeley, California 94720-3140, USA. FAU - Kristiansen, Kristian AU - Kristiansen K AD - Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. Electronic address: ewillerslev@snm.ku.dk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20151022 PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Bacterial) SB - IM MH - Animals MH - Asia MH - DNA, Bacterial/genetics MH - Europe MH - History, Ancient MH - History, Medieval MH - Humans MH - Plague/history/*microbiology/transmission MH - Siphonaptera/microbiology MH - Tooth/microbiology MH - Yersinia pestis/*classification/genetics/*isolation & purification PMC - PMC4644222 EDAT- 2015/10/27 06:00 MHDA- 2016/02/02 06:00 PMCR- 2015/10/22 CRDT- 2015/10/27 06:00 PHST- 2015/08/06 00:00 [received] PHST- 2015/09/30 00:00 [revised] PHST- 2015/10/02 00:00 [accepted] PHST- 2015/10/27 06:00 [entrez] PHST- 2015/10/27 06:00 [pubmed] PHST- 2016/02/02 06:00 [medline] PHST- 2015/10/22 00:00 [pmc-release] AID - S0092-8674(15)01322-7 [pii] AID - 10.1016/j.cell.2015.10.009 [doi] PST - ppublish SO - Cell. 2015 Oct 22;163(3):571-82. doi: 10.1016/j.cell.2015.10.009. Epub 2015 Oct 22. PMID- 26469018 OWN - NLM STAT- MEDLINE DCOM- 20160428 LR - 20181113 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 526 IP - 7573 DP - 2015 Oct 15 TI - Ancient DNA from hot climes yields its secrets. PG - 303 LID - 10.1038/526303a [doi] FAU - Callaway, Ewen AU - Callaway E LA - eng PT - Historical Article PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Climate MH - DNA/genetics/*isolation & purification MH - Ethiopia MH - History, Ancient MH - Hominidae/classification/genetics MH - *Hot Temperature MH - Human Migration/*history MH - Humans MH - Phylogeny MH - Temporal Bone/anatomy & histology MH - Turkey EDAT- 2015/10/16 06:00 MHDA- 2016/04/29 06:00 CRDT- 2015/10/16 06:00 PHST- 2015/10/16 06:00 [entrez] PHST- 2015/10/16 06:00 [pubmed] PHST- 2016/04/29 06:00 [medline] AID - 526303a [pii] AID - 10.1038/526303a [doi] PST - ppublish SO - Nature. 2015 Oct 15;526(7573):303. doi: 10.1038/526303a. PMID- 26458810 OWN - NLM STAT- MEDLINE DCOM- 20160523 LR - 20181113 IS - 1474-760X (Electronic) IS - 1474-7596 (Print) IS - 1474-7596 (Linking) VI - 16 DP - 2015 Oct 12 TI - Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. PG - 224 LID - 10.1186/s13059-015-0776-0 [doi] LID - 224 AB - Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates. AVAILABILITY: https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3. FAU - Renaud, Gabriel AU - Renaud G AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. gabriel.reno@gmail.com. FAU - Slon, Viviane AU - Slon V AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. viviane_slon@eva.mpg.de. FAU - Duggan, Ana T AU - Duggan AT AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St West, Hamilton, ON, L8S 4L9, Canada. duggana@mcmaster.ca. FAU - Kelso, Janet AU - Kelso J AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. janet_kelso@eva.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20151012 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Base Sequence MH - *Consensus Sequence MH - *DNA Contamination MH - DNA, Mitochondrial/*chemistry MH - *Genome, Mitochondrial MH - Humans MH - Neanderthals/genetics MH - Sequence Analysis, DNA/*methods MH - *Software PMC - PMC4601135 EDAT- 2015/10/16 06:00 MHDA- 2016/05/24 06:00 PMCR- 2015/10/12 CRDT- 2015/10/14 06:00 PHST- 2015/06/09 00:00 [received] PHST- 2015/09/10 00:00 [accepted] PHST- 2015/10/14 06:00 [entrez] PHST- 2015/10/16 06:00 [pubmed] PHST- 2016/05/24 06:00 [medline] PHST- 2015/10/12 00:00 [pmc-release] AID - 10.1186/s13059-015-0776-0 [pii] AID - 776 [pii] AID - 10.1186/s13059-015-0776-0 [doi] PST - epublish SO - Genome Biol. 2015 Oct 12;16:224. doi: 10.1186/s13059-015-0776-0. PMID- 26392548 OWN - NLM STAT- MEDLINE DCOM- 20160412 LR - 20181113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 112 IP - 40 DP - 2015 Oct 6 TI - Early human use of anadromous salmon in North America at 11,500 y ago. PG - 12344-8 LID - 10.1073/pnas.1509747112 [doi] AB - Salmon represented a critical resource for prehistoric foragers along the North Pacific Rim, and continue to be economically and culturally important; however, the origins of salmon exploitation remain unresolved. Here we report 11,500-y-old salmon associated with a cooking hearth and human burials from the Upward Sun River Site, near the modern extreme edge of salmon habitat in central Alaska. This represents the earliest known human use of salmon in North America. Ancient DNA analyses establish the species as Oncorhynchus keta (chum salmon), and stable isotope analyses indicate anadromy, suggesting that salmon runs were established by at least the terminal Pleistocene. The early use of this resource has important implications for Paleoindian land use, economy, and expansions into northwest North America. FAU - Halffman, Carrin M AU - Halffman CM AD - Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775; cmhalffman@alaska.edu. FAU - Potter, Ben A AU - Potter BA AD - Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775; FAU - McKinney, Holly J AU - McKinney HJ AD - Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775; FAU - Finney, Bruce P AU - Finney BP AD - Departments of Biological Sciences and Geosciences, Idaho State University, Pocatello, ID 83209; FAU - Rodrigues, Antonia T AU - Rodrigues AT AD - Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada V5A 1S6; FAU - Yang, Dongya Y AU - Yang DY AD - Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada V5A 1S6; FAU - Kemp, Brian M AU - Kemp BM AD - Department of Anthropology, Washington State University, Pullman, WA 99164; School of Biological Sciences, Washington State University, Pullman, WA 99164. LA - eng SI - GENBANK/KT693031 SI - GENBANK/KT693032 SI - GENBANK/KT725810 SI - GENBANK/KT725811 PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20150921 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Carbon Isotopes) RN - 0 (DNA, Mitochondrial) RN - 0 (Fish Proteins) RN - 0 (Nitrogen Isotopes) RN - 9007-49-2 (DNA) RN - 9035-37-4 (Cytochromes b) SB - IM MH - Alaska MH - Animals MH - Base Sequence MH - Carbon Isotopes MH - Cytochromes b/classification/genetics MH - DNA/*chemistry/genetics MH - DNA, Mitochondrial/chemistry/genetics MH - Fish Proteins/genetics MH - *Fossils MH - Geography MH - Haplotypes MH - Humans MH - Molecular Sequence Data MH - Nitrogen Isotopes MH - Oncorhynchus keta/anatomy & histology/*genetics MH - Phylogeny MH - Radiometric Dating/methods MH - Rivers MH - Sequence Analysis, DNA MH - Sequence Homology, Nucleic Acid MH - Spine/anatomy & histology/*metabolism PMC - PMC4603495 OTO - NOTNLM OT - Beringia OT - Paleoindians OT - ancient DNA OT - salmon OT - stable isotopes COIS- The authors declare no conflict of interest. EDAT- 2015/09/24 06:00 MHDA- 2016/04/14 06:00 PMCR- 2016/04/06 CRDT- 2015/09/23 06:00 PHST- 2015/09/23 06:00 [entrez] PHST- 2015/09/24 06:00 [pubmed] PHST- 2016/04/14 06:00 [medline] PHST- 2016/04/06 00:00 [pmc-release] AID - 1509747112 [pii] AID - 201509747 [pii] AID - 10.1073/pnas.1509747112 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):12344-8. doi: 10.1073/pnas.1509747112. Epub 2015 Sep 21. PMID- 26351665 OWN - NLM STAT- MEDLINE DCOM- 20151221 LR - 20181113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 112 IP - 38 DP - 2015 Sep 22 TI - Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. PG - 11917-22 LID - 10.1073/pnas.1509851112 [doi] AB - The consequences of the Neolithic transition in Europe--one of the most important cultural changes in human prehistory--is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter-gatherers. The proportion of hunter-gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people. FAU - Günther, Torsten AU - Günther T AD - Department of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden; FAU - Valdiosera, Cristina AU - Valdiosera C AD - Department of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden; Department of Archaeology and History, La Trobe University, Melbourne, VIC 3086, Australia; Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; FAU - Malmström, Helena AU - Malmström H AD - Department of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden; FAU - Ureña, Irene AU - Ureña I AD - Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain; FAU - Rodriguez-Varela, Ricardo AU - Rodriguez-Varela R AD - Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain; FAU - Sverrisdóttir, Óddny Osk AU - Sverrisdóttir ÓO AD - Department of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden; FAU - Daskalaki, Evangelia A AU - Daskalaki EA AD - Department of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Department of Genetics, Harvard Medical School, Boston, MA 02115; FAU - Naidoo, Thijessen AU - Naidoo T AD - Department of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden; FAU - Svensson, Emma M AU - Svensson EM AD - Department of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; FAU - Bermúdez de Castro, José María AU - Bermúdez de Castro JM AD - Centro Nacional de Investigación sobre la Evolución Humana, 09002 Burgos, Spain; FAU - Carbonell, Eudald AU - Carbonell E AD - Institut Català de Paleoecologia Humana i Evolució Social, CEIP Marcel·lí Domingo, 43007 Tarragona, Spain; FAU - Dunn, Michael AU - Dunn M AD - Department of Linguistics and Philology, Uppsala University, 75238 Uppsala, Sweden; FAU - Storå, Jan AU - Storå J AD - Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; FAU - Iriarte, Eneko AU - Iriarte E AD - Laboratorio de Evolución Humana, Departamento de Ciencias Históricas y Geografía, Universidad de Burgos, 09001 Burgos, Spain; FAU - Arsuaga, Juan Luis AU - Arsuaga JL AD - Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain; FAU - Carretero, José-Miguel AU - Carretero JM AD - Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Laboratorio de Evolución Humana, Departamento de Ciencias Históricas y Geografía, Universidad de Burgos, 09001 Burgos, Spain; FAU - Götherström, Anders AU - Götherström A AD - Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden; Science for Life laboratory, Uppsala University, 75123 Uppsala, Sweden mattias.jakobsson@ebc.uu.se. LA - eng SI - BioProject/PRJEB9783 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150908 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 9007-49-2 (DNA) SB - IM MH - DNA/*genetics MH - Farmers/*history MH - Gene Pool MH - *Genome MH - Geography MH - History, Ancient MH - Humans MH - Population Dynamics MH - Principal Component Analysis MH - Sequence Analysis, DNA MH - Spain PMC - PMC4586848 OTO - NOTNLM OT - Ancient DNA OT - human prehistory OT - population genomics COIS- The authors declare no conflict of interest. EDAT- 2015/09/10 06:00 MHDA- 2015/12/22 06:00 PMCR- 2015/09/08 CRDT- 2015/09/10 06:00 PHST- 2015/09/10 06:00 [entrez] PHST- 2015/09/10 06:00 [pubmed] PHST- 2015/12/22 06:00 [medline] PHST- 2015/09/08 00:00 [pmc-release] AID - 1509851112 [pii] AID - 201509851 [pii] AID - 10.1073/pnas.1509851112 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11917-22. doi: 10.1073/pnas.1509851112. Epub 2015 Sep 8. PMID- 26210385 OWN - NLM STAT- MEDLINE DCOM- 20160609 LR - 20181113 IS - 1435-4373 (Electronic) IS - 0934-9723 (Print) IS - 0934-9723 (Linking) VI - 34 IP - 9 DP - 2015 Sep TI - Molecular studies on ancient M. tuberculosis and M. leprae: methods of pathogen and host DNA analysis. PG - 1733-49 LID - 10.1007/s10096-015-2427-5 [doi] AB - Humans have evolved alongside infectious diseases for millennia. Despite the efforts to reduce their incidence, infectious diseases still pose a tremendous threat to the world population. Fast development of molecular techniques and increasing risk of new epidemics have resulted in several studies that look to the past in order to investigate the origin and evolution of infectious diseases. Tuberculosis and leprosy have become frequent targets of such studies, owing to the persistence of their molecular biomarkers in ancient material and the characteristic skeletal lesions each disease may cause. This review examines the molecular methods used to screen for the presence of M. tuberculosis and M. leprae ancient DNA (aDNA) and their differentiation in ancient human remains. Examples of recent studies, mainly from Europe, that employ the newest techniques of molecular analysis are also described. Moreover, we present a specific approach based on assessing the likely immunological profile of historic populations, in order to further elucidate the influence of M. tuberculosis and M. leprae on historical human populations. FAU - Witas, H W AU - Witas HW AD - Department of Molecular Biology, Medical University of Łódź, Łódź, Poland, henryk.witas@umed.lodz.pl. FAU - Donoghue, H D AU - Donoghue HD FAU - Kubiak, D AU - Kubiak D FAU - Lewandowska, M AU - Lewandowska M FAU - Gładykowska-Rzeczycka, J J AU - Gładykowska-Rzeczycka JJ LA - eng PT - Journal Article PT - Review DEP - 20150726 PL - Germany TA - Eur J Clin Microbiol Infect Dis JT - European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology JID - 8804297 RN - 0 (DNA, Bacterial) SB - IM MH - Archaeology MH - Biological Evolution MH - DNA, Bacterial/genetics MH - Europe MH - Genetic Predisposition to Disease MH - Genome, Bacterial/*genetics MH - Humans MH - Leprosy/*diagnosis/microbiology MH - Molecular Typing/methods MH - Mycobacterium leprae/*genetics MH - Mycobacterium tuberculosis/*genetics MH - Tuberculosis/*diagnosis/microbiology PMC - PMC4545183 EDAT- 2015/07/27 06:00 MHDA- 2016/06/10 06:00 PMCR- 2015/07/26 CRDT- 2015/07/27 06:00 PHST- 2015/03/26 00:00 [received] PHST- 2015/06/09 00:00 [accepted] PHST- 2015/07/27 06:00 [entrez] PHST- 2015/07/27 06:00 [pubmed] PHST- 2016/06/10 06:00 [medline] PHST- 2015/07/26 00:00 [pmc-release] AID - 2427 [pii] AID - 10.1007/s10096-015-2427-5 [doi] PST - ppublish SO - Eur J Clin Microbiol Infect Dis. 2015 Sep;34(9):1733-49. doi: 10.1007/s10096-015-2427-5. Epub 2015 Jul 26. PMID- 26319403 OWN - NLM STAT- MEDLINE DCOM- 20160725 LR - 20181113 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 7 IP - 9 DP - 2015 Aug 28 TI - Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals. PG - 2569-84 LID - 10.1093/gbe/evv166 [doi] AB - Dietary shifts can drive molecular evolution in mammals and a major transition in human history, the agricultural revolution, favored carbohydrate consumption. We investigated the evolutionary history of nine genes encoding brush-border proteins involved in carbohydrate digestion/absorption. Results indicated widespread adaptive evolution in mammals, with several branches experiencing episodic selection, particularly strong in bats. Many positively selected sites map to functional protein regions (e.g., within glucosidase catalytic crevices), with parallel evolution at SI (sucrase-isomaltase) and MGAM (maltase-glucoamylase). In human populations, five genes were targeted by positive selection acting on noncoding variants within regulatory elements. Analysis of ancient DNA samples indicated that most derived alleles were already present in the Paleolithic. Positively selected variants at SLC2A5 (fructose transporter) were an exception and possibly spread following the domestication of specific fruit crops. We conclude that agriculture determined no major selective event at carbohydrate metabolism genes in humans, with implications for susceptibility to metabolic disorders. CI - © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Pontremoli, Chiara AU - Pontremoli C AD - Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy. FAU - Mozzi, Alessandra AU - Mozzi A AD - Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy. FAU - Forni, Diego AU - Forni D AD - Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy. FAU - Cagliani, Rachele AU - Cagliani R AD - Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy. FAU - Pozzoli, Uberto AU - Pozzoli U AD - Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy. FAU - Menozzi, Giorgia AU - Menozzi G AD - Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy. FAU - Vertemara, Jacopo AU - Vertemara J AD - Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy. FAU - Bresolin, Nereo AU - Bresolin N AD - Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy Dino Ferrari Centre, Department of Physiopathology and Transplantation, University of Milan, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico, Italy. FAU - Clerici, Mario AU - Clerici M AD - Department of Physiopathology and Transplantation, University of Milan, Italy Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy. FAU - Sironi, Manuela AU - Sironi M AD - Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy manuela.sironi@bp.lnf.it. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150828 PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 RN - 0 (Dietary Carbohydrates) RN - EC 3.2.1.- (Sucrase-Isomaltase Complex) RN - EC 3.2.1.20 (alpha-Glucosidases) SB - IM MH - Adaptation, Biological/genetics MH - Alleles MH - Animals MH - Carbohydrate Metabolism/genetics MH - Dietary Carbohydrates/*metabolism MH - *Evolution, Molecular MH - Gorilla gorilla/genetics MH - Humans MH - Mammals/*genetics MH - Microvilli/enzymology MH - Pan troglodytes/genetics MH - Protein Structure, Tertiary/genetics MH - *Selection, Genetic MH - Sucrase-Isomaltase Complex/genetics MH - alpha-Glucosidases/genetics PMC - PMC4607523 OTO - NOTNLM OT - LCT OT - MGAM OT - SI OT - SLC2A2 OT - TREH OT - natural selection EDAT- 2015/09/01 06:00 MHDA- 2016/07/28 06:00 PMCR- 2015/09/11 CRDT- 2015/08/31 06:00 PHST- 2015/08/31 06:00 [entrez] PHST- 2015/09/01 06:00 [pubmed] PHST- 2016/07/28 06:00 [medline] PHST- 2015/09/11 00:00 [pmc-release] AID - evv166 [pii] AID - 10.1093/gbe/evv166 [doi] PST - epublish SO - Genome Biol Evol. 2015 Aug 28;7(9):2569-84. doi: 10.1093/gbe/evv166. PMID- 26260087 OWN - NLM STAT- MEDLINE DCOM- 20160414 LR - 20150811 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 59 IP - 2 DP - 2015 Aug TI - Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. PG - 87-93 LID - 10.2144/000114320 [doi] AB - Although great progress has been made in improving methods for generating DNA sequences from ancient biological samples, many, if not most, samples are still not amenable for analyses due to overwhelming contamination with microbial or modern human DNA. Here we explore different DNA decontamination procedures for ancient bones and teeth for use prior to DNA library preparation and high-throughput sequencing. Two procedures showed promising results: (i) the release of surface-bound DNA by phosphate buffer and (ii) the removal of DNA contamination by sodium hypochlorite treatment. Exposure to phosphate removes on average 64% of the microbial DNA from bone powder but only 37% of the endogenous DNA (from the organism under study), increasing the percentage of informative sequences by a factor of two on average. An average 4.6-fold increase, in one case reaching 24-fold, is achieved by sodium hypochlorite treatment, albeit at the expense of destroying 63% of the endogenous DNA preserved in the bone. While both pretreatment methods described here greatly reduce the cost of genome sequencing from ancient material due to efficient depletion of microbial DNA, we find that the removal of human DNA contamination remains a challenging problem. FAU - Korlević, Petra AU - Korlević P AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Gerber, Tobias AU - Gerber T AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Gansauge, Marie-Theres AU - Gansauge MT AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Hajdinjak, Mateja AU - Hajdinjak M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Nagel, Sarah AU - Nagel S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Aximu-Petri, Ayinuer AU - Aximu-Petri A AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Meyer, Matthias AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150801 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 SB - IM MH - Bacteria MH - Bone and Bones MH - *DNA Contamination MH - Decontamination/methods MH - *Fossils MH - Gene Library MH - High-Throughput Nucleotide Sequencing MH - Humans MH - *Paleodontology/methods MH - Tooth OTO - NOTNLM OT - DNA contamination removal OT - DNA extraction OT - ancient DNA OT - paleogenomics EDAT- 2014/01/01 00:00 MHDA- 2016/04/15 06:00 CRDT- 2015/08/12 06:00 PHST- 2015/04/01 00:00 [received] PHST- 2015/07/08 00:00 [accepted] PHST- 2015/08/12 06:00 [entrez] PHST- 2014/01/01 00:00 [pubmed] PHST- 2016/04/15 06:00 [medline] AID - 000114320 [pii] AID - 10.2144/000114320 [doi] PST - epublish SO - Biotechniques. 2015 Aug 1;59(2):87-93. doi: 10.2144/000114320. eCollection 2015 Aug. PMID- 26200455 OWN - NLM STAT- MEDLINE DCOM- 20160501 LR - 20240714 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 7 DP - 2015 TI - Genetic Evidence Supports the Multiethnic Character of Teopancazco, a Neighborhood Center of Teotihuacan, Mexico (AD 200-600). PG - e0132371 LID - 10.1371/journal.pone.0132371 [doi] LID - e0132371 AB - Multiethnicity in Teopancazco, Teotihuacan, is supported by foreign individuals found in the neighborhood center as well as by the diversity observed in funerary rituals at the site. Studies of both stable and strontium isotopes as well as paleodietary analysis, suggest that the population of Teopancazco was composed by three population groups: people from Teotihuacan, people from nearby sites (Tlaxcala-Hidalgo-Puebla), and people from afar, including the coastal plains. In an attempt to understand the genetic dynamics in Teopancazco we conducted an ancient DNA (aDNA) analysis based on mtDNA. Our results show that the level of genetic diversity is consistent with the multiethnicity phenomenon at the neighborhood center. Levels of genetic diversity at different time periods of Teopancazco's history show that multiethnicity was evident since the beginning and lasted until the collapse of the neighborhood center. However, a PCA and a Neighbor-Joining tree suggested the presence of a genetically differentiated group (buried at the Transitional phase) compared to the population from the initial phase (Tlamimilolpa) as well as the population from the final phase (Xolalpan) of the history of Teopancazco. Genetic studies showed no differences in genetic diversity between males and females in the adult population of Teopancazco, this data along with ample archaeological evidence, suggest a neolocal post-marital pattern of residence in Teopancazco. Nevertheless, genetic analyses on the infant population showed that the males are significantly more heterogeneous than the females suggesting a possible differential role in cultural practices by sex in the infant sector. Regarding interpopulation analysis, we found similar indices of genetic diversity between Teopancazco and heterogeneous native groups, which support the multiethnic character of Teopancazco. Finally, our data showed a close genetic relationship between Teopancazco and populations from the "Teotihuacan corridor" and from Oaxaca and the Maya region, in agreement with previous archaeological evidence. FAU - Álvarez-Sandoval, Brenda A AU - Álvarez-Sandoval BA AD - Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico. FAU - Manzanilla, Linda R AU - Manzanilla LR AD - Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico. FAU - González-Ruiz, Mercedes AU - González-Ruiz M AD - Unitat d'Antropologia, Departamento de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain. FAU - Malgosa, Assumpció AU - Malgosa A AD - Unitat d'Antropologia, Departamento de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain. FAU - Montiel, Rafael AU - Montiel R AD - Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150722 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Anthropology, Cultural/*methods MH - DNA, Mitochondrial/*analysis MH - Female MH - Genetic Variation MH - Genetics, Population MH - Human Migration MH - Humans MH - Indians, North American/*ethnology/*genetics MH - Male MH - Mexico/ethnology MH - Phylogeography MH - Principal Component Analysis MH - Young Adult PMC - PMC4511806 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/07/23 06:00 MHDA- 2016/05/02 06:00 PMCR- 2015/07/22 CRDT- 2015/07/23 06:00 PHST- 2015/03/12 00:00 [received] PHST- 2015/06/12 00:00 [accepted] PHST- 2015/07/23 06:00 [entrez] PHST- 2015/07/23 06:00 [pubmed] PHST- 2016/05/02 06:00 [medline] PHST- 2015/07/22 00:00 [pmc-release] AID - PONE-D-15-08186 [pii] AID - 10.1371/journal.pone.0132371 [doi] PST - epublish SO - PLoS One. 2015 Jul 22;10(7):e0132371. doi: 10.1371/journal.pone.0132371. eCollection 2015. PMID- 26399147 OWN - NLM STAT- MEDLINE DCOM- 20151201 LR - 20150924 IS - 0958-6687 (Print) IS - 0958-6687 (Linking) VI - 60 IP - 2 DP - 2015 Jul TI - Unlocking the past: The role of dental analysis in archaeology. PG - 51-62 AB - What can the study of ancient teeth tell us about the life style and dietary habits of our ancestors? Dental palaeopathology is particularly important as it can provide direct evidence of the type of diet an individual consumed during life. An analysis of the angle of tooth wear evident on the crown of the tooth can help to distinguish between early hunter-gatherers and later agriculturists, whilst microwear features on the occlusal surface can help to discern subtle dietary shifts. The distributions of stable isotopes in food webs make it possible to use them to reconstruct ancient diets as well as tracing the geographic origins and migrations of peoples. Plant microfossils have been isolated from calculus which can be identified using light microscopy. Teeth are particularly useful in ancient DNA studies due to the excellent preservation of biomaterials within the enamel shell of the tooth. FAU - Forshaw, Roger AU - Forshaw R LA - eng PT - Historical Article PT - Journal Article PL - England TA - Dent Hist JT - Dental historian : Lindsay Club newsletter JID - 8803742 RN - 9007-49-2 (DNA) MH - DNA/analysis MH - Diet/history MH - History, 15th Century MH - History, Ancient MH - History, Medieval MH - Humans MH - *Paleodontology MH - Periodontal Diseases/history MH - Tooth Diseases/*history EDAT- 2015/09/25 06:00 MHDA- 2015/12/15 06:00 CRDT- 2015/09/25 06:00 PHST- 2015/09/25 06:00 [entrez] PHST- 2015/09/25 06:00 [pubmed] PHST- 2015/12/15 06:00 [medline] PST - ppublish SO - Dent Hist. 2015 Jul;60(2):51-62. PMID- 26329415 OWN - NLM STAT- MEDLINE DCOM- 20170117 LR - 20191027 IS - 1526-3711 (Electronic) IS - 1526-3711 (Linking) VI - 16 IP - 7 DP - 2015 Jul 1 TI - Oral Paleomicrobiology: Study of Ancient Oral Microbiome. PG - 588-94 AB - BACKGROUND: Paleomicrobiology is a special branch of micropaleontology concerned with the study of bacterial fossils. We have used the term 'oral paleomicrobiology', as in this review we have focused on the ancient oral microflora. Recently, dental calculus and dental pulp have been identified as rich sources of ancient microbial DNA. Study of this ancient genetic material opens a new door to the ancient world. This review gives an overview of history of ancient DNA research, various techniques of analyzing ancient DNA in dental calculus and dental pulp, and the implications of the oral paleomicrobiology. MATERIALS AND METHODS: A comprehensive literature search was performed in the following databases-pubmed, medline and google scholar for studies published before 10 April, 2015. The following keywords were used- 'ancient DNA', 'ancient oral flora, 'oral paleomicrobiology' and 'oral microbiome', '16S rRNA sequencing'. To obtain additional data, a manual search was performed using the reference lists of selected articles. RESULT: As a result of literature search, 27 articles were found in pubmed, 12 in google scholar and one in medline. Eight more articles were selected from the reference list of selected articles. CONCLUSION: The combination of microbiology and paleontology has brought a revolution in the study of human evolution and microbial communities. The naturally well-preserved samples of microbial DNA from dental pulp and microbial colonies trapped in dental calculus are a potential source of microbial genetic material, which will prove invaluable in resolving mysteries of the past. This may be a beginning of a new era of oral paleomicrobiology, which will contribute in our studies about prevention of disease by establishing symbiosis between human beings and their microbiome. FAU - Dagli, Namrata AU - Dagli N AD - Former Member of Ethics Committee, Care Institute of Medical Science, Ahmedabad, Gujarat, India, Phone: 8141703838, e-mail: r.j.dagli@gmail.com. FAU - Dagli, Rushabh AU - Dagli R AD - Vyas Dental College and Hospital, Jodhpur, Rajasthan, India. FAU - Baroudi, Kusai AU - Baroudi K AD - Department of Restorative Dental Sciences, Alfarabi Colleges Riyadh, Saudi Arabia. FAU - Tarakji, Bassel AU - Tarakji B AD - Department of Oral and Maxillofacial Sciences, Alfarabi Colleges, Riyadh, Saudi Arabia. LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20150701 PL - India TA - J Contemp Dent Pract JT - The journal of contemporary dental practice JID - 101090552 RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Bacterial/history MH - Dental Calculus/*history/microbiology MH - Dental Pulp/microbiology MH - History, Ancient MH - Humans MH - *Microbiota MH - *Paleodontology MH - Paleontology OTO - NOTNLM OT - Ancient microbiome OT - Oral microbiome OT - Oral paleomicrobiology EDAT- 2015/09/04 06:00 MHDA- 2017/01/18 06:00 CRDT- 2015/09/03 06:00 PHST- 2015/09/03 06:00 [entrez] PHST- 2015/09/04 06:00 [pubmed] PHST- 2017/01/18 06:00 [medline] AID - 1526-3711-1486 [pii] AID - 10.5005/jp-journals-10024-1726 [doi] PST - epublish SO - J Contemp Dent Pract. 2015 Jul 1;16(7):588-94. doi: 10.5005/jp-journals-10024-1726. PMID- 26055157 OWN - NLM STAT- MEDLINE DCOM- 20150820 LR - 20181113 IS - 1471-0064 (Electronic) IS - 1471-0056 (Linking) VI - 16 IP - 7 DP - 2015 Jul TI - Reconstructing ancient genomes and epigenomes. PG - 395-408 LID - 10.1038/nrg3935 [doi] AB - Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes. FAU - Orlando, Ludovic AU - Orlando L AD - 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 allées Jules Guesde, 31000 Toulouse, France. FAU - Gilbert, M Thomas P AU - Gilbert MT AD - 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20150609 PL - England TA - Nat Rev Genet JT - Nature reviews. Genetics JID - 100962779 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*genetics/*history MH - Epigenomics/*methods/trends MH - Genomics/*methods/trends MH - High-Throughput Nucleotide Sequencing/*methods/trends MH - History, Ancient MH - Humans EDAT- 2015/06/10 06:00 MHDA- 2015/08/21 06:00 CRDT- 2015/06/10 06:00 PHST- 2015/06/10 06:00 [entrez] PHST- 2015/06/10 06:00 [pubmed] PHST- 2015/08/21 06:00 [medline] AID - nrg3935 [pii] AID - 10.1038/nrg3935 [doi] PST - ppublish SO - Nat Rev Genet. 2015 Jul;16(7):395-408. doi: 10.1038/nrg3935. Epub 2015 Jun 9. PMID- 26086078 OWN - NLM STAT- MEDLINE DCOM- 20160407 LR - 20181113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 6 DP - 2015 TI - Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone. PG - e0129102 LID - 10.1371/journal.pone.0129102 [doi] LID - e0129102 AB - The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses. FAU - Pinhasi, Ron AU - Pinhasi R AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. FAU - Fernandes, Daniel AU - Fernandes D AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. FAU - Sirak, Kendra AU - Sirak K AD - Department of Anthropology, Emory University, Atlanta, Georgia, United States of America. FAU - Novak, Mario AU - Novak M AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. FAU - Connell, Sarah AU - Connell S AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. FAU - Alpaslan-Roodenberg, Songül AU - Alpaslan-Roodenberg S AD - independent researcher, Santpoort-Noord, The Netherlands. FAU - Gerritsen, Fokke AU - Gerritsen F AD - Netherlands Institute in Turkey, Istiklal Caddesi, Nur-i Ziya Sokak 5, Beyoğlu, Istanbul, Turkey. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Universitetskaya Nab. 3, St. Petersburg, Russia. FAU - Gromov, Andrey AU - Gromov A AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Universitetskaya Nab. 3, St. Petersburg, Russia. FAU - Raczky, Pál AU - Raczky P AD - Eötvös Loránd University University, Faculty of Humanities, Institute of Archaeological Sciences, Múzeum körút 4/b, Budapest, Hungary. FAU - Anders, Alexandra AU - Anders A AD - Eötvös Loránd University University, Faculty of Humanities, Institute of Archaeological Sciences, Múzeum körút 4/b, Budapest, Hungary. FAU - Pietrusewsky, Michael AU - Pietrusewsky M AD - Department of Anthropology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America. FAU - Rollefson, Gary AU - Rollefson G AD - Whitman College, Walla Walla, Washington, United States of America. FAU - Jovanovic, Marija AU - Jovanovic M AD - Museum of Vojvodina, 21 000 Novi Sad, Ulica Dunavska 35, Serbia. FAU - Trinhhoang, Hiep AU - Trinhhoang H AD - Institute of Archaeology, Hoan Kiem District, Hanoi, Vietnam. FAU - Bar-Oz, Guy AU - Bar-Oz G AD - Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Israel. FAU - Oxenham, Marc AU - Oxenham M AD - School of Archaeology and Anthropology, Australian National University, Canberra, Australia. FAU - Matsumura, Hirofumi AU - Matsumura H AD - School of Health Science, Sapporo Medical University, Sapporo, Japan. FAU - Hofreiter, Michael AU - Hofreiter M AD - Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknechtstr. 24-25, 14476 Potsdam Golm, Germany; Department of Biology, University of York, Wentworth Way, Heslington, York, United Kingdom. LA - eng SI - BioProject/PRJNA283950 SI - SRA/SRP058345 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150618 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 9007-49-2 (DNA) SB - IM CIN - Nature. 2017 Aug 9;548(7666):158. doi: 10.1038/548158a. PMID: 28796208 MH - Archaeology MH - DNA/*isolation & purification MH - DNA Damage MH - Ear, Inner/*chemistry MH - *Fossils MH - Humans MH - Petrous Bone/*chemistry MH - Sequence Analysis, DNA/methods PMC - PMC4472748 COIS- Competing Interests: SAR is a self employed freelance osteologist. There are no patents, products in development or marketed products to declare. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. EDAT- 2015/06/19 06:00 MHDA- 2016/04/08 06:00 PMCR- 2015/06/18 CRDT- 2015/06/19 06:00 PHST- 2015/03/15 00:00 [received] PHST- 2015/05/06 00:00 [accepted] PHST- 2015/06/19 06:00 [entrez] PHST- 2015/06/19 06:00 [pubmed] PHST- 2016/04/08 06:00 [medline] PHST- 2015/06/18 00:00 [pmc-release] AID - PONE-D-15-10882 [pii] AID - 10.1371/journal.pone.0129102 [doi] PST - epublish SO - PLoS One. 2015 Jun 18;10(6):e0129102. doi: 10.1371/journal.pone.0129102. eCollection 2015. PMID- 26081994 OWN - NLM STAT- MEDLINE DCOM- 20160324 LR - 20181113 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 5 DP - 2015 Jun 17 TI - Improving access to endogenous DNA in ancient bones and teeth. PG - 11184 LID - 10.1038/srep11184 [doi] LID - 11184 AB - Poor DNA preservation is the most limiting factor in ancient genomic research. In the majority of ancient bones and teeth, endogenous DNA molecules represent a minor fraction of the whole DNA extract, rendering shot-gun sequencing inefficient for obtaining genomic data. Based on ancient human bone samples from temperate and tropical environments, we show that an EDTA-based enzymatic 'pre-digestion' of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we observe an asymptotic increase in endogenous DNA content, with a 2.7-fold average increase reached at 1 hour. We repeat the experiment using a brief pre-digestion (15 or 30 mins) on 21 ancient bones and teeth from a variety of archaeological contexts and observe an improvement in 16 of these. We here advocate the implementation of a brief pre-digestion step as a standard procedure in ancient DNA extractions. Finally, we demonstrate on 14 ancient teeth that by targeting the outer layer of the roots we obtain up to 14 times more endogenous DNA than when using the inner dentine. Our presented methods are likely to increase the proportion of ancient samples that are suitable for genome-scale characterization. FAU - Damgaard, Peter B AU - Damgaard PB AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen. FAU - Margaryan, Ashot AU - Margaryan A AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen. FAU - Schroeder, Hannes AU - Schroeder H AD - 1] Centre for GeoGenetics, Natural History Museum, University of Copenhagen [2] Faculty of Archaeology, Leiden University, PO Box 9515, 2300 Leiden, The Netherlands. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen. FAU - Allentoft, Morten E AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150617 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - *Bone and Bones MH - *DNA, Mitochondrial MH - Fossils MH - Humans MH - *Tooth PMC - PMC4472031 EDAT- 2015/06/18 06:00 MHDA- 2016/03/25 06:00 PMCR- 2015/06/17 CRDT- 2015/06/18 06:00 PHST- 2015/01/06 00:00 [received] PHST- 2015/05/15 00:00 [accepted] PHST- 2015/06/18 06:00 [entrez] PHST- 2015/06/18 06:00 [pubmed] PHST- 2016/03/25 06:00 [medline] PHST- 2015/06/17 00:00 [pmc-release] AID - srep11184 [pii] AID - 10.1038/srep11184 [doi] PST - epublish SO - Sci Rep. 2015 Jun 17;5:11184. doi: 10.1038/srep11184. PMID- 26062506 OWN - NLM STAT- MEDLINE DCOM- 20150702 LR - 20221207 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 522 IP - 7555 DP - 2015 Jun 11 TI - Human evolution: ancient DNA steps into the language debate. PG - 164-5 LID - 10.1038/522164a [doi] FAU - Novembre, John AU - Novembre J AD - Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA. LA - eng PT - Comment PT - Journal Article PL - England TA - Nature JT - Nature JID - 0410462 SB - IM CON - Nature. 2015 Jun 11;522(7555):207-11. doi: 10.1038/nature14317. PMID: 25731166 CON - Nature. 2015 Jun 11;522(7555):167-72. doi: 10.1038/nature14507. PMID: 26062507 MH - Asian People/*genetics MH - Cultural Evolution/*history MH - *Fossils MH - Genome, Human/*genetics MH - *Genomics MH - *Grassland MH - Human Migration/*history MH - Humans MH - Language/*history MH - Male MH - White People/*genetics EDAT- 2015/06/13 06:00 MHDA- 2015/07/03 06:00 CRDT- 2015/06/12 06:00 PHST- 2015/06/12 06:00 [entrez] PHST- 2015/06/13 06:00 [pubmed] PHST- 2015/07/03 06:00 [medline] AID - 522164a [pii] AID - 10.1038/522164a [doi] PST - ppublish SO - Nature. 2015 Jun 11;522(7555):164-5. doi: 10.1038/522164a. PMID- 25731166 OWN - NLM STAT- MEDLINE DCOM- 20150702 LR - 20231111 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 522 IP - 7555 DP - 2015 Jun 11 TI - Massive migration from the steppe was a source for Indo-European languages in Europe. PG - 207-11 LID - 10.1038/nature14317 [doi] AB - We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian. By ∼6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe. FAU - Haak, Wolfgang AU - Haak W AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Lazaridis, Iosif AU - Lazaridis I AD - 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. FAU - Patterson, Nick AU - Patterson N AD - Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. FAU - Rohland, Nadin AU - Rohland N AD - 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. FAU - Mallick, Swapan AU - Mallick S AD - 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Brandt, Guido AU - Brandt G AD - Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany. FAU - Nordenfelt, Susanne AU - Nordenfelt S AD - 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. FAU - Harney, Eadaoin AU - Harney E AD - 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Stewardson, Kristin AU - Stewardson K AD - 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Fu, Qiaomei AU - Fu Q AD - 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany [4] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100049, China. FAU - Mittnik, Alissa AU - Mittnik A AD - Institute for Archaeological Sciences, University of Tübingen, D-72070 Tübingen, Germany. FAU - Bánffy, Eszter AU - Bánffy E AD - 1] Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Science, H-1014 Budapest, Hungary [2] Römisch Germanische Kommission (RGK) Frankfurt, D-60325 Frankfurt, Germany. FAU - Economou, Christos AU - Economou C AD - Archaeological Research Laboratory, Stockholm University, 114 18 Stockholm, Sweden. FAU - Francken, Michael AU - Francken M AD - Departments of Paleoanthropology and Archaeogenetics, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, D-72070 Tübingen, Germany. FAU - Friederich, Susanne AU - Friederich S AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany. FAU - Pena, Rafael Garrido AU - Pena RG AD - Departamento de Prehistoria y Arqueología, Facultad de Filosofía y Letras, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. FAU - Hallgren, Fredrik AU - Hallgren F AD - The Cultural Heritage Foundation, Västerås 722 12, Sweden. FAU - Khartanovich, Valery AU - Khartanovich V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg 199034, Russia. FAU - Khokhlov, Aleksandr AU - Khokhlov A AD - Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia. FAU - Kunst, Michael AU - Kunst M AD - Deutsches Archaeologisches Institut, Abteilung Madrid, E-28002 Madrid, Spain. FAU - Kuznetsov, Pavel AU - Kuznetsov P AD - Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia. FAU - Meller, Harald AU - Meller H AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany. FAU - Mochalov, Oleg AU - Mochalov O AD - Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia. FAU - Moiseyev, Vayacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg 199034, Russia. FAU - Nicklisch, Nicole AU - Nicklisch N AD - 1] Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany [2] State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany [3] Danube Private University, A-3500 Krems, Austria. FAU - Pichler, Sandra L AU - Pichler SL AD - Institute for Prehistory and Archaeological Science, University of Basel, CH-4003 Basel, Switzerland. FAU - Risch, Roberto AU - Risch R AD - Departamento de Prehistòria, Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain. FAU - Rojo Guerra, Manuel A AU - Rojo Guerra MA AD - Departamento de Prehistòria y Arqueolgia, Universidad de Valladolid, E-47002 Valladolid, Spain. FAU - Roth, Christina AU - Roth C AD - Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AD - 1] Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany [2] Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Science, H-1014 Budapest, Hungary. FAU - Wahl, Joachim AU - Wahl J AD - State Office for Cultural Heritage Management Baden-Württemberg, Osteology, D-78467 Konstanz, Germany. FAU - Meyer, Matthias AU - Meyer M AD - Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. FAU - Krause, Johannes AU - Krause J AD - 1] Institute for Archaeological Sciences, University of Tübingen, D-72070 Tübingen, Germany [2] Departments of Paleoanthropology and Archaeogenetics, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, D-72070 Tübingen, Germany [3] Max Planck Institute for the Science of Human History, D-07745 Jena, Germany. FAU - Brown, Dorcas AU - Brown D AD - Anthropology Department, Hartwick College, Oneonta, New York 13820, USA. FAU - Anthony, David AU - Anthony D AD - Anthropology Department, Hartwick College, Oneonta, New York 13820, USA. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Alt, Kurt Werner AU - Alt KW AD - 1] Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany [2] State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany [3] Danube Private University, A-3500 Krems, Austria [4] Institute for Prehistory and Archaeological Science, University of Basel, CH-4003 Basel, Switzerland. FAU - Reich, David AU - Reich D AD - 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. LA - eng GR - HHMI_/Howard Hughes Medical Institute/United States GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - R01 HG006399/HG/NHGRI NIH HHS/United States GR - GM100233/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20150302 PL - England TA - Nature JT - Nature JID - 0410462 SB - IM CIN - Nature. 2015 Jun 11;522(7555):164-5. doi: 10.1038/522164a. PMID: 26062506 MH - Cultural Evolution/*history MH - Europe/ethnology MH - Genome, Human/genetics MH - *Grassland MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Language/*history MH - Male MH - Polymorphism, Genetic/genetics MH - Population Dynamics MH - Russia PMC - PMC5048219 MID - NIHMS801601 EDAT- 2015/03/04 06:00 MHDA- 2015/07/03 06:00 PMCR- 2016/10/04 CRDT- 2015/03/04 06:00 PHST- 2014/12/29 00:00 [received] PHST- 2015/02/12 00:00 [accepted] PHST- 2015/03/04 06:00 [entrez] PHST- 2015/03/04 06:00 [pubmed] PHST- 2015/07/03 06:00 [medline] PHST- 2016/10/04 00:00 [pmc-release] AID - nature14317 [pii] AID - 10.1038/nature14317 [doi] PST - ppublish SO - Nature. 2015 Jun 11;522(7555):207-11. doi: 10.1038/nature14317. Epub 2015 Mar 2. PMID- 26053041 OWN - NLM STAT- MEDLINE DCOM- 20160229 LR - 20200306 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 6 DP - 2015 TI - Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage. PG - e0128810 LID - 10.1371/journal.pone.0128810 [doi] LID - e0128810 AB - The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations. FAU - Hervella, Montserrat AU - Hervella M AD - Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain. FAU - Rotea, Mihai AU - Rotea M AD - National History Museum of Transylvania, Cluj-Napoca, Romania. FAU - Izagirre, Neskuts AU - Izagirre N AD - Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain. FAU - Constantinescu, Mihai AU - Constantinescu M AD - "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, Bucharest, Romania. FAU - Alonso, Santos AU - Alonso S AD - Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain. FAU - Ioana, Mihai AU - Ioana M AD - Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands. FAU - Lazăr, Cătălin AU - Lazăr C AD - National History Museum of Romania, Bucharest, Romania. FAU - Ridiche, Florin AU - Ridiche F AD - Oltenia Museum Craiova, Craiova, Romania. FAU - Soficaru, Andrei Dorian AU - Soficaru AD AD - "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, Bucharest, Romania. FAU - Netea, Mihai G AU - Netea MG AD - Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands. FAU - de-la-Rua, Concepcion AU - de-la-Rua C AD - Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150608 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - *Genetic Variation MH - *Genetics, Population MH - Geography MH - Haplotypes/genetics MH - Humans MH - Multivariate Analysis MH - Principal Component Analysis MH - Romania MH - Time Factors PMC - PMC4460020 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/06/09 06:00 MHDA- 2016/03/02 06:00 PMCR- 2015/06/08 CRDT- 2015/06/09 06:00 PHST- 2014/12/10 00:00 [received] PHST- 2015/04/30 00:00 [accepted] PHST- 2015/06/09 06:00 [entrez] PHST- 2015/06/09 06:00 [pubmed] PHST- 2016/03/02 06:00 [medline] PHST- 2015/06/08 00:00 [pmc-release] AID - PONE-D-14-49607 [pii] AID - 10.1371/journal.pone.0128810 [doi] PST - epublish SO - PLoS One. 2015 Jun 8;10(6):e0128810. doi: 10.1371/journal.pone.0128810. eCollection 2015. PMID- 26310027 OWN - NLM STAT- MEDLINE DCOM- 20151109 LR - 20150827 IS - 0016-6758 (Print) IS - 0016-6758 (Linking) VI - 51 IP - 6 DP - 2015 Jun TI - [Ancient DNA: Results and Prospects (the 30th Anniversary)]. PG - 627-43 AB - Evolutionary genetics has reached a new level of research thanks to the opportunity to study the genomes of not only present-day but also of ancient organisms. The obtaining of reliable data when working with ancient DNA is possible only in the case of interdisciplinary collaboration between archaeologists, paleontologists, molecular geneticists, and bioinformaticians. Despite laborious and high-cost technologies, the results never cease to amaze and can not only fill the gaps in the knowledge of the evolutionary history of different species but can also review the existing ideas on population development and dynamics. In this review, we discuss the history of the development of investigative techniques in ancient DNA research and the most striking results of these studies, including the most recent achievements. FAU - Druzhkova, A S AU - Druzhkova AS FAU - Vorobieva, N V AU - Vorobieva NV FAU - Trifonov, V A AU - Trifonov VA FAU - Graphodatsky, A S AU - Graphodatsky AS LA - rus PT - English Abstract PT - Journal Article PT - Review PL - Russia (Federation) TA - Genetika JT - Genetika JID - 0047354 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*chemistry MH - Evolution, Molecular MH - *Fossils MH - Humans MH - Paleontology/*methods/trends MH - Sequence Analysis, DNA/*methods/trends EDAT- 2015/08/28 06:00 MHDA- 2015/11/10 06:00 CRDT- 2015/08/28 06:00 PHST- 2015/08/28 06:00 [entrez] PHST- 2015/08/28 06:00 [pubmed] PHST- 2015/11/10 06:00 [medline] PST - ppublish SO - Genetika. 2015 Jun;51(6):627-43. PMID- 25998652 OWN - NLM STAT- MEDLINE DCOM- 20160223 LR - 20221207 IS - 1932-8494 (Electronic) IS - 1932-8486 (Linking) VI - 298 IP - 6 DP - 2015 Jun TI - Joseon funerary texts tested using ancient DNA analysis of a Korean mummy. PG - 1191-207 LID - 10.1002/ar.23142 [doi] AB - In Korea, ancient DNA (aDNA) analysis has been applied to investigations into the genetic affiliations of mummies found in Joseon Dynasty tombs (1392-1910 CE), becoming now indispensable tool for researches studying human remains from archaeological sites. In the course of our recent examinations on a Korean mummy of Joseon Dynasty, we discovered many teeth contained in a pouch. And in fact, the historical literature on the topic of Joseon funerals contain general accounts of pouches in which an individual's lost teeth were collected over the course of a lifetime and, after death, placed in the coffin with the body. To test the veracity of the historical texts, the present study undertook aDNA analyses and compared the results between specifically questioned (Q) samples (teeth) and known (K) samples (brain and bone) from the mummy to ensure that they came from the same individual. Although the Q-K comparison of autosomal short tandem repeat results did not show full concordance due to allelic drop-outs in some loci, our statistical calculation indicated that the teeth in the pouch are highly likely those of the mummy. Additionally, Q-K comparison of mitochondrial DNA sequence results showed 100% matches between samples. There results, in short, could not gainsay the conjecture that the teeth samples originated from the person buried in the tomb; and if so, he must have kept his teeth for a long time after their loss. As the application of aDNA analysis to Korean mummy studies develops, there will be other opportunities to test historical documents, particularly those referring to funerary rites. CI - © 2015 Wiley Periodicals, Inc. FAU - Oh, Chang Seok AU - Oh CS AD - Anthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul, 110-799, Korea. FAU - Koh, Bou-Ja AU - Koh BJ AD - Dankook University, 152, Jukjeon-Ro, Suji-Gu, Yongin-Si, Gyeonggi-Do, 448-701, Korea. FAU - Yoo, Dong Soo AU - Yoo DS AD - Department of Radiology, Dankook University College of Medicine, San 29, Anseo-Dong, Chonan City, Chungcheongnam-Do, 330-715, Korea. FAU - Park, Jun Bum AU - Park JB AD - Seoul Institute of Cultural Heritages, 833, Tongil-Ro, Eunpyeong-Gu, Seoul, 122-842, Korea. FAU - Min, So Ri AU - Min SR AD - Korean Institute for Archaeology and Environment, 26, Mogwanamu-1 Gil, Jochiwon-Eup, Sejong-Si, 339-806, Korea. FAU - Kim, Yi-Suk AU - Kim YS AD - Department of Anatomy, Graduate School of Medicine, Ewha Womans University, 911-1, Mok-Dong, Yangcheon-Gu, Seoul, 158-710, Korea. FAU - Lee, Sang Sup AU - Lee SS AD - National Forensic Service, 331-1 Shinwol 7-Dong, Yangcheon-Gu, Seoul, 158-707, Korea. FAU - Ge, Jianye AU - Ge J AD - Department of Forensic and Investigative Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA. FAU - Seo, Seung Bum AU - Seo SB AD - Department of Forensic and Investigative Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA. FAU - Shin, Dong Hoon AU - Shin DH AD - Anthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul, 110-799, Korea. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Anat Rec (Hoboken) JT - Anatomical record (Hoboken, N.J. : 2007) JID - 101292775 SB - IM MH - Asian People MH - *Funeral Rites MH - Humans MH - *Mummies MH - Republic of Korea MH - Sequence Analysis, DNA OTO - NOTNLM OT - Joseon dynasty OT - Korean mummy OT - archaeology OT - mitochondrial DNA OT - short tandem repeats OT - teeth EDAT- 2015/05/23 06:00 MHDA- 2016/02/26 06:00 CRDT- 2015/05/23 06:00 PHST- 2015/01/16 00:00 [received] PHST- 2015/01/30 00:00 [accepted] PHST- 2015/05/23 06:00 [entrez] PHST- 2015/05/23 06:00 [pubmed] PHST- 2016/02/26 06:00 [medline] AID - 10.1002/ar.23142 [doi] PST - ppublish SO - Anat Rec (Hoboken). 2015 Jun;298(6):1191-207. doi: 10.1002/ar.23142. PMID- 25998650 OWN - NLM STAT- MEDLINE DCOM- 20160223 LR - 20150522 IS - 1932-8494 (Electronic) IS - 1932-8486 (Linking) VI - 298 IP - 6 DP - 2015 Jun TI - A code of ethics for evidence-based research with ancient human remains. PG - 1175-81 LID - 10.1002/ar.23126 [doi] AB - As clinical research constantly advances and the concept of evolution becomes a strong and influential part of basic medical research, the absence of a discourse that deals with the use of ancient human remains in evidence-based research is becoming unbearable. While topics such as exhibition and excavation of human remains are established ethical fields of discourse, when faced with instrumentalization of ancient human remains for research (i.e., ancient DNA extractions for disease marker analyses) the answers from traditional ethics or even more practical fields of bio-ethics or more specific biomedical ethics are rare to non-existent. The Centre for Evolutionary Medicine at the University of Zurich solved their needs for discursive action through the writing of a self-given code of ethics which was written in dialogue with the researchers at the Institute and was published online in Sept. 2011: http://evolutionäremedizin.ch/coe/. The philosophico-ethical basis for this a code of conduct and ethics and the methods are published in this article. CI - © 2015 Wiley Periodicals, Inc. FAU - Kreissl Lonfat, Bettina M AU - Kreissl Lonfat BM AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Winterthurerstr. 190, Zürich, 8057, Switzerland. FAU - Kaufmann, Ina Maria AU - Kaufmann IM AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Winterthurerstr. 190, Zürich, 8057, Switzerland. FAU - Rühli, Frank AU - Rühli F AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Winterthurerstr. 190, Zürich, 8057, Switzerland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Anat Rec (Hoboken) JT - Anatomical record (Hoboken, N.J. : 2007) JID - 101292775 SB - IM MH - *Codes of Ethics MH - *Ethics, Research MH - Humans MH - *Mummies OTO - NOTNLM OT - human remains OT - medical ethics OT - personal rights OT - research ethics EDAT- 2015/05/23 06:00 MHDA- 2016/02/26 06:00 CRDT- 2015/05/23 06:00 PHST- 2015/01/16 00:00 [received] PHST- 2015/01/30 00:00 [accepted] PHST- 2015/05/23 06:00 [entrez] PHST- 2015/05/23 06:00 [pubmed] PHST- 2016/02/26 06:00 [medline] AID - 10.1002/ar.23126 [doi] PST - ppublish SO - Anat Rec (Hoboken). 2015 Jun;298(6):1175-81. doi: 10.1002/ar.23126. PMID- 25998631 OWN - NLM STAT- MEDLINE DCOM- 20160223 LR - 20150522 IS - 1932-8494 (Electronic) IS - 1932-8486 (Linking) VI - 298 IP - 6 DP - 2015 Jun TI - PUM I Revisited: Tradeoffs in Preservation and Discovery. PG - 949-53 LID - 10.1002/ar.23133 [doi] AB - An Egyptian mummy designated PUM I (Pennsylvania University Museum) was subjected to a complete autopsy in 1972. Forty-one years later, the senior author (MZ) was invited back to the Penn Museum to identify several packages of material that had been preserved with the mummy joining the project conservator (MG) in the evaluation of these remains. A summary of the 1972 examination reviews the dating of the mummy, about 3,000 years ago. The mummy was poorly preserved and the only significant pathology was a rare skin disease, subcorneal pustular dermatosis, which was not identified by modern medicine until 1956. The review of PUM 1, as the mummy is stabilized during conservation at the Penn Museum (previously called the Pennsylvania University Museum), generates a discussion for researchers who embark on the study of mummified remains. There have been major advances in the study of mummies since 1972, including computed tomography (CT) scanning, with much less invasive endoscopically guided biopsies, analysis for ancient DNA (aDNA), nuclear magnetic resonance technology, chemical analysis, and paleoserology. The value of complete autopsy must now be balanced against preservation of a complete mummy by less invasive techniques that are tissue sampled through guided technology. Indeed it is unlikely that these regions of the skin of PUM 1 would have been sampled and studied if these new tools of analysis had been available and applied. CI - © 2015 Wiley Periodicals, Inc. FAU - Zimmerman, Michael R AU - Zimmerman MR AD - Villanova University Biology Department, Villanova, Pennsylvania. FAU - Gleeson, Molly AU - Gleeson M AD - University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, Pennsylvania. LA - eng PT - Journal Article PL - United States TA - Anat Rec (Hoboken) JT - Anatomical record (Hoboken, N.J. : 2007) JID - 101292775 SB - IM MH - *Autopsy MH - Humans MH - Magnetic Resonance Imaging MH - Mummies/*pathology MH - Skin Diseases/*pathology OTO - NOTNLM OT - Egyptian mummy OT - autopsy OT - mummy conservation OT - skin disease EDAT- 2015/05/23 06:00 MHDA- 2016/02/26 06:00 CRDT- 2015/05/23 06:00 PHST- 2015/01/16 00:00 [received] PHST- 2015/01/30 00:00 [accepted] PHST- 2015/05/23 06:00 [entrez] PHST- 2015/05/23 06:00 [pubmed] PHST- 2016/02/26 06:00 [medline] AID - 10.1002/ar.23133 [doi] PST - ppublish SO - Anat Rec (Hoboken). 2015 Jun;298(6):949-53. doi: 10.1002/ar.23133. PMID- 25963373 OWN - NLM STAT- MEDLINE DCOM- 20150722 LR - 20240516 IS - 1471-0064 (Electronic) IS - 1471-0056 (Print) IS - 1471-0056 (Linking) VI - 16 IP - 6 DP - 2015 Jun TI - Evidence for archaic adaptive introgression in humans. PG - 359-71 LID - 10.1038/nrg3936 [doi] AB - As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments - a process known as adaptive introgression. Within the past few years, a series of studies have identified genomic regions that show strong evidence for archaic adaptive introgression. Here, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans and to determine whether positive selection has acted on these fragments. We review recently reported examples of adaptive introgression, grouped by selection pressure, and consider the level of supporting evidence for each. Finally, we discuss challenges and recommendations for inferring selection on introgressed regions. FAU - Racimo, Fernando AU - Racimo F AD - Department of Integrative Biology, University of California, Berkeley, Berkeley, California 97420, USA. FAU - Sankararaman, Sriram AU - Sankararaman S AD - Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Nielsen, Rasmus AU - Nielsen R AD - 1] Department of Integrative Biology, University of California, Berkeley, Berkeley, California 97420, USA. [2] Department of Statistics, University of California, Berkeley, Berkeley, California 97420, USA. FAU - Huerta-Sánchez, Emilia AU - Huerta-Sánchez E AD - Molecular and Cell Biology Unit, School of Natural Sciences, University of California, Merced, Merced, California 95343, USA. LA - eng GR - R01HG003229-09/HG/NHGRI NIH HHS/United States GR - R01 GM040282/GM/NIGMS NIH HHS/United States GR - R01 HG003229/HG/NHGRI NIH HHS/United States GR - R01‑GM40282/GM/NIGMS NIH HHS/United States GR - K99 GM111744/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20150512 PL - England TA - Nat Rev Genet JT - Nature reviews. Genetics JID - 100962779 SB - IM MH - Adaptation, Biological/genetics MH - Animals MH - Evolution, Molecular MH - Gene Flow MH - Genome, Human MH - Haplotypes MH - Humans MH - Linkage Disequilibrium MH - Markov Chains MH - *Models, Genetic MH - Neanderthals/genetics MH - Phylogeny MH - Selection, Genetic PMC - PMC4478293 MID - NIHMS700823 EDAT- 2015/05/13 06:00 MHDA- 2015/07/23 06:00 PMCR- 2015/06/24 CRDT- 2015/05/13 06:00 PHST- 2015/05/13 06:00 [entrez] PHST- 2015/05/13 06:00 [pubmed] PHST- 2015/07/23 06:00 [medline] PHST- 2015/06/24 00:00 [pmc-release] AID - nrg3936 [pii] AID - 10.1038/nrg3936 [doi] PST - ppublish SO - Nat Rev Genet. 2015 Jun;16(6):359-71. doi: 10.1038/nrg3936. Epub 2015 May 12. PMID- 25912776 OWN - NLM STAT- MEDLINE DCOM- 20160224 LR - 20171128 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 251 DP - 2015 Jun TI - DNA and bone structure preservation in medieval human skeletons. PG - 186-94 LID - S0379-0738(15)00151-6 [pii] LID - 10.1016/j.forsciint.2015.04.005 [doi] AB - Morphological and ultrastructural data from archaeological human bones are scarce, particularly data that have been correlated with information on the preservation of molecules such as DNA. Here we examine the bone structure of macroscopically well-preserved medieval human skeletons by transmission electron microscopy and immunohistochemistry, and the quantity and quality of DNA extracted from these skeletons. DNA technology has been increasingly used for analyzing physical evidence in archaeological forensics; however, the isolation of ancient DNA is difficult since it is highly degraded, extraction yields are low and the co-extraction of PCR inhibitors is a problem. We adapted and optimised a method that is frequently used for isolating DNA from modern samples, Chelex(®) 100 (Bio-Rad) extraction, for isolating DNA from archaeological human bones and teeth. The isolated DNA was analysed by real-time PCR using primers targeting the sex determining region on the Y chromosome (SRY) and STR typing using the AmpFlSTR(®) Identifiler PCR Amplification kit. Our results clearly show the preservation of bone matrix in medieval bones and the presence of intact osteocytes with well preserved encapsulated nuclei. In addition, we show how effective Chelex(®) 100 is for isolating ancient DNA from archaeological bones and teeth. This optimised method is suitable for STR typing using kits aimed specifically at degraded and difficult DNA templates since amplicons of up to 250bp were successfully amplified. CI - Copyright © 2015 Elsevier Ireland Ltd. All rights reserved. FAU - Coulson-Thomas, Yvette M AU - Coulson-Thomas YM AD - Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio 100, São Paulo, 04044-020, Brazil; School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK. Electronic address: ycoulsonthomas@gmail.com. FAU - Norton, Andrew L AU - Norton AL AD - Durham University, Woodland Road, DH7 9RH, Durham, UK. FAU - Coulson-Thomas, Vivien J AU - Coulson-Thomas VJ AD - Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio 100, São Paulo, 04044-020, Brazil; John van Geest Centre for Brain Repair, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0PY, UK. FAU - Florencio-Silva, Rinaldo AU - Florencio-Silva R AD - Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo, 04023-900, Brazil. FAU - Ali, Nadir AU - Ali N AD - School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK. FAU - Elmrghni, Samir AU - Elmrghni S AD - School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK. FAU - Gil, Cristiane D AU - Gil CD AD - Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo, 04023-900, Brazil. FAU - Sasso, Gisela R S AU - Sasso GR AD - Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo, 04023-900, Brazil. FAU - Dixon, Ronald A AU - Dixon RA AD - School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK. FAU - Nader, Helena B AU - Nader HB AD - Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio 100, São Paulo, 04044-020, Brazil. LA - eng PT - Historical Article PT - Journal Article DEP - 20150413 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (Collagen Type III) RN - 0 (DNA Primers) RN - 104982-03-8 (Osteocalcin) RN - 9007-49-2 (DNA) SB - IM EIN - Forensic Sci Int. 2016 Jun;263:213. doi: 10.1016/j.forsciint.2016.04.022. PMID: 27156432 MH - Adult MH - Bone and Bones/*chemistry/*ultrastructure MH - Chromosomes, Human, Y MH - Collagen Type III/analysis MH - DNA/*isolation & purification MH - DNA Fingerprinting MH - DNA Primers MH - Female MH - History, Medieval MH - Humans MH - Immunohistochemistry MH - Male MH - Microsatellite Repeats MH - Microscopy, Electron, Transmission MH - Osteocalcin/analysis MH - Osteocytes/cytology MH - Real-Time Polymerase Chain Reaction MH - Sex Determination Analysis MH - Tooth/chemistry OTO - NOTNLM OT - Ancient DNA OT - Archaeological bone OT - Archaeological teeth OT - Chelex OT - DNA typing OT - Electron microscopy EDAT- 2015/04/29 06:00 MHDA- 2016/02/26 06:00 CRDT- 2015/04/28 06:00 PHST- 2014/09/13 00:00 [received] PHST- 2015/01/29 00:00 [revised] PHST- 2015/04/03 00:00 [accepted] PHST- 2015/04/28 06:00 [entrez] PHST- 2015/04/29 06:00 [pubmed] PHST- 2016/02/26 06:00 [medline] AID - S0379-0738(15)00151-6 [pii] AID - 10.1016/j.forsciint.2015.04.005 [doi] PST - ppublish SO - Forensic Sci Int. 2015 Jun;251:186-94. doi: 10.1016/j.forsciint.2015.04.005. Epub 2015 Apr 13. PMID- 25912182 OWN - NLM STAT- MEDLINE DCOM- 20160224 LR - 20150511 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 251 DP - 2015 Jun TI - Extensive evaluation of DNA polymerase performance for highly degraded human DNA samples. PG - 171-8 LID - S0379-0738(15)00147-4 [pii] LID - 10.1016/j.forsciint.2015.04.001 [doi] AB - Highly degraded human DNA is commonly encountered in the forensic studies. Despite many efforts, the poor quality and quantity of the DNA often result in unsuccessful DNA analysis. There has been no extensive evaluation of DNA polymerase performance for the successful PCR of highly degraded DNA samples. We evaluated the most efficient DNA polymerases, based on real-time PCR and agarose gel electrophoresis analyses for a single copy gene amplification, with 200 ancient DNA (aDNA) samples of various origins. Nine commercially available DNA polymerases were tested, which included enzymes that are reportedly effective for PCR-inhibitory samples. The first screening test for the polymerases with 20 aDNA samples showed that Pico Maxx HF, FastStart Taq, and Ex Taq HS DNA polymerases were the most effective. Further tests with 180 aDNA samples showed that AmpliTaq Gold (control) amplified PCR products from 52 aDNA samples, PicoMaxx HF from 62, FastStart Taq from 64, and Ex Taq HS from 65. The use of two or more of Ex Taq HS, FastStart Taq, and PicoMaxx HF resulted in a significantly higher success rate than that of AmpliTaq Gold alone. With 37 positive samples tested in duplicate, Ex Taq HS showed the highest reproducibility (13 samples) and AmpliTaq Gold, the lowest (four samples); this difference was significant. The data also showed preferential amplification by the enzymes; Ex Taq HS exclusively produced amplification from two samples, FastStart Taq from one, and PicoMaxx HF from one. We suggest that the initial use of these three DNA polymerases will increase the probability of successfully amplifying DNA from highly degraded human DNA samples. CI - Copyright © 2015 Elsevier Ireland Ltd. All rights reserved. FAU - Kim, Kijeong AU - Kim K AD - Institute for Medical Sciences, College of Medicine, Chung-Ang University, Seoul 156-756, Republic of Korea. FAU - Bazarragchaa, Munkhtsetseg AU - Bazarragchaa M AD - Institute for Medical Sciences, College of Medicine, Chung-Ang University, Seoul 156-756, Republic of Korea. FAU - Brenner, Charles H AU - Brenner CH AD - DNA_VIEW, Oakland, CA 94601, USA; School of Public Health, University of California, Berkeley, CA 94720, USA. FAU - Choi, Byung-Sun AU - Choi BS AD - Institute for Medical Sciences, College of Medicine, Chung-Ang University, Seoul 156-756, Republic of Korea. FAU - Kim, Kyung-Yong AU - Kim KY AD - Institute for Medical Sciences, College of Medicine, Chung-Ang University, Seoul 156-756, Republic of Korea. Electronic address: skull@cau.ac.kr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150413 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - EC 2.7.7.7 (DNA-Directed DNA Polymerase) SB - IM MH - *DNA Degradation, Necrotic MH - DNA-Directed DNA Polymerase/*genetics MH - Electrophoresis, Agar Gel MH - Forensic Genetics MH - Humans MH - Real-Time Polymerase Chain Reaction MH - Sequence Analysis, DNA OTO - NOTNLM OT - DNA polymerase OT - Highly degraded DNA OT - Real-time PCR EDAT- 2015/04/29 06:00 MHDA- 2016/02/26 06:00 CRDT- 2015/04/28 06:00 PHST- 2014/11/01 00:00 [received] PHST- 2015/02/04 00:00 [revised] PHST- 2015/04/03 00:00 [accepted] PHST- 2015/04/28 06:00 [entrez] PHST- 2015/04/29 06:00 [pubmed] PHST- 2016/02/26 06:00 [medline] AID - S0379-0738(15)00147-4 [pii] AID - 10.1016/j.forsciint.2015.04.001 [doi] PST - ppublish SO - Forensic Sci Int. 2015 Jun;251:171-8. doi: 10.1016/j.forsciint.2015.04.001. Epub 2015 Apr 13. PMID- 25773651 OWN - NLM STAT- MEDLINE DCOM- 20160325 LR - 20150623 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 95 Suppl 1 DP - 2015 Jun TI - Ancient DNA analysis - An established technique in charting the evolution of tuberculosis and leprosy. PG - S140-4 LID - S1472-9792(15)00021-9 [pii] LID - 10.1016/j.tube.2015.02.020 [doi] AB - Many tuberculosis and leprosy infections are latent or paucibacillary, suggesting a long time-scale for host and pathogen co-existence. Palaeopathology enables recognition of archaeological cases and PCR detects pathogen ancient DNA (aDNA). Mycobacterium tuberculosis and Mycobacterium leprae cell wall lipids are more stable than aDNA and restrict permeability, thereby possibly aiding long-term persistence of pathogen aDNA. Amplification of aDNA, using specific PCR primers designed for short fragments and linked to fluorescent probes, gives good results, especially when designed to target multi-copy loci. Such studies have confirmed tuberculosis and leprosy, including co-infections. Many tuberculosis cases have non-specific or no visible skeletal pathology, consistent with the natural history of this disease. M. tuberculosis and M. leprae are obligate parasites, closely associated with their human host following recent clonal distribution. Therefore genotyping based on single nucleotide polymorphisms (SNPs) can indicate their origins, spread and phylogeny. Knowledge of extant genetic lineages at particular times in past human populations can be obtained from well-preserved specimens where molecular typing is possible, using deletion analysis, microsatellite analysis and whole genome sequencing. Such studies have identified non-bovine tuberculosis from a Pleistocene bison from 17,500 years BP, human tuberculosis from 9000 years ago and leprosy from over 2000 years ago. CI - Copyright © 2015 Elsevier Ltd. All rights reserved. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK; Centre for the History of Medicine, Division of Biosciences, University College London, UK. Electronic address: h.donoghue@ucl.ac.uk. FAU - Spigelman, Mark AU - Spigelman M AD - Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK; Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. Electronic address: spigelman@btinternet.com. FAU - O'Grady, Justin AU - O'Grady J AD - Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK. Electronic address: Justin.OGrady@uea.ac.uk. FAU - Szikossy, Ildikó AU - Szikossy I AD - Department of Anthropology, Hungarian Natural Science Museum, Budapest, Hungary. Electronic address: szikossy@nhmus.hu. FAU - Pap, Ildikó AU - Pap I AD - Department of Anthropology, Hungarian Natural Science Museum, Budapest, Hungary. Electronic address: papildi@hotmail.com. FAU - Lee, Oona Y-C AU - Lee OY AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: o.y.lee@bham.ac.uk. FAU - Wu, Houdini H T AU - Wu HH AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: h.wu.2@bham.ac.uk. FAU - Besra, Gurdyal S AU - Besra GS AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: g.besra@bham.ac.uk. FAU - Minnikin, David E AU - Minnikin DE AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: d.e.minnikin@bham.ac.uk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150213 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 0 (DNA, Bacterial) SB - IM MH - Bacterial Typing Techniques MH - Coinfection/complications/genetics/history MH - DNA, Bacterial/*analysis/genetics MH - *Evolution, Molecular MH - Genome, Bacterial MH - History, Ancient MH - Humans MH - Leprosy/complications/*genetics/history MH - Molecular Typing/methods MH - Mycobacterium leprae/*genetics MH - Mycobacterium tuberculosis/*genetics MH - Nucleic Acid Amplification Techniques MH - Paleopathology/methods MH - Polymerase Chain Reaction MH - Tuberculosis/complications/*genetics/history OTO - NOTNLM OT - Ancient DNA OT - Evolution OT - Molecular typing OT - Mycobacterium leprae OT - Mycobacterium tuberculosis EDAT- 2015/03/17 06:00 MHDA- 2016/03/26 06:00 CRDT- 2015/03/17 06:00 PHST- 2015/03/17 06:00 [entrez] PHST- 2015/03/17 06:00 [pubmed] PHST- 2016/03/26 06:00 [medline] AID - S1472-9792(15)00021-9 [pii] AID - 10.1016/j.tube.2015.02.020 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2015 Jun;95 Suppl 1:S140-4. doi: 10.1016/j.tube.2015.02.020. Epub 2015 Feb 13. PMID- 25771204 OWN - NLM STAT- MEDLINE DCOM- 20160325 LR - 20220129 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 95 Suppl 1 DP - 2015 Jun TI - Morphological and biomolecular evidence for tuberculosis in 8th century AD skeletons from Bélmegyer-Csömöki domb, Hungary. PG - S35-41 LID - S1472-9792(15)00033-5 [pii] LID - 10.1016/j.tube.2015.02.032 [doi] AB - Macromorphological analysis of skeletons, from 20 selected graves of the 8th century AD Bélmegyer-Csömöki domb, revealed 19 cases of possible skeletal tuberculosis. Biomolecular analyses provided general support for such diagnoses, including the individual without pathology, but the data did not show coherent consistency over the range of biomarkers examined. Amplification of ancient DNA fragments found evidence for the Mycobacterium tuberculosis complex DNA only in five graves. In contrast, varying degrees of lipid biomarker presence were recorded in all except two of the skeletons, though most lipid components appeared to be somewhat degraded. Mycobacterial mycolic acid biomarkers were absent in five cases, but the weak, possibly degraded profiles for the remainder were smaller and inconclusive for either tuberculosis or leprosy. The most positive lipid biomarker evidence for tuberculosis was provided by mycolipenic acid, with 13 clear cases, supported by five distinct possible cases. Combinations of mycocerosic acids were present in all but three graves, but in one case a tuberculosis-leprosy co-infection was indicated. In two specimens with pathology, no lipid biomarker evidence was recorded, but one of these specimens provided M. tuberculosis complex DNA fragments. CI - Copyright © 2015 Elsevier Ltd. All rights reserved. FAU - Molnár, Erika AU - Molnár E AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. Electronic address: balinte@bio.u-szeged.hu. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centre for Clinical Microbiology and Centre for the History of Medicine, University College London, London, UK. Electronic address: h.donoghue@ucl.ac.uk. FAU - Lee, Oona Y-C AU - Lee OY AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: o.y.lee@bham.ac.uk. FAU - Wu, Houdini H T AU - Wu HH AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: h.wu.2@bham.ac.uk. FAU - Besra, Gurdyal S AU - Besra GS AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: g.besra@bham.ac.uk. FAU - Minnikin, David E AU - Minnikin DE AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: d.e.minnikin@bham.ac.uk. FAU - Bull, Ian D AU - Bull ID AD - Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK. Electronic address: ian.d.bull@bristol.ac.uk. FAU - Llewellyn, Gareth AU - Llewellyn G AD - National Mass Spectrometry Service Centre, School of Medicine, Grove Building, Swansea University, Swansea, UK. Electronic address: g.llewellyn@swansea.ac.uk. FAU - Williams, Christopher M AU - Williams CM AD - National Mass Spectrometry Service Centre, School of Medicine, Grove Building, Swansea University, Swansea, UK. Electronic address: christopher.matthew.williams@swansea.ac.uk. FAU - Spekker, Olga AU - Spekker O AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. Electronic address: olga.spekker@gmail.com. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. Electronic address: palfigy@bio.u-szeged.hu. LA - eng GR - MR/K012118/1/MRC_/Medical Research Council/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150213 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 0 (Biomarkers) RN - 0 (DNA, Bacterial) RN - 0 (Lipids) RN - 0 (Mycolic Acids) SB - IM MH - Adult MH - Aged MH - Biomarkers/analysis MH - Chromatography, High Pressure Liquid MH - DNA, Bacterial/genetics MH - Female MH - History, Medieval MH - Humans MH - Hungary MH - Lipids/analysis MH - Male MH - Middle Aged MH - Mycobacterium tuberculosis/genetics MH - Mycolic Acids/analysis MH - Nucleic Acid Amplification Techniques MH - Paleopathology MH - Polymerase Chain Reaction MH - Tuberculosis, Osteoarticular/genetics/history/*pathology MH - Young Adult OTO - NOTNLM OT - Ancient DNA OT - Lipid biomarkers OT - Mycobacterium tuberculosis complex OT - PCR OT - Palaeopathology EDAT- 2015/03/17 06:00 MHDA- 2016/03/26 06:00 CRDT- 2015/03/16 06:00 PHST- 2015/03/16 06:00 [entrez] PHST- 2015/03/17 06:00 [pubmed] PHST- 2016/03/26 06:00 [medline] AID - S1472-9792(15)00033-5 [pii] AID - 10.1016/j.tube.2015.02.032 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2015 Jun;95 Suppl 1:S35-41. doi: 10.1016/j.tube.2015.02.032. Epub 2015 Feb 13. PMID- 25771203 OWN - NLM STAT- MEDLINE DCOM- 20160325 LR - 20150623 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 95 Suppl 1 DP - 2015 Jun TI - Evolutionary changes in the genome of Mycobacterium tuberculosis and the human genome from 9000 years BP until modern times. PG - S145-9 LID - S1472-9792(15)00023-2 [pii] LID - 10.1016/j.tube.2015.02.022 [doi] AB - The demonstration of Mycobacterium tuberculosis DNA in ancient skeletons gives researchers an insight into its evolution. Findings of the last two decades sketched the biological relationships between the various species of tubercle bacilli, the time scale involved, their possible origin and dispersal. This paper includes the available evidence and on-going research. In the submerged Eastern Mediterranean Neolithic village of Atlit Yam (9000 BP), a human lineage of M. tuberculosis, defined by the TbD1 deletion in its genome, was demonstrated. An infected infant at the site provides an example of active tuberculosis in a human with a naïve immune system. Over 4000 years later tuberculosis was found in Jericho. Urbanization increases population density encouraging M. tuberculosis/human co-evolution. As susceptible humans die of tuberculosis, survivors develop genetic resistance to disease. Thus in 18th century Hungarian mummies from Vác, 65% were positive for tuberculosis yet a 95-year-old woman had clearly survived a childhood Ghon lesion. Whole genome studies are in progress, to detect changes over the millennia both in bacterial virulence and also host susceptibility/resistance genes that determine the NRAMP protein and Killer Cell Immunoglobulin-like Receptors (KIRs). This paper surveys present evidence and includes initial findings. CI - Copyright © 2015 Elsevier Ltd. All rights reserved. FAU - Spigelman, Mark AU - Spigelman M AD - Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK; Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Kuvin Center for the Study of Infectious & Tropical Diseases and Ancient DNA, Hadassah Medical School, The Hebrew University, Jerusalem, Israel. Electronic address: spigelman@btinternet.com. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK; Centre for the History of Medicine, Division of Biosciences, University College London, London, UK. Electronic address: h.donoghue@ucl.ac.uk. FAU - Abdeen, Ziad AU - Abdeen Z AD - Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University, Abu-Deis, P.O. Box 201760, West Bank, Palestine. Electronic address: zabdeen13@gmail.com. FAU - Ereqat, Suheir AU - Ereqat S AD - Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University, Abu-Deis, P.O. Box 201760, West Bank, Palestine. Electronic address: sereqat@med.alquds.edu. FAU - Sarie, Issa AU - Sarie I AD - Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University, Abu-Deis, P.O. Box 201760, West Bank, Palestine. Electronic address: isarie63@gmail.com. FAU - Greenblatt, Charles L AU - Greenblatt CL AD - Kuvin Center for the Study of Infectious & Tropical Diseases and Ancient DNA, Hadassah Medical School, The Hebrew University, Jerusalem, Israel. Electronic address: charlesg@ekmd.huji.ac.il. FAU - Pap, Ildikó AU - Pap I AD - Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary. Electronic address: papildi@hotmail.com. FAU - Szikossy, Ildikó AU - Szikossy I AD - Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary. FAU - Hershkovitz, Israel AU - Hershkovitz I AD - Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. Electronic address: anatom2@post.tau.ac.il. FAU - Bar-Gal, Gila Kahila AU - Bar-Gal GK AD - Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel. Electronic address: gila.kahila@mail.huji.ac.il. FAU - Matheson, Carney AU - Matheson C AD - Paleo-DNA Laboratory, Departments of Anthropology and Biology, Lakehead University, Thunder Bay, Ontario, Canada. Electronic address: cmatheso@lakehead.ca. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150213 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 0 (Cation Transport Proteins) RN - 0 (natural resistance-associated macrophage protein 1) SB - IM MH - Animals MH - Cation Transport Proteins/genetics MH - Cattle MH - Disease Resistance/genetics MH - *Evolution, Molecular MH - Genetic Predisposition to Disease/genetics/history MH - Genome, Bacterial/*genetics MH - Genome, Human/*genetics MH - Genotype MH - History, 18th Century MH - History, 19th Century MH - History, Ancient MH - Host-Pathogen Interactions/genetics MH - Humans MH - Mummies MH - Mycobacterium tuberculosis/*genetics MH - Paleopathology MH - Tuberculosis/*genetics/history OTO - NOTNLM OT - Ancient DNA OT - Evolution OT - KIR historical specimens OT - Mycobacterium tuberculosis OT - SLC11A1 gene OT - Solute Carrier family genes EDAT- 2015/03/17 06:00 MHDA- 2016/03/26 06:00 CRDT- 2015/03/16 06:00 PHST- 2015/03/16 06:00 [entrez] PHST- 2015/03/17 06:00 [pubmed] PHST- 2016/03/26 06:00 [medline] AID - S1472-9792(15)00023-2 [pii] AID - 10.1016/j.tube.2015.02.022 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2015 Jun;95 Suppl 1:S145-9. doi: 10.1016/j.tube.2015.02.022. Epub 2015 Feb 13. PMID- 25754342 OWN - NLM STAT- MEDLINE DCOM- 20160325 LR - 20150623 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 95 Suppl 1 DP - 2015 Jun TI - Mycobacterium tuberculosis phylogeography in the context of human migration and pathogen's pathobiology: Insights from Beijing and Ural families. PG - S167-76 LID - S1472-9792(15)00032-3 [pii] LID - 10.1016/j.tube.2015.02.031 [doi] AB - Here, I review the population structure and phylogeography of the two contrasting families of Mycobacterium tuberculosis, Beijing and Ural, in the context of strain pathobiology and human history and migration. Proprietary database (12-loci MIRU-VNTR profiles of 3067 Beijing genotype isolates) was subjected to phylogenetic and statistical analysis. The highest rate (90%) and diversity (HGI 0.80-0.95) of the Beijing genotype in North China suggest it to be its area of origin. Under VNTR-based MDS analysis the interpopulation genetic distances correlated with geography over uninterrupted landmasses. In contrast, large water distances together with long time generated remarkable outliers. Weak and less expected affinities of the distant M. tuberculosis populations may reflect hidden epidemiological links due to unknown migration. Association with drug-resistance or increased virulence/transmissibility along with particular human migration flows shape global dissemination of some Beijing clones. The paucity of data on the Ural genotype prevents from high-resolution analysis that was mainly based on the available spoligotyping data. The North/East Pontic area marked with the highest prevalence of the Ural family may have been the area of its origin and primary dispersal in Eurasia. Ural strains are not marked by increased pathogenic capacities, increased transmissibility and association with drug resistance (but most recent reports describe an alarming increase of MDR Ural strains in some parts of eastern Europe and northwestern Russia). Large-scale SNP or WGS population-based studies targeting strains from indigenous populations and, eventually, analysis of ancient DNA will better test these hypotheses. Host genetics factors likely play the most prominent role in differential dissemination of particular M. tuberculosis genotypes. CI - Copyright © 2015 Elsevier Ltd. All rights reserved. FAU - Mokrousov, Igor AU - Mokrousov I AD - St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia. Electronic address: imokrousov@mail.ru. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20150224 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 SB - IM MH - Africa/epidemiology MH - Beijing/ethnology MH - Genotype MH - Global Health MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, 20th Century MH - History, Ancient MH - *Human Migration MH - Humans MH - Japan/epidemiology MH - Mycobacterium tuberculosis/*genetics MH - Oceania/epidemiology MH - Phylogeography MH - Prevalence MH - Russia/ethnology MH - South America/epidemiology MH - Tuberculosis/ethnology/*genetics/history OTO - NOTNLM OT - Beijing genotype OT - Human migration OT - Mycobacterium tuberculosis OT - Phylogeography OT - Ural genotype EDAT- 2015/03/11 06:00 MHDA- 2016/03/26 06:00 CRDT- 2015/03/11 06:00 PHST- 2015/03/11 06:00 [entrez] PHST- 2015/03/11 06:00 [pubmed] PHST- 2016/03/26 06:00 [medline] AID - S1472-9792(15)00032-3 [pii] AID - 10.1016/j.tube.2015.02.031 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2015 Jun;95 Suppl 1:S167-76. doi: 10.1016/j.tube.2015.02.031. Epub 2015 Feb 24. PMID- 25754341 OWN - NLM STAT- MEDLINE DCOM- 20160325 LR - 20221207 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 95 Suppl 1 DP - 2015 Jun TI - Evidence for tuberculosis in 18th/19th century slaves in Anse Sainte-Marguerite (Guadeloupe - French Western Indies). PG - S65-8 LID - S1472-9792(15)00007-4 [pii] LID - 10.1016/j.tube.2015.02.006 [doi] AB - During the American colonization in the 18th and 19th century, Africans were captured and shipped to America. Harsh living and working conditions often led to chronic diseases and high mortality rates. Slaves in the Caribbean were forced to work mainly on sugar plantations. They were buried in cemeteries like Anse Sainte-Marguerite on the isle of Grande-Terre (Guadeloupe) which was examined by archaeologists and physical anthropologists. Morphological studies on osseous remains of 148 individuals revealed 15 cases with signs for bone tuberculosis and a high frequency of periosteal reactions which indicates early stages of the disease. 11 bone samples from these cemeteries were analysed for ancient DNA. The samples were extracted with established procedures and examined for the cytoplasmic multicopy β-actin gene and Mycobacterium tuberculosis complex DNA (IS 6110) by PCR. An amplification product for M. tuberculosis with the size of 123 bp was obtained. Sequencing confirmed the result. This study shows evidence of M. tuberculosis complex DNA in a Caribbean slave population. CI - Copyright © 2015 Elsevier Ltd. All rights reserved. FAU - Lösch, Sandra AU - Lösch S AD - Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Switzerland. Electronic address: sandra.loesch@irm.unibe.ch. FAU - Kim, Mi-Ra AU - Kim MR AD - Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Switzerland; Benedictus Hospital Tutzing, Germany. FAU - Dutour, Olivier AU - Dutour O AD - Laboratoire d'Anthropologie biologique Paul Broca, Ecole Pratique des Hautes Etudes, France; PACEA-A3P, Université Bordeaux1, Talence, France. FAU - Courtaud, Patrice AU - Courtaud P AD - PACEA-A3P, Université Bordeaux1, Talence, France. FAU - Maixner, Frank AU - Maixner F AD - Institute for Mummies and the Iceman, EURAC, Bolzano, Italy. FAU - Romon, Thomas AU - Romon T AD - INRAP GSO, PACEA-A3P, Gourbeyre, Guadeloupe, France. FAU - Sola, Christophe AU - Sola C AD - Institut de Biologie Intégrative de la Cellule I2BC CEA-CNRS-Université Paris-Saclay, UMR9198, Bât. 400 F-91405 ORSAY-Cedex, France. FAU - Zink, Albert AU - Zink A AD - Institute for Mummies and the Iceman, EURAC, Bolzano, Italy. LA - eng PT - Historical Article PT - Journal Article DEP - 20150212 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 0 (Actins) RN - 0 (DNA, Bacterial) SB - IM MH - Actins/genetics MH - Adolescent MH - Adult MH - Black People/genetics MH - Child MH - DNA, Bacterial/genetics MH - Enslaved Persons/*history MH - Female MH - Guadeloupe MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Male MH - Mycobacterium tuberculosis/genetics MH - Nucleic Acid Amplification Techniques MH - Paleopathology MH - Polymerase Chain Reaction MH - Tuberculosis, Osteoarticular/*history MH - Young Adult OTO - NOTNLM OT - Ancient DNA OT - Bones OT - Guadeloupe OT - M. tuberculosis OT - Slaves EDAT- 2015/03/11 06:00 MHDA- 2016/03/26 06:00 CRDT- 2015/03/11 06:00 PHST- 2015/03/11 06:00 [entrez] PHST- 2015/03/11 06:00 [pubmed] PHST- 2016/03/26 06:00 [medline] AID - S1472-9792(15)00007-4 [pii] AID - 10.1016/j.tube.2015.02.006 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2015 Jun;95 Suppl 1:S65-8. doi: 10.1016/j.tube.2015.02.006. Epub 2015 Feb 12. PMID- 25726364 OWN - NLM STAT- MEDLINE DCOM- 20160325 LR - 20150623 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 95 Suppl 1 DP - 2015 Jun TI - Tuberculosis origin: The Neolithic scenario. PG - S122-6 LID - S1472-9792(15)00022-0 [pii] LID - 10.1016/j.tube.2015.02.021 [doi] AB - This paper follows the dramatic changes in scientific research during the last 20 years regarding the relationship between the Mycobacterium tuberculosis complex and its hosts - bovids and/or humans. Once the M. tuberculosis and Mycobacterium bovis genomes were sequenced, it became obvious that the old story of M. bovis evolving into the human pathogen should be reversed, as M. tuberculosis is more ancestral than M. bovis. Nevertheless, the timescale and geographical origin remained an enigma. In the current study human and cattle bone samples were examined for evidence of tuberculosis from the site of Atlit-Yam in the Eastern Mediterranean, dating from 9250 to 8160 (calibrated) years ago. Strict precautions were used to prevent contamination in the DNA analysis, and independent centers used to confirm authenticity of findings. DNA from five M. tuberculosis genetic loci was detected and had characteristics consistent with extant genetic lineages. High performance liquid chromatography was used as an independent method of verification and it directly detected mycolic acid lipid biomarkers, specific for the M. tuberculosis complex. These, together with pathological changes detected in some of the bones, confirm the presence of the disease in the Levantine populations during the Pre-pottery Neolithic C period, more than 8000 years ago. CI - Copyright © 2015 Elsevier Ltd. All rights reserved. FAU - Hershkovitz, Israel AU - Hershkovitz I AD - Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel. Electronic address: anatom2@post.tau.ac.il. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centres for Clinical Microbiology and the History of Medicine, University College London, London, UK. Electronic address: h.donoghue@ucl.ac.uk. FAU - Minnikin, David E AU - Minnikin DE AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: d.e.minnikin@bham.ac.uk. FAU - May, Hila AU - May H AD - Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel. Electronic address: hilamay@gmail.com. FAU - Lee, Oona Y-C AU - Lee OY AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. Electronic address: leeoy@bham.ac.uk. FAU - Feldman, Michal AU - Feldman M AD - Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel. Electronic address: michalfe@gmail.com. FAU - Galili, Ehud AU - Galili E AD - Israel Antiquities Authority, Jerusalem, Israel; Zinman Institute of Archaeology, Haifa University, Israel. Electronic address: udi@israntique.org.il. FAU - Spigelman, Mark AU - Spigelman M AD - Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Kuvin Center for the Study of Infectious and Tropical Diseases, Hebrew University-Hadassah Medical School, Jerusalem, Israel. Electronic address: spigelman@btinternet.com. FAU - Rothschild, Bruce M AU - Rothschild BM AD - Carnegie Museum, Pittsburgh, PA 15702, USA; Biodiversity Institute and Department of Geology, University of Kansas, Lawrence, KS 66045, USA. Electronic address: bmr@ku.edu. FAU - Bar-Gal, Gila Kahila AU - Bar-Gal GK AD - The Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel. Electronic address: gila.kahila@mail.huji.ac.il. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150213 PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 0 (Biomarkers) RN - 0 (DNA, Bacterial) RN - 0 (Lipids) RN - 0 (Mycolic Acids) SB - IM MH - Adult MH - Animals MH - Biomarkers/analysis MH - Cattle MH - Chromatography, High Pressure Liquid MH - DNA, Bacterial/analysis/genetics MH - Female MH - History, Ancient MH - Humans MH - Infant MH - Lipids/analysis MH - Male MH - Mycobacterium tuberculosis/genetics MH - Mycolic Acids/analysis MH - Paleopathology/*methods MH - Tuberculosis, Osteoarticular/genetics/*history/pathology OTO - NOTNLM OT - Ancient DNA OT - Neolithic OT - Origin of tuberculosis OT - Paleopathology EDAT- 2015/03/03 06:00 MHDA- 2016/03/26 06:00 CRDT- 2015/03/02 06:00 PHST- 2015/03/02 06:00 [entrez] PHST- 2015/03/03 06:00 [pubmed] PHST- 2016/03/26 06:00 [medline] AID - S1472-9792(15)00022-0 [pii] AID - 10.1016/j.tube.2015.02.021 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2015 Jun;95 Suppl 1:S122-6. doi: 10.1016/j.tube.2015.02.021. Epub 2015 Feb 13. PMID- 26016479 OWN - NLM STAT- MEDLINE DCOM- 20160425 LR - 20200306 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 5 DP - 2015 TI - Detection of Cytosine methylation in ancient DNA from five native american populations using bisulfite sequencing. PG - e0125344 LID - 10.1371/journal.pone.0125344 [doi] LID - e0125344 AB - While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/μL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches. FAU - Smith, Rick W A AU - Smith RW AD - Department of Anthropology, University of Texas at Austin, Austin, Texas, United States of America. FAU - Monroe, Cara AU - Monroe C AD - Department of Anthropology, Washington State University, Pullman, Washington, United States of America; Department of Anthropology, University of California Santa Barbara, Santa Barbara, California, United States of America. FAU - Bolnick, Deborah A AU - Bolnick DA AD - Department of Anthropology, University of Texas at Austin, Austin, Texas, United States of America; Population Research Center, University of Texas at Austin, Austin, Texas, United States of America. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150527 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Retroelements) RN - 0 (Sulfites) RN - 8J337D1HZY (Cytosine) RN - TZX5469Z6I (sodium bisulfite) SB - IM MH - CpG Islands/genetics MH - Cytosine/*metabolism MH - DNA Methylation/*genetics/physiology MH - Humans MH - Indians, North American/*genetics MH - Retroelements/genetics MH - Sequence Analysis, DNA MH - Sulfites/*chemistry PMC - PMC4445908 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/05/29 06:00 MHDA- 2016/04/26 06:00 PMCR- 2015/05/27 CRDT- 2015/05/29 06:00 PHST- 2014/10/14 00:00 [received] PHST- 2015/03/14 00:00 [accepted] PHST- 2015/05/29 06:00 [entrez] PHST- 2015/05/29 06:00 [pubmed] PHST- 2016/04/26 06:00 [medline] PHST- 2015/05/27 00:00 [pmc-release] AID - PONE-D-14-41204 [pii] AID - 10.1371/journal.pone.0125344 [doi] PST - epublish SO - PLoS One. 2015 May 27;10(5):e0125344. doi: 10.1371/journal.pone.0125344. eCollection 2015. PMID- 25999485 OWN - NLM STAT- MEDLINE DCOM- 20150918 LR - 20150522 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 348 IP - 6237 DP - 2015 May 22 TI - Human evolution. Ancient DNA pinpoints Paleolithic liaison in Europe. PG - 847 LID - 10.1126/science.348.6237.847 [doi] FAU - Gibbons, Ann AU - Gibbons A LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Biological Evolution MH - DNA/*genetics MH - Europe MH - *Fossils MH - Humans MH - *Mandible MH - Neanderthals/*genetics EDAT- 2015/05/23 06:00 MHDA- 2015/09/19 06:00 CRDT- 2015/05/23 06:00 PHST- 2015/05/23 06:00 [entrez] PHST- 2015/05/23 06:00 [pubmed] PHST- 2015/09/19 06:00 [medline] AID - 348/6237/847 [pii] AID - 10.1126/science.348.6237.847 [doi] PST - ppublish SO - Science. 2015 May 22;348(6237):847. doi: 10.1126/science.348.6237.847. PMID- 25992635 OWN - NLM STAT- MEDLINE DCOM- 20160415 LR - 20181113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 5 DP - 2015 TI - Differential nuclear and mitochondrial DNA preservation in post-mortem teeth with implications for forensic and ancient DNA studies. PG - e0126935 LID - 10.1371/journal.pone.0126935 [doi] LID - e0126935 AB - Major advances in genetic analysis of skeletal remains have been made over the last decade, primarily due to improvements in post-DNA-extraction techniques. Despite this, a key challenge for DNA analysis of skeletal remains is the limited yield of DNA recovered from these poorly preserved samples. Enhanced DNA recovery by improved sampling and extraction techniques would allow further advancements. However, little is known about the post-mortem kinetics of DNA degradation and whether the rate of degradation varies between nuclear and mitochondrial DNA or across different skeletal tissues. This knowledge, along with information regarding ante-mortem DNA distribution within skeletal elements, would inform sampling protocols facilitating development of improved extraction processes. Here we present a combined genetic and histological examination of DNA content and rates of DNA degradation in the different tooth tissues of 150 human molars over short-medium post-mortem intervals. DNA was extracted from coronal dentine, root dentine, cementum and pulp of 114 teeth via a silica column method and the remaining 36 teeth were examined histologically. Real time quantification assays based on two nuclear DNA fragments (67 bp and 156 bp) and one mitochondrial DNA fragment (77 bp) showed nuclear and mitochondrial DNA degraded exponentially, but at different rates, depending on post-mortem interval and soil temperature. In contrast to previous studies, we identified differential survival of nuclear and mtDNA in different tooth tissues. Furthermore histological examination showed pulp and dentine were rapidly affected by loss of structural integrity, and pulp was completely destroyed in a relatively short time period. Conversely, cementum showed little structural change over the same time period. Finally, we confirm that targeted sampling of cementum from teeth buried for up to 16 months can provide a reliable source of nuclear DNA for STR-based genotyping using standard extraction methods, without the need for specialised equipment or large-volume demineralisation steps. FAU - Higgins, Denice AU - Higgins D AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences and Environment Institute, University of Adelaide, South Australia, 5005, Australia. FAU - Rohrlach, Adam B AU - Rohrlach AB AD - School of Mathematical Sciences, University of Adelaide, South Australia, 5005, Australia. FAU - Kaidonis, John AU - Kaidonis J AD - School of Dentistry, University of Adelaide, South Australia, 5005, Australia. FAU - Townsend, Grant AU - Townsend G AD - School of Dentistry, University of Adelaide, South Australia, 5005, Australia. FAU - Austin, Jeremy J AU - Austin JJ AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences and Environment Institute, University of Adelaide, South Australia, 5005, Australia. LA - eng SI - figshare/10.6084/M9.FIGSHARE.1355825 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150519 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Cell Nucleus/*genetics MH - DNA/*genetics MH - DNA, Mitochondrial/*genetics MH - *Forensic Genetics MH - Humans MH - Microsatellite Repeats/genetics MH - *Postmortem Changes MH - Tooth/*metabolism PMC - PMC4438076 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/05/21 06:00 MHDA- 2016/04/16 06:00 PMCR- 2015/05/19 CRDT- 2015/05/21 06:00 PHST- 2015/02/05 00:00 [received] PHST- 2015/04/09 00:00 [accepted] PHST- 2015/05/21 06:00 [entrez] PHST- 2015/05/21 06:00 [pubmed] PHST- 2016/04/16 06:00 [medline] PHST- 2015/05/19 00:00 [pmc-release] AID - PONE-D-15-04985 [pii] AID - 10.1371/journal.pone.0126935 [doi] PST - epublish SO - PLoS One. 2015 May 19;10(5):e0126935. doi: 10.1371/journal.pone.0126935. eCollection 2015. PMID- 25908660 OWN - NLM STAT- MEDLINE DCOM- 20150623 LR - 20150515 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 348 IP - 6236 DP - 2015 May 15 TI - Archaeology. The makers of the Protoaurignacian and implications for Neandertal extinction. PG - 793-6 LID - 10.1126/science.aaa2773 [doi] AB - The Protoaurignacian culture is pivotal to the debate about the timing of the arrival of modern humans in western Europe and the demise of Neandertals. However, which group is responsible for this culture remains uncertain. We investigated dental remains associated with the Protoaurignacian. The lower deciduous incisor from Riparo Bombrini is modern human, based on its morphology. The upper deciduous incisor from Grotta di Fumane contains ancient mitochondrial DNA of a modern human type. These teeth are the oldest human remains in an Aurignacian-related archaeological context, confirming that by 41,000 calendar years before the present, modern humans bearing Protoaurignacian culture spread into southern Europe. Because the last Neandertals date to 41,030 to 39,260 calendar years before the present, we suggest that the Protoaurignacian triggered the demise of Neandertals in this area. CI - Copyright © 2015, American Association for the Advancement of Science. FAU - Benazzi, S AU - Benazzi S AD - Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. stefano.benazzi@unibo.it. FAU - Slon, V AU - Slon V AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Talamo, S AU - Talamo S AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Negrino, F AU - Negrino F AD - Dipartimento di Antichità, Filosofia, Storia e Geografia, Università di Genova, Via Balbi 2, 16126 Genova, Italy. FAU - Peresani, M AU - Peresani M AD - Sezione di Scienze Preistoriche e Antropologiche, Dipartimento di Studi Umanistici, Corso Ercole I d'Este 32, Università di Ferrara, 44100 Ferrara, Italy. FAU - Bailey, S E AU - Bailey SE AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA. FAU - Sawyer, S AU - Sawyer S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Panetta, D AU - Panetta D AD - CNR Institute of Clinical Physiology, National Research Council, Via G. Moruzzi 1, 56124 Pisa, Italy. FAU - Vicino, G AU - Vicino G AD - Museo Archeologico del Finale, Chiostri di Santa Caterina, 17024 Finale Ligure Borgo, Italy. FAU - Starnini, E AU - Starnini E AD - Scuola di Scienze Umanistiche, Dipartimento di Studi Storici, Università di Torino, via S. Ottavio 20, 10124 Torino, Italy. Museo Preistorico Nazionale dei Balzi Rossi, Via Balzi Rossi 9, 18039 Ventimiglia, Italy. FAU - Mannino, M A AU - Mannino MA AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Salvadori, P A AU - Salvadori PA AD - CNR Institute of Clinical Physiology, National Research Council, Via G. Moruzzi 1, 56124 Pisa, Italy. FAU - Meyer, M AU - Meyer M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Pääbo, S AU - Pääbo S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. FAU - Hublin, J-J AU - Hublin JJ AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. LA - eng SI - GENBANK/KP718913 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150423 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM CIN - Science. 2015 May 15;348(6236):754-6. doi: 10.1126/science.aab0234. PMID: 25908661 MH - Animals MH - Archaeology MH - Base Sequence MH - DNA, Mitochondrial/analysis/genetics MH - Dental Enamel/chemistry MH - *Extinction, Biological MH - Genome, Mitochondrial/genetics MH - Humans MH - Incisor/anatomy & histology/chemistry MH - Molecular Sequence Data MH - Neanderthals/anatomy & histology/*classification/*genetics MH - *Phylogeny MH - Tooth, Deciduous/anatomy & histology/chemistry EDAT- 2015/04/25 06:00 MHDA- 2015/06/24 06:00 CRDT- 2015/04/25 06:00 PHST- 2014/11/11 00:00 [received] PHST- 2015/03/16 00:00 [accepted] PHST- 2015/04/25 06:00 [entrez] PHST- 2015/04/25 06:00 [pubmed] PHST- 2015/06/24 06:00 [medline] AID - science.aaa2773 [pii] AID - 10.1126/science.aaa2773 [doi] PST - ppublish SO - Science. 2015 May 15;348(6236):793-6. doi: 10.1126/science.aaa2773. Epub 2015 Apr 23. PMID- 25970602 OWN - NLM STAT- MEDLINE DCOM- 20160205 LR - 20231104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 5 DP - 2015 TI - Osteological, biomolecular and geochemical examination of an early anglo-saxon case of lepromatous leprosy. PG - e0124282 LID - 10.1371/journal.pone.0124282 [doi] LID - e0124282 AB - We have examined a 5th to 6th century inhumation from Great Chesterford, Essex, UK. The incomplete remains are those of a young male, aged around 21-35 years at death. The remains show osteological evidence of lepromatous leprosy (LL) and this was confirmed by lipid biomarker analysis and ancient DNA (aDNA) analysis, which provided evidence for both multi-copy and single copy loci from the Mycobacterium leprae genome. Genotyping showed the strain belonged to the 3I lineage, but the Great Chesterford isolate appeared to be ancestral to 3I strains found in later medieval cases in southern Britain and also continental Europe. While a number of contemporaneous cases exist, at present, this case of leprosy is the earliest radiocarbon dated case in Britain confirmed by both aDNA and lipid biomarkers. Importantly, Strontium and Oxygen isotope analysis suggest that the individual is likely to have originated from outside Britain. This potentially sheds light on the origins of the strain in Britain and its subsequent spread to other parts of the world, including the Americas where the 3I lineage of M. leprae is still found in some southern states of America. FAU - Inskip, Sarah A AU - Inskip SA AD - Faculteit Archaeologie, Universiteit Leiden, 2311 BE, Leiden, The Netherlands. FAU - Taylor, G Michael AU - Taylor GM AD - Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7TE, United Kingdom. FAU - Zakrzewski, Sonia R AU - Zakrzewski SR AD - Department of Archaeology, University of Southampton, Avenue Campus, Highfield, Southampton, SO17 1BF, United Kingdom. FAU - Mays, Simon A AU - Mays SA AD - Ancient Monuments Laboratory, English Heritage Centre for Archaeology, Fort Cumberland, Fort Cumberland Road, Eastney, Portsmouth PO4 9LD, United Kingdom. FAU - Pike, Alistair W G AU - Pike AW AD - Department of Archaeology, University of Southampton, Avenue Campus, Highfield, Southampton, SO17 1BF, United Kingdom. FAU - Llewellyn, Gareth AU - Llewellyn G AD - EPSRC National Mass Spectrometry Facility, Institute of Mass Spectrometry, College of Medicine, Swansea University, Swansea, SA2 8PP, United Kingdom. FAU - Williams, Christopher M AU - Williams CM AD - EPSRC National Mass Spectrometry Facility, Institute of Mass Spectrometry, College of Medicine, Swansea University, Swansea, SA2 8PP, United Kingdom. FAU - Lee, Oona Y-C AU - Lee OY AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom. FAU - Wu, Houdini H T AU - Wu HH AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom. FAU - Minnikin, David E AU - Minnikin DE AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom. FAU - Besra, Gurdyal S AU - Besra GS AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom. FAU - Stewart, Graham R AU - Stewart GR AD - Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7TE, United Kingdom. LA - eng GR - MR/K012118/1/MRC_/Medical Research Council/United Kingdom PT - Case Reports PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150513 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Carbon Radioisotopes) RN - 0 (Lipids) SB - IM MH - Adult MH - Carbon Radioisotopes MH - Fibula/microbiology/pathology MH - *Genes, Bacterial MH - *Genome, Bacterial MH - Genotype MH - History, Medieval MH - Humans MH - Leprosy, Lepromatous/*history/microbiology/pathology MH - Lipids/isolation & purification MH - Male MH - Metatarsal Bones/microbiology/pathology MH - Mycobacterium leprae/classification/*genetics/isolation & purification/metabolism MH - Osteology MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA MH - Talus/microbiology/pathology MH - United Kingdom PMC - PMC4430215 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/05/15 06:00 MHDA- 2016/02/06 06:00 PMCR- 2015/05/13 CRDT- 2015/05/14 06:00 PHST- 2015/01/19 00:00 [received] PHST- 2015/03/12 00:00 [accepted] PHST- 2015/05/14 06:00 [entrez] PHST- 2015/05/15 06:00 [pubmed] PHST- 2016/02/06 06:00 [medline] PHST- 2015/05/13 00:00 [pmc-release] AID - PONE-D-15-00561 [pii] AID - 10.1371/journal.pone.0124282 [doi] PST - epublish SO - PLoS One. 2015 May 13;10(5):e0124282. doi: 10.1371/journal.pone.0124282. eCollection 2015. PMID- 25938511 OWN - NLM STAT- MEDLINE DCOM- 20160404 LR - 20221207 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 5 DP - 2015 TI - Ancient DNA reveals that the genetic structure of the northern Han Chinese was shaped prior to 3,000 years ago. PG - e0125676 LID - 10.1371/journal.pone.0125676 [doi] LID - e0125676 AB - The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area. FAU - Zhao, Yong-Bin AU - Zhao YB AD - College of Life Science, Jilin University, Changchun, China; College of Life Science, Jilin Normal University, Siping, China. FAU - Zhang, Ye AU - Zhang Y AD - College of Life Science, Jilin University, Changchun, China. FAU - Zhang, Quan-Chao AU - Zhang QC AD - Laboratory of Ancient DNA, Research Center for Chinese Frontier Archaeology of Jilin University, Changchun, China. FAU - Li, Hong-Jie AU - Li HJ AD - Laboratory of Ancient DNA, Research Center for Chinese Frontier Archaeology of Jilin University, Changchun, China. FAU - Cui, Ying-Qiu AU - Cui YQ AD - College of Life Science, Jilin University, Changchun, China. FAU - Xu, Zhi AU - Xu Z AD - Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China. FAU - Jin, Li AU - Jin L AD - Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China. FAU - Zhou, Hui AU - Zhou H AD - College of Life Science, Jilin University, Changchun, China; Laboratory of Ancient DNA, Research Center for Chinese Frontier Archaeology of Jilin University, Changchun, China. FAU - Zhu, Hong AU - Zhu H AD - Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150504 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/*genetics MH - Base Sequence MH - DNA, Mitochondrial/*history MH - Ethnicity/*genetics MH - Geography MH - Haplotypes MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - Polymorphism, Single Nucleotide/genetics MH - Principal Component Analysis PMC - PMC4418768 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/05/06 06:00 MHDA- 2016/04/05 06:00 PMCR- 2015/05/04 CRDT- 2015/05/05 06:00 PHST- 2014/09/23 00:00 [received] PHST- 2015/03/21 00:00 [accepted] PHST- 2015/05/05 06:00 [entrez] PHST- 2015/05/06 06:00 [pubmed] PHST- 2016/04/05 06:00 [medline] PHST- 2015/05/04 00:00 [pmc-release] AID - PONE-D-14-41345 [pii] AID - 10.1371/journal.pone.0125676 [doi] PST - epublish SO - PLoS One. 2015 May 4;10(5):e0125676. doi: 10.1371/journal.pone.0125676. eCollection 2015. PMID- 25546319 OWN - NLM STAT- MEDLINE DCOM- 20151029 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 157 IP - 1 DP - 2015 May TI - Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age. PG - 71-80 LID - 10.1002/ajpa.22690 [doi] AB - Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty-nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y-chromosomal DNA analyses combined with the archaeological studies revealed that the Di-qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age. CI - © 2014 Wiley Periodicals, Inc. FAU - Gao, Shi-Zhu AU - Gao SZ AD - Laboratory of Ancient DNA, Department of Molecular Biology, School of Life Sciences, Jilin University, Changchun, 130012, China; Department of Biopharmacy, College of Pharmacia Sciences, School of Life Sciences, Jilin University, Changchun, 130012, China. FAU - Zhang, Ye AU - Zhang Y FAU - Wei, Dong AU - Wei D FAU - Li, Hong-Jie AU - Li HJ FAU - Zhao, Yong-Bin AU - Zhao YB FAU - Cui, Yin-Qiu AU - Cui YQ FAU - Zhou, Hui AU - Zhou H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141229 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - Asian People/*genetics MH - China MH - Chromosomes, Human, Y/*genetics MH - DNA, Mitochondrial/*genetics MH - Female MH - *Human Migration MH - Humans MH - Male MH - Microsatellite Repeats/genetics MH - Polymorphism, Single Nucleotide/genetics OTO - NOTNLM OT - Tianshanbeilu site OT - Y-DNA OT - ancient DNA OT - mtDNA EDAT- 2014/12/30 06:00 MHDA- 2015/10/30 06:00 CRDT- 2014/12/30 06:00 PHST- 2014/06/24 00:00 [received] PHST- 2014/12/10 00:00 [revised] PHST- 2014/12/11 00:00 [accepted] PHST- 2014/12/30 06:00 [entrez] PHST- 2014/12/30 06:00 [pubmed] PHST- 2015/10/30 06:00 [medline] AID - 10.1002/ajpa.22690 [doi] PST - ppublish SO - Am J Phys Anthropol. 2015 May;157(1):71-80. doi: 10.1002/ajpa.22690. Epub 2014 Dec 29. PMID- 25808890 OWN - NLM STAT- MEDLINE DCOM- 20151201 LR - 20181113 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 282 IP - 1805 DP - 2015 Apr 22 TI - Tracing the genetic origin of Europe's first farmers reveals insights into their social organization. LID - 10.1098/rspb.2015.0339 [doi] LID - 20150339 AB - Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis is yet unclear. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (seventh/sixth millennia BC) from the Carpathian Basin and southeastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early southeastern European and Carpathian Basin farming cultures on Central European populations of the sixth-fourth millennia BC. Comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through southeastern Europe and the Carpathian Basin into Central Europe. However, our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting a system of patrilineal descent and patrilocal residential rules among the early farmers. CI - © 2015 The Author(s) Published by the Royal Society. All rights reserved. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AUID- ORCID: 0000-0003-2095-738X AD - Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany Laboratory of Archaeogenetics, Hungarian Academy of Sciences, Budapest 1014, Hungary szecsenyi-nagy.anna@btk.mta.hu. FAU - Brandt, Guido AU - Brandt G AD - Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany. FAU - Haak, Wolfgang AU - Haak W AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Keerl, Victoria AU - Keerl V AD - Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany. FAU - Jakucs, János AU - Jakucs J AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary. FAU - Möller-Rieker, Sabine AU - Möller-Rieker S AD - Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany. FAU - Köhler, Kitti AU - Köhler K AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary. FAU - Mende, Balázs Gusztáv AU - Mende BG AD - Laboratory of Archaeogenetics, Hungarian Academy of Sciences, Budapest 1014, Hungary. FAU - Oross, Krisztián AU - Oross K AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary. FAU - Marton, Tibor AU - Marton T AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary. FAU - Osztás, Anett AU - Osztás A AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary. FAU - Kiss, Viktória AU - Kiss V AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary. FAU - Fecher, Marc AU - Fecher M AD - Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany. FAU - Pálfi, György AU - Pálfi G AD - Department of Biological Anthropology, University of Szeged, Szeged 6726, Hungary. FAU - Molnár, Erika AU - Molnár E AD - Department of Biological Anthropology, University of Szeged, Szeged 6726, Hungary. FAU - Sebők, Katalin AU - Sebők K AD - Institute of Archaeological Sciences, Eötvös Loránd University, Budapest 1088, Hungary. FAU - Czene, András AU - Czene A AD - Salisbury Archaeological Ltd, Budaörs 2040, Hungary. FAU - Paluch, Tibor AU - Paluch T AD - Móra Ferenc Museum, Szeged 6720, Hungary. FAU - Šlaus, Mario AU - Šlaus M AD - Anthropological Center, Croatian Academy of Sciences and Arts, Zagreb 10000, Croatia. FAU - Novak, Mario AU - Novak M AD - School of Archaeology, University College Dublin, Dublin 4, Ireland. FAU - Pećina-Šlaus, Nives AU - Pećina-Šlaus N AD - Department of Biology, School of Medicine, University of Zagreb, Zagreb 10000, Croatia. FAU - Ősz, Brigitta AU - Ősz B AD - Department Pécs, National Heritage Protection Centre of the Hungarian National Museum, Pécs 7621, Hungary. FAU - Voicsek, Vanda AU - Voicsek V AD - Department Pécs, National Heritage Protection Centre of the Hungarian National Museum, Pécs 7621, Hungary. FAU - Somogyi, Krisztina AU - Somogyi K AD - Institute of Archaeological Sciences, Eötvös Loránd University, Budapest 1088, Hungary. FAU - Tóth, Gábor AU - Tóth G AD - Biology Department, University of West Hungary, Szombathely 9700, Hungary. FAU - Kromer, Bernd AU - Kromer B AD - Curt-Engelhorn-Centre for Archaeometry, Mannheim 68159, Germany. FAU - Bánffy, Eszter AU - Bánffy E AD - Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary German Archaeological Institute, Roman-Germanic Commission, Frankfurt am Main 0325, Germany. FAU - Alt, Kurt W AU - Alt KW AD - Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany Institute for Integrative Prehistory and Archaeological Science, University of Basel, Basel 4003, Switzerland Center of Natural and Cultural History of Teeth, Danube Private University, Krems 3500, Austria. LA - eng SI - GENBANK/KP828071 SI - GENBANK/KP828072 SI - GENBANK/KP828073 SI - GENBANK/KP828074 SI - GENBANK/KP828075 SI - GENBANK/KP828076 SI - GENBANK/KP828077 SI - GENBANK/KP828078 SI - GENBANK/KP828079 SI - GENBANK/KP828080 SI - GENBANK/KP828081 SI - GENBANK/KP828082 SI - GENBANK/KP828083 SI - GENBANK/KP828084 SI - GENBANK/KP828085 SI - GENBANK/KP828086 SI - GENBANK/KP828087 SI - GENBANK/KP828088 SI - GENBANK/KP828089 SI - GENBANK/KP828090 SI - GENBANK/KP828091 SI - GENBANK/KP828092 SI - GENBANK/KP828093 SI - GENBANK/KP828094 SI - GENBANK/KP828095 SI - GENBANK/KP828096 SI - GENBANK/KP828097 SI - GENBANK/KP828098 SI - GENBANK/KP828099 SI - GENBANK/KP828100 SI - GENBANK/KP828101 SI - GENBANK/KP828102 SI - GENBANK/KP828103 SI - GENBANK/KP828104 SI - GENBANK/KP828105 SI - GENBANK/KP828106 SI - GENBANK/KP828107 SI - GENBANK/KP828108 SI - GENBANK/KP828109 SI - GENBANK/KP828110 SI - GENBANK/KP828111 SI - GENBANK/KP828112 SI - GENBANK/KP828113 SI - GENBANK/KP828114 SI - GENBANK/KP828115 SI - GENBANK/KP828116 SI - GENBANK/KP828117 SI - GENBANK/KP828118 SI - GENBANK/KP828119 SI - GENBANK/KP828120 SI - GENBANK/KP828121 SI - GENBANK/KP828122 SI - GENBANK/KP828123 SI - GENBANK/KP828124 SI - GENBANK/KP828125 SI - GENBANK/KP828126 SI - GENBANK/KP828127 SI - GENBANK/KP828128 SI - GENBANK/KP828129 SI - GENBANK/KP828130 SI - GENBANK/KP828131 SI - GENBANK/KP828132 SI - GENBANK/KP828133 SI - GENBANK/KP828134 SI - GENBANK/KP828135 SI - GENBANK/KP828136 SI - GENBANK/KP828137 SI - GENBANK/KP828138 SI - GENBANK/KP828139 SI - GENBANK/KP828140 SI - GENBANK/KP828141 SI - GENBANK/KP828142 SI - GENBANK/KP828143 SI - GENBANK/KP828144 SI - GENBANK/KP828145 SI - GENBANK/KP828146 SI - GENBANK/KP828147 SI - GENBANK/KP828148 SI - GENBANK/KP828149 SI - GENBANK/KP828150 SI - GENBANK/KP828151 SI - GENBANK/KP828152 SI - GENBANK/KP828153 SI - GENBANK/KP828154 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture MH - Archaeology MH - Chromosomes, Human, Y/*genetics MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration MH - Europe MH - *Farmers MH - Female MH - Genetic Variation MH - Humans MH - Male MH - Molecular Sequence Data MH - Sequence Analysis, DNA MH - *Social Behavior MH - Social Environment PMC - PMC4389623 OTO - NOTNLM OT - Carpathian Basin OT - Central Europe OT - Neolithization OT - Y chromosomal DNA OT - ancient DNA OT - mitochondrial DNA EDAT- 2015/03/27 06:00 MHDA- 2015/12/15 06:00 PMCR- 2016/04/22 CRDT- 2015/03/27 06:00 PHST- 2015/03/27 06:00 [entrez] PHST- 2015/03/27 06:00 [pubmed] PHST- 2015/12/15 06:00 [medline] PHST- 2016/04/22 00:00 [pmc-release] AID - rspb.2015.0339 [pii] AID - rspb20150339 [pii] AID - 10.1098/rspb.2015.0339 [doi] PST - ppublish SO - Proc Biol Sci. 2015 Apr 22;282(1805):20150339. doi: 10.1098/rspb.2015.0339. PMID- 26829294 OWN - NLM STAT- MEDLINE DCOM- 20161114 LR - 20161230 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 87 IP - 2 DP - 2015 Apr TI - Origins of an Unmarked Georgia Cemetery Using Ancient DNA Analysis. PG - 109-21 LID - 10.13110/humanbiology.87.2.0109 [doi] AB - Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and, in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the cemetery. Through examination of hypervariable region I (HVR1) in the mitochondrial genome (mtDNA), we determined haplotypes for all 20 of these individuals. Eighteen of these individuals belong to the L or U haplogroups, suggesting that Avondale Burial Place was most likely used primarily as a resting place for African Americans. After the surrounding Bibb County community expressed interest in investigating potential ancestral relationships to those within the cemetery, eight potential descendants provided saliva to obtain mtDNA HVR1 information. Three individuals from Avondale Burial Place matched three individuals with oral history ties to the cemetery. Using the online tool EMPOP, we calculated the likelihood of these exact matches occurring by chance alone (< 1%). The present findings exhibit the importance of genetic analysis of cemetery origins when archaeological and osteological data are inconclusive for estimating ancestry of anonymous historical individuals. FAU - Ozga, Andrew T AU - Ozga AT AD - 1 University of Oklahoma, Norman, Oklahoma. FAU - Tito, Raúl Y AU - Tito RY AD - 1 University of Oklahoma, Norman, Oklahoma. FAU - Kemp, Brian M AU - Kemp BM AD - Department of Anthropology and the School of Biological Sciences, Washington State University, Pullman, Washington. FAU - Matternes, Hugh AU - Matternes H AD - 3 New South Associates, Inc., Stone Mountain, Georgia. FAU - Obregon-Tito, Alexandra AU - Obregon-Tito A AD - 1 University of Oklahoma, Norman, Oklahoma. FAU - Neal, Leslie AU - Neal L AD - 1 University of Oklahoma, Norman, Oklahoma. FAU - Lewis, Cecil M Jr AU - Lewis CM Jr AD - 1 University of Oklahoma, Norman, Oklahoma. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology/*methods MH - *Cemeteries MH - DNA, Mitochondrial/*genetics MH - Genetics, Population MH - Georgia MH - Haplotypes MH - Humans OTO - NOTNLM OT - AFRICAN AMERICAN CEMETERY OT - GENETICS OT - MITOCHONDRIAL HAPLOTYPES EDAT- 2016/02/02 06:00 MHDA- 2016/11/15 06:00 CRDT- 2016/02/02 06:00 PHST- 2016/02/02 06:00 [entrez] PHST- 2016/02/02 06:00 [pubmed] PHST- 2016/11/15 06:00 [medline] AID - 10.13110/humanbiology.87.2.0109 [doi] PST - ppublish SO - Hum Biol. 2015 Apr;87(2):109-21. doi: 10.13110/humanbiology.87.2.0109. PMID- 25994097 OWN - NLM STAT- MEDLINE DCOM- 20160310 LR - 20181113 IS - 1563-258X (Electronic) IS - 0043-5341 (Linking) VI - 165 IP - 7-8 DP - 2015 Apr TI - Ancient pathogens in museal dry bone specimens: analysis of paleocytology and aDNA. PG - 133-9 LID - 10.1007/s10354-015-0357-6 [doi] AB - Bone samples investigated in this study derive from the pathologic-anatomical collection of the Natural History Museum of Vienna. In order to explore the survival of treponemes and treponemal ancient DNA in museal dry bone specimens, we analyzed three individuals known to have been infected with Treponema pallidum pallidum. No reproducible evidence of surviving pathogen's ancient DNA (aDNA) was obtained, despite the highly sensitive extraction and amplification techniques (TPP15 and arp). Additionally, decalcification fluid of bone sections was smear stained with May-Gruenwald-Giemsa. The slides were examined using direct light microscope and dark field illumination. Remnants of spirochetal structures were detectable in every smear. Our results demonstrate that aDNA is unlikely to survive, but spirochetal remains are stainable and thus detectable. FAU - Gaul, Johanna Sophia AU - Gaul JS AD - Department of Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria, karl.grossschmidt@meduniwien.ac.at. FAU - Winter, Eduard AU - Winter E FAU - Grossschmidt, Karl AU - Grossschmidt K LA - eng PT - Historical Article PT - Journal Article DEP - 20150521 PL - Austria TA - Wien Med Wochenschr JT - Wiener medizinische Wochenschrift (1946) JID - 8708475 RN - 0 (DNA, Bacterial) SB - IM MH - Austria MH - Bone and Bones/*microbiology/*pathology MH - DNA, Bacterial/*genetics/*history MH - History, Ancient MH - Humans MH - Museums/*history MH - Paleopathology/*history MH - Treponema pallidum/*genetics MH - Treponemal Infections/*genetics/*history EDAT- 2015/05/23 06:00 MHDA- 2016/03/11 06:00 CRDT- 2015/05/22 06:00 PHST- 2014/11/20 00:00 [received] PHST- 2015/04/16 00:00 [accepted] PHST- 2015/05/22 06:00 [entrez] PHST- 2015/05/23 06:00 [pubmed] PHST- 2016/03/11 06:00 [medline] AID - 10.1007/s10354-015-0357-6 [doi] PST - ppublish SO - Wien Med Wochenschr. 2015 Apr;165(7-8):133-9. doi: 10.1007/s10354-015-0357-6. Epub 2015 May 21. PMID- 25925186 OWN - NLM STAT- MEDLINE DCOM- 20160126 LR - 20190108 IS - 1738-0006 (Electronic) IS - 0023-4001 (Print) IS - 0023-4001 (Linking) VI - 53 IP - 2 DP - 2015 Apr TI - Ancient mitochondrial DNA analyses of ascaris eggs discovered in coprolites from joseon tomb. PG - 237-42 LID - 10.3347/kjp.2015.53.2.237 [doi] AB - Analysis of ancient DNA (aDNA) extracted from Ascaris is very important for understanding the phylogenetic lineage of the parasite species. When aDNAs obtained from a Joseon tomb (SN2-19-1) coprolite in which Ascaris eggs were identified were amplified with primers for cytochrome b (cyt b) and 18S small subunit ribosomal RNA (18S rRNA) gene, the outcome exhibited Ascaris specific amplicon bands. By cloning, sequencing, and analysis of the amplified DNA, we obtained information valuable for comprehending genetic lineage of Ascaris prevalent among pre-modern Joseon peoples. FAU - Oh, Chang Seok AU - Oh CS AD - Bioanthropology and Paleopathology Lab, Institute of Forensic Science, Seoul National University College of Medicine, Seoul 110-799, Korea. FAU - Seo, Min AU - Seo M AD - Department of Parasitology and Research Center for Mummy, Dankook University, Cheonan 330-715, Korea. FAU - Hong, Jong Ha AU - Hong JH AD - Bioanthropology and Paleopathology Lab, Institute of Forensic Science, Seoul National University College of Medicine, Seoul 110-799, Korea. FAU - Chai, Jong-Yil AU - Chai JY AD - Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, Seoul 110-799, Korea. FAU - Oh, Seung Whan AU - Oh SW AD - Hangang Institute of Cultural Heritage, Seoul 143-904, Korea. FAU - Park, Jun Bum AU - Park JB AD - Sangmyung University, Seoul 110-743, Korea. FAU - Shin, Dong Hoon AU - Shin DH AD - Bioanthropology and Paleopathology Lab, Institute of Forensic Science, Seoul National University College of Medicine, Seoul 110-799, Korea. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150422 PL - Korea (South) TA - Korean J Parasitol JT - The Korean journal of parasitology JID - 9435800 RN - 0 (DNA Primers) RN - 0 (DNA, Helminth) RN - 0 (DNA, Mitochondrial) RN - 0 (RNA, Ribosomal, 18S) RN - 9035-37-4 (Cytochromes b) SB - IM MH - Adult MH - Animals MH - Ascariasis/diagnosis/history/*parasitology MH - Ascaris/classification/genetics/*isolation & purification MH - Base Sequence MH - Cytochromes b/genetics MH - DNA Primers/genetics MH - DNA, Helminth/*genetics MH - DNA, Mitochondrial/*genetics/history MH - Female MH - Fossils/history/parasitology MH - History, Ancient MH - Humans MH - Male MH - Molecular Sequence Data MH - Mummies/history/*parasitology MH - Ovum/chemistry/classification MH - Phylogeny MH - RNA, Ribosomal, 18S/genetics PMC - PMC4416368 OTO - NOTNLM OT - 18S rRNA OT - Ascaris OT - Korean mummy OT - ancient DNA OT - cytochrome b COIS- We have no conflict of interest related to this work. EDAT- 2015/05/01 06:00 MHDA- 2016/01/27 06:00 PMCR- 2015/04/01 CRDT- 2015/05/01 06:00 PHST- 2014/12/11 00:00 [received] PHST- 2015/02/25 00:00 [revised] PHST- 2015/03/03 00:00 [accepted] PHST- 2015/05/01 06:00 [entrez] PHST- 2015/05/01 06:00 [pubmed] PHST- 2016/01/27 06:00 [medline] PHST- 2015/04/01 00:00 [pmc-release] AID - kjp-53-2-237 [pii] AID - 10.3347/kjp.2015.53.2.237 [doi] PST - ppublish SO - Korean J Parasitol. 2015 Apr;53(2):237-42. doi: 10.3347/kjp.2015.53.2.237. Epub 2015 Apr 22. PMID- 25770088 OWN - NLM STAT- MEDLINE DCOM- 20160516 LR - 20221111 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 25 IP - 4 DP - 2015 Apr TI - A recent bottleneck of Y chromosome diversity coincides with a global change in culture. PG - 459-66 LID - 10.1101/gr.186684.114 [doi] AB - It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males. CI - © 2015 Karmin et al.; Published by Cold Spring Harbor Laboratory Press. FAU - Karmin, Monika AU - Karmin M AD - Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; tk331@cam.ac.uk monika.karmin@gmail.com. FAU - Saag, Lauri AU - Saag L AD - Estonian Biocentre, Tartu, 51010, Estonia; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51010, Estonia; FAU - Vicente, Mário AU - Vicente M AD - Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom; FAU - Wilson Sayres, Melissa A AU - Wilson Sayres MA AD - Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; School of Life Sciences and The Biodesign Institute, Tempe, Arizona 85287-5001, USA; FAU - Järve, Mari AU - Järve M AD - Estonian Biocentre, Tartu, 51010, Estonia; FAU - Talas, Ulvi Gerst AU - Talas UG AD - Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; FAU - Rootsi, Siiri AU - Rootsi S AD - Estonian Biocentre, Tartu, 51010, Estonia; FAU - Ilumäe, Anne-Mai AU - Ilumäe AM AD - Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; FAU - Mägi, Reedik AU - Mägi R AD - Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia; FAU - Mitt, Mario AU - Mitt M AD - Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia; Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; FAU - Pagani, Luca AU - Pagani L AD - Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom; FAU - Puurand, Tarmo AU - Puurand T AD - Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; FAU - Faltyskova, Zuzana AU - Faltyskova Z AD - Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom; FAU - Clemente, Florian AU - Clemente F AD - Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom; FAU - Cardona, Alexia AU - Cardona A AD - Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom; FAU - Metspalu, Ene AU - Metspalu E AD - Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; FAU - Sahakyan, Hovhannes AU - Sahakyan H AD - Estonian Biocentre, Tartu, 51010, Estonia; Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia; FAU - Yunusbayev, Bayazit AU - Yunusbayev B AD - Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; FAU - Hudjashov, Georgi AU - Hudjashov G AD - Estonian Biocentre, Tartu, 51010, Estonia; Department of Psychology, University of Auckland, Auckland, 1142, New Zealand; FAU - DeGiorgio, Michael AU - DeGiorgio M AD - Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA; FAU - Loogväli, Eva-Liis AU - Loogväli EL AD - Estonian Biocentre, Tartu, 51010, Estonia; FAU - Eichstaedt, Christina AU - Eichstaedt C AD - Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom; FAU - Eelmets, Mikk AU - Eelmets M AD - Estonian Biocentre, Tartu, 51010, Estonia; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; FAU - Chaubey, Gyaneshwer AU - Chaubey G AD - Estonian Biocentre, Tartu, 51010, Estonia; FAU - Tambets, Kristiina AU - Tambets K AD - Estonian Biocentre, Tartu, 51010, Estonia; FAU - Litvinov, Sergei AU - Litvinov S AD - Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; FAU - Mormina, Maru AU - Mormina M AD - Department of Applied Social Sciences, University of Winchester, Winchester, SO22 4NR, United Kingdom; FAU - Xue, Yali AU - Xue Y AD - The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom; FAU - Ayub, Qasim AU - Ayub Q AD - The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom; FAU - Zoraqi, Grigor AU - Zoraqi G AD - Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, ALB1005, Albania; FAU - Korneliussen, Thorfinn Sand AU - Korneliussen TS AD - Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark; FAU - Akhatova, Farida AU - Akhatova F AD - Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia; FAU - Lachance, Joseph AU - Lachance J AD - Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA; School of Biology, Georgia Institute of Technology, Atlanta, 30332, Georgia, USA; FAU - Tishkoff, Sarah AU - Tishkoff S AD - Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA; Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6313, USA; FAU - Momynaliev, Kuvat AU - Momynaliev K AD - DNcode Laboratories, Moscow, 119992, Russia; FAU - Ricaut, François-Xavier AU - Ricaut FX AD - Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France; FAU - Kusuma, Pradiptajati AU - Kusuma P AD - Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France; Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia; FAU - Razafindrazaka, Harilanto AU - Razafindrazaka H AD - Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France; FAU - Pierron, Denis AU - Pierron D AD - Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France; FAU - Cox, Murray P AU - Cox MP AD - Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand; FAU - Sultana, Gazi Nurun Nahar AU - Sultana GN AD - Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Dhaka-1000, Bangladesh; FAU - Willerslev, Rane AU - Willerslev R AD - Arctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmark; FAU - Muller, Craig AU - Muller C AD - Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark; FAU - Westaway, Michael AU - Westaway M AD - Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia; FAU - Lambert, David AU - Lambert D AD - Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia; FAU - Skaro, Vedrana AU - Skaro V AD - Genos, DNA Laboratory, Zagreb, 10000, Croatia; University of Osijek, Medical School, Osijek, 31000, Croatia; FAU - Kovačevic, Lejla AU - Kovačevic L AD - Centogene AG, Rostock, 18057, Germany; FAU - Turdikulova, Shahlo AU - Turdikulova S AD - Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan; FAU - Dalimova, Dilbar AU - Dalimova D AD - Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan; FAU - Khusainova, Rita AU - Khusainova R AD - Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia; FAU - Trofimova, Natalya AU - Trofimova N AD - Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; FAU - Akhmetova, Vita AU - Akhmetova V AD - Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; FAU - Khidiyatova, Irina AU - Khidiyatova I AD - Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia; FAU - Lichman, Daria V AU - Lichman DV AD - Institute of Cytology and Genetics, Novosibirsk, 630090, Russia; FAU - Isakova, Jainagul AU - Isakova J AD - Institute of Molecular Biology and Medicine, Bishkek, 720040, Kyrgyzstan; FAU - Pocheshkhova, Elvira AU - Pocheshkhova E AD - Kuban State Medical University, Krasnodar, 350063, Russia; FAU - Sabitov, Zhaxylyk AU - Sabitov Z AD - L.N. Gumilyov Eurasian National University, Astana, 010008, Kazakhstan; Center for Life Sciences, Nazarbayev University, Astana, 010000, Kazakhstan; FAU - Barashkov, Nikolay A AU - Barashkov NA AD - Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia; Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia; FAU - Nymadawa, Pagbajabyn AU - Nymadawa P AD - Mongolian Academy of Medical Sciences, Ulaanbaatar, 210620, Mongolia; FAU - Mihailov, Evelin AU - Mihailov E AD - Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia; FAU - Seng, Joseph Wee Tien AU - Seng JW AD - National Cancer Centre Singapore, 169610, Singapore; FAU - Evseeva, Irina AU - Evseeva I AD - Northern State Medical University, Arkhangelsk, 163000, Russia; Anthony Nolan, London, NW3 2NU, United Kingdom; FAU - Migliano, Andrea Bamberg AU - Migliano AB AD - Department of Anthropology, University College London, London, WC1E 6BT, United Kingdom; FAU - Abdullah, Syafiq AU - Abdullah S AD - RIPAS Hospital, Bandar Seri Begawan, BE1518, Brunei; FAU - Andriadze, George AU - Andriadze G AD - Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, 0162, Georgia; FAU - Primorac, Dragan AU - Primorac D AD - University of Osijek, Medical School, Osijek, 31000, Croatia; St. Catherine Specialty Hospital, Zabok, 49210, Croatia; Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania 16802, USA; University of Split, Medical School, Split, 21000, Croatia; FAU - Atramentova, Lubov AU - Atramentova L AD - V.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine; FAU - Utevska, Olga AU - Utevska O AD - V.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine; FAU - Yepiskoposyan, Levon AU - Yepiskoposyan L AD - Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia; FAU - Marjanovic, Damir AU - Marjanovic D AD - Genos, DNA Laboratory, Zagreb, 10000, Croatia; Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, 71000, Bosnia and Herzegovina; FAU - Kushniarevich, Alena AU - Kushniarevich A AD - Estonian Biocentre, Tartu, 51010, Estonia; Institute of Genetics and Cytology, National Academy of Sciences, Minsk, 220072, Belarus; FAU - Behar, Doron M AU - Behar DM AD - Estonian Biocentre, Tartu, 51010, Estonia; FAU - Gilissen, Christian AU - Gilissen C AD - Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands; FAU - Vissers, Lisenka AU - Vissers L AD - Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands; FAU - Veltman, Joris A AU - Veltman JA AD - Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands; FAU - Balanovska, Elena AU - Balanovska E AD - Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia; FAU - Derenko, Miroslava AU - Derenko M AD - Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia; FAU - Malyarchuk, Boris AU - Malyarchuk B AD - Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia; FAU - Metspalu, Andres AU - Metspalu A AD - Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia; FAU - Fedorova, Sardana AU - Fedorova S AD - Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia; Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia; FAU - Eriksson, Anders AU - Eriksson A AD - Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom; Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia; FAU - Manica, Andrea AU - Manica A AD - Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom; FAU - Mendez, Fernando L AU - Mendez FL AD - Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA; FAU - Karafet, Tatiana M AU - Karafet TM AD - ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA; FAU - Veeramah, Krishna R AU - Veeramah KR AD - Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA; FAU - Bradman, Neil AU - Bradman N AD - The Henry Stewart Group, London, WC1A 2HN, United Kingdom; FAU - Hammer, Michael F AU - Hammer MF AD - ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA; FAU - Osipova, Ludmila P AU - Osipova LP AD - Institute of Cytology and Genetics, Novosibirsk, 630090, Russia; FAU - Balanovsky, Oleg AU - Balanovsky O AD - Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia; Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia; FAU - Khusnutdinova, Elza K AU - Khusnutdinova EK AD - Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia; FAU - Johnsen, Knut AU - Johnsen K AD - University Hospital of North Norway, Tromsøe, N-9038, Norway; FAU - Remm, Maido AU - Remm M AD - Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; FAU - Thomas, Mark G AU - Thomas MG AD - Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom; FAU - Tyler-Smith, Chris AU - Tyler-Smith C AD - The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom; FAU - Underhill, Peter A AU - Underhill PA AD - Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA; FAU - Willerslev, Eske AU - Willerslev E AD - Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark; FAU - Nielsen, Rasmus AU - Nielsen R AD - Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; FAU - Metspalu, Mait AU - Metspalu M AD - Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; FAU - Villems, Richard AU - Villems R AD - Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; Estonian Academy of Sciences, Tallinn, 10130, Estonia. FAU - Kivisild, Toomas AU - Kivisild T AD - Estonian Biocentre, Tartu, 51010, Estonia; Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom; tk331@cam.ac.uk monika.karmin@gmail.com. LA - eng GR - 261213/ERC_/European Research Council/International GR - 098051/WT_/Wellcome Trust/United Kingdom GR - WT_/Wellcome Trust/United Kingdom GR - R01 GM113657/GM/NIGMS NIH HHS/United States GR - BB/H005854/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150313 PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - Chromosomes, Human, Y/*genetics MH - DNA, Mitochondrial/genetics MH - *Evolution, Molecular MH - Genetic Variation/genetics MH - Genetics, Population MH - Haplotypes/genetics MH - Humans MH - Male MH - Models, Genetic MH - Phylogeny MH - Racial Groups/*genetics MH - Sequence Analysis, DNA PMC - PMC4381518 EDAT- 2015/03/15 06:00 MHDA- 2016/05/18 06:00 PMCR- 2015/10/01 CRDT- 2015/03/15 06:00 PHST- 2014/11/06 00:00 [received] PHST- 2015/02/13 00:00 [accepted] PHST- 2015/03/15 06:00 [entrez] PHST- 2015/03/15 06:00 [pubmed] PHST- 2016/05/18 06:00 [medline] PHST- 2015/10/01 00:00 [pmc-release] AID - gr.186684.114 [pii] AID - 10.1101/gr.186684.114 [doi] PST - ppublish SO - Genome Res. 2015 Apr;25(4):459-66. doi: 10.1101/gr.186684.114. Epub 2015 Mar 13. PMID- 25735209 OWN - NLM STAT- MEDLINE DCOM- 20150521 LR - 20180808 IS - 1365-294X (Electronic) IS - 0962-1083 (Linking) VI - 24 IP - 7 DP - 2015 Apr TI - Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA. PG - 1485-98 LID - 10.1111/mec.13136 [doi] AB - Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA-based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high-elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall-herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long-term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long-term ecosystem dynamics under the influence of human-induced and environmental drivers. CI - © 2015 John Wiley & Sons Ltd. FAU - Pansu, Johan AU - Pansu J AD - Univ. Grenoble Alpes, LECA, F-38000, Grenoble, France; CNRS, LECA, F-38000, Grenoble, France. FAU - Giguet-Covex, Charline AU - Giguet-Covex C FAU - Ficetola, Gentile Francesco AU - Ficetola GF FAU - Gielly, Ludovic AU - Gielly L FAU - Boyer, Frédéric AU - Boyer F FAU - Zinger, Lucie AU - Zinger L FAU - Arnaud, Fabien AU - Arnaud F FAU - Poulenard, Jérôme AU - Poulenard J FAU - Taberlet, Pierre AU - Taberlet P FAU - Choler, Philippe AU - Choler P LA - eng SI - Dryad/10.5061/dryad.6171J SI - Dryad/10.5061/dryad.H11H7 SI - Dryad/10.5061/dryad.PH8S5 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150323 PL - England TA - Mol Ecol JT - Molecular ecology JID - 9214478 RN - 0 (DNA, Plant) SB - IM MH - Agriculture MH - Climate Change MH - DNA Barcoding, Taxonomic MH - DNA, Plant/genetics MH - *Ecosystem MH - Geologic Sediments/*analysis MH - High-Throughput Nucleotide Sequencing MH - Humans MH - *Lakes MH - Plants/*classification/genetics MH - Population Dynamics OTO - NOTNLM OT - anthropocene OT - environmental DNA OT - landscape history OT - metabarcoding OT - paleoecology OT - pastoralism EDAT- 2015/03/05 06:00 MHDA- 2015/05/23 06:00 CRDT- 2015/03/05 06:00 PHST- 2014/10/06 00:00 [received] PHST- 2015/02/24 00:00 [revised] PHST- 2015/02/27 00:00 [accepted] PHST- 2015/03/05 06:00 [entrez] PHST- 2015/03/05 06:00 [pubmed] PHST- 2015/05/23 06:00 [medline] AID - 10.1111/mec.13136 [doi] PST - ppublish SO - Mol Ecol. 2015 Apr;24(7):1485-98. doi: 10.1111/mec.13136. Epub 2015 Mar 23. PMID- 25680828 OWN - NLM STAT- MEDLINE DCOM- 20151201 LR - 20220129 IS - 1567-7257 (Electronic) IS - 1567-1348 (Linking) VI - 31 DP - 2015 Apr TI - A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe. PG - 250-6 LID - S1567-1348(15)00044-1 [pii] LID - 10.1016/j.meegid.2015.02.001 [doi] AB - Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th-11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th-8th century Northern Italy, 7th-11th century Hungary, 8th-9th century Austria, the Slavic Greater Moravian Empire of the 9th-10th century and 8th-10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor. CI - Copyright © 2015 Elsevier B.V. All rights reserved. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, UK. Electronic address: h.donoghue@ucl.ac.uk. FAU - Michael Taylor, G AU - Michael Taylor G AD - Department of Microbial and Cellular Science, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK. FAU - Marcsik, Antónia AU - Marcsik A AD - University of Szeged, Mályva utca 23, H-6771 Szeged, Hungary. FAU - Molnár, Erika AU - Molnár E AD - Department of Biological Anthropology, University of Szeged, Hungary. FAU - Pálfi, Gyorgy AU - Pálfi G AD - Department of Biological Anthropology, University of Szeged, Hungary. FAU - Pap, Ildikó AU - Pap I AD - Department of Anthropology, Natural History Museum, Budapest, Hungary. FAU - Teschler-Nicola, Maria AU - Teschler-Nicola M AD - Department of Anthropology, Natural History Museum, Vienna, Austria. FAU - Pinhasi, Ron AU - Pinhasi R AD - School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. FAU - Erdal, Yilmaz S AU - Erdal YS AD - Department of Anthropology, Hacettepe University, Ankara, Turkey. FAU - Velemínsky, Petr AU - Velemínsky P AD - Department of Anthropology, National Museum, Prague, Czech Republic. FAU - Likovsky, Jakub AU - Likovsky J AD - Department of the Archaeology of Landscape and Archaeobiology, Institute of Archaeology, Academy of Sciences of the Czech Republic, Prague, Czech Republic. FAU - Belcastro, Maria Giovanna AU - Belcastro MG AD - Laboratorio di Bioarcheologia e Osteologia Forense, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Via Selmi 3, 40126 Bologna, Italy; Centro Fermi, Piazza del Viminale 1, 00184 Rome, Italy. FAU - Mariotti, Valentina AU - Mariotti V AD - Laboratorio di Bioarcheologia e Osteologia Forense, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Via Selmi 3, 40126 Bologna, Italy; ADES, UMR 7268 CNRS/Université de la Méditerranée/EFS, Université de la Méditerranée, CS80011, Bd Pierre Dramard,13344 Marseille Cedex 15, France. FAU - Riga, Alessandro AU - Riga A AD - Laboratorio di Bioarcheologia e Osteologia Forense, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Via Selmi 3, 40126 Bologna, Italy. FAU - Rubini, Mauro AU - Rubini M AD - Department of Archaeology, Foggia University, Tivoli, Italy; Anthropological Service of S.B.A.L. (Ministry of Culture), Rome, Italy. FAU - Zaio, Paola AU - Zaio P AD - Department of Archaeology, Foggia University, Tivoli, Italy. FAU - Besra, Gurdyal S AU - Besra GS AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. FAU - Lee, Oona Y-C AU - Lee OY AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. FAU - Wu, Houdini H T AU - Wu HH AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. FAU - Minnikin, David E AU - Minnikin DE AD - Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK. FAU - Bull, Ian D AU - Bull ID AD - Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK. FAU - O'Grady, Justin AU - O'Grady J AD - Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, UK. FAU - Spigelman, Mark AU - Spigelman M AD - Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, UK; Department of Anatomy and Anthropology Sackler Medical School, Tel Aviv University, Israel. LA - eng GR - MR/K012118/1/MRC_/Medical Research Council/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150211 PL - Netherlands TA - Infect Genet Evol JT - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JID - 101084138 SB - IM MH - Adult MH - Europe/epidemiology MH - Female MH - Genotype MH - History, Medieval MH - *Human Migration MH - Humans MH - Leprosy/*epidemiology/history/*transmission MH - Male MH - Middle Aged MH - *Models, Statistical MH - Mycobacterium leprae/genetics MH - Paleopathology MH - Young Adult OTO - NOTNLM OT - Ancient DNA OT - Genotyping OT - Human migrations OT - Lipid biomarkers OT - Mycobacterium leprae OT - Mycobacterium tuberculosis EDAT- 2015/02/15 06:00 MHDA- 2015/12/15 06:00 CRDT- 2015/02/15 06:00 PHST- 2014/11/22 00:00 [received] PHST- 2015/02/01 00:00 [revised] PHST- 2015/02/03 00:00 [accepted] PHST- 2015/02/15 06:00 [entrez] PHST- 2015/02/15 06:00 [pubmed] PHST- 2015/12/15 06:00 [medline] AID - S1567-1348(15)00044-1 [pii] AID - 10.1016/j.meegid.2015.02.001 [doi] PST - ppublish SO - Infect Genet Evol. 2015 Apr;31:250-6. doi: 10.1016/j.meegid.2015.02.001. Epub 2015 Feb 11. PMID- 25755263 OWN - NLM STAT- MEDLINE DCOM- 20150615 LR - 20221207 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 112 IP - 12 DP - 2015 Mar 24 TI - Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean. PG - 3669-73 LID - 10.1073/pnas.1421784112 [doi] AB - Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions. FAU - Schroeder, Hannes AU - Schroeder H AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; Faculty of Archaeology, Leiden University, 2300 Leiden, The Netherlands; hschroeder@snm.ku.dk tgilbert@snm.ku.dk. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; Department of Genetics, Stanford University, Stanford, CA 94305; FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; FAU - Poznik, G David AU - Poznik GD AUID- ORCID: 0000-0003-4427-3556 AD - Program in Biomedical Informatics and Department of Statistics, Stanford University, Stanford, CA 94305; FAU - Sandoval-Velasco, Marcela AU - Sandoval-Velasco M AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; FAU - Carpenter, Meredith L AU - Carpenter ML AD - Department of Genetics, Stanford University, Stanford, CA 94305; FAU - Moreno-Mayar, José Víctor AU - Moreno-Mayar JV AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; FAU - Sikora, Martin AU - Sikora M AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; Department of Genetics, Stanford University, Stanford, CA 94305; FAU - Johnson, Philip L F AU - Johnson PL AD - Department of Biology, Emory University, Atlanta, GA 30322; FAU - Allentoft, Morten Erik AU - Allentoft ME AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; FAU - Samaniego, José Alfredo AU - Samaniego JA AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; FAU - Haviser, Jay B AU - Haviser JB AD - St. Maarten Archaeological Center, Philipsburg, Saint Martin; FAU - Dee, Michael W AU - Dee MW AD - Research Laboratory for Archaeology and the History of Art, University of Oxford, OX1 3QY Oxford, United Kingdom; FAU - Stafford, Thomas W Jr AU - Stafford TW Jr AD - AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus, Denmark; and. FAU - Salas, Antonio AU - Salas A AD - Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; FAU - Willerslev, Eske AU - Willerslev E AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; FAU - Bustamante, Carlos D AU - Bustamante CD AD - Department of Genetics, Stanford University, Stanford, CA 94305; FAU - Gilbert, M Thomas P AU - Gilbert MT AD - Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; hschroeder@snm.ku.dk tgilbert@snm.ku.dk. LA - eng GR - R00 GM104158/GM/NIGMS NIH HHS/United States GR - F32 HG007342/HG/NHGRI NIH HHS/United States GR - K99 GM104158/GM/NIGMS NIH HHS/United States GR - R01 GM090087/GM/NIGMS NIH HHS/United States GR - T15 LM007033/LM/NLM NIH HHS/United States GR - 5F32HG007342/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20150309 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - Africa/ethnology MH - Algorithms MH - Archaeology MH - Bayes Theorem MH - Black People/genetics MH - Caribbean Region/ethnology MH - Chromosomes, Human, Y/genetics MH - Cluster Analysis MH - DNA, Mitochondrial/genetics MH - *Enslaved Persons MH - Enslavement MH - Ethnicity/genetics MH - Genetic Markers MH - *Genetics, Population MH - Genome, Human MH - *Genome-Wide Association Study MH - Haplotypes MH - Humans MH - Likelihood Functions MH - Principal Component Analysis MH - Probability MH - Sequence Analysis, DNA PMC - PMC4378422 OTO - NOTNLM OT - ancient DNA OT - genomics OT - slave trade COIS- Conflict of interest statement: C.D.B. is the founder of IdentifyGenomics, LLC, and is on the Scientific Advisory Boards of Personalis, Inc., and Ancestry.com as well as the Medical Advisory Board of InVitae. M.L.C. is now the Chief Scientific Officer at IdentifyGenomics, LLC. None of this played a role in the design, execution, or interpretation of experiments and results presented here. EDAT- 2015/03/11 06:00 MHDA- 2015/06/16 06:00 PMCR- 2015/03/09 CRDT- 2015/03/11 06:00 PHST- 2015/03/11 06:00 [entrez] PHST- 2015/03/11 06:00 [pubmed] PHST- 2015/06/16 06:00 [medline] PHST- 2015/03/09 00:00 [pmc-release] AID - 1421784112 [pii] AID - 201421784 [pii] AID - 10.1073/pnas.1421784112 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):3669-73. doi: 10.1073/pnas.1421784112. Epub 2015 Mar 9. PMID- 25799293 OWN - NLM STAT- MEDLINE DCOM- 20160218 LR - 20231104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 3 DP - 2015 TI - When data sharing gets close to 100%: what human paleogenetics can teach the open science movement. PG - e0121409 LID - 10.1371/journal.pone.0121409 [doi] LID - e0121409 AB - This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals' editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers' awareness of the importance of openness and transparency for scientific progress may complement stakeholders' policies in achieving very high sharing rates. Second, widespread data sharing does not necessarily coincide with a prevalent use of practices which maximize data findability, accessibility, useability and preservation. A detailed look at the different ways in which data are released can be very useful to detect failures to adopt the best sharing modalities and understand how to correct them. Third and finally, the case of human paleogenetics tells us that a widespread awareness of the importance of Open Science may be important to build reliable scientific practices even in the presence of complex experimental challenges. FAU - Anagnostou, Paolo AU - Anagnostou P AD - Dipartimento di Biologia Ambientale, "Sapienza" Università di Roma, Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy. FAU - Capocasa, Marco AU - Capocasa M AD - Istituto Italiano di Antropologia, Rome, Italy; Dipartimento Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Rome, Italy. FAU - Milia, Nicola AU - Milia N AD - Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy. FAU - Sanna, Emanuele AU - Sanna E AD - Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy. FAU - Battaggia, Cinzia AU - Battaggia C AD - Dipartimento di Biologia Ambientale, "Sapienza" Università di Roma, Rome, Italy. FAU - Luzi, Daniela AU - Luzi D AD - Istituto di Ricerche sulla Popolazione e le Politiche Sociali, Consiglio Nazionale delle Ricerche, Rome, Italy. FAU - Destro Bisol, Giovanni AU - Destro Bisol G AD - Dipartimento di Biologia Ambientale, "Sapienza" Università di Roma, Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150323 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 9007-49-2 (DNA) SB - IM MH - Chromosomes, Human, Y/genetics MH - DNA/*genetics MH - Humans MH - *Information Dissemination MH - Mitochondria/genetics MH - *Paleontology MH - Polymorphism, Genetic MH - Publications MH - *Science MH - Surveys and Questionnaires PMC - PMC4370607 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/03/24 06:00 MHDA- 2016/02/19 06:00 PMCR- 2015/03/23 CRDT- 2015/03/24 06:00 PHST- 2014/08/01 00:00 [received] PHST- 2015/02/02 00:00 [accepted] PHST- 2015/03/24 06:00 [entrez] PHST- 2015/03/24 06:00 [pubmed] PHST- 2016/02/19 06:00 [medline] PHST- 2015/03/23 00:00 [pmc-release] AID - PONE-D-14-34200 [pii] AID - 10.1371/journal.pone.0121409 [doi] PST - epublish SO - PLoS One. 2015 Mar 23;10(3):e0121409. doi: 10.1371/journal.pone.0121409. eCollection 2015. PMID- 25819058 OWN - NLM STAT- MEDLINE DCOM- 20161215 LR - 20190816 IS - 2532-8689 (Electronic) IS - 1124-9390 (Linking) VI - 23 IP - 1 DP - 2015 Mar TI - [Mycobacterium infection in prehistoric humans: co-evolution in remote ages]. PG - 83-93 AB - The introduction of agriculture and animal husbandry at the end of the Mesolithic era, despite enabling a significant demographic growth through an increase in food storage and availability, caused new infectious noxae to enter the pathocoenosis. However in the Palaeolithic era, hunter-gatherers were already in contact with infectious diseases of animal origin, albeit episodically. Modern biomedical technologies allow us to estimate, with better approximation, how long mankind has been in contact with Mycobacterium tuberculosis. Archaeological finds, including human and animal remains (especially the aurochs), are particularly studied by palaeopathologists, as mycobacteria frequently cause bone involvement and this characteristic is of particular interest for palaeopathological (even macroscopic) studies; the interest is to detect the ancient DNA of MT, which is the cause of bone tuberculosis in skeletal remains as well as in mummies. According to our present knowledge, palaeopathological findings, confirmed by molecular techniques, suggest that tuberculosis in human skeletons goes back at most to 9000 years ago, while, in a veterinary environment, the most ancient DNA of MTBC to be detected in an American bison dates back about 17,000 years. The possibility of discovering archaeological finds making even more ancient human remains available leaves opens up the possibility of dating back to previous eras the transmission of MTBC infection to mankind. Phylogenetic works examining the available materials (DNAa) suggest that Mycobacterium tuberculosis, the cause of tuberculosis infection in humans and cattle (Aurochs), would have had a co-evolutionary process. On the basis of recent phylogenetic studies, the MTBC genome would have had a wide span of time to reach a suitable adjustment, co-evolving in geographical environments both at high and low host density. It is likely that the strains that did not show this strong "flexibility" underwent extinction, in favour of more versatile, adaptable strains, that are able to infect susceptible hosts "always" and in any environmental condition. FAU - Sabbatani, Sandro AU - Sabbatani S AD - U.O. Malattie Infettive, Policlinico S. Orsola-Malpighi; U.O. di Medicina Interna Ospedale di Budrio, Bologna, Italy. FAU - Fiorini, Sirio AU - Fiorini S AD - U.O. Malattie Infettive, Policlinico S. Orsola-Malpighi; U.O. di Medicina Interna Ospedale di Budrio, Bologna, Italy. LA - ita PT - Historical Article PT - Journal Article TT - L'infezione da micobatteri nell'uomo preistorico. Un cammino parallelo (co-evoluzione) dimostrato già in epoche remote. PL - Italy TA - Infez Med JT - Le infezioni in medicina JID - 9613961 RN - 0 (DNA, Bacterial) SB - IM MH - Africa MH - Ancient Lands MH - Animal Husbandry/history MH - Animals MH - Cattle MH - Cattle Diseases/*history/microbiology MH - Cultural Evolution/history MH - DNA, Bacterial/*history MH - Emigration and Immigration/*history MH - *Genome, Bacterial MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, 20th Century MH - History, 21st Century MH - History, Ancient MH - History, Medieval MH - Humans MH - Medical Illustration/*history MH - *Mycobacterium tuberculosis/genetics MH - North America MH - Paleopathology/history/methods MH - Phylogeny MH - Phylogeography MH - Tuberculosis/*history EDAT- 2015/03/31 06:00 MHDA- 2016/12/16 06:00 CRDT- 2015/03/31 06:00 PHST- 2015/03/31 06:00 [entrez] PHST- 2015/03/31 06:00 [pubmed] PHST- 2016/12/16 06:00 [medline] PST - ppublish SO - Infez Med. 2015 Mar;23(1):83-93. PMID- 25466970 OWN - NLM STAT- MEDLINE DCOM- 20150925 LR - 20150120 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 15 DP - 2015 Mar TI - Genetic research at a fivefold children's burial from medieval Berlin. PG - 90-7 LID - S1872-4973(14)00238-5 [pii] LID - 10.1016/j.fsigen.2014.10.022 [doi] AB - Berlin originated from the two twin cities Berlin and Cölln, which both were founded at the beginning of the 13th century. However the real date of their foundation as well as the origin of the first settlers is still unknown. On the Berlin site the historic city center is still visible in the Nikolaiviertel, but the medieval origin of Cölln disappeared almost completely. In 2007 a large scale excavation, which comprised an area of about 1700m(2) of the historical center of the St. Peters church, recovers the remains of Cölln's first citizens and span a period of 500 years of medieval population. Here we present the first genetic analysis of a fivefold children's burial from excavations in Berlin. The genetic data unveiled next to ancestry and eye color data also the kinship and the gender of the five individuals. Together with the archeological context the new gained information help to shed more light on the possible reasons for this burial. CI - Copyright © 2014 Elsevier Ireland Ltd. All rights reserved. FAU - Rothe, Jessica AU - Rothe J AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Germany. Electronic address: jessica.rothe@charite.de. FAU - Melisch, Claudia AU - Melisch C AD - Humboldt University Berlin, Germany. FAU - Powers, Natasha AU - Powers N AD - MOLA (Museum of London Archaeology), London, United Kingdom. FAU - Geppert, Maria AU - Geppert M AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Germany. FAU - Zander, Judith AU - Zander J AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Germany. FAU - Purps, Josephine AU - Purps J AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Germany. FAU - Spors, Birgit AU - Spors B AD - Department of Pediatrician Radiology, Charité-Universitätsmedizin Berlin, Germany. FAU - Nagy, Marion AU - Nagy M AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Germany. LA - eng PT - Historical Article PT - Journal Article DEP - 20141108 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Mitochondrial) SB - IM MH - Child MH - Chromosomes, Human, Y MH - DNA, Mitochondrial/genetics MH - Family MH - *Funeral Rites MH - *Genetics, Medical MH - Germany MH - History, Medieval MH - Humans OTO - NOTNLM OT - Ancient DNA OT - Medieval multiple burial OT - Medieval population of Berlin OT - St. Peters square (Petriplatz) EDAT- 2014/12/04 06:00 MHDA- 2015/09/26 06:00 CRDT- 2014/12/04 06:00 PHST- 2014/08/18 00:00 [received] PHST- 2014/10/20 00:00 [revised] PHST- 2014/10/24 00:00 [accepted] PHST- 2014/12/04 06:00 [entrez] PHST- 2014/12/04 06:00 [pubmed] PHST- 2015/09/26 06:00 [medline] AID - S1872-4973(14)00238-5 [pii] AID - 10.1016/j.fsigen.2014.10.022 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2015 Mar;15:90-7. doi: 10.1016/j.fsigen.2014.10.022. Epub 2014 Nov 8. PMID- 25418693 OWN - NLM STAT- MEDLINE DCOM- 20151105 LR - 20150219 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 156 IP - 3 DP - 2015 Mar TI - Ancient DNA from the Schild site in Illinois: Implications for the Mississippian transition in the Lower Illinois River Valley. PG - 434-48 LID - 10.1002/ajpa.22668 [doi] AB - Archaeologists have long debated whether rapid cultural change in the archaeological record is due to in situ developments, migration of a new group into the region, or the spread of new cultural practices into an area through existing social networks, with the local peoples adopting and adapting practices from elsewhere as they see fit (acculturation). Researchers have suggested each of these explanations for the major cultural transition that occurred at the beginning of the Mississippian period (AD 1050) across eastern North America. In this study, we used ancient DNA to test competing hypotheses of migration and acculturation for the culture change that occurred between the Late Woodland (AD 400-1050) and Mississippian (AD 1050-1500) periods in the Lower Illinois River Valley. We obtained sequences of the first hypervariable segment of the mitochondrial genome (mtDNA) from 39 individuals (17 Late Woodland, 22 Mississippian) interred in the Schild cemetery in western Illinois, and compared these lineages to ancient mtDNA lineages present at other sites in the region. Computer simulations were used to test a null hypothesis of population continuity from Late Woodland to Mississippian times at the Schild site and to investigate the possibility of gene flow from elsewhere in the region. Our results suggest that the Late Woodland to Mississippian cultural transition at Schild was not due to an influx of people from elsewhere. Instead, it is more likely that the transition to Mississippian cultural practices at this site was due to a process of acculturation. CI - © 2014 Wiley Periodicals, Inc. FAU - Reynolds, Austin W AU - Reynolds AW AD - Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712; Department of Anthropology, University of Texas at Austin, Austin, TX, 78712. FAU - Raff, Jennifer A AU - Raff JA FAU - Bolnick, Deborah A AU - Bolnick DA FAU - Cook, Della C AU - Cook DC FAU - Kaestle, Frederika A AU - Kaestle FA LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20141124 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - Female MH - *Genetics, Population MH - Haplotypes MH - *Human Migration MH - Humans MH - Illinois MH - Male MH - Mississippi MH - Paleontology MH - Rivers OTO - NOTNLM OT - Late Woodland OT - Native American OT - US Midwest OT - mitochondrial DNA OT - population history EDAT- 2014/11/25 06:00 MHDA- 2015/11/06 06:00 CRDT- 2014/11/25 06:00 PHST- 2014/09/30 00:00 [received] PHST- 2014/11/01 00:00 [accepted] PHST- 2014/11/25 06:00 [entrez] PHST- 2014/11/25 06:00 [pubmed] PHST- 2015/11/06 06:00 [medline] AID - 10.1002/ajpa.22668 [doi] PST - ppublish SO - Am J Phys Anthropol. 2015 Mar;156(3):434-48. doi: 10.1002/ajpa.22668. Epub 2014 Nov 24. PMID- 25413709 OWN - NLM STAT- MEDLINE DCOM- 20150930 LR - 20150218 IS - 1521-1878 (Electronic) IS - 0265-9247 (Linking) VI - 37 IP - 3 DP - 2015 Mar TI - The future of ancient DNA: Technical advances and conceptual shifts. PG - 284-93 LID - 10.1002/bies.201400160 [doi] AB - Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics. CI - © 2015 WILEY Periodicals, Inc. FAU - Hofreiter, Michael AU - Hofreiter M AD - Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Department of Biology, University of York, York, UK. FAU - Paijmans, Johanna L A AU - Paijmans JL FAU - Goodchild, Helen AU - Goodchild H FAU - Speller, Camilla F AU - Speller CF FAU - Barlow, Axel AU - Barlow A FAU - Fortes, Gloria G AU - Fortes GG FAU - Thomas, Jessica A AU - Thomas JA FAU - Ludwig, Arne AU - Ludwig A FAU - Collins, Matthew J AU - Collins MJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20141121 PL - United States TA - Bioessays JT - BioEssays : news and reviews in molecular, cellular and developmental biology JID - 8510851 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*genetics/isolation & purification MH - DNA Damage MH - Genome MH - *High-Throughput Nucleotide Sequencing MH - Humans MH - Multilocus Sequence Typing MH - Temperature OTO - NOTNLM OT - ancient DNA OT - hybridisation capture OT - multi-locus data OT - next generation sequencing (NGS) OT - palaeogenomics OT - population genomics EDAT- 2014/11/22 06:00 MHDA- 2015/10/01 06:00 CRDT- 2014/11/22 06:00 PHST- 2014/11/22 06:00 [entrez] PHST- 2014/11/22 06:00 [pubmed] PHST- 2015/10/01 06:00 [medline] AID - 10.1002/bies.201400160 [doi] PST - ppublish SO - Bioessays. 2015 Mar;37(3):284-93. doi: 10.1002/bies.201400160. Epub 2014 Nov 21. PMID- 25700511 OWN - NLM STAT- MEDLINE DCOM- 20150313 LR - 20181202 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 347 IP - 6224 DP - 2015 Feb 20 TI - Anthropology. Response to Comment on "Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans". PG - 835 LID - 10.1126/science.1261188 [doi] AB - Prüfer and Meyer raise concerns over the mitochondrial DNA (mtDNA) results we reported for the Hoyo Negro individual, citing failure of a portion of these data to conform to their expectations of ancient DNA (aDNA). Because damage patterns in aDNA vary, outright rejection of our findings on this basis is unwarranted, especially in light of our other observations. CI - Copyright © 2015, American Association for the Advancement of Science. FAU - Kemp, Brian M AU - Kemp BM AD - Department of Anthropology and School of Biological Sciences, Washington State University, Pullman, WA 99164, USA. paleosci@gmail.com bmkemp@wsu.edu. FAU - Lindo, John AU - Lindo J AD - Department of Anthropology, University of Illinois, Urbana, IL 61801, USA. FAU - Bolnick, Deborah A AU - Bolnick DA AD - Department of Anthropology and Population Research Center, University of Texas at Austin, Austin, TX 78712, USA. FAU - Malhi, Ripan S AU - Malhi RS AD - Department of Anthropology, University of Illinois, Urbana, IL 61801, USA. Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA. FAU - Chatters, James C AU - Chatters JC AD - Applied Paleoscience and DirectAMS, 10322 Northeast 190th Street, Bothell, WA 98011, USA. paleosci@gmail.com bmkemp@wsu.edu. LA - eng PT - Comment PT - Journal Article PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 SB - IM CON - Science. 2014 May 16;344(6185):750-4. doi: 10.1126/science.1252619. PMID: 24833392 CON - Science. 2015 Feb 20;347(6224):835. doi: 10.1126/science.1260617. PMID: 25700510 MH - *Biological Evolution MH - Humans MH - Indians, North American/*genetics MH - *Skeleton EDAT- 2015/02/24 06:00 MHDA- 2015/03/17 06:00 CRDT- 2015/02/21 06:00 PHST- 2015/02/21 06:00 [entrez] PHST- 2015/02/24 06:00 [pubmed] PHST- 2015/03/17 06:00 [medline] AID - 347/6224/835-b [pii] AID - 10.1126/science.1261188 [doi] PST - ppublish SO - Science. 2015 Feb 20;347(6224):835. doi: 10.1126/science.1261188. PMID- 25700495 OWN - NLM STAT- MEDLINE DCOM- 20150313 LR - 20150221 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 347 IP - 6224 DP - 2015 Feb 20 TI - Ancient DNA. Indo-European languages tied to herders. PG - 814-5 LID - 10.1126/science.347.6224.814 [doi] FAU - Balter, Michael AU - Balter M FAU - Gibbons, Ann AU - Gibbons A LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 9007-49-2 (DNA) SB - IM MH - DNA/genetics/*history MH - DNA Fingerprinting/methods MH - Europe MH - Genome, Human/*genetics MH - Grassland MH - History, Ancient MH - *Human Migration MH - Humans MH - India MH - Language/*history MH - Skeleton EDAT- 2015/02/24 06:00 MHDA- 2015/03/17 06:00 CRDT- 2015/02/21 06:00 PHST- 2015/02/21 06:00 [entrez] PHST- 2015/02/24 06:00 [pubmed] PHST- 2015/03/17 06:00 [medline] AID - 347/6224/814 [pii] AID - 10.1126/science.347.6224.814 [doi] PST - ppublish SO - Science. 2015 Feb 20;347(6224):814-5. doi: 10.1126/science.347.6224.814. PMID- 25649153 OWN - NLM STAT- MEDLINE DCOM- 20160107 LR - 20220311 IS - 1756-3305 (Electronic) IS - 1756-3305 (Linking) VI - 8 DP - 2015 Feb 4 TI - Leishmania tarentolae molecular signatures in a 300 hundred-years-old human Brazilian mummy. PG - 72 LID - 10.1186/s13071-015-0666-z [doi] LID - 72 AB - BACKGROUND: L. tarentolae, the lizard-infecting species of Old World geckos, has been classified as non-pathogenic to man. While it has been demonstrated that L. tarentolae is capable of infecting human phagocytic cells and to differentiate into amastigote-like forms, there is no clear evidence for its efficient replication within macrophages. Here we provide first evidence for L. tarentolae ancient DNA sequences from bone marrow and intestines of a 300yo adult male. METHODS: We identified molecular signatures of Leishmania tarentolae, the lizard-infecting species of Old World geckos, in hard and soft tissue biopsies from a Brazilian mummy (A74) uncovered in Itacambira (Brazil) and dating to the Colonial Period (end of 18th/beginning of the 19th century). RESULTS: Our results imply that efficient replication of the parasite occurred within human macrophage and to lead to a systemic spread and visceralization in this individual. The ancient sequences show a 100% similarity with those of isolated L. tarentolae parasites grown on artificial nutrient media and a 99% similarity with two modern sequences isolated from reptiles. CONCLUSIONS: De facto, our findings re-open the debate about the potential survival of ancient L. tarentolae strain within human macrophage and its ability to spread systemically. They also raise ecological issues since it is unknown whether this parasite circulates in the reptilian reservoir in modern day Brazil or not. Investigations on fossil fauna and arthropods are needed to shed light on the interactions between saurian Leishmania and lizards in Brazil's remote and recent past. FAU - Novo, Shênia P C AU - Novo SP AD - Departamento de Endemias Samuel Pessoa, Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Fiocruz, rua Leopoldo Bulhões, 1480, Térreo, Manguinhos, 21041-210, Rio de Janeiro, Brasil. shenia@ensp.fiocruz.br. FAU - Leles, Daniela AU - Leles D AD - Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Laboratório de Biologia Molecular de Parasitos, Rua Professor Hernani Melo 101, São domingos, Niterói, Rio de Janeiro, 24210-130, Brazil. dleles@id.uff.br. FAU - Bianucci, Raffaella AU - Bianucci R AD - Department of Public Health and Paediatric Sciences, Laboratory of Physical Anthropology, University of Turin, Corso Galileo Galilei, 22, 10126, Turin, Italy. raffaella.bianucci@unito.it. AD - Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316, Oslo, Norway. raffaella.bianucci@unito.it. AD - Anthropologie bioculturelle, Droit, Ethique et Santé, Aix-Marseille Université, 15, boulevard Pierre Dramard, Faculté de Médecine-Nord, Cedex 15, 13344, Marseille, France. raffaella.bianucci@unito.it. FAU - Araujo, Adauto AU - Araujo A AD - Departamento de Endemias Samuel Pessoa, Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Fiocruz, rua Leopoldo Bulhões, 1480, Térreo, Manguinhos, 21041-210, Rio de Janeiro, Brasil. adauto@ensp.fiocruz.br. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150204 PL - England TA - Parasit Vectors JT - Parasites & vectors JID - 101462774 RN - 0 (DNA, Protozoan) SB - IM MH - Bone Marrow/parasitology MH - Brazil MH - DNA, Protozoan/genetics MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Leishmania/classification/genetics/*isolation & purification MH - Leishmaniasis/history/*parasitology MH - Male MH - Mummies/history/*parasitology PMC - PMC4328655 EDAT- 2015/02/05 06:00 MHDA- 2016/01/08 06:00 PMCR- 2015/02/04 CRDT- 2015/02/05 06:00 PHST- 2014/07/23 00:00 [received] PHST- 2015/01/16 00:00 [accepted] PHST- 2015/02/05 06:00 [entrez] PHST- 2015/02/05 06:00 [pubmed] PHST- 2016/01/08 06:00 [medline] PHST- 2015/02/04 00:00 [pmc-release] AID - s13071-015-0666-z [pii] AID - 666 [pii] AID - 10.1186/s13071-015-0666-z [doi] PST - epublish SO - Parasit Vectors. 2015 Feb 4;8:72. doi: 10.1186/s13071-015-0666-z. PMID- 25640964 OWN - NLM STAT- MEDLINE DCOM- 20150824 LR - 20160418 IS - 1365-294X (Electronic) IS - 0962-1083 (Linking) VI - 24 IP - 4 DP - 2015 Feb TI - Lack of support for the time-dependent molecular evolution hypothesis. PG - 702-9 LID - 10.1111/mec.13070 [doi] AB - There is increasing momentum surrounding the hypothesis that rates of molecular evolution between individuals within contemporary populations are high, and that these rates decrease as a function of time, perhaps over several millions of years, before reaching stationarity. The implications of this are powerful, potentially reshaping our view of how climate history impacts upon both species distribution patterns and the geographic structuring of genetic variation within species. However, our assessment of the hypothesis reveals a lack of theoretical support and empirical evidence for hypothesized magnitudes of time-dependent rates of molecular evolution, with much of the apparent rate changes coming from artefacts and biases inherent in the methods of rate estimation. Our assessment also reveals a problem with how serial sampling is implemented for mutation rate estimation using ancient DNA samples, rendering published estimates unreliable. CI - © 2015 John Wiley & Sons Ltd. FAU - Emerson, Brent C AU - Emerson BC AD - Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain. FAU - Hickerson, Michael J AU - Hickerson MJ LA - eng PT - Journal Article PL - England TA - Mol Ecol JT - Molecular ecology JID - 9214478 SB - IM CIN - Mol Ecol. 2015 Dec;24(24):6007-12. doi: 10.1111/mec.13450. PMID: 26769402 CIN - Mol Ecol. 2015 Dec;24(24):6013-20. doi: 10.1111/mec.13451. PMID: 26769403 MH - Animals MH - *Evolution, Molecular MH - Genetics, Population MH - Humans MH - *Models, Genetic MH - *Mutation Rate MH - Selection, Genetic MH - Sequence Analysis, DNA OTO - NOTNLM OT - Bayesian inference OT - ancestral polymorphism OT - ancient DNA OT - calibration OT - coalescent OT - mutation rate EDAT- 2015/02/03 06:00 MHDA- 2015/08/25 06:00 CRDT- 2015/02/03 06:00 PHST- 2014/08/28 00:00 [received] PHST- 2014/12/17 00:00 [revised] PHST- 2014/12/30 00:00 [accepted] PHST- 2015/02/03 06:00 [entrez] PHST- 2015/02/03 06:00 [pubmed] PHST- 2015/08/25 06:00 [medline] AID - 10.1111/mec.13070 [doi] PST - ppublish SO - Mol Ecol. 2015 Feb;24(4):702-9. doi: 10.1111/mec.13070. PMID- 25619123 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20150131 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - Ancient DNA and human evolution. PG - 1-3 LID - S0047-2484(14)00299-1 [pii] LID - 10.1016/j.jhevol.2014.12.002 [doi] FAU - Perry, George H AU - Perry GH AD - Departments of Anthropology and Biology, Pennsylvania State University, USA. Electronic address: ghp3@psu.edu. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark. Electronic address: lorlando@snm.ku.dk. LA - eng PT - Editorial DEP - 20150122 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Biological Evolution MH - *DNA/analysis/genetics MH - Fossils MH - Hominidae/*genetics MH - Humans MH - *Paleontology EDAT- 2015/01/27 06:00 MHDA- 2015/09/22 06:00 CRDT- 2015/01/27 06:00 PHST- 2015/01/27 06:00 [entrez] PHST- 2015/01/27 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] AID - S0047-2484(14)00299-1 [pii] AID - 10.1016/j.jhevol.2014.12.002 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:1-3. doi: 10.1016/j.jhevol.2014.12.002. Epub 2015 Jan 22. PMID- 25601038 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20150131 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - Ancient human genomics: the methodology behind reconstructing evolutionary pathways. PG - 21-34 LID - S0047-2484(14)00269-3 [pii] LID - 10.1016/j.jhevol.2014.11.003 [doi] AB - High-throughput sequencing (HTS) has radically altered approaches to human evolutionary research. Recent contributions highlight that HTS is able to reach depths of the human lineage previously thought to be impossible. In this paper, we outline the methodological advances afforded by recent developments in DNA recovery, data output, scalability, speed, and resolution of the current sequencing technology. We review and critically evaluate the 'DNA pipeline' for ancient samples: from DNA extraction, to constructing immortalized sequence libraries, to enrichment strategies (e.g., polymerase chain reaction [PCR] and hybridization capture), and finally, to bioinformatic analyses of sequence data. We argue that continued evaluations and improvements to this process are essential to ensure sequence data validity. Also, we highlight the role of contamination and authentication in ancient DNA-HTS, which is particularly relevant to ancient human genomics, since sequencing the genomes of hominins such as Homo erectus and Homo heidelbergensis may soon be within the realm of possibility. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Marciniak, Stephanie AU - Marciniak S AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada. Electronic address: marcis@mcmaster.ca. FAU - Klunk, Jennifer AU - Klunk J AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada. FAU - Devault, Alison AU - Devault A AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; MYcroarray, Ann Arbor, MI, USA. FAU - Enk, Jacob AU - Enk J AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada; MYcroarray, Ann Arbor, MI, USA. FAU - Poinar, Hendrik N AU - Poinar HN AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada. Electronic address: poinarh@mcmaster.ca. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150115 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Anthropology, Physical MH - *Biological Evolution MH - DNA/analysis/genetics MH - *Fossils MH - *Genomics MH - *High-Throughput Nucleotide Sequencing MH - Hominidae/*genetics MH - Humans OTO - NOTNLM OT - Ancient DNA OT - High-throughput sequencing OT - Human evolution EDAT- 2015/01/21 06:00 MHDA- 2015/09/22 06:00 CRDT- 2015/01/21 06:00 PHST- 2014/05/15 00:00 [received] PHST- 2014/09/09 00:00 [revised] PHST- 2014/11/07 00:00 [accepted] PHST- 2015/01/21 06:00 [entrez] PHST- 2015/01/21 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] AID - S0047-2484(14)00269-3 [pii] AID - 10.1016/j.jhevol.2014.11.003 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:21-34. doi: 10.1016/j.jhevol.2014.11.003. Epub 2015 Jan 15. PMID- 25563409 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20250103 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data. PG - 55-63 LID - S0047-2484(14)00264-4 [pii] LID - 10.1016/j.jhevol.2014.10.018 [doi] AB - Nuclear genome sequence data from Neandertals, Denisovans, and archaic anatomically modern humans can be used to complement our understanding of hominin evolutionary biology and ecology through i) direct inference of archaic hominin phenotypes, ii) indirect inference of those phenotypes by identifying the effects of previously-introgressed alleles still present among modern humans, or iii) determining the evolutionary timing of relevant hominin-specific genetic changes. Here we review and reanalyze published Neandertal and Denisovan genome sequence data to illustrate an example of the third approach. Specifically, we infer the timing of five human gene presence/absence changes that may be related to particular hominin-specific dietary changes and discuss these results in the context of our broader reconstructions of hominin evolutionary ecology. We show that pseudogenizing (gene loss) mutations in the TAS2R62 and TAS2R64 bitter taste receptor genes and the MYH16 masticatory myosin gene occurred after the hominin-chimpanzee divergence but before the divergence of the human and Neandertal/Denisovan lineages. The absence of a functional MYH16 protein may explain our relatively reduced jaw muscles; this gene loss may have followed the adoption of cooking behavior. In contrast, salivary amylase gene (AMY1) duplications were not observed in the Neandertal and Denisovan genomes, suggesting a relatively recent origin for the AMY1 copy number gains that are observed in modern humans. Thus, if earlier hominins were consuming large quantities of starch-rich underground storage organs, as previously hypothesized, then they were likely doing so without the digestive benefits of increased salivary amylase production. Our most surprising result was the observation of a heterozygous mutation in the first codon of the TAS2R38 bitter taste receptor gene in the Neandertal individual, which likely would have resulted in a non-functional protein and inter-individual PTC (phenylthiocarbamide) taste sensitivity variation, as also observed in both humans and chimpanzees. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Perry, George H AU - Perry GH AD - Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address: ghp3@psu.edu. FAU - Kistler, Logan AU - Kistler L AD - Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA. FAU - Kelaita, Mary A AU - Kelaita MA AD - Department of Anthropology, University of Texas at San Antonio, San Antonio, TX 78249, USA. FAU - Sams, Aaron J AU - Sams AJ AD - Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20150103 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 0 (Receptors, G-Protein-Coupled) RN - 0 (Taste Receptors, Type 2) RN - 9007-49-2 (DNA) RN - EC 3.6.4.1 (Myosin Heavy Chains) SB - IM MH - Animals MH - Base Sequence MH - *Biological Evolution MH - DNA/analysis/genetics MH - DNA Copy Number Variations MH - Feeding Behavior/*physiology MH - Fossils MH - Genetic Variation MH - Genomics MH - Hominidae/*genetics/*physiology MH - Humans MH - Molecular Sequence Data MH - Myosin Heavy Chains/genetics MH - Neanderthals MH - Paleontology MH - Phenotype MH - Receptors, G-Protein-Coupled/genetics MH - Sequence Alignment MH - Sequence Analysis, DNA MH - Taste Receptors, Type 2 OTO - NOTNLM OT - Copy number variation OT - Gene content variation OT - Hominin evolutionary ecology OT - Paleogenomics EDAT- 2015/01/08 06:00 MHDA- 2015/09/22 06:00 CRDT- 2015/01/08 06:00 PHST- 2014/02/21 00:00 [received] PHST- 2014/09/21 00:00 [revised] PHST- 2014/10/28 00:00 [accepted] PHST- 2015/01/08 06:00 [entrez] PHST- 2015/01/08 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] AID - S0047-2484(14)00264-4 [pii] AID - 10.1016/j.jhevol.2014.10.018 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:55-63. doi: 10.1016/j.jhevol.2014.10.018. Epub 2015 Jan 3. PMID- 25559298 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20240610 IS - 1095-8606 (Electronic) IS - 0047-2484 (Print) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - Ancient human microbiomes. PG - 125-36 LID - S0047-2484(14)00262-0 [pii] LID - 10.1016/j.jhevol.2014.10.016 [doi] AB - Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Warinner, Christina AU - Warinner C AD - Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA. FAU - Speller, Camilla AU - Speller C AD - Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK. FAU - Collins, Matthew J AU - Collins MJ AD - Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK. FAU - Lewis, Cecil M Jr AU - Lewis CM Jr AD - Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA. Electronic address: cmlewis@ou.edu. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - R01 GM089886/GM/NIGMS NIH HHS/United States GR - R01 GM089886)/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20150103 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 SB - IM MH - Dental Calculus/microbiology MH - Diet MH - Feces/microbiology MH - Health/history MH - High-Throughput Nucleotide Sequencing MH - History, Ancient MH - Humans MH - Metagenomics MH - *Microbiota MH - *Paleontology PMC - PMC4312737 MID - NIHMS652822 OTO - NOTNLM OT - Ancient DNA OT - Coprolite OT - Dental calculus OT - Feces OT - Metagenomics OT - Metaproteomics EDAT- 2015/01/07 06:00 MHDA- 2015/09/22 06:00 PMCR- 2016/02/01 CRDT- 2015/01/07 06:00 PHST- 2014/03/04 00:00 [received] PHST- 2014/07/06 00:00 [revised] PHST- 2014/10/29 00:00 [accepted] PHST- 2015/01/07 06:00 [entrez] PHST- 2015/01/07 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] PHST- 2016/02/01 00:00 [pmc-release] AID - S0047-2484(14)00262-0 [pii] AID - 10.1016/j.jhevol.2014.10.016 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:125-36. doi: 10.1016/j.jhevol.2014.10.016. Epub 2015 Jan 3. PMID- 25556846 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20150131 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - Ancient DNA and the human settlement of the Pacific: a review. PG - 93-104 LID - S0047-2484(14)00263-2 [pii] LID - 10.1016/j.jhevol.2014.10.017 [doi] AB - The Pacific region provides unique opportunities to study human evolution including through analyses of ancient DNA. While some of the earliest studies involving ancient DNA from skeletal remains focused on Pacific samples, in the following 25 years, several factors meant that little aDNA research, particularly research focused on human populations, has emerged. This paper briefly presents the genetic evidence for population origins, reviews what ancient DNA work has been undertaken to address human history and evolution in the Pacific region, and argues that the future is bright but research requires a collaborative approach between academic disciplines but also with local communities. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Matisoo-Smith, Elizabeth AU - Matisoo-Smith E AD - Department of Anatomy and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, PO Box 913, Dunedin 9054, New Zealand. Electronic address: matisoo-smith@otago.ac.nz. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20150101 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 9007-49-2 (DNA) SB - IM MH - Archaeology MH - DNA/analysis/*genetics MH - *Evolution, Molecular MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Polynesia OTO - NOTNLM OT - Commensal models OT - Human migration OT - Lapita OT - Polynesia OT - Sahul EDAT- 2015/01/06 06:00 MHDA- 2015/09/22 06:00 CRDT- 2015/01/06 06:00 PHST- 2014/02/25 00:00 [received] PHST- 2014/09/01 00:00 [revised] PHST- 2014/10/28 00:00 [accepted] PHST- 2015/01/06 06:00 [entrez] PHST- 2015/01/06 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] AID - S0047-2484(14)00263-2 [pii] AID - 10.1016/j.jhevol.2014.10.017 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:93-104. doi: 10.1016/j.jhevol.2014.10.017. Epub 2015 Jan 1. PMID- 25532803 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20150131 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - DNA analysis of ancient dogs of the Americas: identifying possible founding haplotypes and reconstructing population histories. PG - 105-18 LID - S0047-2484(14)00257-7 [pii] LID - 10.1016/j.jhevol.2014.10.012 [doi] AB - As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) of mitochondrial DNA (mtDNA) to indicate that prior to European contact the dogs of Native Americans originated in Eurasia. In this study, we summarize past DNA studies of both humans and dogs to discuss their population histories in the Americas. We then sequenced a portion of the mtDNA HVR of 42 pre-Columbian dogs from three sites located in Illinois, coastal British Columbia, and Colorado, and identify four novel dog mtDNA haplotypes. Next, we analyzed a dataset comprised of all available ancient dog sequences from the Americas to infer the pre-Columbian population history of dogs in the Americas. Interestingly, we found low levels of genetic diversity for some populations consistent with the possibility of deliberate breeding practices. Furthermore, we identified multiple putative founding haplotypes in addition to dog haplotypes that closely resemble those of wolves, suggesting admixture with North American wolves or perhaps a second domestication of canids in the Americas. Notably, initial effective population size estimates suggest at least 1000 female dogs likely existed in the Americas at the time of the first known canid burial, and that population size increased gradually over time before stabilizing roughly 1200 years before present. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Witt, Kelsey E AU - Witt KE AD - School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA. FAU - Judd, Kathleen AU - Judd K AD - Kemp Lab of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, WA 99164, USA. FAU - Kitchen, Andrew AU - Kitchen A AD - Department of Anthropology, University of Iowa, Iowa City, IA 52242, USA. FAU - Grier, Colin AU - Grier C AD - Department of Anthropology, Washington State University, Pullman, WA 99164, USA. FAU - Kohler, Timothy A AU - Kohler TA AD - Department of Anthropology, Washington State University, Pullman, WA 99164, USA; Santa Fe Institute, Santa Fe, NM 87501, USA; Crow Canyon Archaeological Center, 23390 Road K, Cortez, CO 81321-9408, USA. FAU - Ortman, Scott G AU - Ortman SG AD - Department of Anthropology, University of Colorado, Boulder, CO 80309, USA. FAU - Kemp, Brian M AU - Kemp BM AD - Department of Anthropology, Washington State University, Pullman, WA 99164, USA; School of Biological Sciences, Washington State University, Pullman, WA 99164, USA. FAU - Malhi, Ripan S AU - Malhi RS AD - School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology and Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA. Electronic address: malhi@illinois.edu. LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20141218 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 0 (DNA, Mitochondrial) SB - IM MH - Americas MH - Animals MH - DNA, Mitochondrial/*genetics MH - *Databases, Genetic MH - Dogs/*genetics MH - *Evolution, Molecular MH - Female MH - Genetic Variation/genetics MH - Haplotypes/*genetics MH - Humans OTO - NOTNLM OT - Ancient DNA OT - Canis lupus familiaris OT - Domestication OT - Mitochondrial DNA OT - New World OT - Population genetics EDAT- 2014/12/24 06:00 MHDA- 2015/09/22 06:00 CRDT- 2014/12/24 06:00 PHST- 2014/01/22 00:00 [received] PHST- 2014/06/16 00:00 [revised] PHST- 2014/10/22 00:00 [accepted] PHST- 2014/12/24 06:00 [entrez] PHST- 2014/12/24 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] AID - S0047-2484(14)00257-7 [pii] AID - 10.1016/j.jhevol.2014.10.012 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:105-18. doi: 10.1016/j.jhevol.2014.10.012. Epub 2014 Dec 18. PMID- 25532802 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20150131 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - Ancient pathogen genomics: insights into timing and adaptation. PG - 137-49 LID - S0047-2484(14)00268-1 [pii] LID - 10.1016/j.jhevol.2014.11.002 [doi] AB - Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Harkins, Kelly M AU - Harkins KM AD - Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, United States. Electronic address: kmharkin@ucsc.edu. FAU - Stone, Anne C AU - Stone AC AD - Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, United States. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20141218 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Archaeology MH - Bacteria/*genetics/pathogenicity MH - Bacterial Infections/history/microbiology MH - *Biological Evolution MH - DNA/genetics MH - *Genomics MH - History, Ancient MH - Humans MH - Parasites/*genetics/pathogenicity MH - Parasitic Diseases/history/parasitology OTO - NOTNLM OT - Ancient DNA OT - Human disease OT - Pathogen evolution EDAT- 2014/12/24 06:00 MHDA- 2015/09/22 06:00 CRDT- 2014/12/24 06:00 PHST- 2014/02/13 00:00 [received] PHST- 2014/09/08 00:00 [revised] PHST- 2014/11/05 00:00 [accepted] PHST- 2014/12/24 06:00 [entrez] PHST- 2014/12/24 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] AID - S0047-2484(14)00268-1 [pii] AID - 10.1016/j.jhevol.2014.11.002 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:137-49. doi: 10.1016/j.jhevol.2014.11.002. Epub 2014 Dec 18. PMID- 25532800 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20150131 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - Major transitions in human evolution revisited: a tribute to ancient DNA. PG - 4-20 LID - S0047-2484(14)00251-6 [pii] LID - 10.1016/j.jhevol.2014.06.015 [doi] AB - The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Ermini, Luca AU - Ermini L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark. FAU - Der Sarkissian, Clio AU - Der Sarkissian C AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark. Electronic address: orlando.ludovic@gmail.com. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141219 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Biological Evolution MH - *DNA/analysis/genetics MH - Fossils MH - Genome, Human/genetics MH - *Genomics MH - Hominidae/*genetics MH - Humans MH - Paleontology/*methods OTO - NOTNLM OT - Admixture OT - Archaic hominins OT - Epidemics OT - Epigenomics OT - Metagenomics OT - Migration OT - Neolithic transition OT - Paleodemography OT - Paleogenomics OT - Selection EDAT- 2014/12/24 06:00 MHDA- 2015/09/22 06:00 CRDT- 2014/12/24 06:00 PHST- 2014/01/14 00:00 [received] PHST- 2014/06/06 00:00 [revised] PHST- 2014/06/19 00:00 [accepted] PHST- 2014/12/24 06:00 [entrez] PHST- 2014/12/24 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] AID - S0047-2484(14)00251-6 [pii] AID - 10.1016/j.jhevol.2014.06.015 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:4-20. doi: 10.1016/j.jhevol.2014.06.015. Epub 2014 Dec 19. PMID- 25476244 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20150131 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - Ancient DNA analysis of dental calculus. PG - 119-24 LID - S0047-2484(14)00254-1 [pii] LID - 10.1016/j.jhevol.2014.06.018 [doi] AB - Dental calculus (calcified tartar or plaque) is today widespread on modern human teeth around the world. A combination of soft starchy foods, changing acidity of the oral environment, genetic pre-disposition, and the absence of dental hygiene all lead to the build-up of microorganisms and food debris on the tooth crown, which eventually calcifies through a complex process of mineralisation. Millions of oral microbes are trapped and preserved within this mineralised matrix, including pathogens associated with the oral cavity and airways, masticated food debris, and other types of extraneous particles that enter the mouth. As a result, archaeologists and anthropologists are increasingly using ancient human dental calculus to explore broad aspects of past human diet and health. Most recently, high-throughput DNA sequencing of ancient dental calculus has provided valuable insights into the evolution of the oral microbiome and shed new light on the impacts of some of the major biocultural transitions on human health throughout history and prehistory. Here, we provide a brief historical overview of archaeological dental calculus research, and discuss the current approaches to ancient DNA sampling and sequencing. Novel applications of ancient DNA from dental calculus are discussed, highlighting the considerable scope of this new research field for evolutionary biology and modern medicine. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Weyrich, Laura S AU - Weyrich LS AD - The Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, Australia. FAU - Dobney, Keith AU - Dobney K AD - Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK. FAU - Cooper, Alan AU - Cooper A AD - The Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, Australia. Electronic address: Alan.cooper@adelaide.edu.au. LA - eng PT - Historical Article PT - Journal Article DEP - 20141201 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 0 (DNA, Bacterial) SB - IM MH - Archaeology MH - DNA, Bacterial/*genetics MH - Dental Calculus/history/*microbiology MH - Diet MH - Evolution, Molecular MH - History, Ancient MH - Humans MH - Microbiota/genetics MH - Oral Health/history OTO - NOTNLM OT - Ancient bacteria OT - Dietary analysis OT - Disease evolution OT - Microbiome EDAT- 2014/12/06 06:00 MHDA- 2015/09/22 06:00 CRDT- 2014/12/06 06:00 PHST- 2014/01/16 00:00 [received] PHST- 2014/05/19 00:00 [revised] PHST- 2014/06/19 00:00 [accepted] PHST- 2014/12/06 06:00 [entrez] PHST- 2014/12/06 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] AID - S0047-2484(14)00254-1 [pii] AID - 10.1016/j.jhevol.2014.06.018 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:119-24. doi: 10.1016/j.jhevol.2014.06.018. Epub 2014 Dec 1. PMID- 25467114 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20150131 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - Human paleogenetics of Europe--the known knowns and the known unknowns. PG - 73-92 LID - S0047-2484(14)00253-X [pii] LID - 10.1016/j.jhevol.2014.06.017 [doi] AB - The number of ancient human DNA studies has drastically increased in recent years. This results in a substantial record of mitochondrial sequences available from many prehistoric sites across Western Eurasia, but also growing Y-chromosome and autosomal sequence data. We review the current state of research with specific emphasis on the Holocene population events that likely have shaped the present-day genetic variation in Europe. We reconcile observations from the genetic data with hypotheses about the peopling and settlement history from anthropology and archaeology for various key regions, and also discuss the data in light of evidence from related disciplines, such as modern human genetics, climatology and linguistics. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Brandt, Guido AU - Brandt G AD - Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany. FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A AD - Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany; Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1014 Budapest, Hungary. FAU - Roth, Christina AU - Roth C AD - Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany. FAU - Alt, Kurt Werner AU - Alt KW AD - State Office for Heritage Management and Archaeology Saxony-Anhalt and State Heritage Museum, Richard-Wagner-Straße 9, D-06114 Halle, Germany; Institute for Prehistory and Archaeological Science, Basel University, Petersplatz 1, 4003 Basel, Switzerland; Danube Private University, Faculty of Medicine and Dentistry, Doktor-Karl-Dorrek-Straße 23, 3500 Krems an der Donau, Austria. FAU - Haak, Wolfgang AU - Haak W AD - Australian Centre for Ancient DNA, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia. Electronic address: wolfgang.haak@adelaide.edu.au. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141113 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - *Archaeology MH - Chromosomes, Human/genetics MH - DNA/*genetics MH - DNA, Mitochondrial/genetics MH - Europe MH - Genetic Variation/*genetics MH - Humans MH - *Paleontology OTO - NOTNLM OT - Ancient DNA OT - Archaeology OT - Mesolithic OT - Neolithic OT - Paleolithic EDAT- 2014/12/04 06:00 MHDA- 2015/09/22 06:00 CRDT- 2014/12/04 06:00 PHST- 2014/02/04 00:00 [received] PHST- 2014/03/25 00:00 [revised] PHST- 2014/06/19 00:00 [accepted] PHST- 2014/12/04 06:00 [entrez] PHST- 2014/12/04 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] AID - S0047-2484(14)00253-X [pii] AID - 10.1016/j.jhevol.2014.06.017 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:73-92. doi: 10.1016/j.jhevol.2014.06.017. Epub 2014 Nov 13. PMID- 25467111 OWN - NLM STAT- MEDLINE DCOM- 20150921 LR - 20181113 IS - 1095-8606 (Electronic) IS - 0047-2484 (Print) IS - 0047-2484 (Linking) VI - 79 DP - 2015 Feb TI - The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection. PG - 64-72 LID - S0047-2484(14)00250-4 [pii] LID - 10.1016/j.jhevol.2014.10.009 [doi] AB - The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Sams, Aaron J AU - Sams AJ AD - Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA. Electronic address: as2847@cornell.edu. FAU - Hawks, John AU - Hawks J AD - Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA. FAU - Keinan, Alon AU - Keinan A AD - Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA. LA - eng GR - R01 GM108805/GM/NIGMS NIH HHS/United States GR - R01GM108805/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20141115 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Anthropology, Physical MH - DNA/analysis/*genetics MH - Europe MH - *Evolution, Molecular MH - Genetics, Population/*methods MH - Humans MH - Male MH - Neanderthals/*genetics MH - Selection, Genetic PMC - PMC4381881 MID - NIHMS672641 OTO - NOTNLM OT - Europe OT - Neandertals OT - Ötzi EDAT- 2014/12/04 06:00 MHDA- 2015/09/22 06:00 PMCR- 2015/04/01 CRDT- 2014/12/04 06:00 PHST- 2014/01/14 00:00 [received] PHST- 2014/09/07 00:00 [revised] PHST- 2014/10/22 00:00 [accepted] PHST- 2014/12/04 06:00 [entrez] PHST- 2014/12/04 06:00 [pubmed] PHST- 2015/09/22 06:00 [medline] PHST- 2015/04/01 00:00 [pmc-release] AID - S0047-2484(14)00250-4 [pii] AID - 10.1016/j.jhevol.2014.10.009 [doi] PST - ppublish SO - J Hum Evol. 2015 Feb;79:64-72. doi: 10.1016/j.jhevol.2014.10.009. Epub 2014 Nov 15. PMID- 25357228 OWN - NLM STAT- MEDLINE DCOM- 20150507 LR - 20150224 IS - 1937-2345 (Electronic) IS - 0022-3395 (Linking) VI - 101 IP - 1 DP - 2015 Feb TI - DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement. PG - 57-63 LID - 10.1645/14-650.1 [doi] AB - Ancient parasite eggs were recovered from environmental samples collected at a Viking-age settlement in Viborg, Denmark, dated 1018-1030 A.D. Morphological examination identified Ascaris sp., Trichuris sp., and Fasciola sp. eggs, but size and shape did not allow species identification. By carefully selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura , using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology. The identification of T. trichiura eggs indicates that human fecal material is present and, hence, that the Ascaris sp. haplotype 07 was most likely a human variant in Viking-age Denmark. The location of the F. hepatica finding suggests that sheep or cattle are the most likely hosts. Further, we sequenced the Ascaris sp. 18S rRNA gene in recent isolates from humans and pigs of global distribution and show that this is not a suited marker for species-specific identification. Finally, we discuss ancient parasitism in Denmark and the implementation of aDNA analysis methods in paleoparasitological studies. We argue that when employing species-specific identification, soil samples offer excellent opportunities for studies of human parasite infections and of human and animal interactions of the past. FAU - Søe, Martin Jensen AU - Søe MJ AD - Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 2-70, 3rd Floor, DK-1871 Frederiksberg C, Denmark. FAU - Nejsum, Peter AU - Nejsum P FAU - Fredensborg, Brian Lund AU - Fredensborg BL FAU - Kapel, Christian Moliin Outzen AU - Kapel CM LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141030 PL - United States TA - J Parasitol JT - The Journal of parasitology JID - 7803124 SB - IM MH - Animals MH - Ascariasis/*history MH - Ascaris/classification/genetics/isolation & purification MH - Cattle MH - Cattle Diseases/*history/parasitology MH - DNA Fingerprinting MH - Denmark MH - Fasciola hepatica/classification/genetics/isolation & purification MH - Fascioliasis/*history MH - History, Medieval MH - Humans MH - Molecular Sequence Data MH - Ovum/classification MH - Paleopathology MH - Sheep MH - Sheep Diseases/*history/parasitology MH - Trichuriasis/*history MH - Trichuris/classification/genetics/isolation & purification EDAT- 2014/10/31 06:00 MHDA- 2015/05/08 06:00 CRDT- 2014/10/31 06:00 PHST- 2014/10/31 06:00 [entrez] PHST- 2014/10/31 06:00 [pubmed] PHST- 2015/05/08 06:00 [medline] AID - 10.1645/14-650.1 [doi] PST - ppublish SO - J Parasitol. 2015 Feb;101(1):57-63. doi: 10.1645/14-650.1. Epub 2014 Oct 30. PMID- 25487342 OWN - NLM STAT- MEDLINE DCOM- 20150810 LR - 20190130 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 370 IP - 1660 DP - 2015 Jan 19 TI - Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. PG - 20130624 LID - 10.1098/rstb.2013.0624 [doi] LID - 20130624 AB - The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 ancient human samples. CI - © 2014 The Author(s) Published by the Royal Society. All rights reserved. FAU - Rohland, Nadin AU - Rohland N AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA nrohland@genetics.med.harvard.edu. FAU - Harney, Eadaoin AU - Harney E AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Howard Hughes Medical Institute, Boston, MA 02115, USA. FAU - Mallick, Swapan AU - Mallick S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Howard Hughes Medical Institute, Boston, MA 02115, USA. FAU - Nordenfelt, Susanne AU - Nordenfelt S AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Howard Hughes Medical Institute, Boston, MA 02115, USA. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 9007-49-2 (DNA) RN - EC 3.2.2.- (Uracil-DNA Glycosidase) SB - IM MH - Base Sequence MH - DNA/*genetics/history MH - DNA Barcoding, Taxonomic/methods MH - *Fossils MH - *Gene Library MH - Genetic Testing/*methods MH - Genetics, Population/methods MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - Sequence Analysis, DNA/*methods MH - Uracil-DNA Glycosidase/*chemistry PMC - PMC4275898 OTO - NOTNLM OT - ancient DNA OT - authenticity OT - barcodes OT - flexibility OT - library preparation OT - target capture EDAT- 2014/12/10 06:00 MHDA- 2015/08/11 06:00 PMCR- 2016/01/19 CRDT- 2014/12/10 06:00 PHST- 2014/12/10 06:00 [entrez] PHST- 2014/12/10 06:00 [pubmed] PHST- 2015/08/11 06:00 [medline] PHST- 2016/01/19 00:00 [pmc-release] AID - rstb.2013.0624 [pii] AID - rstb20130624 [pii] AID - 10.1098/rstb.2013.0624 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130624. doi: 10.1098/rstb.2013.0624. PMID- 25487341 OWN - NLM STAT- MEDLINE DCOM- 20150810 LR - 20240326 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 370 IP - 1660 DP - 2015 Jan 19 TI - Screening ancient tuberculosis with qPCR: challenges and opportunities. PG - 20130622 LID - 10.1098/rstb.2013.0622 [doi] LID - 20130622 AB - The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the Mycobacterium tuberculosis complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies. CI - © 2014 The Author(s) Published by the Royal Society. All rights reserved. FAU - Harkins, Kelly M AU - Harkins KM AUID- ORCID: 0000-0002-0756-4250 AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. FAU - Buikstra, Jane E AU - Buikstra JE AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. FAU - Campbell, Tessa AU - Campbell T AD - Department of Archaeology, University of Cape Town, Cape Town, South Africa. FAU - Bos, Kirsten I AU - Bos KI AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Johnson, Eric D AU - Johnson ED AD - School of Life Sciences, Arizona State University, Tempe, AZ, USA. FAU - Krause, Johannes AU - Krause J AD - Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. FAU - Stone, Anne C AU - Stone AC AD - School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA acstone@asu.edu. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA Primers) RN - 0 (DNA, Bacterial) SB - IM MH - Bone and Bones/*chemistry MH - DNA Primers/genetics MH - DNA, Bacterial/*genetics/history MH - *Fossils MH - History, Ancient MH - Humans MH - Mycobacterium tuberculosis/*genetics MH - Paleopathology/*methods/trends MH - Real-Time Polymerase Chain Reaction/*methods PMC - PMC4275897 OTO - NOTNLM OT - ancient DNA OT - bioarchaeology OT - qPCR OT - tuberculosis EDAT- 2014/12/10 06:00 MHDA- 2015/08/11 06:00 PMCR- 2016/01/19 CRDT- 2014/12/10 06:00 PHST- 2014/12/10 06:00 [entrez] PHST- 2014/12/10 06:00 [pubmed] PHST- 2015/08/11 06:00 [medline] PHST- 2016/01/19 00:00 [pmc-release] AID - rstb.2013.0622 [pii] AID - rstb20130622 [pii] AID - 10.1098/rstb.2013.0622 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130622. doi: 10.1098/rstb.2013.0622. PMID- 25487339 OWN - NLM STAT- MEDLINE DCOM- 20150810 LR - 20211203 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 370 IP - 1660 DP - 2015 Jan 19 TI - Where are the Caribs? Ancient DNA from ceramic period human remains in the Lesser Antilles. PG - 20130388 LID - 10.1098/rstb.2013.0388 [doi] LID - 20130388 AB - The identity and history of the indigenous groups who occupied the Lesser Antilles during the ceramic periods remain highly controversial. Although recent archaeological evidence has challenged hypotheses concerning the organization of human groups in this region, more biological data are needed to fully inform the discussion. Our study provides, to our knowledge, the first palaeogenetic data for Late Ceramic groups of the Guadeloupe archipelago, yielding crucial information concerning the identities of these groups. Despite the generally poor DNA preservation in the tested remains, we were able to retrieve Hypervariable Region 1 sequences from 11 individuals and mitochondrial single-nucleotide polymorphisms from 13 individuals. These novel data provide interesting preliminary results in favour of a common origin for all Saladoid Caribbean communities, i.e. the first ceramic groups of the region, as well as for a local continuity between the Saladoid and post-Saladoid groups. A combination of the genetic data obtained and several pieces of cultural evidence allows us to propose that two different groups inhabited the Guadeloupe archipelago during the Late Ceramic period, with the possible occupation of the La Désirade and Marie-Galante islands by groups affiliated with the Taíno communities. The working hypotheses proposed here appear consistent with recent archaeological evidence. CI - © 2014 The Author(s) Published by the Royal Society. All rights reserved. FAU - Mendisco, F AU - Mendisco F AD - Université de Bordeaux, UMR 5199 PACEA, Equipe Anthropologie des Populations Passées et Présentes, Allée Geoffroy ST Hilaire, Pessac Cedex 33615, France fanny.mendisco@gmail.com. FAU - Pemonge, M H AU - Pemonge MH AD - Université de Bordeaux, UMR 5199 PACEA, Equipe Anthropologie des Populations Passées et Présentes, Allée Geoffroy ST Hilaire, Pessac Cedex 33615, France. FAU - Leblay, E AU - Leblay E AD - Université de Bordeaux, UMR 5199 PACEA, Equipe Anthropologie des Populations Passées et Présentes, Allée Geoffroy ST Hilaire, Pessac Cedex 33615, France. FAU - Romon, T AU - Romon T AD - Institut National de Recherches Archéologiques Préventives Guadeloupe, centre de Saint-Claude, rue des Gommiers Blancs Parnasse, Saint-Claude 97120, France. FAU - Richard, G AU - Richard G AD - Conseil regional de la Guadeloupe, Avenue Paul Lacavé, Basse-Terre 97100, France. FAU - Courtaud, P AU - Courtaud P AD - Université de Bordeaux, UMR 5199 PACEA, Equipe Anthropologie des Populations Passées et Présentes, Allée Geoffroy ST Hilaire, Pessac Cedex 33615, France. FAU - Deguilloux, M F AU - Deguilloux MF AD - Université de Bordeaux, UMR 5199 PACEA, Equipe Anthropologie des Populations Passées et Présentes, Allée Geoffroy ST Hilaire, Pessac Cedex 33615, France. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (Complementarity Determining Regions) RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Base Sequence MH - Cloning, Molecular MH - Complementarity Determining Regions/genetics MH - DNA/*genetics/history MH - DNA, Mitochondrial/genetics MH - Ethnicity/*genetics MH - *Fossils MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - Nucleic Acid Amplification Techniques/methods MH - Polymorphism, Single Nucleotide/genetics MH - Principal Component Analysis MH - Sequence Analysis, DNA MH - West Indies PMC - PMC4275895 OTO - NOTNLM OT - Caribbean region OT - Guadeloupe archipelago OT - Late Ceramic Age OT - ancient DNA OT - mitochondrial DNA EDAT- 2014/12/10 06:00 MHDA- 2015/08/11 06:00 PMCR- 2016/01/19 CRDT- 2014/12/10 06:00 PHST- 2014/12/10 06:00 [entrez] PHST- 2014/12/10 06:00 [pubmed] PHST- 2015/08/11 06:00 [medline] PHST- 2016/01/19 00:00 [pmc-release] AID - rstb.2013.0388 [pii] AID - rstb20130388 [pii] AID - 10.1098/rstb.2013.0388 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130388. doi: 10.1098/rstb.2013.0388. PMID- 25487338 OWN - NLM STAT- MEDLINE DCOM- 20150810 LR - 20240326 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 370 IP - 1660 DP - 2015 Jan 19 TI - Ancient genomics. PG - 20130387 LID - 10.1098/rstb.2013.0387 [doi] LID - 20130387 AB - The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. FAU - Der Sarkissian, Clio AU - Der Sarkissian C AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Allentoft, Morten E AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Ávila-Arcos, María C AU - Ávila-Arcos MC AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Barnett, Ross AU - Barnett R AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Campos, Paula F AU - Campos PF AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Cappellini, Enrico AU - Cappellini E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Ermini, Luca AU - Ermini L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Fernández, Ruth AU - Fernández R AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - da Fonseca, Rute AU - da Fonseca R AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Ginolhac, Aurélien AU - Ginolhac A AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Hansen, Anders J AU - Hansen AJ AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Jónsson, Hákon AU - Jónsson H AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Korneliussen, Thorfinn AU - Korneliussen T AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Margaryan, Ashot AU - Margaryan A AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Martin, Michael D AU - Martin MD AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Moreno-Mayar, J Víctor AU - Moreno-Mayar JV AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Raghavan, Maanasa AU - Raghavan M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Rasmussen, Morten AU - Rasmussen M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Velasco, Marcela Sandoval AU - Velasco MS AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Schroeder, Hannes AU - Schroeder H AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Schubert, Mikkel AU - Schubert M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Seguin-Orlando, Andaine AU - Seguin-Orlando A AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Wales, Nathan AU - Wales N AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Gilbert, M Thomas P AU - Gilbert MT AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Orlando, Ludovic AU - Orlando L AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark lorlando@snm.ku.dk. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*genetics/*history MH - Genomics/*methods/trends MH - High-Throughput Nucleotide Sequencing/*methods/trends MH - History, Ancient MH - Humans PMC - PMC4275894 OTO - NOTNLM OT - ancient DNA OT - genomics OT - next generation sequencing EDAT- 2014/12/10 06:00 MHDA- 2015/08/11 06:00 PMCR- 2015/01/19 CRDT- 2014/12/10 06:00 PHST- 2014/12/10 06:00 [entrez] PHST- 2014/12/10 06:00 [pubmed] PHST- 2015/08/11 06:00 [medline] PHST- 2015/01/19 00:00 [pmc-release] AID - rstb.2013.0387 [pii] AID - rstb20130387 [pii] AID - 10.1098/rstb.2013.0387 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130387. doi: 10.1098/rstb.2013.0387. PMID- 25487336 OWN - NLM STAT- MEDLINE DCOM- 20150810 LR - 20240326 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 370 IP - 1660 DP - 2015 Jan 19 TI - The ancient Yakuts: a population genetic enigma. PG - 20130385 LID - 10.1098/rstb.2013.0385 [doi] LID - 20130385 AB - This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages. CI - © 2014 The Author(s) Published by the Royal Society. All rights reserved. FAU - Keyser, Christine AU - Keyser C AD - Institut de Médecine Légale, Laboratoire AMIS, CNRS UMR 5288, Université de Strasbourg, Strasbourg, France Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France ckeyser@unistra.fr. FAU - Hollard, Clémence AU - Hollard C AD - Institut de Médecine Légale, Laboratoire AMIS, CNRS UMR 5288, Université de Strasbourg, Strasbourg, France Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. FAU - Gonzalez, Angela AU - Gonzalez A AD - Institut de Médecine Légale, Laboratoire AMIS, CNRS UMR 5288, Université de Strasbourg, Strasbourg, France. FAU - Fausser, Jean-Luc AU - Fausser JL AD - Institut de Médecine Légale, Laboratoire AMIS, CNRS UMR 5288, Université de Strasbourg, Strasbourg, France. FAU - Rivals, Eric AU - Rivals E AD - LIRMM, CNRS UMR 5506, Université Montpellier 2, Montpellier, France Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France. FAU - Alexeev, Anatoly Nikolayevich AU - Alexeev AN AD - Medical Institute, Yakutsk University, Sakha Republic, Russia. FAU - Riberon, Alexandre AU - Riberon A AD - Laboratoire Evolution et Diversité Biologique, CNRS UMR 5174, Université de Toulouse, Toulouse, France. FAU - Crubézy, Eric AU - Crubézy E AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France. FAU - Ludes, Bertrand AU - Ludes B AD - Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France Institut Médico-Légal, Université Paris Descartes, Paris, France. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - Bone and Bones/chemistry MH - Chromosomes, Human, Y/*genetics MH - DNA, Mitochondrial/*genetics/history MH - Ethnicity/*genetics/*history MH - *Fossils MH - Genetics, Population MH - Haplotypes/genetics MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Likelihood Functions MH - Male MH - Microsatellite Repeats/genetics MH - Molecular Sequence Data MH - Pedigree MH - Polymorphism, Single Nucleotide/genetics MH - Sequence Analysis, DNA MH - Siberia PMC - PMC4275892 OTO - NOTNLM OT - Yakuts OT - ancient DNA OT - kinship OT - short tandem repeats EDAT- 2014/12/10 06:00 MHDA- 2015/08/11 06:00 PMCR- 2016/01/19 CRDT- 2014/12/10 06:00 PHST- 2014/12/10 06:00 [entrez] PHST- 2014/12/10 06:00 [pubmed] PHST- 2015/08/11 06:00 [medline] PHST- 2016/01/19 00:00 [pmc-release] AID - rstb.2013.0385 [pii] AID - rstb20130385 [pii] AID - 10.1098/rstb.2013.0385 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130385. doi: 10.1098/rstb.2013.0385. PMID- 25487335 OWN - NLM STAT- MEDLINE DCOM- 20150810 LR - 20190130 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 370 IP - 1660 DP - 2015 Jan 19 TI - Mitochondrial DNA variation in the Viking age population of Norway. PG - 20130384 LID - 10.1098/rstb.2013.0384 [doi] LID - 20130384 AB - The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland. CI - © 2014 The Author(s) Published by the Royal Society. All rights reserved. FAU - Krzewińska, Maja AU - Krzewińska M AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden Department of Biosciences, University of Oslo, 0316 Oslo, Norway Museum of Cultural History, University of Oslo, 0130 Oslo, Norway maja.krzewinska@arklab.su.se. FAU - Bjørnstad, Gro AU - Bjørnstad G AD - Department of Forensic Biology, Norwegian Institute of Public Health, 0403 Oslo, Norway Department of Archaeology, Conservation and History, University of Oslo, 0315 Oslo, Norway. FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden. FAU - Olason, Pall Isolfur AU - Olason PI AD - Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden. FAU - Bill, Jan AU - Bill J AD - Museum of Cultural History, University of Oslo, 0130 Oslo, Norway. FAU - Götherström, Anders AU - Götherström A AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden. FAU - Hagelberg, Erika AU - Hagelberg E AD - Department of Biosciences, University of Oslo, 0316 Oslo, Norway erika.hagelberg@ibv.uio.no. LA - eng SI - GENBANK/KM656396 SI - GENBANK/KM656397 SI - GENBANK/KM656398 SI - GENBANK/KM656399 SI - GENBANK/KM656400 SI - GENBANK/KM656401 SI - GENBANK/KM656402 SI - GENBANK/KM656403 SI - GENBANK/KM656404 SI - GENBANK/KM656405 SI - GENBANK/KM656406 SI - GENBANK/KM656407 SI - GENBANK/KM656408 SI - GENBANK/KM656409 SI - GENBANK/KM656410 SI - GENBANK/KM656411 SI - GENBANK/KM656412 SI - GENBANK/KM656413 SI - GENBANK/KM656414 SI - GENBANK/KM656415 SI - GENBANK/KM656416 SI - GENBANK/KM656417 SI - GENBANK/KM656418 SI - GENBANK/KM656419 SI - GENBANK/KM656420 SI - GENBANK/KM656421 SI - GENBANK/KM656422 SI - GENBANK/KM656423 SI - GENBANK/KM656424 SI - GENBANK/KM656425 SI - GENBANK/KM656426 SI - GENBANK/KM656427 SI - GENBANK/KM656428 SI - GENBANK/KM656429 SI - GENBANK/KM656430 SI - GENBANK/KM656431 SI - GENBANK/KM656432 SI - GENBANK/KM656433 SI - GENBANK/KM656434 SI - GENBANK/KM656435 SI - GENBANK/KM656436 SI - GENBANK/KM656437 SI - GENBANK/KM656438 SI - GENBANK/KM656439 SI - GENBANK/KM656440 SI - GENBANK/KM656441 SI - GENBANK/KM656442 SI - GENBANK/KM656443 SI - GENBANK/KM656444 SI - GENBANK/KM656445 SI - GENBANK/KM656446 SI - GENBANK/KM656447 SI - GENBANK/KM656448 SI - GENBANK/KM656449 SI - GENBANK/KM656450 SI - GENBANK/KM656451 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - Base Sequence MH - Bone and Bones/chemistry MH - DNA, Mitochondrial/*genetics/history MH - Female MH - *Fossils MH - Genetic Markers/*genetics MH - *Genetic Variation MH - Haplotypes/genetics MH - History, Medieval MH - Human Migration/*history MH - Humans MH - Molecular Sequence Data MH - Norway MH - Nucleic Acid Amplification Techniques MH - Sequence Alignment MH - Sequence Analysis, DNA MH - Tooth/chemistry PMC - PMC4275891 OTO - NOTNLM OT - Norway OT - Scandinavia OT - Vikings OT - ancient DNA OT - human mitochondrial DNA EDAT- 2014/12/10 06:00 MHDA- 2015/08/11 06:00 PMCR- 2016/01/19 CRDT- 2014/12/10 06:00 PHST- 2014/12/10 06:00 [entrez] PHST- 2014/12/10 06:00 [pubmed] PHST- 2015/08/11 06:00 [medline] PHST- 2016/01/19 00:00 [pmc-release] AID - rstb.2013.0384 [pii] AID - rstb20130384 [pii] AID - 10.1098/rstb.2013.0384 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130384. doi: 10.1098/rstb.2013.0384. PMID- 25487330 OWN - NLM STAT- MEDLINE DCOM- 20150810 LR - 20240326 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 370 IP - 1660 DP - 2015 Jan 19 TI - Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach. PG - 20130378 LID - 10.1098/rstb.2013.0378 [doi] LID - 20130378 AB - The Yuan Dynasty (AD 1271-1368) was the first dynasty in Chinese history where a minority ethnic group (Mongols) ruled. Few cemeteries containing Mongolian nobles have been found owing to their tradition of keeping burial grounds secret and their lack of historical records. Archaeological excavations at the Shuzhuanglou site in the Hebei province of China led to the discovery of 13 skeletons in six separate tombs. The style of the artefacts and burials indicate the cemetery occupants were Mongol nobles. However, the origin, relationships and status of the chief occupant (M1m) are unclear. To shed light on the identity of the principal occupant and resolve the kin relationships between individuals, a multidisciplinary approach was adopted, combining archaeological information, stable isotope data and molecular genetic data. Analysis of autosomal, mitochondrial and Y-chromosomal DNA show that some of the occupants were related. The available evidence strongly suggests that the principal occupant may have been the Mongol noble Korguz. Our study demonstrates the power of a multidisciplinary approach in elucidating information about the inhabitants of ancient historical sites. CI - © 2014 The Author(s) Published by the Royal Society. All rights reserved. FAU - Cui, Yinqiu AU - Cui Y AD - School of Life Sciences, Jilin University, Changchun 130012, People's Republic of China Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China. FAU - Song, Li AU - Song L AD - School of Life Sciences, Jilin University, Changchun 130012, People's Republic of China. FAU - Wei, Dong AU - Wei D AD - Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China. FAU - Pang, Yuhong AU - Pang Y AD - Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, People's Republic of China. FAU - Wang, Ning AU - Wang N AD - Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Palaeontology and Palaeoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China. FAU - Ning, Chao AU - Ning C AD - School of Life Sciences, Jilin University, Changchun 130012, People's Republic of China. FAU - Li, Chunmei AU - Li C AD - Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, People's Republic of China. FAU - Feng, Binxiao AU - Feng B AD - Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, People's Republic of China. FAU - Tang, Wentao AU - Tang W AD - School of Life Sciences, Jilin University, Changchun 130012, People's Republic of China. FAU - Li, Hongjie AU - Li H AD - School of Life Sciences, Jilin University, Changchun 130012, People's Republic of China Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China. FAU - Ren, Yashan AU - Ren Y AD - Hebei Provincial Centre for Cultural Relics Protection, Shijiazhuang 050031, People's Republic of China. FAU - Zhang, Chunchang AU - Zhang C AD - Hebei Provincial Institute of Cultural Relics, Shijiazhuang 050031, People's Republic of China. FAU - Huang, Yanyi AU - Huang Y AD - Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, People's Republic of China College of Engineering, Peking University, Beijing 100871, People's Republic of China yanyi@pku.edu.cn. FAU - Hu, Yaowu AU - Hu Y AD - Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Palaeontology and Palaeoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China Department of Scientific History and Archaeometry, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China ywhu@ucas.ac.cn. FAU - Zhou, Hui AU - Zhou H AD - School of Life Sciences, Jilin University, Changchun 130012, People's Republic of China Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China zhouhui@jlu.edu.cn. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA, Mitochondrial) RN - 0 (Oxygen Isotopes) RN - 10028-17-8 (Tritium) RN - 9007-34-5 (Collagen) SB - IM MH - Archaeology/*methods MH - Asian People/*genetics MH - Base Sequence MH - Burial/*history MH - China MH - Chromosomes, Human, Y/*genetics MH - Collagen/chemistry MH - DNA, Mitochondrial/*genetics/history MH - *Genetic Techniques MH - History, Medieval MH - Humans MH - Microsatellite Repeats/genetics MH - Molecular Sequence Data MH - Oxygen Isotopes/analysis MH - Pedigree MH - Phylogeny MH - Polymorphism, Single Nucleotide/genetics MH - Sequence Analysis, DNA MH - Tritium/analysis PMC - PMC4275886 OTO - NOTNLM OT - ancient DNA OT - archaeology OT - kinship OT - mitochondrial DNA OT - stable isotopes EDAT- 2014/12/10 06:00 MHDA- 2015/08/11 06:00 PMCR- 2016/01/19 CRDT- 2014/12/10 06:00 PHST- 2014/12/10 06:00 [entrez] PHST- 2014/12/10 06:00 [pubmed] PHST- 2015/08/11 06:00 [medline] PHST- 2016/01/19 00:00 [pmc-release] AID - rstb.2013.0378 [pii] AID - rstb20130378 [pii] AID - 10.1098/rstb.2013.0378 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130378. doi: 10.1098/rstb.2013.0378. PMID- 25487328 OWN - NLM STAT- MEDLINE DCOM- 20150810 LR - 20240326 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 370 IP - 1660 DP - 2015 Jan 19 TI - A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome. PG - 20130376 LID - 10.1098/rstb.2013.0376 [doi] LID - 20130376 AB - The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes. FAU - Warinner, Christina AU - Warinner C AUID- ORCID: 0000-0002-4528-5877 AD - Department of Anthropology, University of Oklahoma, Norman, OK, USA christina.warinner@ou.edu. FAU - Speller, Camilla AU - Speller C AUID- ORCID: 0000-0001-7128-9903 AD - Department of Archaeology, University of York, York, UK. FAU - Collins, Matthew J AU - Collins MJ AUID- ORCID: 0000-0003-4226-5501 AD - Department of Archaeology, University of York, York, UK. LA - eng GR - 097829/Z/11/A/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 SB - IM MH - Archaeology/*methods/trends MH - Dental Calculus/*microbiology MH - *Fossils MH - High-Throughput Nucleotide Sequencing/methods/trends MH - Humans MH - Microbiological Techniques/*methods/trends MH - Microbiota/*genetics MH - Paleodontology/*methods/trends PMC - PMC4275884 OTO - NOTNLM OT - ancient DNA OT - dental calculus OT - metagenomics OT - metaproteomics OT - oral microbiome OT - palaeomicrobiology EDAT- 2014/12/10 06:00 MHDA- 2015/08/11 06:00 PMCR- 2015/01/19 CRDT- 2014/12/10 06:00 PHST- 2014/12/10 06:00 [entrez] PHST- 2014/12/10 06:00 [pubmed] PHST- 2015/08/11 06:00 [medline] PHST- 2015/01/19 00:00 [pmc-release] AID - rstb.2013.0376 [pii] AID - rstb20130376 [pii] AID - 10.1098/rstb.2013.0376 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130376. doi: 10.1098/rstb.2013.0376. PMID- 25487325 OWN - NLM STAT- MEDLINE DCOM- 20150810 LR - 20190130 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 370 IP - 1660 DP - 2015 Jan 19 TI - Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process. PG - 20130373 LID - 10.1098/rstb.2013.0373 [doi] LID - 20130373 AB - The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers. CI - © 2014 The Author(s) Published by the Royal Society. All rights reserved. FAU - Malmström, Helena AU - Malmström H AD - Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden helena.malmstrom@ebc.uu.se. FAU - Linderholm, Anna AU - Linderholm A AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, South Road, Durham DH1 3LE, UK. FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden. FAU - Storå, Jan AU - Storå J AD - Osteolarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden. FAU - Sjödin, Per AU - Sjödin P AD - Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden. FAU - Gilbert, M Thomas P AU - Gilbert MT AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350 Copenhagen, Denmark. FAU - Holmlund, Gunilla AU - Holmlund G AD - Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping University, Artillerigatan 12, 587 58, Linköping, Sweden Department of Clinical and Experimental Medicine, Linköping University, Artillerigatan 12, 587 58, Linköping, Sweden. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350 Copenhagen, Denmark. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden Science for Life Laboratory, Uppsala University, Uppsala, Sweden. FAU - Lidén, Kerstin AU - Lidén K AD - Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden. FAU - Götherström, Anders AU - Götherström A AD - Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden. LA - eng SI - GENBANK/KJ873248 SI - GENBANK/KJ873249 SI - GENBANK/KJ873250 SI - GENBANK/KJ873251 SI - GENBANK/KJ873252 SI - GENBANK/KJ873253 SI - GENBANK/KJ873254 SI - GENBANK/KJ873255 SI - GENBANK/KJ873256 SI - GENBANK/KJ873257 SI - GENBANK/KJ873258 SI - GENBANK/KJ873259 SI - GENBANK/KJ873260 SI - GENBANK/KJ873261 SI - GENBANK/KJ873262 SI - GENBANK/KJ873263 SI - GENBANK/KJ873264 SI - GENBANK/KJ873265 SI - GENBANK/KJ873266 SI - GENBANK/KJ873267 SI - GENBANK/KJ873268 SI - GENBANK/KJ873269 SI - GENBANK/KJ873270 SI - GENBANK/KJ873271 SI - GENBANK/KJ873272 SI - GENBANK/KJ873273 SI - GENBANK/KJ873274 SI - GENBANK/KJ873275 PT - Historical Article PT - Journal Article PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/history MH - Base Sequence MH - Computational Biology MH - DNA Primers/genetics MH - DNA, Mitochondrial/*genetics/history MH - Gene Flow MH - *Genetic Variation MH - Genetics, Population MH - High-Throughput Nucleotide Sequencing MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Models, Genetic MH - Molecular Sequence Data MH - Population Dynamics MH - Real-Time Polymerase Chain Reaction MH - Sweden PMC - PMC4275881 OTO - NOTNLM OT - Battle Axe Culture OT - Funnel Beaker Culture OT - Neolithic OT - Pitted Ware Culture OT - ancient DNA OT - mtDNA EDAT- 2014/12/10 06:00 MHDA- 2015/08/11 06:00 PMCR- 2016/01/19 CRDT- 2014/12/10 06:00 PHST- 2014/12/10 06:00 [entrez] PHST- 2014/12/10 06:00 [pubmed] PHST- 2015/08/11 06:00 [medline] PHST- 2016/01/19 00:00 [pmc-release] AID - rstb.2013.0373 [pii] AID - rstb20130373 [pii] AID - 10.1098/rstb.2013.0373 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130373. doi: 10.1098/rstb.2013.0373. PMID- 26450112 OWN - NLM STAT- MEDLINE DCOM- 20160704 LR - 20240323 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 16 Suppl 10 IP - Suppl 10 DP - 2015 TI - Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence. PG - S9 LID - 10.1186/1471-2164-16-S10-S9 [doi] AB - BACKGROUND: We propose the computational reconstruction of a whole bacterial ancestral genome at the nucleotide scale, and its validation by a sequence of ancient DNA. This rare possibility is offered by an ancient sequence of the late middle ages plague agent. It has been hypothesized to be ancestral to extant Yersinia pestis strains based on the pattern of nucleotide substitutions. But the dynamics of indels, duplications, insertion sequences and rearrangements has impacted all genomes much more than the substitution process, which makes the ancestral reconstruction task challenging. RESULTS: We use a set of gene families from 13 Yersinia species, construct reconciled phylogenies for all of them, and determine gene orders in ancestral species. Gene trees integrate information from the sequence, the species tree and gene order. We reconstruct ancestral sequences for ancestral genic and intergenic regions, providing nearly a complete genome sequence for the ancestor, containing a chromosome and three plasmids. CONCLUSION: The comparison of the ancestral and ancient sequences provides a unique opportunity to assess the quality of ancestral genome reconstruction methods. But the quality of the sequencing and assembly of the ancient sequence can also be questioned by this comparison. FAU - Duchemin, Wandrille AU - Duchemin W FAU - Daubin, Vincent AU - Daubin V FAU - Tannier, Eric AU - Tannier E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20151002 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 SB - IM MH - *Evolution, Molecular MH - *Genome, Bacterial MH - Humans MH - *Phylogeny MH - Plague/genetics/microbiology MH - Plasmids/genetics MH - Species Specificity MH - Yersinia pestis/*genetics/pathogenicity PMC - PMC4603589 EDAT- 2015/10/10 06:00 MHDA- 2016/07/05 06:00 PMCR- 2015/10/02 CRDT- 2015/10/10 06:00 PHST- 2015/10/10 06:00 [entrez] PHST- 2015/10/10 06:00 [pubmed] PHST- 2016/07/05 06:00 [medline] PHST- 2015/10/02 00:00 [pmc-release] AID - 1471-2164-16-S10-S9 [pii] AID - 10.1186/1471-2164-16-S10-S9 [doi] PST - ppublish SO - BMC Genomics. 2015;16 Suppl 10(Suppl 10):S9. doi: 10.1186/1471-2164-16-S10-S9. Epub 2015 Oct 2. PMID- 26416323 OWN - NLM STAT- MEDLINE DCOM- 20160420 LR - 20191113 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 87 IP - 1 DP - 2015 Jan TI - Low Mitochondrial DNA Diversity in an Ancient Population from China: Insight into Social Organization at the Fujia Site. PG - 71-84 AB - To gain insight into the social organization of a population associated with the Dawenkou period, we performed ancient DNA analysis of 18 individuals from human remains from the Fujia site in Shandong Province, China. Directly radiocarbon dated to 4800-4500 cal BP, the Fujia site is assumed to be associated with a transitional phase from matrilineal clans to patrilineal monogamous families. Our results reveal a low mitochondrial DNA diversity from the site and population. Combined with Y chromosome data, the pattern observed at the Fujia site is most consistent with a matrilineal community. The patterns also suggest that the bond of marriage was de-emphasized compared with the bonds of descent at Fujia. FAU - Dong, Yu AU - Dong Y AD - 1 School of History and Culture, Shandong University, Jinan, Shandong, China. AD - 2 Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois. FAU - Li, Chunxiang AU - Li C AD - 3 College of Life Sciences, Jilin University, Changchun, Jilin, China. FAU - Luan, Fengshi AU - Luan F AD - 1 School of History and Culture, Shandong University, Jinan, Shandong, China. FAU - Li, Zhenguang AU - Li Z AD - 4 Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, Shandong, China. FAU - Li, Hongjie AU - Li H AD - 3 College of Life Sciences, Jilin University, Changchun, Jilin, China. FAU - Cui, Yinqiu AU - Cui Y AD - 2 Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois. AD - 3 College of Life Sciences, Jilin University, Changchun, Jilin, China. FAU - Zhou, Hui AU - Zhou H AD - 3 College of Life Sciences, Jilin University, Changchun, Jilin, China. FAU - Malhi, Ripan S AU - Malhi RS AD - 2 Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois. AD - 5 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM MH - China/ethnology MH - DNA, Mitochondrial/*analysis/history MH - Female MH - *Genetic Variation MH - History, Ancient MH - Humans MH - Male MH - Marriage/ethnology/history MH - Sequence Analysis, DNA MH - Social Dominance/*history OTO - NOTNLM OT - ANCIENT DNA OT - KINSHIP OT - MATRILINEAL OT - MTDNA OT - Y CHROMOSOME EDAT- 2015/09/30 06:00 MHDA- 2016/04/21 06:00 CRDT- 2015/09/30 06:00 PHST- 2015/09/30 06:00 [entrez] PHST- 2015/09/30 06:00 [pubmed] PHST- 2016/04/21 06:00 [medline] AID - 10.13110/humanbiology.87.1.0071 [pii] AID - 10.13110/humanbiology.87.1.0071 [doi] PST - ppublish SO - Hum Biol. 2015 Jan;87(1):71-84. doi: 10.13110/humanbiology.87.1.0071. PMID- 26416319 OWN - NLM STAT- MEDLINE DCOM- 20160420 LR - 20221207 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 87 IP - 1 DP - 2015 Jan TI - Mitochondrial DNA Suggests a Western Eurasian Origin for Ancient (Proto-) Bulgarians. PG - 19-28 AB - Ancient (proto-) Bulgarians have long been thought of as a Turkic population. However, evidence found in the past three decades shows that this is not the case. Until now, this evidence has not included ancient mitochondrial DNA (mtDNA) analysis. To fill this void, we collected human remains from the 8th to the 10th century AD located in three necropolises in Bulgaria: Nojarevo (Silistra region) and Monastery of Mostich (Shumen region), both in northeastern Bulgaria, and Tuhovishte (Satovcha region) in southwestern Bulgaria. The phylogenetic analysis of 13 ancient DNA samples (extracted from teeth) identified 12 independent haplotypes, which we further classified into mtDNA haplogroups found in present-day European and western Eurasian populations. Our results suggest a western Eurasian matrilineal origin for proto-Bulgarians, as well as a genetic similarity between proto- and modern Bulgarians. Our future work will provide additional data that will further clarify proto-Bulgarian origins, thereby adding new clues to the current understanding of European genetic evolution. FAU - Nesheva, D V AU - Nesheva DV AD - 1 Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria. FAU - Karachanak-Yankova, S AU - Karachanak-Yankova S AD - 1 Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria. FAU - Lari, M AU - Lari M AD - 2 Department of Biology, Laboratory of Anthropology, Molecular Anthropology/Paleogenetics Unit, University of Florence, Florence, Italy. FAU - Yordanov, Y AU - Yordanov Y AD - 3 Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria. FAU - Galabov, A AU - Galabov A AD - 4 Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria. FAU - Caramelli, D AU - Caramelli D AD - 2 Department of Biology, Laboratory of Anthropology, Molecular Anthropology/Paleogenetics Unit, University of Florence, Florence, Italy. FAU - Toncheva, D AU - Toncheva D AD - 1 Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM MH - Bulgaria/ethnology MH - DNA, Mitochondrial/*history MH - Ethnicity/*genetics MH - *Evolution, Molecular MH - History, Medieval MH - Humans MH - White People/*genetics OTO - NOTNLM OT - ANCIENT DNA OT - HAPLOGROUP OT - HAPLOTYPE OT - MITOCHONDRIAL DNA OT - PROTO-BULGARIANS EDAT- 2015/09/30 06:00 MHDA- 2016/04/21 06:00 CRDT- 2015/09/30 06:00 PHST- 2015/09/30 06:00 [entrez] PHST- 2015/09/30 06:00 [pubmed] PHST- 2016/04/21 06:00 [medline] AID - 10.13110/humanbiology.87.1.0019 [pii] AID - 10.13110/humanbiology.87.1.0019 [doi] PST - ppublish SO - Hum Biol. 2015 Jan;87(1):19-28. doi: 10.13110/humanbiology.87.1.0019. PMID- 26345378 OWN - NLM STAT- MEDLINE DCOM- 20160606 LR - 20181113 IS - 2314-6141 (Electronic) IS - 2314-6133 (Print) VI - 2015 DP - 2015 TI - Frozen Mummies from Andean Mountaintop Shrines: Bioarchaeology and Ethnohistory of Inca Human Sacrifice. PG - 439428 LID - 10.1155/2015/439428 [doi] LID - 439428 AB - This study will focus on frozen mummies of sacrificial victims from mounts Llullaillaco (6739 m), Quehuar (6130 m), El Toro (6160 m), and the Aconcagua massif. These finds provide bioarchaeological data from mountaintop sites that has been recovered in scientifically controlled excavations in the northwest of Argentina, which was once part of the southern province of the Inca Empire. Numerous interdisciplinary studies have been conducted on the Llullaillaco mummies, including radiological evaluations by conventional X-rays and CT scans, which provided information about condition and pathology of the bones and internal organ, as well as dental studies oriented to the estimation of the ages of the three children at the time of death. Ancient DNA studies and hair analysis were also performed in cooperation with the George Mason University, the University of Bradford, and the Laboratory of Biological Anthropology at the University of Copenhagen. Ethnohistorical sources reveal interesting aspects related to the commemorative, expiatory, propitiatory, and dedicatory aspects of human sacrifice performed under Inca rule. The selection of the victims along with the procedures followed during the performance of the capacocha ceremony will be discussed, based on the bioarchaeological evidences from frozen mummies and the accounts recorded by the Spanish chroniclers. FAU - Ceruti, Maria Constanza AU - Ceruti MC AD - Instituto de Investigaciones de Alta Montaña, Universidad Católica de Salta, Campus Castañares, 4400 Salta, Argentina. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20150806 PL - United States TA - Biomed Res Int JT - BioMed research international JID - 101600173 SB - IM MH - Argentina MH - Humans MH - *Indians, South American MH - *Mummies MH - *Religion PMC - PMC4543117 EDAT- 2015/09/09 06:00 MHDA- 2016/06/09 06:00 PMCR- 2015/08/06 CRDT- 2015/09/09 06:00 PHST- 2014/12/22 00:00 [received] PHST- 2015/04/05 00:00 [accepted] PHST- 2015/09/09 06:00 [entrez] PHST- 2015/09/09 06:00 [pubmed] PHST- 2016/06/09 06:00 [medline] PHST- 2015/08/06 00:00 [pmc-release] AID - 10.1155/2015/439428 [doi] PST - ppublish SO - Biomed Res Int. 2015;2015:439428. doi: 10.1155/2015/439428. Epub 2015 Aug 6. PMID- 25806829 OWN - NLM STAT- MEDLINE DCOM- 20151124 LR - 20221207 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 72 IP - 3 DP - 2015 TI - In naming the dead: Autosomal and Y-chromosomal STR typing on human skeletal remains from an 18th/19th century aristocratic crypt in Gallspach, Upper Austria. PG - 335-46 LID - 10.1127/anthranz/2015/0515 [doi] AB - Ancient DNA analyses have shown to be a powerful tool in the joint transdisciplinary assessment of archaeological records involving human remains. In this study we set out to identify single inhumations by synoptically evaluating the historical, archaeological, anthropological and molecular records on human remains from the crypt of the aristocratic family of Hoheneck (or: Hohenegg) dating to the 18(th) and 19(th) century AD. A total of 11 individuals were under investigation, yielding complete autosomal and Y-chromosomal STR profiles for 5 persons clearly showing a family group. DNA results, anthropological data and archaeological records taken together resulted in (almost) unambiguous correlation to historical records on the persons entombed in the crypt. FAU - Schwarz, Reinhard AU - Schwarz R AD - CAMAS - Centre of Archaeometry and Applied Molecular Archaeology - c/o University of Salzburg, Interfaculty Department of Legal Medicine, Salzburg, Austria. FAU - Renhart, Silvia AU - Renhart S AD - Hallersdorf 36a, 8564 Krottendorf, Austria. FAU - Gruber, Heinz AU - Gruber H AD - Austrian Federal Office for the Protection of Monuments, Department for Archeology, Linz, Austria. FAU - Kli Mesch, Wolfgang AU - Kli Mesch W AD - ARCHAEONOVA, Leonding, Austria. FAU - Neuhuber, Franz AU - Neuhuber F AD - University of Salzburg, Interfaculty Department of Legal Medicine, Salzburg, Austria. FAU - Cemper-Kiesslich, Jan AU - Cemper-Kiesslich J AD - University of Salzburg, Interfaculty Department of Legal Medicine, Salzburg, Austria. AD - CAMAS - Centre of Archaeometry and Applied Molecular Archaeology - c/o University of Salzburg, Interfaculty Department of Legal Medicine, Salzburg, Austria. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150217 PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 9007-49-2 (DNA) SB - IM MH - Adolescent MH - Adult MH - Aged MH - Aged, 80 and over MH - Austria/epidemiology MH - Child MH - Chromosomes, Human/*genetics MH - Chromosomes, Human, Y/*genetics MH - DNA/analysis/chemistry/genetics MH - Female MH - Forensic Anthropology MH - Genotype MH - Genotyping Techniques MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Male MH - Microsatellite Repeats/*genetics MH - Middle Aged MH - White People/*genetics/*history EDAT- 2015/03/26 06:00 MHDA- 2015/12/15 06:00 CRDT- 2015/03/26 06:00 PHST- 2014/07/23 00:00 [received] PHST- 2014/10/10 00:00 [accepted] PHST- 2015/03/26 06:00 [entrez] PHST- 2015/03/26 06:00 [pubmed] PHST- 2015/12/15 06:00 [medline] AID - 10.1127/anthranz/2015/0515 [doi] PST - ppublish SO - Anthropol Anz. 2015;72(3):335-46. doi: 10.1127/anthranz/2015/0515. Epub 2015 Feb 17. PMID- 25673485 OWN - NLM STAT- MEDLINE DCOM- 20151109 LR - 20150212 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 1274 DP - 2015 TI - Sex identification of ancient DNA samples using a microfluidic device. PG - 93-8 LID - 10.1007/978-1-4939-2353-3_8 [doi] AB - Ancient DNA is the name given to the degraded, fragmented, and chemically damaged biomolecules that can be recovered from archaeological remains of plants, animals, and humans. Where ancient human DNA has survived at archaeological sites, it can give valuable information and is especially useful for its potential to identify kinship, population affinities, pathogens, and biological sex. Here, we describe the operation of a microfluidic device for the sex identification of ancient DNA samples using an efficient sample handling process. DNA is extracted from powdered bone samples and abasic sites labeled with biotin. Streptavidin-coated superparamagnetic particles are used to isolate the labeled DNA prior to amplification of the Amelogenin sex marker. FAU - Shaw, Kirsty J AU - Shaw KJ AD - Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, M1 5GD, Manchester, UK, K.Shaw@mmu.ac.uk. FAU - Brown, Keri A AU - Brown KA FAU - Brown, Terence A AU - Brown TA FAU - Haswell, Stephen J AU - Haswell SJ LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Bone and Bones/chemistry MH - DNA/*chemistry MH - DNA Fingerprinting/*methods MH - Female MH - Humans MH - Male MH - Microfluidic Analytical Techniques/*methods EDAT- 2015/02/13 06:00 MHDA- 2015/11/10 06:00 CRDT- 2015/02/13 06:00 PHST- 2015/02/13 06:00 [entrez] PHST- 2015/02/13 06:00 [pubmed] PHST- 2015/11/10 06:00 [medline] AID - 10.1007/978-1-4939-2353-3_8 [doi] PST - ppublish SO - Methods Mol Biol. 2015;1274:93-8. doi: 10.1007/978-1-4939-2353-3_8. PMID- 25231926 OWN - NLM STAT- MEDLINE DCOM- 20150824 LR - 20141216 IS - 1464-5033 (Electronic) IS - 0301-4460 (Linking) VI - 42 IP - 1 DP - 2015 Jan TI - Methodological strategies to assess the degree of bone preservation for ancient DNA studies. PG - 10-9 LID - 10.3109/03014460.2014.954614 [doi] AB - BACKGROUND: Archaeological bones contain only small amounts of DNA due to post-mortem DNA degradation and the changes endogenous DNA is subjected to during diagenesis. An important step before undertaking such time-consuming and costly analyses as ancient DNA investigation is to predict the presence of DNA in ancient samples. To date, the leading screening method has been amino acid racemization; however, other analytical techniques can also be used to assess the degree of bone preservation. AIM: The aim of the present study was to relate the presence of DNA with bone preservation in order to select samples potentially suitable for ancient DNA analysis. SUBJECTS AND METHODS: Bones collected from several archaeological sites, different locations (cave, rockshelter or sub divo) and diachronic periods were selected for analytical and spectroscopic analysis in order to correlate bone tissue preservation with the presence of DNA. Different techniques were combined to assess the degree of preservation of organic and inorganic components. RESULTS: As determined by different analytical methods, preservation of the inorganic component was best associated with the presence of DNA. CONCLUSION: Evaluation of the bone preservation state may be an efficient step to predict the presence of DNA in ancient samples prior to aDNA analysis. FAU - Scorrano, Gabriele AU - Scorrano G AD - Centro di Antropologia molecolare per lo studio del DNA antico, Dipartimento di Biologia . FAU - Valentini, Federica AU - Valentini F FAU - Martínez-Labarga, Cristina AU - Martínez-Labarga C FAU - Rolfo, Mario Federico AU - Rolfo MF FAU - Fiammenghi, Antonella AU - Fiammenghi A FAU - Lo Vetro, Domenico AU - Lo Vetro D FAU - Martini, Fabio AU - Martini F FAU - Casoli, Antonella AU - Casoli A FAU - Ferraris, Giovanni AU - Ferraris G FAU - Palleschi, Giuseppe AU - Palleschi G FAU - Palleschi, Antonio AU - Palleschi A FAU - Rickards, Olga AU - Rickards O LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140918 PL - England TA - Ann Hum Biol JT - Annals of human biology JID - 0404024 RN - 9007-49-2 (DNA) SB - IM MH - Bone and Bones/*cytology/*metabolism MH - DNA/*analysis/chemistry/genetics MH - *Fossils MH - Humans OTO - NOTNLM OT - Amino-acid racemization OT - Early Neolithic OT - crystallinity OT - roman imperial age OT - upper paleolithic EDAT- 2014/09/19 06:00 MHDA- 2015/08/25 06:00 CRDT- 2014/09/19 06:00 PHST- 2014/09/19 06:00 [entrez] PHST- 2014/09/19 06:00 [pubmed] PHST- 2015/08/25 06:00 [medline] AID - 10.3109/03014460.2014.954614 [doi] PST - ppublish SO - Ann Hum Biol. 2015 Jan;42(1):10-9. doi: 10.3109/03014460.2014.954614. Epub 2014 Sep 18. PMID- 25047360 OWN - NLM STAT- MEDLINE DCOM- 20151116 LR - 20150114 IS - 1556-4029 (Electronic) IS - 0022-1198 (Linking) VI - 60 IP - 1 DP - 2015 Jan TI - Nondestructive methods for recovery of biological material from human teeth for DNA extraction. PG - 136-41 LID - 10.1111/1556-4029.12568 [doi] AB - The extraction of DNA from human skeletal remains applied to forensic, and evolutionary studies do not exclude risks, which are to be evaluated when working with unique specimens that could be damaged or even destroyed. In the present study were evaluated several nondestructive methods for recovering DNA instead of the most currently used pulverization method. Three different procedures to access inside the dental pieces (occlusal perforation, cervical perforation, and cervical cut) have been compared with the aim of recovering as many cell remains as possible to carry out a DNA extraction. Given the DNA quantitation results, a method was proposed that consists of a cervical cut to facilitate the access to the pulp cavity and a subsequent filing of the root canals down to the apex of the dental root. This methodology allows the recovery of both mitochondrial and nuclear DNA, with the minimum deterioration for the dental pieces. CI - © 2014 American Academy of Forensic Sciences. FAU - Hervella, Montserrat AU - Hervella M AD - Faculty of Science and Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, Leioa, Spain. FAU - Iñiguez, Maitane G AU - Iñiguez MG FAU - Izagirre, Neskuts AU - Izagirre N FAU - Anta, Alberto AU - Anta A FAU - de-la-Rúa, Concepción AU - de-la-Rúa C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140722 PL - United States TA - J Forensic Sci JT - Journal of forensic sciences JID - 0375370 RN - 0 (DNA, Mitochondrial) SB - IM MH - Cuspid MH - DNA Fingerprinting MH - DNA, Mitochondrial/*isolation & purification MH - Dental Pulp/chemistry MH - Forensic Dentistry MH - Humans MH - Molar, Third MH - Polymerase Chain Reaction MH - Specimen Handling/*methods MH - Tooth Root/*chemistry OTO - NOTNLM OT - DNA recovery OT - ancient DNA OT - forensic science OT - human teeth OT - mitochondrial DNA OT - nuclear DNA EDAT- 2014/07/23 06:00 MHDA- 2015/11/17 06:00 CRDT- 2014/07/23 06:00 PHST- 2013/05/03 00:00 [received] PHST- 2013/10/22 00:00 [revised] PHST- 2013/11/02 00:00 [accepted] PHST- 2014/07/23 06:00 [entrez] PHST- 2014/07/23 06:00 [pubmed] PHST- 2015/11/17 06:00 [medline] AID - 10.1111/1556-4029.12568 [doi] PST - ppublish SO - J Forensic Sci. 2015 Jan;60(1):136-41. doi: 10.1111/1556-4029.12568. Epub 2014 Jul 22. PMID- 25130911 OWN - NLM STAT- MEDLINE DCOM- 20150630 LR - 20221207 IS - 1520-6300 (Electronic) IS - 1042-0533 (Linking) VI - 26 IP - 6 DP - 2014 Nov-Dec TI - Ancient DNA evidence reveals that the Y chromosome haplogroup Q1a1 admixed into the Han Chinese 3,000 years ago. PG - 813-21 LID - 10.1002/ajhb.22604 [doi] AB - OBJECTIVES: Y chromosome haplogroup Q1a1 is found almost only in Han Chinese populations. However, it has not been found in ancient Han Chinese samples until now. Thus, the origin of haplogroup Q1a1 in Han Chinese is still obscure. This study attempts to provide answer to this question, and to uncover the origin and paternal genetic structure of the ancestors of the Han Chinese. METHODS: Eighty-nine ancient human remains that were excavated from the presumed geographic source of the Han Chinese and dated to approximately 3,000 years ago were treated by the amelogenin gene polymerase chain reaction test, to determine their sex. Then, Y chromosome single nucleotide polymorphisms were subsequently analyzed from the samples detected as male. RESULTS: Samples from 27 individuals were successfully amplified. Their haplotypes could be attributed to haplogroups N, O*, O2a, O3a, and Q1a1. Analyses showed that the assigned haplogroup of each sample is correlated to the suspected social status and observed burial custom associated with the sample. CONCLUSIONS: The origins of the observed haplotypes and their distribution in present day Han Chinese and in the samples suggest that haplogroup Q1a1 was probably introduced into the Han Chinese population approximately 3,000 years ago. CI - © 2014 Wiley Periodicals, Inc. FAU - Zhao, Yong-Bin AU - Zhao YB AD - College of Life Science, Jilin University, Changchun, China; College of Life Science, Jilin Normal University, Siping, China. FAU - Zhang, Ye AU - Zhang Y FAU - Li, Hong-Jie AU - Li HJ FAU - Cui, Ying-Qiu AU - Cui YQ FAU - Zhu, Hong AU - Zhu H FAU - Zhou, Hui AU - Zhou H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140818 PL - United States TA - Am J Hum Biol JT - American journal of human biology : the official journal of the Human Biology Council JID - 8915029 SB - IM MH - Asian People/*genetics MH - China MH - Chromosomes, Human, Y/*genetics MH - Genetics, Population MH - *Haplotypes MH - Humans MH - Male MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA EDAT- 2014/08/19 06:00 MHDA- 2015/07/01 06:00 CRDT- 2014/08/19 06:00 PHST- 2014/04/11 00:00 [received] PHST- 2014/07/20 00:00 [revised] PHST- 2014/07/29 00:00 [accepted] PHST- 2014/08/19 06:00 [entrez] PHST- 2014/08/19 06:00 [pubmed] PHST- 2015/07/01 06:00 [medline] AID - 10.1002/ajhb.22604 [doi] PST - ppublish SO - Am J Hum Biol. 2014 Nov-Dec;26(6):813-21. doi: 10.1002/ajhb.22604. Epub 2014 Aug 18. PMID- 25337992 OWN - NLM STAT- MEDLINE DCOM- 20150703 LR - 20221207 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 10 DP - 2014 TI - Ancient DNA reveals matrilineal continuity in present-day Poland over the last two millennia. PG - e110839 LID - 10.1371/journal.pone.0110839 [doi] LID - e110839 AB - While numerous ancient human DNA datasets from across Europe have been published till date, modern-day Poland in particular, remains uninvestigated. Besides application in the reconstruction of continent-wide human history, data from this region would also contribute towards our understanding of the history of the Slavs, whose origin is hypothesized to be in East or Central Europe. Here, we present the first population-scale ancient human DNA study from the region of modern-day Poland by establishing mitochondrial DNA profiles for 23 samples dated to 200 BC - 500 AD (Roman Iron Age) and for 20 samples dated to 1000-1400 AD (Medieval Age). Our results show that mitochondrial DNA sequences from both periods belong to haplogroups that are characteristic of contemporary West Eurasia. Haplotype sharing analysis indicates that majority of the ancient haplotypes are widespread in some modern Europeans, including Poles. Notably, the Roman Iron Age samples share more rare haplotypes with Central and Northeast Europeans, whereas the Medieval Age samples share more rare haplotypes with East-Central and South-East Europeans, primarily Slavic populations. Our data demonstrates genetic continuity of certain matrilineages (H5a1 and N1a1a2) in the area of present-day Poland from at least the Roman Iron Age until present. As such, the maternal gene pool of present-day Poles, Czechs and Slovaks, categorized as Western Slavs, is likely to have descended from inhabitants of East-Central Europe during the Roman Iron Age. FAU - Juras, Anna AU - Juras A AD - Department of Human Evolutionary Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland. FAU - Dabert, Miroslawa AU - Dabert M AD - Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland. FAU - Kushniarevich, Alena AU - Kushniarevich A AD - Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia. FAU - Malmström, Helena AU - Malmström H AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden. FAU - Raghavan, Maanasa AU - Raghavan M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Kosicki, Jakub Z AU - Kosicki JZ AD - Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland. FAU - Metspalu, Ene AU - Metspalu E AD - Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia; Department of Evolutionary Biology, University of Tartu, Tartu, Estonia. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. FAU - Piontek, Janusz AU - Piontek J AD - Department of Human Evolutionary Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141022 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - Consensus Sequence MH - DNA, Mitochondrial/*genetics MH - Female MH - *Haplotypes MH - History, Ancient MH - Humans MH - Phylogeny MH - Poland MH - Sequence Analysis, DNA MH - White People/*genetics PMC - PMC4206425 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2014/10/23 06:00 MHDA- 2015/07/04 06:00 PMCR- 2014/10/22 CRDT- 2014/10/23 06:00 PHST- 2014/05/20 00:00 [received] PHST- 2014/09/20 00:00 [accepted] PHST- 2014/10/23 06:00 [entrez] PHST- 2014/10/23 06:00 [pubmed] PHST- 2015/07/04 06:00 [medline] PHST- 2014/10/22 00:00 [pmc-release] AID - PONE-D-14-21869 [pii] AID - 10.1371/journal.pone.0110839 [doi] PST - epublish SO - PLoS One. 2014 Oct 22;9(10):e110839. doi: 10.1371/journal.pone.0110839. eCollection 2014. PMID- 24974206 OWN - NLM STAT- MEDLINE DCOM- 20141203 LR - 20211021 IS - 1367-4811 (Electronic) IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 30 IP - 20 DP - 2014 Oct 15 TI - bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). PG - 2962-4 LID - 10.1093/bioinformatics/btu410 [doi] AB - SUMMARY: We present bammds, a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional scaling algorithm. Our tool is aimed at determining the ancestry of unknown samples-typical of ancient DNA data-particularly when only low amounts of data are available for those samples. AVAILABILITY AND IMPLEMENTATION: The software package is available under GNU General Public License v3 and is freely available together with test datasets https://savannah.nongnu.org/projects/bammds/. It is using R (http://www.r-project.org/), parallel (http://www.gnu.org/software/parallel/), samtools (https://github.com/samtools/samtools). CONTACT: bammds-users@nongnu.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CI - © The Author 2014. Published by Oxford University Press. FAU - Malaspinas, Anna-Sapfo AU - Malaspinas AS AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. FAU - Tange, Ole AU - Tange O AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. FAU - Moreno-Mayar, José Víctor AU - Moreno-Mayar JV AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. FAU - Rasmussen, Morten AU - Rasmussen M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. FAU - DeGiorgio, Michael AU - DeGiorgio M AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. FAU - Wang, Yong AU - Wang Y AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. FAU - Valdiosera, Cristina E AU - Valdiosera CE AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. FAU - Politis, Gustavo AU - Politis G AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. FAU - Nielsen, Rasmus AU - Nielsen R AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140628 PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 SB - IM MH - Genetics, Population MH - Genome, Human/genetics MH - Genomics/*methods MH - Genotype MH - Humans MH - Phylogeography/*methods MH - *Software PMC - PMC4184259 EDAT- 2014/06/30 06:00 MHDA- 2014/12/15 06:00 PMCR- 2014/06/28 CRDT- 2014/06/30 06:00 PHST- 2014/06/30 06:00 [entrez] PHST- 2014/06/30 06:00 [pubmed] PHST- 2014/12/15 06:00 [medline] PHST- 2014/06/28 00:00 [pmc-release] AID - btu410 [pii] AID - 10.1093/bioinformatics/btu410 [doi] PST - ppublish SO - Bioinformatics. 2014 Oct 15;30(20):2962-4. doi: 10.1093/bioinformatics/btu410. Epub 2014 Jun 28. PMID- 25294605 OWN - NLM STAT- MEDLINE DCOM- 20150626 LR - 20211021 IS - 1756-0500 (Electronic) IS - 1756-0500 (Linking) VI - 7 DP - 2014 Oct 7 TI - SNPest: a probabilistic graphical model for estimating genotypes. PG - 698 LID - 10.1186/1756-0500-7-698 [doi] LID - 698 AB - BACKGROUND: As the use of next-generation sequencing technologies is becoming more widespread, the need for robust software to help with the analysis is growing as well. A key challenge when analyzing sequencing data is the prediction of genotypes from the reads, i.e. correct inference of the underlying DNA sequences that gave rise to the sequenced fragments. For diploid organisms, the genotyper should be able to predict both alleles in the individual. Variations between the individual and the population can then be analyzed by looking for SNPs (single nucleotide polymorphisms) in order to investigate diseases or phenotypic features. To perform robust and high confidence genotyping and SNP calling, methods are needed that take the technology specific limitations into account and can model different sources of error. As an example, ancient DNA poses special challenges as the data is often shallow and subject to errors induced by post mortem damage. FINDINGS: We present a novel approach to the genotyping problem where a probabilistic framework describing the process from sampling to sequencing is implemented as a graphical model. This makes it possible to model technology specific errors and other sources of variation that can affect the result. The inferred genotype is given a posterior probability to signify the confidence in the result. SNPest has already been used to genotype large scale projects such as the first ancient human genome published in 2010. CONCLUSIONS: We compare the performance of SNPest to a number of other widely used genotypers on both real and simulated data, covering both haploid and diploid genomes. We investigate the effects of read depth, of removing adapters before mapping and genotyping, of using different mapping tools, and of using the correct model in the genotyping process. We show that the performance of SNPest is comparable to existing methods, and we also illustrate cases where SNPest has an advantage over other methods, e.g. when dealing with simulated ancient DNA. FAU - Lindgreen, Stinus AU - Lindgreen S AD - Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaloes Vej, 2200 Copenhagen, Denmark. stinus@binf.ku.dk. FAU - Krogh, Anders AU - Krogh A FAU - Pedersen, Jakob Skou AU - Pedersen JS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141007 PL - England TA - BMC Res Notes JT - BMC research notes JID - 101462768 SB - IM MH - Computer Simulation MH - Diploidy MH - Escherichia coli/*genetics MH - Gene Frequency MH - Genetic Association Studies MH - *Genome, Bacterial MH - *Genome, Human MH - Genotype MH - Haploidy MH - *High-Throughput Nucleotide Sequencing MH - Humans MH - *Models, Statistical MH - Phenotype MH - *Polymorphism, Single Nucleotide MH - Probability MH - Reproducibility of Results MH - Software Design PMC - PMC4203901 EDAT- 2014/10/09 06:00 MHDA- 2015/06/27 06:00 PMCR- 2014/10/07 CRDT- 2014/10/09 06:00 PHST- 2014/01/29 00:00 [received] PHST- 2014/10/02 00:00 [accepted] PHST- 2014/10/09 06:00 [entrez] PHST- 2014/10/09 06:00 [pubmed] PHST- 2015/06/27 06:00 [medline] PHST- 2014/10/07 00:00 [pmc-release] AID - 1756-0500-7-698 [pii] AID - 3244 [pii] AID - 10.1186/1756-0500-7-698 [doi] PST - epublish SO - BMC Res Notes. 2014 Oct 7;7:698. doi: 10.1186/1756-0500-7-698. PMID- 25100861 OWN - NLM STAT- MEDLINE DCOM- 20150604 LR - 20220129 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 31 IP - 10 DP - 2014 Oct TI - Improved calibration of the human mitochondrial clock using ancient genomes. PG - 2780-92 LID - 10.1093/molbev/msu222 [doi] AB - Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g., the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g., first entry into the Americas). The recent availability of ancient mitochondrial DNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analyzed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive data set of 350 ancient and modern human complete mitochondrial DNA genomes, among which 146 were generated for the purpose of this study and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same data set, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable. CI - © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Rieux, Adrien AU - Rieux A AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom a.rieux@ucl.ac.uk f.balloux@ucl.ac.uk. FAU - Eriksson, Anders AU - Eriksson A AD - Department of Zoology, University of Cambridge, Cambridge, United Kingdom. FAU - Li, Mingkun AU - Li M AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Sobkowiak, Benjamin AU - Sobkowiak B AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom. FAU - Weinert, Lucy A AU - Weinert LA AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom. FAU - Warmuth, Vera AU - Warmuth V AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom. FAU - Ruiz-Linares, Andres AU - Ruiz-Linares A AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom. FAU - Manica, Andrea AU - Manica A AD - Department of Zoology, University of Cambridge, Cambridge, United Kingdom. FAU - Balloux, François AU - Balloux F AD - UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom a.rieux@ucl.ac.uk f.balloux@ucl.ac.uk. LA - eng GR - 260801/ERC_/European Research Council/International GR - BB/H008802/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/H005854/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140805 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 SB - IM MH - *Amino Acid Substitution MH - Animals MH - Bayes Theorem MH - Calibration MH - Computational Biology/*methods MH - Evolution, Molecular MH - Genome, Human MH - *Genome, Mitochondrial MH - Humans MH - Mutation Rate MH - Phylogeny PMC - PMC4166928 OTO - NOTNLM OT - Bayesian phylogenetic inference OT - ancient genomes OT - calibration strategy OT - divergence times OT - human OT - mitochondrial substitution rates OT - molecular clock EDAT- 2014/08/08 06:00 MHDA- 2015/06/05 06:00 PMCR- 2014/08/05 CRDT- 2014/08/08 06:00 PHST- 2014/08/08 06:00 [entrez] PHST- 2014/08/08 06:00 [pubmed] PHST- 2015/06/05 06:00 [medline] PHST- 2014/08/05 00:00 [pmc-release] AID - msu222 [pii] AID - 10.1093/molbev/msu222 [doi] PST - ppublish SO - Mol Biol Evol. 2014 Oct;31(10):2780-92. doi: 10.1093/molbev/msu222. Epub 2014 Aug 5. PMID- 25212860 OWN - NLM STAT- MEDLINE DCOM- 20150706 LR - 20211021 IS - 1759-6653 (Electronic) IS - 1759-6653 (Linking) VI - 6 IP - 10 DP - 2014 Sep 10 TI - First ancient mitochondrial human genome from a prepastoralist southern African. PG - 2647-53 LID - 10.1093/gbe/evu202 [doi] AB - The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semidesert regions of Namibia and Botswana, whereas archeological, historical, and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. No genetic data have been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa prepastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330-year-old male skeleton, confirmed through osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that prepastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins. CI - © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Morris, Alan G AU - Morris AG AD - Department of Human Biology, University of Cape Town, South Africa v.hayes@garvan.org.au andrew.smith@uct.ac.za. FAU - Heinze, Anja AU - Heinze A AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany v.hayes@garvan.org.au andrew.smith@uct.ac.za. FAU - Chan, Eva K F AU - Chan EK AD - Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia v.hayes@garvan.org.au andrew.smith@uct.ac.za. FAU - Smith, Andrew B AU - Smith AB AD - Department of Archeology, University of Cape Town, South Africa v.hayes@garvan.org.au andrew.smith@uct.ac.za. FAU - Hayes, Vanessa M AU - Hayes VM AD - Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia Genomeic Medicine Group, J. Craig Venter Institute, La Jolla, California Central Clinical School, The University of Sydney, Camperdown, New South Wales, Australia Department of Urology, University of Pretoria, South Africa Medical Faculty, University of New South Wales, Randwick, New South Wales, Australia v.hayes@garvan.org.au andrew.smith@uct.ac.za. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140910 PL - England TA - Genome Biol Evol JT - Genome biology and evolution JID - 101509707 SB - IM MH - Africa MH - *Fossils MH - Genome, Mitochondrial/*genetics MH - Humans MH - Phylogeny PMC - PMC4224329 OTO - NOTNLM OT - Khoesan OT - ancient DNA OT - archeological skeletons OT - marine foragers OT - mitochondrial genome OT - southern Africa EDAT- 2014/09/13 06:00 MHDA- 2015/07/07 06:00 PMCR- 2014/09/10 CRDT- 2014/09/13 06:00 PHST- 2014/09/13 06:00 [entrez] PHST- 2014/09/13 06:00 [pubmed] PHST- 2015/07/07 06:00 [medline] PHST- 2014/09/10 00:00 [pmc-release] AID - evu202 [pii] AID - 10.1093/gbe/evu202 [doi] PST - epublish SO - Genome Biol Evol. 2014 Sep 10;6(10):2647-53. doi: 10.1093/gbe/evu202. PMID- 25207979 OWN - NLM STAT- MEDLINE DCOM- 20150521 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 9 DP - 2014 TI - Paleomicrobiology: revealing fecal microbiomes of ancient indigenous cultures. PG - e106833 LID - 10.1371/journal.pone.0106833 [doi] LID - e106833 AB - Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations. FAU - Cano, Raul J AU - Cano RJ AD - Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California, United States of America. FAU - Rivera-Perez, Jessica AU - Rivera-Perez J AD - Department of Biology, University of Puerto Rico, San Juan, Puerto Rico. FAU - Toranzos, Gary A AU - Toranzos GA AD - Department of Biology, University of Puerto Rico, San Juan, Puerto Rico. FAU - Santiago-Rodriguez, Tasha M AU - Santiago-Rodriguez TM AD - Department of Pathology, University of California San Diego, San Diego, California, United States of America. FAU - Narganes-Storde, Yvonne M AU - Narganes-Storde YM AD - Center for Archaeological Research, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico. FAU - Chanlatte-Baik, Luis AU - Chanlatte-Baik L AD - Center for Archaeological Research, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico. FAU - García-Roldán, Erileen AU - García-Roldán E AD - Department of Biology, University of Puerto Rico, San Juan, Puerto Rico. FAU - Bunkley-Williams, Lucy AU - Bunkley-Williams L AD - Department of Biology, University of Puerto Rico, Mayaguez Campus, San Juan, Puerto Rico. FAU - Massey, Steven E AU - Massey SE AD - Department of Biology, University of Puerto Rico, San Juan, Puerto Rico. LA - eng GR - R25 GM061151/GM/NIGMS NIH HHS/United States GR - 5R25GM061151-12/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140910 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (RNA, Ribosomal, 16S) SB - IM MH - Diet MH - Feces/*microbiology/parasitology MH - Humans MH - *Microbiology MH - *Microbiota MH - *Paleontology MH - *Population Groups MH - Puerto Rico/ethnology MH - RNA, Ribosomal, 16S/genetics PMC - PMC4160228 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2014/09/11 06:00 MHDA- 2015/05/23 06:00 PMCR- 2014/09/10 CRDT- 2014/09/11 06:00 PHST- 2014/04/29 00:00 [received] PHST- 2014/07/22 00:00 [accepted] PHST- 2014/09/11 06:00 [entrez] PHST- 2014/09/11 06:00 [pubmed] PHST- 2015/05/23 06:00 [medline] PHST- 2014/09/10 00:00 [pmc-release] AID - PONE-D-14-18828 [pii] AID - 10.1371/journal.pone.0106833 [doi] PST - epublish SO - PLoS One. 2014 Sep 10;9(9):e106833. doi: 10.1371/journal.pone.0106833. eCollection 2014. PMID- 25190770 OWN - NLM STAT- MEDLINE DCOM- 20140922 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 345 IP - 6201 DP - 2014 Sep 5 TI - Ancient DNA. Three-part ancestry for Europeans. PG - 1106-7 LID - 10.1126/science.345.6201.1106 [doi] FAU - Gibbons, Ann AU - Gibbons A LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 9007-49-2 (DNA) SB - IM MH - DNA/*genetics MH - Genome, Human MH - Humans MH - White People/*genetics EDAT- 2014/09/06 06:00 MHDA- 2014/09/23 06:00 CRDT- 2014/09/06 06:00 PHST- 2014/09/06 06:00 [entrez] PHST- 2014/09/06 06:00 [pubmed] PHST- 2014/09/23 06:00 [medline] AID - 345/6201/1106 [pii] AID - 10.1126/science.345.6201.1106 [doi] PST - ppublish SO - Science. 2014 Sep 5;345(6201):1106-7. doi: 10.1126/science.345.6201.1106. PMID- 25168683 OWN - NLM STAT- MEDLINE DCOM- 20150406 LR - 20231110 IS - 0168-9525 (Print) IS - 0168-9525 (Linking) VI - 30 IP - 9 DP - 2014 Sep TI - Toward a new history and geography of human genes informed by ancient DNA. PG - 377-89 LID - S0168-9525(14)00120-6 [pii] LID - 10.1016/j.tig.2014.07.007 [doi] AB - Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture, and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world's human populations. In light of this we argue that it is time to critically reevaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection. CI - Copyright © 2014 Elsevier Ltd. All rights reserved. FAU - Pickrell, Joseph K AU - Pickrell JK AD - New York Genome Center, New York, NY, USA; Department of Biological Sciences, Columbia University, New York, NY, USA. Electronic address: jkpickrell@nygenome.org. FAU - Reich, David AU - Reich D AD - Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA. Electronic address: reich@genetics.med.harvard.edu. LA - eng GR - F32 GM103098/GM/NIGMS NIH HHS/United States GR - R01 GM100233/GM/NIGMS NIH HHS/United States GR - GM100233/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review DEP - 20140826 PL - England TA - Trends Genet JT - Trends in genetics : TIG JID - 8507085 RN - 9007-49-2 (DNA) SB - IM MH - Africa MH - DNA/*genetics/*history MH - Evolution, Molecular MH - *Genetics, Population MH - *Genome, Human MH - *Geography MH - History, Ancient MH - Humans MH - Phenotype MH - Selection, Genetic/*genetics PMC - PMC4163019 MID - NIHMS626145 EDAT- 2014/08/30 06:00 MHDA- 2015/04/07 06:00 PMCR- 2015/09/01 CRDT- 2014/08/30 06:00 PHST- 2014/03/21 00:00 [received] PHST- 2014/07/21 00:00 [revised] PHST- 2014/07/28 00:00 [accepted] PHST- 2014/08/30 06:00 [entrez] PHST- 2014/08/30 06:00 [pubmed] PHST- 2015/04/07 06:00 [medline] PHST- 2015/09/01 00:00 [pmc-release] AID - S0168-9525(14)00120-6 [pii] AID - 10.1016/j.tig.2014.07.007 [doi] PST - ppublish SO - Trends Genet. 2014 Sep;30(9):377-89. doi: 10.1016/j.tig.2014.07.007. Epub 2014 Aug 26. PMID- 25081630 OWN - NLM STAT- MEDLINE DCOM- 20150526 LR - 20211021 IS - 1549-5469 (Electronic) IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 24 IP - 9 DP - 2014 Sep TI - Selective enrichment of damaged DNA molecules for ancient genome sequencing. PG - 1543-9 LID - 10.1101/gr.174201.114 [doi] AB - Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA--the presence of deoxyuracils--for selective enrichment of endogenous DNA against a complex background of contamination during DNA library preparation. By applying the method to Neanderthal DNA extracts that are heavily contaminated with present-day human DNA, we show that the fraction of useful sequence information increases ∼ 10-fold and that the resulting sequences are more efficiently depleted of human contamination than when using purely computational approaches. Furthermore, we show that U selection can lead to a four- to fivefold increase in the proportion of endogenous DNA sequences relative to those of microbial contaminants in some samples. U selection may thus help to lower the costs for ancient genome sequencing of nonhuman samples also. CI - © 2014 Gansauge and Meyer; Published by Cold Spring Harbor Laboratory Press. FAU - Gansauge, Marie-Theres AU - Gansauge MT AD - Max Planck Institute for Evolutionary Anthropology, Evolutionary Genetics Department, Deutscher Platz 6, D-04103 Leipzig, Germany marie_gansauge@eva.mpg.de mmeyer@eva.mpg.de. FAU - Meyer, Matthias AU - Meyer M AD - Max Planck Institute for Evolutionary Anthropology, Evolutionary Genetics Department, Deutscher Platz 6, D-04103 Leipzig, Germany marie_gansauge@eva.mpg.de mmeyer@eva.mpg.de. LA - eng SI - GENBANK/KJ533544 SI - SRA/PRJEB6014 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140731 PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (Deoxyuracil Nucleotides) SB - IM CIN - Nat Rev Genet. 2014 Oct;15(10):642-3. doi: 10.1038/nrg3814. PMID: 25139188 MH - Animals MH - Base Sequence MH - DNA Contamination MH - Deoxyuracil Nucleotides/*chemistry/genetics MH - *Genome MH - Humans MH - Molecular Sequence Data MH - Neanderthals/*genetics MH - Sensitivity and Specificity MH - Sequence Analysis, DNA/*methods PMC - PMC4158764 EDAT- 2014/08/02 06:00 MHDA- 2015/05/27 06:00 PMCR- 2015/03/01 CRDT- 2014/08/02 06:00 PHST- 2014/08/02 06:00 [entrez] PHST- 2014/08/02 06:00 [pubmed] PHST- 2015/05/27 06:00 [medline] PHST- 2015/03/01 00:00 [pmc-release] AID - gr.174201.114 [pii] AID - 10.1101/gr.174201.114 [doi] PST - ppublish SO - Genome Res. 2014 Sep;24(9):1543-9. doi: 10.1101/gr.174201.114. Epub 2014 Jul 31. PMID- 25016250 OWN - NLM STAT- MEDLINE DCOM- 20150402 LR - 20140801 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 12 DP - 2014 Sep TI - Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers. PG - 199-207 LID - S1872-4973(14)00116-1 [pii] LID - 10.1016/j.fsigen.2014.05.012 [doi] AB - The Altai Mountains have been a long-term boundary zone between the Eurasian Steppe populations and South and East Asian populations. To disentangle some of the historical population movements in this area, 14 ancient human specimens excavated in the westernmost part of the Mongolian Altai were studied. Thirteen of them were dated from the Middle to the End of the Bronze Age and one of them to the Eneolithic period. The environmental conditions encountered in this region led to the good preservation of DNA in the human remains. Therefore, a multi-markers approach was adopted for the genetic analysis of identity, ancestry and phenotype markers. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages. To go further in the search of the origin of these ancient specimens, phenotypical characters (i.e. hair and eye color) were determined. For this purpose, we adapted the HIrisPlex assay recently described to MALDI-TOF mass spectrometry. In addition, some ancestry informative markers were analyzed with this assay. The results revealed mixed phenotypes among this group confirming the probable admixed ancestry of the studied Altaian population at the Middle Bronze Age. The good results obtained from ancient DNA samples suggest that this approach might be relevant for forensic casework too. CI - Copyright © 2014 Elsevier Ireland Ltd. All rights reserved. FAU - Hollard, Clémence AU - Hollard C AD - Laboratoire AMIS, CNRS, UMR 5288, Institut de Médecine Légale, Université de Strasbourg, France. Electronic address: clemence.hollard@etu.unistra.fr. FAU - Keyser, Christine AU - Keyser C AD - Laboratoire AMIS, CNRS, UMR 5288, Institut de Médecine Légale, Université de Strasbourg, France; Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier, Toulouse, France. Electronic address: ckeyser@unistra.fr. FAU - Giscard, Pierre-Henri AU - Giscard PH AD - Institut des Déserts et des Steppes, Paris, France. Electronic address: institutdesdeserts@gmail.com. FAU - Tsagaan, Turbat AU - Tsagaan T AD - Institute of Archaeology, Mongolian Academy of Sciences, Mongolia. Electronic address: ts_turbat@yahoo.com. FAU - Bayarkhuu, Noost AU - Bayarkhuu N AD - Institute of Archaeology, Mongolian Academy of Sciences, Mongolia. Electronic address: n_bayaraa2001@yahoo.com. FAU - Bemmann, Jan AU - Bemmann J AD - Vor- und Frühgeschichtliche Archäologie, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany. Electronic address: Jan.Bemmann@uni-bonn.de. FAU - Crubézy, Eric AU - Crubézy E AD - Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier, Toulouse, France. Electronic address: crubezy.eric@free.fr. FAU - Ludes, Bertrand AU - Ludes B AD - Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier, Toulouse, France; Université Paris Descartes, Institut Médico-Légal de Paris, France. Electronic address: ludes@unistra.fr. LA - eng PT - Journal Article DEP - 20140602 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - Asia MH - Chromosomes, Human, Y MH - DNA, Mitochondrial/*genetics MH - Europe MH - Female MH - Genetic Markers MH - Humans MH - Male MH - Microsatellite Repeats OTO - NOTNLM OT - Admixture OT - Altai Mountains OT - Ancient DNA OT - Bronze Age EDAT- 2014/07/13 06:00 MHDA- 2015/04/04 06:00 CRDT- 2014/07/13 06:00 PHST- 2014/01/02 00:00 [received] PHST- 2014/05/21 00:00 [revised] PHST- 2014/05/25 00:00 [accepted] PHST- 2014/07/13 06:00 [entrez] PHST- 2014/07/13 06:00 [pubmed] PHST- 2015/04/04 06:00 [medline] AID - S1872-4973(14)00116-1 [pii] AID - 10.1016/j.fsigen.2014.05.012 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2014 Sep;12:199-207. doi: 10.1016/j.fsigen.2014.05.012. Epub 2014 Jun 2. PMID- 24962720 OWN - NLM STAT- MEDLINE DCOM- 20150408 LR - 20140813 IS - 1469-1809 (Electronic) IS - 0003-4800 (Linking) VI - 78 IP - 5 DP - 2014 Sep TI - Genetic diversity of a late prehispanic group of the Quebrada de Humahuaca, northwestern Argentina. PG - 367-80 LID - 10.1111/ahg.12075 [doi] AB - This palaeogenetic study focused on the analysis of a late prehispanic Argentinean group from the Humahuaca valley, with the main aim of reconstructing its (micro)evolutionary history. The Humahuaca valley, a natural passageway from the eastern plains to the highlands, was the living environment of Andean societies whose cultural but especially biological diversity is still poorly understood. We analyzed the DNA extracted from 39 individuals who populated this upper valley during the Regional Development period (RDP) (between the 11th and 15th centuries CE), to determine their maternal and paternal genetic ancestry. Some mitochondrial and Y-chromosomal haplotypes specific to the Andean region are consistent with an origin in the highlands of Central Andes. On the other hand, a significant genetic affinity with contemporary admixed communities of the Chaco area was detected. Expectedly, recent demographic events, such as the expansion of the Inca Empire or the European colonization, have changed the original mitochondrial gene pool of the ancient Humahuaca Valley community. Finally, we identified a particular geographical organization of the prehispanic populations of Northwestern Argentina. Our results suggest that the communities of the region were divided between two different spheres of interaction, which is consistent with assumptions made by means of craniometric traits. CI - © 2014 John Wiley & Sons Ltd/University College London. FAU - Mendisco, Fanny AU - Mendisco F AD - Institut de Médecine Légale, AMIS, CNRS UMR 5288, Université de Strasbourg, F-67085, Strasbourg, France; Université Paul Sabatier, AMIS, CNRS UMR 5288, F-31073, Toulouse, France. FAU - Keyser, Christine AU - Keyser C FAU - Seldes, Veronica AU - Seldes V FAU - Rivolta, Clara AU - Rivolta C FAU - Mercolli, Pablo AU - Mercolli P FAU - Cruz, Pablo AU - Cruz P FAU - Nielsen, Axel E AU - Nielsen AE FAU - Crubezy, Eric AU - Crubezy E FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Historical Article PT - Journal Article DEP - 20140624 PL - England TA - Ann Hum Genet JT - Annals of human genetics JID - 0416661 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology/methods MH - Argentina MH - Base Sequence MH - *Biological Evolution MH - Chromosomes, Human, Y/*genetics MH - DNA, Mitochondrial/*genetics MH - *Fossils MH - *Genetic Variation MH - Genetics, Population MH - Haplotypes/genetics MH - History, Medieval MH - Humans MH - Indians, South American/*genetics MH - Molecular Sequence Data MH - Sequence Analysis, DNA OTO - NOTNLM OT - Andes OT - Palaeogenetics OT - Y-chromosome OT - ancient DNA OT - microevolution OT - migration OT - mitochondrial DNA EDAT- 2014/06/26 06:00 MHDA- 2015/04/09 06:00 CRDT- 2014/06/26 06:00 PHST- 2013/12/10 00:00 [received] PHST- 2014/05/13 00:00 [accepted] PHST- 2014/06/26 06:00 [entrez] PHST- 2014/06/26 06:00 [pubmed] PHST- 2015/04/09 06:00 [medline] AID - 10.1111/ahg.12075 [doi] PST - ppublish SO - Ann Hum Genet. 2014 Sep;78(5):367-80. doi: 10.1111/ahg.12075. Epub 2014 Jun 24. PMID- 24939468 OWN - NLM STAT- MEDLINE DCOM- 20160307 LR - 20231110 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 31 IP - 9 DP - 2014 Sep TI - Investigating population history using temporal genetic differentiation. PG - 2516-27 LID - 10.1093/molbev/msu192 [doi] AB - The rapid advance of sequencing technology, coupled with improvements in molecular methods for obtaining genetic data from ancient sources, holds the promise of producing a wealth of genomic data from time-separated individuals. However, the population-genetic properties of time-structured samples have not been extensively explored. Here, we consider the implications of temporal sampling for analyses of genetic differentiation and use a temporal coalescent framework to show that complex historical events such as size reductions, population replacements, and transient genetic barriers between populations leave a footprint of genetic differentiation that can be traced through history using temporal samples. Our results emphasize explicit consideration of the temporal structure when making inferences and indicate that genomic data from ancient individuals will greatly increase our ability to reconstruct population history. CI - © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden skoglund@genetics.med.harvard.edu mattias.jakobsson@ebc.uu.se. FAU - Sjödin, Per AU - Sjödin P AD - Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden. FAU - Skoglund, Tobias AU - Skoglund T AD - Department of Evolutionary Biology, Uppsala University, Uppsala, SwedenDepartment of Information Technology, Uppsala University, Uppsala, Sweden. FAU - Lascoux, Martin AU - Lascoux M AD - Department of Ecology and Genetics, Program in Plant Ecology and Evolution, Uppsala University, Uppsala, SwedenScience for Life Laboratory, Uppsala, Sweden. FAU - Jakobsson, Mattias AU - Jakobsson M AD - Department of Evolutionary Biology, Uppsala University, Uppsala, SwedenScience for Life Laboratory, Uppsala, Sweden skoglund@genetics.med.harvard.edu mattias.jakobsson@ebc.uu.se. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140617 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 SB - IM MH - Algorithms MH - Animals MH - Computational Biology/methods MH - Genetic Drift MH - *Genetic Variation MH - Humans MH - *Phylogeny MH - Population Dynamics MH - Sampling Studies PMC - PMC4137715 OTO - NOTNLM OT - FST OT - ancient DNA OT - genetic differentiation OT - population structure OT - time-serial sampling EDAT- 2014/06/19 06:00 MHDA- 2016/03/08 06:00 PMCR- 2014/06/17 CRDT- 2014/06/19 06:00 PHST- 2014/06/19 06:00 [entrez] PHST- 2014/06/19 06:00 [pubmed] PHST- 2016/03/08 06:00 [medline] PHST- 2014/06/17 00:00 [pmc-release] AID - msu192 [pii] AID - 10.1093/molbev/msu192 [doi] PST - ppublish SO - Mol Biol Evol. 2014 Sep;31(9):2516-27. doi: 10.1093/molbev/msu192. Epub 2014 Jun 17. PMID- 25162694 OWN - NLM STAT- MEDLINE DCOM- 20151106 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 8 DP - 2014 TI - Molecular paleoparasitological hybridization approach as effective tool for diagnosing human intestinal parasites from scarce archaeological remains. PG - e105910 LID - 10.1371/journal.pone.0105910 [doi] LID - e105910 AB - Paleoparasitology is the science that uses parasitological techniques for diagnosing parasitic diseases in the past. Advances in molecular biology brought new insights into this field allowing the study of archaeological material. However, due to technical limitations a proper diagnosis and confirmation of the presence of parasites is not always possible, especially in scarce and degraded archaeological remains. In this study, we developed a Molecular Paleoparasitological Hybridization (MPH) approach using ancient DNA (aDNA) hybridization to confirm and complement paleoparasitological diagnosis. Eight molecular targets from four helminth parasites were included: Ascaris sp., Trichuris trichiura, Enterobius vermicularis, and Strongyloides stercoralis. The MPH analysis using 18th century human remains from Praça XV cemetery (CPXV), Rio de Janeiro, Brazil, revealed for the first time the presence E. vermicularis aDNA (50%) in archaeological sites of Brazil. Besides, the results confirmed T. trichiura and Ascaris sp. infections. The prevalence of infection by Ascaris sp. and E. vermicularis increased considerably when MPH was applied. However, a lower aDNA detection of T. trichiura (40%) was observed when compared to the diagnosis by paleoparasitological analysis (70%). Therefore, based on these data, we suggest a combination of Paleoparasitological and MPH approaches to verify the real panorama of intestinal parasite infection in human archeological samples. FAU - Jaeger, Lauren Hubert AU - Jaeger LH AD - Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil. FAU - Iñiguez, Alena Mayo AU - Iñiguez AM AD - Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140827 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Helminth) SB - IM MH - Animals MH - Anthropology/methods MH - Ascaris/classification/*genetics MH - Brazil MH - Cemeteries MH - DNA, Helminth/*genetics/isolation & purification MH - Enterobius/classification/*genetics MH - Exhumation MH - Helminthiasis/diagnosis/*history/parasitology MH - History, 18th Century MH - Humans MH - Hybridization, Genetic MH - Intestinal Diseases, Parasitic/diagnosis/*history/parasitology MH - Parasitology/methods MH - Strongyloides stercoralis/classification/*genetics MH - Trichuris/classification/*genetics PMC - PMC4146586 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2014/08/28 06:00 MHDA- 2015/11/07 06:00 PMCR- 2014/08/27 CRDT- 2014/08/28 06:00 PHST- 2014/06/11 00:00 [received] PHST- 2014/07/24 00:00 [accepted] PHST- 2014/08/28 06:00 [entrez] PHST- 2014/08/28 06:00 [pubmed] PHST- 2015/11/07 06:00 [medline] PHST- 2014/08/27 00:00 [pmc-release] AID - PONE-D-14-25765 [pii] AID - 10.1371/journal.pone.0105910 [doi] PST - epublish SO - PLoS One. 2014 Aug 27;9(8):e105910. doi: 10.1371/journal.pone.0105910. eCollection 2014. PMID- 25098828 OWN - NLM STAT- MEDLINE DCOM- 20151130 LR - 20220331 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 8 DP - 2014 TI - Sex determination in highly fragmented human DNA by high-resolution melting (HRM) analysis. PG - e104629 LID - 10.1371/journal.pone.0104629 [doi] LID - e104629 AB - Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp) of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM). HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design. FAU - Álvarez-Sandoval, Brenda A AU - Álvarez-Sandoval BA AD - Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico. FAU - Manzanilla, Linda R AU - Manzanilla LR AD - Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico. FAU - Montiel, Rafael AU - Montiel R AD - Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140806 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (AMELX protein, human) RN - 0 (Amelogenin) RN - 9007-49-2 (DNA) SB - IM MH - Adult MH - Amelogenin/*genetics MH - Chromosomes, Human, X/*genetics MH - Chromosomes, Human, Y/*genetics MH - DNA/*genetics MH - Female MH - Humans MH - Male MH - Real-Time Polymerase Chain Reaction/*methods MH - Sex Determination Analysis/*methods PMC - PMC4123986 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2014/08/08 06:00 MHDA- 2015/12/15 06:00 PMCR- 2014/08/06 CRDT- 2014/08/08 06:00 PHST- 2014/01/14 00:00 [received] PHST- 2014/07/15 00:00 [accepted] PHST- 2014/08/08 06:00 [entrez] PHST- 2014/08/08 06:00 [pubmed] PHST- 2015/12/15 06:00 [medline] PHST- 2014/08/06 00:00 [pmc-release] AID - PONE-D-13-47573 [pii] AID - 10.1371/journal.pone.0104629 [doi] PST - epublish SO - PLoS One. 2014 Aug 6;9(8):e104629. doi: 10.1371/journal.pone.0104629. eCollection 2014. PMID- 24780138 OWN - NLM STAT- MEDLINE DCOM- 20150115 LR - 20140530 IS - 1873-0329 (Electronic) IS - 1383-5769 (Linking) VI - 63 IP - 4 DP - 2014 Aug TI - Insights about echinostomiasis by paleomolecular diagnosis. PG - 646-9 LID - S1383-5769(14)00053-1 [pii] LID - 10.1016/j.parint.2014.04.005 [doi] AB - Echinostomiasis is a zoonosis caused by intestinal trematodes and transmitted by the ingestion of mollusks, crustaceans, fish, amphibians, and reptiles, either raw or poorly cooked. Today human infection is endemic in Southeast Asia and the Far East, but has been reported more recently in other regions of the world. Interestingly eggs identified as Echinostoma sp. were found in coprolites from a mummified body human in Brazil, dated 560 ± 40 BP (before present). However, the specific diagnosis based on morphology of the eggs has not been resolved at the species level. As a follow-up to the previous finding, the current study now aims to standardize the methodology for molecular diagnosis and apply it to the coprolite, using current Echinostoma paraensei-positive feces as the reference, and also the same fecal material dried in a stove as an experimental coprolite model. Isolated eggs of E. paraensei and adult worm were included to verify the sensibility and as positive control, respectively. An adult worm of E. luisreyi was used for comparison. PCR using primers in-house for ITS1 region (126 bp) and cox1 (123 bp) of Echinostoma spp. and subsequent nucleotide sequencing were performed. This is the first molecular paleoparasitological diagnosis for echinostomiasis. The methodology was able to amplify specific DNA fragments for the genus Echinostoma sp. in all samples: adult worm, feces, and a single egg of the parasite, in both the experimental coprolite and archaeological sample. Additionally we observed that ancient DNA can also be retrieved without rehydrating the material. The nucleotide sequences from E. paraensei and E. luisreyi are very similar in the fragment analyzed that difficult the differentiation these species, but DNA sequence analysis recovered in the parasite found in the mummy showed more similarity with the species E. paraensei. CI - Copyright © 2014 Elsevier B.V. All rights reserved. FAU - Leles, Daniela AU - Leles D AD - Universidade Federal Fluminense, Instituto Biomédico, Departamento de Microbiologia e Parasitologia, Laboratório de Biologia Molecular de Parasitos, Rua Professor Hernani Melo 101, São Domingos, Niterói, RJ, CEP 24.210-130, Brazil. Electronic address: dleles@id.uff.br. FAU - Cascardo, Paula AU - Cascardo P AD - Universidade Federal Fluminense, Instituto Biomédico, Departamento de Microbiologia e Parasitologia, Laboratório de Biologia Molecular de Parasitos, Rua Professor Hernani Melo 101, São Domingos, Niterói, RJ, CEP 24.210-130, Brazil. FAU - Freire, Andressa Dos Santos AU - Freire Ados S AD - Universidade Federal Fluminense, Instituto Biomédico, Departamento de Microbiologia e Parasitologia, Laboratório de Biologia Molecular de Parasitos, Rua Professor Hernani Melo 101, São Domingos, Niterói, RJ, CEP 24.210-130, Brazil. FAU - Maldonado, Arnaldo Jr AU - Maldonado A Jr AD - Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Av. Brasil, 4365, Rio de Janeiro, RJ, CEP 21.045-900, Brazil. FAU - Sianto, Luciana AU - Sianto L AD - Laboratório de Paleoparasitologia, Escola Nacional de Saúde Pública-Fundação Oswaldo Cruz, Rua Leopoldo Bulhões 1480, Rio de Janeiro, RJ, CEP 21.041-210, Brazil. FAU - Araújo, Adauto AU - Araújo A AD - Laboratório de Paleoparasitologia, Escola Nacional de Saúde Pública-Fundação Oswaldo Cruz, Rua Leopoldo Bulhões 1480, Rio de Janeiro, RJ, CEP 21.041-210, Brazil. LA - eng SI - GENBANK/KC111440 SI - GENBANK/KF663568 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140426 PL - Netherlands TA - Parasitol Int JT - Parasitology international JID - 9708549 RN - 0 (DNA, Ribosomal Spacer) RN - 0 (Helminth Proteins) RN - EC 1.9.3.1 (Electron Transport Complex IV) SB - IM MH - Animals MH - Base Sequence MH - Brazil MH - DNA, Ribosomal Spacer/genetics MH - Echinostoma/*genetics/*isolation & purification MH - Echinostomiasis/*parasitology MH - Electron Transport Complex IV/genetics MH - Feces/parasitology MH - Helminth Proteins/genetics MH - Humans MH - Molecular Sequence Data MH - Polymerase Chain Reaction MH - Sequence Alignment OTO - NOTNLM OT - Ancient DNA OT - Ancient parasites OT - Coprolite OT - Echinostoma OT - Mummy OT - Paleoparasitology EDAT- 2014/05/02 06:00 MHDA- 2015/01/16 06:00 CRDT- 2014/05/01 06:00 PHST- 2013/12/01 00:00 [received] PHST- 2014/04/01 00:00 [revised] PHST- 2014/04/17 00:00 [accepted] PHST- 2014/05/01 06:00 [entrez] PHST- 2014/05/02 06:00 [pubmed] PHST- 2015/01/16 06:00 [medline] AID - S1383-5769(14)00053-1 [pii] AID - 10.1016/j.parint.2014.04.005 [doi] PST - ppublish SO - Parasitol Int. 2014 Aug;63(4):646-9. doi: 10.1016/j.parint.2014.04.005. Epub 2014 Apr 26. PMID- 24979787 OWN - NLM STAT- MEDLINE DCOM- 20140923 LR - 20240507 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 111 IP - 26 DP - 2014 Jul 1 TI - Climate change underlies global demographic, genetic, and cultural transitions in pre-Columbian southern Peru. PG - 9443-8 LID - 10.1073/pnas.1403466111 [doi] AB - Several archaeological studies in the Central Andes have pointed at the temporal coincidence of climatic fluctuations (both long- and short-term) and episodes of cultural transition and changes of socioeconomic structures throughout the pre-Columbian period. Although most scholars explain the connection between environmental and cultural changes by the impact of climatic alterations on the capacities of the ecosystems inhabited by pre-Columbian cultures, direct evidence for assumed demographic consequences is missing so far. In this study, we address directly the impact of climatic changes on the spatial population dynamics of the Central Andes. We use a large dataset of pre-Columbian mitochondrial DNA sequences from the northern Rio Grande de Nasca drainage (RGND) in southern Peru, dating from ∼840 BC to 1450 AD. Alternative demographic scenarios are tested using Bayesian serial coalescent simulations in an approximate Bayesian computational framework. Our results indicate migrations from the lower coastal valleys of southern Peru into the Andean highlands coincident with increasing climate variability at the end of the Nasca culture at ∼640 AD. We also find support for a back-migration from the highlands to the coast coincident with droughts in the southeastern Andean highlands and improvement of climatic conditions on the coast after the decline of the Wari and Tiwanaku empires (∼1200 AD), leading to a genetic homogenization in the RGND and probably southern Peru as a whole. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AD - Department of Anthropology, University of California, Santa Cruz, CA 95064;Historical Anthropology and Human Ecology, University of Göttingen, D-37073 Göttingen, Germany; lfehrens@ucsc.edu. FAU - Haak, Wolfgang AU - Haak W AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia; FAU - Mächtle, Bertil AU - Mächtle B AD - Geographisches Institut, Universität Heidelberg, D-69120 Heidelberg, Germany; FAU - Masch, Florian AU - Masch F AD - Historical Anthropology and Human Ecology, University of Göttingen, D-37073 Göttingen, Germany; FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia; FAU - Cagigao, Elsa Tomasto AU - Cagigao ET AD - Departmento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Perú; FAU - Sossna, Volker AU - Sossna V AD - German Archaeological Institute (DAI), Commission for Archaeology of Non-European Cultures (KAAK), D-53173 Bonn, Germany; FAU - Schittek, Karsten AU - Schittek K AD - Seminar of Geography and Geographical Education, University of Cologne, D-50931 Cologne, Germany; and. FAU - Isla Cuadrado, Johny AU - Isla Cuadrado J AD - Centro de Investigación para la Arqueología y el Desarrollo (ANDES), Lima 11, Perú FAU - Eitel, Bernhard AU - Eitel B AD - Geographisches Institut, Universität Heidelberg, D-69120 Heidelberg, Germany; FAU - Reindel, Markus AU - Reindel M AD - German Archaeological Institute (DAI), Commission for Archaeology of Non-European Cultures (KAAK), D-53173 Bonn, Germany; LA - eng SI - GENBANK/KJ489100 SI - GENBANK/KJ489101 SI - GENBANK/KJ489102 SI - GENBANK/KJ489103 SI - GENBANK/KJ489104 SI - GENBANK/KJ489105 SI - GENBANK/KJ489106 SI - GENBANK/KJ489107 SI - GENBANK/KJ489108 SI - GENBANK/KJ489109 SI - GENBANK/KJ489110 SI - GENBANK/KJ489111 SI - GENBANK/KJ489112 SI - GENBANK/KJ489113 SI - GENBANK/KJ489114 SI - GENBANK/KJ489115 SI - GENBANK/KJ489116 SI - GENBANK/KJ489117 SI - GENBANK/KJ489118 SI - GENBANK/KJ489119 SI - GENBANK/KJ489120 SI - GENBANK/KJ489121 SI - GENBANK/KJ489122 SI - GENBANK/KJ489123 SI - GENBANK/KJ489124 SI - GENBANK/KJ489125 SI - 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GENBANK/KJ489218 SI - GENBANK/KJ489219 SI - GENBANK/KJ489220 SI - GENBANK/KJ489221 SI - GENBANK/KJ489222 SI - GENBANK/KJ489223 SI - GENBANK/KJ489224 SI - GENBANK/KJ489225 SI - GENBANK/KJ489226 SI - GENBANK/KJ489227 SI - GENBANK/KJ489228 SI - GENBANK/KJ489229 SI - GENBANK/KJ489230 SI - GENBANK/KJ489231 SI - GENBANK/KJ489232 SI - GENBANK/KJ489233 SI - GENBANK/KJ489234 SI - GENBANK/KJ489235 SI - GENBANK/KJ489236 SI - GENBANK/KJ489237 SI - GENBANK/KJ489238 SI - GENBANK/KJ489239 SI - GENBANK/KJ489240 SI - GENBANK/KJ489241 SI - GENBANK/KJ489242 SI - GENBANK/KJ489243 SI - GENBANK/KJ489244 SI - GENBANK/KJ489245 SI - GENBANK/KJ489246 SI - GENBANK/KJ489247 SI - GENBANK/KJ489248 SI - GENBANK/KJ489249 SI - GENBANK/KJ489250 SI - GENBANK/KJ489251 SI - GENBANK/KJ489252 SI - GENBANK/KJ489253 SI - GENBANK/KJ489254 SI - GENBANK/KJ489255 SI - GENBANK/KJ489256 SI - GENBANK/KJ489257 SI - GENBANK/KJ489258 SI - GENBANK/KJ489259 SI - GENBANK/KJ489260 SI - GENBANK/KJ489261 SI - GENBANK/KJ489262 SI - GENBANK/KJ489263 SI - GENBANK/KJ489264 SI - GENBANK/KJ489265 SI - GENBANK/KJ489266 SI - GENBANK/KJ489267 SI - GENBANK/KJ489268 SI - GENBANK/KJ489269 SI - GENBANK/KJ489270 SI - GENBANK/KJ489271 SI - GENBANK/KJ489272 SI - GENBANK/KJ489273 SI - GENBANK/KJ489274 SI - GENBANK/KJ489275 SI - GENBANK/KJ489276 SI - GENBANK/KJ489277 SI - GENBANK/KJ489278 SI - GENBANK/KJ489279 SI - GENBANK/KJ489280 SI - GENBANK/KJ489281 SI - GENBANK/KJ489282 SI - GENBANK/KJ489283 SI - GENBANK/KJ489284 SI - GENBANK/KJ489285 SI - GENBANK/KJ489286 SI - GENBANK/KJ489287 SI - GENBANK/KJ489288 SI - GENBANK/KJ489289 SI - GENBANK/KJ489290 SI - GENBANK/KJ489291 SI - GENBANK/KJ489292 SI - GENBANK/KJ489293 SI - GENBANK/KJ489294 SI - GENBANK/KJ489295 SI - GENBANK/KJ489296 SI - GENBANK/KJ489297 SI - GENBANK/KJ489298 SI - GENBANK/KJ489299 SI - GENBANK/KJ489300 SI - GENBANK/KJ489301 SI - GENBANK/KJ489302 SI - GENBANK/KJ489303 SI - GENBANK/KJ489304 SI - GENBANK/KJ489305 SI - GENBANK/KJ489306 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140616 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology/methods MH - Base Sequence MH - Bayes Theorem MH - Climate Change/*history MH - Computer Simulation MH - Cultural Evolution/*history MH - DNA, Mitochondrial/isolation & purification MH - Droughts/*history MH - Haplotypes/genetics MH - History, 15th Century MH - History, Ancient MH - History, Medieval MH - Human Migration/*history MH - Humans MH - Models, Genetic MH - Molecular Sequence Data MH - Peru MH - Population Dynamics/*history MH - Sequence Analysis, DNA PMC - PMC4084453 OTO - NOTNLM OT - South America OT - ancient DNA OT - population history COIS- The authors declare no conflict of interest. EDAT- 2014/07/01 06:00 MHDA- 2014/09/24 06:00 PMCR- 2015/01/01 CRDT- 2014/07/01 06:00 PHST- 2014/07/01 06:00 [entrez] PHST- 2014/07/01 06:00 [pubmed] PHST- 2014/09/24 06:00 [medline] PHST- 2015/01/01 00:00 [pmc-release] AID - 1403466111 [pii] AID - 201403466 [pii] AID - 10.1073/pnas.1403466111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9443-8. doi: 10.1073/pnas.1403466111. Epub 2014 Jun 16. PMID- 24838416 OWN - NLM STAT- MEDLINE DCOM- 20150511 LR - 20160512 IS - 1618-2650 (Electronic) IS - 1618-2642 (Linking) VI - 406 IP - 19 DP - 2014 Jul TI - Novel contribution on the diagenetic physicochemical features of bone and teeth minerals, as substrates for ancient DNA typing. PG - 4691-704 LID - 10.1007/s00216-014-7863-z [doi] AB - The extraction of DNA from skeletal remains is a major step in archeological or forensic contexts. However, diagenesis of mineralized tissues often compromises this task although bones and teeth may represent preservation niches allowing DNA to persist over a wide timescale. This exceptional persistence is not only explained on the basis of complex organo-mineral interactions through DNA adsorption on apatite crystals composing the mineral part of bones and teeth but is also linked to environmental factors such as low temperatures and/or a dry environment. The preservation of the apatite phase itself, as an adsorption substrate, is another crucial factor susceptible to significantly impact the retrieval of DNA. With the view to bring physicochemical evidence of the preservation or alteration of diagenetic biominerals, we developed here an analytical approach on various skeletal specimens (ranging from ancient archeological samples to recent forensic specimens), allowing us to highlight several diagenetic indices so as to better apprehend the complexity of bone diagenesis. Based on complementary techniques (X-ray diffraction (XRD), Fourier transform infrared (FTIR), calcium and phosphate titrations, SEM-EDX, and gravimetry), we have identified specific indices that allow differentiating 11 biological samples, primarily according to the crystallinity and maturation state of the apatite phase. A good correlation was found between FTIR results from the analysis of the v3(PO4) and v4(PO4) vibrational domains and XRD-based crystallinity features. A maximal amount of information has been sought from this analytical approach, by way of optimized posttreatment of the data (spectral subtraction and enhancement of curve-fitting parameters). The good overall agreement found between all techniques leads to a rather complete picture of the diagenetic changes undergone by these 11 skeletal specimens. Although the heterogeneity and scarcity of the studied samples did not allow us to seek direct correlations with DNA persistence, the physicochemical parameters described in this work permit a fine differentiation of key properties of apatite crystals among post mortem samples. As a perspective, this analytical approach could be extended to more numerous sets of specimens so as to draw statistical relationships between mineral and molecular conservation. FAU - Grunenwald, A AU - Grunenwald A AD - CIRIMAT Carnot Institute  -  Phosphates, Pharmacotechnics, Biomaterials, University of Toulouse, CNRS/INPT/UPS, ENSIACET, 4 allée Emile Monso, 31030, Toulouse Cedex 4, France. FAU - Keyser, C AU - Keyser C FAU - Sautereau, A M AU - Sautereau AM FAU - Crubézy, E AU - Crubézy E FAU - Ludes, B AU - Ludes B FAU - Drouet, C AU - Drouet C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140517 PL - Germany TA - Anal Bioanal Chem JT - Analytical and bioanalytical chemistry JID - 101134327 RN - 0 (Phosphates) RN - SY7Q814VUP (Calcium) SB - IM MH - Aged, 80 and over MH - Anthropology, Physical/methods MH - Bone and Bones/*chemistry MH - Calcium/*analysis MH - DNA Fingerprinting/*methods MH - Female MH - Humans MH - Male MH - Middle Aged MH - Phosphates/*analysis MH - Spectroscopy, Fourier Transform Infrared/*methods MH - Tooth/*chemistry MH - X-Ray Diffraction/*methods EDAT- 2014/05/20 06:00 MHDA- 2015/05/12 06:00 CRDT- 2014/05/20 06:00 PHST- 2014/02/09 00:00 [received] PHST- 2014/04/28 00:00 [accepted] PHST- 2014/04/25 00:00 [revised] PHST- 2014/05/20 06:00 [entrez] PHST- 2014/05/20 06:00 [pubmed] PHST- 2015/05/12 06:00 [medline] AID - 10.1007/s00216-014-7863-z [doi] PST - ppublish SO - Anal Bioanal Chem. 2014 Jul;406(19):4691-704. doi: 10.1007/s00216-014-7863-z. Epub 2014 May 17. PMID- 24801631 OWN - NLM STAT- MEDLINE DCOM- 20141219 LR - 20140616 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 154 IP - 3 DP - 2014 Jul TI - Locals, resettlers, and pilgrims: a genetic portrait of three pre-Columbian Andean populations. PG - 402-12 LID - 10.1002/ajpa.22524 [doi] AB - The common practice of resettlement and the development of administrative and ceremonial systems shaped the population landscape of the Andean region under the Inca rule. The area surrounding Coropuna and Solimana volcanoes, in the Arequipa region (Peru), carried a high-density, multiethnic population. We studied the genetic variation among three pre-Columbian populations from three functionally diverse archaeological sites excavated in this region. By analyzing the genetic composition of a large ceremonial center (Acchaymarca), an isolated pastoral settlement (Tompullo 2), and an agricultural settlement characterized by architectural features rare in the region (Puca), we investigated the patterns of population movements and the distribution of genetic diversity. We obtained mitochondrial DNA sequences for 25 individuals and autosomal microsatellite profiles for 20 individuals from Acchaymarca and Puca sites. These were compared with previously published genetic data for Tompullo 2 and other pre-Columbian populations. We found differences among the genetic portraits of the three populations, congruent with the archaeologically described functions and characteristics of the sites. The Acchaymarca population had the highest genetic diversity and possessed the lowest number of unique mtDNA haplotypes. The Tompullo 2 population exhibited the lowest level of genetic diversity. The Puca population was distinct from the other two populations owing to a high frequency of haplogroup A haplotypes, what potentially explains the non-local character of the burial architecture. Our analyses of microsatellite data suggest that gene flow between sites was mostly mediated by females, which is consistent with ethnohistorical knowledge of the social organization of the pre-Columbian communities. CI - © 2014 Wiley Periodicals, Inc. FAU - Baca, Mateusz AU - Baca M AD - Centre for Pre-Columbian Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927, Warsaw, Poland. FAU - Molak, Martyna AU - Molak M FAU - Sobczyk, Maciej AU - Sobczyk M FAU - Węgleński, Piotr AU - Węgleński P FAU - Stankovic, Anna AU - Stankovic A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140506 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Cemeteries MH - DNA, Mitochondrial/genetics MH - Female MH - Genetic Variation/*genetics MH - *Genetics, Population MH - Haplotypes MH - Human Migration MH - Humans MH - Indians, South American/*genetics MH - Male MH - Microsatellite Repeats MH - Peru MH - Sex Determination Analysis OTO - NOTNLM OT - Acchaymarca OT - Puca OT - Tompullo 2 OT - ancient DNA OT - microsatellites EDAT- 2014/05/08 06:00 MHDA- 2014/12/20 06:00 CRDT- 2014/05/08 06:00 PHST- 2013/11/26 00:00 [received] PHST- 2014/04/18 00:00 [accepted] PHST- 2014/05/08 06:00 [entrez] PHST- 2014/05/08 06:00 [pubmed] PHST- 2014/12/20 06:00 [medline] AID - 10.1002/ajpa.22524 [doi] PST - ppublish SO - Am J Phys Anthropol. 2014 Jul;154(3):402-12. doi: 10.1002/ajpa.22524. Epub 2014 May 6. PMID- 24906487 OWN - NLM STAT- MEDLINE DCOM- 20150130 LR - 20211021 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 15 IP - 1 DP - 2014 Jun 6 TI - Improved multiple displacement amplification (iMDA) and ultraclean reagents. PG - 443 LID - 10.1186/1471-2164-15-443 [doi] LID - 443 AB - BACKGROUND: Next-generation sequencing sample preparation requires nanogram to microgram quantities of DNA; however, many relevant samples are comprised of only a few cells. Genomic analysis of these samples requires a whole genome amplification method that is unbiased and free of exogenous DNA contamination. To address these challenges we have developed protocols for the production of DNA-free consumables including reagents and have improved upon multiple displacement amplification (iMDA). RESULTS: A specialized ethylene oxide treatment was developed that renders free DNA and DNA present within Gram positive bacterial cells undetectable by qPCR. To reduce DNA contamination in amplification reagents, a combination of ion exchange chromatography, filtration, and lot testing protocols were developed. Our multiple displacement amplification protocol employs a second strand-displacing DNA polymerase, improved buffers, improved reaction conditions and DNA free reagents. The iMDA protocol, when used in combination with DNA-free laboratory consumables and reagents, significantly improved efficiency and accuracy of amplification and sequencing of specimens with moderate to low levels of DNA. The sensitivity and specificity of sequencing of amplified DNA prepared using iMDA was compared to that of DNA obtained with two commercial whole genome amplification kits using 10 fg (~1-2 bacterial cells worth) of bacterial genomic DNA as a template. Analysis showed >99% of the iMDA reads mapped to the template organism whereas only 0.02% of the reads from the commercial kits mapped to the template. To assess the ability of iMDA to achieve balanced genomic coverage, a non-stochastic amount of bacterial genomic DNA (1 pg) was amplified and sequenced, and data obtained were compared to sequencing data obtained directly from genomic DNA. The iMDA DNA and genomic DNA sequencing had comparable coverage 99.98% of the reference genome at ≥1X coverage and 99.9% at ≥5X coverage while maintaining both balance and representation of the genome. CONCLUSIONS: The iMDA protocol in combination with DNA-free laboratory consumables, significantly improved the ability to sequence specimens with low levels of DNA. iMDA has broad utility in metagenomics, diagnostics, ancient DNA analysis, pre-implantation embryo screening, single-cell genomics, whole genome sequencing of unculturable organisms, and forensic applications for both human and microbial targets. FAU - Motley, S Timothy AU - Motley ST FAU - Picuri, John M AU - Picuri JM FAU - Crowder, Chris D AU - Crowder CD FAU - Minich, Jeremiah J AU - Minich JJ FAU - Hofstadler, Steven A AU - Hofstadler SA FAU - Eshoo, Mark W AU - Eshoo MW AD - Ibis Biosciences an Abbott Company, 2251 Faraday Ave, Suite 150, Carlsbad, CA 92008, USA. Mark.eshoo@abbott.com. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140606 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (Indicators and Reagents) RN - 9007-49-2 (DNA) RN - JJH7GNN18P (Ethylene Oxide) SB - IM MH - DNA/analysis MH - *DNA Contamination MH - Ethylene Oxide/pharmacology MH - Genome, Bacterial MH - Genome, Human MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Indicators and Reagents MH - Polymerase Chain Reaction MH - Reproducibility of Results MH - Sequence Analysis, DNA/*methods PMC - PMC4061449 EDAT- 2014/06/08 06:00 MHDA- 2015/01/31 06:00 PMCR- 2014/06/06 CRDT- 2014/06/08 06:00 PHST- 2013/10/23 00:00 [received] PHST- 2014/05/29 00:00 [accepted] PHST- 2014/06/08 06:00 [entrez] PHST- 2014/06/08 06:00 [pubmed] PHST- 2015/01/31 06:00 [medline] PHST- 2014/06/06 00:00 [pmc-release] AID - 1471-2164-15-443 [pii] AID - 6118 [pii] AID - 10.1186/1471-2164-15-443 [doi] PST - epublish SO - BMC Genomics. 2014 Jun 6;15(1):443. doi: 10.1186/1471-2164-15-443. PMID- 24901650 OWN - NLM STAT- MEDLINE DCOM- 20150623 LR - 20211203 IS - 1553-7404 (Electronic) IS - 1553-7390 (Print) IS - 1553-7390 (Linking) VI - 10 IP - 6 DP - 2014 Jun TI - Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands. PG - e1004401 LID - 10.1371/journal.pgen.1004401 [doi] LID - e1004401 AB - The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700-6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization. FAU - Fernández, Eva AU - Fernández E AD - Research Centre in Evolutionary Anthropology and Paleoecology, Liverpool John Moores University, Liverpool, United Kingdom; Laboratorio de Genética Forense y Genética de Poblaciones, Dpto. Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain. FAU - Pérez-Pérez, Alejandro AU - Pérez-Pérez A AD - Dpto. Biología Animal-Unidad de Antropología, Facultad de Biología, Universitat de Barcelona, Barcelona, Spain. FAU - Gamba, Cristina AU - Gamba C AD - Laboratorio de Genética Forense y Genética de Poblaciones, Dpto. Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain. FAU - Prats, Eva AU - Prats E AD - Centro de Investigación y Desarrollo, Consejo Superior de Investigaciones Científicas, Barcelona, Spain. FAU - Cuesta, Pedro AU - Cuesta P AD - Dpto. de Apoyo a la Investigación, Servicios informáticos de la Universidad Complutense de Madrid, Madrid, Spain. FAU - Anfruns, Josep AU - Anfruns J AD - Dep. Prehistoria, Facultad de Filosofía y Letras, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain. FAU - Molist, Miquel AU - Molist M AD - Dep. Prehistoria, Facultad de Filosofía y Letras, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain. FAU - Arroyo-Pardo, Eduardo AU - Arroyo-Pardo E AD - Laboratorio de Genética Forense y Genética de Poblaciones, Dpto. Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain. FAU - Turbón, Daniel AU - Turbón D AD - Dpto. Biología Animal-Unidad de Antropología, Facultad de Biología, Universitat de Barcelona, Barcelona, Spain. LA - eng SI - GENBANK/KF601411 SI - GENBANK/KF601412 SI - GENBANK/KF601413 SI - GENBANK/KF601414 SI - GENBANK/KF601415 SI - GENBANK/KF601416 SI - GENBANK/KF601417 SI - GENBANK/KF601418 SI - GENBANK/KF601419 SI - GENBANK/KF601420 SI - GENBANK/KF601421 SI - GENBANK/KF601422 SI - GENBANK/KF601423 SI - GENBANK/KF601424 SI - GENBANK/KF601425 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140605 PL - United States TA - PLoS Genet JT - PLoS genetics JID - 101239074 RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture MH - Archaeology MH - Base Sequence MH - Cyprus MH - DNA, Mitochondrial/*genetics MH - Ethnicity/*genetics MH - Europe MH - Gene Frequency MH - Gene Pool MH - Genetics, Population MH - Greece, Ancient MH - Haplotypes/genetics MH - History, Ancient MH - *Human Migration MH - Humans MH - Mitochondria/*genetics MH - Molecular Sequence Data MH - Principal Component Analysis MH - Sequence Analysis, DNA MH - Skeleton PMC - PMC4046922 COIS- The authors have declared that no competing interests exist. EDAT- 2014/06/06 06:00 MHDA- 2015/06/24 06:00 PMCR- 2014/06/05 CRDT- 2014/06/06 06:00 PHST- 2013/09/05 00:00 [received] PHST- 2014/04/09 00:00 [accepted] PHST- 2014/06/06 06:00 [entrez] PHST- 2014/06/06 06:00 [pubmed] PHST- 2015/06/24 06:00 [medline] PHST- 2014/06/05 00:00 [pmc-release] AID - PGENETICS-D-13-02446 [pii] AID - 10.1371/journal.pgen.1004401 [doi] PST - epublish SO - PLoS Genet. 2014 Jun 5;10(6):e1004401. doi: 10.1371/journal.pgen.1004401. eCollection 2014 Jun. PMID- 24924389 OWN - NLM STAT- MEDLINE DCOM- 20150126 LR - 20140613 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 56 IP - 6 DP - 2014 Jun TI - Library construction for ancient genomics: single strand or double strand? PG - 289-90, 292-6, 298, passim LID - 10.2144/000114176 [doi] AB - A novel method of library construction that takes advantage of a single-stranded DNA ligase has been recently described and used to generate high-resolution genomes from ancient DNA samples. While this method is effective and appears to recover a greater fraction of endogenous ancient material, there has been no direct comparison of results from different library construction methods on a diversity of ancient DNA samples. In addition, the single-stranded method is limited by high cost and lengthy preparation time and is restricted to the Illumina sequencing platform. Here we present in-depth comparisons of the different available library construction methods for DNA purified from 16 ancient and modern faunal and human remains, covering a range of different taphonomic and climatic conditions. We further present a DNA purification method for ancient samples that permits the concentration of a large volume of dissolved extract with minimal manipulation and methodological improvements to the single-stranded method to render it more economical and versatile, in particular to expand its use to both the Illumina and the Ion Torrent sequencing platforms. We show that the single-stranded library construction method improves the relative recovery of endogenous to exogenous DNA for most, but not all, of our ancient extracts. FAU - Bennett, E Andrew AU - Bennett EA AD - Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France. FAU - Massilani, Diyendo AU - Massilani D AD - Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France. FAU - Lizzo, Giulia AU - Lizzo G AD - Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France. FAU - Daligault, Julien AU - Daligault J AD - Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France. FAU - Geigl, Eva-Maria AU - Geigl EM AD - Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France. FAU - Grange, Thierry AU - Grange T AD - Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140601 PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Single-Stranded) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Cattle MH - DNA/*genetics MH - DNA, Single-Stranded/*genetics MH - *Gene Library MH - Genomics/*methods MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Mammoths MH - Paleontology/*methods MH - Pan troglodytes MH - Sequence Analysis, DNA/methods OTO - NOTNLM OT - DNA library preparation OT - ancient DNA OT - next-generation sequencing OT - palaeogenomics EDAT- 2014/06/14 06:00 MHDA- 2015/01/27 06:00 CRDT- 2014/06/14 06:00 PHST- 2013/12/02 00:00 [received] PHST- 2014/05/27 00:00 [accepted] PHST- 2014/06/14 06:00 [entrez] PHST- 2014/06/14 06:00 [pubmed] PHST- 2015/01/27 06:00 [medline] AID - 000114176 [pii] AID - 10.2144/000114176 [doi] PST - epublish SO - Biotechniques. 2014 Jun 1;56(6):289-90, 292-6, 298, passim. doi: 10.2144/000114176. eCollection 2014 Jun. PMID- 24471807 OWN - NLM STAT- MEDLINE DCOM- 20140801 LR - 20140614 IS - 1937-2345 (Electronic) IS - 0022-3395 (Linking) VI - 100 IP - 3 DP - 2014 Jun TI - Detection of ancient DNA of Encephalitozoon intestinalis (Microsporidia) in archaeological material. PG - 356-9 LID - 10.1645/13-232.1 [doi] AB - Ancient DNA (aDNA) of Encephalitozoon intestinalis (Microsporidia, Fungi) was detected in archaeological material originated from New Town of Prague (Czech Republic) with the use of molecular methods. Microsporidial aDNA was found in 3 samples originating from 2 objects, in a well/cesspit (samples from layers from the 18th century) and in a well from the 18th/19th century. The ability to use molecular methods to detect microsporidia extends the range of paleoparasitological inquiry, and could contribute to a better understanding of parasites shared between human and animals. FAU - Myšková, Eva AU - Myšková E AD - Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, České Budějovice 370 05, Czech Republic; FAU - Ditrich, Oleg AU - Ditrich O FAU - Sak, Bohumil AU - Sak B FAU - Kváč, Martin AU - Kváč M FAU - Cymbalak, Tomasz AU - Cymbalak T LA - eng SI - GENBANK/JX204837 SI - GENBANK/JX204838 SI - GENBANK/JX204839 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140128 PL - United States TA - J Parasitol JT - The Journal of parasitology JID - 7803124 RN - 0 (DNA, Fungal) SB - IM MH - Animals MH - Base Sequence MH - Czech Republic MH - DNA, Fungal/chemistry/history/*isolation & purification MH - Encephalitozoon/*genetics/isolation & purification MH - Encephalitozoonosis/*history MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Molecular Sequence Data EDAT- 2014/01/30 06:00 MHDA- 2014/08/02 06:00 CRDT- 2014/01/30 06:00 PHST- 2014/01/30 06:00 [entrez] PHST- 2014/01/30 06:00 [pubmed] PHST- 2014/08/02 06:00 [medline] AID - 10.1645/13-232.1 [doi] PST - ppublish SO - J Parasitol. 2014 Jun;100(3):356-9. doi: 10.1645/13-232.1. Epub 2014 Jan 28. PMID- 24865457 OWN - NLM STAT- MEDLINE DCOM- 20151203 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 5 DP - 2014 TI - Back to BaySICS: a user-friendly program for Bayesian Statistical Inference from Coalescent Simulations. PG - e98011 LID - 10.1371/journal.pone.0098011 [doi] LID - e98011 AB - Inference of population demographic history has vastly improved in recent years due to a number of technological and theoretical advances including the use of ancient DNA. Approximate Bayesian computation (ABC) stands among the most promising methods due to its simple theoretical fundament and exceptional flexibility. However, limited availability of user-friendly programs that perform ABC analysis renders it difficult to implement, and hence programming skills are frequently required. In addition, there is limited availability of programs able to deal with heterochronous data. Here we present the software BaySICS: Bayesian Statistical Inference of Coalescent Simulations. BaySICS provides an integrated and user-friendly platform that performs ABC analyses by means of coalescent simulations from DNA sequence data. It estimates historical demographic population parameters and performs hypothesis testing by means of Bayes factors obtained from model comparisons. Although providing specific features that improve inference from datasets with heterochronous data, BaySICS also has several capabilities making it a suitable tool for analysing contemporary genetic datasets. Those capabilities include joint analysis of independent tables, a graphical interface and the implementation of Markov-chain Monte Carlo without likelihoods. FAU - Sandoval-Castellanos, Edson AU - Sandoval-Castellanos E AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Department of Zoology, Stockholm University, Stockholm, Sweden. FAU - Palkopoulou, Eleftheria AU - Palkopoulou E AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Department of Zoology, Stockholm University, Stockholm, Sweden. FAU - Dalén, Love AU - Dalén L AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140527 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - *Bayes Theorem MH - *Computer Simulation MH - *Genetics, Population MH - Humans MH - Markov Chains MH - *Models, Theoretical MH - Population Groups/genetics MH - *Software PMC - PMC4035278 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2014/05/29 06:00 MHDA- 2015/12/15 06:00 PMCR- 2014/05/27 CRDT- 2014/05/29 06:00 PHST- 2013/11/12 00:00 [received] PHST- 2014/04/28 00:00 [accepted] PHST- 2014/05/29 06:00 [entrez] PHST- 2014/05/29 06:00 [pubmed] PHST- 2015/12/15 06:00 [medline] PHST- 2014/05/27 00:00 [pmc-release] AID - PONE-D-13-47391 [pii] AID - 10.1371/journal.pone.0098011 [doi] PST - epublish SO - PLoS One. 2014 May 27;9(5):e98011. doi: 10.1371/journal.pone.0098011. eCollection 2014. PMID- 24753607 OWN - NLM STAT- MEDLINE DCOM- 20140702 LR - 20211021 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 111 IP - 18 DP - 2014 May 6 TI - Patterns of coding variation in the complete exomes of three Neandertals. PG - 6666-71 LID - 10.1073/pnas.1405138111 [doi] AB - We present the DNA sequence of 17,367 protein-coding genes in two Neandertals from Spain and Croatia and analyze them together with the genome sequence recently determined from a Neandertal from southern Siberia. Comparisons with present-day humans from Africa, Europe, and Asia reveal that genetic diversity among Neandertals was remarkably low, and that they carried a higher proportion of amino acid-changing (nonsynonymous) alleles inferred to alter protein structure or function than present-day humans. Thus, Neandertals across Eurasia had a smaller long-term effective population than present-day humans. We also identify amino acid substitutions in Neandertals and present-day humans that may underlie phenotypic differences between the two groups. We find that genes involved in skeletal morphology have changed more in the lineage leading to Neandertals than in the ancestral lineage common to archaic and modern humans, whereas genes involved in behavior and pigmentation have changed more on the modern human lineage. FAU - Castellano, Sergi AU - Castellano S AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. FAU - Parra, Genís AU - Parra G FAU - Sánchez-Quinto, Federico A AU - Sánchez-Quinto FA FAU - Racimo, Fernando AU - Racimo F FAU - Kuhlwilm, Martin AU - Kuhlwilm M FAU - Kircher, Martin AU - Kircher M FAU - Sawyer, Susanna AU - Sawyer S FAU - Fu, Qiaomei AU - Fu Q FAU - Heinze, Anja AU - Heinze A FAU - Nickel, Birgit AU - Nickel B FAU - Dabney, Jesse AU - Dabney J FAU - Siebauer, Michael AU - Siebauer M FAU - White, Louise AU - White L FAU - Burbano, Hernán A AU - Burbano HA FAU - Renaud, Gabriel AU - Renaud G FAU - Stenzel, Udo AU - Stenzel U FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C FAU - de la Rasilla, Marco AU - de la Rasilla M FAU - Rosas, Antonio AU - Rosas A FAU - Rudan, Pavao AU - Rudan P FAU - Brajković, Dejana AU - Brajković D FAU - Kucan, Željko AU - Kucan Ž FAU - Gušic, Ivan AU - Gušic I FAU - Shunkov, Michael V AU - Shunkov MV FAU - Derevianko, Anatoli P AU - Derevianko AP FAU - Viola, Bence AU - Viola B FAU - Meyer, Matthias AU - Meyer M FAU - Kelso, Janet AU - Kelso J FAU - Andrés, Aida M AU - Andrés AM FAU - Pääbo, Svante AU - Pääbo S LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140421 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Substitution MH - Animals MH - Croatia MH - DNA/genetics MH - *Exome MH - Gene Frequency MH - *Genetic Variation MH - Humans MH - Neanderthals/*genetics MH - Paleontology MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Siberia MH - Spain PMC - PMC4020111 OTO - NOTNLM OT - ancient DNA OT - exome capture OT - paleogenetics OT - site frequency spectra COIS- The authors declare no conflict of interest. EDAT- 2014/04/23 06:00 MHDA- 2014/07/06 06:00 PMCR- 2014/11/06 CRDT- 2014/04/23 06:00 PHST- 2014/04/23 06:00 [entrez] PHST- 2014/04/23 06:00 [pubmed] PHST- 2014/07/06 06:00 [medline] PHST- 2014/11/06 00:00 [pmc-release] AID - 1405138111 [pii] AID - 201405138 [pii] AID - 10.1073/pnas.1405138111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 May 6;111(18):6666-71. doi: 10.1073/pnas.1405138111. Epub 2014 Apr 21. PMID- 24786081 OWN - NLM STAT- MEDLINE DCOM- 20140623 LR - 20150107 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 344 IP - 6183 DP - 2014 May 2 TI - Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. PG - 523-7 LID - 10.1126/science.1250368 [doi] AB - Ancient DNA sequencing has recently provided high-coverage archaic human genomes. However, the evolution of epigenetic regulation along the human lineage remains largely unexplored. We reconstructed the full DNA methylation maps of the Neandertal and the Denisovan by harnessing the natural degradation processes of methylated and unmethylated cytosines. Comparing these ancient methylation maps to those of present-day humans, we identified ~2000 differentially methylated regions (DMRs). Particularly, we found substantial methylation changes in the HOXD cluster that may explain anatomical differences between archaic and present-day humans. Additionally, we found that DMRs are significantly more likely to be associated with diseases. This study provides insight into the epigenetic landscape of our closest evolutionary relatives and opens a window to explore the epigenomes of extinct species. FAU - Gokhman, David AU - Gokhman D AD - Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel. FAU - Lavi, Eitan AU - Lavi E FAU - Prüfer, Kay AU - Prüfer K FAU - Fraga, Mario F AU - Fraga MF FAU - Riancho, José A AU - Riancho JA FAU - Kelso, Janet AU - Kelso J FAU - Pääbo, Svante AU - Pääbo S FAU - Meshorer, Eran AU - Meshorer E FAU - Carmel, Liran AU - Carmel L LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140417 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 SB - IM CIN - Brain Behav Evol. 2014;84(3):169-71. doi: 10.1159/000365650. PMID: 25277105 CIN - Nature. 2019 Sep;573(7775):475-476. doi: 10.1038/d41586-019-02820-0. PMID: 31551547 MH - Animals MH - *DNA Methylation MH - *Epigenesis, Genetic MH - *Evolution, Molecular MH - *Genome, Human MH - Humans MH - Neanderthals/*genetics EDAT- 2014/05/03 06:00 MHDA- 2014/06/24 06:00 CRDT- 2014/05/03 06:00 PHST- 2014/05/03 06:00 [entrez] PHST- 2014/05/03 06:00 [pubmed] PHST- 2014/06/24 06:00 [medline] AID - science.1250368 [pii] AID - 10.1126/science.1250368 [doi] PST - ppublish SO - Science. 2014 May 2;344(6183):523-7. doi: 10.1126/science.1250368. Epub 2014 Apr 17. PMID- 25757334 OWN - NLM STAT- MEDLINE DCOM- 20150320 LR - 20191113 IS - 0555-1099 (Print) IS - 0555-1099 (Linking) VI - 50 IP - 3 DP - 2014 May-Jun TI - [Application of repair enzymes to improve the quality of degraded DNA templates for PCR amplification]. PG - 264-72 AB - PCR amplification of severely degraded DNA, including ancient DNA, forensic samples, and preparations from deeply processed foodstuffs, is a serious problem. Living organisms have a set of enzymes to repair lesions in their DNA. In this work, we have developed and characterized model systems of degraded high-molecular-weight DNA with a predominance of different types of damage. It was shown that depurination and oxidation of the model plasmid DNA template led to a decrease in the PCR efficiency. A set of enzymes performing a full cycle of excision repair of some lesions was determined. The treatment of model-damaged substrates with this set of enzymes resulted in an increased PCR product yield as compared with that of the unrepaired samples. FAU - Dovgerd, A P AU - Dovgerd AP FAU - Zharkov, D O AU - Zharkov DO LA - rus PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Russia (Federation) TA - Prikl Biokhim Mikrobiol JT - Prikladnaia biokhimiia i mikrobiologiia JID - 0023416 RN - 0 (Bacterial Proteins) RN - 0 (DNA, Bacterial) RN - 0 (Viral Proteins) RN - EC 2.7.1.78 (Polynucleotide 5'-Hydroxyl-Kinase) RN - EC 2.7.7.- (Taq Polymerase) RN - EC 3.1.- (Ribonucleases) RN - EC 3.2.2.- (DNA Glycosylases) RN - EC 3.2.2.- (oxoguanine glycosylase 1, human) RN - EC 4.2.99.18 (APEX1 protein, human) RN - EC 4.2.99.18 (DNA-(Apurinic or Apyrimidinic Site) Lyase) RN - EC 6.5.1.- (DNA Ligases) RN - EC 6.5.1.1 (DNA Ligase ATP) SB - IM MH - Animals MH - Bacterial Proteins/*chemistry MH - Bacteriophage T4/chemistry MH - Cattle MH - DNA Damage MH - DNA Glycosylases/chemistry MH - DNA Ligase ATP MH - DNA Ligases/chemistry MH - *DNA Repair MH - DNA, Bacterial/*chemistry MH - DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry MH - Escherichia coli/chemistry MH - Humans MH - Pancreas/chemistry/enzymology MH - Plasmids/*chemistry MH - Polymerase Chain Reaction/*methods MH - Polynucleotide 5'-Hydroxyl-Kinase/chemistry MH - Ribonucleases/chemistry MH - Taq Polymerase/chemistry MH - Viral Proteins/*chemistry EDAT- 2015/03/12 06:00 MHDA- 2015/03/21 06:00 CRDT- 2015/03/12 06:00 PHST- 2015/03/12 06:00 [entrez] PHST- 2015/03/12 06:00 [pubmed] PHST- 2015/03/21 06:00 [medline] AID - 10.7868/s0555109914030210 [doi] PST - ppublish SO - Prikl Biokhim Mikrobiol. 2014 May-Jun;50(3):264-72. doi: 10.7868/s0555109914030210. PMID- 24702983 OWN - NLM STAT- MEDLINE DCOM- 20141231 LR - 20140428 IS - 1872-8383 (Electronic) IS - 0169-5347 (Linking) VI - 29 IP - 5 DP - 2014 May TI - Why we are not all multiregionalists now. PG - 248-51 LID - S0169-5347(14)00047-0 [pii] LID - 10.1016/j.tree.2014.03.001 [doi] AB - Recent revelations that human genomes contain DNA introgressed through interbreeding with archaic populations outside of Africa have led to reassessments of models for the origins of our species. The fact that small portions of the DNA of recent Homo sapiens derive from ancient populations in more than one region of the world makes our origins 'multiregional', but does that mean that the multiregional model of modern human origins has been proved correct? The extent of archaic assimilation in living humans remains modest, and fossil evidence outside of Africa shows little sign of the long-term morphological continuity through to recent humans expected from the multiregional model. Thus, rather than multiregionalism, a recent African origin (RAO) model for modern humans is still supported by the data. CI - Copyright © 2014. Published by Elsevier Ltd. FAU - Stringer, Chris AU - Stringer C AD - Department of Earth Sciences, The Natural History Museum, London, SW7 5BD, UK. Electronic address: c.stringer@nhm.ac.uk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140401 PL - England TA - Trends Ecol Evol JT - Trends in ecology & evolution JID - 8805125 SB - IM MH - Animals MH - *Biological Evolution MH - Gene Flow MH - Genetic Speciation MH - Genetics, Population MH - Hominidae/genetics MH - Humans/genetics MH - *Hybridization, Genetic MH - Neanderthals OTO - NOTNLM OT - Africa OT - Homo sapiens OT - ancient DNA OT - human evolution OT - human origins OT - hybridisation OT - modern humans OT - multiregionalism EDAT- 2014/04/08 06:00 MHDA- 2015/01/01 06:00 CRDT- 2014/04/08 06:00 PHST- 2014/01/21 00:00 [received] PHST- 2014/03/01 00:00 [revised] PHST- 2014/03/04 00:00 [accepted] PHST- 2014/04/08 06:00 [entrez] PHST- 2014/04/08 06:00 [pubmed] PHST- 2015/01/01 06:00 [medline] AID - S0169-5347(14)00047-0 [pii] AID - 10.1016/j.tree.2014.03.001 [doi] PST - ppublish SO - Trends Ecol Evol. 2014 May;29(5):248-51. doi: 10.1016/j.tree.2014.03.001. Epub 2014 Apr 1. PMID- 24497031 OWN - NLM STAT- MEDLINE DCOM- 20140926 LR - 20141120 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 31 IP - 5 DP - 2014 May TI - Assessing the maximum contribution from ancient populations. PG - 1248-60 LID - 10.1093/molbev/msu059 [doi] AB - Ancestral relationships between populations separated by time represent an often neglected dimension in population genetics, a field which historically has focused on analysis of spatially distributed samples from the same point in time. Models are usually straightforward when two time-separated populations are assumed to be completely isolated from all other populations. However, this is usually an unrealistically stringent assumption when there is gene flow with other populations. Here, we investigate continuity in the presence of gene flow from unknown populations. This setup allows a more nuanced treatment of questions regarding population continuity in terms of "level of contribution" from a particular ancient population to a more recent population. We propose a statistical framework which makes use of a biallelic marker sampled at two different points in time to assess population contribution, and present two different interpretations of the concept. We apply the approach to published data from a prehistoric human population in Scandinavia (Malmström H, Gilbert MTP, Thomas MG, Brandström M, Storå J, Molnar P, Andersen PK, Bendixen C, Holmlund G, Götherström A, et al. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol. 19:1758-1762) and Pleistocene woolly mammoth (Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG. 2007. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol. 17:1072-1075; Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Gröcke DR, Matheus P, Zazula G, et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326). FAU - Sjödin, Per AU - Sjödin P AD - Department of Evolutionary Biology, Uppsala University, Norbyvägen, Sweden. FAU - Skoglund, Pontus AU - Skoglund P FAU - Jakobsson, Mattias AU - Jakobsson M LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140203 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Computer Simulation MH - DNA, Mitochondrial/genetics/history MH - *Evolution, Molecular MH - Fossils MH - Gene Flow MH - Gene Frequency MH - Genetic Drift MH - *Genetics, Population MH - History, Ancient MH - Humans MH - Mammoths/genetics MH - *Models, Genetic MH - Scandinavian and Nordic Countries MH - Siberia OTO - NOTNLM OT - ancient DNA OT - continuity OT - population genetics EDAT- 2014/02/06 06:00 MHDA- 2014/09/27 06:00 CRDT- 2014/02/06 06:00 PHST- 2014/02/06 06:00 [entrez] PHST- 2014/02/06 06:00 [pubmed] PHST- 2014/09/27 06:00 [medline] AID - msu059 [pii] AID - 10.1093/molbev/msu059 [doi] PST - ppublish SO - Mol Biol Evol. 2014 May;31(5):1248-60. doi: 10.1093/molbev/msu059. Epub 2014 Feb 3. PMID- 24573854 OWN - NLM STAT- MEDLINE DCOM- 20141021 LR - 20211021 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 281 IP - 1781 DP - 2014 Apr 22 TI - Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity. PG - 20133236 LID - 10.1098/rspb.2013.3236 [doi] LID - 20133236 AB - The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second-nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth-nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis. FAU - Müller, Romy AU - Müller R AD - Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, , 131 Princess Street, Manchester M1 7DN, UK, Department of Archaeology, Durham University, , South Road, Durham DH1 3LE, UK. FAU - Roberts, Charlotte A AU - Roberts CA FAU - Brown, Terence A AU - Brown TA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140226 PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 SB - IM MH - Base Sequence MH - Bone and Bones/chemistry MH - Cluster Analysis MH - Europe MH - *Evolution, Molecular MH - Genetic Variation/*genetics MH - Genotype MH - Humans MH - Molecular Sequence Data MH - Mycobacterium tuberculosis/*genetics MH - Phylogeny MH - Polymorphism, Genetic/genetics MH - Sequence Analysis, DNA MH - Species Specificity PMC - PMC3953847 OTO - NOTNLM OT - ancient DNA OT - mixed infection OT - single nucleotide polymorphisms OT - strain typing OT - tuberculosis EDAT- 2014/02/28 06:00 MHDA- 2014/10/22 06:00 PMCR- 2014/04/22 CRDT- 2014/02/28 06:00 PHST- 2014/02/28 06:00 [entrez] PHST- 2014/02/28 06:00 [pubmed] PHST- 2014/10/22 06:00 [medline] PHST- 2014/04/22 00:00 [pmc-release] AID - rspb.2013.3236 [pii] AID - rspb20133236 [pii] AID - 10.1098/rspb.2013.3236 [doi] PST - epublish SO - Proc Biol Sci. 2014 Feb 26;281(1781):20133236. doi: 10.1098/rspb.2013.3236. Print 2014 Apr 22. PMID- 24744352 OWN - NLM STAT- MEDLINE DCOM- 20140428 LR - 20140418 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 344 IP - 6181 DP - 2014 Apr 18 TI - Epigenetics. Ancient DNA holds clues to gene activity in extinct humans. PG - 245-6 LID - 10.1126/science.344.6181.245 [doi] FAU - Pennisi, Elizabeth AU - Pennisi E LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Bone and Bones/anatomy & histology MH - DNA/*genetics MH - *DNA Methylation MH - *Epigenesis, Genetic MH - Extinction, Biological MH - Female MH - *Fossils MH - Gene Silencing MH - *Genome MH - *Genome, Human MH - Humans MH - Neanderthals/*genetics MH - Sequence Analysis, DNA EDAT- 2014/04/20 06:00 MHDA- 2014/04/29 06:00 CRDT- 2014/04/19 06:00 PHST- 2014/04/19 06:00 [entrez] PHST- 2014/04/20 06:00 [pubmed] PHST- 2014/04/29 06:00 [medline] AID - 344/6181/245 [pii] AID - 10.1126/science.344.6181.245 [doi] PST - ppublish SO - Science. 2014 Apr 18;344(6181):245-6. doi: 10.1126/science.344.6181.245. PMID- 24639531 OWN - NLM STAT- MEDLINE DCOM- 20140602 LR - 20211021 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 111 IP - 13 DP - 2014 Apr 1 TI - Extinct New Zealand megafauna were not in decline before human colonization. PG - 4922-7 LID - 10.1073/pnas.1314972111 [doi] AB - The extinction of New Zealand's moa (Aves: Dinornithiformes) followed the arrival of humans in the late 13th century and was the final event of the prehistoric Late Quaternary megafauna extinctions. Determining the state of the moa populations in the pre-extinction period is fundamental to understanding the causes of the event. We sampled 281 moa individuals and combined radiocarbon dating with ancient DNA analyses to help resolve the extinction debate and gain insights into moa biology. The samples, which were predominantly from the last 4,000 years preceding the extinction, represent four sympatric moa species excavated from five adjacent fossil deposits. We characterized the moa assemblage using mitochondrial DNA and nuclear microsatellite markers developed specifically for moa. Although genetic diversity differed significantly among the four species, we found that the millennia preceding the extinction were characterized by a remarkable degree of genetic stability in all species, with no loss of heterozygosity and no shifts in allele frequencies over time. The extinction event itself was too rapid to be manifested in the moa gene pools. Contradicting previous claims of a decline in moa before Polynesian settlement in New Zealand, our findings indicate that the populations were large and stable before suddenly disappearing. This interpretation is supported by approximate Bayesian computation analyses. Our analyses consolidate the disappearance of moa as the most rapid, human-facilitated megafauna extinction documented to date. FAU - Allentoft, Morten Erik AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen,1350 Copenhagen K, Denmark. FAU - Heller, Rasmus AU - Heller R FAU - Oskam, Charlotte L AU - Oskam CL FAU - Lorenzen, Eline D AU - Lorenzen ED FAU - Hale, Marie L AU - Hale ML FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Jacomb, Christopher AU - Jacomb C FAU - Holdaway, Richard N AU - Holdaway RN FAU - Bunce, Michael AU - Bunce M LA - eng SI - GENBANK/KJ533749 SI - GENBANK/KJ533750 SI - GENBANK/KJ533751 SI - GENBANK/KJ533752 SI - GENBANK/KJ533753 SI - GENBANK/KJ533754 SI - GENBANK/KJ533755 SI - GENBANK/KJ533756 SI - GENBANK/KJ533757 SI - GENBANK/KJ533758 SI - GENBANK/KJ533759 SI - GENBANK/KJ533760 SI - GENBANK/KJ533761 SI - GENBANK/KJ533762 SI - GENBANK/KJ533763 SI - GENBANK/KJ533764 SI - GENBANK/KJ533765 SI - GENBANK/KJ533766 SI - GENBANK/KJ533767 SI - GENBANK/KJ533768 SI - GENBANK/KJ533769 SI - GENBANK/KJ533770 SI - GENBANK/KJ533771 SI - GENBANK/KJ533772 SI - GENBANK/KJ533773 SI - GENBANK/KJ533774 SI - GENBANK/KJ533775 SI - GENBANK/KJ533776 SI - GENBANK/KJ533777 SI - GENBANK/KJ533778 SI - GENBANK/KJ533779 SI - GENBANK/KJ533780 SI - GENBANK/KJ533781 SI - GENBANK/KJ533782 SI - GENBANK/KJ533783 SI - GENBANK/KJ533784 SI - GENBANK/KJ533785 SI - GENBANK/KJ533786 SI - GENBANK/KJ533787 SI - GENBANK/KJ533788 SI - GENBANK/KJ533789 SI - GENBANK/KJ533790 SI - GENBANK/KJ533791 SI - GENBANK/KJ533792 SI - GENBANK/KJ533793 SI - GENBANK/KJ533794 SI - GENBANK/KJ533795 SI - GENBANK/KJ533796 SI - GENBANK/KJ533797 SI - GENBANK/KJ533798 SI - GENBANK/KJ533799 SI - GENBANK/KJ533800 SI - GENBANK/KJ533801 SI - GENBANK/KJ533802 SI - GENBANK/KJ533803 SI - GENBANK/KJ533804 SI - GENBANK/KJ533805 SI - GENBANK/KJ533806 SI - GENBANK/KJ533807 SI - GENBANK/KJ533808 SI - GENBANK/KJ533809 SI - GENBANK/KJ533810 SI - GENBANK/KJ533811 SI - GENBANK/KJ533812 SI - GENBANK/KJ533813 SI - GENBANK/KJ533814 SI - GENBANK/KJ533815 SI - GENBANK/KJ533816 SI - GENBANK/KJ533817 SI - GENBANK/KJ533818 SI - GENBANK/KJ533819 SI - GENBANK/KJ533820 SI - GENBANK/KJ533821 SI - GENBANK/KJ533822 SI - GENBANK/KJ533823 SI - GENBANK/KJ533824 SI - GENBANK/KJ533825 SI - GENBANK/KJ533826 SI - GENBANK/KJ533827 SI - GENBANK/KJ533828 SI - GENBANK/KJ533829 SI - GENBANK/KJ533830 SI - GENBANK/KJ533831 SI - GENBANK/KJ533832 SI - GENBANK/KJ533833 SI - GENBANK/KJ533834 SI - GENBANK/KJ533835 SI - GENBANK/KJ533836 SI - GENBANK/KJ533837 SI - GENBANK/KJ533838 SI - GENBANK/KJ533839 SI - GENBANK/KJ533840 SI - GENBANK/KJ533841 SI - GENBANK/KJ533842 SI - GENBANK/KJ533843 SI - GENBANK/KJ533844 SI - GENBANK/KJ533845 SI - GENBANK/KJ533846 SI - GENBANK/KJ533847 SI - GENBANK/KJ533848 SI - GENBANK/KJ533849 SI - GENBANK/KJ533850 SI - GENBANK/KJ533851 SI - GENBANK/KJ533852 SI - GENBANK/KJ533853 SI - GENBANK/KJ533854 SI - GENBANK/KJ533855 SI - GENBANK/KJ533856 SI - GENBANK/KJ533857 SI - GENBANK/KJ533858 SI - GENBANK/KJ533859 SI - GENBANK/KJ533860 SI - GENBANK/KJ533861 SI - GENBANK/KJ533862 SI - GENBANK/KJ533863 SI - GENBANK/KJ533864 SI - GENBANK/KJ533865 SI - GENBANK/KJ533866 SI - GENBANK/KJ533867 SI - GENBANK/KJ533868 SI - GENBANK/KJ533869 SI - GENBANK/KJ533870 SI - GENBANK/KJ533871 SI - 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GENBANK/KJ534010 SI - GENBANK/KJ534011 SI - GENBANK/KJ534012 SI - GENBANK/KJ534013 SI - GENBANK/KJ534014 SI - GENBANK/KJ534015 SI - GENBANK/KJ534016 SI - GENBANK/KJ534017 SI - GENBANK/KJ534018 SI - GENBANK/KJ534019 SI - GENBANK/KJ534020 SI - GENBANK/KJ534021 SI - GENBANK/KJ534022 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140317 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Bayes Theorem MH - Birds/genetics/*physiology MH - Calibration MH - DNA, Mitochondrial/genetics MH - *Extinction, Biological MH - Genetic Variation MH - Geography MH - Humans MH - Molecular Sequence Data MH - New Zealand MH - Time Factors PMC - PMC3977255 COIS- The authors declare no conflict of interest. EDAT- 2014/03/19 06:00 MHDA- 2014/06/03 06:00 PMCR- 2014/10/01 CRDT- 2014/03/19 06:00 PHST- 2014/03/19 06:00 [entrez] PHST- 2014/03/19 06:00 [pubmed] PHST- 2014/06/03 06:00 [medline] PHST- 2014/10/01 00:00 [pmc-release] AID - 1314972111 [pii] AID - 201314972 [pii] AID - 10.1073/pnas.1314972111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4922-7. doi: 10.1073/pnas.1314972111. Epub 2014 Mar 17. PMID- 24616518 OWN - NLM STAT- MEDLINE DCOM- 20140602 LR - 20221207 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 111 IP - 13 DP - 2014 Apr 1 TI - Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. PG - 4832-7 LID - 10.1073/pnas.1316513111 [doi] AB - Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways--HERC2, SLC45A2, and TYR--using allele frequency estimates from Eneolithic, Bronze Age, and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied, with point estimates of selection ranging from around 2-10% per generation. Our results provide direct evidence that strong selection favoring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 y. FAU - Wilde, Sandra AU - Wilde S AD - Institute of Anthropology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany. FAU - Timpson, Adrian AU - Timpson A FAU - Kirsanow, Karola AU - Kirsanow K FAU - Kaiser, Elke AU - Kaiser E FAU - Kayser, Manfred AU - Kayser M FAU - Unterländer, Martina AU - Unterländer M FAU - Hollfelder, Nina AU - Hollfelder N FAU - Potekhina, Inna D AU - Potekhina ID FAU - Schier, Wolfram AU - Schier W FAU - Thomas, Mark G AU - Thomas MG FAU - Burger, Joachim AU - Burger J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140310 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Antigens, Neoplasm) RN - 0 (Membrane Transport Proteins) RN - 0 (SLC45A2 protein, human) SB - IM MH - Alleles MH - Antigens, Neoplasm/genetics MH - Eye Color/*genetics MH - Gene Frequency/genetics MH - Hair Color/*genetics MH - Humans MH - Membrane Transport Proteins/genetics MH - Polymorphism, Single Nucleotide/genetics MH - *Selection, Genetic MH - Skin Pigmentation/*genetics MH - Time Factors MH - White People/*genetics PMC - PMC3977302 OTO - NOTNLM OT - Eastern Europe OT - Neolithic/Bronze Age OT - ancient DNA OT - computer simulations OT - natural selection COIS- The authors declare no conflict of interest. EDAT- 2014/03/13 06:00 MHDA- 2014/06/03 06:00 PMCR- 2014/03/10 CRDT- 2014/03/12 06:00 PHST- 2014/03/12 06:00 [entrez] PHST- 2014/03/13 06:00 [pubmed] PHST- 2014/06/03 06:00 [medline] PHST- 2014/03/10 00:00 [pmc-release] AID - 1316513111 [pii] AID - 201316513 [pii] AID - 10.1073/pnas.1316513111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4832-7. doi: 10.1073/pnas.1316513111. Epub 2014 Mar 10. PMID- 24448642 OWN - NLM STAT- MEDLINE DCOM- 20141117 LR - 20140324 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 31 IP - 4 DP - 2014 Apr TI - Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe. PG - 975-83 LID - 10.1093/molbev/msu049 [doi] AB - Lactase persistence (LP) is a genetically determined trait whereby the enzyme lactase is expressed throughout adult life. Lactase is necessary for the digestion of lactose--the main carbohydrate in milk--and its production is downregulated after the weaning period in most humans and all other mammals studied. Several sources of evidence indicate that LP has evolved independently, in different parts of the world over the last 10,000 years, and has been subject to strong natural selection in dairying populations. In Europeans, LP is strongly associated with, and probably caused by, a single C to T mutation 13,910 bp upstream of the lactase (LCT) gene (-13,910*T). Despite a considerable body of research, the reasons why LP should provide such a strong selective advantage remain poorly understood. In this study, we examine one of the most widely cited hypotheses for selection on LP--that fresh milk consumption supplemented the poor vitamin D and calcium status of northern Europe's early farmers (the calcium assimilation hypothesis). We do this by testing for natural selection on -13,910*T using ancient DNA data from the skeletal remains of eight late Neolithic Iberian individuals, whom we would not expect to have poor vitamin D and calcium status because of relatively high incident UVB light levels. None of the eight samples successfully typed in the study had the derived T-allele. In addition, we reanalyze published data from French Neolithic remains to both test for population continuity and further examine the evolution of LP in the region. Using simulations that accommodate genetic drift, natural selection, uncertainty in calibrated radiocarbon dates, and sampling error, we find that natural selection is still required to explain the observed increase in allele frequency. We conclude that the calcium assimilation hypothesis is insufficient to explain the spread of LP in Europe. FAU - Sverrisdóttir, Oddny Ósk AU - Sverrisdóttir OÓ AD - Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. FAU - Timpson, Adrian AU - Timpson A FAU - Toombs, Jamie AU - Toombs J FAU - Lecoeur, Cecile AU - Lecoeur C FAU - Froguel, Philippe AU - Froguel P FAU - Carretero, Jose Miguel AU - Carretero JM FAU - Arsuaga Ferreras, Juan Luis AU - Arsuaga Ferreras JL FAU - Götherström, Anders AU - Götherström A FAU - Thomas, Mark G AU - Thomas MG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140121 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) RN - EC 3.2.1.108 (Lactase) RN - SY7Q814VUP (Calcium) SB - IM CIN - Mol Biol Evol. 2014 Apr;31(4):1056. doi: 10.1093/molbev/msu052. PMID: 24515723 MH - Calcium/*metabolism MH - DNA, Mitochondrial/genetics MH - Evolution, Molecular MH - Female MH - France MH - Gene Frequency MH - Genetic Drift MH - Humans MH - Intestinal Absorption/*genetics MH - Lactase/*genetics MH - Models, Genetic MH - Polymorphism, Single Nucleotide MH - *Selection, Genetic MH - Sequence Analysis, DNA MH - Spain OTO - NOTNLM OT - Iberia OT - Neolithic OT - ancient DNA OT - forward simulation OT - lactase persistence OT - natural selection EDAT- 2014/01/23 06:00 MHDA- 2014/11/18 06:00 CRDT- 2014/01/23 06:00 PHST- 2014/01/23 06:00 [entrez] PHST- 2014/01/23 06:00 [pubmed] PHST- 2014/11/18 06:00 [medline] AID - msu049 [pii] AID - 10.1093/molbev/msu049 [doi] PST - ppublish SO - Mol Biol Evol. 2014 Apr;31(4):975-83. doi: 10.1093/molbev/msu049. Epub 2014 Jan 21. PMID- 24608104 OWN - NLM STAT- MEDLINE DCOM- 20141230 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 3 DP - 2014 TI - Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA. PG - e89676 LID - 10.1371/journal.pone.0089676 [doi] LID - e89676 AB - Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting of reverse complementary sequence at the 5' and 3'-ends of sequencing reads. The palindromic sequences themselves have specific properties - the bases at the 5'-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3'-end. The terminal 3' bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA), which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3'-end of DNA strands, with the 5'-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA) datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias. FAU - Star, Bastiaan AU - Star B AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. FAU - Nederbragt, Alexander J AU - Nederbragt AJ AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. FAU - Hansen, Marianne H S AU - Hansen MH AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. FAU - Skage, Morten AU - Skage M AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. FAU - Gilfillan, Gregor D AU - Gilfillan GD AD - Department of Medical Genetics, Oslo University Hospital, Oslo, Norway. FAU - Bradbury, Ian R AU - Bradbury IR AD - Fisheries and Oceans Canada, St. John's, Newfoundland, Canada. FAU - Pampoulie, Christophe AU - Pampoulie C AD - Marine Research Institute, Reykjavík, Iceland. FAU - Stenseth, Nils Chr AU - Stenseth NC AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. FAU - Jakobsen, Kjetill S AU - Jakobsen KS AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. FAU - Jentoft, Sissel AU - Jentoft S AD - Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140307 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Single-Stranded) RN - 9007-49-2 (DNA) SB - IM EIN - PLoS One. 2014;9(7):e103170 MH - Animals MH - *Artifacts MH - DNA/*genetics MH - DNA, Single-Stranded/genetics MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Sequence Analysis, DNA/methods PMC - PMC3946424 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2014/03/13 06:00 MHDA- 2014/12/31 06:00 PMCR- 2014/03/07 CRDT- 2014/03/11 06:00 PHST- 2013/11/19 00:00 [received] PHST- 2014/01/21 00:00 [accepted] PHST- 2014/03/11 06:00 [entrez] PHST- 2014/03/13 06:00 [pubmed] PHST- 2014/12/31 06:00 [medline] PHST- 2014/03/07 00:00 [pmc-release] AID - PONE-D-13-48659 [pii] AID - 10.1371/journal.pone.0089676 [doi] PST - epublish SO - PLoS One. 2014 Mar 7;9(3):e89676. doi: 10.1371/journal.pone.0089676. eCollection 2014. PMID- 24528593 OWN - NLM STAT- MEDLINE DCOM- 20150127 LR - 20191210 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 9 DP - 2014 Mar TI - Developmental validation of the HIrisPlex system: DNA-based eye and hair colour prediction for forensic and anthropological usage. PG - 150-61 LID - S1872-4973(13)00253-6 [pii] LID - 10.1016/j.fsigen.2013.12.006 [doi] AB - Forensic DNA Phenotyping or 'DNA intelligence' tools are expected to aid police investigations and find unknown individuals by providing information on externally visible characteristics of unknown suspects, perpetrators and missing persons from biological samples. This is especially useful in cases where conventional DNA profiling or other means remain non-informative. Recently, we introduced the HIrisPlex system, capable of predicting both eye and hair colour from DNA. In the present developmental validation study, we demonstrate that the HIrisPlex assay performs in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines providing an essential prerequisite for future HIrisPlex applications to forensic casework. The HIrisPlex assay produces complete profiles down to only 63 pg of DNA. Species testing revealed human specificity for a complete HIrisPlex profile, while only non-human primates showed the closest full profile at 20 out of the 24 DNA markers, in all animals tested. Rigorous testing of simulated forensic casework samples such as blood, semen, saliva stains, hairs with roots as well as extremely low quantity touch (trace) DNA samples, produced complete profiles in 88% of cases. Concordance testing performed between five independent forensic laboratories displayed consistent reproducible results on varying types of DNA samples. Due to its design, the assay caters for degraded samples, underlined here by results from artificially degraded DNA and from simulated casework samples of degraded DNA. This aspect was also demonstrated previously on DNA samples from human remains up to several hundreds of years old. With this paper, we also introduce enhanced eye and hair colour prediction models based on enlarged underlying databases of HIrisPlex genotypes and eye/hair colour phenotypes (eye colour: N = 9188 and hair colour: N = 1601). Furthermore, we present an online web-based system for individual eye and hair colour prediction from full and partial HIrisPlex DNA profiles. By demonstrating that the HIrisPlex assay is fully compatible with the SWGDAM guidelines, we provide the first forensically validated DNA test system for parallel eye and hair colour prediction now available to forensic laboratories for immediate casework application, including missing person cases. Given the robustness and sensitivity described here and in previous work, the HIrisPlex system is also suitable for analysing old and ancient DNA in anthropological and evolutionary studies. CI - Copyright © 2013 Elsevier Ireland Ltd. All rights reserved. FAU - Walsh, Susan AU - Walsh S AD - Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands. FAU - Chaitanya, Lakshmi AU - Chaitanya L AD - Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands. FAU - Clarisse, Lindy AU - Clarisse L AD - Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands. FAU - Wirken, Laura AU - Wirken L AD - Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. FAU - Draus-Barini, Jolanta AU - Draus-Barini J AD - Section of Forensic Genetics, Institute of Forensic Research, Kraków, Poland. FAU - Kovatsi, Leda AU - Kovatsi L AD - Laboratory of Forensic Medicine & Toxicology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece. FAU - Maeda, Hitoshi AU - Maeda H AD - Department of Legal Medicine, Osaka City University, Medical School, Osaka, Japan. FAU - Ishikawa, Takaki AU - Ishikawa T AD - Department of Legal Medicine, Osaka City University, Medical School, Osaka, Japan; Division of Legal Medicine, Faculty of Medicine, Tottori University, 86 Nichicho Yonago, Japan. FAU - Sijen, Titia AU - Sijen T AD - Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands. FAU - de Knijff, Peter AU - de Knijff P AD - Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. FAU - Branicki, Wojciech AU - Branicki W AD - Section of Forensic Genetics, Institute of Forensic Research, Kraków, Poland; Department of Genetics and Evolution, Institute of Zoology, Jagiellonian University, Kraków, Poland. FAU - Liu, Fan AU - Liu F AD - Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands. FAU - Kayser, Manfred AU - Kayser M AD - Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands. Electronic address: m.kayser@erasmusmc.nl. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Validation Study DEP - 20131227 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 9007-49-2 (DNA) SB - IM MH - Alleles MH - Blood Chemical Analysis MH - DNA/*genetics/isolation & purification MH - Eye Color/*genetics MH - *Forensic Genetics MH - Genotype MH - Hair/chemistry MH - Hair Color/*genetics MH - Heterozygote MH - Humans MH - Polymorphism, Single Nucleotide MH - Saliva/chemistry MH - Semen/chemistry OTO - NOTNLM OT - Developmental validation OT - Eye colour prediction OT - Forensic DNA Phenotyping, FDP OT - HIrisPlex OT - Hair colour prediction OT - SNP OT - SWGDAM EDAT- 2014/02/18 06:00 MHDA- 2015/01/28 06:00 CRDT- 2014/02/18 06:00 PHST- 2013/10/24 00:00 [received] PHST- 2013/12/13 00:00 [revised] PHST- 2013/12/17 00:00 [accepted] PHST- 2014/02/18 06:00 [entrez] PHST- 2014/02/18 06:00 [pubmed] PHST- 2015/01/28 06:00 [medline] AID - S1872-4973(13)00253-6 [pii] AID - 10.1016/j.fsigen.2013.12.006 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2014 Mar;9:150-61. doi: 10.1016/j.fsigen.2013.12.006. Epub 2013 Dec 27. PMID- 24438205 OWN - NLM STAT- MEDLINE DCOM- 20150130 LR - 20140213 IS - 1469-0691 (Electronic) IS - 1198-743X (Linking) VI - 20 IP - 3 DP - 2014 Mar TI - The rediscovery of smallpox. PG - 210-8 LID - 10.1111/1469-0691.12536 [doi] AB - Smallpox is an infectious disease that is unique to humans, caused by a poxvirus. It is one of the most lethal of diseases; the virus variant Variola major has a mortality rate of 30%. People surviving this disease have life-long consequences, but also assured immunity. Historically, smallpox was recognized early in human populations. This led to prevention attempts--variolation, quarantine, and the isolation of infected subjects--until Jenner's discovery of the first steps of vaccination in the 18th century. After vaccination campaigns throughout the 19th and 20th centuries, the WHO declared the eradication of smallpox in 1980. With the development of microscopy techniques, the structural characterization of the virus began in the early 20th century. In 1990, the genomes of different smallpox viruses were determined; viruses could be classified in order to investigate their origin, diffusion, and evolution. To study the evolution and possible re-emergence of this viral pathogen, however, researchers can only use viral genomes collected during the 20th century. Cases of smallpox in ancient periods are sometimes well documented, so palaeomicrobiology and, more precisely, the study of ancient smallpox viral strains could be an exceptional opportunity. The analysis of poxvirus fragmented genomes could give new insights into the genetic evolution of the poxvirus. Recently, small fragments of the poxvirus genome were detected. With the genetic information obtained, a new phylogeny of smallpox virus was described. The interest in conducting studies on ancient strains is discussed, in order to explore the natural history of this disease. CI - © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases. FAU - Thèves, C AU - Thèves C AD - AMIS Laboratory, UMR 5288, CNRS, University of Toulouse, University of Strasbourg, Toulouse , France. FAU - Biagini, P AU - Biagini P FAU - Crubézy, E AU - Crubézy E LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Clin Microbiol Infect JT - Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases JID - 9516420 SB - IM MH - Animals MH - Biological Evolution MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, 20th Century MH - Humans MH - Smallpox/diagnosis/epidemiology/*history/virology MH - Variola virus/genetics/isolation & purification OTO - NOTNLM OT - Ancient DNA OT - Yakut population OT - evolution OT - palaeomicrobiology OT - smallpox EDAT- 2014/01/21 06:00 MHDA- 2015/01/31 06:00 CRDT- 2014/01/21 06:00 PHST- 2014/01/21 06:00 [entrez] PHST- 2014/01/21 06:00 [pubmed] PHST- 2015/01/31 06:00 [medline] AID - S1198-743X(14)60860-0 [pii] AID - 10.1111/1469-0691.12536 [doi] PST - ppublish SO - Clin Microbiol Infect. 2014 Mar;20(3):210-8. doi: 10.1111/1469-0691.12536. PMID- 24586848 OWN - NLM STAT- MEDLINE DCOM- 20150303 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 2 DP - 2014 TI - Reconstructing the life of an unknown (ca. 500 years-old South American Inca) mummy--multidisciplinary study of a Peruvian Inca mummy suggests severe Chagas disease and ritual homicide. PG - e89528 LID - 10.1371/journal.pone.0089528 [doi] LID - e89528 AB - The paleopathological, paleoradiological, histological, molecular and forensic investigation of a female mummy (radiocarbon dated 1451-1642 AD) provides circumstantial evidence for massive skull trauma affecting a young adult female individual shortly before death along with chronic infection by Trypanosoma cruzi (Chagas disease). The mummy (initially assumed to be a German bog body) was localized by stable isotope analysis to South America at/near the Peruvian/Northern Chilean coast line. This is further supported by New World camelid fibers attached to her plaits, typical Inca-type skull deformation and the type of Wormian bone at her occiput. Despite an only small transverse wound of the supraorbital region computed tomography scans show an almost complete destruction of face and frontal skull bones with terrace-like margins, but without evidence for tissue reaction. The type of destruction indicates massive blunt force applied to the center of the face. Stable isotope analysis indicates South American origin: Nitrogen and hydrogen isotope patterns indicate an extraordinarily high marine diet along with C4-plant alimentation which fits best to the coastal area of Pacific South America. A hair strand over the last ten months of her life indicates a shift to a more "terrestric" nutrition pattern suggesting either a move from the coast or a change in her nutrition. Paleoradiology further shows extensive hypertrophy of the heart muscle and a distended large bowel/rectum. Histologically, in the rectum wall massive fibrosis alternates with residual smooth muscle. The latter contains multiple inclusions of small intracellular parasites as confirmed by immunohistochemical and molecular ancient DNA analysis to represent a chronic Trypanosoma cruzi infection. This case shows a unique paleopathological setting with massive blunt force trauma to the skull nurturing the hypothesis of a ritual homicide as previously described in South American mummies in an individual that suffered from severe chronic Chagas disease. FAU - Panzer, Stephanie AU - Panzer S AD - Department of Radiology, Trauma Center Murnau, Murnau, Germany and Biomechanics Laboratory, Paracelsus Medical University Salzburg and Trauma Center Murnau, Murnau, Germany. FAU - Peschel, Oliver AU - Peschel O AD - Institute of Legal Medicine, Ludwig-Maximilians University, Munich, Germany. FAU - Haas-Gebhard, Brigitte AU - Haas-Gebhard B AD - Bavarian State Archaeological Collection and Museum, Munich, Germany. FAU - Bachmeier, Beatrice E AU - Bachmeier BE AD - Institute of Laboratory Medicine, Ludwig-Maximilians University Munich, Germany. FAU - Pusch, Carsten M AU - Pusch CM AD - Institute of Anthropology and Human Genetics, Eberhard-Karls-University Tübingen, Germany. FAU - Nerlich, Andreas G AU - Nerlich AG AD - Institute of Pathology, Academic Clinic München-Bogenhausen, Munich, Germany. LA - eng PT - Historical Article PT - Journal Article DEP - 20140226 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 9007-49-2 (DNA) SB - IM MH - Adult MH - *Ceremonial Behavior MH - Chagas Disease/*parasitology MH - *Craniocerebral Trauma MH - DNA/*analysis MH - Female MH - Hair/chemistry MH - History, Medieval MH - *Homicide MH - Humans MH - Image Processing, Computer-Assisted MH - Mummies/history/*parasitology/pathology MH - Paleopathology MH - South America MH - Tomography, X-Ray Computed MH - Trypanosoma cruzi/pathogenicity MH - Young Adult PMC - PMC3935882 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2014/03/04 06:00 MHDA- 2015/03/04 06:00 PMCR- 2014/02/26 CRDT- 2014/03/04 06:00 PHST- 2013/12/17 00:00 [received] PHST- 2014/01/20 00:00 [accepted] PHST- 2014/03/04 06:00 [entrez] PHST- 2014/03/04 06:00 [pubmed] PHST- 2015/03/04 06:00 [medline] PHST- 2014/02/26 00:00 [pmc-release] AID - PONE-D-13-50531 [pii] AID - 10.1371/journal.pone.0089528 [doi] PST - epublish SO - PLoS One. 2014 Feb 26;9(2):e89528. doi: 10.1371/journal.pone.0089528. eCollection 2014. PMID- 24568097 OWN - NLM STAT- MEDLINE DCOM- 20141028 LR - 20211021 IS - 1756-0500 (Electronic) IS - 1756-0500 (Linking) VI - 7 DP - 2014 Feb 25 TI - False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing. PG - 111 LID - 10.1186/1756-0500-7-111 [doi] AB - BACKGROUND: Identification of historic pathogens is challenging since false positives and negatives are a serious risk. Environmental non-pathogenic contaminants are ubiquitous. Furthermore, public genetic databases contain limited information regarding these species. High-throughput sequencing may help reliably detect and identify historic pathogens. RESULTS: We shotgun-sequenced 8 16th-century Mixtec individuals from the site of Teposcolula Yucundaa (Oaxaca, Mexico) who are reported to have died from the huey cocoliztli ('Great Pestilence' in Nahautl), an unknown disease that decimated native Mexican populations during the Spanish colonial period, in order to identify the pathogen. Comparison of these sequences with those deriving from the surrounding soil and from 4 precontact individuals from the site found a wide variety of contaminant organisms that confounded analyses. Without the comparative sequence data from the precontact individuals and soil, false positives for Yersinia pestis and rickettsiosis could have been reported. CONCLUSIONS: False positives and negatives remain problematic in ancient DNA analyses despite the application of high-throughput sequencing. Our results suggest that several studies claiming the discovery of ancient pathogens may need further verification. Additionally, true single molecule sequencing's short read lengths, inability to sequence through DNA lesions, and limited ancient-DNA-specific technical development hinder its application to palaeopathology. FAU - Campana, Michael G AU - Campana MG AD - Department of Human Evolutionary Biology, Harvard University, Peabody Museum, 11 Divinity Avenue, Cambridge, MA 02138, USA. mcampana63@gmail.com. FAU - Robles García, Nelly AU - Robles García N FAU - Rühli, Frank J AU - Rühli FJ FAU - Tuross, Noreen AU - Tuross N LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140225 PL - England TA - BMC Res Notes JT - BMC research notes JID - 101462768 SB - IM MH - Adolescent MH - Adult MH - Bacteria/classification/*genetics MH - Bacterial Infections/genetics/history/microbiology MH - Child, Preschool MH - False Positive Reactions MH - Female MH - Genome, Human/genetics MH - High-Throughput Nucleotide Sequencing/*methods MH - History, 16th Century MH - Humans MH - Male MH - Metagenome/genetics MH - Mexico MH - Reproducibility of Results MH - Sequence Analysis, DNA/*methods MH - Soil Microbiology MH - Virus Diseases/genetics/history/virology MH - Viruses/classification/*genetics MH - Young Adult PMC - PMC3938818 EDAT- 2014/02/27 06:00 MHDA- 2014/10/29 06:00 PMCR- 2014/02/25 CRDT- 2014/02/27 06:00 PHST- 2014/02/19 00:00 [received] PHST- 2014/02/20 00:00 [accepted] PHST- 2014/02/27 06:00 [entrez] PHST- 2014/02/27 06:00 [pubmed] PHST- 2014/10/29 06:00 [medline] PHST- 2014/02/25 00:00 [pmc-release] AID - 1756-0500-7-111 [pii] AID - 10.1186/1756-0500-7-111 [doi] PST - epublish SO - BMC Res Notes. 2014 Feb 25;7:111. doi: 10.1186/1756-0500-7-111. PMID- 24516122 OWN - NLM STAT- MEDLINE DCOM- 20140422 LR - 20240318 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 111 IP - 8 DP - 2014 Feb 25 TI - Transoceanic drift and the domestication of African bottle gourds in the Americas. PG - 2937-41 LID - 10.1073/pnas.1318678111 [doi] AB - Bottle gourd (Lagenaria siceraria) was one of the first domesticated plants, and the only one with a global distribution during pre-Columbian times. Although native to Africa, bottle gourd was in use by humans in east Asia, possibly as early as 11,000 y ago (BP) and in the Americas by 10,000 BP. Despite its utilitarian importance to diverse human populations, it remains unresolved how the bottle gourd came to be so widely distributed, and in particular how and when it arrived in the New World. A previous study using ancient DNA concluded that Paleoindians transported already domesticated gourds to the Americas from Asia when colonizing the New World [Erickson et al. (2005) Proc Natl Acad Sci USA 102(51):18315-18320]. However, this scenario requires the propagation of tropical-adapted bottle gourds across the Arctic. Here, we isolate 86,000 base pairs of plastid DNA from a geographically broad sample of archaeological and living bottle gourds. In contrast to the earlier results, we find that all pre-Columbian bottle gourds are most closely related to African gourds, not Asian gourds. Ocean-current drift modeling shows that wild African gourds could have simply floated across the Atlantic during the Late Pleistocene. Once they arrived in the New World, naturalized gourd populations likely became established in the Neotropics via dispersal by megafaunal mammals. These wild populations were domesticated in several distinct New World locales, most likely near established centers of food crop domestication. FAU - Kistler, Logan AU - Kistler L AD - Department of Anthropology and Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802. FAU - Montenegro, Alvaro AU - Montenegro A FAU - Smith, Bruce D AU - Smith BD FAU - Gifford, John A AU - Gifford JA FAU - Green, Richard E AU - Green RE FAU - Newsom, Lee A AU - Newsom LA FAU - Shapiro, Beth AU - Shapiro B LA - eng SI - GENBANK/KJ399838 SI - GENBANK/KJ399839 SI - GENBANK/KJ399840 SI - GENBANK/KJ399841 SI - GENBANK/KJ399842 SI - GENBANK/KJ399843 SI - GENBANK/KJ399844 SI - GENBANK/KJ399845 SI - GENBANK/KJ399846 SI - GENBANK/KJ399847 SI - GENBANK/KJ399848 SI - GENBANK/KJ399849 SI - GENBANK/KJ399850 SI - GENBANK/KJ399851 SI - GENBANK/KJ399852 SI - GENBANK/KJ399853 SI - GENBANK/KJ399854 SI - GENBANK/KJ399855 SI - GENBANK/KJ399856 SI - GENBANK/KJ399857 SI - GENBANK/KJ399858 SI - GENBANK/KJ399859 SI - GENBANK/KJ399860 SI - GENBANK/KJ399861 SI - GENBANK/KJ399862 SI - GENBANK/KJ399863 SI - GENBANK/KJ399864 SI - GENBANK/KJ399865 SI - GENBANK/KJ399866 SI - GENBANK/KJ399867 SI - GENBANK/KJ399868 SI - GENBANK/KJ399869 SI - GENBANK/KJ399870 SI - GENBANK/KJ399871 SI - GENBANK/KJ399872 SI - GENBANK/KJ399873 SI - GENBANK/KJ399874 SI - GENBANK/KJ399875 SI - GENBANK/KJ399876 SI - GENBANK/KJ399877 SI - GENBANK/KJ399878 SI - GENBANK/KJ399879 SI - GENBANK/KJ399880 SI - GENBANK/KJ399881 SI - GENBANK/KJ399882 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140210 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Africa MH - Agriculture/*history MH - Americas MH - Asia MH - Base Sequence MH - Bayes Theorem MH - Computer Simulation MH - Cucurbitaceae/*genetics/physiology MH - *Demography MH - History, Ancient MH - Human Migration/*history MH - Humans MH - Models, Genetic MH - Molecular Sequence Data MH - Oceans and Seas MH - *Phylogeny MH - Plastids/genetics MH - Sequence Analysis, DNA MH - *Water Movements PMC - PMC3939861 OTO - NOTNLM OT - New World domestication OT - archaeogenomics OT - long-distance dispersal COIS- The authors declare no conflict of interest. EDAT- 2014/02/12 06:00 MHDA- 2014/04/23 06:00 PMCR- 2014/08/25 CRDT- 2014/02/12 06:00 PHST- 2014/02/12 06:00 [entrez] PHST- 2014/02/12 06:00 [pubmed] PHST- 2014/04/23 06:00 [medline] PHST- 2014/08/25 00:00 [pmc-release] AID - 1318678111 [pii] AID - 201318678 [pii] AID - 10.1073/pnas.1318678111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):2937-41. doi: 10.1073/pnas.1318678111. Epub 2014 Feb 10. PMID- 24550262 OWN - NLM STAT- MEDLINE DCOM- 20140415 LR - 20211021 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 111 IP - 7 DP - 2014 Feb 18 TI - Sequencing ancient DNA. PG - 2401 LID - 10.1073/pnas.1322476111 [doi] FAU - Nair, Prashant AU - Nair P LA - eng PT - Journal Article PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 9007-49-2 (DNA) SB - IM MH - DNA/*genetics MH - Humans MH - *Mummies MH - Sequence Analysis, DNA/*methods PMC - PMC3932904 EDAT- 2014/02/20 06:00 MHDA- 2014/04/16 06:00 PMCR- 2014/02/18 CRDT- 2014/02/20 06:00 PHST- 2014/02/20 06:00 [entrez] PHST- 2014/02/20 06:00 [pubmed] PHST- 2014/04/16 06:00 [medline] PHST- 2014/02/18 00:00 [pmc-release] AID - 111/7/2401 [pii] AID - 201322476 [pii] AID - 10.1073/pnas.1322476111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2401. doi: 10.1073/pnas.1322476111. PMID- 24522580 OWN - NLM STAT- MEDLINE DCOM- 20140219 LR - 20140213 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 506 IP - 7487 DP - 2014 Feb 13 TI - Ancient genome stirs ethics debate. PG - 142-3 LID - 10.1038/506142a [doi] FAU - Callaway, Ewen AU - Callaway E LA - eng PT - News PL - England TA - Nature JT - Nature JID - 0410462 SB - IM MH - Asia/ethnology MH - Child MH - *Ethics, Research MH - Genome, Human/*genetics MH - Humans MH - Indians, North American/classification/*genetics/psychology MH - Male MH - Montana MH - Negotiating MH - Phylogeny EDAT- 2014/02/14 06:00 MHDA- 2014/02/20 06:00 CRDT- 2014/02/14 06:00 PHST- 2014/02/14 06:00 [entrez] PHST- 2014/02/14 06:00 [pubmed] PHST- 2014/02/20 06:00 [medline] AID - 506142a [pii] AID - 10.1038/506142a [doi] PST - ppublish SO - Nature. 2014 Feb 13;506(7487):142-3. doi: 10.1038/506142a. PMID- 24469802 OWN - NLM STAT- MEDLINE DCOM- 20140515 LR - 20211021 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 111 IP - 6 DP - 2014 Feb 11 TI - Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. PG - 2229-34 LID - 10.1073/pnas.1318934111 [doi] AB - One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation-summarized in a postmortem degradation score-which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material. FAU - Skoglund, Pontus AU - Skoglund P AD - Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden. FAU - Northoff, Bernd H AU - Northoff BH FAU - Shunkov, Michael V AU - Shunkov MV FAU - Derevianko, Anatoli P AU - Derevianko AP FAU - Pääbo, Svante AU - Pääbo S FAU - Krause, Johannes AU - Krause J FAU - Jakobsson, Mattias AU - Jakobsson M LA - eng SI - GENBANK/KF982693 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140127 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - DNA, Mitochondrial/genetics/*isolation & purification MH - Humans MH - Molecular Sequence Data MH - Neanderthals/*genetics MH - Siberia PMC - PMC3926038 OTO - NOTNLM OT - human evolution OT - paleogenomics COIS- The authors declare no conflict of interest. EDAT- 2014/01/29 06:00 MHDA- 2014/05/16 06:00 PMCR- 2014/08/11 CRDT- 2014/01/29 06:00 PHST- 2014/01/29 06:00 [entrez] PHST- 2014/01/29 06:00 [pubmed] PHST- 2014/05/16 06:00 [medline] PHST- 2014/08/11 00:00 [pmc-release] AID - 1318934111 [pii] AID - 201318934 [pii] AID - 10.1073/pnas.1318934111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2229-34. doi: 10.1073/pnas.1318934111. Epub 2014 Jan 27. PMID- 24503968 OWN - NLM STAT- MEDLINE DCOM- 20141228 LR - 20221207 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 2 DP - 2014 TI - Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1. PG - e87612 LID - 10.1371/journal.pone.0087612 [doi] LID - e87612 AB - The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. Three individuals from the 7,500 year old Mesolithic site of Yuzhnyy Oleni Ostrov, Western Russia, could be assigned to haplogroup C1 based on mitochondrial hypervariable region I sequences. However, hypervariable region I data alone could not provide enough resolution to establish the phylogenetic relationship of these Mesolithic haplotypes with haplogroup C1 mitochondrial DNA sequences found today in populations of Europe, Asia and the Americas. In order to obtain high-resolution data and shed light on the origin of this European Mesolithic C1 haplotype, we target-enriched and sequenced the complete mitochondrial genome of one Yuzhnyy Oleni Ostrov C1 individual. The updated phylogeny of C1 haplogroups indicated that the Yuzhnyy Oleni Ostrov haplotype represents a new distinct clade, provisionally coined "C1f". We show that all three C1 carriers of Yuzhnyy Oleni Ostrov belong to this clade. No haplotype closely related to the C1f sequence could be found in the large current database of ancient and present-day mitochondrial genomes. Hence, we have discovered past human mitochondrial diversity that has not been observed in modern-day populations so far. The lack of positive matches in modern populations may be explained by under-sampling of rare modern C1 carriers or by demographic processes, population extinction or replacement, that may have impacted on populations of Northeast Europe since prehistoric times. FAU - Der Sarkissian, Clio AU - Der Sarkissian C AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Brotherton, Paul AU - Brotherton P AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Balanovsky, Oleg AU - Balanovsky O AD - Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia ; Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia. FAU - Templeton, Jennifer E L AU - Templeton JE AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Llamas, Bastien AU - Llamas B AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Soubrier, Julien AU - Soubrier J AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Moiseyev, Vyacheslav AU - Moiseyev V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg, Russia. FAU - Khartanovich, Valery AU - Khartanovich V AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg, Russia. FAU - Cooper, Alan AU - Cooper A AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Haak, Wolfgang AU - Haak W AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia. CN - Genographic Consortium LA - eng SI - SRA/SRP033724 GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140204 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Cluster Analysis MH - *DNA, Mitochondrial MH - Europe MH - Genetics, Population MH - *Genome, Mitochondrial MH - Geography MH - *Haplotypes MH - Humans MH - Phylogeny MH - Population Dynamics MH - Sequence Analysis, DNA MH - White People/*genetics PMC - PMC3913659 COIS- Competing Interests: The authors declare having received funding from a commercial partner (IBM). This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials. FIR - Adler, Christina J IR - Adler CJ FIR - Bertranpetit, Jaume IR - Bertranpetit J FIR - Clarke, Andrew C IR - Clarke AC FIR - Comas, David IR - Comas D FIR - Dulik, Matthew C IR - Dulik MC FIR - Gaieski, Jill B IR - Gaieski JB FIR - Prasad, Arun Kumar Ganesh IR - Prasad AK FIR - Haber, Marc IR - Haber M FIR - Jin, Li IR - Jin L FIR - Kaplan, Matthew E IR - Kaplan ME FIR - Li, Shilin IR - Li S FIR - Martínez-Cruz, Begoña IR - Martínez-Cruz B FIR - Matisoo-Smith, Elizabeth A IR - Matisoo-Smith EA FIR - Merchant, Nirav C IR - Merchant NC FIR - Mitchell, R John IR - Mitchell R FIR - Owings, Amanda C IR - Owings AC FIR - Parida, Laxmi IR - Parida L FIR - Pitchappan, Ramasamy IR - Pitchappan R FIR - Platt, Daniel E IR - Platt DE FIR - Quintana-Murci, Lluis IR - Quintana-Murci L FIR - Renfrew, Colin IR - Renfrew C FIR - Lacerda, Daniela R IR - Lacerda DR FIR - Horizonte, Belo IR - Horizonte B FIR - Royyuru, Ajay K IR - Royyuru AK FIR - Santos, Fabrício R IR - Santos FR FIR - Horizonte, Belo IR - Horizonte B FIR - Schurr, Theodore G IR - Schurr TG FIR - Soodyall, Himla IR - Soodyall H FIR - Hernanz, David F Soria IR - Hernanz DF FIR - Swamikrishnan, Pandikumar IR - Swamikrishnan P FIR - Tyler-Smith, Chris IR - Tyler-Smith C FIR - Santhakumari, Arun Varatharajan IR - Santhakumari AV FIR - Vieira, Pedro Paulo IR - Vieira PP FIR - Vilar, Miguel G IR - Vilar MG FIR - Wells, R Spencer IR - Wells R FIR - Zalloua, Pierre A IR - Zalloua PA FIR - Ziegle, Janet S IR - Ziegle JS EDAT- 2014/02/08 06:00 MHDA- 2014/12/30 06:00 PMCR- 2014/02/04 CRDT- 2014/02/08 06:00 PHST- 2013/11/04 00:00 [received] PHST- 2013/12/23 00:00 [accepted] PHST- 2014/02/08 06:00 [entrez] PHST- 2014/02/08 06:00 [pubmed] PHST- 2014/12/30 06:00 [medline] PHST- 2014/02/04 00:00 [pmc-release] AID - PONE-D-13-45021 [pii] AID - 10.1371/journal.pone.0087612 [doi] PST - epublish SO - PLoS One. 2014 Feb 4;9(2):e87612. doi: 10.1371/journal.pone.0087612. eCollection 2014. PMID- 24616928 OWN - NLM STAT- MEDLINE DCOM- 20140930 LR - 20191112 IS - 1618-1301 (Electronic) IS - 0018-442X (Linking) VI - 65 IP - 1 DP - 2014 Feb TI - Purported medical diagnoses of Pharaoh Tutankhamun, c. 1325 BC-. PG - 51-63 AB - King Tutankhamun is one of the most famous rulers of antiquity,thus it is not surprising that a plethora of scientific studies have put forth possible medical diagnoses and causes of his death. Diseases(autologous or infectious), metabolic disorders, trauma (possibly even murder-related), or tumorous conditions have been postulated, frequently only based on secondary data sources. The aim of this article is to critically review all these diagnoses. Since the initial examination of the mummy in the mid 1920s by Howard Carter and others, several dozens of medical diagnoses based on various levels of evidence have been proposed. While some studies did not support any sign of a major disease, others suggested diseases whose existence cannot be proven with the little tissue that is preserved for study. In the last c. five years new examinations of the mummy were performed by computed tomography and ancient DNA analyses,now allowing not only to exclude certain diagnoses that had been postulated earlier, but also to arrive at new theories with a higher degree of certainty concerning the state of health and the early death of this most famous ruler. FAU - Rühli, F J AU - Rühli FJ FAU - Ikram, S AU - Ikram S LA - eng PT - Case Reports PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Germany TA - Homo JT - Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen JID - 0374655 SB - IM MH - Adolescent MH - Egypt, Ancient MH - History, Ancient MH - Homicide MH - Humans MH - Male MH - Metabolic Diseases/diagnosis/mortality MH - Mummies/diagnostic imaging/*history/pathology MH - Tomography, X-Ray Computed MH - Wounds and Injuries/diagnosis/mortality MH - Young Adult EDAT- 2014/03/13 06:00 MHDA- 2014/10/01 06:00 CRDT- 2014/03/12 06:00 PHST- 2014/03/12 06:00 [entrez] PHST- 2014/03/13 06:00 [pubmed] PHST- 2014/10/01 06:00 [medline] AID - S0018-442X(13)00128-5 [pii] AID - 10.1016/j.jchb.2013.08.006 [doi] PST - ppublish SO - Homo. 2014 Feb;65(1):51-63. doi: 10.1016/j.jchb.2013.08.006. PMID- 24461411 OWN - NLM STAT- MEDLINE DCOM- 20151124 LR - 20140127 IS - 1878-3554 (Electronic) IS - 0099-2399 (Linking) VI - 40 IP - 2 DP - 2014 Feb TI - Preservation of bacterial DNA by human dentin. PG - 241-5 LID - S0099-2399(13)00752-8 [pii] LID - 10.1016/j.joen.2013.08.025 [doi] AB - INTRODUCTION: The capacity of dentin and collagen to bind DNA and protect against spontaneous and nuclease-induced degradation was evaluated individually and by the incubation of DNA with nuclease-producing bacteria in a mixed culture. METHODS: Extracted Fusobacterium nucleatum DNA was incubated with dentin shavings or collagen for 90 minutes. The DNA-bound substrates were incubated in different media (water, sera, and DNase I) for up to 3 months. Amplifiable DNA was released from dentin using EDTA,or from collagen using proteinase K, and evaluated by polymerase chain reaction (PCR). The stability of dentin-bound DNA was also assessed in a mixed culture (Parvimonas micra and Pseudoramibacter alactolyticus) containing a DNase-producing species, Prevotella intermedia. Samples were analyzed for amplifiable DNA. RESULTS: In water, dentin-bound DNA was recoverable by PCR at 3 months compared with no detectable DNA after 4 weeks in controls (no dentin). DNA bound to collagen was detectable by PCR after 3 months of incubation in water. In 10% human sera, amplifiable DNA was detectable at 3 months when dentin bound and in controls (no dentin). In mixed bacterial culture, dentin-bound DNA was recoverable throughout the experimental period (3 months), compared with no recoverable F. nucleatum DNA within 24 hours in controls (no dentin). CONCLUSIONS: There is a strong binding affinity between DNA and dentin, and between DNA and serum proteins or collagen. These substrates preserve DNA against natural decomposition and protect DNA from nuclease activity, factors that may confound molecular analysis of the endodontic microbiota yet favor paleomicrobiological studies of ancient DNA. CI - Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved. FAU - Brundin, Malin AU - Brundin M AD - Department of Odontology/Endodontics, Faculty of Medicine, Umeå University, Umeå, Sweden. Electronic address: malin.brundin@odont.umu.se. FAU - Figdor, David AU - Figdor D AD - Department of Microbiology, Monash University, Melbourne, Australia. FAU - Johansson, Anders AU - Johansson A AD - Department of Odontology/Molecular Periodontology, Faculty of Medicine, Umeå University, Umeå, Sweden. FAU - Sjögren, Ulf AU - Sjögren U AD - Department of Odontology/Endodontics, Faculty of Medicine, Umeå University, Umeå, Sweden. LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131018 PL - United States TA - J Endod JT - Journal of endodontics JID - 7511484 RN - 0 (Blood Proteins) RN - 0 (Culture Media) RN - 0 (DNA, Bacterial) RN - 059QF0KO0R (Water) RN - 9007-34-5 (Collagen) RN - 9G34HU7RV0 (Edetic Acid) RN - EC 3.1.21.1 (Deoxyribonuclease I) RN - EC 3.4.21.64 (Endopeptidase K) MH - Blood MH - Blood Proteins/metabolism MH - Coculture Techniques MH - Collagen/drug effects/metabolism MH - Culture Media MH - DNA, Bacterial/analysis/*metabolism MH - Dentin/drug effects/*microbiology MH - Deoxyribonuclease I/metabolism MH - Edetic Acid/pharmacology MH - Endopeptidase K/pharmacology MH - Eubacterium/genetics MH - Fusobacterium nucleatum/*genetics MH - Humans MH - Humidity MH - Microbial Consortia MH - Peptostreptococcus/genetics MH - Polymerase Chain Reaction/methods MH - Prevotella intermedia/genetics MH - Protein Binding MH - Temperature MH - Time Factors MH - Water OTO - NOTNLM OT - Bacterial nucleases OT - DNA binding affinity OT - DNA decomposition OT - DNA preservation OT - dentin OT - polymerase chain reaction EDAT- 2014/01/28 06:00 MHDA- 2015/12/15 06:00 CRDT- 2014/01/28 06:00 PHST- 2013/07/20 00:00 [received] PHST- 2013/08/22 00:00 [revised] PHST- 2013/08/23 00:00 [accepted] PHST- 2014/01/28 06:00 [entrez] PHST- 2014/01/28 06:00 [pubmed] PHST- 2015/12/15 06:00 [medline] AID - S0099-2399(13)00752-8 [pii] AID - 10.1016/j.joen.2013.08.025 [doi] PST - ppublish SO - J Endod. 2014 Feb;40(2):241-5. doi: 10.1016/j.joen.2013.08.025. Epub 2013 Oct 18. PMID- 24226751 OWN - NLM STAT- MEDLINE DCOM- 20140707 LR - 20161125 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 153 IP - 2 DP - 2014 Feb TI - Biomolecular identification of ancient Mycobacterium tuberculosis complex DNA in human remains from Britain and continental Europe. PG - 178-89 LID - 10.1002/ajpa.22417 [doi] AB - Tuberculosis is known to have afflicted humans throughout history and re-emerged towards the end of the 20th century, to an extent that it was declared a global emergency in 1993. The aim of this study was to apply a rigorous analytical regime to the detection of Mycobacterium tuberculosis complex (MTBC) DNA in 77 bone and tooth samples from 70 individuals from Britain and continental Europe, spanning the 1st-19th centuries AD. We performed the work in dedicated ancient DNA facilities designed to prevent all types of modern contamination, we checked the authenticity of all products obtained by the polymerase chain reaction, and we based our conclusions on up to four replicate experiments for each sample, some carried out in an independent laboratory. We identified 12 samples that, according to our strict criteria, gave definite evidence for the presence of MTBC DNA, and another 22 that we classified as "probable" or "possible." None of the definite samples came from vertebrae displaying lesions associated with TB. Instead, eight were from ribs displaying visceral new bone formation, one was a tooth from a skeleton with rib lesions, one was taken from a skeleton with endocranial lesions, one from an individual with lesions to the sacrum and sacroiliac joint and the last was from an individual with no lesions indicative of TB or possible TB. Our results add to information on the past temporal and geographical distribution of TB and affirm the suitability of ribs for studying ancient TB. CI - Copyright © 2013 Wiley Periodicals, Inc. FAU - Müller, Romy AU - Müller R AD - Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, M1 7DN, UK. FAU - Roberts, Charlotte A AU - Roberts CA FAU - Brown, Terence A AU - Brown TA LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131114 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Bacterial) SB - IM MH - Adolescent MH - Adult MH - Bone and Bones/microbiology MH - DNA, Bacterial/*isolation & purification MH - Europe MH - Female MH - Forensic Anthropology MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, Ancient MH - History, Medieval MH - Humans MH - Male MH - Middle Aged MH - Mycobacterium tuberculosis/*genetics/*isolation & purification MH - Tuberculosis/*history/microbiology MH - United Kingdom MH - Young Adult OTO - NOTNLM OT - IS elements OT - PCR OT - infectious disease OT - skeletal pathology OT - visceral surface new bone EDAT- 2013/11/15 06:00 MHDA- 2014/07/08 06:00 CRDT- 2013/11/15 06:00 PHST- 2013/10/13 00:00 [received] PHST- 2013/10/21 00:00 [accepted] PHST- 2013/11/15 06:00 [entrez] PHST- 2013/11/15 06:00 [pubmed] PHST- 2014/07/08 06:00 [medline] AID - 10.1002/ajpa.22417 [doi] PST - ppublish SO - Am J Phys Anthropol. 2014 Feb;153(2):178-89. doi: 10.1002/ajpa.22417. Epub 2013 Nov 14. PMID- 24458647 OWN - NLM STAT- MEDLINE DCOM- 20140224 LR - 20140124 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 343 IP - 6169 DP - 2014 Jan 24 TI - A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. PG - 1236573 LID - 10.1126/science.1236573 [doi] AB - The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events. FAU - Shapiro, B AU - Shapiro B AD - Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA. FAU - Hofreiter, M AU - Hofreiter M LA - eng PT - Journal Article PT - Review PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Classification MH - Columbidae/genetics MH - DNA/*genetics MH - *Evolution, Molecular MH - Extinction, Biological MH - Genomics/*trends MH - Hominidae/genetics MH - Humans MH - Mammoths/genetics MH - Mastodons/genetics MH - Paleontology/*trends EDAT- 2014/01/25 06:00 MHDA- 2014/02/25 06:00 CRDT- 2014/01/25 06:00 PHST- 2014/01/25 06:00 [entrez] PHST- 2014/01/25 06:00 [pubmed] PHST- 2014/02/25 06:00 [medline] AID - 343/6169/1236573 [pii] AID - 10.1126/science.1236573 [doi] PST - ppublish SO - Science. 2014 Jan 24;343(6169):1236573. doi: 10.1126/science.1236573. PMID- 24465990 OWN - NLM STAT- MEDLINE DCOM- 20141111 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 1 DP - 2014 TI - Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe. PG - e86251 LID - 10.1371/journal.pone.0086251 [doi] LID - e86251 AB - Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications. FAU - Krüttli, Annina AU - Krüttli A AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland ; Department of Pre- and Protohistory, Institute of History, University of Zurich, Zurich, Switzerland. FAU - Bouwman, Abigail AU - Bouwman A AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland. FAU - Akgül, Gülfirde AU - Akgül G AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland. FAU - Della Casa, Philippe AU - Della Casa P AD - Department of Pre- and Protohistory, Institute of History, University of Zurich, Zurich, Switzerland. FAU - Rühli, Frank AU - Rühli F AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland. FAU - Warinner, Christina AU - Warinner C AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland ; Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140123 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) RN - EC 3.2.1.108 (Lactase) SB - IM MH - Alleles MH - Animals MH - DNA, Mitochondrial/genetics MH - Evolution, Molecular MH - Female MH - Gene Frequency MH - Germany MH - History, Medieval MH - Humans MH - Lactase/*genetics MH - Lactose Intolerance/*genetics/history MH - Male MH - Milk MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA PMC - PMC3900515 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2014/01/28 06:00 MHDA- 2014/11/12 06:00 PMCR- 2014/01/23 CRDT- 2014/01/28 06:00 PHST- 2013/08/07 00:00 [received] PHST- 2013/12/10 00:00 [accepted] PHST- 2014/01/28 06:00 [entrez] PHST- 2014/01/28 06:00 [pubmed] PHST- 2014/11/12 06:00 [medline] PHST- 2014/01/23 00:00 [pmc-release] AID - PONE-D-13-32430 [pii] AID - 10.1371/journal.pone.0086251 [doi] PST - epublish SO - PLoS One. 2014 Jan 23;9(1):e86251. doi: 10.1371/journal.pone.0086251. eCollection 2014. PMID- 25277105 OWN - NLM STAT- MEDLINE DCOM- 20150521 LR - 20181202 IS - 1421-9743 (Electronic) IS - 0006-8977 (Linking) VI - 84 IP - 3 DP - 2014 TI - Epigenetic information from ancient DNA provides new insights into human evolution. Commentary on Gokhman D et al. (2014): Reconstructing the DNA methylation maps of the Neanderthal and the Denisovan. Science 344:523-527. PG - 169-71 LID - 10.1159/000365650 [doi] FAU - Schneider, Eberhard AU - Schneider E AD - Institute of Human Genetics, Julius Maximilian University of Würzburg, Würzburg, Germany. FAU - El Hajj, Nady AU - El Hajj N FAU - Haaf, Thomas AU - Haaf T LA - eng PT - Comment PT - Journal Article DEP - 20140924 PL - Switzerland TA - Brain Behav Evol JT - Brain, behavior and evolution JID - 0151620 SB - IM CON - Science. 2014 May 2;344(6183):523-7. doi: 10.1126/science.1250368. PMID: 24786081 MH - Animals MH - *DNA Methylation MH - *Epigenesis, Genetic MH - *Evolution, Molecular MH - *Genome, Human MH - Humans MH - Neanderthals/*genetics EDAT- 2014/10/04 06:00 MHDA- 2015/05/23 06:00 CRDT- 2014/10/04 06:00 PHST- 2014/10/04 06:00 [entrez] PHST- 2014/10/04 06:00 [pubmed] PHST- 2015/05/23 06:00 [medline] AID - 000365650 [pii] AID - 10.1159/000365650 [doi] PST - ppublish SO - Brain Behav Evol. 2014;84(3):169-71. doi: 10.1159/000365650. Epub 2014 Sep 24. PMID- 24355295 OWN - NLM STAT- MEDLINE DCOM- 20140919 LR - 20140131 IS - 1872-8278 (Electronic) IS - 1567-7249 (Linking) VI - 14 IP - 1 DP - 2014 Jan TI - Relic excavated in western India is probably of Georgian Queen Ketevan. PG - 1-6 LID - S1567-7249(13)00279-1 [pii] LID - 10.1016/j.mito.2013.12.002 [doi] AB - History has well documented the execution of Queen Ketevan of Georgia by the Persian Emperor of modern day Iran. Based on historical records, in 1624 two Augustinian friars unearthed the queen's remains and one of them brought the relic to the St. Augustine convent in Goa, India. We carried out ancient DNA analysis on the human bone remains excavated from the St. Augustine convent by sequencing and genotyping of the mitochondrial DNA. The investigations of the remains revealed a unique mtDNA haplogroup U1b, which is absent in India, but present in Georgia and surrounding regions. Since our genetic analysis corroborates archaeological and literary evidence, it is likely that the excavated bone belongs to Queen Ketevan of Georgia. CI - Copyright © 2013 Elsevier B.V. All rights reserved. FAU - Rai, Niraj AU - Rai N AD - CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India. Electronic address: nirajrai@ccmb.res.in. FAU - Taher, Nizamuddin AU - Taher N AD - Archeological Survey of India, Bhopal Circle India. Electronic address: n_taher2000@yahoo.com. FAU - Singh, Manvendra AU - Singh M AD - CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India. Electronic address: mnujnu@gmail.com. FAU - Chaubey, Gyaneshwer AU - Chaubey G AD - Estonian Biocentre, Riia23, Tartu, 51010, Estonia. Electronic address: gyanc@ebc.ee. FAU - Jha, Aditya Nath AU - Jha AN AD - CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India. Electronic address: adityanjha@ccmb.res.in. FAU - Singh, Lalji AU - Singh L AD - CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India; Banaras Hindu University, Varanasi 221005, India. Electronic address: lalji@ccmb.res.in. FAU - Thangaraj, Kumarasamy AU - Thangaraj K AD - CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India. Electronic address: thangs@ccmb.res.in. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131216 PL - Netherlands TA - Mitochondrion JT - Mitochondrion JID - 100968751 RN - 0 (DNA, Mitochondrial) SB - IM MH - Bone and Bones/*chemistry MH - DNA, Mitochondrial/*genetics/*isolation & purification MH - Female MH - *Forensic Anthropology MH - *Fossils MH - Genotyping Techniques MH - Haplotypes MH - Humans MH - India MH - Sequence Analysis, DNA OTO - NOTNLM OT - Ancestry OT - Ancient DNA OT - Queen Ketevan OT - Relic EDAT- 2013/12/21 06:00 MHDA- 2014/09/23 06:00 CRDT- 2013/12/21 06:00 PHST- 2013/09/02 00:00 [received] PHST- 2013/12/06 00:00 [revised] PHST- 2013/12/06 00:00 [accepted] PHST- 2013/12/21 06:00 [entrez] PHST- 2013/12/21 06:00 [pubmed] PHST- 2014/09/23 06:00 [medline] AID - S1567-7249(13)00279-1 [pii] AID - 10.1016/j.mito.2013.12.002 [doi] PST - ppublish SO - Mitochondrion. 2014 Jan;14(1):1-6. doi: 10.1016/j.mito.2013.12.002. Epub 2013 Dec 16. PMID- 24331083 OWN - NLM STAT- MEDLINE DCOM- 20140829 LR - 20140110 IS - 1095-8606 (Electronic) IS - 0047-2484 (Linking) VI - 66 DP - 2014 Jan TI - A reassessment of the presumed Neandertal remains from San Bernardino Cave, Italy. PG - 89-94 LID - S0047-2484(13)00239-X [pii] LID - 10.1016/j.jhevol.2013.09.009 [doi] AB - In 1986-1987, three human remains were unearthed from macro-unit II of San Bernardino Cave (Berici Hills, Veneto, Italy), a deposit containing a late Mousterian lithic assemblage. The human remains (a distal phalanx, a lower right third molar and a lower right second deciduous incisor) do not show diagnostic morphological features that could be used to determine whether they were from Homo neanderthalensis or Homo sapiens. Despite being of small size, and thus more similar to recent H. sapiens, the specimens were attributed to Neandertals, primarily because they were found in Mousterian layers. We carried out a taxonomic reassessment of the lower right third molar (LRM3; San Bernardino 4) using digital morphometric analysis of the root, ancient DNA analysis, carbon and nitrogen isotope analyses, and direct accelerator mass spectrometry (AMS) radiocarbon dating of dentine collagen. Mitochondrial DNA analysis and root morphology show that the molar belongs to a modern human and not to a Neandertal. Carbon 14 ((14)C) dating of the molar attributes it to the end of the Middle Ages (1420-1480 cal AD, 2 sigma). Carbon and nitrogen isotope analyses suggest that the individual in question had a diet similar to that of Medieval Italians. These results show that the molar, as well as the other two human remains, belong to recent H. sapiens and were introduced in the Mousterian levels post-depositionally. CI - Copyright © 2013 Elsevier Ltd. All rights reserved. FAU - Benazzi, Stefano AU - Benazzi S AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. Electronic address: stefano_benazzi@eva.mpg.de. FAU - Peresani, Marco AU - Peresani M AD - Sezione di Preistoria e Antropologia, Dipartimento di Studi Umanistici, Corso Ercole I d'Este 32, Università di Ferrara, I-44100 Ferrara, Italy. FAU - Talamo, Sahra AU - Talamo S AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. FAU - Fu, Qiaomei AU - Fu Q AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany; Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. FAU - Mannino, Marcello A AU - Mannino MA AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. FAU - Richards, Michael P AU - Richards MP AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany; Department of Anthropology, University of British Columbia, Vancouver, British Columbia, V6T 1Z1 Canada. FAU - Hublin, Jean-Jacques AU - Hublin JJ AD - Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131209 PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 0 (Carbon Isotopes) RN - 0 (DNA, Mitochondrial) RN - 0 (Nitrogen Isotopes) SB - IM MH - Animals MH - Carbon Isotopes/analysis MH - Caves MH - Chronology as Topic MH - DNA, Mitochondrial/*genetics MH - Fossils MH - Humans/classification MH - Italy MH - Mass Spectrometry MH - Molar/*anatomy & histology/*chemistry MH - Molecular Sequence Data MH - Neanderthals/*classification MH - Nitrogen Isotopes/analysis MH - Paleodontology MH - Phylogeny MH - Radiometric Dating MH - Sequence Analysis, DNA MH - Sequence Homology MH - Tooth Root/*anatomy & histology OTO - NOTNLM OT - AMS radiocarbon dating OT - Ancient DNA OT - Homo neanderthalensis OT - Isotope analyses OT - Modern human OT - Root morphometry EDAT- 2013/12/18 06:00 MHDA- 2014/08/30 06:00 CRDT- 2013/12/17 06:00 PHST- 2013/06/07 00:00 [received] PHST- 2013/08/08 00:00 [revised] PHST- 2013/09/23 00:00 [accepted] PHST- 2013/12/17 06:00 [entrez] PHST- 2013/12/18 06:00 [pubmed] PHST- 2014/08/30 06:00 [medline] AID - S0047-2484(13)00239-X [pii] AID - 10.1016/j.jhevol.2013.09.009 [doi] PST - ppublish SO - J Hum Evol. 2014 Jan;66:89-94. doi: 10.1016/j.jhevol.2013.09.009. Epub 2013 Dec 9. PMID- 24337269 OWN - NLM STAT- MEDLINE DCOM- 20131224 LR - 20131216 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 342 IP - 6164 DP - 2013 Dec 13 TI - Ancient DNA. Fossilized teeth offer mouthful on ancient microbiome. PG - 1303 LID - 10.1126/science.342.6164.1303 [doi] FAU - Curry, Andrew AU - Curry A LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Bacterial/*isolation & purification MH - Dental Calculus/*microbiology MH - *Fossils MH - Humans MH - *Microbiota MH - Paleodontology MH - Spirochaetales/classification/genetics/isolation & purification MH - Tetracycline Resistance/genetics MH - Tooth/*microbiology EDAT- 2013/12/18 06:00 MHDA- 2013/12/25 06:00 CRDT- 2013/12/17 06:00 PHST- 2013/12/17 06:00 [entrez] PHST- 2013/12/18 06:00 [pubmed] PHST- 2013/12/25 06:00 [medline] AID - 342/6164/1303 [pii] AID - 10.1126/science.342.6164.1303 [doi] PST - ppublish SO - Science. 2013 Dec 13;342(6164):1303. doi: 10.1126/science.342.6164.1303. PMID- 25079126 OWN - NLM STAT- MEDLINE DCOM- 20151110 LR - 20211203 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 85 IP - 6 DP - 2013 Dec TI - Letter to the editor: Genetics and the archaeology of ancient Israel. PG - 925-40 AB - This letter is a call for DNA testing on ancient skeletal materials from the southern Levant to begin a database of genetic information of the inhabitants of this crossroads region. In this region, during the Iron I period traditionally dated to circa 1200-1000 BCE, archaeologists and biblical historians view the earliest presence of a group that called itself Israel. They lived in villages in the varied hill countries of the region, contemporary with urban settlements in the coastal plains, inland valleys, and central hill country attributed to varied indigenous groups collectively called Canaanite. The remnants of Egyptian imperial presence in the region lasted until around 1150 BCE, postdating the arrival of an immigrant group from the Aegean called the Philistines circa 1175 BCE. The period that follows in the southern Levant is marked by the development of territorial states throughout the region, circa 1000-800 BCE. These patrimonial kingdoms, including the United Kingdom of Israel and the divided kingdoms of northern Israel and Judah, coalesced varied peoples under central leadership and newly founded administrative and religious bureaucracies. Ancient DNA testing will give us a further refined understanding of the individuals who peopled the region of the southern Levant throughout its varied archaeological and historic periods and provide scientific data that will support, refute, or nuance our sociohistoric reconstruction of ancient group identities. These social identities may or may not map onto genetic data, but without sampling of ancient DNA we may never know. A database of ancient DNA will also allow for comparisons with modern DNA samples collected throughout the greater region and the Mediterranean littoral, giving a more robust understanding of the long historical trajectories of regional human genetics and the genetics of varied ancestral groups of today's Jewish populations and other cultural groups in the modern Middle East and Mediterranean. CI - Copyright © 2014 Wayne State University Press, Detroit, Michigan 48201-1309. FAU - Brody, Aaron J AU - Brody AJ AD - Badè Museum of Biblical Archaeology, Pacific School of Religion, Berkeley, CA. FAU - King, Roy J AU - King RJ AD - Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA. LA - eng PT - Historical Article PT - Letter PL - United States TA - Hum Biol JT - Human biology JID - 0116717 SB - IM MH - Chromosomes, Human, Y/genetics MH - Emigration and Immigration/history MH - Ethnicity/*genetics/history MH - Genetics, Population/history MH - Haplotypes MH - History, Ancient MH - Humans MH - Israel/ethnology MH - Middle East/ethnology EDAT- 2014/08/01 06:00 MHDA- 2015/11/11 06:00 CRDT- 2014/08/01 06:00 PHST- 2013/09/24 00:00 [accepted] PHST- 2014/08/01 06:00 [entrez] PHST- 2014/08/01 06:00 [pubmed] PHST- 2015/11/11 06:00 [medline] AID - 10.3378/027.085.0606 [doi] PST - ppublish SO - Hum Biol. 2013 Dec;85(6):925-40. doi: 10.3378/027.085.0606. PMID- 24035510 OWN - NLM STAT- MEDLINE DCOM- 20140519 LR - 20200728 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 7 IP - 6 DP - 2013 Dec TI - Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jörg Jenatsch (1596-1639). PG - 610-617 LID - S1872-4973(13)00180-4 [pii] LID - 10.1016/j.fsigen.2013.08.006 [doi] AB - Jörg Jenatsch was a Swiss defender of independence and a fighter for liberty in the 17th century. With the help of three living male members of the Jenatsch family, we successfully identified a skeleton exhumed from Chur cathedral as the remains of Jörg Jenatsch. Our conclusion was based upon complete Y-STR and Y-SNP profiles that could be generated by replicate analyses of a bone sample available to us. The skeleton and the three living family members carried the same Y-SNP haplogroup, but were discordant at three of 23 Y-STR loci. This notwithstanding, conservative biostatistical evaluation of the data suggests that the Chur skeleton is at least 20 times more likely than not to be Jörg Jenatsch. CI - Copyright © 2013 Elsevier Ireland Ltd. All rights reserved. FAU - Haas, Cordula AU - Haas C AD - Institute of Legal Medicine, University of Zurich, Switzerland. Electronic address: cordula.haas@irm.uzh.ch. FAU - Shved, Natallia AU - Shved N AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Switzerland. FAU - Rühli, Frank Jakobus AU - Rühli FJ AD - Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Switzerland. FAU - Papageorgopoulou, Christina AU - Papageorgopoulou C AD - Laboratory of Anthropology, Department of History and Ethnology, Demokritus University of Thrace, Greece. FAU - Purps, Josephine AU - Purps J AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany. FAU - Geppert, Maria AU - Geppert M AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany. FAU - Willuweit, Sascha AU - Willuweit S AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany. FAU - Roewer, Lutz AU - Roewer L AD - Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany. FAU - Krawczak, Michael AU - Krawczak M AD - Institute of Medical Informatics and Statistics, Christian-Albrechts University of Kiel, Germany. LA - eng PT - Biography PT - Historical Article PT - Journal Article PT - Portrait PT - Research Support, Non-U.S. Gov't DEP - 20130827 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA Primers) SB - IM MH - Base Sequence MH - *Chromosomes, Human, Y MH - DNA Primers MH - *Forensic Anthropology MH - History, 16th Century MH - History, 17th Century MH - Humans MH - Male MH - Pedigree MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Switzerland PS - Jenatsch J FPS - Jenatsch, Jorg OTO - NOTNLM OT - Ancient DNA OT - Identification OT - Likelihood OT - Mutation OT - Y-SNP OT - Y-STR EDAT- 2013/09/17 06:00 MHDA- 2014/05/20 06:00 CRDT- 2013/09/17 06:00 PHST- 2013/03/15 00:00 [received] PHST- 2013/08/13 00:00 [revised] PHST- 2013/08/14 00:00 [accepted] PHST- 2013/09/17 06:00 [entrez] PHST- 2013/09/17 06:00 [pubmed] PHST- 2014/05/20 06:00 [medline] AID - S1872-4973(13)00180-4 [pii] AID - 10.1016/j.fsigen.2013.08.006 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2013 Dec;7(6):610-617. doi: 10.1016/j.fsigen.2013.08.006. Epub 2013 Aug 27. PMID- 24568772 OWN - NLM STAT- MEDLINE DCOM- 20140422 LR - 20211021 IS - 1537-6605 (Electronic) IS - 0002-9297 (Print) IS - 0002-9297 (Linking) VI - 93 IP - 5 DP - 2013 Nov 7 TI - Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. PG - 852-64 LID - S0002-9297(13)00459-X [pii] LID - 10.1016/j.ajhg.2013.10.002 [doi] AB - Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062-147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217-73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples. CI - Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. FAU - Carpenter, Meredith L AU - Carpenter ML AD - Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. FAU - Buenrostro, Jason D AU - Buenrostro JD AD - Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. FAU - Valdiosera, Cristina AU - Valdiosera C AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark; Department of Archaeology, Environment, and Community Planning, Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia. FAU - Schroeder, Hannes AU - Schroeder H AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark. FAU - Allentoft, Morten E AU - Allentoft ME AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark. FAU - Sikora, Martin AU - Sikora M AD - Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. FAU - Rasmussen, Morten AU - Rasmussen M AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark. FAU - Gravel, Simon AU - Gravel S AD - Department of Human Genetics and Génome Québec Innovation Centre, McGill University, Montréal, QC H3A 0G1, Canada. FAU - Guillén, Sonia AU - Guillén S AD - Centro Mallqui, Calle Ugarte y Moscoso 165, San Isidro, Lima 27, Peru. FAU - Nekhrizov, Georgi AU - Nekhrizov G AD - Bulgarian Academy of Sciences, National Institute of Archaeology, Sofia 1000, Bulgaria. FAU - Leshtakov, Krasimir AU - Leshtakov K AD - Department of Archaeology, Sofia University St. Kliment Ohridski, Sofia 1504, Bulgaria. FAU - Dimitrova, Diana AU - Dimitrova D AD - Bulgarian Academy of Sciences, National Institute of Archaeology, Sofia 1000, Bulgaria. FAU - Theodossiev, Nikola AU - Theodossiev N AD - Department of Archaeology, Sofia University St. Kliment Ohridski, Sofia 1504, Bulgaria. FAU - Pettener, Davide AU - Pettener D AD - Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy. FAU - Luiselli, Donata AU - Luiselli D AD - Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy. FAU - Sandoval, Karla AU - Sandoval K AD - Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. FAU - Moreno-Estrada, Andrés AU - Moreno-Estrada A AD - Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. FAU - Li, Yingrui AU - Li Y AD - BGI-Shenzhen, Shenzhen 518083, China. FAU - Wang, Jun AU - Wang J AD - BGI-Shenzhen, Shenzhen 518083, China; King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark; Macau University of Science and Technology, Taipa, Macau 999078, China. FAU - Gilbert, M Thomas P AU - Gilbert MT AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark; Ancient DNA Laboratory, Murdoch University, South Street, Perth, WA 6150, Australia. FAU - Willerslev, Eske AU - Willerslev E AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark. FAU - Greenleaf, William J AU - Greenleaf WJ AD - Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: wjg@stanford.edu. FAU - Bustamante, Carlos D AU - Bustamante CD AD - Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: cdbustam@stanford.edu. LA - eng GR - F32 HG007342/HG/NHGRI NIH HHS/United States GR - U01 HG005715/HG/NHGRI NIH HHS/United States GR - HG003220/HG/NHGRI NIH HHS/United States GR - HG005715/HG/NHGRI NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20131025 PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 63231-63-0 (RNA) RN - 9007-49-2 (DNA) SB - IM MH - Adolescent MH - Bone and Bones MH - Child MH - DNA/chemistry/genetics/*isolation & purification MH - *Fossils MH - Gene Library MH - *Genomics MH - Hair MH - High-Throughput Nucleotide Sequencing MH - History, Ancient MH - Humans MH - Male MH - *Mummies MH - Nucleic Acid Hybridization MH - Principal Component Analysis MH - RNA/genetics MH - Sequence Analysis, DNA/*methods MH - Tooth PMC - PMC3824117 EDAT- 2014/02/27 06:00 MHDA- 2014/04/23 06:00 PMCR- 2014/05/07 CRDT- 2014/02/27 06:00 PHST- 2013/08/03 00:00 [received] PHST- 2013/09/27 00:00 [revised] PHST- 2013/10/02 00:00 [accepted] PHST- 2014/02/27 06:00 [entrez] PHST- 2014/02/27 06:00 [pubmed] PHST- 2014/04/23 06:00 [medline] PHST- 2014/05/07 00:00 [pmc-release] AID - S0002-9297(13)00459-X [pii] AID - 10.1016/j.ajhg.2013.10.002 [doi] PST - ppublish SO - Am J Hum Genet. 2013 Nov 7;93(5):852-64. doi: 10.1016/j.ajhg.2013.10.002. Epub 2013 Oct 25. PMID- 24186332 OWN - NLM STAT- MEDLINE DCOM- 20151026 LR - 20211021 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 3 DP - 2013 Nov 4 TI - Ancient DNA and population turnover in southern levantine pigs--signature of the sea peoples migration? PG - 3035 LID - 10.1038/srep03035 [doi] LID - 3035 AB - Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have the DNA sequences of European wild boars and domestic pigs. To understand how this anomaly evolved, we sequenced DNA from ancient and modern pigs from Israel. Pigs from Late Bronze Age (until ca. 1150 BCE) in Israel shared haplotypes of modern and ancient Near Eastern pigs. European haplotypes became dominant only during the Iron Age (ca. 900 BCE). This raises the possibility that European pigs were brought to the region by the Sea Peoples who migrated to the Levant at that time. Then, a complete genetic turnover took place, most likely because of repeated admixture between local and introduced European domestic pigs that went feral. Severe population bottlenecks likely accelerated this process. Introductions by humans have strongly affected the phylogeography of wild animals, and interpretations of phylogeography based on modern DNA alone should be taken with caution. FAU - Meiri, Meirav AU - Meiri M AD - 1] Institute of Archaeology, Tel Aviv University, Tel Aviv 69978, Israel [2] Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel. FAU - Huchon, Dorothée AU - Huchon D FAU - Bar-Oz, Guy AU - Bar-Oz G FAU - Boaretto, Elisabetta AU - Boaretto E FAU - Horwitz, Liora Kolska AU - Horwitz LK FAU - Maeir, Aren M AU - Maeir AM FAU - Sapir-Hen, Lidar AU - Sapir-Hen L FAU - Larson, Greger AU - Larson G FAU - Weiner, Steve AU - Weiner S FAU - Finkelstein, Israel AU - Finkelstein I LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131104 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Archaeology MH - *DNA MH - DNA, Mitochondrial/genetics MH - *Genetics, Population MH - Geography MH - Haplotypes MH - *Human Migration MH - Humans MH - Israel MH - Phylogeny MH - Sus scrofa/*classification/*genetics PMC - PMC3816294 EDAT- 2013/11/05 06:00 MHDA- 2015/10/27 06:00 PMCR- 2013/11/04 CRDT- 2013/11/05 06:00 PHST- 2013/05/30 00:00 [received] PHST- 2013/07/23 00:00 [accepted] PHST- 2013/11/05 06:00 [entrez] PHST- 2013/11/05 06:00 [pubmed] PHST- 2015/10/27 06:00 [medline] PHST- 2013/11/04 00:00 [pmc-release] AID - srep03035 [pii] AID - 10.1038/srep03035 [doi] PST - epublish SO - Sci Rep. 2013 Nov 4;3:3035. doi: 10.1038/srep03035. PMID- 24179194 OWN - NLM STAT- MEDLINE DCOM- 20131114 LR - 20131101 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 342 IP - 6158 DP - 2013 Nov 1 TI - Genetics. RNA helps resurrect ancient DNA. PG - 543 LID - 10.1126/science.342.6158.543 [doi] FAU - Kaiser, Jocelyn AU - Kaiser J LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (RNA Probes) RN - 63231-63-0 (RNA) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/chemistry/*genetics/history MH - *Genetic Code MH - Genome, Human/*genetics MH - History, Ancient MH - Humans MH - Mummies MH - Peru MH - RNA/chemical synthesis/*chemistry/genetics MH - RNA Probes/chemical synthesis/*chemistry/genetics MH - Sequence Analysis, DNA/*methods EDAT- 2013/11/02 06:00 MHDA- 2013/11/15 06:00 CRDT- 2013/11/02 06:00 PHST- 2013/11/02 06:00 [entrez] PHST- 2013/11/02 06:00 [pubmed] PHST- 2013/11/15 06:00 [medline] AID - 342/6158/543 [pii] AID - 10.1126/science.342.6158.543 [doi] PST - ppublish SO - Science. 2013 Nov 1;342(6158):543. doi: 10.1126/science.342.6158.543. PMID- 24002647 OWN - NLM STAT- MEDLINE DCOM- 20140602 LR - 20240321 IS - 1943-2631 (Electronic) IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 195 IP - 3 DP - 2013 Nov TI - The characteristic trajectory of a fixing allele: a consequence of fictitious selection that arises from conditioning. PG - 993-1006 LID - 10.1534/genetics.113.156059 [doi] AB - This work is concerned with the historical progression, to fixation, of an allele in a finite population. This progression is characterized by the average frequency trajectory of alleles that achieve fixation before a given time, T. Under a diffusion analysis, the average trajectory, conditional on fixation by time T, is shown to be equivalent to the average trajectory in an unconditioned problem involving additional selection. We call this additional selection "fictitious selection"; it plays the role of a selective force in the unconditioned problem but does not exist in reality. It is a consequence of conditioning on fixation. The fictitious selection is frequency dependent and can be very large compared with any real selection that is acting. We derive an approximation for the characteristic trajectory of a fixing allele, when subject to real additive selection, from an unconditioned problem, where the total selection is a combination of real and fictitious selection. Trying to reproduce the characteristic trajectory from the action of additive selection, in an infinite population, can lead to estimates of the strength of the selection that deviate from the real selection by >1000% or have the opposite sign. Strong evolutionary forces may be invoked in problems where conditioning has been carried out, but these forces may largely be an outcome of the conditioning and hence may not have a real existence. The work presented here clarifies these issues and provides two useful tools for future analyses: the characteristic trajectory of a fixing allele and the force that primarily drives this, namely fictitious selection. These should prove useful in a number of areas of interest including coalescence with selection, experimental evolution, time series analyses of ancient DNA, game theory in finite populations, and the historical dynamics of selected alleles in wild populations. FAU - Zhao, Lei AU - Zhao L AD - Centre for Computational Systems Biology, Fudan University, Shanghai 200433, People's Republic of China. FAU - Lascoux, Martin AU - Lascoux M FAU - Overall, Andrew D J AU - Overall AD FAU - Waxman, David AU - Waxman D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130903 PL - United States TA - Genetics JT - Genetics JID - 0374636 SB - IM MH - *Alleles MH - Animals MH - Gene Frequency MH - Genetic Drift MH - *Genetics, Population MH - Humans MH - *Models, Genetic MH - Mutation MH - Population Density MH - *Selection, Genetic PMC - PMC3813879 OTO - NOTNLM OT - allele fixation OT - diffusion analysis OT - genetic disease progression OT - population genetics theory OT - random genetic drift OT - stochastic population dynamics EDAT- 2013/09/05 06:00 MHDA- 2014/06/03 06:00 PMCR- 2014/11/01 CRDT- 2013/09/05 06:00 PHST- 2013/09/05 06:00 [entrez] PHST- 2013/09/05 06:00 [pubmed] PHST- 2014/06/03 06:00 [medline] PHST- 2014/11/01 00:00 [pmc-release] AID - genetics.113.156059 [pii] AID - 156059 [pii] AID - 10.1534/genetics.113.156059 [doi] PST - ppublish SO - Genetics. 2013 Nov;195(3):993-1006. doi: 10.1534/genetics.113.156059. Epub 2013 Sep 3. PMID- 24205173 OWN - NLM STAT- MEDLINE DCOM- 20150223 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 10 DP - 2013 TI - Osteological and biomolecular evidence of a 7000-year-old case of hypertrophic pulmonary osteopathy secondary to tuberculosis from neolithic hungary. PG - e78252 LID - 10.1371/journal.pone.0078252 [doi] LID - e78252 AB - Seventy-one individuals from the late Neolithic population of the 7000-year-old site of Hódmezővásárhely-Gorzsa were examined for their skeletal palaeopathology. This revealed numerous cases of infections and non-specific stress indicators in juveniles and adults, metabolic diseases in juveniles, and evidence of trauma and mechanical changes in adults. Several cases showed potential signs of tuberculosis, particularly the remains of the individual HGO-53. This is an important finding that has significant implications for our understanding of this community. The aim of the present study was to seek biomolecular evidence to confirm this diagnosis. HGO-53 was a young male with a striking case of hypertrophic pulmonary osteopathy (HPO), revealing rib changes and cavitations in the vertebral bodies. The initial macroscopic diagnosis of HPO secondary to tuberculosis was confirmed by analysis of Mycobacterium tuberculosis complex specific cell wall lipid biomarkers and corroborated by ancient DNA (aDNA) analysis. This case is the earliest known classical case of HPO on an adult human skeleton and is one of the oldest palaeopathological and palaeomicrobiological tuberculosis cases to date. FAU - Masson, Muriel AU - Masson M AD - Archaeology, University of Edinburgh, Edinburgh, Scotland, United Kingdom ; Department of Biological Anthropology, University of Szeged, Szeged, Hungary. FAU - Molnár, Erika AU - Molnár E FAU - Donoghue, Helen D AU - Donoghue HD FAU - Besra, Gurdyal S AU - Besra GS FAU - Minnikin, David E AU - Minnikin DE FAU - Wu, Houdini H T AU - Wu HH FAU - Lee, Oona Y-C AU - Lee OY FAU - Bull, Ian D AU - Bull ID FAU - Pálfi, György AU - Pálfi G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131030 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Biomarkers) RN - 0 (DNA, Bacterial) SB - IM MH - Biomarkers/*metabolism MH - DNA, Bacterial/genetics MH - Humans MH - Hungary MH - Hypertrophy/genetics/*metabolism/microbiology/*pathology MH - Male MH - Mycobacterium tuberculosis/genetics MH - Osteology/methods MH - Paleopathology/methods MH - Ribs/microbiology/pathology MH - Spine/microbiology/pathology MH - Tuberculosis/genetics/metabolism/microbiology/*pathology PMC - PMC3813517 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2013/11/10 06:00 MHDA- 2015/02/24 06:00 PMCR- 2013/10/30 CRDT- 2013/11/09 06:00 PHST- 2013/05/29 00:00 [received] PHST- 2013/09/04 00:00 [accepted] PHST- 2013/11/09 06:00 [entrez] PHST- 2013/11/10 06:00 [pubmed] PHST- 2015/02/24 06:00 [medline] PHST- 2013/10/30 00:00 [pmc-release] AID - PONE-D-13-22233 [pii] AID - 10.1371/journal.pone.0078252 [doi] PST - epublish SO - PLoS One. 2013 Oct 30;8(10):e78252. doi: 10.1371/journal.pone.0078252. eCollection 2013. PMID- 24159019 OWN - NLM STAT- MEDLINE DCOM- 20131105 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 342 IP - 6157 DP - 2013 Oct 25 TI - Genomes. Ancient DNA links Native Americans with Europe. PG - 409-10 LID - 10.1126/science.342.6157.409 [doi] FAU - Balter, Michael AU - Balter M LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 9007-49-2 (DNA) SB - IM MH - Child, Preschool MH - DNA/*genetics MH - Genome, Human/*genetics MH - Haplotypes MH - Humans MH - Indians, North American/*genetics MH - Male MH - Siberia/ethnology MH - White People/*genetics EDAT- 2013/10/26 06:00 MHDA- 2013/11/06 06:00 CRDT- 2013/10/26 06:00 PHST- 2013/10/26 06:00 [entrez] PHST- 2013/10/26 06:00 [pubmed] PHST- 2013/11/06 06:00 [medline] AID - 342/6157/409 [pii] AID - 10.1126/science.342.6157.409 [doi] PST - ppublish SO - Science. 2013 Oct 25;342(6157):409-10. doi: 10.1126/science.342.6157.409. PMID- 24115443 OWN - NLM STAT- MEDLINE DCOM- 20131115 LR - 20211021 IS - 1095-9203 (Electronic) IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 342 IP - 6155 DP - 2013 Oct 11 TI - Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. PG - 257-61 LID - 10.1126/science.1241844 [doi] AB - The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity. FAU - Brandt, Guido AU - Brandt G AD - Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany. brandtg@uni-mainz.de FAU - Haak, Wolfgang AU - Haak W FAU - Adler, Christina J AU - Adler CJ FAU - Roth, Christina AU - Roth C FAU - Szécsényi-Nagy, Anna AU - Szécsényi-Nagy A FAU - Karimnia, Sarah AU - Karimnia S FAU - Möller-Rieker, Sabine AU - Möller-Rieker S FAU - Meller, Harald AU - Meller H FAU - Ganslmeier, Robert AU - Ganslmeier R FAU - Friederich, Susanne AU - Friederich S FAU - Dresely, Veit AU - Dresely V FAU - Nicklisch, Nicole AU - Nicklisch N FAU - Pickrell, Joseph K AU - Pickrell JK FAU - Sirocko, Frank AU - Sirocko F FAU - Reich, David AU - Reich D FAU - Cooper, Alan AU - Cooper A FAU - Alt, Kurt W AU - Alt KW CN - Genographic Consortium LA - eng SI - GENBANK/KF600801 SI - GENBANK/KF600802 SI - GENBANK/KF600803 SI - GENBANK/KF600804 SI - GENBANK/KF600805 SI - GENBANK/KF600806 SI - GENBANK/KF600807 SI - GENBANK/KF600808 SI - GENBANK/KF600809 SI - GENBANK/KF600810 SI - GENBANK/KF600811 SI - GENBANK/KF600812 SI - GENBANK/KF600813 SI - GENBANK/KF600814 SI - GENBANK/KF600815 SI - GENBANK/KF600816 SI - GENBANK/KF600817 SI - GENBANK/KF600818 SI - GENBANK/KF600819 SI - GENBANK/KF600820 SI - GENBANK/KF600821 SI - GENBANK/KF600822 SI - GENBANK/KF600823 SI - GENBANK/KF600824 SI - GENBANK/KF600825 SI - GENBANK/KF600826 SI - GENBANK/KF600827 SI - GENBANK/KF600828 SI - GENBANK/KF600829 SI - GENBANK/KF600830 SI - GENBANK/KF600831 SI - GENBANK/KF600832 SI - GENBANK/KF600833 SI - GENBANK/KF600834 SI - GENBANK/KF600835 SI - GENBANK/KF600836 SI - GENBANK/KF600837 SI - GENBANK/KF600838 SI - GENBANK/KF600839 SI - GENBANK/KF600840 SI - GENBANK/KF600841 SI - GENBANK/KF600842 SI - GENBANK/KF600843 SI - GENBANK/KF600844 SI - GENBANK/KF600845 SI - GENBANK/KF600846 SI - GENBANK/KF600847 SI - GENBANK/KF600848 SI - GENBANK/KF600849 SI - GENBANK/KF600850 SI - GENBANK/KF600851 SI - GENBANK/KF600852 SI - GENBANK/KF600853 SI - GENBANK/KF600854 SI - GENBANK/KF600855 SI - GENBANK/KF600856 SI - GENBANK/KF600857 SI - GENBANK/KF600858 SI - GENBANK/KF600859 SI - GENBANK/KF600860 SI - GENBANK/KF600861 SI - GENBANK/KF600862 SI - GENBANK/KF600863 SI - GENBANK/KF600864 SI - GENBANK/KF600865 SI - GENBANK/KF600866 SI - GENBANK/KF600867 SI - GENBANK/KF600868 SI - GENBANK/KF600869 SI - GENBANK/KF600870 SI - GENBANK/KF600871 SI - GENBANK/KF600872 SI - GENBANK/KF600873 SI - GENBANK/KF600874 SI - GENBANK/KF600875 SI - GENBANK/KF600876 SI - GENBANK/KF600877 SI - GENBANK/KF600878 SI - GENBANK/KF600879 SI - GENBANK/KF600880 SI - GENBANK/KF600881 SI - GENBANK/KF600882 SI - GENBANK/KF600883 SI - GENBANK/KF600884 SI - GENBANK/KF600885 SI - GENBANK/KF600886 SI - GENBANK/KF600887 SI - GENBANK/KF600888 SI - GENBANK/KF600889 SI - GENBANK/KF600890 SI - GENBANK/KF600891 SI - GENBANK/KF600892 SI - GENBANK/KF600893 SI - GENBANK/KF600894 SI - GENBANK/KF600895 SI - GENBANK/KF600896 SI - GENBANK/KF600897 SI - GENBANK/KF600898 SI - GENBANK/KF600899 SI - GENBANK/KF600900 SI - GENBANK/KF600901 SI - GENBANK/KF600902 SI - GENBANK/KF600903 SI - GENBANK/KF600904 SI - GENBANK/KF600905 SI - GENBANK/KF600906 SI - GENBANK/KF600907 SI - GENBANK/KF600908 SI - GENBANK/KF600909 SI - GENBANK/KF600910 SI - GENBANK/KF600911 SI - GENBANK/KF600912 SI - GENBANK/KF600913 SI - GENBANK/KF600914 SI - GENBANK/KF600915 SI - GENBANK/KF600916 SI - GENBANK/KF600917 SI - GENBANK/KF600918 SI - GENBANK/KF600919 SI - GENBANK/KF600920 SI - GENBANK/KF600921 SI - GENBANK/KF600922 SI - GENBANK/KF600923 SI - GENBANK/KF600924 SI - GENBANK/KF600925 SI - GENBANK/KF600926 SI - GENBANK/KF600927 SI - GENBANK/KF600928 SI - GENBANK/KF600929 SI - GENBANK/KF600930 SI - GENBANK/KF600931 SI - GENBANK/KF600932 SI - GENBANK/KF600933 SI - GENBANK/KF600934 SI - GENBANK/KF600935 SI - GENBANK/KF600936 SI - GENBANK/KF600937 SI - GENBANK/KF600938 SI - GENBANK/KF600939 SI - GENBANK/KF600940 SI - GENBANK/KF600941 SI - GENBANK/KF600942 SI - GENBANK/KF600943 SI - GENBANK/KF600944 SI - GENBANK/KF600945 SI - GENBANK/KF600946 SI - GENBANK/KF600947 SI - GENBANK/KF600948 SI - GENBANK/KF600949 SI - GENBANK/KF600950 SI - GENBANK/KF600951 SI - GENBANK/KF600952 SI - GENBANK/KF600953 SI - GENBANK/KF600954 SI - GENBANK/KF600955 SI - GENBANK/KF600956 SI - GENBANK/KF600957 SI - GENBANK/KF600958 SI - GENBANK/KF600959 SI - GENBANK/KF600960 SI - GENBANK/KF600961 SI - GENBANK/KF600962 SI - GENBANK/KF600963 SI - GENBANK/KF600964 SI - GENBANK/KF600965 SI - GENBANK/KF600966 SI - GENBANK/KF600967 SI - GENBANK/KF600968 SI - GENBANK/KF600969 SI - GENBANK/KF600970 SI - GENBANK/KF600971 SI - GENBANK/KF600972 SI - GENBANK/KF600973 SI - GENBANK/KF600974 SI - GENBANK/KF600975 SI - GENBANK/KF600976 SI - GENBANK/KF600977 SI - GENBANK/KF600978 SI - GENBANK/KF600979 SI - GENBANK/KF600980 SI - GENBANK/KF600981 SI - GENBANK/KF600982 SI - GENBANK/KF600983 SI - GENBANK/KF600984 SI - GENBANK/KF600985 SI - GENBANK/KF600986 SI - GENBANK/KF600987 SI - GENBANK/KF600988 SI - GENBANK/KF600989 SI - GENBANK/KF600990 SI - GENBANK/KF600991 SI - GENBANK/KF600992 SI - GENBANK/KF600993 SI - GENBANK/KF600994 SI - GENBANK/KF600995 SI - GENBANK/KF600996 SI - GENBANK/KF600997 SI - GENBANK/KF600998 SI - GENBANK/KF600999 SI - GENBANK/KF601000 SI - GENBANK/KF601001 SI - GENBANK/KF601002 SI - GENBANK/KF601003 SI - GENBANK/KF601004 SI - GENBANK/KF601005 SI - GENBANK/KF601006 SI - GENBANK/KF601007 SI - GENBANK/KF601008 SI - GENBANK/KF601009 SI - GENBANK/KF601010 SI - GENBANK/KF601011 SI - GENBANK/KF601012 SI - GENBANK/KF601013 SI - GENBANK/KF601014 SI - GENBANK/KF601015 SI - GENBANK/KF601016 SI - GENBANK/KF601017 SI - GENBANK/KF601018 SI - GENBANK/KF601019 SI - GENBANK/KF601020 SI - GENBANK/KF601021 SI - GENBANK/KF601022 SI - GENBANK/KF601023 SI - GENBANK/KF601024 SI - GENBANK/KF601025 SI - GENBANK/KF601026 SI - GENBANK/KF601027 SI - GENBANK/KF601028 SI - GENBANK/KF601029 SI - GENBANK/KF601030 SI - GENBANK/KF601031 SI - GENBANK/KF601032 SI - GENBANK/KF601033 SI - GENBANK/KF601034 SI - GENBANK/KF601035 SI - GENBANK/KF601036 SI - GENBANK/KF601037 SI - GENBANK/KF601038 SI - GENBANK/KF601039 SI - GENBANK/KF601040 SI - GENBANK/KF601041 SI - GENBANK/KF601042 SI - GENBANK/KF601043 SI - GENBANK/KF601044 SI - GENBANK/KF601045 SI - GENBANK/KF601046 SI - GENBANK/KF601047 SI - GENBANK/KF601048 SI - GENBANK/KF601049 SI - GENBANK/KF601050 SI - GENBANK/KF601051 SI - GENBANK/KF601052 SI - GENBANK/KF601053 SI - GENBANK/KF601054 SI - GENBANK/KF601055 SI - GENBANK/KF601056 SI - GENBANK/KF601057 SI - GENBANK/KF601058 SI - GENBANK/KF601059 SI - GENBANK/KF601060 SI - GENBANK/KF601061 SI - GENBANK/KF601062 SI - GENBANK/KF601063 SI - GENBANK/KF601064 SI - GENBANK/KF601065 SI - GENBANK/KF601066 SI - GENBANK/KF601067 SI - GENBANK/KF601068 SI - GENBANK/KF601069 SI - GENBANK/KF601070 SI - GENBANK/KF601071 SI - GENBANK/KF601072 SI - GENBANK/KF601073 SI - GENBANK/KF601074 SI - GENBANK/KF601075 SI - GENBANK/KF601076 SI - GENBANK/KF601077 SI - GENBANK/KF601078 SI - GENBANK/KF601079 SI - GENBANK/KF601080 SI - GENBANK/KF601081 SI - GENBANK/KF601082 SI - GENBANK/KF601083 SI - GENBANK/KF601084 SI - GENBANK/KF601085 SI - GENBANK/KF601086 SI - GENBANK/KF601087 SI - GENBANK/KF601088 SI - GENBANK/KF601089 SI - GENBANK/KF601090 SI - GENBANK/KF601091 SI - GENBANK/KF601092 SI - GENBANK/KF601093 SI - GENBANK/KF601094 SI - GENBANK/KF601095 SI - GENBANK/KF601096 SI - GENBANK/KF601097 SI - GENBANK/KF601098 SI - GENBANK/KF601099 SI - GENBANK/KF601100 SI - GENBANK/KF601101 SI - GENBANK/KF601102 SI - GENBANK/KF601103 SI - GENBANK/KF601104 SI - GENBANK/KF601105 SI - GENBANK/KF601106 SI - GENBANK/KF601107 SI - GENBANK/KF601108 SI - GENBANK/KF601109 SI - GENBANK/KF601110 SI - GENBANK/KF601111 SI - GENBANK/KF601112 SI - GENBANK/KF601113 SI - GENBANK/KF601114 SI - GENBANK/KF601115 SI - GENBANK/KF601116 SI - GENBANK/KF601117 SI - GENBANK/KF601118 SI - GENBANK/KF601119 SI - GENBANK/KF601120 SI - GENBANK/KF601121 SI - GENBANK/KF601122 SI - GENBANK/KF601123 SI - GENBANK/KF601124 SI - GENBANK/KF601125 SI - GENBANK/KF601126 SI - GENBANK/KF601127 SI - GENBANK/KF601128 SI - GENBANK/KF601129 SI - GENBANK/KF601130 SI - GENBANK/KF601131 SI - GENBANK/KF601132 SI - GENBANK/KF601133 SI - GENBANK/KF601134 SI - GENBANK/KF601135 SI - GENBANK/KF601136 SI - GENBANK/KF601137 SI - GENBANK/KF601138 SI - GENBANK/KF601139 SI - GENBANK/KF601140 SI - GENBANK/KF601141 SI - GENBANK/KF601142 SI - GENBANK/KF601143 SI - GENBANK/KF601144 SI - GENBANK/KF601145 SI - GENBANK/KF601146 SI - GENBANK/KF601147 SI - GENBANK/KF601148 SI - GENBANK/KF601149 SI - GENBANK/KF601150 SI - GENBANK/KF601151 SI - GENBANK/KF601152 SI - GENBANK/KF601153 SI - GENBANK/KF601154 SI - GENBANK/KF601155 SI - GENBANK/KF601156 SI - GENBANK/KF601157 SI - GENBANK/KF601158 SI - GENBANK/KF601159 SI - GENBANK/KF601160 SI - GENBANK/KF601161 SI - GENBANK/KF601162 SI - GENBANK/KF601163 SI - GENBANK/KF601164 SI - GENBANK/KF601165 SI - GENBANK/KF601166 SI - GENBANK/KF601167 SI - GENBANK/KF601168 SI - GENBANK/KF601169 SI - GENBANK/KF601170 SI - GENBANK/KF601171 SI - GENBANK/KF601172 SI - GENBANK/KF601173 SI - GENBANK/KF601174 SI - GENBANK/KF601175 SI - GENBANK/KF601176 SI - GENBANK/KF601177 SI - GENBANK/KF601178 SI - GENBANK/KF601179 SI - GENBANK/KF601180 SI - GENBANK/KF601181 SI - GENBANK/KF601182 SI - GENBANK/KF601183 SI - GENBANK/KF601184 SI - GENBANK/KF601185 SI - GENBANK/KF601186 SI - GENBANK/KF601187 SI - GENBANK/KF601188 SI - GENBANK/KF601189 SI - GENBANK/KF601190 SI - GENBANK/KF601191 SI - GENBANK/KF601192 SI - GENBANK/KF601193 GR - R01 GM100233/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/history MH - Base Sequence MH - DNA, Mitochondrial/*genetics/history MH - Europe MH - *Genetic Drift MH - *Genetic Variation MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - Population/*genetics MH - Transients and Migrants PMC - PMC4039305 MID - NIHMS584043 FIR - Der Sarkissian, Clio IR - Der Sarkissian C FIR - Adhikarla, Syama IR - Adhikarla S FIR - Prasad, Arun Kumar Ganesh IR - Prasad AK FIR - Pitchappan, Ramasamy IR - Pitchappan R FIR - Santhakumari, Arun Varatharajan IR - Santhakumari AV FIR - Balanovska, Elena IR - Balanovska E FIR - Balanovsky, Oleg IR - Balanovsky O FIR - Bertranpetit, Jaume IR - Bertranpetit J FIR - Comas, David IR - Comas D FIR - Martínez-Cruz, Begoña IR - Martínez-Cruz B FIR - Melé, Marta IR - Melé M FIR - Clarke, Andrew C IR - Clarke AC FIR - Matisoo-Smith, Elizabeth A IR - Matisoo-Smith EA FIR - Dulik, Matthew C IR - Dulik MC FIR - Gaieski, Jill B IR - Gaieski JB FIR - Owings, Amanda C IR - Owings AC FIR - Schurr, Theodore G IR - Schurr TG FIR - Vilar, Miguel G IR - Vilar MG FIR - Hobbs, Angela IR - Hobbs A FIR - Soodyall, Himla IR - Soodyall H FIR - Javed, Asif IR - Javed A FIR - Parida, Laxmi IR - Parida L FIR - Platt, Daniel E IR - Platt DE FIR - Royyuru, Ajay K IR - Royyuru AK FIR - Jin, Li IR - Jin L FIR - Li, Shilin IR - Li S FIR - Kaplan, Matthew E IR - Kaplan ME FIR - Merchant, Nirav C IR - Merchant NC FIR - Mitchell, R John IR - Mitchell RJ FIR - Quintana-Murci, Lluis IR - Quintana-Murci L FIR - Renfrew, Colin IR - Renfrew C FIR - Lacerda, Daniela R IR - Lacerda DR FIR - Santos, Fabrício R IR - Santos FR FIR - Hernanz, David F Soria IR - Hernanz DF FIR - Wells, Spencer IR - Wells S FIR - Swamikrishnan, Pandikumar IR - Swamikrishnan P FIR - Tyler-Smith, Chris IR - Tyler-Smith C FIR - Vieira, Pedro Paulo IR - Vieira PP FIR - Ziegle, Janet S IR - Ziegle JS EDAT- 2013/10/12 06:00 MHDA- 2013/11/16 06:00 PMCR- 2014/05/30 CRDT- 2013/10/12 06:00 PHST- 2013/10/12 06:00 [entrez] PHST- 2013/10/12 06:00 [pubmed] PHST- 2013/11/16 06:00 [medline] PHST- 2014/05/30 00:00 [pmc-release] AID - 342/6155/257 [pii] AID - 10.1126/science.1241844 [doi] PST - ppublish SO - Science. 2013 Oct 11;342(6155):257-61. doi: 10.1126/science.1241844. PMID- 24115417 OWN - NLM STAT- MEDLINE DCOM- 20131115 LR - 20131011 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 342 IP - 6155 DP - 2013 Oct 11 TI - Ancient DNA. Farming's tangled European roots. PG - 181-2 LID - 10.1126/science.342.6155.181 [doi] FAU - Balter, Michael AU - Balter M LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/*history/trends MH - DNA, Mitochondrial/genetics/*history MH - Europe MH - History, Ancient MH - Humans MH - Middle East MH - Paleontology MH - Skeleton EDAT- 2013/10/12 06:00 MHDA- 2013/11/16 06:00 CRDT- 2013/10/12 06:00 PHST- 2013/10/12 06:00 [entrez] PHST- 2013/10/12 06:00 [pubmed] PHST- 2013/11/16 06:00 [medline] AID - 342/6155/181 [pii] AID - 10.1126/science.342.6155.181 [doi] PST - ppublish SO - Science. 2013 Oct 11;342(6155):181-2. doi: 10.1126/science.342.6155.181. PMID- 23900195 OWN - NLM STAT- MEDLINE DCOM- 20131105 LR - 20130830 IS - 1879-0038 (Electronic) IS - 0378-1119 (Linking) VI - 528 IP - 2 DP - 2013 Oct 10 TI - Emulsion PCR-coupled target enrichment: an effective fishing method for high-throughput sequencing of poorly preserved ancient DNA. PG - 347-51 LID - S0378-1119(13)00929-3 [pii] LID - 10.1016/j.gene.2013.07.040 [doi] AB - Due to the difficulties in deep sequencing, high-throughput sequencing of ancient DNA has been limited to exceptionally well-preserved ancient materials. The primary factor is microbial attack popularly observed in the buried materials, and it causes drastic increase in relative ratio of microbial DNA in the extracted DNA. We present a unified strategy in which emulsion PCR is coupled with target enrichment followed by next-generation sequencing. The method made it possible to obtain efficiently non-duplicated reads mapped to target sequences of interest, and this can achieve deep and reliable sequencing of ancient DNA from typical materials, even though poorly preserved. CI - © 2013. FAU - Kihana, Makio AU - Kihana M AD - Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. FAU - Mizuno, Fuzuki AU - Mizuno F FAU - Sawafuji, Rikai AU - Sawafuji R FAU - Wang, Li AU - Wang L FAU - Ueda, Shintaroh AU - Ueda S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130727 PL - Netherlands TA - Gene JT - Gene JID - 7706761 RN - 0 (DNA, Mitochondrial) RN - 0 (Emulsions) SB - IM MH - DNA Damage MH - DNA, Mitochondrial/*genetics MH - Emulsions MH - Gene Library MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Polymerase Chain Reaction/*methods MH - Preservation, Biological MH - Sequence Analysis, DNA/*methods OTO - NOTNLM OT - Ancient DNA OT - Emulsion PCR OT - Microbial attack OT - NGS OT - Next-generation sequencing OT - PCR OT - Target enrichment OT - UV OT - double-stranded DNA OT - dsDNA OT - kDa OT - kilo-dalton OT - next-generation sequencing OT - polymerase-chain reaction OT - ultraviolet EDAT- 2013/08/01 06:00 MHDA- 2013/11/06 06:00 CRDT- 2013/08/01 06:00 PHST- 2013/02/22 00:00 [received] PHST- 2013/07/09 00:00 [revised] PHST- 2013/07/18 00:00 [accepted] PHST- 2013/08/01 06:00 [entrez] PHST- 2013/08/01 06:00 [pubmed] PHST- 2013/11/06 06:00 [medline] AID - S0378-1119(13)00929-3 [pii] AID - 10.1016/j.gene.2013.07.040 [doi] PST - ppublish SO - Gene. 2013 Oct 10;528(2):347-51. doi: 10.1016/j.gene.2013.07.040. Epub 2013 Jul 27. PMID- 23792062 OWN - NLM STAT- MEDLINE DCOM- 20131113 LR - 20130826 IS - 1879-0038 (Electronic) IS - 0378-1119 (Linking) VI - 528 IP - 1 DP - 2013 Oct 1 TI - Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations. PG - 33-40 LID - S0378-1119(13)00770-1 [pii] LID - 10.1016/j.gene.2013.06.017 [doi] AB - The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future. CI - Copyright © 2013 Elsevier B.V. All rights reserved. FAU - Anastasiou, Evilena AU - Anastasiou E AD - Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge CB2 1QH, UK. FAU - Mitchell, Piers D AU - Mitchell PD LA - eng PT - Journal Article PT - Review DEP - 20130619 PL - Netherlands TA - Gene JT - Gene JID - 7706761 RN - 9007-49-2 (DNA) SB - IM MH - Bacterial Infections/genetics/microbiology MH - Communicable Diseases/*genetics MH - DNA/genetics/isolation & purification MH - Fossils MH - Genetics, Population/*methods MH - Humans MH - Mummies MH - Paleopathology/*methods MH - Parasitic Diseases/genetics/parasitology MH - Virus Diseases/genetics/virology OTO - NOTNLM OT - Ancient DNA OT - Ancient disease OT - HIV OT - HPV OT - HTLV-1 OT - Human T-cell lymphotrophic virus type I OT - Human immunodeficiency virus OT - Human papilloma virus OT - MNI OT - Minimum number of individuals OT - Mummies OT - PCR OT - Palaeomicrobiology OT - Palaeoparasitology OT - Palaeopathology OT - Polymerase chain reaction OT - RLEP OT - Repetitive elements OT - SNPs OT - Single nucleotide polymorphisms OT - TB OT - Tuberculosis OT - aDNA EDAT- 2013/06/25 06:00 MHDA- 2013/11/14 06:00 CRDT- 2013/06/25 06:00 PHST- 2013/01/18 00:00 [received] PHST- 2013/05/23 00:00 [revised] PHST- 2013/06/01 00:00 [accepted] PHST- 2013/06/25 06:00 [entrez] PHST- 2013/06/25 06:00 [pubmed] PHST- 2013/11/14 06:00 [medline] AID - S0378-1119(13)00770-1 [pii] AID - 10.1016/j.gene.2013.06.017 [doi] PST - ppublish SO - Gene. 2013 Oct 1;528(1):33-40. doi: 10.1016/j.gene.2013.06.017. Epub 2013 Jun 19. PMID- 23792014 OWN - NLM STAT- MEDLINE DCOM- 20131113 LR - 20130826 IS - 1879-0038 (Electronic) IS - 0378-1119 (Linking) VI - 528 IP - 1 DP - 2013 Oct 1 TI - Evolutionary anthropology and genes: investigating the genetics of human evolution from excavated skeletal remains. PG - 27-32 LID - S0378-1119(13)00762-2 [pii] LID - 10.1016/j.gene.2013.06.011 [doi] AB - The development of molecular tools for the extraction, analysis and interpretation of DNA from the remains of ancient organisms (paleogenetics) has revolutionised a range of disciplines as diverse as the fields of human evolution, bioarchaeology, epidemiology, microbiology, taxonomy and population genetics. The paper draws attention to some of the challenges associated with the extraction and interpretation of ancient DNA from archaeological material, and then reviews the influence of paleogenetics on the field of human evolution. It discusses the main contributions of molecular studies to reconstructing the evolutionary and phylogenetic relationships between extinct hominins (human ancestors) and anatomically modern humans. It also explores the evidence for evolutionary changes in the genetic structure of anatomically modern humans in recent millennia. This breadth of research has led to discoveries that would never have been possible using traditional approaches to human evolution. CI - Copyright © 2013 Elsevier B.V. All rights reserved. FAU - Anastasiou, Evilena AU - Anastasiou E AD - Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge CB2 1QH, UK. FAU - Mitchell, Piers D AU - Mitchell PD LA - eng PT - Journal Article DEP - 20130618 PL - Netherlands TA - Gene JT - Gene JID - 7706761 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Anthropology/*methods MH - Cell Nucleus/genetics MH - DNA/analysis/*genetics/isolation & purification MH - DNA, Mitochondrial/analysis/genetics/isolation & purification MH - *Evolution, Molecular MH - Fossils MH - Genetics, Population/methods MH - Hominidae/*genetics MH - Humans MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA OTO - NOTNLM OT - Ancient DNA OT - Asp OT - Aspartic Acid OT - HVR OT - Human evolution OT - Human remains OT - Hypervariable Region OT - NGS OT - Next Generation Sequencing OT - PCR OT - Paleogenetics OT - Polymerase Chain Reaction OT - RFLP OT - Restriction Length Fragment Polymorphism OT - aDNA OT - ancient DNA OT - base pair OT - bp EDAT- 2013/06/25 06:00 MHDA- 2013/11/14 06:00 CRDT- 2013/06/25 06:00 PHST- 2013/01/11 00:00 [received] PHST- 2013/05/23 00:00 [revised] PHST- 2013/06/01 00:00 [accepted] PHST- 2013/06/25 06:00 [entrez] PHST- 2013/06/25 06:00 [pubmed] PHST- 2013/11/14 06:00 [medline] AID - S0378-1119(13)00762-2 [pii] AID - 10.1016/j.gene.2013.06.011 [doi] PST - ppublish SO - Gene. 2013 Oct 1;528(1):27-32. doi: 10.1016/j.gene.2013.06.011. Epub 2013 Jun 18. PMID- 24069445 OWN - NLM STAT- MEDLINE DCOM- 20140615 LR - 20240313 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 9 DP - 2013 TI - Strategy for sensitive and specific detection of Yersinia pestis in skeletons of the black death pandemic. PG - e75742 LID - 10.1371/journal.pone.0075742 [doi] LID - e75742 AB - Yersinia pestis has been identified as the causative agent of the Black Death pandemic in the 14(th) century. However, retrospective diagnostics in human skeletons after more than 600 years are critical. We describe a strategy following a modern diagnostic algorithm and working under strict ancient DNA regime for the identification of medieval human plague victims. An initial screening and DNA quantification assay detected the Y. pestis specific pla gene of the high copy number plasmid pPCP1. Results were confirmed by conventional PCR and sequence analysis targeting both Y. pestis specific virulence plasmids pPCP1 and pMT1. All assays were meticulously validated according to human clinical diagnostics requirements (ISO 15189) regarding efficiency, sensitivity, specificity, and limit of detection (LOD). Assay specificity was 100% tested on 41 clinically relevant bacteria and 29 Y. pseudotuberculosis strains as well as for DNA of 22 Y. pestis strains and 30 previously confirmed clinical human plague samples. The optimized LOD was down to 4 gene copies. 29 individuals from three different multiple inhumations were initially assessed as possible victims of the Black Death pandemic. 7 samples (24%) were positive in the pPCP1 specific screening assay. Confirmation through second target pMT1 specific PCR was successful for 4 of the positive individuals (14%). A maximum of 700 and 560 copies per µl aDNA were quantified in two of the samples. Those were positive in all assays including all repetitions, and are candidates for future continuative investigations such as whole genome sequencing. We discuss that all precautions taken here for the work with aDNA are sufficient to prevent external sample contamination and fulfill the criteria of authenticity. With regard to retrospective diagnostics of a human pathogen and the uniqueness of ancient material we strongly recommend using a careful strategy and validated assays as presented in our study. FAU - Seifert, Lisa AU - Seifert L AD - Ludwig Maximilian University of Munich, Department Biology I, Biodiversity research/Anthropology, Martinsried, Germany. FAU - Harbeck, Michaela AU - Harbeck M FAU - Thomas, Astrid AU - Thomas A FAU - Hoke, Nadja AU - Hoke N FAU - Zöller, Lothar AU - Zöller L FAU - Wiechmann, Ingrid AU - Wiechmann I FAU - Grupe, Gisela AU - Grupe G FAU - Scholz, Holger C AU - Scholz HC FAU - Riehm, Julia M AU - Riehm JM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130917 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Bacterial Proteins) RN - 0 (DNA, Bacterial) RN - EC 3.4.21.- (Pla protease, Yersinia pestis) RN - EC 3.4.21.- (Plasminogen Activators) SB - IM EIN - PLoS One. 2013;8(10). doi:10.1371/annotation/190eceb9-03c6-4d5f-b861-83d44f2a0e53 MH - Archaeology/methods MH - Bacterial Proteins/genetics MH - Bone and Bones/*microbiology MH - DNA, Bacterial/genetics MH - Germany MH - Humans MH - Plague/*diagnosis/epidemiology MH - Plasmids/genetics MH - Plasminogen Activators/genetics MH - Polymerase Chain Reaction/methods MH - Reproducibility of Results MH - Sensitivity and Specificity MH - Switzerland MH - Yersinia pestis/*genetics PMC - PMC3775804 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2013/09/27 06:00 MHDA- 2014/06/16 06:00 PMCR- 2013/09/17 CRDT- 2013/09/27 06:00 PHST- 2013/02/21 00:00 [received] PHST- 2013/08/19 00:00 [accepted] PHST- 2013/09/27 06:00 [entrez] PHST- 2013/09/27 06:00 [pubmed] PHST- 2014/06/16 06:00 [medline] PHST- 2013/09/17 00:00 [pmc-release] AID - PONE-D-13-07989 [pii] AID - 10.1371/journal.pone.0075742 [doi] PST - epublish SO - PLoS One. 2013 Sep 17;8(9):e75742. doi: 10.1371/journal.pone.0075742. eCollection 2013. PMID- 24040024 OWN - NLM STAT- MEDLINE DCOM- 20140702 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 9 DP - 2013 TI - mtDNA from the early Bronze Age to the Roman period suggests a genetic link between the Indian subcontinent and Mesopotamian cradle of civilization. PG - e73682 LID - 10.1371/journal.pone.0073682 [doi] LID - e73682 AB - Ancient DNA methodology was applied to analyse sequences extracted from freshly unearthed remains (teeth) of 4 individuals deeply deposited in slightly alkaline soil of the Tell Ashara (ancient Terqa) and Tell Masaikh (ancient Kar-Assurnasirpal) Syrian archaeological sites, both in the middle Euphrates valley. Dated to the period between 2.5 Kyrs BC and 0.5 Kyrs AD the studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Paleolithic and are absent in people living today in Syria. However, they are present in people inhabiting today's Tibet, Himalayas, India and Pakistan. We anticipate that the analysed remains from Mesopotamia belonged to people with genetic affinity to the Indian subcontinent since the distribution of identified ancient haplotypes indicates solid link with populations from the region of South Asia-Tibet (Trans-Himalaya). They may have been descendants of migrants from much earlier times, spreading the clades of the macrohaplogroup M throughout Eurasia and founding regional Mesopotamian groups like that of Terqa or just merchants moving along trade routes passing near or through the region. None of the successfully identified nuclear alleles turned out to be ΔF508 CFTR, LCT-13910T or Δ32 CCR5. FAU - Witas, Henryk W AU - Witas HW AD - Department of Molecular Biology, Medical University of Łódź, Łódź, Poland. FAU - Tomczyk, Jacek AU - Tomczyk J FAU - Jędrychowska-Dańska, Krystyna AU - Jędrychowska-Dańska K FAU - Chaubey, Gyaneshwer AU - Chaubey G FAU - Płoszaj, Tomasz AU - Płoszaj T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130911 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - Base Sequence MH - *Civilization MH - DNA, Mitochondrial/chemistry/classification/*genetics MH - Emigration and Immigration MH - Female MH - Fossils MH - Genetic Variation MH - *Genetics, Population MH - Geography MH - Haplotypes/*genetics MH - Humans MH - India MH - Male MH - Mesopotamia MH - Pakistan MH - Phylogeny MH - Population Dynamics MH - Sequence Analysis, DNA MH - Syria MH - Tibet MH - Time Factors MH - Tooth/metabolism PMC - PMC3770703 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2013/09/17 06:00 MHDA- 2014/07/06 06:00 PMCR- 2013/09/11 CRDT- 2013/09/17 06:00 PHST- 2013/05/22 00:00 [received] PHST- 2013/07/20 00:00 [accepted] PHST- 2013/09/17 06:00 [entrez] PHST- 2013/09/17 06:00 [pubmed] PHST- 2014/07/06 06:00 [medline] PHST- 2013/09/11 00:00 [pmc-release] AID - PONE-D-13-21225 [pii] AID - 10.1371/journal.pone.0073682 [doi] PST - epublish SO - PLoS One. 2013 Sep 11;8(9):e73682. doi: 10.1371/journal.pone.0073682. eCollection 2013. PMID- 23900768 OWN - NLM STAT- MEDLINE DCOM- 20140303 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 152 IP - 1 DP - 2013 Sep TI - Genetic evidence does not support an Etruscan origin in Anatolia. PG - 11-8 LID - 10.1002/ajpa.22319 [doi] AB - The debate on the origins of Etruscans, documented in central Italy between the eighth century BC and the first century AD, dates back to antiquity. Herodotus described them as a group of immigrants from Lydia, in Western Anatolia, whereas for Dionysius of Halicarnassus they were an indigenous population. Dionysius' view is shared by most modern archeologists, but the observation of similarities between the (modern) mitochondrial DNAs (mtDNAs) of Turks and Tuscans was interpreted as supporting an Anatolian origin of the Etruscans. However, ancient DNA evidence shows that only some isolates, and not the bulk of the modern Tuscan population, are genetically related to the Etruscans. In this study, we tested alternative models of Etruscan origins by Approximate Bayesian Computation methods, comparing levels of genetic diversity in the mtDNAs of modern and ancient populations with those obtained by millions of computer simulations. The results show that the observed genetic similarities between modern Tuscans and Anatolians cannot be attributed to an immigration wave from the East leading to the onset of the Etruscan culture in Italy. Genetic links between Tuscany and Anatolia do exist, but date back to a remote stage of prehistory, possibly but not necessarily to the spread of farmers during the Neolithic period. CI - Copyright © 2013 Wiley Periodicals, Inc. FAU - Tassi, Francesca AU - Tassi F AD - Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy. FAU - Ghirotto, Silvia AU - Ghirotto S FAU - Caramelli, David AU - Caramelli D FAU - Barbujani, Guido AU - Barbujani G LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130730 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - Bayes Theorem MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration/*history MH - *Genetic Variation MH - Genetics, Population MH - History, 21st Century MH - History, Ancient MH - History, Medieval MH - Humans MH - Italy MH - Models, Statistical MH - Turkey MH - White People/*genetics OTO - NOTNLM OT - ancient DNA OT - approximate Bayesian computation OT - coalescent simulations OT - mitochondrial DNA EDAT- 2013/08/01 06:00 MHDA- 2014/03/04 06:00 CRDT- 2013/08/01 06:00 PHST- 2013/01/11 00:00 [received] PHST- 2013/05/20 00:00 [accepted] PHST- 2013/08/01 06:00 [entrez] PHST- 2013/08/01 06:00 [pubmed] PHST- 2014/03/04 06:00 [medline] AID - 10.1002/ajpa.22319 [doi] PST - ppublish SO - Am J Phys Anthropol. 2013 Sep;152(1):11-8. doi: 10.1002/ajpa.22319. Epub 2013 Jul 30. PMID- 23868176 OWN - NLM STAT- MEDLINE DCOM- 20131017 LR - 20130722 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 151 IP - 4 DP - 2013 Aug TI - Brief communication: Evolution of a specific O allele (O1vG542A) supports unique ancestry of Native Americans. PG - 649-57 LID - 10.1002/ajpa.22292 [doi] AB - In this study, we explore the geographic and temporal distribution of a unique variant of the O blood group allele called O1v(G542A) , which has been shown to be shared among Native Americans but is rare in other populations. O1v(G542A) was previously reported in Native American populations in Mesoamerica and South America, and has been proposed as an ancestry informative marker. We investigated whether this allele is also found in the Tlingit and Haida, two contemporary indigenous populations from Alaska, and a pre-Columbian population from California. If O1v(G542A) is present in Na-Dene speakers (i.e., Tlingits), it would indicate that Na-Dene speaking groups share close ancestry with other Native American groups and support a Beringian origin of the allele, consistent with the Beringian Incubation Model. If O1v(G542A) is found in pre-Columbian populations, it would further support a Beringian origin of the allele, rather than a more recent introduction of the allele into the Americas via gene flow from one or more populations which have admixed with Native Americans over the past five centuries. We identified this allele in one Na-Dene population at a frequency of 0.11, and one ancient California population at a frequency of 0.20. Our results support a Beringian origin of O1v(G542A) , which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus. This result is consistent with the hypothesis that Na-Dene and other Native American populations primarily derive their ancestry from a single source population. CI - Copyright © 2013 Wiley Periodicals, Inc. FAU - Villanea, Fernando A AU - Villanea FA AD - School of Biological Sciences, Washington State University, Pullman, WA 99164-4910, USA. FAU - Bolnick, Deborah A AU - Bolnick DA FAU - Monroe, Cara AU - Monroe C FAU - Worl, Rosita AU - Worl R FAU - Cambra, Rosemary AU - Cambra R FAU - Leventhal, Alan AU - Leventhal A FAU - Kemp, Brian M AU - Kemp BM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (ABO Blood-Group System) RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - ABO Blood-Group System/*genetics MH - Alaska MH - *Alleles MH - Base Sequence MH - *Biological Evolution MH - California MH - DNA Primers/genetics MH - DNA, Mitochondrial/genetics MH - Demography MH - Gene Flow/*genetics MH - Genetics, Population MH - Haplotypes/genetics MH - Humans MH - Indians, North American/*genetics MH - Molecular Sequence Data MH - Sequence Analysis, DNA OTO - NOTNLM OT - ABO blood group OT - ancestry informative markers OT - ancient DNA OT - entrance of humans into the Americas EDAT- 2013/07/23 06:00 MHDA- 2013/10/18 06:00 CRDT- 2013/07/23 06:00 PHST- 2013/02/18 00:00 [received] PHST- 2013/04/16 00:00 [accepted] PHST- 2013/07/23 06:00 [entrez] PHST- 2013/07/23 06:00 [pubmed] PHST- 2013/10/18 06:00 [medline] AID - 10.1002/ajpa.22292 [doi] PST - ppublish SO - Am J Phys Anthropol. 2013 Aug;151(4):649-57. doi: 10.1002/ajpa.22292. PMID- 23703035 OWN - NLM STAT- MEDLINE DCOM- 20140113 LR - 20130715 IS - 1521-1878 (Electronic) IS - 0265-9247 (Linking) VI - 35 IP - 8 DP - 2013 Aug TI - Phenotypes from ancient DNA: approaches, insights and prospects. PG - 690-5 LID - 10.1002/bies.201300036 [doi] AB - The great majority of phenotypic characteristics are complex traits, complicating the identification of the genes underlying their expression. However, both methodological and theoretical progress in genome-wide association studies have resulted in a much better understanding of the underlying genetics of many phenotypic traits, including externally visible characteristics (EVCs) such as eye and hair color. Consequently, it has become possible to predict EVCs from human samples lacking phenotypic information. Predicting EVCs from genetic evidence is clearly appealing for forensic applications involving the personal identification of human remains. Now, a recent paper has reported the genetic determination of eye and hair color in samples up to 800 years old. The ability to predict EVCs from ancient human remains opens up promising perspectives for ancient DNA research, as this could allow studies to directly address archaeological and evolutionary questions related to the temporal and geographical origins of the genetic variants underlying phenotypes. CI - © 2013 WILEY Periodicals, Inc. FAU - Fortes, Gloria G AU - Fortes GG AD - Department of Biology, University of York, York, UK. FAU - Speller, Camilla F AU - Speller CF FAU - Hofreiter, Michael AU - Hofreiter M FAU - King, Turi E AU - King TE LA - eng PT - Journal Article PT - Review DEP - 20130523 PL - United States TA - Bioessays JT - BioEssays : news and reviews in molecular, cellular and developmental biology JID - 8510851 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Archaeology/methods MH - DNA/*genetics MH - DNA Fingerprinting MH - DNA, Mitochondrial/*genetics MH - Eye Color MH - Fossils MH - Genome, Human MH - Hair MH - Humans MH - Paleontology/methods MH - *Phenotype MH - Pigmentation/*genetics MH - Polymorphism, Single Nucleotide OTO - NOTNLM OT - EVC OT - HIrisPlex OT - NGS OT - ancient DNA OT - genotypes OT - phenotypes EDAT- 2013/05/25 06:00 MHDA- 2014/01/15 06:00 CRDT- 2013/05/25 06:00 PHST- 2013/05/25 06:00 [entrez] PHST- 2013/05/25 06:00 [pubmed] PHST- 2014/01/15 06:00 [medline] AID - 10.1002/bies.201300036 [doi] PST - ppublish SO - Bioessays. 2013 Aug;35(8):690-5. doi: 10.1002/bies.201300036. Epub 2013 May 23. PMID- 23553074 OWN - NLM STAT- MEDLINE DCOM- 20140114 LR - 20211021 IS - 2190-3883 (Electronic) IS - 1234-1983 (Linking) VI - 54 IP - 3 DP - 2013 Aug TI - First insights into the metagenome of Egyptian mummies using next-generation sequencing. PG - 309-25 LID - 10.1007/s13353-013-0145-1 [doi] AB - We applied, for the first time, next-generation sequencing (NGS) technology on Egyptian mummies. Seven NGS datasets obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC-124AD) and two unearthed pre-contact Bolivian lowland skeletons were generated and characterised. The datasets were contrasted to three recently published NGS datasets obtained from cold-climate regions, i.e. the Saqqaq, the Denisova hominid and the Alpine Iceman. Analysis was done using one million reads of each newly generated or published dataset. Blastn and megablast results were analysed using MEGAN software. Distinct NGS results were replicated by specific and sensitive polymerase chain reaction (PCR) protocols in ancient DNA dedicated laboratories. Here, we provide unambiguous identification of authentic DNA in Egyptian mummies. The NGS datasets showed variable contents of endogenous DNA harboured in tissues. Three of five mummies displayed a human DNA proportion comparable to the human read count of the Saqqaq permafrost-preserved specimen. Furthermore, a metagenomic signature unique to mummies was displayed. By applying a "bacterial fingerprint", discrimination among mummies and other remains from warm areas outside Egypt was possible. Due to the absence of an adequate environment monitoring, a bacterial bloom was identified when analysing different biopsies from the same mummies taken after a lapse of time of 1.5 years. Plant kingdom representation in all mummy datasets was unique and could be partially associated with their use in embalming materials. Finally, NGS data showed the presence of Plasmodium falciparum and Toxoplasma gondii DNA sequences, indicating malaria and toxoplasmosis in these mummies. We demonstrate that endogenous ancient DNA can be extracted from mummies and serve as a proper template for the NGS technique, thus, opening new pathways of investigation for future genome sequencing of ancient Egyptian individuals. FAU - Khairat, Rabab AU - Khairat R AD - Institute of Human Genetics, University of Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany. FAU - Ball, Markus AU - Ball M FAU - Chang, Chun-Chi Hsieh AU - Chang CC FAU - Bianucci, Raffaella AU - Bianucci R FAU - Nerlich, Andreas G AU - Nerlich AG FAU - Trautmann, Martin AU - Trautmann M FAU - Ismail, Somaia AU - Ismail S FAU - Shanab, Gamila M L AU - Shanab GM FAU - Karim, Amr M AU - Karim AM FAU - Gad, Yehia Z AU - Gad YZ FAU - Pusch, Carsten M AU - Pusch CM LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130404 PL - England TA - J Appl Genet JT - Journal of applied genetics JID - 9514582 SB - IM MH - Base Sequence MH - Biopsy MH - Egypt, Ancient MH - Embalming/history/*methods MH - Gene Library MH - History, Ancient MH - Humans MH - *Metagenome MH - Molecular Sequence Data MH - *Mummies MH - Phylogeny MH - Plasmodium falciparum/genetics MH - Polymerase Chain Reaction/methods MH - Sequence Analysis, DNA/methods MH - Temperature MH - Toxoplasma/genetics EDAT- 2013/04/05 06:00 MHDA- 2014/01/15 06:00 CRDT- 2013/04/05 06:00 PHST- 2012/07/09 00:00 [received] PHST- 2013/03/11 00:00 [accepted] PHST- 2013/03/08 00:00 [revised] PHST- 2013/04/05 06:00 [entrez] PHST- 2013/04/05 06:00 [pubmed] PHST- 2014/01/15 06:00 [medline] AID - 10.1007/s13353-013-0145-1 [doi] PST - ppublish SO - J Appl Genet. 2013 Aug;54(3):309-25. doi: 10.1007/s13353-013-0145-1. Epub 2013 Apr 4. PMID- 23843972 OWN - NLM STAT- MEDLINE DCOM- 20140207 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 7 DP - 2013 TI - Ancient DNA analysis of mid-holocene individuals from the Northwest Coast of North America reveals different evolutionary paths for mitogenomes. PG - e66948 LID - 10.1371/journal.pone.0066948 [doi] LID - e66948 AB - To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga'a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor-descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast. FAU - Cui, Yinqiu AU - Cui Y AD - Department of Anthropology, University of Illinois, Urbana, Ilinois, United States of America. FAU - Lindo, John AU - Lindo J FAU - Hughes, Cris E AU - Hughes CE FAU - Johnson, Jesse W AU - Johnson JW FAU - Hernandez, Alvaro G AU - Hernandez AG FAU - Kemp, Brian M AU - Kemp BM FAU - Ma, Jian AU - Ma J FAU - Cunningham, Ryan AU - Cunningham R FAU - Petzelt, Barbara AU - Petzelt B FAU - Mitchell, Joycellyn AU - Mitchell J FAU - Archer, David AU - Archer D FAU - Cybulski, Jerome S AU - Cybulski JS FAU - Malhi, Ripan S AU - Malhi RS LA - eng SI - GENBANK/KC998701 SI - GENBANK/KC998702 SI - GENBANK/KC998703 SI - GENBANK/KC998704 SI - GENBANK/KC998705 SI - GENBANK/KC998706 SI - GENBANK/KC998707 PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130703 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - Adult MH - Canada MH - *Evolution, Molecular MH - Female MH - *Genome, Mitochondrial MH - Haplotypes MH - Humans MH - Indians, North American/*genetics MH - Male MH - Molecular Sequence Data MH - Mutation MH - North America MH - Phylogeny MH - Young Adult PMC - PMC3700925 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2013/07/12 06:00 MHDA- 2014/02/08 06:00 PMCR- 2013/07/03 CRDT- 2013/07/12 06:00 PHST- 2013/03/11 00:00 [received] PHST- 2013/05/10 00:00 [accepted] PHST- 2013/07/12 06:00 [entrez] PHST- 2013/07/12 06:00 [pubmed] PHST- 2014/02/08 06:00 [medline] PHST- 2013/07/03 00:00 [pmc-release] AID - PONE-D-13-10171 [pii] AID - 10.1371/journal.pone.0066948 [doi] PST - epublish SO - PLoS One. 2013 Jul 3;8(7):e66948. doi: 10.1371/journal.pone.0066948. Print 2013. PMID- 23613487 OWN - NLM STAT- MEDLINE DCOM- 20131217 LR - 20211021 IS - 1367-4811 (Electronic) IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 29 IP - 13 DP - 2013 Jul 1 TI - mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. PG - 1682-4 LID - 10.1093/bioinformatics/btt193 [doi] AB - MOTIVATION: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples. RESULTS: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (λ), nick frequency (ν) and cytosine deamination rates in both double-stranded regions ( ) and overhangs ( ). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols. AVAILABILITY: mapDamage 2.0 is available at ginolhac.github.io/mapDamage/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk/publications/mapdamage2.0/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. FAU - Jónsson, Hákon AU - Jónsson H AD - Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 København K, Denmark. jonsson.hakon@gmail.com FAU - Ginolhac, Aurélien AU - Ginolhac A FAU - Schubert, Mikkel AU - Schubert M FAU - Johnson, Philip L F AU - Johnson PL FAU - Orlando, Ludovic AU - Orlando L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130423 PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 8J337D1HZY (Cytosine) SB - IM MH - Bayes Theorem MH - Cytosine/metabolism MH - *DNA Damage MH - Deamination MH - Fossils MH - *High-Throughput Nucleotide Sequencing MH - Humans MH - *Sequence Analysis, DNA MH - *Software PMC - PMC3694634 EDAT- 2013/04/25 06:00 MHDA- 2013/12/18 06:00 PMCR- 2013/04/23 CRDT- 2013/04/25 06:00 PHST- 2013/04/25 06:00 [entrez] PHST- 2013/04/25 06:00 [pubmed] PHST- 2013/12/18 06:00 [medline] PHST- 2013/04/23 00:00 [pmc-release] AID - btt193 [pii] AID - 10.1093/bioinformatics/btt193 [doi] PST - ppublish SO - Bioinformatics. 2013 Jul 1;29(13):1682-4. doi: 10.1093/bioinformatics/btt193. Epub 2013 Apr 23. PMID- 23052219 OWN - NLM STAT- MEDLINE DCOM- 20130826 LR - 20240525 IS - 1420-9071 (Electronic) IS - 1420-682X (Print) IS - 1420-682X (Linking) VI - 70 IP - 14 DP - 2013 Jul TI - Ancestry of modern Europeans: contributions of ancient DNA. PG - 2473-87 LID - 10.1007/s00018-012-1180-5 [doi] AB - Understanding the peopling history of Europe is crucial to comprehend the origins of modern populations. Of course, the analysis of current genetic data offers several explanations about human migration patterns which occurred on this continent, but it fails to explain precisely the impact of each demographic event. In this context, direct access to the DNA of ancient specimens allows the overcoming of recent demographic phenomena, which probably highly modified the constitution of the current European gene pool. In recent years, several DNA studies have been successfully conducted from ancient human remains thanks to the improvement of molecular techniques. They have brought new fundamental information on the peopling of Europe and allowed us to refine our understanding of European prehistory. In this review, we will detail all the ancient DNA studies performed to date on ancient European DNA from the Middle Paleolithic to the beginning of the protohistoric period. FAU - Lacan, Marie AU - Lacan M AD - Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde,Toulouse cedex 3, France. lacan.marie@netcourrier.com FAU - Keyser, Christine AU - Keyser C FAU - Crubézy, Eric AU - Crubézy E FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20121011 PL - Switzerland TA - Cell Mol Life Sci JT - Cellular and molecular life sciences : CMLS JID - 9705402 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - DNA, Mitochondrial/analysis/*genetics MH - Genetics, Population MH - Genome MH - Haplotypes MH - History, Ancient MH - Humans MH - Neanderthals/genetics MH - Paleopathology MH - White People/*genetics/history PMC - PMC11113793 EDAT- 2012/10/12 06:00 MHDA- 2013/08/27 06:00 PMCR- 2012/10/11 CRDT- 2012/10/12 06:00 PHST- 2012/04/05 00:00 [received] PHST- 2012/09/24 00:00 [accepted] PHST- 2012/09/21 00:00 [revised] PHST- 2012/10/12 06:00 [entrez] PHST- 2012/10/12 06:00 [pubmed] PHST- 2013/08/27 06:00 [medline] PHST- 2012/10/11 00:00 [pmc-release] AID - 1180 [pii] AID - 10.1007/s00018-012-1180-5 [doi] PST - ppublish SO - Cell Mol Life Sci. 2013 Jul;70(14):2473-87. doi: 10.1007/s00018-012-1180-5. Epub 2012 Oct 11. PMID- 23697340 OWN - NLM STAT- MEDLINE DCOM- 20131029 LR - 20221207 IS - 1080-6059 (Electronic) IS - 1080-6040 (Print) IS - 1080-6040 (Linking) VI - 19 IP - 5 DP - 2013 May TI - Mycobacterium tuberculosis complex in remains of 18th-19th century slaves, Brazil. PG - 837-9 LID - 10.3201/eid1905.120193 [doi] FAU - Jaeger, Lauren H AU - Jaeger LH FAU - de Souza, Sheila M F M AU - de Souza SM FAU - Dias, Ondemar F AU - Dias OF FAU - Iñiguez, Alena M AU - Iñiguez AM LA - eng SI - GENBANK/JQ639893 SI - GENBANK/JQ639894 SI - GENBANK/JQ639895 PT - Historical Article PT - Letter PT - Research Support, Non-U.S. Gov't PL - United States TA - Emerg Infect Dis JT - Emerging infectious diseases JID - 9508155 RN - 0 (DNA, Bacterial) RN - 0 (DNA, Mitochondrial) SB - IM MH - Adolescent MH - Adult MH - Base Sequence MH - *Black People MH - Brazil/epidemiology MH - DNA, Bacterial/classification/*genetics/isolation & purification MH - DNA, Mitochondrial/classification/*genetics/isolation & purification MH - Forensic Anthropology MH - Haplotypes MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Male MH - Molecular Sequence Data MH - Mycobacterium tuberculosis/classification/*genetics/isolation & purification MH - Paleopathology MH - Social Problems MH - Tuberculosis/ethnology/history/*microbiology PMC - PMC3647487 OTO - NOTNLM OT - Brazil OT - MTC OT - Mycobacterium tuberculosis complex OT - Rio de Janeiro OT - TB OT - aDNA OT - ancient DNA OT - bacteria OT - mitochondrial DNA OT - mtDNA OT - paleogenetic analysis OT - slavery OT - tuberculosis OT - tuberculosis and other mycobacteria EDAT- 2013/05/24 06:00 MHDA- 2013/10/30 06:00 PMCR- 2013/05/01 CRDT- 2013/05/24 06:00 PHST- 2013/05/24 06:00 [entrez] PHST- 2013/05/24 06:00 [pubmed] PHST- 2013/10/30 06:00 [medline] PHST- 2013/05/01 00:00 [pmc-release] AID - 12-0193 [pii] AID - 10.3201/eid1905.120193 [doi] PST - ppublish SO - Emerg Infect Dis. 2013 May;19(5):837-9. doi: 10.3201/eid1905.120193. PMID- 23622484 OWN - NLM STAT- MEDLINE DCOM- 20140109 LR - 20130429 IS - 1878-7487 (Electronic) IS - 1752-928X (Linking) VI - 20 IP - 4 DP - 2013 May TI - Vanadium accelerates polymerase chain reaction and expands the applicability of forensic DNA testing. PG - 326-33 LID - S1752-928X(12)00203-X [pii] LID - 10.1016/j.jflm.2012.09.006 [doi] AB - Polymerase chain reaction (PCR) has been rapidly established as one of the most widely used techniques in molecular biology. Because most DNA analysis is PCR-based, the analysis of unamplifiable DNA of poor quality or low quantity is nearly impossible. However, we observed that if an appropriate concentration of vanadium chloride is added to the standard reaction mixture, the enzymatic amplification of DNA could be enhanced. Using multiplex PCR with the addition of vanadium, DNA typing was possible from even trace amounts of DNA that we were unable to amplify using normal reaction conditions. This method might be an effective tool for not only criminal investigations and ancient DNA analysis, but also for nearly all fields using DNA technology. CI - Copyright © 2012 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved. FAU - Kaminiwa, Junko AU - Kaminiwa J AD - Department of Legal Medicine, University of Tsukuba, 1-1-1 Tenodai, Tsukuba, Ibaraki Prefecture 305-0003, Japan. FAU - Honda, Katsuya AU - Honda K FAU - Sugano, Yukiko AU - Sugano Y FAU - Yano, Shizue AU - Yano S FAU - Nishi, Takeki AU - Nishi T FAU - Sekine, Yuko AU - Sekine Y LA - eng PT - Journal Article DEP - 20121012 PL - England TA - J Forensic Leg Med JT - Journal of forensic and legal medicine JID - 101300022 RN - 0 (DNA, Mitochondrial) RN - 0 (Vanadium Compounds) SB - IM MH - Chromosomes, Human, Y MH - DNA Fingerprinting/*methods MH - DNA, Mitochondrial/genetics MH - Humans MH - Microsatellite Repeats MH - *Multiplex Polymerase Chain Reaction MH - Real-Time Polymerase Chain Reaction MH - Vanadium Compounds/*chemistry EDAT- 2013/04/30 06:00 MHDA- 2014/01/10 06:00 CRDT- 2013/04/30 06:00 PHST- 2012/05/05 00:00 [received] PHST- 2012/07/11 00:00 [revised] PHST- 2012/09/07 00:00 [accepted] PHST- 2013/04/30 06:00 [entrez] PHST- 2013/04/30 06:00 [pubmed] PHST- 2014/01/10 06:00 [medline] AID - S1752-928X(12)00203-X [pii] AID - 10.1016/j.jflm.2012.09.006 [doi] PST - ppublish SO - J Forensic Leg Med. 2013 May;20(4):326-33. doi: 10.1016/j.jflm.2012.09.006. Epub 2012 Oct 12. PMID- 23407348 OWN - NLM STAT- MEDLINE DCOM- 20131115 LR - 20181202 IS - 1435-232X (Electronic) IS - 1434-5161 (Linking) VI - 58 IP - 4 DP - 2013 Apr TI - Ancient DNA of Emperor CAO Cao's granduncle matches those of his present descendants: a commentary on present Y chromosomes reveal the ancestry of Emperor CAO Cao of 1800 years ago. PG - 238-9 LID - 10.1038/jhg.2013.5 [doi] FAU - Wang, Chuan-Chao AU - Wang CC FAU - Yan, Shi AU - Yan S FAU - Yao, Can AU - Yao C FAU - Huang, Xiu-Yuan AU - Huang XY FAU - Ao, Xue AU - Ao X FAU - Wang, Zhanfeng AU - Wang Z FAU - Han, Sheng AU - Han S FAU - Jin, Li AU - Jin L FAU - Li, Hui AU - Li H LA - eng PT - Comment PT - Letter PT - Research Support, Non-U.S. Gov't DEP - 20130214 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 SB - IM CON - J Hum Genet. 2012 Mar;57(3):216-8. doi: 10.1038/jhg.2011.147. PMID: 22189622 MH - *Chromosomes, Human, Y MH - Humans EDAT- 2013/02/15 06:00 MHDA- 2013/11/16 06:00 CRDT- 2013/02/15 06:00 PHST- 2013/02/15 06:00 [entrez] PHST- 2013/02/15 06:00 [pubmed] PHST- 2013/11/16 06:00 [medline] AID - jhg20135 [pii] AID - 10.1038/jhg.2013.5 [doi] PST - ppublish SO - J Hum Genet. 2013 Apr;58(4):238-9. doi: 10.1038/jhg.2013.5. Epub 2013 Feb 14. PMID- 23315957 OWN - NLM STAT- MEDLINE DCOM- 20130903 LR - 20161125 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 30 IP - 4 DP - 2013 Apr TI - Neandertal origin of genetic variation at the cluster of OAS immunity genes. PG - 798-801 LID - 10.1093/molbev/mst004 [doi] AB - Analyses of ancient DNA from extinct humans reveal signals of at least two independent hybridization events in the history of non-African populations. To date, there are very few examples of specific genetic variants that have been rigorously identified as introgressive. Here, we survey DNA sequence variation in the OAS gene cluster on chromosome 12 and provide strong evidence that a haplotype extending for ~185 kb introgressed from Neandertals. This haplotype is nearly restricted to Eurasians and is estimated to have diverged from the Neandertal sequence ~125 kya. Despite the potential for novel functional variation, the observed frequency of this haplotype is consistent with neutral introgression. This is the second locus in the human genome, after STAT2, carrying distinct haplotypes that appear to have introgressed separately from both Neandertals and Denisova. FAU - Mendez, Fernando L AU - Mendez FL AD - Department of Ecology and Evolutionary Biology, University of Arizona, Arizona, USA. FAU - Watkins, Joseph C AU - Watkins JC FAU - Hammer, Michael F AU - Hammer MF LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130112 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - EC 2.7.7.- (OAS1 protein, human) RN - EC 2.7.7.84 (2',5'-Oligoadenylate Synthetase) SB - IM MH - 2',5'-Oligoadenylate Synthetase/*genetics MH - Animals MH - Evolution, Molecular MH - Genetic Loci/*immunology MH - Genetic Speciation MH - Gorilla gorilla/genetics MH - Haplotypes MH - Humans MH - Linkage Disequilibrium MH - Models, Genetic MH - Multigene Family MH - Neanderthals/*genetics MH - Pan troglodytes/genetics MH - Phylogeography MH - *Polymorphism, Single Nucleotide EDAT- 2013/01/15 06:00 MHDA- 2013/09/04 06:00 CRDT- 2013/01/15 06:00 PHST- 2013/01/15 06:00 [entrez] PHST- 2013/01/15 06:00 [pubmed] PHST- 2013/09/04 06:00 [medline] AID - mst004 [pii] AID - 10.1093/molbev/mst004 [doi] PST - ppublish SO - Mol Biol Evol. 2013 Apr;30(4):798-801. doi: 10.1093/molbev/mst004. Epub 2013 Jan 12. PMID- 23180578 OWN - NLM STAT- MEDLINE DCOM- 20130903 LR - 20211021 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 30 IP - 4 DP - 2013 Apr TI - Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. PG - 824-32 LID - 10.1093/molbev/mss261 [doi] AB - Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ~8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages. FAU - Ottoni, Claudio AU - Ottoni C AD - Center for Archaeological Sciences, Department of Earth and Environmental Sciences, University of Leuven, Leuven, Belgium. FAU - Flink, Linus Girdland AU - Flink LG FAU - Evin, Allowen AU - Evin A FAU - Geörg, Christina AU - Geörg C FAU - De Cupere, Bea AU - De Cupere B FAU - Van Neer, Wim AU - Van Neer W FAU - Bartosiewicz, László AU - Bartosiewicz L FAU - Linderholm, Anna AU - Linderholm A FAU - Barnett, Ross AU - Barnett R FAU - Peters, Joris AU - Peters J FAU - Decorte, Ronny AU - Decorte R FAU - Waelkens, Marc AU - Waelkens M FAU - Vanderheyden, Nancy AU - Vanderheyden N FAU - Ricaut, François-Xavier AU - Ricaut FX FAU - Cakirlar, Canan AU - Cakirlar C FAU - Cevik, Ozlem AU - Cevik O FAU - Hoelzel, A Rus AU - Hoelzel AR FAU - Mashkour, Marjan AU - Mashkour M FAU - Karimlu, Azadeh Fatemeh Mohaseb AU - Karimlu AF FAU - Seno, Shiva Sheikhi AU - Seno SS FAU - Daujat, Julie AU - Daujat J FAU - Brock, Fiona AU - Brock F FAU - Pinhasi, Ron AU - Pinhasi R FAU - Hongo, Hitomi AU - Hongo H FAU - Perez-Enciso, Miguel AU - Perez-Enciso M FAU - Rasmussen, Morten AU - Rasmussen M FAU - Frantz, Laurent AU - Frantz L FAU - Megens, Hendrik-Jan AU - Megens HJ FAU - Crooijmans, Richard AU - Crooijmans R FAU - Groenen, Martien AU - Groenen M FAU - Arbuckle, Benjamin AU - Arbuckle B FAU - Benecke, Nobert AU - Benecke N FAU - Vidarsdottir, Una Strand AU - Vidarsdottir US FAU - Burger, Joachim AU - Burger J FAU - Cucchi, Thomas AU - Cucchi T FAU - Dobney, Keith AU - Dobney K FAU - Larson, Greger AU - Larson G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121122 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animal Distribution MH - Animals MH - Animals, Domestic/genetics MH - Asia MH - DNA, Mitochondrial/*genetics MH - Europe MH - Humans MH - Molar/*anatomy & histology MH - Phylogeography MH - Sequence Analysis, DNA MH - Sus scrofa/*genetics MH - Swine/genetics PMC - PMC3603306 EDAT- 2012/11/28 06:00 MHDA- 2013/09/04 06:00 PMCR- 2012/11/22 CRDT- 2012/11/28 06:00 PHST- 2012/11/28 06:00 [entrez] PHST- 2012/11/28 06:00 [pubmed] PHST- 2013/09/04 06:00 [medline] PHST- 2012/11/22 00:00 [pmc-release] AID - mss261 [pii] AID - 10.1093/molbev/mss261 [doi] PST - ppublish SO - Mol Biol Evol. 2013 Apr;30(4):824-32. doi: 10.1093/molbev/mss261. Epub 2012 Nov 22. PMID- 23201231 OWN - NLM STAT- MEDLINE DCOM- 20130823 LR - 20130213 IS - 1873-4162 (Electronic) IS - 1344-6223 (Linking) VI - 15 IP - 2 DP - 2013 Mar TI - Sub-population structure evident in forensic Y-STR profiles from Armenian geographical groups. PG - 85-90 LID - S1344-6223(12)00166-6 [pii] LID - 10.1016/j.legalmed.2012.10.003 [doi] AB - Over the course of its long history, Armenia has acted as both a source of numerous indigenous cultures and as a recipient of foreign invasions. As a result of this complex history among populations, the gene pool of the Armenian population may contain traces of historically well-documented ancient migrations. Furthermore, the regions within the historical boundaries of Armenia possess unique demographic histories, having hosted both autochthonous and specific exogenous genetic influences. In the present study, we analyze the Armenian population sub-structure utilizing 17 Y-chromosome short tandem repeat (Y-STR) loci of 412 Armenians from four geographically and anthropologically well-defined groups (Ararat Valley, Gardman, Lake Van and Sasun). To place the genetic composition of Armenia in a regional and historic context, we have compared the Y-STR profiles from these four Armenian collections to 18 current-day Eurasian populations and two ancient DNA collections. Our results illustrate regional trends in Armenian paternal lineages and locale-specific patterns of affinities with neighboring regions. Additionally, we observe a phylogenetic relationship between the Northern Caucasus and the group from Sasun, which offers an explanation for the genetic divergence of this group from other three Armenian collections. These findings highlight the importance of analyzing both general populations as well as geographically defined sub-populations when utilizing Y-STRs for forensic analyses and population genetics studies. CI - Copyright © 2012 Elsevier Ireland Ltd. All rights reserved. FAU - Lowery, Robert K AU - Lowery RK AD - Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA. FAU - Herrera, Kristian AU - Herrera K FAU - Uribe, Gabriel AU - Uribe G FAU - Reguiero, Maria AU - Reguiero M FAU - Herrera, Rene J AU - Herrera RJ LA - eng PT - Journal Article DEP - 20121130 PL - Ireland TA - Leg Med (Tokyo) JT - Legal medicine (Tokyo, Japan) JID - 100889186 SB - IM MH - Armenia MH - *Chromosomes, Human, Y MH - DNA Fingerprinting MH - Gene Frequency MH - Genetic Variation MH - *Genetics, Population MH - Genotype MH - Haplotypes MH - Humans MH - *Microsatellite Repeats MH - Multiplex Polymerase Chain Reaction MH - Phylogeography MH - Principal Component Analysis EDAT- 2012/12/04 06:00 MHDA- 2013/08/24 06:00 CRDT- 2012/12/04 06:00 PHST- 2012/07/18 00:00 [received] PHST- 2012/10/05 00:00 [revised] PHST- 2012/10/10 00:00 [accepted] PHST- 2012/12/04 06:00 [entrez] PHST- 2012/12/04 06:00 [pubmed] PHST- 2013/08/24 06:00 [medline] AID - S1344-6223(12)00166-6 [pii] AID - 10.1016/j.legalmed.2012.10.003 [doi] PST - ppublish SO - Leg Med (Tokyo). 2013 Mar;15(2):85-90. doi: 10.1016/j.legalmed.2012.10.003. Epub 2012 Nov 30. PMID- 23180580 OWN - NLM STAT- MEDLINE DCOM- 20130716 LR - 20220311 IS - 1537-1719 (Electronic) IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 30 IP - 3 DP - 2013 Mar TI - Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. PG - 713-24 LID - 10.1093/molbev/mss265 [doi] AB - Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a Gaussian Markov random field (GMRF) model for a single gene locus. Here, we present a generalization of the GMRF model that allows for the analysis of multilocus sequence data. Using simulated data, we demonstrate the improved performance of our method to recover true population trajectories and the time to the most recent common ancestor (TMRCA). We analyze a multilocus alignment of HIV-1 CRF02_AG gene sequences sampled from Cameroon. Our results are consistent with HIV prevalence data and uncover some aspects of the population history that go undetected in Bayesian parametric estimation. Finally, we recover an older and more reconcilable TMRCA for a classic ancient DNA data set. FAU - Gill, Mandev S AU - Gill MS AD - Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, USA. FAU - Lemey, Philippe AU - Lemey P FAU - Faria, Nuno R AU - Faria NR FAU - Rambaut, Andrew AU - Rambaut A FAU - Shapiro, Beth AU - Shapiro B FAU - Suchard, Marc A AU - Suchard MA LA - eng GR - T32 AI007370/AI/NIAID NIH HHS/United States GR - R01 GM086887/GM/NIGMS NIH HHS/United States GR - R01 HG006139/HG/NHGRI NIH HHS/United States GR - 260864/ERC_/European Research Council/International GR - 5T32AI007370-22/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20121122 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 SB - IM MH - Algorithms MH - Bayes Theorem MH - Computer Simulation MH - Evolution, Molecular MH - Genes, Viral MH - *Genetic Loci MH - Genetic Speciation MH - HIV-1/genetics MH - Humans MH - Markov Chains MH - *Models, Genetic MH - Monte Carlo Method MH - Mutation MH - Population Density MH - Population Dynamics MH - Statistics, Nonparametric PMC - PMC3563973 EDAT- 2012/11/28 06:00 MHDA- 2013/07/17 06:00 PMCR- 2014/03/01 CRDT- 2012/11/28 06:00 PHST- 2012/11/28 06:00 [entrez] PHST- 2012/11/28 06:00 [pubmed] PHST- 2013/07/17 06:00 [medline] PHST- 2014/03/01 00:00 [pmc-release] AID - mss265 [pii] AID - 10.1093/molbev/mss265 [doi] PST - ppublish SO - Mol Biol Evol. 2013 Mar;30(3):713-24. doi: 10.1093/molbev/mss265. Epub 2012 Nov 22. PMID- 23453014 OWN - NLM STAT- MEDLINE DCOM- 20130712 LR - 20211021 IS - 2210-3244 (Electronic) IS - 1672-0229 (Print) IS - 1672-0229 (Linking) VI - 11 IP - 1 DP - 2013 Feb TI - My journey to DNA repair. PG - 2-7 LID - S1672-0229(12)00097-6 [pii] LID - 10.1016/j.gpb.2012.12.001 [doi] AB - I completed my medical studies at the Karolinska Institute in Stockholm but have always been devoted to basic research. My longstanding interest is to understand fundamental DNA repair mechanisms in the fields of cancer therapy, inherited human genetic disorders and ancient DNA. I initially measured DNA decay, including rates of base loss and cytosine deamination. I have discovered several important DNA repair proteins and determined their mechanisms of action. The discovery of uracil-DNA glycosylase defined a new category of repair enzymes with each specialized for different types of DNA damage. The base excision repair pathway was first reconstituted with human proteins in my group. Cell-free analysis for mammalian nucleotide excision repair of DNA was also developed in my laboratory. I found multiple distinct DNA ligases in mammalian cells, and led the first genetic and biochemical work on DNA ligases I, III and IV. I discovered the mammalian exonucleases DNase III (TREX1) and IV (FEN1). Interestingly, expression of TREX1 was altered in some human autoimmune diseases. I also showed that the mutagenic DNA adduct O(6)-methylguanine (O(6)mG) is repaired without removing the guanine from DNA, identifying a surprising mechanism by which the methyl group is transferred to a residue in the repair protein itself. A further novel process of DNA repair discovered by my research group is the action of AlkB as an iron-dependent enzyme carrying out oxidative demethylation. CI - Copyright © 2013. Production and hosting by Elsevier Ltd. FAU - Lindahl, Tomas AU - Lindahl T AD - Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms EN6 3LD, United Kingdom. tomas.lindahl@cancer.org.uk LA - eng PT - Autobiography PT - Biography PT - Historical Article PT - Journal Article PT - Review DEP - 20121221 PL - England TA - Genomics Proteomics Bioinformatics JT - Genomics, proteomics & bioinformatics JID - 101197608 RN - EC 3.1.- (Exodeoxyribonucleases) RN - EC 3.2.2.- (DNA Glycosylases) RN - EC 6.5.1.- (DNA Ligases) SB - IM MH - Animals MH - DNA Damage MH - DNA Glycosylases/history/metabolism MH - DNA Ligases/history/metabolism MH - *DNA Repair MH - Exodeoxyribonucleases/history/metabolism MH - History, 20th Century MH - History, 21st Century MH - Humans MH - United Kingdom PS - Lindahl T FPS - Lindahl, Tomas PMC - PMC4357663 EDAT- 2013/03/05 06:00 MHDA- 2013/07/16 06:00 PMCR- 2012/12/21 CRDT- 2013/03/05 06:00 PHST- 2012/12/06 00:00 [received] PHST- 2012/12/07 00:00 [accepted] PHST- 2013/03/05 06:00 [entrez] PHST- 2013/03/05 06:00 [pubmed] PHST- 2013/07/16 06:00 [medline] PHST- 2012/12/21 00:00 [pmc-release] AID - S1672-0229(12)00097-6 [pii] AID - 10.1016/j.gpb.2012.12.001 [doi] PST - ppublish SO - Genomics Proteomics Bioinformatics. 2013 Feb;11(1):2-7. doi: 10.1016/j.gpb.2012.12.001. Epub 2012 Dec 21. PMID- 23321233 OWN - NLM STAT- MEDLINE DCOM- 20140109 LR - 20130116 IS - 1878-3554 (Electronic) IS - 0099-2399 (Linking) VI - 39 IP - 2 DP - 2013 Feb TI - DNA binding to hydroxyapatite: a potential mechanism for preservation of microbial DNA. PG - 211-6 LID - S0099-2399(12)00903-X [pii] LID - 10.1016/j.joen.2012.09.013 [doi] AB - INTRODUCTION: Molecular methods are increasingly being deployed for analysis of the microbial flora in the root canal. Such methods are based on the assumption that recovered DNA is associated with the active endodontic infection, yet paleomicrobiology research is based on the recovery of ancient DNA from centuries-old tooth and bone samples, which points to considerable longevity of the DNA molecule in these tissues. The main component of dentin and bone is the mineral hydroxyapatite. This study assessed DNA binding to hydroxyapatite and whether this binding affinity stabilizes the DNA molecule in various media. METHODS: DNA was extracted from Fusobacterium nucleatum and added to ceramic hydroxyapatite for 90 minutes. The DNA-bound hydroxyapatite was incubated in different media (ie, water, sera, and DNase I) for up to 3 months. At predetermined intervals, the recovery of detectable DNA was assessed by releasing the DNA from the hydroxyapatite using EDTA and evaluating the presence of DNA by gel electrophoresis and polymerase chain reaction (PCR) amplification. RESULTS: When incubated with hydroxyapatite, nonamplified DNA was detectable after 3 months in water, sera, and DNase I. In contrast, DNA incubated in the same media (without hydroxyapatite) decomposed to levels below the detection level of PCR within 3 weeks, with the exception of DNA in sera in which PCR revealed a weak positive amplification product. CONCLUSIONS: These results confirm a specific binding affinity of hydroxyapatite for DNA. Hydroxyapatite-bound DNA is more resistant to decay and less susceptible to degradation by serum and nucleases, which may account for the long-term persistence of DNA in bone and tooth. CI - Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved. FAU - Brundin, Malin AU - Brundin M AD - Department of Odontology/Endodontics, Faculty of Medicine, Umeå University, Umeå, Sweden. malin.brundin@odont.umu.se FAU - Figdor, David AU - Figdor D FAU - Sundqvist, Göran AU - Sundqvist G FAU - Sjögren, Ulf AU - Sjögren U LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121025 PL - United States TA - J Endod JT - Journal of endodontics JID - 7511484 RN - 0 (Chelating Agents) RN - 0 (DNA, Bacterial) RN - 0 (Immobilized Nucleic Acids) RN - 0 (RNA, Ribosomal, 16S) RN - 059QF0KO0R (Water) RN - 91D9GV0Z28 (Durapatite) RN - 9G34HU7RV0 (Edetic Acid) RN - EC 3.1.21.1 (Deoxyribonuclease I) MH - Adult MH - Base Pairing/genetics MH - Blood MH - Chelating Agents/chemistry MH - DNA, Bacterial/analysis/*chemistry MH - Deoxyribonuclease I/chemistry MH - Durapatite/*chemistry MH - Edetic Acid/chemistry MH - Electrophoresis, Agar Gel MH - Fusobacterium nucleatum/genetics MH - Humans MH - *Immobilized Nucleic Acids MH - Polymerase Chain Reaction MH - RNA, Ribosomal, 16S/genetics MH - Temperature MH - Time Factors MH - Water/chemistry EDAT- 2013/01/17 06:00 MHDA- 2014/01/10 06:00 CRDT- 2013/01/17 06:00 PHST- 2012/07/06 00:00 [received] PHST- 2012/09/23 00:00 [revised] PHST- 2012/09/24 00:00 [accepted] PHST- 2013/01/17 06:00 [entrez] PHST- 2013/01/17 06:00 [pubmed] PHST- 2014/01/10 06:00 [medline] AID - S0099-2399(12)00903-X [pii] AID - 10.1016/j.joen.2012.09.013 [doi] PST - ppublish SO - J Endod. 2013 Feb;39(2):211-6. doi: 10.1016/j.joen.2012.09.013. Epub 2012 Oct 25. PMID- 25807700 OWN - NLM STAT- MEDLINE DCOM- 20150522 LR - 20170330 IS - 0394-9001 (Print) IS - 0394-9001 (Linking) VI - 25 IP - 1 DP - 2013 TI - [Ancient DNA: principles and methodologies]. PG - 51-83 AB - Paleogenetics is providing increasing evidence about the biological characteristics of ancient populations. This paper examines the guiding principles and methodologies to the study of ancient DNA with constant references to the state of the art in this fascinating disciplin. FAU - De Angelis, Flavio AU - De Angelis F AD - Centro di Antropologia Molecolare per lo Studio del DNA Antico- Dipartimento di Biologi,a Università degli Studi di Roma Tor Vergata, Roma, I. flavio.de.angelis@uniroma2.it FAU - Scorrano, Gabriele AU - Scorrano G FAU - Rickards, Olga AU - Rickards O LA - ita PT - English Abstract PT - Journal Article TT - DNA antico: principi e metodologie. PL - Italy TA - Med Secoli JT - Medicina nei secoli JID - 0176472 RN - 9007-49-2 (DNA) MH - Archaeology/*methods MH - DNA/analysis/*genetics MH - Humans MH - Paleontology/*methods MH - Sequence Analysis, DNA EDAT- 2013/01/01 00:00 MHDA- 2015/05/23 06:00 CRDT- 2015/03/27 06:00 PHST- 2015/03/27 06:00 [entrez] PHST- 2013/01/01 00:00 [pubmed] PHST- 2015/05/23 06:00 [medline] PST - ppublish SO - Med Secoli. 2013;25(1):51-83. PMID- 24861860 OWN - NLM STAT- MEDLINE DCOM- 20150106 LR - 20140527 IS - 1423-0062 (Electronic) IS - 0001-5652 (Linking) VI - 76 IP - 3-4 DP - 2013 TI - The onset of lactase persistence in Europe. PG - 154-61 LID - 10.1159/000360136 [doi] AB - The genomic region containing the lactase (LCT) gene shows one of the strongest signals of positive selection in Europeans, detectable using a range of approaches including haplotype length, linked microsatellite variation and population-differentiation-based tests. Lactase is the enzyme that carries out the digestion of the milk sugar lactose. Its expression decreases at some point after the weaning period is over in most mammals and in around 68% of all living adult humans. However, in some humans, particularly those from populations with a history of dairying, lactase is expressed throughout adulthood. This trait is called lactase persistence (LP), and in people of European ancestry, it is associated with a single mutation (-13910*T). Evidence from the detection of dairy fat residues in potsherds, and allele frequencies in ancient DNA samples suggest that LP arose after dairying practices had developed. However, the reasons why LP may have been advantageous are still debated, and the respective contribution of demography and natural selection remains to be disentangled. This paper discusses various studies, from archaeology to population genetics, that have shed some light on the subject by investigating the evolution of LP in Europe. FAU - Gerbault, Pascale AU - Gerbault P AD - Research Department of Genetics, Evolution and Environment, University College London, London, UK. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20140521 PL - Switzerland TA - Hum Hered JT - Human heredity JID - 0200525 RN - EC 3.2.1.108 (Lactase) SB - IM MH - Dairying MH - Demography MH - Europe MH - Humans MH - Lactase/*genetics MH - *Quantitative Trait, Heritable MH - Selection, Genetic EDAT- 2013/01/01 00:00 MHDA- 2015/01/07 06:00 CRDT- 2014/05/28 06:00 PHST- 2014/05/28 06:00 [entrez] PHST- 2013/01/01 00:00 [pubmed] PHST- 2015/01/07 06:00 [medline] AID - 000360136 [pii] AID - 10.1159/000360136 [doi] PST - ppublish SO - Hum Hered. 2013;76(3-4):154-61. doi: 10.1159/000360136. Epub 2014 May 21. PMID- 24861859 OWN - NLM STAT- MEDLINE DCOM- 20150106 LR - 20221207 IS - 1423-0062 (Electronic) IS - 0001-5652 (Linking) VI - 76 IP - 3-4 DP - 2013 TI - Investigating European genetic history through computer simulations. PG - 142-53 LID - 10.1159/000360162 [doi] AB - BACKGROUND/AIMS: The genetic diversity of Europeans has been shaped by various evolutionary forces including their demographic history. Genetic data can thus be used to draw inferences on the population history of Europe using appropriate statistical methods such as computer simulation, which constitutes a powerful tool to study complex models. METHODS: Here, we focus on spatially explicit simulation, a method which takes population movements over space and time into account. We present its main principles and then describe a series of studies using this approach that we consider as particularly significant in the context of European prehistory. RESULTS AND CONCLUSION: All simulation studies agree that ancient demographic events played a significant role in the establishment of the European gene pool; but while earlier works support a major genetic input from the Near East during the Neolithic transition, the most recent ones revalue positively the contribution of pre-Neolithic hunter-gatherers and suggest a possible impact of very ancient demographic events. This result of a substantial genetic continuity from pre-Neolithic times to the present challenges some recent studies analyzing ancient DNA. We discuss the possible reasons for this discrepancy and identify future lines of investigation in order to get a better understanding of European evolution. FAU - Currat, Mathias AU - Currat M AD - Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland. FAU - Silva, Nuno M AU - Silva NM LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20140521 PL - Switzerland TA - Hum Hered JT - Human heredity JID - 0200525 RN - 9007-49-2 (DNA) SB - IM MH - *Computer Simulation MH - DNA/genetics MH - Europe MH - *Genetic Variation MH - Genetics, Population/*history MH - History, Ancient MH - Humans MH - White People/*genetics EDAT- 2013/01/01 00:00 MHDA- 2015/01/07 06:00 CRDT- 2014/05/28 06:00 PHST- 2014/05/28 06:00 [entrez] PHST- 2013/01/01 00:00 [pubmed] PHST- 2015/01/07 06:00 [medline] AID - 000360162 [pii] AID - 10.1159/000360162 [doi] PST - ppublish SO - Hum Hered. 2013;76(3-4):142-53. doi: 10.1159/000360162. Epub 2014 May 21. PMID- 24861858 OWN - NLM STAT- MEDLINE DCOM- 20150106 LR - 20140527 IS - 1423-0062 (Electronic) IS - 0001-5652 (Linking) VI - 76 IP - 3-4 DP - 2013 TI - Genetic evidence for prehistoric demographic changes in Europe. PG - 133-41 LID - 10.1159/000357957 [doi] AB - OBJECTIVES: Two main models have been proposed to explain the origins of the patterns of genetic variation in Europe, one emphasizing Paleolithic and the other Neolithic immigration from the Southeast. In this paper, I summarize how the models developed and how they can help address some open questions. METHODS: The rationale of the methods traditionally supporting the Neolithic and the Paleolithic models is discussed, and the evidence supporting either of them is reviewed. RESULTS: Ancient DNA evidence proves for good that the studies traditionally supporting the Paleolithic model had serious methodological flaws. This does not imply that the alternative model is right, but rather calls for further analyses explicitly testing the two models against the genomic information now available. CONCLUSIONS: Questions that need to be addressed include whether the two main models differ enough to be discriminated by analyses of modern DNA diversity, and to what extent inferences from ancient mitochondrial DNA can be trusted in the absence of sufficient datasets of ancient nuclear DNA. The time seems ripe for the construction of a more complex (and hence more realistic) model, incorporating the possibility of different processes affecting different geographic locations at different times. FAU - Barbujani, Guido AU - Barbujani G AD - Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20140521 PL - Switzerland TA - Hum Hered JT - Human heredity JID - 0200525 SB - IM MH - *Demography MH - Europe MH - Founder Effect MH - *Genetics, Population MH - Humans MH - Models, Biological MH - Time Factors EDAT- 2013/01/01 00:00 MHDA- 2015/01/07 06:00 CRDT- 2014/05/28 06:00 PHST- 2014/05/28 06:00 [entrez] PHST- 2013/01/01 00:00 [pubmed] PHST- 2015/01/07 06:00 [medline] AID - 000357957 [pii] AID - 10.1159/000357957 [doi] PST - ppublish SO - Hum Hered. 2013;76(3-4):133-41. doi: 10.1159/000357957. Epub 2014 May 21. PMID- 24861857 OWN - NLM STAT- MEDLINE DCOM- 20150106 LR - 20140527 IS - 1423-0062 (Electronic) IS - 0001-5652 (Linking) VI - 76 IP - 3-4 DP - 2013 TI - Ancient DNA: A window to the past of Europe. PG - 121-32 LID - 10.1159/000356933 [doi] AB - OBJECTIVES: The history of European populations is characterised by numerous migrations or demographic events that are likely to have had major impacts on the European gene pool patterns. This paper will focus on how ancient DNA (aDNA) data contribute to our understanding of past population dynamics in Europe. METHODS: Technological challenges of the palaeogenetic approach will be discussed. With these limitations in mind, it will be shown that the acquisition of aDNA now permits a glimpse of how human genetic diversity has changed, spatially and temporally, in Europe, from the Palaeolithic through to the present day. RESULTS: Although early modern human DNA sequences come only from rare exceptionally well-preserved specimens, genetic samples of a reasonable size are becoming available for the Mesolithic and the Neolithic periods, permitting a discussion of regional variation in the inferred mode of the spread of farming. Palaeogenetic data collected for ancient and more recent periods regularly demonstrate genetic discontinuity between past and present populations. CONCLUSIONS: The results indicate that only large diachronic aDNA datasets from throughout Europe will permit researchers to reliably identify all demographic and evolutionary events that shaped the modern European gene pool. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - Equipe Anthropologie des Populations Passées et Présentes, Université Bordeaux 1, UMR 5199 PACEA, Talence, France. FAU - Mendisco, Fanny AU - Mendisco F LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20140521 PL - Switzerland TA - Hum Hered JT - Human heredity JID - 0200525 RN - 9007-49-2 (DNA) SB - IM MH - Biological Evolution MH - DNA/*genetics MH - Europe MH - Gene Pool MH - Geography MH - History, Ancient MH - Humans MH - Time Factors EDAT- 2013/01/01 00:00 MHDA- 2015/01/07 06:00 CRDT- 2014/05/28 06:00 PHST- 2014/05/28 06:00 [entrez] PHST- 2013/01/01 00:00 [pubmed] PHST- 2015/01/07 06:00 [medline] AID - 000356933 [pii] AID - 10.1159/000356933 [doi] PST - ppublish SO - Hum Hered. 2013;76(3-4):121-32. doi: 10.1159/000356933. Epub 2014 May 21. PMID- 23658525 OWN - NLM STAT- MEDLINE DCOM- 20131209 LR - 20211021 IS - 1553-7374 (Electronic) IS - 1553-7366 (Print) IS - 1553-7366 (Linking) VI - 9 IP - 5 DP - 2013 TI - Yersinia pestis DNA from skeletal remains from the 6(th) century AD reveals insights into Justinianic Plague. PG - e1003349 LID - 10.1371/journal.ppat.1003349 [doi] LID - e1003349 AB - Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19(th) and 20(th) centuries, during which plague was spread around the world, and the second pandemic of the 14(th)-17(th) centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6(th)-8(th) centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics. FAU - Harbeck, Michaela AU - Harbeck M AD - State Collection for Anthropology and Palaeoanatomy, Munich, Germany. M.Harbeck@lrz.uni-muenchen.de FAU - Seifert, Lisa AU - Seifert L FAU - Hänsch, Stephanie AU - Hänsch S FAU - Wagner, David M AU - Wagner DM FAU - Birdsell, Dawn AU - Birdsell D FAU - Parise, Katy L AU - Parise KL FAU - Wiechmann, Ingrid AU - Wiechmann I FAU - Grupe, Gisela AU - Grupe G FAU - Thomas, Astrid AU - Thomas A FAU - Keim, Paul AU - Keim P FAU - Zöller, Lothar AU - Zöller L FAU - Bramanti, Barbara AU - Bramanti B FAU - Riehm, Julia M AU - Riehm JM FAU - Scholz, Holger C AU - Scholz HC LA - eng SI - GENBANK/KC170159 SI - GENBANK/KC170160 SI - GENBANK/KC170161 SI - GENBANK/KC170162 SI - GENBANK/KC170163 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130502 PL - United States TA - PLoS Pathog JT - PLoS pathogens JID - 101238921 RN - 0 (DNA, Bacterial) SB - IM MH - Base Sequence MH - Bone and Bones/*microbiology MH - DNA, Bacterial/*genetics MH - Female MH - Genotype MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 19th Century MH - History, 20th Century MH - History, Medieval MH - Humans MH - Male MH - Molecular Sequence Data MH - Pandemics/*history MH - *Phylogeny MH - *Plague/epidemiology/etiology/genetics/history/microbiology MH - Yersinia pestis/*genetics PMC - PMC3642051 COIS- The authors have declared that no competing interests exist. EDAT- 2013/05/10 06:00 MHDA- 2013/12/16 06:00 PMCR- 2013/05/02 CRDT- 2013/05/10 06:00 PHST- 2012/12/19 00:00 [received] PHST- 2013/03/24 00:00 [accepted] PHST- 2013/05/10 06:00 [entrez] PHST- 2013/05/10 06:00 [pubmed] PHST- 2013/12/16 06:00 [medline] PHST- 2013/05/02 00:00 [pmc-release] AID - PPATHOGENS-D-13-00017 [pii] AID - 10.1371/journal.ppat.1003349 [doi] PST - ppublish SO - PLoS Pathog. 2013;9(5):e1003349. doi: 10.1371/journal.ppat.1003349. Epub 2013 May 2. PMID- 23590114 OWN - NLM STAT- MEDLINE DCOM- 20130618 LR - 20191112 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 70 IP - 1 DP - 2013 TI - Revision of tuberculous lesions in the Bácsalmás-Oalmás series--preliminary morphological and biomolecular studies. PG - 83-100 AB - Previous investigations carried out in some parts of the 16th-17th century AD series of Bácsalmás-Oalmás (southern Hungary) have already provided interesting paleopathological cases of tuberculosis (e.g. Molnár & Pálfi 1994). These studies were essentially based on macromorphological analysis, biomolecular methods were used only in a few cases (e.g. Haas et al. 2000). From a macromorphological point of view, former investigations have only considered 'classical' tuberculosis (TB) alterations (advanced-stage lesions in common skeletal locations). However, due to the recent development of diagnostic criteria in the field of the paleopathology of infectious diseases, new approaches have been introduced in the identification of skeletal TB lesions (Pálfi et al. 1999, Maczel 2003). Molecular methods for the detection of mycobacterial aDNA have also been developed considerably in the last few years (e.g. Donoghue 2008, Donoghue 2011). The good state of preservation of the material, the important chronological period of the series and the relative high prevalence of TB reported in preliminary studies encouraged us to carry out a revision of TB-related lesions in the complete Bácsalmás-Oalmás series. A five year international research program--including both macroscopic and biomolecular studies of the series--was recently started. The present paper summarizes the results ofa pilot project conducted to optimize the further systematic paleopathological and paleomicrobial studies. Skeletal material of 205 individuals was chosen forthe macromorphological test-investigation, which was focused both on classical/advanced stage skeletal TB alterations (tuberculous spondylitis, tuberculous arthritis) and atypical/early-stage TB lesions (rib lesions, superficial vertebral changes, endocranial alterations, early-stage spondylodiscitis). In addition, the association of possible stress factors (long bone periostitis, cribra orbitalia, cribra cranii) were also considered. Paleomicrobiological analysis was used to study the presence of Mycobacterium tuberculosis ancient DNA (aDNA) in morphologically positive and negative cases. A comparative paleomicrobial analysis was carried out on different samples, to test the presence of MTB DNA in different skeletal regions. FAU - Pósa, Annamária AU - Pósa A AD - Department of Biological Anthropology, University of Szeged, Szeged, Hungary. posa.annamaria@gmail.com FAU - Maixner, Frank AU - Maixner F FAU - Lovász, Gabriella AU - Lovász G FAU - Molnár, Erika AU - Molnár E FAU - Bereczki, Zsolt AU - Bereczki Z FAU - Perrin, Pascale AU - Perrin P FAU - Zink, Albert AU - Zink A FAU - Pálfi, György AU - Pálfi G LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (DNA, Bacterial) SB - IM MH - Adult MH - Bone and Bones/chemistry/*microbiology/*pathology MH - Child MH - DNA, Bacterial/analysis/isolation & purification MH - Female MH - History, 16th Century MH - History, 17th Century MH - Humans MH - Hungary MH - Infant MH - Male MH - Molecular Typing MH - Mycobacterium tuberculosis/genetics/*isolation & purification MH - Paleopathology MH - Polymerase Chain Reaction MH - Tuberculosis, Osteoarticular/*history/microbiology/pathology EDAT- 2013/04/18 06:00 MHDA- 2013/06/19 06:00 CRDT- 2013/04/18 06:00 PHST- 2013/04/18 06:00 [entrez] PHST- 2013/04/18 06:00 [pubmed] PHST- 2013/06/19 06:00 [medline] AID - 10.1127/0003-5548/2012/0260 [doi] PST - ppublish SO - Anthropol Anz. 2013;70(1):83-100. doi: 10.1127/0003-5548/2012/0260. PMID- 23590113 OWN - NLM STAT- MEDLINE DCOM- 20130618 LR - 20191112 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 70 IP - 1 DP - 2013 TI - Amplification of DNA remnants in mummified human brains from medieval Joseon tombs of Korea. PG - 57-81 AB - Recently, a number of mummified brains obtained from the remains of medieval Joseon Koreans have been subjected to biological investigations. Although the morphology of the organs had been perfectly maintained on gross examination, we still do not know how well biomolecules such as DNA were preserved. In the present study, the preservation status of remnant DNA in mummified brain tissue was determined by means of comparisons with corresponding DNA taken from the femurs of the same subjects. Quantifiler analysis revealed that DNA from the mummified brain was less fragmented than that contained in the femurs. The better preservation status of the brain DNA was shown also in MiniFiler assays: the number of short tandem repeat (STR) locus profiles for the mummified brain was far higher than in the case of the femur bones. In the case of the mtDNA analysis, longer DNA fragments (821 bp) could be successfully amplified with brain samples, whereas only shorter PCR amplicons (221-263 bp) were seen with the femur samples. Indeed mummified brain tissue, if discovered in amounts suitable for ancient DNA analysis, promises to be the preferred source for genetic analysis of individuals from pre-modern Korean tombs. FAU - Oh, Chang Seok AU - Oh CS AD - Anthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, 28, Yongon-dong, Chongno-Gu, Seoul 110-799, Republic of Korea. drdoogi@snu.ac.kr FAU - Lee, Sang Jun AU - Lee SJ FAU - Lee, Soong Deok AU - Lee SD FAU - Kim, Myeung Ju AU - Kim MJ FAU - Kim, Yi-Suk AU - Kim YS FAU - Lim, Do-Seon AU - Lim DS FAU - Shin, Dong Hoon AU - Shin DH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Base Sequence MH - Brain/anatomy & histology/pathology MH - *Brain Chemistry MH - DNA/*analysis/*genetics/isolation & purification MH - DNA, Mitochondrial/genetics MH - Female MH - Femur/chemistry MH - Humans MH - Male MH - Microsatellite Repeats MH - Middle Aged MH - Molecular Sequence Data MH - *Mummies MH - Polymerase Chain Reaction MH - Republic of Korea MH - Young Adult EDAT- 2013/04/18 06:00 MHDA- 2013/06/19 06:00 CRDT- 2013/04/18 06:00 PHST- 2013/04/18 06:00 [entrez] PHST- 2013/04/18 06:00 [pubmed] PHST- 2013/06/19 06:00 [medline] AID - 10.1127/0003-5548/2012/0225 [doi] PST - ppublish SO - Anthropol Anz. 2013;70(1):57-81. doi: 10.1127/0003-5548/2012/0225. PMID- 23459685 OWN - NLM STAT- MEDLINE DCOM- 20130613 LR - 20221207 IS - 1553-7404 (Electronic) IS - 1553-7390 (Print) IS - 1553-7390 (Linking) VI - 9 IP - 2 DP - 2013 TI - Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe. PG - e1003296 LID - 10.1371/journal.pgen.1003296 [doi] LID - e1003296 AB - North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans. FAU - Der Sarkissian, Clio AU - Der Sarkissian C AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia. FAU - Balanovsky, Oleg AU - Balanovsky O FAU - Brandt, Guido AU - Brandt G FAU - Khartanovich, Valery AU - Khartanovich V FAU - Buzhilova, Alexandra AU - Buzhilova A FAU - Koshel, Sergey AU - Koshel S FAU - Zaporozhchenko, Valery AU - Zaporozhchenko V FAU - Gronenborn, Detlef AU - Gronenborn D FAU - Moiseyev, Vyacheslav AU - Moiseyev V FAU - Kolpakov, Eugen AU - Kolpakov E FAU - Shumkin, Vladimir AU - Shumkin V FAU - Alt, Kurt W AU - Alt KW FAU - Balanovska, Elena AU - Balanovska E FAU - Cooper, Alan AU - Cooper A FAU - Haak, Wolfgang AU - Haak W CN - Genographic Consortium LA - eng GR - WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130214 PL - United States TA - PLoS Genet JT - PLoS genetics JID - 101239074 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA, Mitochondrial/*genetics MH - Europe MH - *Gene Flow MH - *Genetic Variation MH - Genetics, Population MH - *Genome, Mitochondrial MH - Genotype MH - Haplotypes MH - Humans MH - Population Dynamics MH - Russia MH - Scandinavian and Nordic Countries MH - Siberia MH - White People/genetics PMC - PMC3573127 COIS- The authors declare that no competing interests exist. FIR - Adhikarla, Syama IR - Adhikarla S FIR - Adler, Christina J IR - Adler CJ FIR - Bertranpetit, Jaume IR - Bertranpetit J FIR - Clarke, Andrew C IR - Clarke AC FIR - Comas, David IR - Comas D FIR - Dulik, Matthew C IR - Dulik MC FIR - Gaieski, Jill B IR - Gaieski JB FIR - Haber, Marc IR - Haber M FIR - Jin, Li IR - Jin L FIR - Kaplan, Matthew E IR - Kaplan ME FIR - Li, Shilin IR - Li S FIR - Martínez-Cruz, Begonã IR - Martínez-Cruz B FIR - Matisoo-Smith, Elizabeth A IR - Matisoo-Smith EA FIR - Mitchell, R John IR - Mitchell R FIR - Owings, Amanda C IR - Owings AC FIR - Parida, Laxmi IR - Parida L FIR - Pitchappan, Ramasamy IR - Pitchappan R FIR - Platt, Daniel E IR - Platt DE FIR - Quintana-Murci, Lluis IR - Quintana-Murci L FIR - Renfrew, Colin IR - Renfrew C FIR - Lacerda, Daniela R IR - Lacerda DR FIR - Royyuru, Ajay K IR - Royyuru AK FIR - Santos, Fabrício R IR - Santos FR FIR - Schurr, Theodore G IR - Schurr TG FIR - Soodyall, Himla IR - Soodyall H FIR - Hernanz, David F Soria IR - Hernanz DF FIR - Swamikrishnan, Pandikumar IR - Swamikrishnan P FIR - Tyler-Smith, Chris IR - Tyler-Smith C FIR - Santhakumari, Arun Varatharajan IR - Santhakumari AV FIR - Vieira, Pedro Paulo IR - Vieira PP FIR - Vilar, Miguel G IR - Vilar MG FIR - Wells, R Spencer IR - Wells R FIR - Zalloua, Pierre A IR - Zalloua PA FIR - Ziegle, Janet S IR - Ziegle JS FIR - GaneshPrasad, ArunKumar IR - GaneshPrasad A FIR - Merchant, Nirav C IR - Merchant NC EDAT- 2013/03/06 06:00 MHDA- 2013/06/14 06:00 PMCR- 2013/02/01 CRDT- 2013/03/06 06:00 PHST- 2012/09/11 00:00 [received] PHST- 2012/12/18 00:00 [accepted] PHST- 2013/03/06 06:00 [entrez] PHST- 2013/03/06 06:00 [pubmed] PHST- 2013/06/14 06:00 [medline] PHST- 2013/02/01 00:00 [pmc-release] AID - PGENETICS-D-12-02275 [pii] AID - 10.1371/journal.pgen.1003296 [doi] PST - ppublish SO - PLoS Genet. 2013;9(2):e1003296. doi: 10.1371/journal.pgen.1003296. Epub 2013 Feb 14. PMID- 23372650 OWN - NLM STAT- MEDLINE DCOM- 20130722 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 1 DP - 2013 TI - Monitoring DNA contamination in handled vs. directly excavated ancient human skeletal remains. PG - e52524 LID - 10.1371/journal.pone.0052524 [doi] LID - e52524 AB - Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14(th) century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as "virgin samples" (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called "lab samples"(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from "lab samples" are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the "virgin samples" set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between "lab" and "virgin" samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history. FAU - Pilli, Elena AU - Pilli E AD - Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy. FAU - Modi, Alessandra AU - Modi A FAU - Serpico, Ciro AU - Serpico C FAU - Achilli, Alessandro AU - Achilli A FAU - Lancioni, Hovirag AU - Lancioni H FAU - Lippi, Barbara AU - Lippi B FAU - Bertoldi, Francesca AU - Bertoldi F FAU - Gelichi, Sauro AU - Gelichi S FAU - Lari, Martina AU - Lari M FAU - Caramelli, David AU - Caramelli D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130125 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Archaeology/methods/standards MH - *Artifacts MH - Bone and Bones/chemistry MH - Burial MH - DNA/*analysis MH - *DNA Contamination MH - DNA, Mitochondrial MH - *Fossils MH - Hair/chemistry MH - Humans MH - Polymerase Chain Reaction MH - Specimen Handling/*standards MH - Tooth/*chemistry PMC - PMC3556025 COIS- Competing Interests: Co-author David Caramelli is a PLOS ONE Editorial Board member. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. EDAT- 2013/02/02 06:00 MHDA- 2013/07/23 06:00 PMCR- 2013/01/25 CRDT- 2013/02/02 06:00 PHST- 2012/08/31 00:00 [received] PHST- 2012/11/15 00:00 [accepted] PHST- 2013/02/02 06:00 [entrez] PHST- 2013/02/02 06:00 [pubmed] PHST- 2013/07/23 06:00 [medline] PHST- 2013/01/25 00:00 [pmc-release] AID - PONE-D-12-26640 [pii] AID - 10.1371/journal.pone.0052524 [doi] PST - ppublish SO - PLoS One. 2013;8(1):e52524. doi: 10.1371/journal.pone.0052524. Epub 2013 Jan 25. PMID- 22237796 OWN - NLM STAT- MEDLINE DCOM- 20130614 LR - 20211021 IS - 1437-1596 (Electronic) IS - 0937-9827 (Linking) VI - 127 IP - 1 DP - 2013 Jan TI - A real-time PCR-based amelogenin Y allele dropout assessment model in gender typing of degraded DNA samples. PG - 55-61 LID - 10.1007/s00414-011-0663-5 [doi] AB - Allelic dropout due to stochastic variation in degraded small quantity DNA appears to be one of the most serious genotyping errors. Most methods require PCR replication to address this problem. The small amounts of valuable samples are often a limitation for such replications. We report a real-time PCR-based amelogonin Y (AMELY) allele dropout estimation model in an AMEL-based gender typing. We examined 915 replicates of AMELY-positive modern male DNA with varying amounts of DNA and humic acid. A male-specific AMEL fragment (AMELy) dropped out in 143 genuine male replicates, leading to gender typing errors. By graphing a scatter plot of the crossing point versus the end cycle fluorescence of the male replicates, a standard graph model for the estimation of the AMELy allele dropout was constructed with the dropout-prone and dropout-free zones. This model was then applied to ancient DNA (aDNA) samples. Nine samples identified as female were found in the dropout-prone zone; with higher DNA concentrations, six were shifted to the dropout-free zone. Among them, two female identifications were converted to male. All the aDNA gender was confirmed by sex-determination region Y marker amplification. Our data suggest that this model could be a basic approach for securing AMELy allele dropout-safe data from the stochastic variation of degraded inhibitory DNA samples. FAU - Kim, Kyung-Yong AU - Kim KY AD - Institute for Medical Sciences, Chung-Ang University, Seoul, 156-756, South Korea. FAU - Kwon, Younghyuk AU - Kwon Y FAU - Bazarragchaa, Munkhtsetseg AU - Bazarragchaa M FAU - Park, Ae-Ja AU - Park AJ FAU - Bang, Hyowon AU - Bang H FAU - Lee, Won-Bok AU - Lee WB FAU - Lee, Junyoung AU - Lee J FAU - Lee, Kwang-Ho AU - Lee KH FAU - Kim, Bum-Joon AU - Kim BJ FAU - Kim, Kijeong AU - Kim K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120112 PL - Germany TA - Int J Legal Med JT - International journal of legal medicine JID - 9101456 RN - 0 (Amelogenin) RN - 0 (Humic Substances) SB - IM MH - Alleles MH - Amelogenin/*genetics MH - *Chromosomes, Human, Y MH - *DNA Degradation, Necrotic MH - Female MH - Forensic Genetics MH - Humans MH - Humic Substances MH - Male MH - *Real-Time Polymerase Chain Reaction MH - Sex Determination Analysis/*methods EDAT- 2012/01/13 06:00 MHDA- 2013/06/15 06:00 CRDT- 2012/01/13 06:00 PHST- 2011/10/13 00:00 [received] PHST- 2011/12/20 00:00 [accepted] PHST- 2012/01/13 06:00 [entrez] PHST- 2012/01/13 06:00 [pubmed] PHST- 2013/06/15 06:00 [medline] AID - 10.1007/s00414-011-0663-5 [doi] PST - ppublish SO - Int J Legal Med. 2013 Jan;127(1):55-61. doi: 10.1007/s00414-011-0663-5. Epub 2012 Jan 12. PMID- 23076995 OWN - NLM STAT- MEDLINE DCOM- 20130423 LR - 20121120 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 149 IP - 4 DP - 2012 Dec TI - The genetic impact of Aztec imperialism: ancient mitochondrial DNA evidence from Xaltocan, Mexico. PG - 504-16 LID - 10.1002/ajpa.22152 [doi] AB - In AD 1428, the city-states of Tenochtitlan, Texcoco, and Tlacopan formed the Triple Alliance, laying the foundations of the Aztec empire. Although it is well documented that the Aztecs annexed numerous polities in the Basin of Mexico over the following years, the demographic consequences of this expansion remain unclear. At the city-state capital of Xaltocan, 16th century documents suggest that the site's conquest and subsequent incorporation into the Aztec empire led to a replacement of the original Otomí population, whereas archaeological evidence suggests that some of the original population may have remained at the town under Aztec rule. To help address questions about Xaltocan's demographic history during this period, we analyzed ancient DNA from 25 individuals recovered from three houses rebuilt over time and occupied between AD 1240 and 1521. These individuals were divided into two temporal groups that predate and postdate the site's conquest. We determined the mitochondrial DNA haplogroup of each individual and identified haplotypes based on 372 base pair sequences of first hypervariable region. Our results indicate that the residents of these houses before and after the Aztec conquest have distinct haplotypes that are not closely related, and the mitochondrial compositions of the temporal groups are statistically different. Altogether, these results suggest that the matrilines present in the households were replaced following the Aztec conquest. This study therefore indicates that the Aztec expansion may have been associated with significant demographic and genetic changes within Xaltocan. CI - Copyright © 2012 Wiley Periodicals, Inc. FAU - Mata-Míguez, Jaime AU - Mata-Míguez J AD - Department of Anthropology, University of Texas at Austin, Austin, TX 78712, USA. jaime.mata.miguez@utexas.edu FAU - Overholtzer, Lisa AU - Overholtzer L FAU - Rodríguez-Alegría, Enrique AU - Rodríguez-Alegría E FAU - Kemp, Brian M AU - Kemp BM FAU - Bolnick, Deborah A AU - Bolnick DA LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121017 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Bayes Theorem MH - Bone and Bones/chemistry MH - Child MH - Child, Preschool MH - DNA, Mitochondrial/analysis/*genetics MH - Genetic Variation MH - Haplotypes/genetics MH - History, Medieval MH - Humans MH - Indians, Central American/*genetics/*history MH - Infant MH - Infant, Newborn MH - Mexico MH - Middle Aged MH - Phylogeny MH - Tooth/chemistry EDAT- 2012/10/19 06:00 MHDA- 2013/04/24 06:00 CRDT- 2012/10/19 06:00 PHST- 2012/04/05 00:00 [received] PHST- 2012/08/28 00:00 [accepted] PHST- 2012/10/19 06:00 [entrez] PHST- 2012/10/19 06:00 [pubmed] PHST- 2013/04/24 06:00 [medline] AID - 10.1002/ajpa.22152 [doi] PST - ppublish SO - Am J Phys Anthropol. 2012 Dec;149(4):504-16. doi: 10.1002/ajpa.22152. Epub 2012 Oct 17. PMID- 22976345 OWN - NLM STAT- MEDLINE DCOM- 20130522 LR - 20121129 IS - 1528-1159 (Electronic) IS - 0362-2436 (Linking) VI - 37 IP - 25 DP - 2012 Dec 1 TI - A case of spinal tuberculosis from the middle ages in Transylvania (Romania). PG - E1598-601 LID - 10.1097/BRS.0b013e31827300dc [doi] AB - STUDY DESIGN: Case report. OBJECTIVE: To characterize the paleopathology presented in the skeleton of a 45- to 50-year-old man indicative of tuberculous spondylitis and to confirm by the detection of ancient DNA. SUMMARY OF BACKGROUND DATA: Tuberculosis (TB) is an infectious disease prevalent in both present and ancient human populations. The disease is primarily located within the lungs; although characteristic bone lesions can lead to a clear diagnosis, skeletal TB occurs in only 5% to 6% of TB infections, even in historical cases. In addition, the visual appearance of human skeletal remains may be influenced by the environmental conditions at the burial site. However, it is important to recognize ancient skeletal TB because it can provide important data on the history of Mycobacterium tuberculosis and give a unique opportunity for physicians to observe the natural outcome of the infection of the preantibiotic era. METHODS: Paleopathological analysis was carried out using careful visual observation supported by ancient DNA analysis. Approximately 60 mg of bone powder from rib fragments was examined and DNA from the M. tuberculosis complex was detected by polymerase chain reaction (PCR) targeting specific genetic loci of the IS6110 and IS1081 regions. RESULTS: The skeleton is part of a human osteoarchaeological collection (n = 274) from the 12th- to 13th-century Transylvanian archaeological site of Peteni, in modern-day Romania. The individual, a 45- to 50-year-old man, showed gross pathology typical of tuberculous spondylitis. The paleopathological diagnosis was supported by analysis for M. tuberculosis complex ancient DNA. CONCLUSIONS: This case demonstrates that TB was present in Transylvania (Romania) during the 12th and 13th centuries and adds to the growing body of knowledge on the history of this disease. FAU - Hajdu, Tamás AU - Hajdu T AD - Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary. hajdut@elte.hu FAU - Donoghue, Helen D AU - Donoghue HD FAU - Bernert, Zsolt AU - Bernert Z FAU - Fóthi, Erzsébet AU - Fóthi E FAU - Kővári, Ivett AU - Kővári I FAU - Marcsik, Antónia AU - Marcsik A LA - eng PT - Historical Article PT - Journal Article PL - United States TA - Spine (Phila Pa 1976) JT - Spine JID - 7610646 RN - 0 (DNA, Bacterial) SB - IM MH - Adult MH - Base Sequence MH - *DNA, Bacterial/isolation & purification MH - History, Medieval MH - Humans MH - Hungary MH - Male MH - Middle Aged MH - Molecular Sequence Data MH - *Mycobacterium tuberculosis/genetics MH - Paleopathology MH - Polymerase Chain Reaction MH - Romania MH - Sequence Analysis, DNA MH - *Spine/microbiology/pathology MH - Spondylitis/diagnosis/*history/microbiology MH - Tuberculosis, Spinal/complications/diagnosis/*history/microbiology EDAT- 2012/09/15 06:00 MHDA- 2013/05/23 06:00 CRDT- 2012/09/15 06:00 PHST- 2012/09/15 06:00 [entrez] PHST- 2012/09/15 06:00 [pubmed] PHST- 2013/05/23 06:00 [medline] AID - 10.1097/BRS.0b013e31827300dc [doi] PST - ppublish SO - Spine (Phila Pa 1976). 2012 Dec 1;37(25):E1598-601. doi: 10.1097/BRS.0b013e31827300dc. PMID- 23091009 OWN - NLM STAT- MEDLINE DCOM- 20130117 LR - 20211021 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 109 IP - 45 DP - 2012 Nov 6 TI - Genotype of a historic strain of Mycobacterium tuberculosis. PG - 18511-6 LID - 10.1073/pnas.1209444109 [doi] AB - The use of ancient DNA in paleopathological studies of tuberculosis has largely been restricted to confirmation of disease identifications made by skeletal analysis; few attempts at obtaining genotype data from archaeological samples have been made because of the need to perform different PCRs for each genetic locus being studied in an ancient DNA extract. We used a next generation sequencing approach involving hybridization capture directed at specific polymorphic regions of the Mycobacterium tuberculosis genome to identify a detailed genotype for a historic strain of M. tuberculosis from an individual buried in the 19th century St. George's Crypt, Leeds, West Yorkshire, England. We obtained 664,500 sequencing by oligonucleotide ligation and detection (SOLiD) reads that mapped to the targeted regions of the M. tuberculosis genome; the coverage included 218 of 247 SNPs, 10 of 11 insertion/deletion regions, and the repeat elements IS1081 and IS6110. The accuracy of the SOLiD data was checked by conventional PCRs directed at 11 SNPs and two insertion/deletions. The data placed the historic strain of M. tuberculosis in a group that is uncommon today, but it is known to have been present in North America in the early 20th century. Our results show the use of hybridization capture followed by next generation sequencing as a means of obtaining detailed genotypes of ancient varieties of M. tuberculosis, potentially enabling meaningful comparisons between strains from different geographic locations and different periods in the past. FAU - Bouwman, Abigail S AU - Bouwman AS AD - Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom. FAU - Kennedy, Sandra L AU - Kennedy SL FAU - Müller, Romy AU - Müller R FAU - Stephens, Richard H AU - Stephens RH FAU - Holst, Malin AU - Holst M FAU - Caffell, Anwen C AU - Caffell AC FAU - Roberts, Charlotte A AU - Roberts CA FAU - Brown, Terence A AU - Brown TA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121022 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Oligonucleotides) SB - IM MH - Bacterial Typing Techniques MH - Base Sequence MH - England MH - Female MH - Genome, Bacterial/genetics MH - Genotype MH - Humans MH - Molecular Sequence Data MH - Mycobacterium tuberculosis/*genetics MH - Oligonucleotides/genetics MH - *Paleontology MH - Phylogeny MH - Polymerase Chain Reaction MH - Sequence Alignment MH - Sequence Analysis, DNA PMC - PMC3494915 COIS- The authors declare no conflict of interest. EDAT- 2012/10/24 06:00 MHDA- 2013/01/18 06:00 PMCR- 2013/05/06 CRDT- 2012/10/24 06:00 PHST- 2012/10/24 06:00 [entrez] PHST- 2012/10/24 06:00 [pubmed] PHST- 2013/01/18 06:00 [medline] PHST- 2013/05/06 00:00 [pmc-release] AID - 1209444109 [pii] AID - 201209444 [pii] AID - 10.1073/pnas.1209444109 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18511-6. doi: 10.1073/pnas.1209444109. Epub 2012 Oct 22. PMID- 23066327 OWN - NLM STAT- MEDLINE DCOM- 20130328 LR - 20211021 IS - 2219-2840 (Electronic) IS - 1007-9327 (Print) IS - 1007-9327 (Linking) VI - 18 IP - 37 DP - 2012 Oct 7 TI - Origin of celiac disease: how old are predisposing haplotypes? PG - 5300-4 LID - 10.3748/wjg.v18.i37.5300 [doi] AB - We recently presented the case of a first century AD young woman, found in the archaeological site of Cosa, showing clinical signs of malnutrition, such as short height, osteoporosis, dental enamel hypoplasia and cribra orbitalia, indirect sign of anemia, all strongly suggestive for celiac disease (CD). However, whether these findings were actually associated to CD was not shown based on genetic parameters. To investigate her human leukocyte antigen (HLA) class II polymorphism, we extracted DNA from a bone sample and a tooth and genotyped HLA using three HLA-tagging single nucleotide polymorphisms for DQ8, DQ2.2 and DQ2.5, specifically associated to CD. She displayed HLA DQ 2.5, the haplotype associated to the highest risk of CD. This is the first report showing the presence of a HLA haplotype compatible for CD in archaeological specimens. FAU - Gasbarrini, Giovanni AU - Gasbarrini G AD - Ricerca in Medicina Foundation NGO, Falcone and Borsellino Gallery, 40123 Bologna, Italy. agasbarrini@rm.unicatt.it FAU - Rickards, Olga AU - Rickards O FAU - Martínez-Labarga, Cristina AU - Martínez-Labarga C FAU - Pacciani, Elsa AU - Pacciani E FAU - Chilleri, Filiberto AU - Chilleri F FAU - Laterza, Lucrezia AU - Laterza L FAU - Marangi, Giuseppe AU - Marangi G FAU - Scaldaferri, Franco AU - Scaldaferri F FAU - Gasbarrini, Antonio AU - Gasbarrini A LA - eng PT - Case Reports PT - Journal Article PL - United States TA - World J Gastroenterol JT - World journal of gastroenterology JID - 100883448 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) RN - 0 (HLA Antigens) RN - 0 (HLA-DQ Antigens) SB - IM MH - Archaeology/methods MH - Celiac Disease/*diagnosis/*genetics MH - DNA Primers/genetics MH - DNA, Mitochondrial/genetics MH - Female MH - *Genetic Predisposition to Disease MH - Genotype MH - HLA Antigens/metabolism MH - HLA-DQ Antigens/genetics MH - *Haplotypes MH - Humans MH - Italy MH - Malabsorption Syndromes/genetics MH - Polymorphism, Genetic MH - Risk PMC - PMC3468865 OTO - NOTNLM OT - Ancient DNA OT - Celiac disease OT - Human leukocyte antigen haplotype OT - Malabsorption OT - Single nucleotide polymorphisms EDAT- 2012/10/16 06:00 MHDA- 2013/03/30 06:00 PMCR- 2012/10/07 CRDT- 2012/10/16 06:00 PHST- 2012/02/24 00:00 [received] PHST- 2012/06/29 00:00 [revised] PHST- 2012/07/09 00:00 [accepted] PHST- 2012/10/16 06:00 [entrez] PHST- 2012/10/16 06:00 [pubmed] PHST- 2013/03/30 06:00 [medline] PHST- 2012/10/07 00:00 [pmc-release] AID - 10.3748/wjg.v18.i37.5300 [doi] PST - ppublish SO - World J Gastroenterol. 2012 Oct 7;18(37):5300-4. doi: 10.3748/wjg.v18.i37.5300. PMID- 23298497 OWN - NLM STAT- MEDLINE DCOM- 20130423 LR - 20170214 IS - 0394-6320 (Print) IS - 0394-6320 (Linking) VI - 25 IP - 4 DP - 2012 Oct-Dec TI - Immunogenetics and HPLC analyses contribute to understanding the etiopathology of rheumatoid arthritis through studies on ancient human remains. PG - 1075-82 AB - Genetic investigations on ancient human remains affected by rheumatological pathologies are a research field of particular interest for identifying origins and the etiopathology of diseases, especially those having an autoimmune background such as rheumatoid arthritis (RA). We wish to demonstrate how reliable studies concerning this topic require collaboration between multiple disciplines, usually starting from paleopathologic observations up to immunogenetic screening, even involving analytical chemistry. Here, we focused our investigation on the skeleton of Cardinal Carlo de'Medici (1595-1666) for whom RA and psoriatic arthritis (PsA) were postulated after paleopathologic examination. RA susceptibility is linked to specific HLA alleles belonging to DRB1 04 locus, such as DRB1 0401, while Cw 0602 and DRB1 07 predispose to PsA. Thus, we genotyped the Cardinal?s remains to search for RA or PsA risk genes. Ancient DNA is often subjected to hydrolysis followed by fragmentation. For this reason, all immunogenetic tests were preceded by an original RP-HPLC-FL method able to inform on the ancient DNA preservation and the extent of contamination, with the purpose of avoiding the risk of false positive results. After DNA isolation from a piece of bone from the Cardinal, PCR-SSP and reverse-SSO hybridization assays were applied to perform genomic HLA-typing. RP-HPLC-FL analysis revealed a good preservation of DNA without contamination by exogenous genomes. Molecular tests assigned to the Cardinal the genotype DRB1 0401/1102 for HLA-DRB locus and Cw 04/ 12 for HLA-C locus, data that support a genetic predisposition for RA but not for PsA. This multidisciplinary study has allowed us: (i) to ascertain that the remains undoubtedly belonged to the specific subject, Cardinal Carlo de?Medici; (ii) to sustain that the subject suffered from RA rather then that PsA, and (iii) to state that RA was already widespread in Europe at the Renaissance age, despite some authors claiming that the disease was introduced to the Old Continent from America after colonization during the 18th century. FAU - Poma, A AU - Poma A AD - Dipartimento di Medicina Clinica, Universita' degli Studi di L'Aquila, Coppito, L'Aquila, Italy. annamaria.poma@univaq.it FAU - Carlucci, G AU - Carlucci G FAU - Fontecchio, G AU - Fontecchio G LA - eng PT - Journal Article PL - England TA - Int J Immunopathol Pharmacol JT - International journal of immunopathology and pharmacology JID - 8911335 RN - 0 (HLA-DRB1 Chains) RN - 9007-49-2 (DNA) SB - IM MH - Arthritis, Psoriatic/etiology/genetics MH - Arthritis, Rheumatoid/*etiology/genetics MH - Chromatography, High Pressure Liquid/*methods MH - DNA/*analysis MH - HLA-DRB1 Chains/genetics MH - Humans MH - Immunogenetics/*methods MH - *Paleopathology EDAT- 2013/01/10 06:00 MHDA- 2013/04/24 06:00 CRDT- 2013/01/10 06:00 PHST- 2013/01/10 06:00 [entrez] PHST- 2013/01/10 06:00 [pubmed] PHST- 2013/04/24 06:00 [medline] AID - 24 [pii] AID - 10.1177/039463201202500424 [doi] PST - ppublish SO - Int J Immunopathol Pharmacol. 2012 Oct-Dec;25(4):1075-82. doi: 10.1177/039463201202500424. PMID- 22889475 OWN - NLM STAT- MEDLINE DCOM- 20121226 LR - 20221207 IS - 0168-9525 (Print) IS - 0168-9525 (Linking) VI - 28 IP - 10 DP - 2012 Oct TI - The genetic history of Europeans. PG - 496-505 LID - S0168-9525(12)00095-9 [pii] LID - 10.1016/j.tig.2012.06.006 [doi] AB - The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data. CI - Copyright © 2012 Elsevier Ltd. All rights reserved. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Archaeology, University College Cork, Cork, Ireland. ron_pinhasi@yahoo.com FAU - Thomas, Mark G AU - Thomas MG FAU - Hofreiter, Michael AU - Hofreiter M FAU - Currat, Mathias AU - Currat M FAU - Burger, Joachim AU - Burger J LA - eng GR - 263441/ERC_/European Research Council/International PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20120810 PL - England TA - Trends Genet JT - Trends in genetics : TIG JID - 8507085 SB - IM MH - Animals MH - *Biological Evolution MH - Bone and Bones/anatomy & histology/metabolism MH - Fossils MH - Genetic Variation MH - Humans MH - White People/*genetics EDAT- 2012/08/15 06:00 MHDA- 2012/12/27 06:00 CRDT- 2012/08/15 06:00 PHST- 2012/02/27 00:00 [received] PHST- 2012/06/16 00:00 [revised] PHST- 2012/06/22 00:00 [accepted] PHST- 2012/08/15 06:00 [entrez] PHST- 2012/08/15 06:00 [pubmed] PHST- 2012/12/27 06:00 [medline] AID - S0168-9525(12)00095-9 [pii] AID - 10.1016/j.tig.2012.06.006 [doi] PST - ppublish SO - Trends Genet. 2012 Oct;28(10):496-505. doi: 10.1016/j.tig.2012.06.006. Epub 2012 Aug 10. PMID- 22673688 OWN - NLM STAT- MEDLINE DCOM- 20130211 LR - 20221207 IS - 1435-232X (Electronic) IS - 1434-5161 (Linking) VI - 57 IP - 9 DP - 2012 Sep TI - Mitochondrial haplogroup C in ancient mitochondrial DNA from Ukraine extends the presence of East Eurasian genetic lineages in Neolithic Central and Eastern Europe. PG - 610-2 LID - 10.1038/jhg.2012.69 [doi] AB - Recent studies of ancient mitochondrial DNA (mtDNA) lineages have revealed the presence of East Eurasian mtDNA haplogroups in the Central European Neolithic. Here we report the finding of East Eurasian lineages in ancient mtDNA from two Neolithic cemeteries of the North Pontic Region (NPR) in Ukraine. In our study, comprehensive haplotyping information was obtained for 7 out of 18 specimens. Although the majority of identified mtDNA haplogroups belonged to the traditional West Eurasian lineages of H and U, three specimens were determined to belong to the lineages of mtDNA haplogroup C. This find extends the presence of East Eurasian lineages in Neolithic Europe from the Carpathian Mountains to the northern shores of the Black Sea and provides the first genetic account of Neolithic mtDNA lineages from the NPR. FAU - Nikitin, Alexey G AU - Nikitin AG AD - Biology Department, Grand Valley State University, Allendale, MI 49401, USA. nikitin@gvsu.edu FAU - Newton, Jeremy R AU - Newton JR FAU - Potekhina, Inna D AU - Potekhina ID LA - eng SI - GENBANK/JN873355 SI - GENBANK/JN873356 SI - GENBANK/JN873357 SI - GENBANK/JN873358 SI - GENBANK/JN873359 SI - GENBANK/JN873360 SI - GENBANK/JN873361 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120607 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adolescent MH - Adult MH - Child MH - Child, Preschool MH - DNA, Mitochondrial/*genetics MH - Europe, Eastern MH - Female MH - *Genetic Linkage MH - Geography MH - *Haplotypes MH - Humans MH - Male MH - Middle Aged MH - Molecular Sequence Data MH - Polymorphism, Single Nucleotide MH - White People/*genetics MH - Young Adult EDAT- 2012/06/08 06:00 MHDA- 2013/02/12 06:00 CRDT- 2012/06/08 06:00 PHST- 2012/06/08 06:00 [entrez] PHST- 2012/06/08 06:00 [pubmed] PHST- 2013/02/12 06:00 [medline] AID - jhg201269 [pii] AID - 10.1038/jhg.2012.69 [doi] PST - ppublish SO - J Hum Genet. 2012 Sep;57(9):610-2. doi: 10.1038/jhg.2012.69. Epub 2012 Jun 7. PMID- 22427706 OWN - NLM STAT- MEDLINE DCOM- 20130614 LR - 20120823 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 29 IP - 9 DP - 2012 Sep TI - Statistical guidelines for detecting past population shifts using ancient DNA. PG - 2241-51 LID - 10.1093/molbev/mss094 [doi] AB - Populations carry a genetic signal of their demographic past, providing an opportunity for investigating the processes that shaped their evolution. Our ability to infer population histories can be enhanced by including ancient DNA data. Using serial-coalescent simulations and a range of both quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast post-bottleneck recoveries. In contrast, nuclear SNPs can detect bottlenecks followed by rapid recovery, although bottlenecks involving reduction of less than half the population are generally detected with low power unless extensive genetic information from ancient individuals is available. Our results provide useful guidelines for scaling sampling schemes and for optimizing our ability to infer past population dynamics. In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when based solely on mitochondrial information. FAU - Mourier, Tobias AU - Mourier T AD - Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. tmourier@snm.ku.dk FAU - Ho, Simon Y W AU - Ho SY FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Willerslev, Eske AU - Willerslev E FAU - Orlando, Ludovic AU - Orlando L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120316 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Computer Simulation MH - *DNA, Mitochondrial MH - Genetics, Population MH - Guidelines as Topic MH - Humans MH - *Models, Genetic MH - *Models, Statistical MH - Polymorphism, Single Nucleotide MH - Population Dynamics EDAT- 2012/03/20 06:00 MHDA- 2013/06/15 06:00 CRDT- 2012/03/20 06:00 PHST- 2012/03/20 06:00 [entrez] PHST- 2012/03/20 06:00 [pubmed] PHST- 2013/06/15 06:00 [medline] AID - mss094 [pii] AID - 10.1093/molbev/mss094 [doi] PST - ppublish SO - Mol Biol Evol. 2012 Sep;29(9):2241-51. doi: 10.1093/molbev/mss094. Epub 2012 Mar 16. PMID- 22936748 OWN - NLM STAT- MEDLINE DCOM- 20120917 LR - 20120831 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 337 IP - 6098 DP - 2012 Aug 31 TI - Ancient DNA. A crystal-clear view of an extinct girl's genome. PG - 1028-9 LID - 10.1126/science.337.6098.1028 [doi] FAU - Gibbons, Ann AU - Gibbons A LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Single-Stranded) SB - IM MH - Animals MH - DNA, Single-Stranded/*genetics/history/*isolation & purification MH - Evolution, Molecular MH - Female MH - *Fossils MH - Genome, Human/*genetics MH - History, Ancient MH - Humans MH - Sequence Analysis, DNA/history/*methods EDAT- 2012/09/01 06:00 MHDA- 2012/09/18 06:00 CRDT- 2012/09/01 06:00 PHST- 2012/09/01 06:00 [entrez] PHST- 2012/09/01 06:00 [pubmed] PHST- 2012/09/18 06:00 [medline] AID - 337/6098/1028 [pii] AID - 10.1126/science.337.6098.1028 [doi] PST - ppublish SO - Science. 2012 Aug 31;337(6098):1028-9. doi: 10.1126/science.337.6098.1028. PMID- 22748318 OWN - NLM STAT- MEDLINE DCOM- 20130110 LR - 20120824 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 22 IP - 16 DP - 2012 Aug 21 TI - Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. PG - 1494-9 LID - 10.1016/j.cub.2012.06.005 [doi] AB - The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic is poorly understood, both due to the scarcity of human remains from that period and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain). The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe. CI - Copyright © 2012 Elsevier Ltd. All rights reserved. FAU - Sánchez-Quinto, Federico AU - Sánchez-Quinto F AD - Institut de Biologia Evolutiva, CSIC-UPF, Dr. Aiguader 88, 08003 Barcelona, Spain. FAU - Schroeder, Hannes AU - Schroeder H FAU - Ramirez, Oscar AU - Ramirez O FAU - Avila-Arcos, María C AU - Avila-Arcos MC FAU - Pybus, Marc AU - Pybus M FAU - Olalde, Iñigo AU - Olalde I FAU - Velazquez, Amhed M V AU - Velazquez AM FAU - Marcos, María Encina Prada AU - Marcos ME FAU - Encinas, Julio Manuel Vidal AU - Encinas JM FAU - Bertranpetit, Jaume AU - Bertranpetit J FAU - Orlando, Ludovic AU - Orlando L FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C LA - eng SI - GENBANK/JX186998 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120628 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) SB - IM CIN - Curr Biol. 2012 Aug 21;22(16):R631-3. doi: 10.1016/j.cub.2012.06.033. PMID: 22917508 MH - Base Sequence MH - *DNA, Mitochondrial MH - *Fossils MH - *Genome, Human MH - *Genome, Mitochondrial MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - Spain EDAT- 2012/07/04 06:00 MHDA- 2013/01/11 06:00 CRDT- 2012/07/04 06:00 PHST- 2012/02/23 00:00 [received] PHST- 2012/05/08 00:00 [revised] PHST- 2012/06/04 00:00 [accepted] PHST- 2012/07/04 06:00 [entrez] PHST- 2012/07/04 06:00 [pubmed] PHST- 2013/01/11 06:00 [medline] AID - S0960-9822(12)00650-1 [pii] AID - 10.1016/j.cub.2012.06.005 [doi] PST - ppublish SO - Curr Biol. 2012 Aug 21;22(16):1494-9. doi: 10.1016/j.cub.2012.06.005. Epub 2012 Jun 28. PMID- 23249313 OWN - NLM STAT- MEDLINE DCOM- 20131206 LR - 20221207 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 84 IP - 4 DP - 2012 Aug TI - Genetic data suggests that the Jinggouzi people are associated with the Donghu, an ancient nomadic group of North China. PG - 365-78 LID - 10.3378/027.084.0402 [doi] AB - Nomadic populations have played a significant role in the history of not only China but also in many nations worldwide. Because they had no written language, an important aspect in the study of these people is the discovery of their tombs. It has been generally accepted that Xiongnu was the first empire created by a nomadic tribe in the 3rd century BC. However, little population genetic information is available concerning the Donghu, another flourishing nomadic tribe at the same period because of the restriction of materials until the Jinggouzi site was excavated. In order to test the genetic characteristics of ancient people in this site and to explore the relationship between Jinggouzis and Donghus, two uniparentally inherited markers were analyzed from 42 human remains in this site, which was located in northern China, dated approximately 2500 years ago. With ancient DNA technology, four mtDNA haplogroups (D, G, C, and M10) and one Y chromosome haplogroup (C) were identified using mitochondrial DNA and Y-chromosome single nucleotide polymorphisms. Those haplogroups are common in North Asia and East Asia. The Jinggouzi people were genetically closest to the Xianbeis in ancient populations and to the Oroqens among extant populations, who were all pastoralists. This might indicate that ancient Jinggouzi people were nomads. Meanwhile, according to the genetic data and the evidences in archaeology, we inferred that Jinggouzi people were associated with Donghu. It is of much value to trace the history of the Donghu tribe and this might show some insight into the ancient nomadic society. FAU - Wang, Haijing AU - Wang H AD - Key Laboratory for Evolution of Past Life and Environment in Northeast Asia, Jilin University, Ministry of Education, Changchun, People's Republic of China. FAU - Chen, Lu AU - Chen L FAU - Ge, Binwen AU - Ge B FAU - Zhang, Ye AU - Zhang Y FAU - Zhu, Hong AU - Zhu H FAU - Zhou, Hui AU - Zhou H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - Asian People/*genetics MH - China MH - DNA, Mitochondrial MH - Female MH - Genetic Markers MH - Genotyping Techniques MH - *Haplotypes MH - *Human Migration MH - Humans MH - Male MH - Phylogeography MH - Polymorphism, Single Nucleotide MH - *Transients and Migrants EDAT- 2012/12/20 06:00 MHDA- 2013/12/16 06:00 CRDT- 2012/12/20 06:00 PHST- 2012/12/20 06:00 [entrez] PHST- 2012/12/20 06:00 [pubmed] PHST- 2013/12/16 06:00 [medline] AID - 10.3378/027.084.0402 [doi] PST - ppublish SO - Hum Biol. 2012 Aug;84(4):365-78. doi: 10.3378/027.084.0402. PMID- 22552938 OWN - NLM STAT- MEDLINE DCOM- 20121226 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 148 IP - 4 DP - 2012 Aug TI - Emerging genetic patterns of the European Neolithic: perspectives from a late Neolithic Bell Beaker burial site in Germany. PG - 571-9 LID - 10.1002/ajpa.22074 [doi] AB - The transition from hunting and gathering to agriculture in Europe is associated with demographic changes that may have shifted the human gene pool of the region as a result of an influx of Neolithic farmers from the Near East. However, the genetic composition of populations after the earliest Neolithic, when a diverse mosaic of societies that had been fully engaged in agriculture for some time appeared in central Europe, is poorly known. At this period during the Late Neolithic (ca. 2,800-2,000 BC), regionally distinctive burial patterns associated with two different cultural groups emerge, Bell Beaker and Corded Ware, and may reflect differences in how these societies were organized. Ancient DNA analyses of human remains from the Late Neolithic Bell Beaker site of Kromsdorf, Germany showed distinct mitochondrial haplotypes for six individuals, which were classified under the haplogroups I1, K1, T1, U2, U5, and W5, and two males were identified as belonging to the Y haplogroup R1b. In contrast to other Late Neolithic societies in Europe emphasizing maintenance of biological relatedness in mortuary contexts, the diversity of maternal haplotypes evident at Kromsdorf suggests that burial practices of Bell Beaker communities operated outside of social norms based on shared maternal lineages. Furthermore, our data, along with those from previous studies, indicate that modern U5-lineages may have received little, if any, contribution from the Mesolithic or Neolithic mitochondrial gene pool. CI - Copyright © 2012 Wiley Periodicals, Inc. FAU - Lee, Esther J AU - Lee EJ AD - Graduate School "Human Development in Landscapes," Christian-Albrechts-University of Kiel, Germany. FAU - Makarewicz, Cheryl AU - Makarewicz C FAU - Renneberg, Rebecca AU - Renneberg R FAU - Harder, Melanie AU - Harder M FAU - Krause-Kyora, Ben AU - Krause-Kyora B FAU - Müller, Stephanie AU - Müller S FAU - Ostritz, Sven AU - Ostritz S FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L FAU - Schreiber, Stefan AU - Schreiber S FAU - Müller, Johannes AU - Müller J FAU - von Wurmb-Schwark, Nicole AU - von Wurmb-Schwark N FAU - Nebel, Almut AU - Nebel A LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120503 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - *Cemeteries MH - Cultural Evolution MH - DNA, Mitochondrial/genetics MH - Emigration and Immigration MH - Germany MH - Haplotypes MH - History, Ancient MH - Humans MH - Male MH - White People/*genetics/*history EDAT- 2012/05/04 06:00 MHDA- 2012/12/27 06:00 CRDT- 2012/05/04 06:00 PHST- 2011/11/21 00:00 [received] PHST- 2012/03/08 00:00 [revised] PHST- 2012/03/12 00:00 [accepted] PHST- 2012/05/04 06:00 [entrez] PHST- 2012/05/04 06:00 [pubmed] PHST- 2012/12/27 06:00 [medline] AID - 10.1002/ajpa.22074 [doi] PST - ppublish SO - Am J Phys Anthropol. 2012 Aug;148(4):571-9. doi: 10.1002/ajpa.22074. Epub 2012 May 3. PMID- 22697611 OWN - NLM STAT- MEDLINE DCOM- 20121024 LR - 20211021 IS - 1297-9686 (Electronic) IS - 0999-193X (Print) IS - 0999-193X (Linking) VI - 44 IP - 1 DP - 2012 Jul 6 TI - Ancient DNA studies: new perspectives on old samples. PG - 21 LID - 10.1186/1297-9686-44-21 [doi] AB - In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field. FAU - Rizzi, Ermanno AU - Rizzi E AD - Institute for Biomedical Technologies, National Research Council, Via F.lli Cervi 93, Segrate, Milan 20090, Italy. FAU - Lari, Martina AU - Lari M FAU - Gigli, Elena AU - Gigli E FAU - De Bellis, Gianluca AU - De Bellis G FAU - Caramelli, David AU - Caramelli D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20120706 PL - France TA - Genet Sel Evol JT - Genetics, selection, evolution : GSE JID - 9114088 RN - 0 (DNA, Mitochondrial) SB - IM EIN - Genet Sel Evol. 2013;45:4 MH - Animals MH - Base Sequence MH - Cell Nucleus/genetics MH - DNA Damage MH - DNA, Mitochondrial/analysis/*genetics MH - *Evolution, Molecular MH - Extinction, Biological MH - Genome, Human MH - Humans MH - Mitochondria/genetics MH - Polymerase Chain Reaction/methods/standards MH - Sequence Analysis, DNA/*methods MH - Time Factors PMC - PMC3390907 EDAT- 2012/06/16 06:00 MHDA- 2012/10/25 06:00 PMCR- 2012/07/06 CRDT- 2012/06/16 06:00 PHST- 2011/09/06 00:00 [received] PHST- 2012/06/14 00:00 [accepted] PHST- 2012/06/16 06:00 [entrez] PHST- 2012/06/16 06:00 [pubmed] PHST- 2012/10/25 06:00 [medline] PHST- 2012/07/06 00:00 [pmc-release] AID - 1297-9686-44-21 [pii] AID - 10.1186/1297-9686-44-21 [doi] PST - epublish SO - Genet Sel Evol. 2012 Jul 6;44(1):21. doi: 10.1186/1297-9686-44-21. PMID- 22673687 OWN - NLM STAT- MEDLINE DCOM- 20121127 LR - 20221207 IS - 1435-232X (Electronic) IS - 1434-5161 (Linking) VI - 57 IP - 7 DP - 2012 Jul TI - 'Early Neolithic' graves of the Carpathian Basin are in fact 6000 years younger-appeal for real interdisciplinarity between archaeology and ancient DNA research. PG - 467-9; author reply 470-1 LID - 10.1038/jhg.2012.36 [doi] FAU - Bánffy, Eszter AU - Bánffy E FAU - Brandt, Guido AU - Brandt G FAU - Alt, Kurt W AU - Alt KW LA - eng PT - Comment PT - Letter DEP - 20120607 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (DNA, Mitochondrial) SB - IM CON - J Hum Genet. 2011 Nov;56(11):784-96. doi: 10.1038/jhg.2011.103. PMID: 21918529 MH - Asian People/*genetics MH - DNA, Mitochondrial/*chemistry MH - *Haplotypes MH - Humans MH - *Polymorphism, Single Nucleotide EDAT- 2012/06/08 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/06/08 06:00 PHST- 2012/06/08 06:00 [entrez] PHST- 2012/06/08 06:00 [pubmed] PHST- 2012/12/10 06:00 [medline] AID - jhg201236 [pii] AID - 10.1038/jhg.2012.36 [doi] PST - ppublish SO - J Hum Genet. 2012 Jul;57(7):467-9; author reply 470-1. doi: 10.1038/jhg.2012.36. Epub 2012 Jun 7. PMID- 22516743 OWN - NLM STAT- MEDLINE DCOM- 20120926 LR - 20120618 IS - 1879-3096 (Electronic) IS - 0167-7799 (Linking) VI - 30 IP - 7 DP - 2012 Jul TI - Next-generation sequencing offers new insights into DNA degradation. PG - 364-8 LID - 10.1016/j.tibtech.2012.03.007 [doi] AB - The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation rates that previously were obtained only from extrapolations of results from in vitro kinetic experiments performed over short timescales. For example, recent next-generation sequencing of ancient DNA reveals purine bases as one of the main targets of postmortem hydrolytic damage, through base elimination and strand breakage. It also shows substantially increased rates of DNA base-loss at guanosine. In this review, we argue that the latter results from an electron resonance structure unique to guanosine rather than adenosine having an extra resonance structure over guanosine as previously suggested. CI - Copyright © 2012 Elsevier Ltd. All rights reserved. FAU - Overballe-Petersen, Søren AU - Overballe-Petersen S AD - Centre for GeoGenetics, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark. FAU - Orlando, Ludovic AU - Orlando L FAU - Willerslev, Eske AU - Willerslev E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20120417 PL - England TA - Trends Biotechnol JT - Trends in biotechnology JID - 8310903 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/analysis/chemistry/*genetics MH - DNA Damage/*genetics MH - Fossils MH - Horses MH - Humans MH - Mammals MH - *Models, Genetic MH - Nucleic Acid Conformation MH - Sequence Analysis, DNA/*methods EDAT- 2012/04/21 06:00 MHDA- 2012/09/27 06:00 CRDT- 2012/04/21 06:00 PHST- 2012/01/09 00:00 [received] PHST- 2012/03/02 00:00 [revised] PHST- 2012/03/21 00:00 [accepted] PHST- 2012/04/21 06:00 [entrez] PHST- 2012/04/21 06:00 [pubmed] PHST- 2012/09/27 06:00 [medline] AID - S0167-7799(12)00039-X [pii] AID - 10.1016/j.tibtech.2012.03.007 [doi] PST - ppublish SO - Trends Biotechnol. 2012 Jul;30(7):364-8. doi: 10.1016/j.tibtech.2012.03.007. Epub 2012 Apr 17. PMID- 22457070 OWN - NLM STAT- MEDLINE DCOM- 20121022 LR - 20211021 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 40 IP - 13 DP - 2012 Jul TI - A mostly traditional approach improves alignment of bisulfite-converted DNA. PG - e100 LID - 10.1093/nar/gks275 [doi] AB - Cytosines in genomic DNA are sometimes methylated. This affects many biological processes and diseases. The standard way of measuring methylation is to use bisulfite, which converts unmethylated cytosines to thymines, then sequence the DNA and compare it to a reference genome sequence. We describe a method for the critical step of aligning the DNA reads to the correct genomic locations. Our method builds on classic alignment techniques, including likelihood-ratio scores and spaced seeds. In a realistic benchmark, our method has a better combination of sensitivity, specificity and speed than nine other high-throughput bisulfite aligners. This study enables more accurate and rational analysis of DNA methylation. It also illustrates how to adapt general-purpose alignment methods to a special case with distorted base patterns: this should be informative for other special cases such as ancient DNA and AT-rich genomes. FAU - Frith, Martin C AU - Frith MC AD - Computational Biology Research Center, National Institute for Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan. martin@cbrc.jp FAU - Mori, Ryota AU - Mori R FAU - Asai, Kiyoshi AU - Asai K LA - eng PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120328 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Sulfites) RN - 9007-49-2 (DNA) RN - OJ9787WBLU (hydrogen sulfite) SB - IM MH - DNA/chemistry MH - *DNA Methylation MH - Genome, Human MH - Humans MH - Repetitive Sequences, Nucleic Acid MH - Sequence Alignment/*methods MH - *Sequence Analysis, DNA MH - *Sulfites PMC - PMC3401460 EDAT- 2012/03/30 06:00 MHDA- 2012/10/23 06:00 PMCR- 2012/03/28 CRDT- 2012/03/30 06:00 PHST- 2012/03/30 06:00 [entrez] PHST- 2012/03/30 06:00 [pubmed] PHST- 2012/10/23 06:00 [medline] PHST- 2012/03/28 00:00 [pmc-release] AID - gks275 [pii] AID - 10.1093/nar/gks275 [doi] PST - ppublish SO - Nucleic Acids Res. 2012 Jul;40(13):e100. doi: 10.1093/nar/gks275. Epub 2012 Mar 28. PMID- 23596858 OWN - NLM STAT- MEDLINE DCOM- 20130730 LR - 20130419 IS - 0001-4079 (Print) IS - 0001-4079 (Linking) VI - 196 IP - 6 DP - 2012 Jun TI - [Modern biology, imagery and forensic medicine: contributions and limitations in examination of skeletal remains]. PG - 1103-15; discussion 1116 AB - Forensic examination is often requested when skeletal remains are discovered. Detailed visual observation can provide much information, such as the human or animal origin, sex, age, stature, and ancestry, and approximate time since death. New three-dimensional imaging techniques can provide further information (osteometry, facial reconstruction). Bone chemistry, and particularly measurement of stable or unstable carbon and nitrogen isotopes, yields information on diet and time since death, respectively. Genetic analyses of ancient DNA are also developing rapidly. Although seldom used in a judicial context, these modern anthropologic techniques are nevertheless available for the most complex cases. FAU - Lecomte, Dominique AU - Lecomte D AD - Institut médico-légal, 2 place Mazas, 75012 Paris. dominique.lecomte@interieur.gouv.fr FAU - Plu, Isabelle AU - Plu I FAU - Froment, Alain AU - Froment A LA - fre PT - English Abstract PT - Journal Article PT - Review TT - La biologie moderne, l'imagerie et la médecine légale: apports et limites dans l'étude des ossements. PL - Netherlands TA - Bull Acad Natl Med JT - Bulletin de l'Academie nationale de medecine JID - 7503383 RN - 9007-49-2 (DNA) SB - IM MH - Adult MH - Age Determination by Skeleton MH - Anthropometry/*methods MH - Blood Stains MH - Body Height MH - Bone and Bones/chemistry MH - Cause of Death MH - Child MH - DNA/genetics MH - Face MH - Female MH - Forensic Anthropology/methods MH - Forensic Medicine/*methods MH - Humans MH - Image Processing, Computer-Assisted MH - Imaging, Three-Dimensional/*methods MH - Male MH - Radiometric Dating MH - Sex Characteristics MH - *Skeleton MH - Time Factors MH - Tomography, X-Ray Computed/methods EDAT- 2013/04/20 06:00 MHDA- 2013/07/31 06:00 CRDT- 2013/04/20 06:00 PHST- 2013/04/20 06:00 [entrez] PHST- 2013/04/20 06:00 [pubmed] PHST- 2013/07/31 06:00 [medline] PST - ppublish SO - Bull Acad Natl Med. 2012 Jun;196(6):1103-15; discussion 1116. PMID- 21896337 OWN - NLM STAT- MEDLINE DCOM- 20120815 LR - 20120423 IS - 1567-7257 (Electronic) IS - 1567-1348 (Linking) VI - 12 IP - 4 DP - 2012 Jun TI - Mycobacterium tuberculosis complex detection in human remains: tuberculosis spread since the 17th century in Rio de Janeiro, Brazil. PG - 642-8 LID - 10.1016/j.meegid.2011.08.021 [doi] AB - Paleogenetic analysis for tuberculosis (TB) was conducted on bone and sediment samples dating from the 17th to 19th centuries from the archeological site of Nossa Senhora do Carmo Church in Rio de Janeiro, Brazil. Forty samples were analyzed, corresponding to 32 individuals from 28 burials, 22 of primary type and 6 of secondary type. The samples were collected following strict paleogenetic investigation guidelines and submitted to ancient DNA (aDNA) extraction. In order to detect TB infection, aDNA hybridizations with the molecular targets of Mycobacterium tuberculosis complex (MTC) IS6110 and IS1081 were applied. Additionally, the ancestry of individuals was assessed by human mitochondrial DNA (mtDNA) analysis of hypervariable segment I (HVS-I) sequence polymorphisms. The results of aDNA hybridizations demonstrated varying levels of MTC intensity in 17/32 individuals (53.1%), using the IS6110 target. The IS1081 MTC target showed lower sensitivity, confirming TB positivity in 10/32 (31.2%) individuals. The mtDNA analysis allowed the recovery of HVS-I sequences in 23/32 individuals (71.8%). The majority of these individuals (21/23, 91.3%) were of European ancestry, especially in primary burials. Haplogroups U, J, V, T, K, N, H and R, were identified with haplogroup U being the most frequent at 6/23 (26.1%). African and Amerindian mtDNA haplogroups were observed in two individuals in secondary burials. In spite of the ecclesiastic and aristocratic bias of the population of the study, human ancestry analysis revealed the prominent contribution of Europeans in the introduction or spread of TB in the New World. CI - Copyright © 2011 Elsevier B.V. All rights reserved. FAU - Jaeger, Lauren Hubert AU - Jaeger LH AD - Laboratório de Genética Molecular de Microorganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21045-900, Brazil. FAU - Leles, Daniela AU - Leles D FAU - Lima, Valdirene dos Santos AU - Lima Vdos S FAU - da Silva, Laura da Piedade AU - da Silva Lda P FAU - Dias, Ondemar AU - Dias O FAU - Iñiguez, Alena Mayo AU - Iñiguez AM LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110827 PL - Netherlands TA - Infect Genet Evol JT - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JID - 101084138 RN - 0 (DNA, Bacterial) RN - 0 (DNA, Mitochondrial) SB - IM MH - Brazil/epidemiology MH - DNA, Bacterial/history MH - DNA, Mitochondrial/history MH - History, 17th Century MH - Humans MH - Mycobacterium tuberculosis/genetics/isolation & purification MH - Nucleic Acid Hybridization MH - Tuberculosis/epidemiology/*history EDAT- 2011/09/08 06:00 MHDA- 2012/08/16 06:00 CRDT- 2011/09/08 06:00 PHST- 2011/05/01 00:00 [received] PHST- 2011/08/18 00:00 [revised] PHST- 2011/08/20 00:00 [accepted] PHST- 2011/09/08 06:00 [entrez] PHST- 2011/09/08 06:00 [pubmed] PHST- 2012/08/16 06:00 [medline] AID - S1567-1348(11)00301-7 [pii] AID - 10.1016/j.meegid.2011.08.021 [doi] PST - ppublish SO - Infect Genet Evol. 2012 Jun;12(4):642-8. doi: 10.1016/j.meegid.2011.08.021. Epub 2011 Aug 27. PMID- 22574660 OWN - NLM STAT- MEDLINE DCOM- 20130206 LR - 20211021 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 13 DP - 2012 May 10 TI - Improving ancient DNA read mapping against modern reference genomes. PG - 178 LID - 10.1186/1471-2164-13-178 [doi] AB - BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. RESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. CONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material. FAU - Schubert, Mikkel AU - Schubert M AD - Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 Øster Voldgade, 1350, Kobenhavns K, Denmark. FAU - Ginolhac, Aurelien AU - Ginolhac A FAU - Lindgreen, Stinus AU - Lindgreen S FAU - Thompson, John F AU - Thompson JF FAU - Al-Rasheid, Khaled A S AU - Al-Rasheid KA FAU - Willerslev, Eske AU - Willerslev E FAU - Krogh, Anders AU - Krogh A FAU - Orlando, Ludovic AU - Orlando L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120510 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 SB - IM MH - DNA Damage/genetics MH - Fossils MH - Genotype MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Sequence Analysis, DNA/*methods PMC - PMC3468387 EDAT- 2012/05/12 06:00 MHDA- 2013/02/07 06:00 PMCR- 2012/05/10 CRDT- 2012/05/12 06:00 PHST- 2011/11/24 00:00 [received] PHST- 2012/04/30 00:00 [accepted] PHST- 2012/05/12 06:00 [entrez] PHST- 2012/05/12 06:00 [pubmed] PHST- 2013/02/07 06:00 [medline] PHST- 2012/05/10 00:00 [pmc-release] AID - 1471-2164-13-178 [pii] AID - 10.1186/1471-2164-13-178 [doi] PST - epublish SO - BMC Genomics. 2012 May 10;13:178. doi: 10.1186/1471-2164-13-178. PMID- 22268568 OWN - NLM STAT- MEDLINE DCOM- 20120813 LR - 20120420 IS - 1556-4029 (Electronic) IS - 0022-1198 (Linking) VI - 57 IP - 3 DP - 2012 May TI - Autosomal short tandem repeat analysis of ancient DNA by coupled use of mini- and conventional STR kits. PG - 820-5 LID - 10.1111/j.1556-4029.2011.02044.x [doi] AB - Multiplex autosomal short tandem repeat (STR) genotyping enables researchers to obtain genetic information from ancient human samples. In this study, we tested newly developed AmpFℓSTR(®) MiniFiler™ kit for autosomal STR analysis of ancient DNA (aDNA), using human femurs (n = 8) collected from medieval Korean tombs. After extracting aDNA from the bones, autosomal STR analyses were repeated for each sample using the AmpFℓSTR(®) MiniFiler™ and Identifiler™ kits. Whereas only 21.87% of larger-sized loci profiles could be obtained with the Identifiler™ kit, 75% of the same loci profiles were determined by MiniFiler™ kit analysis. This very successful amplification of large-sized STR markers from highly degraded aDNA suggests that the MiniFiler™ kit could be a useful complement to conventional STR kit analysis of ancient samples. CI - © 2012 American Academy of Forensic Sciences. FAU - Oh, Chang Seok AU - Oh CS AD - Institute of Forensic Medicine, Seoul National University College of Medicine, 28, Yongon-Dong, Chongno-Gu, Seoul 110-799, South Korea. FAU - Lee, Sang Jun AU - Lee SJ FAU - Park, Jun Bum AU - Park JB FAU - Lee, Soong Deok AU - Lee SD FAU - Seo, Seung Bum AU - Seo SB FAU - Kim, Hye Yeon AU - Kim HY FAU - Kim, Jaehyup AU - Kim J FAU - Kim, Yi-Suk AU - Kim YS FAU - Shin, Dong Hoon AU - Shin DH LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120123 PL - United States TA - J Forensic Sci JT - Journal of forensic sciences JID - 0375370 RN - 9007-49-2 (DNA) SB - IM MH - DNA/isolation & purification MH - *DNA Degradation, Necrotic MH - DNA Fingerprinting/*instrumentation/methods MH - Femur/chemistry MH - Genotyping Techniques/instrumentation/methods MH - History, 16th Century MH - History, 18th Century MH - Humans MH - *Microsatellite Repeats MH - Polymerase Chain Reaction EDAT- 2012/01/25 06:00 MHDA- 2012/08/14 06:00 CRDT- 2012/01/25 06:00 PHST- 2012/01/25 06:00 [entrez] PHST- 2012/01/25 06:00 [pubmed] PHST- 2012/08/14 06:00 [medline] AID - 10.1111/j.1556-4029.2011.02044.x [doi] PST - ppublish SO - J Forensic Sci. 2012 May;57(3):820-5. doi: 10.1111/j.1556-4029.2011.02044.x. Epub 2012 Jan 23. PMID- 22524324 OWN - NLM STAT- MEDLINE DCOM- 20130220 LR - 20240505 IS - 1471-2156 (Electronic) IS - 1471-2156 (Linking) VI - 13 DP - 2012 Apr 23 TI - Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community. PG - 30 LID - 10.1186/1471-2156-13-30 [doi] AB - BACKGROUND: A detailed genetic study of the pre-Columbian population inhabiting the Tompullo 2 archaeological site (department Arequipa, Peru) was undertaken to resolve the kin relationships between individuals buried in six different chullpas. Kin relationships were an important factor shaping the social organization in the pre-Columbian Andean communities, centering on the ayllu, a group of relatives that shared a common land and responsibilities. The aim of this study was to evaluate whether this Andean model of a social organization had an influence on mortuary practices, in particular to determine whether chullpas served as family graves. RESULTS: The remains of forty-one individuals were analyzed with both uniparental (mtDNA, Y-chromosome) and biparental (autosomal microsatellites) markers. Reproducible HVRI sequences, autosomal and Y chromosomal STR profiles were obtained for 24, 16 and 11 individuals, respectively. Mitochondrial DNA diversity was comparable to that of ancient and contemporary Andean populations. The Tompullo 2 population exhibited the closest relationship with the modern population from the same region. A kinship analysis revealed complex pattern of relations within and between the graves. However mean relatedness coefficients regarding the pairs of individuals buried in the same grave were significantly higher than those regarding pairs buried in different graves. The Y chromosome profiles of 11 males suggest that only members of one male line were buried in the same grave. CONCLUSIONS: Genetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site was organized into extended family groups that were buried in different graves. This finding is in congruence with known models of social organization of Andean communities. FAU - Baca, Mateusz AU - Baca M AD - Center for Precolumbian Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927, Warsaw, Poland. bacamat@gmail.com FAU - Doan, Karolina AU - Doan K FAU - Sobczyk, Maciej AU - Sobczyk M FAU - Stankovic, Anna AU - Stankovic A FAU - Węgleński, Piotr AU - Węgleński P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120423 PL - England TA - BMC Genet JT - BMC genetics JID - 100966978 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - *Archaeology MH - Burial MH - DNA/*analysis MH - DNA, Mitochondrial/analysis MH - *Family MH - Genetics, Population MH - Humans MH - Indians, South American/*genetics MH - Male MH - Microsatellite Repeats/immunology MH - Peru PMC - PMC3470988 EDAT- 2012/04/25 06:00 MHDA- 2013/02/21 06:00 PMCR- 2012/04/23 CRDT- 2012/04/25 06:00 PHST- 2011/09/06 00:00 [received] PHST- 2012/03/27 00:00 [accepted] PHST- 2012/04/25 06:00 [entrez] PHST- 2012/04/25 06:00 [pubmed] PHST- 2013/02/21 06:00 [medline] PHST- 2012/04/23 00:00 [pmc-release] AID - 1471-2156-13-30 [pii] AID - 10.1186/1471-2156-13-30 [doi] PST - epublish SO - BMC Genet. 2012 Apr 23;13:30. doi: 10.1186/1471-2156-13-30. PMID- 22312053 OWN - NLM STAT- MEDLINE DCOM- 20120521 LR - 20211021 IS - 1471-2970 (Electronic) IS - 0962-8436 (Print) IS - 0962-8436 (Linking) VI - 367 IP - 1590 DP - 2012 Mar 19 TI - Insights from genomic comparisons of genetically monomorphic bacterial pathogens. PG - 860-7 LID - 10.1098/rstb.2011.0303 [doi] AB - Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called 'genetically monomorphic bacteria'. It has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. The genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. Some genetically monomorphic lineages have evolved in the last decades, e.g. antibiotic-resistant Staphylococcus aureus, whereas others have evolved over several millennia, e.g. the cause of plague, Yersinia pestis. Based on recent results, it is now possible to reconstruct the sources and the history of pandemic waves of plague by a combined analysis of phylogeographic signals in Y. pestis plus polymorphisms found in ancient DNA. Different from historical accounts based exclusively on human disease, Y. pestis evolved in China, or the vicinity, and has spread globally on multiple occasions. These routes of transmission can be reconstructed from the genealogy, most precisely for the most recent pandemic that was spread from Hong Kong in multiple independent waves in 1894. FAU - Achtman, Mark AU - Achtman M AD - Environmental Research Institute and Department of Microbiology, University College Cork, Cork, Ireland. m.achtman@ucc.ie LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 SB - IM MH - Epidemics/*history MH - *Evolution, Molecular MH - *Genetic Variation MH - Genetics, Population/*methods MH - Genome, Bacterial/*genetics MH - History, 19th Century MH - History, Ancient MH - History, Medieval MH - Humans MH - Phylogeography MH - Plague/*epidemiology/microbiology MH - Polymorphism, Single Nucleotide/genetics MH - Selection, Genetic MH - Yersinia pestis/*genetics/*pathogenicity PMC - PMC3267118 EDAT- 2012/02/09 06:00 MHDA- 2012/05/23 06:00 PMCR- 2013/03/19 CRDT- 2012/02/08 06:00 PHST- 2012/02/08 06:00 [entrez] PHST- 2012/02/09 06:00 [pubmed] PHST- 2012/05/23 06:00 [medline] PHST- 2013/03/19 00:00 [pmc-release] AID - rstb.2011.0303 [pii] AID - rstb20110303 [pii] AID - 10.1098/rstb.2011.0303 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 2012 Mar 19;367(1590):860-7. doi: 10.1098/rstb.2011.0303. PMID- 22452428 OWN - NLM STAT- MEDLINE DCOM- 20120730 LR - 20120328 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 84 IP - 1 DP - 2012 Feb TI - A craniometric perspective on the transition to agriculture in Europe. PG - 45-66 LID - 10.3378/027.084.0102 [doi] AB - Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centered on two opposing models: a "demic" diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities, and an "indigenist" model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East but with little or no gene flow. The extreme versions of these dichotomous models were heavily contested primarily on the basis of archeological and modern genetic data. However, in recent years a growing acceptance has arisen of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe. Craniometric data were particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships among Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe. FAU - Pinhasi, Ron AU - Pinhasi R AD - Department of Archaeology, University College Cork, Cork, Ireland. r.pinhasi@ucc.ie FAU - von Cramon-Taubadel, Noreen AU - von Cramon-Taubadel N LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 9007-49-2 (DNA) SB - IM MH - Agriculture/*history/statistics & numerical data MH - Cephalometry/*instrumentation/methods MH - *Culture MH - DNA/analysis/genetics MH - Demography MH - Europe MH - Genetics, Population/statistics & numerical data MH - History, Ancient MH - Humans MH - Models, Theoretical MH - Skull EDAT- 2012/03/29 06:00 MHDA- 2012/07/31 06:00 CRDT- 2012/03/29 06:00 PHST- 2012/03/29 06:00 [entrez] PHST- 2012/03/29 06:00 [pubmed] PHST- 2012/07/31 06:00 [medline] AID - 10.3378/027.084.0102 [doi] PST - ppublish SO - Hum Biol. 2012 Feb;84(1):45-66. doi: 10.3378/027.084.0102. PMID- 22313406 OWN - NLM STAT- MEDLINE DCOM- 20121001 LR - 20220408 IS - 1940-9818 (Electronic) IS - 0736-6205 (Linking) VI - 52 IP - 2 DP - 2012 Feb TI - Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. PG - 87-94 LID - 10.2144/000113809 [doi] AB - High-throughput sequencing technologies frequently necessitate the use of PCR for sequencing library amplification. PCR is a sometimes enigmatic process and is known to introduce biases. Here we perform a simple amplification-sequencing assay using 10 commercially available polymerase-buffer systems to amplify libraries prepared from both modern and ancient DNA. We compare the performance of the polymerases with respect to a previously uncharacterized template length bias, as well as GC-content bias, and find that simply avoiding certain polymerase can dramatically decrease the occurrence of both. For amplification of ancient DNA, we found that some commonly used polymerases strongly bias against amplification of endogenous DNA in favor of GC-rich microbial contamination, in our case reducing the fraction of endogenous sequences to almost half. FAU - Dabney, Jesse AU - Dabney J AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. jesse_dabney@eva.mpg.de FAU - Meyer, Matthias AU - Meyer M LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (Buffers) RN - EC 2.7.7.7 (DNA-Directed DNA Polymerase) SB - IM MH - Base Composition/*genetics MH - Buffers MH - DNA-Directed DNA Polymerase/*genetics MH - *Gene Library MH - Humans MH - Nucleic Acid Amplification Techniques/*methods MH - Sequence Analysis, DNA/*methods EDAT- 2012/02/09 06:00 MHDA- 2012/10/02 06:00 CRDT- 2012/02/09 06:00 PHST- 2011/10/28 00:00 [received] PHST- 2011/12/16 00:00 [accepted] PHST- 2012/02/09 06:00 [entrez] PHST- 2012/02/09 06:00 [pubmed] PHST- 2012/10/02 06:00 [medline] AID - 000113809 [pii] AID - 10.2144/000113809 [doi] PST - ppublish SO - Biotechniques. 2012 Feb;52(2):87-94. doi: 10.2144/000113809. PMID- 22183740 OWN - NLM STAT- MEDLINE DCOM- 20120308 LR - 20120112 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 147 IP - 2 DP - 2012 Feb TI - Nondestructive sampling of human skeletal remains yields ancient nuclear and mitochondrial DNA. PG - 293-300 LID - 10.1002/ajpa.21647 [doi] AB - Museum curators and living communities are sometimes reluctant to permit ancient DNA (aDNA) studies of human skeletal remains because the extraction of aDNA usually requires the destruction of at least some skeletal material. Whether these views stem from a desire to conserve precious materials or an objection to destroying ancestral remains, they limit the potential of aDNA research. To help address concerns about destructive analysis and to minimize damage to valuable specimens, we describe a nondestructive method for extracting DNA from ancient human remains. This method can be used with both teeth and bone, but it preserves the structural integrity of teeth much more effectively than that of bone. Using this method, we demonstrate that it is possible to extract both mitochondrial and nuclear DNA from human remains dating between 300 BC and 1600 AD. Importantly, the method does not expose the remains to hazardous chemicals, allowing them to be safely returned to curators, custodians, and/or owners of the samples. We successfully amplified mitochondrial DNA from 90% of the individuals tested, and we were able to analyze 1-9 nuclear loci in 70% of individuals. We also show that repeated nondestructive extractions from the same tooth can yield amplifiable mitochondrial and nuclear DNA. The high success rate of this method and its ability to yield DNA from samples spanning a wide geographic and temporal range without destroying the structural integrity of the sampled material may make possible the genetic study of skeletal collections that are not available for destructive analysis. CI - Copyright © 2011 Wiley Periodicals, Inc. FAU - Bolnick, Deborah A AU - Bolnick DA AD - Department of Anthropology, University of Texas at Austin, 1 University Station, Austin, TX 78712, USA. deborah.bolnick@mail.utexas.edu FAU - Bonine, Holly M AU - Bonine HM FAU - Mata-Míguez, Jaime AU - Mata-Míguez J FAU - Kemp, Brian M AU - Kemp BM FAU - Snow, Meradeth H AU - Snow MH FAU - LeBlanc, Steven A AU - LeBlanc SA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111220 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Archaeology/*methods MH - Bone and Bones/*chemistry MH - DNA/*isolation & purification MH - DNA, Mitochondrial/*isolation & purification MH - Humans MH - North America MH - Polymerase Chain Reaction MH - Tooth/*chemistry EDAT- 2011/12/21 06:00 MHDA- 2012/03/09 06:00 CRDT- 2011/12/21 06:00 PHST- 2011/06/07 00:00 [received] PHST- 2011/10/28 00:00 [accepted] PHST- 2011/12/21 06:00 [entrez] PHST- 2011/12/21 06:00 [pubmed] PHST- 2012/03/09 06:00 [medline] AID - 10.1002/ajpa.21647 [doi] PST - ppublish SO - Am J Phys Anthropol. 2012 Feb;147(2):293-300. doi: 10.1002/ajpa.21647. Epub 2011 Dec 20. PMID- 22169595 OWN - NLM STAT- MEDLINE DCOM- 20120502 LR - 20240229 IS - 1618-0402 (Electronic) IS - 0940-9602 (Linking) VI - 194 IP - 1 DP - 2012 Jan 20 TI - Ancient human DNA. PG - 121-32 LID - 10.1016/j.aanat.2011.11.002 [doi] AB - The contribution of palaeogenetic data to the study of various aspects of hominin biology and evolution has been significant, and has the potential to increase substantially with the widespread implementation of next generation sequencing techniques. Here we discuss the present state-of-the-art of ancient human DNA analysis and the characteristics of hominin aDNA that make sequence validation particularly complex. A brief overview of the development of anthropological palaeogenetic analysis is given to illustrate the technical challenges motivating recent technological advancements. CI - Copyright © 2011 Elsevier GmbH. All rights reserved. FAU - Kirsanow, Karola AU - Kirsanow K AD - Johannes Gutenberg-University Mainz, Institute of Anthropology, Germany. FAU - Burger, Joachim AU - Burger J LA - eng PT - Journal Article PT - Review DEP - 20111118 PL - Germany TA - Ann Anat JT - Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft JID - 100963897 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Biological Evolution MH - *DNA/chemistry/genetics MH - *Hominidae/genetics MH - *Paleontology/methods MH - Phenotype MH - Phylogeny MH - Population Dynamics MH - Reproducibility of Results MH - Specimen Handling MH - Humans EDAT- 2011/12/16 06:00 MHDA- 2012/05/02 06:00 CRDT- 2011/12/16 06:00 PHST- 2011/07/05 00:00 [received] PHST- 2011/11/07 00:00 [revised] PHST- 2011/11/08 00:00 [accepted] PHST- 2011/12/16 06:00 [entrez] PHST- 2011/12/16 06:00 [pubmed] PHST- 2012/05/02 06:00 [medline] AID - S0940-9602(11)00222-6 [pii] AID - 10.1016/j.aanat.2011.11.002 [doi] PST - ppublish SO - Ann Anat. 2012 Jan 20;194(1):121-32. doi: 10.1016/j.aanat.2011.11.002. Epub 2011 Nov 18. PMID- 21641784 OWN - NLM STAT- MEDLINE DCOM- 20120501 LR - 20120110 IS - 1618-0402 (Electronic) IS - 0940-9602 (Linking) VI - 194 IP - 1 DP - 2012 Jan 20 TI - Museums and disease: using tissue archive and museum samples to study pathogens. PG - 58-73 LID - 10.1016/j.aanat.2011.04.003 [doi] AB - Molecular studies of archival and fossil samples have traditionally focused on the nucleic acids derived from the host species. However, there has recently been an increase in ancient DNA research on the identification and characterization of infectious agents within the hosts. The study of pathogens from the past provides great opportunities for discovering the causes of historical infection events, characterizing host-microorganism co-evolution and directly investigating the evolution of specific pathogens. Several research teams have been able to isolate and characterize a variety of different bacterial, parasite and viral microorganisms. However, this emerging field is not without obstacles. The diagenetic processes that make ancient DNA research generally difficult are also impediments to ancient pathogen research and perhaps more so given that their DNA may represent an even rarer proportion of the remaining nucleic acids in a fossil sample than host DNA. However, studies performed under controlled conditions and following stringent ancient DNA protocols can and have yielded reliable and often surprising results. This article reviews the advantages, problems, and failures of ancient microbiological research. CI - Copyright © 2011 Elsevier GmbH. All rights reserved. FAU - Tsangaras, Kyriakos AU - Tsangaras K AD - Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany. FAU - Greenwood, Alex D AU - Greenwood AD LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20110511 PL - Germany TA - Ann Anat JT - Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft JID - 100963897 RN - 0 (DNA, Bacterial) SB - IM MH - Animals MH - Ascariasis/history/parasitology MH - Bacteria/*genetics MH - Bacterial Infections/*history/*microbiology MH - DNA, Bacterial/genetics MH - Disease/*history MH - Enterobiasis/history/parasitology MH - History, Ancient MH - Humans MH - Malaria/history/parasitology MH - *Museums MH - Mycobacterium/genetics MH - Mycobacterium Infections/history/microbiology MH - Mycoses/*history/*microbiology MH - Parasitic Diseases/*history/*parasitology MH - Phytophthora infestans MH - Plague/history/microbiology MH - Plant Diseases/history/microbiology MH - Plasmodium falciparum/genetics MH - Trypanosomiasis/history/parasitology MH - Virus Diseases/*history/*virology MH - Yersinia pestis/genetics EDAT- 2011/06/07 06:00 MHDA- 2012/05/02 06:00 CRDT- 2011/06/07 06:00 PHST- 2010/12/09 00:00 [received] PHST- 2011/04/06 00:00 [revised] PHST- 2011/04/06 00:00 [accepted] PHST- 2011/06/07 06:00 [entrez] PHST- 2011/06/07 06:00 [pubmed] PHST- 2012/05/02 06:00 [medline] AID - S0940-9602(11)00083-5 [pii] AID - 10.1016/j.aanat.2011.04.003 [doi] PST - ppublish SO - Ann Anat. 2012 Jan 20;194(1):58-73. doi: 10.1016/j.aanat.2011.04.003. Epub 2011 May 11. PMID- 21641192 OWN - NLM STAT- MEDLINE DCOM- 20120501 LR - 20120110 IS - 1618-0402 (Electronic) IS - 0940-9602 (Linking) VI - 194 IP - 1 DP - 2012 Jan 20 TI - Special issue ancient DNA. PG - 1-2 LID - 10.1016/j.aanat.2011.04.011 [doi] FAU - Hofreiter, Michael AU - Hofreiter M LA - eng PT - Editorial PT - Introductory Journal Article DEP - 20110513 PL - Germany TA - Ann Anat JT - Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft JID - 100963897 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*genetics MH - DNA, Mitochondrial/genetics MH - Equidae MH - Humans MH - Paleontology/*methods MH - Plants/genetics MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA/methods/trends EDAT- 2011/06/07 06:00 MHDA- 2012/05/02 06:00 CRDT- 2011/06/07 06:00 PHST- 2011/04/19 00:00 [received] PHST- 2011/04/20 00:00 [accepted] PHST- 2011/06/07 06:00 [entrez] PHST- 2011/06/07 06:00 [pubmed] PHST- 2012/05/02 06:00 [medline] AID - S0940-9602(11)00117-8 [pii] AID - 10.1016/j.aanat.2011.04.011 [doi] PST - ppublish SO - Ann Anat. 2012 Jan 20;194(1):1-2. doi: 10.1016/j.aanat.2011.04.011. Epub 2011 May 13. PMID- 21596538 OWN - NLM STAT- MEDLINE DCOM- 20120501 LR - 20120110 IS - 1618-0402 (Electronic) IS - 0940-9602 (Linking) VI - 194 IP - 1 DP - 2012 Jan 20 TI - Finding the founder of Stockholm - a kinship study based on Y-chromosomal, autosomal and mitochondrial DNA. PG - 138-45 LID - 10.1016/j.aanat.2011.03.014 [doi] AB - Historical records claim that Birger Magnusson (died 1266), famous regent of Sweden and the founder of Stockholm, was buried in Varnhem Abbey in Västergötland. After being lost for centuries, his putative grave was rediscovered during restoration work in the 1920s. Morphological analyses of the three individuals in the grave concluded that the older male, the female and the younger male found in the grave were likely to be Birger, his second wife Mechtild of Holstein and his son Erik from a previous marriage. More recent evaluations of the data from the 1920s seriously questioned these conclusions, ultimately leading to the reopening and reexamination of the grave in 2002. Ancient DNA-analyses were performed to investigate if the relationship between the three individuals matched what we would expect if the individuals were Birger, Erik and Mechtild. We used pyrosequencing of Y-chromosomal and autosomal SNPs and compared the results with haplogroup frequencies of modern Swedes to investigate paternal relations. Possible maternal kinship was investigated by deep FLX-sequencing of overlapping mtDNA amplicons. The authenticity of the sequences was examined using data from independent extractions, massive clonal data, the c-statistics, and real-time quantitative data. We show that the males carry the same Y-chromosomal haplogroup and thus we cannot reject a father-son type of relation. Further, as shown by the mtDNA analyses, none of the individuals are maternally related. We conclude that the graves indeed belong to Birger, Erik and Mechtild, or to three individuals with the exact same kind of biological relatedness. CI - Copyright © 2011 Elsevier GmbH. All rights reserved. FAU - Malmström, Helena AU - Malmström H AD - Department of Evolutionary Biology, Uppsala, Sweden. hjmalmstrom@gmail.com FAU - Vretemark, Maria AU - Vretemark M FAU - Tillmar, Andreas AU - Tillmar A FAU - Durling, Mikael Brandström AU - Durling MB FAU - Skoglund, Pontus AU - Skoglund P FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Willerslev, Eske AU - Willerslev E FAU - Holmlund, Gunilla AU - Holmlund G FAU - Götherström, Anders AU - Götherström A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110405 PL - Germany TA - Ann Anat JT - Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft JID - 100963897 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Adult MH - Algorithms MH - Chromosomes, Human, Y/*genetics MH - Cloning, Molecular MH - DNA/chemistry MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - Family MH - Female MH - Gene Dosage MH - Humans MH - Male MH - Paleodontology MH - Polymorphism, Single Nucleotide MH - Real-Time Polymerase Chain Reaction MH - Sequence Analysis, DNA/methods MH - Sweden MH - Tooth/chemistry EDAT- 2011/05/21 06:00 MHDA- 2012/05/02 06:00 CRDT- 2011/05/21 06:00 PHST- 2010/12/31 00:00 [received] PHST- 2011/03/27 00:00 [revised] PHST- 2011/03/27 00:00 [accepted] PHST- 2011/05/21 06:00 [entrez] PHST- 2011/05/21 06:00 [pubmed] PHST- 2012/05/02 06:00 [medline] AID - S0940-9602(11)00079-3 [pii] AID - 10.1016/j.aanat.2011.03.014 [doi] PST - ppublish SO - Ann Anat. 2012 Jan 20;194(1):138-45. doi: 10.1016/j.aanat.2011.03.014. Epub 2011 Apr 5. PMID- 21514120 OWN - NLM STAT- MEDLINE DCOM- 20120501 LR - 20220408 IS - 1618-0402 (Electronic) IS - 0940-9602 (Linking) VI - 194 IP - 1 DP - 2012 Jan 20 TI - Setting the stage - building and working in an ancient DNA laboratory. PG - 3-6 LID - 10.1016/j.aanat.2011.03.008 [doi] AB - With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can contribute significantly to our understanding of evolution in general and the development of our own species in particular. While the amount of sequence data available from ancient human, other animal and plant remains has increased dramatically over the past five years, some key limitations of ancient DNA research remain. Most notably, reduction of contamination and the authentication of results are of utmost importance. A number of studies have addressed different aspects of sampling, DNA extraction and DNA manipulation in order to establish protocols that most efficiently generate reproducible and authentic results. As increasing numbers of researchers from different backgrounds become interested in using ancient DNA technology to address key questions, the need for practical guidelines on how to construct and use an ancient DNA facility arises. The aim of this article is therefore to provide practical tips for building a state-of-the-art ancient DNA facility. It is intended to help researchers new to the field of ancient DNA research generally, and those considering the application of next generation sequencing, in their planning process. CI - Copyright © 2011 Elsevier GmbH. All rights reserved. FAU - Knapp, Michael AU - Knapp M AD - Department of Anatomy and Structural Biology, Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand. michael.knapp@otago.ac.nz FAU - Clarke, Andrew C AU - Clarke AC FAU - Horsburgh, K Ann AU - Horsburgh KA FAU - Matisoo-Smith, Elizabeth A AU - Matisoo-Smith EA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110331 PL - Germany TA - Ann Anat JT - Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft JID - 100963897 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Biological Evolution MH - DNA/chemistry/*genetics MH - Humans MH - Laboratories/organization & administration MH - Paleontology/*methods/organization & administration MH - Plants/chemistry/genetics MH - Polymerase Chain Reaction/methods MH - Sequence Analysis, DNA/methods MH - Specimen Handling EDAT- 2011/04/26 06:00 MHDA- 2012/05/02 06:00 CRDT- 2011/04/26 06:00 PHST- 2011/01/20 00:00 [received] PHST- 2011/03/15 00:00 [revised] PHST- 2011/03/15 00:00 [accepted] PHST- 2011/04/26 06:00 [entrez] PHST- 2011/04/26 06:00 [pubmed] PHST- 2012/05/02 06:00 [medline] AID - S0940-9602(11)00073-2 [pii] AID - 10.1016/j.aanat.2011.03.008 [doi] PST - ppublish SO - Ann Anat. 2012 Jan 20;194(1):3-6. doi: 10.1016/j.aanat.2011.03.008. Epub 2011 Mar 31. PMID- 22000492 OWN - NLM STAT- MEDLINE DCOM- 20120913 LR - 20211020 IS - 1096-0961 (Electronic) IS - 1079-9796 (Print) IS - 1079-9796 (Linking) VI - 48 IP - 1 DP - 2012 Jan 15 TI - A search for β thalassemia mutations in 4000 year old ancient DNAs of Minoan Cretans. PG - 7-10 LID - 10.1016/j.bcmd.2011.09.006 [doi] AB - Ancient DNA methodologies can be applied in the investigation of the genetics of extinct populations. A search for beta thalassemia mutations was performed on 49 Minoan individuals from the Bronze Age who were living in the island of Crete approximately 4000 Years Before Present (YBP). Standard precautionary measures were employed in the laboratory to ensure authenticity of the DNA extracted from the ancient bones, resulting in the successful analysis of DNA of 24 Minoans. DNA sequencing focused on the Intervening Sequence 1 (IVS-1) of the beta globin gene and its splicing junctions. 63% of the thalassemia mutations observed among modern Cretans reside in beta IVS-1. None of the Minoan individuals carried one of the IVS-1 mutations known to cause beta thalassemia; however, only one was expected to be observed if the average frequency of beta thalassemia heterozygotes in the Minoan population was the same with that of modern day Cretans (7.6%). One individual contained a C to G substitution in position 91 of the IVS-1, located 40 bp 5' to the intron 1/exon 2 junction. Functional studies indicated that the mutation did not affect mRNA splicing or stability, and most likely represented an innocent single nucleotide polymorphism. CI - Copyright © 2011 Elsevier Inc. All rights reserved. FAU - Hughey, Jeffery R AU - Hughey JR AD - University of Washington, Department of Medicine, 1705 NE Pacific St., K-240 Health Sciences Building, Box 357720, Seattle, WA 98195-7720, USA. FAU - Du, Meijun AU - Du M FAU - Li, Qiliang AU - Li Q FAU - Michalodimitrakis, Manolis AU - Michalodimitrakis M FAU - Stamatoyannopoulos, George AU - Stamatoyannopoulos G LA - eng GR - R56 DK045365/DK/NIDDK NIH HHS/United States GR - T32 GM007454/GM/NIGMS NIH HHS/United States GR - R90 HG004152-01/HG/NHGRI NIH HHS/United States GR - R37 DK045365/DK/NIDDK NIH HHS/United States GR - DK 045365/DK/NIDDK NIH HHS/United States GR - R01 DK045365/DK/NIDDK NIH HHS/United States GR - GM 007454/GM/NIGMS NIH HHS/United States GR - R90 HG004152/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20111014 PL - United States TA - Blood Cells Mol Dis JT - Blood cells, molecules & diseases JID - 9509932 RN - 0 (beta-Globins) RN - 9007-49-2 (DNA) SB - IM MH - DNA/chemistry/*genetics MH - Exons MH - *Fossils MH - Greece MH - HeLa Cells MH - Heterozygote MH - Humans MH - Introns/*genetics MH - *Mutation MH - Phylogeography MH - Polymorphism, Single Nucleotide MH - RNA Splicing MH - beta-Globins/chemistry/*genetics MH - beta-Thalassemia/*genetics PMC - PMC3249513 MID - NIHMS333117 EDAT- 2011/10/18 06:00 MHDA- 2012/09/14 06:00 PMCR- 2013/01/15 CRDT- 2011/10/18 06:00 PHST- 2011/09/12 00:00 [received] PHST- 2011/09/12 00:00 [accepted] PHST- 2011/10/18 06:00 [entrez] PHST- 2011/10/18 06:00 [pubmed] PHST- 2012/09/14 06:00 [medline] PHST- 2013/01/15 00:00 [pmc-release] AID - S1079-9796(11)00174-4 [pii] AID - 10.1016/j.bcmd.2011.09.006 [doi] PST - ppublish SO - Blood Cells Mol Dis. 2012 Jan 15;48(1):7-10. doi: 10.1016/j.bcmd.2011.09.006. Epub 2011 Oct 14. PMID- 23350155 OWN - NLM STAT- MEDLINE DCOM- 20130212 LR - 20191112 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 69 IP - 4 DP - 2012 TI - Multiplex analysis of genetic markers related to body mass index (BMI) and bone mineral density (BMD). PG - 423-38 AB - The multiplex analysis system described here allows simultaneous typing of one short tandem repeat (STR) and three single nucleotide polymorphisms (SNPs) that are associated with obesity and/or osteoporosis. Genes that are related to a high body mass index (BMI) and/or a high bone mineral density (BMD) are presumed to give an advantage in surviving famines. This analysis system makes it possible to genotype the (TTTA)n polymorphism of CYP19 and three SNPs, namely the rs1800795 polymorphism of IL6, the rs373 6228 polymorphism of LRP5 and the rs993 9609 polymorphism of FTO, in a single PCR amplification in recent and ancient DNA samples. Furthermore, it allows a synchronous authentication of the results with the (TATC)n polymorphism of D13S317, the (TCTA)n polymorphism of D21S11 and the (TTTC)n polymorphism of FGA in a partial genetic fingerprinting. For this purpose, PCR products for fragment-length analysis, as well as those for sequence analysis, were amplified together. After amplification, the PCR product was split into two aliquots. The first aliquot was used for fragment-length analysis and the second one for sequence analysis. The analysis system described here has been optimized for analysing ancient samples, since only minimal amounts of material are available. FAU - Fromm-Dornieden, Carolin AU - Fromm-Dornieden C AD - Historical Anthropology and Human Ecology, Institute of Zoology and Anthropology, University of Goettingen, Germany. cfromm@gwdg.de FAU - Pepperl, Jutta AU - Pepperl J FAU - Herrmann, Bernd AU - Herrmann B FAU - Hummel, Susanne AU - Hummel S LA - eng PT - Historical Article PT - Journal Article PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (Genetic Markers) RN - 0 (IL6 protein, human) RN - 0 (Interleukin-6) RN - 0 (LRP5 protein, human) RN - 0 (Low Density Lipoprotein Receptor-Related Protein-5) RN - 0 (Proteins) RN - 9007-49-2 (DNA) RN - EC 1.14.11.33 (Alpha-Ketoglutarate-Dependent Dioxygenase FTO) RN - EC 1.14.11.33 (FTO protein, human) RN - EC 1.14.14.1 (Aromatase) SB - IM MH - Adult MH - Alpha-Ketoglutarate-Dependent Dioxygenase FTO MH - Aromatase/genetics MH - Base Sequence MH - *Body Mass Index MH - Bone Density/*genetics MH - Cemeteries MH - DNA MH - Female MH - Genetic Markers/*genetics MH - Genotyping Techniques/*methods MH - Germany MH - History, Medieval MH - Humans MH - Interleukin-6/genetics MH - Low Density Lipoprotein Receptor-Related Protein-5/genetics MH - Male MH - *Microsatellite Repeats MH - Molecular Sequence Data MH - Paleopathology MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Proteins/genetics EDAT- 2013/01/29 06:00 MHDA- 2013/02/13 06:00 CRDT- 2013/01/29 06:00 PHST- 2013/01/29 06:00 [entrez] PHST- 2013/01/29 06:00 [pubmed] PHST- 2013/02/13 06:00 [medline] AID - 10.1127/0003-5548/2012/0161 [doi] PST - ppublish SO - Anthropol Anz. 2012;69(4):423-38. doi: 10.1127/0003-5548/2012/0161. PMID- 23152818 OWN - NLM STAT- MEDLINE DCOM- 20130501 LR - 20221207 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 11 DP - 2012 TI - Tracing the origin of the east-west population admixture in the Altai region (Central Asia). PG - e48904 LID - 10.1371/journal.pone.0048904 [doi] LID - e48904 AB - A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a 'contact zone' between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia. FAU - González-Ruiz, Mercedes AU - González-Ruiz M AD - Unitat d'Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain. FAU - Santos, Cristina AU - Santos C FAU - Jordana, Xavier AU - Jordana X FAU - Simón, Marc AU - Simón M FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C FAU - Gigli, Elena AU - Gigli E FAU - Aluja, Maria Pilar AU - Aluja MP FAU - Malgosa, Assumpció AU - Malgosa A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121109 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asia, Central MH - Asian People/*genetics MH - China MH - DNA, Mitochondrial MH - Female MH - Gene Frequency MH - Genetic Variation MH - Genetics, Population MH - Haplotypes MH - Humans MH - *Hybridization, Genetic MH - Male MH - Mongolia MH - Phylogeography MH - Russia MH - Sex Determination Processes MH - White People/*genetics PMC - PMC3494716 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2012/11/16 06:00 MHDA- 2013/05/02 06:00 PMCR- 2012/11/09 CRDT- 2012/11/16 06:00 PHST- 2012/07/17 00:00 [received] PHST- 2012/10/02 00:00 [accepted] PHST- 2012/11/16 06:00 [entrez] PHST- 2012/11/16 06:00 [pubmed] PHST- 2013/05/02 06:00 [medline] PHST- 2012/11/09 00:00 [pmc-release] AID - PONE-D-12-21040 [pii] AID - 10.1371/journal.pone.0048904 [doi] PST - ppublish SO - PLoS One. 2012;7(11):e48904. doi: 10.1371/journal.pone.0048904. Epub 2012 Nov 9. PMID- 22665278 OWN - NLM STAT- MEDLINE DCOM- 20120926 LR - 20120605 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 888 DP - 2012 TI - Roche genome sequencer FLX based high-throughput sequencing of ancient DNA. PG - 109-18 LID - 10.1007/978-1-61779-870-2_7 [doi] AB - Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred to as "ancient DNA," using the Roche GS FLX 454 platform. FAU - Alquezar-Planas, David E AU - Alquezar-Planas DE AD - Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. dalquezar@snm.ku.dk FAU - Fordyce, Sarah L AU - Fordyce SL LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Biological Specimen Banks MH - Chromosome Mapping MH - DNA/*analysis/chemistry MH - DNA Fragmentation MH - Extinction, Biological MH - Gene Library MH - *Genome MH - *High-Throughput Nucleotide Sequencing/instrumentation/methods MH - Humans MH - Mammoths/genetics MH - Neanderthals/genetics MH - Nucleic Acid Amplification Techniques/*methods MH - *Sequence Analysis, DNA/instrumentation/methods MH - Ursidae/genetics EDAT- 2012/06/06 06:00 MHDA- 2012/09/27 06:00 CRDT- 2012/06/06 06:00 PHST- 2012/06/06 06:00 [entrez] PHST- 2012/06/06 06:00 [pubmed] PHST- 2012/09/27 06:00 [medline] AID - 10.1007/978-1-61779-870-2_7 [doi] PST - ppublish SO - Methods Mol Biol. 2012;888:109-18. doi: 10.1007/978-1-61779-870-2_7. PMID- 22615879 OWN - NLM STAT- MEDLINE DCOM- 20130108 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 5 DP - 2012 TI - The loss of functional caspase-12 in Europe is a pre-neolithic event. PG - e37022 LID - 10.1371/journal.pone.0037022 [doi] LID - e37022 AB - BACKGROUND: Caspase-12 (CASP12) modulates the susceptibility to sepsis. In humans, the "C" allele at CASP12 rs497116 has been associated with an increased risk of sepsis. Instead, the derived "T" allele encodes for an inactive caspase-12. Interestingly, Eurasians are practically fixed for the inactive variant, whereas in Sub-Saharan Africa the active variant is still common (~24%). This marked structure has been explained as a function of the selective advantage that the inactive caspase-12 confers by increasing resistance to infection. As regards to both when positive selection started acting and as to the speed with which fixation was achieved in Eurasia, estimates depend on the method and assumptions used, and can vary substantially. Using experimental evidence, we propose that, least in Eurasia, the increase in the frequency of the T allele might be related to the selective pressure exerted by the increase in zoonotic diseases transmission caused by the interplay between increased human population densities and a closer contact with animals during the Neolithic. METHODOLOG/PRINCIPAL FINDINGS: We genotyped CASP12 rs497116 in prehistoric individuals from 6 archaeological sites from the North of the Iberian Peninsula that date from Late Upper Paleolithic to Late Neolithic. DNA extraction was done from teeth lacking cavities or breakages using standard anti-contamination procedures, including processing of the samples in a positive pressure, ancient DNA-only chamber, quantitation of DNAs by qPCR, duplication, replication, genotyping of associated animals, or cloning of PCR products. Out of 50, 24 prehistoric individuals could finally be genotyped for rs497116. Only the inactive form of CASP12 was found. CONCLUSIONS/SIGNIFICANCE: We demonstrate that the loss of caspase-12 in Europe predates animal domestication and that consequently CASP12 loss is unlikely to be related to the impact of zoonotic infections transmitted by livestock. FAU - Hervella, Montserrat AU - Hervella M AD - Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain. montse.hervella@ehu.es FAU - Plantinga, Theo S AU - Plantinga TS FAU - Alonso, Santos AU - Alonso S FAU - Ferwerda, Bart AU - Ferwerda B FAU - Izagirre, Neskuts AU - Izagirre N FAU - Fontecha, Lara AU - Fontecha L FAU - Fregel, Rosa AU - Fregel R FAU - van der Meer, Jos W M AU - van der Meer JW FAU - de-la-Rúa, Concepcion AU - de-la-Rúa C FAU - Netea, Mihai G AU - Netea MG LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120516 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - EC 3.4.22.- (CASP12 protein, human) RN - EC 3.4.22.- (Caspase 12) SB - IM MH - Alleles MH - Caspase 12/genetics/*physiology MH - Europe MH - Genetics, Population MH - Genotype MH - History, Ancient MH - Humans MH - Sepsis/enzymology/genetics PMC - PMC3353979 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2012/05/23 06:00 MHDA- 2013/01/09 06:00 PMCR- 2012/05/16 CRDT- 2012/05/23 06:00 PHST- 2011/12/16 00:00 [received] PHST- 2012/04/12 00:00 [accepted] PHST- 2012/05/23 06:00 [entrez] PHST- 2012/05/23 06:00 [pubmed] PHST- 2013/01/09 06:00 [medline] PHST- 2012/05/16 00:00 [pmc-release] AID - PONE-D-11-25359 [pii] AID - 10.1371/journal.pone.0037022 [doi] PST - ppublish SO - PLoS One. 2012;7(5):e37022. doi: 10.1371/journal.pone.0037022. Epub 2012 May 16. PMID- 22567153 OWN - NLM STAT- MEDLINE DCOM- 20120917 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 5 DP - 2012 TI - Neonate human remains: a window of opportunity to the molecular study of ancient syphilis. PG - e36371 LID - 10.1371/journal.pone.0036371 [doi] LID - e36371 AB - Ancient DNA (aDNA) analysis can be a useful tool in bacterial disease diagnosis in human remains. However, while the recovery of Mycobacterium spp. has been widely successful, several authors report unsuccessful results regarding ancient treponemal DNA, casting doubts on the usefulness of this technique for the diagnosis of ancient syphilis. Here, we present results from an analysis of four newborn specimens recovered from the crypt of "La Ermita de la Soledad" (XVI-XVII centuries), located in the province of Huelva in the southwest of Spain. We extracted and analyzed aDNA in three independent laboratories, following specific procedures generally practiced in the aDNA field, including cloning of the amplified DNA fragments and sequencing of several clones. This is the most ancient case, reported to date, from which detection of DNA from T. pallidum subspecies pallidum has been successful in more than one individual, and we put forward a hypothesis to explain this result, taking into account the course of the disease in neonate individuals. FAU - Montiel, Rafael AU - Montiel R AD - Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico. FAU - Solórzano, Eduvigis AU - Solórzano E FAU - Díaz, Nancy AU - Díaz N FAU - Álvarez-Sandoval, Brenda A AU - Álvarez-Sandoval BA FAU - González-Ruiz, Mercedes AU - González-Ruiz M FAU - Cañadas, Mari Pau AU - Cañadas MP FAU - Simões, Nelson AU - Simões N FAU - Isidro, Albert AU - Isidro A FAU - Malgosa, Assumpció AU - Malgosa A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120502 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology/methods MH - DNA, Mitochondrial/genetics MH - Humans MH - Infant, Newborn MH - Spain MH - Syphilis/*genetics PMC - PMC3342265 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2012/05/09 06:00 MHDA- 2012/09/18 06:00 PMCR- 2012/05/02 CRDT- 2012/05/09 06:00 PHST- 2011/12/22 00:00 [received] PHST- 2012/03/30 00:00 [accepted] PHST- 2012/05/09 06:00 [entrez] PHST- 2012/05/09 06:00 [pubmed] PHST- 2012/09/18 06:00 [medline] PHST- 2012/05/02 00:00 [pmc-release] AID - PONE-D-12-00631 [pii] AID - 10.1371/journal.pone.0036371 [doi] PST - ppublish SO - PLoS One. 2012;7(5):e36371. doi: 10.1371/journal.pone.0036371. Epub 2012 May 2. PMID- 22563371 OWN - NLM STAT- MEDLINE DCOM- 20120917 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 4 DP - 2012 TI - Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe. PG - e34417 LID - 10.1371/journal.pone.0034417 [doi] LID - e34417 AB - BACKGROUND/PRINCIPAL FINDINGS: The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe. METHODOLOGY/SIGNIFICANCE: Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples) and replication of the results (43% of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe. CONCLUSION: The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study) suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different impact on the various geographic regions, and thus contradicts the more simplistic total acculturation and replacement models proposed so far to explain Neolithisation. FAU - Hervella, Montserrat AU - Hervella M AD - Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Bizkaia, Spain. FAU - Izagirre, Neskuts AU - Izagirre N FAU - Alonso, Santos AU - Alonso S FAU - Fregel, Rosa AU - Fregel R FAU - Alonso, Antonio AU - Alonso A FAU - Cabrera, Vicente M AU - Cabrera VM FAU - de la Rúa, Concepción AU - de la Rúa C LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120425 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM EIN - PLoS One. 2012;7(7). doi:10.1371/annotation/3dac0b4f-f76e-4bc1-8559-acb41b87b02c MH - Agriculture MH - Archaeology MH - DNA, Mitochondrial/*genetics/history MH - Europe MH - Genetic Heterogeneity MH - Genetic Variation MH - Genetics, Population/classification MH - Haplotypes MH - History, Ancient MH - Humans MH - *Models, Theoretical MH - Phylogeny MH - Spain PMC - PMC3340892 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2012/05/09 06:00 MHDA- 2012/09/18 06:00 PMCR- 2012/04/25 CRDT- 2012/05/08 06:00 PHST- 2011/09/14 00:00 [received] PHST- 2012/02/28 00:00 [accepted] PHST- 2012/05/08 06:00 [entrez] PHST- 2012/05/09 06:00 [pubmed] PHST- 2012/09/18 06:00 [medline] PHST- 2012/04/25 00:00 [pmc-release] AID - PONE-D-11-18075 [pii] AID - 10.1371/journal.pone.0034417 [doi] PST - ppublish SO - PLoS One. 2012;7(4):e34417. doi: 10.1371/journal.pone.0034417. Epub 2012 Apr 25. PMID- 22479540 OWN - NLM STAT- MEDLINE DCOM- 20121105 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 3 DP - 2012 TI - Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PG - e34131 LID - 10.1371/journal.pone.0034131 [doi] LID - e34131 AB - DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5'-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments. FAU - Sawyer, Susanna AU - Sawyer S AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. susanna_sawyer@eva.mpg.de FAU - Krause, Johannes AU - Krause J FAU - Guschanski, Katerina AU - Guschanski K FAU - Savolainen, Vincent AU - Savolainen V FAU - Pääbo, Svante AU - Pääbo S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120330 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Composition MH - DNA/*genetics MH - DNA Damage MH - *DNA Fragmentation MH - DNA, Mitochondrial/*genetics MH - Gene Library MH - Gorilla gorilla MH - Humans MH - Paleontology/methods MH - Polymerase Chain Reaction/methods MH - Sequence Analysis, DNA MH - Time Factors PMC - PMC3316601 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2012/04/06 06:00 MHDA- 2012/11/06 06:00 PMCR- 2012/03/30 CRDT- 2012/04/06 06:00 PHST- 2011/12/14 00:00 [received] PHST- 2012/02/22 00:00 [accepted] PHST- 2012/04/06 06:00 [entrez] PHST- 2012/04/06 06:00 [pubmed] PHST- 2012/11/06 06:00 [medline] PHST- 2012/03/30 00:00 [pmc-release] AID - PONE-D-11-25055 [pii] AID - 10.1371/journal.pone.0034131 [doi] PST - ppublish SO - PLoS One. 2012;7(3):e34131. doi: 10.1371/journal.pone.0034131. Epub 2012 Mar 30. PMID- 22427842 OWN - NLM STAT- MEDLINE DCOM- 20120820 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 3 DP - 2012 TI - Complete mitochondrial genomes reveal neolithic expansion into Europe. PG - e32473 LID - 10.1371/journal.pone.0032473 [doi] LID - e32473 AB - The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available. FAU - Fu, Qiaomei AU - Fu Q AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. qiaomei_fu@eva.mpg.de FAU - Rudan, Pavao AU - Rudan P FAU - Pääbo, Svante AU - Pääbo S FAU - Krause, Johannes AU - Krause J LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120313 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/*history MH - Base Sequence MH - Bayes Theorem MH - Computational Biology MH - *Cultural Evolution MH - DNA, Mitochondrial/*genetics MH - *Demography MH - Emigration and Immigration/*history MH - Europe MH - Evolution, Molecular MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Models, Genetic MH - Molecular Sequence Data MH - *Phylogeny MH - *Population Dynamics MH - Sequence Analysis, DNA PMC - PMC3302788 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2012/03/20 06:00 MHDA- 2012/08/21 06:00 PMCR- 2012/03/13 CRDT- 2012/03/20 06:00 PHST- 2011/11/03 00:00 [received] PHST- 2012/01/31 00:00 [accepted] PHST- 2012/03/20 06:00 [entrez] PHST- 2012/03/20 06:00 [pubmed] PHST- 2012/08/21 06:00 [medline] PHST- 2012/03/13 00:00 [pmc-release] AID - PONE-D-11-22121 [pii] AID - 10.1371/journal.pone.0032473 [doi] PST - ppublish SO - PLoS One. 2012;7(3):e32473. doi: 10.1371/journal.pone.0032473. Epub 2012 Mar 13. PMID- 22307722 OWN - NLM STAT- MEDLINE DCOM- 20120327 LR - 20221207 IS - 1520-6505 (Electronic) IS - 1060-1538 (Linking) VI - 21 IP - 1 DP - 2012 Jan-Feb TI - European neolithization and ancient DNA: an assessment. PG - 24-37 LID - 10.1002/evan.20341 [doi] AB - Neolithic processes underlying the distribution of genetic diversity among European populations have been the subject of intense debate since the first genetic data became available. However, patterns observed in the current European gene pool are the outcome of Paleolithic and Neolithic processes, overlaid with four millennia of further developments. This observation encouraged paleogeneticists to contribute to the debate by directly comparing genetic variation from the ancient inhabitants of Europe to their contemporary counterparts. Pre-Neolithic and Neolithic paleogenetic data are becoming increasingly available for north and northwest European populations. Despite the numerous problems inherent in the paleogenetic approach, the accumulation of ancient DNA datasets offers new perspectives from which to interpret the interactions between hunter-gatherer and farming communities. In light of information emerging from diverse disciplines, including recent paleogenetic studies, the most plausible model explaining the movement of Neolithic pioneer groups in central Europe is that of leapfrog migration. CI - Copyright © 2012 Wiley Periodicals, Inc. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - Paleogenetic Platform, UMR PACEA, Bordeaux University. mf.deguilloux@pacea.u-bordeaux1.fr FAU - Leahy, Rachael AU - Leahy R FAU - Pemonge, Marie-Hélène AU - Pemonge MH FAU - Rottier, Stéphane AU - Rottier S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Evol Anthropol JT - Evolutionary anthropology JID - 9306331 RN - 9007-49-2 (DNA) SB - IM MH - Agriculture MH - Anthropology, Physical MH - DNA/*genetics MH - *Emigration and Immigration MH - Humans MH - *Phylogeography MH - White People/*genetics EDAT- 2012/02/07 06:00 MHDA- 2012/03/28 06:00 CRDT- 2012/02/07 06:00 PHST- 2012/02/07 06:00 [entrez] PHST- 2012/02/07 06:00 [pubmed] PHST- 2012/03/28 06:00 [medline] AID - 10.1002/evan.20341 [doi] PST - ppublish SO - Evol Anthropol. 2012 Jan-Feb;21(1):24-37. doi: 10.1002/evan.20341. PMID- 22237515 OWN - NLM STAT- MEDLINE DCOM- 20120502 LR - 20120112 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 840 DP - 2012 TI - Setting up an ancient DNA laboratory. PG - 1-11 LID - 10.1007/978-1-61779-516-9_1 [doi] AB - Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential for contamination of ancient samples and DNA extracts with modern DNA is considerable. To minimize the risk associated with working with ancient DNA, experimental protocols specific to handling ancient specimens have been introduced. Here, I outline the challenges associated with working with ancient DNA and describe guidelines for setting up a new ancient DNA laboratory. I also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination with exogenous sources of DNA. FAU - Fulton, Tara L AU - Fulton TL AD - Department of Biology, The Pennsylvania State University, 320 Mueller Laboratory, University Park, PA 16802, USA. tlf19@psu.edu LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *DNA/chemistry/genetics/isolation & purification MH - Fossils MH - *Genetic Techniques MH - Humans MH - *Laboratories MH - Paleontology/*methods EDAT- 2012/01/13 06:00 MHDA- 2012/05/04 06:00 CRDT- 2012/01/13 06:00 PHST- 2012/01/13 06:00 [entrez] PHST- 2012/01/13 06:00 [pubmed] PHST- 2012/05/04 06:00 [medline] AID - 10.1007/978-1-61779-516-9_1 [doi] PST - ppublish SO - Methods Mol Biol. 2012;840:1-11. doi: 10.1007/978-1-61779-516-9_1. PMID- 22117930 OWN - NLM STAT- MEDLINE DCOM- 20120412 LR - 20111220 IS - 1365-294X (Electronic) IS - 0962-1083 (Linking) VI - 21 IP - 1 DP - 2012 Jan TI - Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers. PG - 45-56 LID - 10.1111/j.1365-294X.2011.05361.x [doi] AB - The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations-N* and X1-are found at higher frequencies in our Early Neolithic population (∼31%). Genetic differentiation between Early and Middle Neolithic populations was significant (F(ST) ∼0.13, P<10(-5)), suggesting that genetic drift played an important role at this time. To improve our understanding of the Neolithic demographic processes, we used a Bayesian coalescence-based simulation approach to identify the most likely of three demographic scenarios that might explain the genetic data. The three scenarios were chosen to reflect archaeological knowledge and previous genetic studies using similar inferential approaches. We found that models that ignore population structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East. CI - © 2011 Blackwell Publishing Ltd. FAU - Gamba, C AU - Gamba C AD - Laboratorio de Genética Forense y Genética de Poblaciones, Facultad de Medicina, Pabellón 7, 4ª Planta, Universidad Complutense de Madrid, Avenida Complutense s/n, 28040 Madrid, Spain. cristinagamba@med.ucm.es FAU - Fernández, E AU - Fernández E FAU - Tirado, M AU - Tirado M FAU - Deguilloux, M F AU - Deguilloux MF FAU - Pemonge, M H AU - Pemonge MH FAU - Utrilla, P AU - Utrilla P FAU - Edo, M AU - Edo M FAU - Molist, M AU - Molist M FAU - Rasteiro, R AU - Rasteiro R FAU - Chikhi, L AU - Chikhi L FAU - Arroyo-Pardo, E AU - Arroyo-Pardo E LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111125 PL - England TA - Mol Ecol JT - Molecular ecology JID - 9214478 RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/history MH - Archaeology MH - DNA, Mitochondrial/genetics/*history MH - Genetic Drift MH - Haplotypes/*genetics MH - History, Ancient MH - Humans MH - Middle East MH - Phylogeography/history MH - Spain EDAT- 2011/11/29 06:00 MHDA- 2012/04/13 06:00 CRDT- 2011/11/29 06:00 PHST- 2011/11/29 06:00 [entrez] PHST- 2011/11/29 06:00 [pubmed] PHST- 2012/04/13 06:00 [medline] AID - 10.1111/j.1365-294X.2011.05361.x [doi] PST - ppublish SO - Mol Ecol. 2012 Jan;21(1):45-56. doi: 10.1111/j.1365-294X.2011.05361.x. Epub 2011 Nov 25. PMID- 21968286 OWN - NLM STAT- MEDLINE DCOM- 20120620 LR - 20221207 IS - 1662-8128 (Electronic) IS - 1662-811X (Print) IS - 1662-811X (Linking) VI - 4 IP - 2 DP - 2012 TI - The evolutionary history of TLR4 polymorphisms in Europe. PG - 168-75 LID - 10.1159/000329492 [doi] AB - Infections exert important evolutionary pressures shaping the human genome, especially on genes involved in host defense. A crucial step for host defense is recognition of pathogens by pattern recognition receptors on innate immune cells, among which Toll-like receptor 4 (TLR4) is one of the best known. Genetic variation in TLR4 (Asp299Gly, Thr399Ile) has been recently described. Haplotype frequencies of these polymorphisms differ among African, Asian and European populations, suggesting evolutionary pressures exerted by local infections. The TLR4 299Gly/399Ile haplotype, characteristic mainly of European populations, has relatively high frequency in the Iberian peninsula. This region is also described as refuge area during the last glacial maximum 20,000 years ago, from which repopulation of Europe took place. We speculate that a genetic bottleneck in the Iberian peninsula could have promoted the increased frequency of this haplotype by genetic drift. This hypothesis is supported by three arguments: (1) the West-East gradient of prevalence in the haplotype among European populations; (2) ancient DNA from Neolithic burials in the Iberian peninsula, dated 6,600-4,500 years before present, confirmed the relatively high frequency of this haplotype in the region, and (3) no functional differences between this haplotype and wild-type TLR4 have been found. In contrast, the disappearance of the 299Gly/399Thr haplotype in Europe is most likely due to negative selection due to sepsis. In conclusion, differences in distribution of TLR4 polymorphisms Asp299Gly and Thr399Ile in European populations are most likely due to a combination of population migration events combined with selection due to sepsis. CI - Copyright © 2012 S. Karger AG, Basel. FAU - Plantinga, Theo S AU - Plantinga TS AD - Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands. FAU - Ioana, Mihai AU - Ioana M FAU - Alonso, Santos AU - Alonso S FAU - Izagirre, Neskuts AU - Izagirre N FAU - Hervella, Montserrat AU - Hervella M FAU - Joosten, Leo A B AU - Joosten LA FAU - van der Meer, Jos W M AU - van der Meer JW FAU - de la Rúa, Concepcion AU - de la Rúa C FAU - Netea, Mihai G AU - Netea MG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110930 PL - Switzerland TA - J Innate Immun JT - Journal of innate immunity JID - 101469471 RN - 0 (TLR4 protein, human) RN - 0 (Toll-Like Receptor 4) SB - IM MH - Europe MH - *Evolution, Molecular MH - Genetic Drift MH - Genetic Predisposition to Disease MH - Haplotypes MH - Humans MH - Immunity, Innate/*genetics MH - *Polymorphism, Single Nucleotide MH - Toll-Like Receptor 4/*genetics MH - White People/genetics PMC - PMC6741577 EDAT- 2011/10/05 06:00 MHDA- 2012/06/21 06:00 PMCR- 2011/09/30 CRDT- 2011/10/05 06:00 PHST- 2011/05/13 00:00 [received] PHST- 2011/05/13 00:00 [accepted] PHST- 2011/10/05 06:00 [entrez] PHST- 2011/10/05 06:00 [pubmed] PHST- 2012/06/21 06:00 [medline] PHST- 2011/09/30 00:00 [pmc-release] AID - 000329492 [pii] AID - jin-0004-0168 [pii] AID - 10.1159/000329492 [doi] PST - ppublish SO - J Innate Immun. 2012;4(2):168-75. doi: 10.1159/000329492. Epub 2011 Sep 30. PMID- 22192823 OWN - NLM STAT- MEDLINE DCOM- 20120419 LR - 20111223 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 21 IP - 24 DP - 2011 Dec 20 TI - Paleogenomics of archaic hominins. PG - R1002-9 LID - 10.1016/j.cub.2011.11.021 [doi] AB - In order to understand the genetic basis for the evolutionary success of modern humans, it is necessary to compare their genetic makeup to that of closely related species. Unfortunately, our closest living relatives, the chimpanzees, are evolutionarily quite distant. With the advent of ancient DNA study and more recently paleogenomics - the study of the genomes of ancient organisms - it has become possible to compare human genomes to those of much more closely related groups. Our closest known relatives are the Neanderthals, which evolved and lived in Europe and Western Asia, from about 600,000 years ago until their disappearance around 30,000 years ago following the expansion of anatomically modern humans into their range. The closely related Denisovans are only known by virtue of their DNA, which has been extracted from bone fragments dating around 30,000 to 50,000 years ago found in a single Siberian cave. Analyses of Neanderthal and Denisovan nuclear and mitochondrial genomes have revealed surprising insights into these archaic humans as well as our own species. The genomes provide a preliminary catalogue of derived amino acids that are specific to all extant modern humans, thus offering insights into the functional differences between the three lineages. In addition, the genomes provide evidence of gene flow between the three lineages after anatomically modern humans left Africa, drastically changing our view of human evolution. CI - Copyright © 2011 Elsevier Ltd. All rights reserved. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C AD - Institute of Evolutionary Biology, 08003 Barcelona, Spain. carles.lalueza@upf.edu FAU - Gilbert, M Thomas P AU - Gilbert MT LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - *Biological Evolution MH - Cell Nucleus/genetics MH - DNA, Mitochondrial/genetics MH - Demography MH - *Evolution, Molecular MH - Fossils MH - Gene Flow MH - Genetic Variation MH - Genome, Human MH - Hominidae/anatomy & histology/*genetics/physiology MH - Humans/anatomy & histology/genetics/physiology MH - Neanderthals/anatomy & histology/*genetics/physiology MH - Phylogeny MH - Species Specificity EDAT- 2011/12/24 06:00 MHDA- 2012/04/20 06:00 CRDT- 2011/12/24 06:00 PHST- 2011/12/24 06:00 [entrez] PHST- 2011/12/24 06:00 [pubmed] PHST- 2012/04/20 06:00 [medline] AID - S0960-9822(11)01270-X [pii] AID - 10.1016/j.cub.2011.11.021 [doi] PST - ppublish SO - Curr Biol. 2011 Dec 20;21(24):R1002-9. doi: 10.1016/j.cub.2011.11.021. PMID- 21990065 OWN - NLM STAT- MEDLINE DCOM- 20120126 LR - 20111108 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 146 IP - 4 DP - 2011 Dec TI - High genetic diversity on a sample of pre-Columbian bone remains from Guane territories in northwestern Colombia. PG - 637-49 LID - 10.1002/ajpa.21626 [doi] AB - Ancient DNA was recovered from 17 individuals found in a rock shelter in the district of "La Purnia" (Santander, Colombia). This region is the homeland of pre-Columbian Guane, whom spread over the "Río Suarez" to the "Río de Oro", and were surrounded to the west by the Central Andes, south and east by foothills of Eastern Andes, and north by the "Chicamocha" river canyon. Guanes established in a region that straddles the Andes and the northern Amazon basin, possibly making it an unavoidable conduit for people moving to and from South America. We amplified mtDNA hypervariable region I (HVI) segments from ancient bone remains, and the resulting sequences were compared with both ancient and modern mitochondrial haplogroups from American and non-American populations. Samples showed a distribution of 35% for haplogroup A, 41% for haplogroup B and 24% for haplogroup D. Nine haplotypes were found in 17 samples, indicating an unusually high genetic diversity on a single site ancient population. Among them, three haplotypes have not been previously found in America, two are shared in Asia, and one is a private haplotype. Despite geographical barriers that eventually isolated them, an important influence of gene flow from neighboring pre-Columbian communities, mainly Muiscas, could explain the high genetic polymorphism of this community before the Spanish conquest, and argues against Guanes as being a genetic isolate. CI - 2011 Wiley Periodicals, Inc. FAU - Casas-Vargas, Andrea AU - Casas-Vargas A AD - Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia. FAU - Gómez, Alberto AU - Gómez A FAU - Briceño, Ignacio AU - Briceño I FAU - Díaz-Matallana, Marcela AU - Díaz-Matallana M FAU - Bernal, Jaime E AU - Bernal JE FAU - Rodríguez, José Vicente AU - Rodríguez JV LA - eng PT - Historical Article PT - Journal Article DEP - 20111012 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Americas MH - Anthropology, Physical MH - Bone and Bones/*chemistry MH - Colombia MH - DNA, Mitochondrial/analysis/*genetics MH - Emigration and Immigration MH - *Genetic Variation MH - Haplotypes MH - History, Medieval MH - Humans MH - Indians, South American/*genetics/history MH - Phylogeography MH - Principal Component Analysis EDAT- 2011/10/13 06:00 MHDA- 2012/01/27 06:00 CRDT- 2011/10/13 06:00 PHST- 2011/04/02 00:00 [received] PHST- 2011/08/30 00:00 [accepted] PHST- 2011/10/13 06:00 [entrez] PHST- 2011/10/13 06:00 [pubmed] PHST- 2012/01/27 06:00 [medline] AID - 10.1002/ajpa.21626 [doi] PST - ppublish SO - Am J Phys Anthropol. 2011 Dec;146(4):637-49. doi: 10.1002/ajpa.21626. Epub 2011 Oct 12. PMID- 21938002 OWN - NLM STAT- MEDLINE DCOM- 20120727 LR - 20221207 IS - 1435-232X (Electronic) IS - 1434-5161 (Linking) VI - 56 IP - 12 DP - 2011 Dec TI - Genetic characteristics and migration history of a bronze culture population in the West Liao-River valley revealed by ancient DNA. PG - 815-22 LID - 10.1038/jhg.2011.102 [doi] AB - In order to study the genetic characteristics of the Lower Xiajiadian culture (LXC) population, a main bronze culture branch in northern China dated 4500-3500 years ago, two uniparentally inherited markers, mitochondrial DNA and Y-chromosome single-nucleotide polymorphisms (Y-SNPs), were analyzed on 14 human remains excavated from the Dadianzi site. The 14 sequences, which contained 13 haplotypes, were assigned to 9 haplogroups, and Y-SNP typing of 5 male individuals assigned them to haplogroups N (M231) and O3 (M122). The results indicate that the LXC population mainly included people carrying haplogroups from northern Asia who had lived in this region since the Neolithic period, as well as genetic evidence of immigration from the Central Plain. Later in the Bronze Age, part of the population migrated to the south away from a cooler climate, which ultimately influenced the gene pool in the Central Plain. Thus, climate change is an important factor, which drove the population migration during the Bronze Age in northern China. Based on these results, the local genetic continuity did not seem to be affected by outward migration, although more data are needed especially from other ancient populations to determine the influence of return migration on genetic continuity. FAU - Li, Hongjie AU - Li H AD - College of Life Science, Jilin University, Changchun, PR China. FAU - Zhao, Xin AU - Zhao X FAU - Zhao, Yongbin AU - Zhao Y FAU - Li, Chunxiang AU - Li C FAU - Si, Dayong AU - Si D FAU - Zhou, Hui AU - Zhou H FAU - Cui, Yinqiu AU - Cui Y LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110922 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Asian People/*genetics/history MH - China MH - Chromosomes, Human, Y MH - DNA/chemistry MH - DNA, Mitochondrial/chemistry MH - Emigration and Immigration/*history MH - Female MH - Geography MH - History, Ancient MH - Humans MH - Male MH - Polymorphism, Single Nucleotide MH - Population/genetics MH - Sequence Analysis, DNA EDAT- 2011/09/23 06:00 MHDA- 2012/07/28 06:00 CRDT- 2011/09/23 06:00 PHST- 2011/09/23 06:00 [entrez] PHST- 2011/09/23 06:00 [pubmed] PHST- 2012/07/28 06:00 [medline] AID - jhg2011102 [pii] AID - 10.1038/jhg.2011.102 [doi] PST - ppublish SO - J Hum Genet. 2011 Dec;56(12):815-22. doi: 10.1038/jhg.2011.102. Epub 2011 Sep 22. PMID- 21913177 OWN - NLM STAT- MEDLINE DCOM- 20120126 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 146 IP - 4 DP - 2011 Dec TI - Ancient DNA perspectives on American colonization and population history. PG - 503-14 LID - 10.1002/ajpa.21594 [doi] AB - Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history. CI - 2011 Wiley Periodicals, Inc. FAU - Raff, Jennifer A AU - Raff JA AD - Department of Anthropology, University of Utah, Salt Lake City, UT, USA. jenny@northwestern.edu FAU - Bolnick, Deborah A AU - Bolnick DA FAU - Tackney, Justin AU - Tackney J FAU - O'Rourke, Dennis H AU - O'Rourke DH LA - eng PT - Historical Article PT - Journal Article PT - Review DEP - 20110913 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - American Indian or Alaska Native/*genetics/*history MH - Americas MH - Analysis of Variance MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration/*history MH - Haplotypes MH - History, 21st Century MH - History, Ancient MH - Humans MH - Polymorphism, Single Nucleotide MH - Principal Component Analysis EDAT- 2011/09/14 06:00 MHDA- 2012/01/27 06:00 CRDT- 2011/09/14 06:00 PHST- 2011/03/25 00:00 [received] PHST- 2011/07/07 00:00 [accepted] PHST- 2011/09/14 06:00 [entrez] PHST- 2011/09/14 06:00 [pubmed] PHST- 2012/01/27 06:00 [medline] AID - 10.1002/ajpa.21594 [doi] PST - ppublish SO - Am J Phys Anthropol. 2011 Dec;146(4):503-14. doi: 10.1002/ajpa.21594. Epub 2011 Sep 13. PMID- 22042855 OWN - NLM STAT- MEDLINE DCOM- 20120125 LR - 20211020 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 108 IP - 45 DP - 2011 Nov 8 TI - Ancient DNA suggests the leading role played by men in the Neolithic dissemination. PG - 18255-9 LID - 10.1073/pnas.1113061108 [doi] AB - The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a "multimarkers" approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated. FAU - Lacan, Marie AU - Lacan M AD - Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5288, 31073 Toulouse, France. lacan.marie@netcourrier.com FAU - Keyser, Christine AU - Keyser C FAU - Ricaut, François-Xavier AU - Ricaut FX FAU - Brucato, Nicolas AU - Brucato N FAU - Tarrús, Josep AU - Tarrús J FAU - Bosch, Angel AU - Bosch A FAU - Guilaine, Jean AU - Guilaine J FAU - Crubézy, Eric AU - Crubézy E FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Historical Article PT - Journal Article DEP - 20111031 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 9007-49-2 (DNA) SB - IM MH - Cell Nucleus/genetics MH - Chromosomes, Human, Y MH - DNA/*genetics MH - *Fossils MH - History, Ancient MH - Humans MH - Male MH - Mitochondria/genetics MH - *Role PMC - PMC3215063 COIS- The authors declare no conflict of interest. EDAT- 2011/11/02 06:00 MHDA- 2012/01/26 06:00 PMCR- 2012/05/08 CRDT- 2011/11/02 06:00 PHST- 2011/11/02 06:00 [entrez] PHST- 2011/11/02 06:00 [pubmed] PHST- 2012/01/26 06:00 [medline] PHST- 2012/05/08 00:00 [pmc-release] AID - 1113061108 [pii] AID - 201113061 [pii] AID - 10.1073/pnas.1113061108 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18255-9. doi: 10.1073/pnas.1113061108. Epub 2011 Oct 31. PMID- 21953438 OWN - NLM STAT- MEDLINE DCOM- 20120106 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 146 IP - 3 DP - 2011 Nov TI - Mitochondrial DNA analysis of Hokkaido Jomon skeletons: remnants of archaic maternal lineages at the southwestern edge of former Beringia. PG - 346-60 LID - 10.1002/ajpa.21561 [doi] AB - To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present. CI - Copyright © 2011 Wiley-Liss, Inc. FAU - Adachi, Noboru AU - Adachi N AD - Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi, Japan. nadachi@yamanashi.ac.jp FAU - Shinoda, Ken-ichi AU - Shinoda K FAU - Umetsu, Kazuo AU - Umetsu K FAU - Kitano, Takashi AU - Kitano T FAU - Matsumura, Hirofumi AU - Matsumura H FAU - Fujiyama, Ryuzo AU - Fujiyama R FAU - Sawada, Junmei AU - Sawada J FAU - Tanaka, Masashi AU - Tanaka M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110927 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - *Asian People MH - Bone and Bones/chemistry MH - DNA, Mitochondrial/*analysis MH - Genetics, Population MH - Haplotypes MH - Humans MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Reproducibility of Results MH - Siberia MH - *Skeleton MH - Tooth/chemistry EDAT- 2011/09/29 06:00 MHDA- 2012/01/10 06:00 CRDT- 2011/09/29 06:00 PHST- 2010/10/13 00:00 [received] PHST- 2011/04/26 00:00 [revised] PHST- 2011/09/29 06:00 [entrez] PHST- 2011/09/29 06:00 [pubmed] PHST- 2012/01/10 06:00 [medline] AID - 10.1002/ajpa.21561 [doi] PST - ppublish SO - Am J Phys Anthropol. 2011 Nov;146(3):346-60. doi: 10.1002/ajpa.21561. Epub 2011 Sep 27. PMID- 21993626 OWN - NLM STAT- MEDLINE DCOM- 20120126 LR - 20220317 IS - 1476-4687 (Electronic) IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 478 IP - 7370 DP - 2011 Oct 12 TI - A draft genome of Yersinia pestis from victims of the Black Death. PG - 506-10 LID - 10.1038/nature10549 [doi] AB - Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348-1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347-1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections. FAU - Bos, Kirsten I AU - Bos KI AD - McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada. FAU - Schuenemann, Verena J AU - Schuenemann VJ FAU - Golding, G Brian AU - Golding GB FAU - Burbano, Hernán A AU - Burbano HA FAU - Waglechner, Nicholas AU - Waglechner N FAU - Coombes, Brian K AU - Coombes BK FAU - McPhee, Joseph B AU - McPhee JB FAU - DeWitte, Sharon N AU - DeWitte SN FAU - Meyer, Matthias AU - Meyer M FAU - Schmedes, Sarah AU - Schmedes S FAU - Wood, James AU - Wood J FAU - Earn, David J D AU - Earn DJ FAU - Herring, D Ann AU - Herring DA FAU - Bauer, Peter AU - Bauer P FAU - Poinar, Hendrik N AU - Poinar HN FAU - Krause, Johannes AU - Krause J LA - eng GR - R24 HD044943/HD/NICHD NIH HHS/United States GR - CAPMC/CIHR/Canada PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111012 PL - England TA - Nature JT - Nature JID - 0410462 SB - IM EIN - Nature. 2011 Dec 8;480(7376):278 CIN - Nature. 2011 Oct 26;478(7370):465-6. doi: 10.1038/478465a. PMID: 22031436 MH - Chromosomes, Bacterial/genetics MH - Contig Mapping MH - Dental Pulp/microbiology MH - Evolution, Molecular MH - Genome, Bacterial/*genetics MH - History, Medieval MH - Humans MH - London/epidemiology MH - Molecular Sequence Data MH - Phylogeny MH - Plague/epidemiology/*microbiology/transmission MH - Plasmids/genetics MH - Sequence Alignment MH - Sequence Analysis, DNA MH - Virulence/genetics MH - Yersinia pestis/classification/*genetics/*isolation & purification PMC - PMC3690193 MID - NIHMS478452 EDAT- 2011/10/14 06:00 MHDA- 2012/01/27 06:00 PMCR- 2013/06/23 CRDT- 2011/10/14 06:00 PHST- 2011/07/25 00:00 [received] PHST- 2011/09/09 00:00 [accepted] PHST- 2011/10/14 06:00 [entrez] PHST- 2011/10/14 06:00 [pubmed] PHST- 2012/01/27 06:00 [medline] PHST- 2013/06/23 00:00 [pmc-release] AID - nature10549 [pii] AID - 10.1038/nature10549 [doi] PST - epublish SO - Nature. 2011 Oct 12;478(7370):506-10. doi: 10.1038/nature10549. PMID- 21658464 OWN - NLM STAT- MEDLINE DCOM- 20111216 LR - 20221207 IS - 1769-714X (Electronic) IS - 1286-4579 (Linking) VI - 13 IP - 11 DP - 2011 Oct TI - Multiple loci variable number tandem repeat (VNTR) analysis (MLVA) of Mycobacterium leprae isolates amplified from European archaeological human remains with lepromatous leprosy. PG - 923-9 LID - 10.1016/j.micinf.2011.05.003 [doi] AB - Molecular typing methods based on polymorphisms in single nucleotides and short tandem repeat motifs have been developed as epidemiological typing tools for Mycobacterium leprae. We have used a variable number tandem repeat method based on three variable loci to identify strain variation in archaeological cases of lepromatous leprosy. The panel of polymorphic loci used revealed unique profiles in five cases of leprosy, including those with identical SNP type and subtype. These were also different from profiles of three previously studied lepromatous skeletons. Whilst examination with SNP typing provides evidence for disease origins, dissemination and phylogeny, tandem repeat typing may be useful for studying cases from within a defined area or community where SNP types may be identical due to geographical constraints. We envisage the technique may be useful in studying contemporaneous burials such as those associated with leprosaria and will prove invaluable in authentication of ancient DNA analyses. CI - Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved. FAU - Taylor, G Michael AU - Taylor GM AD - Department of Microbial Sciences, Faculty of Health and Medical Sciences, AW Building, University of Surrey, Guildford, Surrey GU27TE, UK. gm.taylor@surrey.ac.uk FAU - Donoghue, Helen D AU - Donoghue HD LA - eng PT - Journal Article DEP - 20110527 PL - France TA - Microbes Infect JT - Microbes and infection JID - 100883508 SB - IM MH - Adult MH - Archaeology/*methods MH - Child MH - Female MH - Humans MH - Leprosy, Lepromatous/*microbiology MH - Male MH - Middle Aged MH - *Minisatellite Repeats MH - *Molecular Typing MH - Mycobacterium leprae/*classification/*genetics MH - Polymorphism, Genetic MH - *White People EDAT- 2011/06/11 06:00 MHDA- 2011/12/17 06:00 CRDT- 2011/06/11 06:00 PHST- 2011/02/10 00:00 [received] PHST- 2011/05/06 00:00 [revised] PHST- 2011/05/10 00:00 [accepted] PHST- 2011/06/11 06:00 [entrez] PHST- 2011/06/11 06:00 [pubmed] PHST- 2011/12/17 06:00 [medline] AID - S1286-4579(11)00123-7 [pii] AID - 10.1016/j.micinf.2011.05.003 [doi] PST - ppublish SO - Microbes Infect. 2011 Oct;13(11):923-9. doi: 10.1016/j.micinf.2011.05.003. Epub 2011 May 27. PMID- 21834072 OWN - NLM STAT- MEDLINE DCOM- 20120214 LR - 20111118 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 146 IP - 1 DP - 2011 Sep TI - Brief communication: Conjoined twins at angel mounds? an ancient DNA perspective. PG - 138-42 LID - 10.1002/ajpa.21557 [doi] AB - Conjoined twins are born when a single fertilized egg partially splits into two fetuses. A hypothetical case of infant conjoined twins from Angel Mounds, a Middle Mississippian site (A.D. 1050-1400) on the Ohio River near Evansville, Indiana, was discovered in 1941. Morphological analysis does not rule out the field interpretation of this double burial as twins. Ancient mitochondrial DNA recovered from both infants demonstrates that they were not maternal relatives, and hence that they cannot have been conjoined twins. CI - 2011 Wiley-Liss, Inc. FAU - Marshall, Charla AU - Marshall C AD - Department of Anthropology, Indiana University-Bloomington, Bloomington, IN 47405, USA. ckmccorm@umail.iu.edu FAU - Tench, Patricia A AU - Tench PA FAU - Cook, Della Collins AU - Cook DC FAU - Kaestle, Frederika A AU - Kaestle FA LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - *Anthropology, Physical MH - Burial/*history MH - DNA, Mitochondrial/*genetics MH - Femur MH - Haplotypes MH - History, Medieval MH - Humans MH - Indiana MH - Infant MH - *Twins, Conjoined EDAT- 2011/08/13 06:00 MHDA- 2012/02/15 06:00 CRDT- 2011/08/12 06:00 PHST- 2011/08/12 06:00 [entrez] PHST- 2011/08/13 06:00 [pubmed] PHST- 2012/02/15 06:00 [medline] AID - 10.1002/ajpa.21557 [doi] PST - ppublish SO - Am J Phys Anthropol. 2011 Sep;146(1):138-42. doi: 10.1002/ajpa.21557. PMID- 21732320 OWN - NLM STAT- MEDLINE DCOM- 20120214 LR - 20111118 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 146 IP - 1 DP - 2011 Sep TI - Modeling neolithic dispersal in central Europe: demographic implications. PG - 104-15 LID - 10.1002/ajpa.21572 [doi] AB - On the basis of new examination of ancient DNA and craniometric analyses, Neolithic dispersal in Central Europe has been recently explained as reflecting colonization or at least a major influx of near eastern farmers. Given the fact that Neolithic dispersal in Central Europe was very rapid and extended into a large area, colonization would have to be associated with high population growth and fertility rates of an expanding Neolithic population. We built three demographic models to test whether the growth and fertility rates of Neolithic farmers were high enough to allow them to colonize Central Europe without admixture with foragers. The principle of the models is based on stochastic population projections. Our results demonstrate that colonization is an unlikely explanation for the Neolithic dispersal in Central Europe, as the majority of fertility and growth rate estimates obtained in all three models are higher than levels expected in the early Neolithic population. On the basis of our models, we derived that colonization would be possible only if (1) more than 37% of women survived to mean age at childbearing, (2) Neolithic expansion in Central Europe lasted more than 150 years, and (3) the population of farmers grew in the entire settled area. These settings, however, represent very favorable demographic conditions that seem unlikely given current archaeological and demographic evidence. Therefore, our results support the view that Neolithic dispersal in Central Europe involved admixture of expanding farmers with local foragers. We estimate that the admixture contribution from foragers may have been between 55% and 72%. CI - 2011 Wiley-Liss, Inc. FAU - Galeta, Patrik AU - Galeta P AD - Department of Anthropology, University of West Bohemia, 306 14 Pilsen, Czech Republic. galeta@sci.muni.cz FAU - Sládek, Vladimír AU - Sládek V FAU - Sosna, Daniel AU - Sosna D FAU - Bruzek, Jaroslav AU - Bruzek J LA - eng PT - Historical Article PT - Journal Article PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 9007-49-2 (DNA) SB - IM MH - Agriculture MH - Anthropology, Physical MH - Cephalometry MH - DNA/analysis/genetics MH - *Emigration and Immigration MH - Europe MH - Female MH - History, Ancient MH - Humans MH - *Models, Biological MH - Parity MH - Population Dynamics/*history MH - Regression Analysis MH - Stochastic Processes MH - Survival Analysis EDAT- 2011/07/07 06:00 MHDA- 2012/02/15 06:00 CRDT- 2011/07/07 06:00 PHST- 2011/07/07 06:00 [entrez] PHST- 2011/07/07 06:00 [pubmed] PHST- 2012/02/15 06:00 [medline] AID - 10.1002/ajpa.21572 [doi] PST - ppublish SO - Am J Phys Anthropol. 2011 Sep;146(1):104-15. doi: 10.1002/ajpa.21572. PMID- 21833062 OWN - NLM STAT- MEDLINE DCOM- 20110916 LR - 20211020 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 476 IP - 7359 DP - 2011 Aug 9 TI - Ancient DNA reveals secrets of human history. PG - 136-7 LID - 10.1038/476136a [doi] FAU - Callaway, Ewen AU - Callaway E LA - eng PT - News DEP - 20110809 PL - England TA - Nature JT - Nature JID - 0410462 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*analysis/*genetics MH - Genetic Predisposition to Disease MH - Genome, Human/*genetics MH - Genomics MH - Hominidae/genetics/physiology MH - Humans MH - *Phylogeny MH - *Phylogeography EDAT- 2011/08/13 06:00 MHDA- 2011/09/17 06:00 CRDT- 2011/08/12 06:00 PHST- 2011/08/12 06:00 [entrez] PHST- 2011/08/13 06:00 [pubmed] PHST- 2011/09/17 06:00 [medline] AID - 476136a [pii] AID - 10.1038/476136a [doi] PST - epublish SO - Nature. 2011 Aug 9;476(7359):136-7. doi: 10.1038/476136a. PMID- 21753768 OWN - NLM STAT- MEDLINE DCOM- 20120125 LR - 20110825 IS - 1435-232X (Electronic) IS - 1434-5161 (Linking) VI - 56 IP - 8 DP - 2011 Aug TI - Genetic features of ancient West Siberian people of the Middle Ages, revealed by mitochondrial DNA haplogroup analysis. PG - 602-8 LID - 10.1038/jhg.2011.68 [doi] AB - In order to investigate the genetic features of ancient West Siberian people of the Middle Ages, we studied ancient DNA from bone remains excavated from two archeological sites in West Siberia: Saigatinsky 6 (eighth to eleventh centuries) and Zeleny Yar (thirteenth century). Polymerase chain reaction amplification and nucleotide sequencing of mitochondrial DNA (mtDNA) succeeded for 9 of 67 specimens examined, and the sequences were assigned to mtDNA haplogroups B4, C4, G2, H and U. This distribution pattern of mtDNA haplogroups in medieval West Siberian people was similar to those previously reported in modern populations living in West Siberia, such as the Mansi, Ket and Nganasan. Exact tests of population differentiation showed no significant differences between the medieval people and modern populations in West Siberia. The findings suggest that some medieval West Siberian people analyzed in the present study are included in direct ancestral lineages of modern populations native to West Siberia. FAU - Sato, Takehiro AU - Sato T AD - Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Kita-ku, Sapporo, Japan. FAU - Razhev, Dmitry AU - Razhev D FAU - Amano, Tetsuya AU - Amano T FAU - Masuda, Ryuichi AU - Masuda R LA - eng SI - GENBANK/AB598647 SI - GENBANK/AB598648 SI - GENBANK/AB598649 SI - GENBANK/AB598650 SI - GENBANK/AB598651 SI - GENBANK/AB598652 SI - GENBANK/AB598653 SI - GENBANK/AB598654 SI - GENBANK/AB598655 SI - GENBANK/AB598656 SI - GENBANK/AB598657 SI - GENBANK/AB598658 SI - GENBANK/AB598659 SI - GENBANK/AB598660 SI - GENBANK/AB598661 SI - GENBANK/AB598662 SI - GENBANK/AB598663 SI - GENBANK/AB598664 SI - GENBANK/AB598665 SI - GENBANK/AB598666 SI - GENBANK/AB598667 SI - GENBANK/AB598668 SI - GENBANK/AB598669 SI - GENBANK/AB598670 SI - GENBANK/AB598671 SI - GENBANK/AB598672 SI - GENBANK/AB598673 SI - GENBANK/AB598674 SI - GENBANK/AB598675 SI - GENBANK/AB598676 SI - GENBANK/AB598677 SI - GENBANK/AB598678 SI - GENBANK/AB598679 SI - GENBANK/AB598680 SI - GENBANK/AB598681 SI - GENBANK/AB598682 SI - GENBANK/AB598683 SI - GENBANK/AB598684 SI - GENBANK/AB598685 SI - GENBANK/AB598686 SI - GENBANK/AB598687 SI - GENBANK/AB598688 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110714 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology/methods MH - DNA, Mitochondrial/chemistry/classification/*genetics MH - Genetic Variation MH - Genetics, Population/*methods MH - Geography MH - Haplotypes/*genetics MH - Humans MH - Molecular Sequence Data MH - *Phylogeny MH - Polymerase Chain Reaction MH - Principal Component Analysis MH - Sequence Analysis, DNA MH - Siberia EDAT- 2011/07/15 06:00 MHDA- 2012/01/26 06:00 CRDT- 2011/07/15 06:00 PHST- 2011/07/15 06:00 [entrez] PHST- 2011/07/15 06:00 [pubmed] PHST- 2012/01/26 06:00 [medline] AID - jhg201168 [pii] AID - 10.1038/jhg.2011.68 [doi] PST - ppublish SO - J Hum Genet. 2011 Aug;56(8):602-8. doi: 10.1038/jhg.2011.68. Epub 2011 Jul 14. PMID- 21659319 OWN - NLM STAT- MEDLINE DCOM- 20111007 LR - 20181201 IS - 1367-4811 (Electronic) IS - 1367-4803 (Linking) VI - 27 IP - 15 DP - 2011 Aug 1 TI - mapDamage: testing for damage patterns in ancient DNA sequences. PG - 2153-5 LID - 10.1093/bioinformatics/btr347 [doi] AB - SUMMARY: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences. AVAILABILITY AND IMPLEMENTATION: The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems. FAU - Ginolhac, Aurelien AU - Ginolhac A AD - Centre for Geogenetics, Natural History Museum of Denmark, Copenhagen University, 1350 København K, Denmark. aginolhac@snm.ku.dk FAU - Rasmussen, Morten AU - Rasmussen M FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Willerslev, Eske AU - Willerslev E FAU - Orlando, Ludovic AU - Orlando L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110609 PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - EC 3.1.21.- (DNA Restriction Enzymes) SB - IM MH - Base Sequence MH - Computational Biology/methods MH - *DNA Contamination MH - DNA Damage/*genetics MH - DNA Restriction Enzymes MH - Genome, Human MH - Humans MH - Paleontology MH - Reference Standards MH - Sequence Analysis, DNA/*methods MH - *Software EDAT- 2011/06/11 06:00 MHDA- 2011/10/08 06:00 CRDT- 2011/06/11 06:00 PHST- 2011/06/11 06:00 [entrez] PHST- 2011/06/11 06:00 [pubmed] PHST- 2011/10/08 06:00 [medline] AID - btr347 [pii] AID - 10.1093/bioinformatics/btr347 [doi] PST - ppublish SO - Bioinformatics. 2011 Aug 1;27(15):2153-5. doi: 10.1093/bioinformatics/btr347. Epub 2011 Jun 9. PMID- 21367547 OWN - NLM STAT- MEDLINE DCOM- 20111103 LR - 20110628 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 210 IP - 1-3 DP - 2011 Jul 15 TI - Analysis of ancient human DNA and primer contamination: one step backward one step forward. PG - 102-9 LID - 10.1016/j.forsciint.2011.02.010 [doi] AB - The analysis of DNA from archaeological human remains is plagued by a unique set of methodological problems concerning contamination with modern exogenous DNA. Through an original approach, we propose complementary methods to identify all potential sources of contamination and complete guidelines for the validation of ancient human sequences. The study presented was conducted on non-European human samples (Polynesian and Amerindian) which were collected with all precautions during excavation. This permitted us to distinguish without ambiguity authentic and contaminant sequences. The samples' origins and histories were perfectly known, allowing us to trace all potential contamination sources and to determine the efficiency of precautions followed during all steps of the study. The data obtained confirm that precautions taken during sampling effectively prevent contamination. However, we demonstrate that human contamination can also be introduced during genetic analyses even if all precautions are strictly followed. Indeed, numerous human contaminations were detected in template-PCR products and negative controls, resulting in a striking diversity of contaminant mitochondrial DNA sequences. We argue that this contamination partly derives from the primers. To our knowledge, no previous experiment has been performed to investigate primers as a possible source of human contamination despite the fact that this specific type of contamination poses a real problem in terms of validating ancient human DNA studies. Finally, we confirm that the detection of contaminants in negative controls is clearly related to the number of PCR cycles used. This study enhances our understanding of contamination processes and confirms that, in reality, an absolutely contamination-free situation cannot be obtained. As a consequence, we propose improvements to the guidelines usually followed in the field in order to take the highly probable contamination of PCR reagents, including primers, into account. CI - Copyright © 2011 Elsevier Ireland Ltd. All rights reserved. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - Université Bordeaux 1, UMR 5199 PACEA, Laboratoire d'Anthropologie des Populations du Passé, Avenue des Facultés, 33405 Talence Cedex, France.mf.deguilloux@anthropologie.u-bordeaux1.fr FAU - Ricaud, Séverine AU - Ricaud S FAU - Leahy, Rachael AU - Leahy R FAU - Pemonge, Marie-Hélène AU - Pemonge MH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110301 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (Complementarity Determining Regions) RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - Complementarity Determining Regions/genetics MH - *DNA Contamination MH - *DNA Primers MH - DNA, Mitochondrial/*genetics MH - Humans MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA MH - Specimen Handling EDAT- 2011/03/04 06:00 MHDA- 2011/11/04 06:00 CRDT- 2011/03/04 06:00 PHST- 2010/08/30 00:00 [received] PHST- 2010/12/14 00:00 [revised] PHST- 2011/02/06 00:00 [accepted] PHST- 2011/03/04 06:00 [entrez] PHST- 2011/03/04 06:00 [pubmed] PHST- 2011/11/04 06:00 [medline] AID - S0379-0738(11)00072-7 [pii] AID - 10.1016/j.forsciint.2011.02.010 [doi] PST - ppublish SO - Forensic Sci Int. 2011 Jul 15;210(1-3):102-9. doi: 10.1016/j.forsciint.2011.02.010. Epub 2011 Mar 1. PMID- 21592108 OWN - NLM STAT- MEDLINE DCOM- 20110930 LR - 20240323 IS - 1469-1809 (Electronic) IS - 0003-4800 (Print) IS - 0003-4800 (Linking) VI - 75 IP - 4 DP - 2011 Jul TI - Diversification of the ADH1B gene during expansion of modern humans. PG - 497-507 LID - 10.1111/j.1469-1809.2011.00651.x [doi] AB - A variant allele, ADH1B*48His, also known as ADH1B*2, at the human Alcohol Dehydrogenase 1B gene (ADH1B) is strongly associated with alcoholism in some populations and has an unusual geographic distribution. Strong evidence implies selection has increased the frequency of this allele in some East Asian populations but does not fully explain its geographic pattern. We have studied haplotypes of 10 single nucleotide polymorphisms (SNPs) and two short tandem repeat polymorphisms (STRPs) in the ADH1B region in 2,206 individuals from a worldwide set of populations. These SNPs and STRPs define nine common haplogroups most of which have distinct geographic patterns. The haplogroups H5 and H6, both with the derived ADH1B*48His allele, appear restricted to the Middle East and East Asia, respectively. The positively selected H7 is derived from H6 by a new regulatory region variant defining SNP rs3811801 restricted to East Asia. Age estimates of the haplogroups based on the STRPs also agree with the time of the migration events estimated by other studies. H7 is estimated to have expanded recently, around 2,800 years ago, and ancient DNA samples from North China confirm its presence about that time. The dating of the H7 expansion may help understand the selective force on the ADH1B gene. CI - © 2011 The Authors Annals of Human Genetics © 2011 Blackwell Publishing Ltd/University College London. FAU - Li, Hui AU - Li H AD - Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520-8005, USA. FAU - Gu, Sheng AU - Gu S FAU - Han, Yi AU - Han Y FAU - Xu, Zhi AU - Xu Z FAU - Pakstis, Andrew J AU - Pakstis AJ FAU - Jin, Li AU - Jin L FAU - Kidd, Judith R AU - Kidd JR FAU - Kidd, Kenneth K AU - Kidd KK LA - eng GR - P01 GM057672/GM/NIGMS NIH HHS/United States GR - R01 AA009379/AA/NIAAA NIH HHS/United States GR - AA009379/AA/NIAAA NIH HHS/United States GR - GM057672/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20110518 PL - England TA - Ann Hum Genet JT - Annals of human genetics JID - 0416661 RN - EC 1.1.1.1 (ADH1B protein, human) RN - EC 1.1.1.1 (Alcohol Dehydrogenase) SB - IM MH - Africa MH - Alcohol Dehydrogenase/*genetics MH - Americas MH - Asian People/genetics MH - China MH - Europe MH - Asia, Eastern MH - Gene Frequency MH - *Genetics, Population MH - Haplotypes MH - Humans MH - Middle East MH - *Polymorphism, Genetic MH - Polymorphism, Single Nucleotide MH - Selection, Genetic MH - Time Factors PMC - PMC3722864 MID - NIHMS474006 COIS- None of the authors has any conflicts of interest related to the data presented here. EDAT- 2011/05/20 06:00 MHDA- 2011/10/01 06:00 PMCR- 2013/07/25 CRDT- 2011/05/20 06:00 PHST- 2011/05/20 06:00 [entrez] PHST- 2011/05/20 06:00 [pubmed] PHST- 2011/10/01 06:00 [medline] PHST- 2013/07/25 00:00 [pmc-release] AID - 10.1111/j.1469-1809.2011.00651.x [doi] PST - ppublish SO - Ann Hum Genet. 2011 Jul;75(4):497-507. doi: 10.1111/j.1469-1809.2011.00651.x. Epub 2011 May 18. PMID- 21628562 OWN - NLM STAT- MEDLINE DCOM- 20110929 LR - 20221207 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 108 IP - 24 DP - 2011 Jun 14 TI - Ancient DNA reveals male diffusion through the Neolithic Mediterranean route. PG - 9788-91 LID - 10.1073/pnas.1100723108 [doi] AB - The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition. FAU - Lacan, Marie AU - Lacan M AD - Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5288, 31073 Toulouse, France. lacan.marie@netcourrier.com FAU - Keyser, Christine AU - Keyser C FAU - Ricaut, François-Xavier AU - Ricaut FX FAU - Brucato, Nicolas AU - Brucato N FAU - Duranthon, Francis AU - Duranthon F FAU - Guilaine, Jean AU - Guilaine J FAU - Crubézy, Eric AU - Crubézy E FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Journal Article DEP - 20110531 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - DNA/*analysis/genetics MH - DNA, Mitochondrial/analysis/genetics MH - *Emigration and Immigration MH - Europe MH - *Fossils MH - France MH - Genetics, Population MH - Geography MH - Humans MH - Mediterranean Region MH - Polymerase Chain Reaction MH - Population Dynamics MH - Time Factors MH - White People/*genetics PMC - PMC3116412 COIS- The authors declare no conflict of interest. EDAT- 2011/06/02 06:00 MHDA- 2011/10/01 06:00 PMCR- 2011/12/14 CRDT- 2011/06/02 06:00 PHST- 2011/06/02 06:00 [entrez] PHST- 2011/06/02 06:00 [pubmed] PHST- 2011/10/01 06:00 [medline] PHST- 2011/12/14 00:00 [pmc-release] AID - 1100723108 [pii] AID - 201100723 [pii] AID - 10.1073/pnas.1100723108 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9788-91. doi: 10.1073/pnas.1100723108. Epub 2011 May 31. PMID- 21639832 OWN - NLM STAT- MEDLINE DCOM- 20110919 LR - 20221207 IS - 1608-3040 (Electronic) IS - 0006-2979 (Linking) VI - 76 IP - 5 DP - 2011 May TI - Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history". PG - 517-33 LID - 10.1134/S0006297911050026 [doi] AB - This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the foundation for "molecular history", in which the principal tool is high-technology analysis of DNA molecules of both our contemporaries and excavated ancient DNA samples, along with their biological kinetics. FAU - Klyosov, A A AU - Klyosov AA AD - MIR International, Inc., Newton, Massachusetts 02459, USA. aklyosov@comcast.net LA - eng PT - Evaluation Study PT - Historical Article PT - Journal Article PT - Review PL - United States TA - Biochemistry (Mosc) JT - Biochemistry. Biokhimiia JID - 0376536 RN - 9007-49-2 (DNA) SB - IM MH - Biology/instrumentation/*methods MH - Chemistry/history/*methods MH - DNA/*genetics MH - *Genealogy and Heraldry MH - Genetics, Population/history/*methods MH - History, Ancient MH - Humans MH - *Phylogeny MH - White People/ethnology/genetics/history EDAT- 2011/06/07 06:00 MHDA- 2011/09/20 06:00 CRDT- 2011/06/07 06:00 PHST- 2011/06/07 06:00 [entrez] PHST- 2011/06/07 06:00 [pubmed] PHST- 2011/09/20 06:00 [medline] AID - BCM76050636 [pii] AID - 10.1134/S0006297911050026 [doi] PST - ppublish SO - Biochemistry (Mosc). 2011 May;76(5):517-33. doi: 10.1134/S0006297911050026. PMID- 21224890 OWN - NLM STAT- MEDLINE DCOM- 20110801 LR - 20211020 IS - 1476-5438 (Electronic) IS - 1018-4813 (Print) IS - 1018-4813 (Linking) VI - 19 IP - 5 DP - 2011 May TI - Mitochondrial analysis of a Byzantine population reveals the differential impact of multiple historical events in South Anatolia. PG - 571-6 LID - 10.1038/ejhg.2010.230 [doi] AB - The archaeological site of Sagalassos is located in Southwest Turkey, in the western part of the Taurus mountain range. Human occupation of its territory is attested from the late 12th millennium BP up to the 13th century AD. By analysing the mtDNA variation in 85 skeletons from Sagalassos dated to the 11th-13th century AD, this study attempts to reconstruct the genetic signature potentially left in this region of Anatolia by the many civilizations, which succeeded one another over the centuries until the mid-Byzantine period (13th century BC). Authentic ancient DNA data were determined from the control region and some SNPs in the coding region of the mtDNA in 53 individuals. Comparative analyses with up to 157 modern populations allowed us to reconstruct the origin of the mid-Byzantine people still dwelling in dispersed hamlets in Sagalassos, and to detect the maternal contribution of their potential ancestors. By integrating the genetic data with historical and archaeological information, we were able to attest in Sagalassos a significant maternal genetic signature of Balkan/Greek populations, as well as ancient Persians and populations from the Italian peninsula. Some contribution from the Levant has been also detected, whereas no contribution from Central Asian population could be ascertained. FAU - Ottoni, Claudio AU - Ottoni C AD - Laboratory of Forensic Genetics and Molecular Archaeology, Universitaire Ziekenhuizen, Leuven, Belgium. claudio.ottoni@med.kuleuven.be FAU - Ricaut, François-X AU - Ricaut FX FAU - Vanderheyden, Nancy AU - Vanderheyden N FAU - Brucato, Nicolas AU - Brucato N FAU - Waelkens, Marc AU - Waelkens M FAU - Decorte, Ronny AU - Decorte R LA - eng SI - GENBANK/HQ007946 SI - GENBANK/HQ007947 SI - GENBANK/HQ007948 SI - GENBANK/HQ007949 SI - GENBANK/HQ007950 SI - GENBANK/HQ007951 SI - GENBANK/HQ007952 SI - GENBANK/HQ007953 SI - GENBANK/HQ007954 SI - GENBANK/HQ007955 SI - GENBANK/HQ007956 SI - GENBANK/HQ007957 SI - GENBANK/HQ007958 SI - GENBANK/HQ007959 SI - GENBANK/HQ007960 SI - GENBANK/HQ007961 SI - GENBANK/HQ007962 SI - GENBANK/HQ007963 SI - GENBANK/HQ007964 SI - GENBANK/HQ007965 SI - GENBANK/HQ007966 SI - GENBANK/HQ007967 SI - GENBANK/HQ007968 SI - GENBANK/HQ007969 SI - GENBANK/HQ007970 SI - GENBANK/HQ007971 SI - GENBANK/HQ007972 SI - GENBANK/HQ007973 SI - GENBANK/HQ007974 SI - GENBANK/HQ007975 SI - GENBANK/HQ007976 SI - GENBANK/HQ007977 SI - GENBANK/HQ007978 SI - GENBANK/HQ007979 SI - GENBANK/HQ007980 SI - GENBANK/HQ007981 SI - GENBANK/HQ007982 SI - GENBANK/HQ007983 SI - GENBANK/HQ007984 SI - GENBANK/HQ007985 SI - GENBANK/HQ007986 SI - GENBANK/HQ007987 SI - GENBANK/HQ007988 SI - GENBANK/HQ007989 SI - GENBANK/HQ007990 SI - GENBANK/HQ007991 SI - GENBANK/HQ007992 SI - GENBANK/HQ007993 SI - GENBANK/HQ007994 SI - GENBANK/HQ007995 SI - GENBANK/HQ007996 SI - GENBANK/HQ007997 SI - GENBANK/HQ007998 SI - GENBANK/HQ007999 SI - GENBANK/HQ008000 SI - GENBANK/HQ008001 SI - GENBANK/HQ008002 SI - GENBANK/HQ008003 SI - GENBANK/HQ008004 SI - GENBANK/HQ008005 SI - GENBANK/HQ008006 SI - GENBANK/HQ008007 SI - GENBANK/HQ008008 SI - GENBANK/HQ008009 SI - GENBANK/HQ008010 SI - GENBANK/HQ008011 SI - GENBANK/HQ008012 SI - GENBANK/HQ008013 SI - GENBANK/HQ008014 SI - GENBANK/HQ008015 SI - GENBANK/HQ008016 SI - GENBANK/HQ008017 SI - GENBANK/HQ008018 SI - GENBANK/HQ008019 SI - GENBANK/HQ008020 SI - GENBANK/HQ008021 SI - GENBANK/HQ008022 SI - GENBANK/HQ008023 SI - GENBANK/HQ008024 SI - GENBANK/HQ008025 SI - GENBANK/HQ008026 SI - GENBANK/HQ008027 SI - GENBANK/HQ008028 SI - GENBANK/HQ008029 SI - GENBANK/HQ008030 SI - GENBANK/HQ008031 SI - GENBANK/HQ008032 SI - GENBANK/HQ008033 SI - GENBANK/HQ008034 SI - GENBANK/HQ008035 SI - GENBANK/HQ008036 SI - GENBANK/HQ008037 SI - GENBANK/HQ008038 SI - GENBANK/HQ008039 SI - GENBANK/HQ008040 SI - GENBANK/HQ008041 SI - GENBANK/HQ008042 SI - GENBANK/HQ008043 SI - GENBANK/HQ008044 SI - GENBANK/HQ008045 SI - GENBANK/HQ008046 SI - GENBANK/HQ008047 SI - GENBANK/HQ008048 SI - GENBANK/HQ008049 SI - GENBANK/HQ008050 SI - GENBANK/HQ008051 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110112 PL - England TA - Eur J Hum Genet JT - European journal of human genetics : EJHG JID - 9302235 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/genetics MH - *Genes, Mitochondrial MH - *Genetics, Population MH - Humans MH - Molecular Sequence Data MH - Turkey PMC - PMC3083616 EDAT- 2011/01/13 06:00 MHDA- 2011/08/02 06:00 PMCR- 2012/05/01 CRDT- 2011/01/13 06:00 PHST- 2011/01/13 06:00 [entrez] PHST- 2011/01/13 06:00 [pubmed] PHST- 2011/08/02 06:00 [medline] PHST- 2012/05/01 00:00 [pmc-release] AID - ejhg2010230 [pii] AID - 10.1038/ejhg.2010.230 [doi] PST - ppublish SO - Eur J Hum Genet. 2011 May;19(5):571-6. doi: 10.1038/ejhg.2010.230. Epub 2011 Jan 12. PMID- 21525906 OWN - NLM STAT- MEDLINE DCOM- 20110621 LR - 20211020 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 472 IP - 7344 DP - 2011 Apr 28 TI - Ancient DNA: Curse of the Pharaoh's DNA. PG - 404-6 LID - 10.1038/472404a [doi] FAU - Marchant, Jo AU - Marchant J LA - eng PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Cold Climate MH - DNA/*analysis/*genetics/isolation & purification MH - DNA, Mitochondrial/genetics MH - Egypt MH - Female MH - Hot Temperature MH - Humans MH - Male MH - *Mummies MH - Reproducibility of Results MH - *Sequence Analysis, DNA/methods/standards/trends MH - Y Chromosome/genetics EDAT- 2011/04/29 06:00 MHDA- 2011/06/22 06:00 CRDT- 2011/04/29 06:00 PHST- 2011/04/29 06:00 [entrez] PHST- 2011/04/29 06:00 [pubmed] PHST- 2011/06/22 06:00 [medline] AID - 472404a [pii] AID - 10.1038/472404a [doi] PST - ppublish SO - Nature. 2011 Apr 28;472(7344):404-6. doi: 10.1038/472404a. PMID- 20851541 OWN - NLM STAT- MEDLINE DCOM- 20110922 LR - 20110330 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 207 IP - 1-3 DP - 2011 Apr 15 TI - Sex determination of early medieval individuals through nested PCR using a new primer set in the SRY gene. PG - 1-5 LID - 10.1016/j.forsciint.2010.08.012 [doi] AB - One of the first questions asked about excavated human skeletal remains is the sex. As the morphological sex determination is complicated in cases involving fragmentary bones and in skeletons from infants and children, the development of DNA-based techniques has led to improvements in sex determination. This study is focused on sex determination from ancient DNA obtained from 25 skeletons found in Middle Aged burials in western Slovakia. We performed separate amplifications of DXZ4 repetitive satellite sequences on the X chromosome, and SRY gene - testis determined factor on the Y chromosome, using nested PCR. Our results showed that DXZ4 was amplified in the case of 23 individuals. With newly designed internal and external primer sets for SRY detection with internal PCR products in lengths of 102 bp and 85 bp we succeeded in detecting the SRY locus in 9 samples. Finally, the gender was determined in 23 individuals (14 females and 9 males). In 20 samples, the gender was determined by morphological and molecular methods. Sex determination of 17 samples using nested PCR matched the morphological one, providing evidence of the authenticity and ancient origin of the PCR amplifications. The DXZ4/SRY nested PCR method represents a useful technique in sex determination of medieval human remains and it is a critical addition to anthropological studies. CI - Copyright © 2010 Elsevier Ireland Ltd. All rights reserved. FAU - Luptáková, Lenka AU - Luptáková L AD - Katedra antropológie, Prírodovedecká fakulta, Univerzita Komenského, Mlynská dolina B2, 842 15 Bratislava, Slovakia. luptakova@fns.uniba.sk FAU - Bábelová, Andrea AU - Bábelová A FAU - Omelka, Radoslav AU - Omelka R FAU - Kolena, Branislav AU - Kolena B FAU - Vondráková, Mária AU - Vondráková M FAU - Bauerová, Mária AU - Bauerová M LA - eng PT - Historical Article PT - Journal Article DEP - 20100918 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (Amelogenin) RN - 0 (DNA Primers) RN - 0 (SRY protein, human) RN - 0 (Sex-Determining Region Y Protein) SB - IM MH - Amelogenin/genetics MH - Chromosomes, Human, X MH - Chromosomes, Human, Y MH - DNA Primers MH - Female MH - Forensic Genetics/methods MH - History, Medieval MH - Humans MH - Male MH - Polymerase Chain Reaction/*methods MH - Sex Determination Analysis/*methods MH - Sex-Determining Region Y Protein/*genetics MH - Slovakia EDAT- 2010/09/21 06:00 MHDA- 2011/09/23 06:00 CRDT- 2010/09/21 06:00 PHST- 2009/06/15 00:00 [received] PHST- 2010/07/02 00:00 [revised] PHST- 2010/08/15 00:00 [accepted] PHST- 2010/09/21 06:00 [entrez] PHST- 2010/09/21 06:00 [pubmed] PHST- 2011/09/23 06:00 [medline] AID - S0379-0738(10)00400-7 [pii] AID - 10.1016/j.forsciint.2010.08.012 [doi] PST - ppublish SO - Forensic Sci Int. 2011 Apr 15;207(1-3):1-5. doi: 10.1016/j.forsciint.2010.08.012. Epub 2010 Sep 18. PMID- 21302275 OWN - NLM STAT- MEDLINE DCOM- 20110527 LR - 20110208 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 144 IP - 3 DP - 2011 Mar TI - Brief communication: Ancient nuclear DNA and kinship analysis: the case of a medieval burial in San Esteban Church in Cuellar (Segovia, Central Spain). PG - 485-91 LID - 10.1002/ajpa.21451 [doi] AB - The aim of this work was to investigate a very common situation in the archaeological and anthropological context: the study of a burial site containing several individuals, probably related genetically, using ancient DNA techniques. We used available ancient DNA and forensic protocols to obtain reliable results on archaeological material. The results also enabled molecular sex determination to be compared with osteological data. Specifically, a modified ancient DNA extraction method combined with the amplification of nuclear markers with the AmpFlSTR®MiniFiler™ kit(Applied Biosystems) was used. Seven medieval individuals buried in four niches dated in the 15th Century at San Esteban Church in Cuellar (Segovia, Central Spain) were analyzed by the proposed method, and four of seven provided complete autosomal short tandem repeat (STRs) profiles. Kinship analyses comprising paternity and sibship relations were carried out with pedigree-specific software used in forensic casework. A 99.98% paternity probability was established between two individuals, although lower percentages (68%) were obtained in other cases, and some hypothetical kinship relations were excluded. The overall results could eventually provide evidence for reconstructing the historical record. CI - Copyright © 2010 Wiley-Liss, Inc. FAU - Gamba, Cristina AU - Gamba C AD - Laboratory of Forensic and Population Genetics, Toxicology and Health Legislation Department, Complutense University of Madrid, Madrid, Spain. cristinagamba@med.ucm.es FAU - Fernández, Eva AU - Fernández E FAU - Tirado, Mirian AU - Tirado M FAU - Pastor, Francisco AU - Pastor F FAU - Arroyo-Pardo, Eduardo AU - Arroyo-Pardo E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101217 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Genetic Markers) RN - 9007-49-2 (DNA) SB - IM MH - *Anthropology, Physical MH - Cemeteries MH - Computational Biology MH - DNA/*genetics MH - Female MH - Genetic Markers/genetics MH - Humans MH - Male MH - Minisatellite Repeats/genetics MH - *Pedigree MH - Polymerase Chain Reaction MH - *Sequence Analysis, DNA MH - Spain EDAT- 2011/02/09 06:00 MHDA- 2011/05/28 06:00 CRDT- 2011/02/09 06:00 PHST- 2010/08/09 00:00 [received] PHST- 2010/10/19 00:00 [accepted] PHST- 2011/02/09 06:00 [entrez] PHST- 2011/02/09 06:00 [pubmed] PHST- 2011/05/28 06:00 [medline] AID - 10.1002/ajpa.21451 [doi] PST - ppublish SO - Am J Phys Anthropol. 2011 Mar;144(3):485-91. doi: 10.1002/ajpa.21451. Epub 2010 Dec 17. PMID- 21453001 OWN - NLM STAT- MEDLINE DCOM- 20110805 LR - 20110401 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 83 IP - 1 DP - 2011 Feb TI - Drafting human ancestry: what does the Neanderthal genome tell us about hominid evolution? Commentary on Green et al. (2010). PG - 1-11 LID - 10.3378/027.083.0101 [doi] AB - Ten years after the first draft versions of the human genome were announced, technical progress in both DNA sequencing and ancient DNA analyses has allowed a research team around Ed Green and Svante Pääbo to complete this task from infinitely more difficult hominid samples: a few pieces of bone originating from our closest, albeit extinct, relatives, the Neanderthals. Pulling the Neanderthal sequences out of a sea of contaminating environmental DNA impregnating the bones and at the same time avoiding the problems of contamination with modern human DNA is in itself a remarkable accomplishment. However, the crucial question in the long run is, what can we learn from such genomic data about hominid evolution? FAU - Hofreiter, Michael AU - Hofreiter M AD - Chair for Evolutionary Biology and Ecology, Department of Biology (Area 2), The University of York, Wentworth Way, Heslington, York YO10 5DD, UK. LA - eng PT - Historical Article PT - Journal Article PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - *Biological Evolution MH - DNA, Mitochondrial MH - Gene Flow MH - Genome, Human/*genetics MH - History, Ancient MH - Hominidae/*genetics MH - Humans MH - *Sequence Analysis, DNA EDAT- 2011/04/02 06:00 MHDA- 2011/08/06 06:00 CRDT- 2011/04/02 06:00 PHST- 2011/04/02 06:00 [entrez] PHST- 2011/04/02 06:00 [pubmed] PHST- 2011/08/06 06:00 [medline] AID - 10.3378/027.083.0101 [doi] PST - ppublish SO - Hum Biol. 2011 Feb;83(1):1-11. doi: 10.3378/027.083.0101. PMID- 21298665 OWN - NLM STAT- MEDLINE DCOM- 20110512 LR - 20191210 IS - 1522-2683 (Electronic) IS - 0173-0835 (Linking) VI - 32 IP - 3-4 DP - 2011 Feb TI - Application of the iPLEX™ Gold SNP genotyping method for the analysis of Amerindian ancient DNA samples: benefits for ancient population studies. PG - 386-93 LID - 10.1002/elps.201000483 [doi] AB - Important developments in the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique have generated new perspectives regarding SNP genotyping, which are particularly promising for ancient population-based studies. The main aim of the present study was to investigate the application of a MALDI-TOF MS-based SNP genotyping technique, called iPLEX(®) Gold, to analyze Amerindian ancient DNA samples. The first objective was to test the sensitivity of the method, which is recommended for DNA quantities between 10 and 5 ng, for ancient biological samples containing DNA molecules that were degraded and present in minute quantities. The second objective was to detail the advantages of this technique for studies on ancient populations. Two multiplexes were designed, allowing the major Amerindian mitochondrial and Y haplogroups to be determined simultaneously. This analysis has never been described before. Results demonstrated the reliability and accuracy of the method; data were obtained for both mitochondrial and nuclear DNA using picogram (pg) quantities of nucleic acid. This technique has the advantages of both MS and minisequencing techniques; thus, it should be included in the protocols for future ancient DNA studies. CI - Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Mendisco, Fanny AU - Mendisco F AD - Laboratoire d'Anthropologie Moléculaire, Université de Strasbourg, Institut de Médecine Légale, Strasbourg, France. fanny.mendisco@neuf.fr FAU - Keyser, Christine AU - Keyser C FAU - Hollard, Clémence AU - Hollard C FAU - Seldes, Veronica AU - Seldes V FAU - Nielsen, Axel E AU - Nielsen AE FAU - Crubézy, Eric AU - Crubézy E FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Journal Article PT - Validation Study DEP - 20110111 PL - Germany TA - Electrophoresis JT - Electrophoresis JID - 8204476 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - DNA/*analysis/genetics MH - DNA, Mitochondrial/*analysis/genetics MH - Fossils MH - Gene Frequency/genetics MH - Genetic Variation/genetics MH - Genetics, Population/methods MH - Genotype MH - Humans MH - Indians, North American/*genetics MH - Microsatellite Repeats/*genetics MH - Polymerase Chain Reaction/methods MH - Polymorphism, Single Nucleotide/*genetics MH - Sequence Analysis, DNA/methods MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods EDAT- 2011/02/08 06:00 MHDA- 2011/05/13 06:00 CRDT- 2011/02/08 06:00 PHST- 2010/09/20 00:00 [received] PHST- 2010/11/16 00:00 [revised] PHST- 2010/11/17 00:00 [accepted] PHST- 2011/02/08 06:00 [entrez] PHST- 2011/02/08 06:00 [pubmed] PHST- 2011/05/13 06:00 [medline] AID - 10.1002/elps.201000483 [doi] PST - ppublish SO - Electrophoresis. 2011 Feb;32(3-4):386-93. doi: 10.1002/elps.201000483. Epub 2011 Jan 11. PMID- 20872743 OWN - NLM STAT- MEDLINE DCOM- 20110525 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 144 IP - 2 DP - 2011 Feb TI - Ancient DNA evidence supports the contribution of Di-Qiang people to the han Chinese gene pool. PG - 258-68 LID - 10.1002/ajpa.21399 [doi] AB - Han Chinese is the largest ethnic group in the world. During its development, it gradually integrated with many neighboring populations. To uncover the origin of the Han Chinese, ancient DNA analysis was performed on the remains of 46 humans (1700 to 1900 years ago) excavated from the Taojiazhai site in Qinghai province, northwest of China, where the Di-Qiang populations had previously lived. In this study, eight mtDNA haplogroups (A, B, D, F, M*, M10, N9a, and Z) and one Y-chromosome haplogroup (O3) were identified. All analyses show that the Taojiazhai population presents close genetic affinity to Tibeto-Burman populations (descendants of Di-Qiang populations) and Han Chinese, suggesting that the Di-Qiang populations may have contributed to the Han Chinese genetic pool. CI - 2010 Wiley-Liss, Inc. FAU - Zhao, Yong-Bin AU - Zhao YB AD - Laboratory of Ancient DNA, Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China. FAU - Li, Hong-Jie AU - Li HJ FAU - Li, Sheng-Nan AU - Li SN FAU - Yu, Chang-Chun AU - Yu CC FAU - Gao, Shi-Zhu AU - Gao SZ FAU - Xu, Zhi AU - Xu Z FAU - Jin, Li AU - Jin L FAU - Zhu, Hong AU - Zhu H FAU - Zhou, Hui AU - Zhou H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100924 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Analysis of Variance MH - Asian People/*genetics MH - Base Sequence MH - Bone and Bones/chemistry MH - China MH - Chromosomes, Human, Y MH - Cluster Analysis MH - DNA, Mitochondrial/*genetics/isolation & purification MH - Female MH - *Fossils MH - Gene Pool MH - Humans MH - Male MH - Molecular Sequence Data MH - Polymorphism, Single Nucleotide MH - Principal Component Analysis MH - Tooth/chemistry EDAT- 2010/09/28 06:00 MHDA- 2011/05/26 06:00 CRDT- 2010/09/28 06:00 PHST- 2010/04/22 00:00 [received] PHST- 2010/07/28 00:00 [accepted] PHST- 2010/09/28 06:00 [entrez] PHST- 2010/09/28 06:00 [pubmed] PHST- 2011/05/26 06:00 [medline] AID - 10.1002/ajpa.21399 [doi] PST - ppublish SO - Am J Phys Anthropol. 2011 Feb;144(2):258-68. doi: 10.1002/ajpa.21399. Epub 2010 Sep 24. PMID- 21904610 OWN - NLM STAT- MEDLINE DCOM- 20120425 LR - 20211020 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 8 DP - 2011 TI - Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics. PG - e24161 LID - 10.1371/journal.pone.0024161 [doi] LID - e24161 AB - BACKGROUND: Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. CONCLUSIONS: We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone. FAU - García-Garcerà, Marc AU - García-Garcerà M AD - Institut de Biologia Evolutiva, CSIC-UPF, Barcelona, Spain. FAU - Gigli, Elena AU - Gigli E FAU - Sanchez-Quinto, Federico AU - Sanchez-Quinto F FAU - Ramirez, Oscar AU - Ramirez O FAU - Calafell, Francesc AU - Calafell F FAU - Civit, Sergi AU - Civit S FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110831 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*genetics MH - *Fossils MH - Genomics/*methods MH - Humans MH - Sequence Analysis, DNA/*methods PMC - PMC3164143 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2011/09/10 06:00 MHDA- 2012/04/26 06:00 PMCR- 2011/08/31 CRDT- 2011/09/10 06:00 PHST- 2011/06/30 00:00 [received] PHST- 2011/08/01 00:00 [accepted] PHST- 2011/09/10 06:00 [entrez] PHST- 2011/09/10 06:00 [pubmed] PHST- 2012/04/26 06:00 [medline] PHST- 2011/08/31 00:00 [pmc-release] AID - PONE-D-11-12298 [pii] AID - 10.1371/journal.pone.0024161 [doi] PST - ppublish SO - PLoS One. 2011;6(8):e24161. doi: 10.1371/journal.pone.0024161. Epub 2011 Aug 31. PMID- 21765907 OWN - NLM STAT- MEDLINE DCOM- 20111109 LR - 20241101 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 7 DP - 2011 TI - Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. PG - e21733 LID - 10.1371/journal.pone.0021733 [doi] LID - e21733 AB - Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17(th) to the 19(th) century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity ≥ 95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17(th) century to the early 18(th) century. FAU - Thèves, Catherine AU - Thèves C AD - Laboratoire AMIS, UMR 5288, Université Toulouse IIII/CNRS/Université de Strasbourg, Toulouse, France. ctheves@cict.fr FAU - Senescau, Alice AU - Senescau A FAU - Vanin, Stefano AU - Vanin S FAU - Keyser, Christine AU - Keyser C FAU - Ricaut, François Xavier AU - Ricaut FX FAU - Alekseev, Anatoly N AU - Alekseev AN FAU - Dabernat, Henri AU - Dabernat H FAU - Ludes, Bertrand AU - Ludes B FAU - Fabre, Richard AU - Fabre R FAU - Crubézy, Eric AU - Crubézy E LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110713 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Bacterial) RN - 0 (DNA, Ribosomal) RN - 9007-49-2 (DNA) SB - IM MH - Bacteria/*classification/*genetics MH - Bacterial Typing Techniques/*methods MH - Base Sequence MH - Bone and Bones/microbiology MH - *Cause of Death MH - DNA/genetics MH - DNA, Bacterial/genetics MH - DNA, Ribosomal/genetics MH - Environmental Microbiology MH - Fossils MH - Freezing MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - Humans MH - Male MH - Molecular Typing/*methods MH - Phylogeny MH - Reproducibility of Results MH - Reverse Transcriptase Polymerase Chain Reaction MH - Sequence Analysis, DNA MH - Siberia PMC - PMC3135582 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2011/07/19 06:00 MHDA- 2011/11/10 06:00 PMCR- 2011/07/13 CRDT- 2011/07/19 06:00 PHST- 2011/01/10 00:00 [received] PHST- 2011/06/09 00:00 [accepted] PHST- 2011/07/19 06:00 [entrez] PHST- 2011/07/19 06:00 [pubmed] PHST- 2011/11/10 06:00 [medline] PHST- 2011/07/13 00:00 [pmc-release] AID - PONE-D-11-01007 [pii] AID - 10.1371/journal.pone.0021733 [doi] PST - ppublish SO - PLoS One. 2011;6(7):e21733. doi: 10.1371/journal.pone.0021733. Epub 2011 Jul 13. PMID- 21738625 OWN - NLM STAT- MEDLINE DCOM- 20111201 LR - 20240313 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 6 DP - 2011 TI - To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples. PG - e21247 LID - 10.1371/journal.pone.0021247 [doi] LID - e21247 AB - The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from "modern" DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be "gold standards" in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones.To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous. FAU - Winters, Misa AU - Winters M AD - School of Biological Sciences, Washington State University, Pullman, Washington, United States of America. FAU - Barta, Jodi Lynn AU - Barta JL FAU - Monroe, Cara AU - Monroe C FAU - Kemp, Brian M AU - Kemp BM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110627 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Cloning, Molecular/*methods MH - DNA/*analysis MH - Humans PMC - PMC3124491 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2011/07/09 06:00 MHDA- 2011/12/13 00:00 PMCR- 2011/06/27 CRDT- 2011/07/09 06:00 PHST- 2011/03/08 00:00 [received] PHST- 2011/05/24 00:00 [accepted] PHST- 2011/07/09 06:00 [entrez] PHST- 2011/07/09 06:00 [pubmed] PHST- 2011/12/13 00:00 [medline] PHST- 2011/06/27 00:00 [pmc-release] AID - PONE-D-11-04580 [pii] AID - 10.1371/journal.pone.0021247 [doi] PST - ppublish SO - PLoS One. 2011;6(6):e21247. doi: 10.1371/journal.pone.0021247. Epub 2011 Jun 27. PMID- 21657943 OWN - NLM STAT- MEDLINE DCOM- 20110930 LR - 20110610 IS - 1549-781X (Electronic) IS - 1040-8363 (Linking) VI - 48 IP - 1 DP - 2011 Jan-Feb TI - Familial hypercholesterolemia: epidemiology, Neolithic origins and modern geographic distribution. PG - 1-18 LID - 10.3109/10408363.2011.565585 [doi] AB - The elucidation of the molecular basis of familial hypercholesterolemia (FH) by Brown and Goldstein about three decades ago provided the most convincing evidence for a causative relationship between a high plasma level of low-density lipoprotein (LDL) cholesterol and the conditions of atherosclerosis and premature atherosclerotic cardiovascular disease. Today, with a prevalence of about one in 500 individuals, FH remains the most common monogenic disorder of lipoprotein metabolism, and is mainly due to mutations in the LDL receptor (LDLR) gene that lead to the plasma accumulation of cholesterol ester-laden LDL particles. Another form of autosomal dominant hypercholesterolemia, familial defective apolipoprotein B-100, a genocopy of FH caused by defects in the APOB gene that lead to decreased clearance of LDL, is now established as a significant cause of coronary heart disease. Yet another form, due to mutations in the proprotein convertase subtilisin/kexin type 9 (PCSK9) gene, has been recently identified that similarly causes decreased clearance of LDL by novel mechanisms also involving the hepatic LDLR endocytotic pathway. Recent advances in molecular genotyping technology have yielded a staggering amount of detail about human genetic diversity at the single nucleotide level in both private and public databases including the International HapMap Consortium. This, as well as the availability of ancient human DNA from burial sites and the development of new statistical methods, now provide an unprecedented capacity to study human demography and the ability to examine the genealogical ties between ancient and modern people. The aim of this article is to review the epidemiology of FH, and to attempt to draw inferences from our knowledge at a DNA level of inherited hypercholesterolemia of contemporary people that may contribute to the understanding of human population history and adaptation that resulted in the massive demographic expansion following the adoption of agriculture in the Neolithic period. FAU - Liyanage, Khemanganee E AU - Liyanage KE AD - School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia. FAU - Burnett, John R AU - Burnett JR FAU - Hooper, Amanda J AU - Hooper AJ FAU - van Bockxmeer, Frank M AU - van Bockxmeer FM LA - eng PT - Historical Article PT - Journal Article PT - Review PL - England TA - Crit Rev Clin Lab Sci JT - Critical reviews in clinical laboratory sciences JID - 8914816 RN - 0 (Apolipoproteins B) SB - IM MH - Apolipoproteins B/genetics MH - Founder Effect MH - Genealogy and Heraldry MH - *Geography MH - History, Ancient MH - Humans MH - Hyperlipoproteinemia Type II/diagnosis/*epidemiology/genetics/*history MH - Mutation/genetics EDAT- 2011/06/11 06:00 MHDA- 2011/10/01 06:00 CRDT- 2011/06/11 06:00 PHST- 2011/06/11 06:00 [entrez] PHST- 2011/06/11 06:00 [pubmed] PHST- 2011/10/01 06:00 [medline] AID - 10.3109/10408363.2011.565585 [doi] PST - ppublish SO - Crit Rev Clin Lab Sci. 2011 Jan-Feb;48(1):1-18. doi: 10.3109/10408363.2011.565585. PMID- 20717990 OWN - NLM STAT- MEDLINE DCOM- 20110303 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 144 IP - 1 DP - 2011 Jan TI - News from the west: ancient DNA from a French megalithic burial chamber. PG - 108-18 LID - 10.1002/ajpa.21376 [doi] AB - Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices. CI - Copyright © 2010 Wiley-Liss, Inc. FAU - Deguilloux, Marie-France AU - Deguilloux MF AD - Université Bordeaux 1, UMR 5199 PACEA, Laboratoire d'Anthropologie des Populations du Passé, B8 Avenue des Facultés, Talence cedex, France. mf.deguilloux@anthropologie.u-bordeaux1.fr FAU - Soler, Ludovic AU - Soler L FAU - Pemonge, Marie-Hélène AU - Pemonge MH FAU - Scarre, Chris AU - Scarre C FAU - Joussaume, Roger AU - Joussaume R FAU - Laporte, Luc AU - Laporte L LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100817 PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Archaeology MH - Base Sequence MH - Cemeteries MH - Child MH - DNA, Mitochondrial/*genetics MH - *Emigration and Immigration MH - France MH - Haplotypes MH - History, Ancient MH - Humans MH - Male MH - Molecular Sequence Data MH - Phylogeny MH - *Polymorphism, Genetic MH - White People/*genetics/history MH - Young Adult EDAT- 2010/08/19 06:00 MHDA- 2011/03/04 06:00 CRDT- 2010/08/19 06:00 PHST- 2010/02/10 00:00 [received] PHST- 2010/06/08 00:00 [accepted] PHST- 2010/08/19 06:00 [entrez] PHST- 2010/08/19 06:00 [pubmed] PHST- 2011/03/04 06:00 [medline] AID - 10.1002/ajpa.21376 [doi] PST - ppublish SO - Am J Phys Anthropol. 2011 Jan;144(1):108-18. doi: 10.1002/ajpa.21376. Epub 2010 Aug 17. PMID- 20306303 OWN - NLM STAT- MEDLINE DCOM- 20110321 LR - 20211020 IS - 1573-4978 (Electronic) IS - 0301-4851 (Linking) VI - 38 IP - 1 DP - 2011 Jan TI - A genetic investigation of Korean mummies from the Joseon Dynasty. PG - 115-21 LID - 10.1007/s11033-010-0084-4 [doi] AB - Two Korean mummies (Danwoong-mirra and Yoon-mirra) found in medieval tombs in the central region of the Korean peninsula were genetically investigated by analysis of mitochondrial DNA (mtDNA), Y-chromosomal short tandem repeat (Y-STR) and the ABO gene. Danwoong-mirra is a male child mummy and Yoon-mirra is a pregnant female mummy, dating back about 550 and 450 years, respectively. DNA was extracted from soft tissues or bones. mtDNA, Y-STR and the ABO gene were amplified using a small size amplicon strategy and were analyzed according to the criteria of ancient DNA analysis to ensure that authentic DNA typing results were obtained from these ancient samples. Analysis of mtDNA hypervariable region sequence and coding region single nucleotide polymorphism (SNP) information revealed that Danwoong-mirra and Yoon-mirra belong to the East Asian mtDNA haplogroups D4 and M7c, respectively. The Y-STRs were analyzed in the male child mummy (Danwoong-mirra) using the AmpFlSTR® Yfiler PCR Amplification Kit and an in-house Y-miniplex plus system, and could be characterized in 4 loci with small amplicon size. The analysis of ABO gene SNPs using multiplex single base extension methods revealed that the ABO blood types of Danwoong-mirra and Yoon-mirra are AO01 and AB, respectively. The small size amplicon strategy and the authentication process in the present study will be effectively applicable to future genetic analyses of various forensic and ancient samples. FAU - Kim, Na Young AU - Kim NY AD - Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, 250 Seongsanno, Seodaemun-Gu, Seoul, 120-752, Korea. FAU - Lee, Hwan Young AU - Lee HY FAU - Park, Myung Jin AU - Park MJ FAU - Yang, Woo Ick AU - Yang WI FAU - Shin, Kyoung-Jin AU - Shin KJ LA - eng PT - Journal Article DEP - 20100321 PL - Netherlands TA - Mol Biol Rep JT - Molecular biology reports JID - 0403234 RN - 0 (ABO Blood-Group System) RN - 0 (DNA, Mitochondrial) SB - IM MH - ABO Blood-Group System/genetics MH - Adult MH - Child MH - Chromosomes, Human, Y/genetics MH - DNA, Mitochondrial/*genetics MH - Electrophoresis MH - Female MH - Genotype MH - Humans MH - Male MH - Microsatellite Repeats/genetics MH - *Mummies MH - Polymorphism, Single Nucleotide/genetics MH - Pregnancy MH - Republic of Korea MH - Sequence Analysis, DNA EDAT- 2010/03/23 06:00 MHDA- 2011/03/22 06:00 CRDT- 2010/03/23 06:00 PHST- 2009/11/12 00:00 [received] PHST- 2010/03/11 00:00 [accepted] PHST- 2010/03/23 06:00 [entrez] PHST- 2010/03/23 06:00 [pubmed] PHST- 2011/03/22 06:00 [medline] AID - 10.1007/s11033-010-0084-4 [doi] PST - ppublish SO - Mol Biol Rep. 2011 Jan;38(1):115-21. doi: 10.1007/s11033-010-0084-4. Epub 2010 Mar 21. PMID- 19617246 OWN - NLM STAT- MEDLINE DCOM- 20110520 LR - 20101116 IS - 1938-2723 (Electronic) IS - 1076-0296 (Linking) VI - 16 IP - 6 DP - 2010 Dec TI - Factor V Leiden in an Urartian, dating back to 1000 BC. PG - 679-83 LID - 10.1177/1076029609338045 [doi] AB - Factor V Leiden (FVL) is the most common monogenic disorder that causes activated protein C (APC) resistance, creating hyper-coagulation. The mutation shows an uneven geographic distribution, significantly high in European populations. The mutation is believed to have originated approximately 20 000 years ago probably from a geographic region close to Anatolia. This fact makes it noteworthy to search for the mutation in ancient populations that once lived in this area. One of these civilizations, Urartu was centered around Van Lake in Eastern Turkey. The archeological remains from the excavations of the region are dated back to 1000 BC. Teeth, taken from the excavations of Van Yoncatepe fortress, were taken into DNA analysis considering all the precautions for ancient DNA analysis. Multiplex STR (Short Tandem Repeats) analysis were performed both to determine the gender of the samples and to conclude that the samples are preserved from modern DNA contamination. After getting an 80% amplification success for amelogenin, a melting curve analysis using lightcycler was performed to determine the FVL genotype of each sample. Of the 60 samples, 1 gave a positive amplification result for FV gene and was found to be heterozygous. To date, the age of this mutation was estimated based on statistical calculations using haplotype frequencies; here for the first time, we report FVL in an ancient population of 3000 years. FAU - Alakoç, Yeşim Doğan AU - Alakoç YD AD - Institute of Biotechnology, Ankara University, Turkey. FAU - Aka, P Sema AU - Aka PS FAU - Eğin, Yonca AU - Eğin Y FAU - Akar, Nejat AU - Akar N LA - eng PT - Journal Article DEP - 20090717 PL - United States TA - Clin Appl Thromb Hemost JT - Clinical and applied thrombosis/hemostasis : official journal of the International Academy of Clinical and Applied Thrombosis/Hemostasis JID - 9508125 RN - 0 (factor V Leiden) RN - 9001-24-5 (Factor V) RN - 9007-49-2 (DNA) SB - IM MH - Activated Protein C Resistance/genetics MH - Archaeology MH - DNA/chemistry/*genetics MH - Factor V/*genetics/metabolism MH - *Fossils MH - Genetic Testing MH - Humans MH - Point Mutation MH - Tooth/*chemistry MH - Turkey EDAT- 2009/07/21 09:00 MHDA- 2011/05/21 06:00 CRDT- 2009/07/21 09:00 PHST- 2009/07/21 09:00 [entrez] PHST- 2009/07/21 09:00 [pubmed] PHST- 2011/05/21 06:00 [medline] AID - 1076029609338045 [pii] AID - 10.1177/1076029609338045 [doi] PST - ppublish SO - Clin Appl Thromb Hemost. 2010 Dec;16(6):679-83. doi: 10.1177/1076029609338045. Epub 2009 Jul 17. PMID- 21103372 OWN - NLM STAT- MEDLINE DCOM- 20110427 LR - 20211020 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 5 IP - 11 DP - 2010 Nov 16 TI - Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PG - e14004 LID - 10.1371/journal.pone.0014004 [doi] LID - e14004 AB - BACKGROUND: To utilize the power of high-throughput sequencers, target enrichment methods have been developed. The majority of these require reagents and equipment that are only available from commercial vendors and are not suitable for the targets that are a few kilobases in length. METHODOLOGY/PRINCIPAL FINDINGS: We describe a novel and economical method in which custom made long-range PCR products are used to capture complete human mitochondrial genomes from complex DNA mixtures. We use the method to capture 46 complete mitochondrial genomes in parallel and we sequence them on a single lane of an Illumina GA(II) instrument. CONCLUSIONS/SIGNIFICANCE: This method is economical and simple and particularly suitable for targets that can be amplified by PCR and do not contain highly repetitive sequences such as mtDNA. It has applications in population genetics and forensics, as well as studies of ancient DNA. FAU - Maricic, Tomislav AU - Maricic T AD - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. tomislav_maricic@eva.mpg.de FAU - Whitten, Mark AU - Whitten M FAU - Pääbo, Svante AU - Pääbo S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101116 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/chemistry/*genetics MH - Forensic Genetics/methods MH - Genetics, Population/methods MH - Genome, Mitochondrial/*genetics MH - Humans MH - Polymerase Chain Reaction/instrumentation/*methods MH - Reproducibility of Results MH - Sequence Analysis, DNA/instrumentation/*methods PMC - PMC2982832 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2010/11/26 06:00 MHDA- 2011/04/28 06:00 PMCR- 2010/11/16 CRDT- 2010/11/25 06:00 PHST- 2010/05/31 00:00 [received] PHST- 2010/10/26 00:00 [accepted] PHST- 2010/11/25 06:00 [entrez] PHST- 2010/11/26 06:00 [pubmed] PHST- 2011/04/28 06:00 [medline] PHST- 2010/11/16 00:00 [pmc-release] AID - 10-PONE-RA-19400R1 [pii] AID - 10.1371/journal.pone.0014004 [doi] PST - epublish SO - PLoS One. 2010 Nov 16;5(11):e14004. doi: 10.1371/journal.pone.0014004. PMID- 21085689 OWN - NLM STAT- MEDLINE DCOM- 20110131 LR - 20230525 IS - 1545-7885 (Electronic) IS - 1544-9173 (Print) IS - 1544-9173 (Linking) VI - 8 IP - 11 DP - 2010 Nov 9 TI - Ancient DNA from European early neolithic farmers reveals their near eastern affinities. PG - e1000536 LID - 10.1371/journal.pbio.1000536 [doi] LID - e1000536 AB - In Europe, the Neolithic transition (8,000-4,000 B.C.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500-4,900 calibrated B.C.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500-4,900 calibrated B.C.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic. FAU - Haak, Wolfgang AU - Haak W AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, Australia. wolfgang.haak@adelaide.edu.au FAU - Balanovsky, Oleg AU - Balanovsky O FAU - Sanchez, Juan J AU - Sanchez JJ FAU - Koshel, Sergey AU - Koshel S FAU - Zaporozhchenko, Valery AU - Zaporozhchenko V FAU - Adler, Christina J AU - Adler CJ FAU - Der Sarkissian, Clio S I AU - Der Sarkissian CS FAU - Brandt, Guido AU - Brandt G FAU - Schwarz, Carolin AU - Schwarz C FAU - Nicklisch, Nicole AU - Nicklisch N FAU - Dresely, Veit AU - Dresely V FAU - Fritsch, Barbara AU - Fritsch B FAU - Balanovska, Elena AU - Balanovska E FAU - Villems, Richard AU - Villems R FAU - Meller, Harald AU - Meller H FAU - Alt, Kurt W AU - Alt KW FAU - Cooper, Alan AU - Cooper A CN - Members of the Genographic Consortium LA - eng GR - WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101109 PL - United States TA - PLoS Biol JT - PLoS biology JID - 101183755 RN - 0 (DNA, Mitochondrial) SB - IM CIN - PLoS Biol. 2010 Nov 09;8(11):e1000535. doi: 10.1371/journal.pbio.1000535. PMID: 21085688 MH - *Agriculture MH - DNA, Mitochondrial/*genetics MH - *Emigration and Immigration MH - Europe MH - *Fossils MH - Humans PMC - PMC2976717 COIS- The authors have declared that no competing interests exist. FIR - Adhikarla, Syama IR - Adhikarla S FIR - Behar, Doron M IR - Behar DM FIR - Bertranpetit, Jaume IR - Bertranpetit J FIR - Clarke, Andrew C IR - Clarke AC FIR - Comas, David IR - Comas D FIR - Dulik, Matthew C IR - Dulik MC FIR - Erasmus, Christoff J IR - Erasmus CJ FIR - Gaieski, Jill B IR - Gaieski JB FIR - GaneshPrasad, ArunKumar IR - GaneshPrasad A FIR - Hobbs, Angela IR - Hobbs A FIR - Javed, Asif IR - Javed A FIR - Jin, Li IR - Jin L FIR - Kaplan, Matthew E IR - Kaplan ME FIR - Li, Shilin IR - Li S FIR - Martínez-Cruz, Begoña IR - Martínez-Cruz B FIR - Matisoo-Smith, Elizabeth A IR - Matisoo-Smith EA FIR - Melé, Marta IR - Melé M FIR - Merchant, Nirav C IR - Merchant NC FIR - Mitchell, R John IR - Mitchell RJ FIR - Owings, Amanda C IR - Owings AC FIR - Parida, Laxmi IR - Parida L FIR - Pitchappan, Ramasamy IR - Pitchappan R FIR - Platt, Daniel E IR - Platt DE FIR - Quintana-Murci, Lluis IR - Quintana-Murci L FIR - Renfrew, Colin IR - Renfrew C FIR - Rodrigues Lacerda, Daniela IR - Rodrigues Lacerda D FIR - Royyuru, Ajay K IR - Royyuru AK FIR - Santos, Fabrício R IR - Santos FR FIR - Schurr, Theodore G IR - Schurr TG FIR - Soodyall, Himla IR - Soodyall H FIR - Soria Hernanz, David F IR - Soria Hernanz DF FIR - Swamikrishnan, Pandikumar IR - Swamikrishnan P FIR - Tyler-Smith, Chris IR - Tyler-Smith C FIR - Valampuri, Kavitha John IR - Valampuri KJ FIR - Varatharajan, Arun Santhakumari IR - Varatharajan AS FIR - Vieira, Pedro Paulo IR - Vieira PP FIR - Wells, R Spencer IR - Wells RS FIR - Ziegle, Janet S IR - Ziegle JS EDAT- 2010/11/19 06:00 MHDA- 2011/02/01 06:00 PMCR- 2010/11/09 CRDT- 2010/11/19 06:00 PHST- 2010/03/18 00:00 [received] PHST- 2010/09/27 00:00 [accepted] PHST- 2010/11/19 06:00 [entrez] PHST- 2010/11/19 06:00 [pubmed] PHST- 2011/02/01 06:00 [medline] PHST- 2010/11/09 00:00 [pmc-release] AID - 10-PLBI-RA-6634R3 [pii] AID - 10.1371/journal.pbio.1000536 [doi] PST - epublish SO - PLoS Biol. 2010 Nov 9;8(11):e1000536. doi: 10.1371/journal.pbio.1000536. PMID- 21085688 OWN - NLM STAT- MEDLINE DCOM- 20110131 LR - 20211020 IS - 1545-7885 (Electronic) IS - 1544-9173 (Print) IS - 1544-9173 (Linking) VI - 8 IP - 11 DP - 2010 Nov 9 TI - Ancient DNA indicates farmers, not just farming, spread West. PG - e1000535 LID - 10.1371/journal.pbio.1000535 [doi] LID - e1000535 FAU - Robinson, Richard AU - Robinson R AD - Freelance Science Writer, Sherborn, Massachusetts, United States of America. rrobinson@nasw.org LA - eng PT - Comment PT - Journal Article DEP - 20101109 PL - United States TA - PLoS Biol JT - PLoS biology JID - 101183755 RN - 0 (DNA, Mitochondrial) SB - IM CON - PLoS Biol. 2010 Nov 09;8(11):e1000536. doi: 10.1371/journal.pbio.1000536. PMID: 21085689 MH - *Agriculture MH - DNA, Mitochondrial/*genetics MH - *Emigration and Immigration MH - Europe MH - Humans PMC - PMC2976716 COIS- The author has declared that no competing interests exist. EDAT- 2010/11/19 06:00 MHDA- 2011/02/01 06:00 PMCR- 2010/11/09 CRDT- 2010/11/19 06:00 PHST- 2010/11/19 06:00 [entrez] PHST- 2010/11/19 06:00 [pubmed] PHST- 2011/02/01 06:00 [medline] PHST- 2010/11/09 00:00 [pmc-release] AID - 10-PLBI-S-9481R2 [pii] AID - 10.1371/journal.pbio.1000535 [doi] PST - epublish SO - PLoS Biol. 2010 Nov 9;8(11):e1000535. doi: 10.1371/journal.pbio.1000535. PMID- 20703243 OWN - NLM STAT- MEDLINE DCOM- 20110211 LR - 20221207 IS - 1435-232X (Electronic) IS - 1434-5161 (Linking) VI - 55 IP - 10 DP - 2010 Oct TI - Polymorphisms and allele frequencies of the ABO blood group gene among the Jomon, Epi-Jomon and Okhotsk people in Hokkaido, northern Japan, revealed by ancient DNA analysis. PG - 691-6 LID - 10.1038/jhg.2010.90 [doi] AB - To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon/ Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon/Epi-Jomon and Okhotsk people were compared with those of the modern Asian, European and Oceanic populations. The genetic relationships inferred from principal component analyses indicated that both Jomon/Epi-Jomon and Okhotsk people are included in the same group as modern Asian populations. However, the genetic characteristics of these ancient populations in Hokkaido were significantly different from each other, which is in agreement with the conclusions from mitochondrial DNA and ABCC11 gene analyses that were previously reported. FAU - Sato, Takehiro AU - Sato T AD - Graduate School of Science, Hokkaido University, Sapporo, Japan. FAU - Kazuta, Hisako AU - Kazuta H FAU - Amano, Tetsuya AU - Amano T FAU - Ono, Hiroko AU - Ono H FAU - Ishida, Hajime AU - Ishida H FAU - Kodera, Haruto AU - Kodera H FAU - Matsumura, Hirofumi AU - Matsumura H FAU - Yoneda, Minoru AU - Yoneda M FAU - Dodo, Yukio AU - Dodo Y FAU - Masuda, Ryuichi AU - Masuda R LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100812 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (ABO Blood-Group System) SB - IM MH - ABO Blood-Group System/*genetics MH - Alleles MH - Archaeology MH - Asian People/*genetics MH - Ethnicity/*genetics MH - *Gene Frequency MH - History, Ancient MH - Humans MH - Japan MH - *Polymorphism, Genetic MH - Principal Component Analysis EDAT- 2010/08/13 06:00 MHDA- 2011/02/12 06:00 CRDT- 2010/08/13 06:00 PHST- 2010/08/13 06:00 [entrez] PHST- 2010/08/13 06:00 [pubmed] PHST- 2011/02/12 06:00 [medline] AID - jhg201090 [pii] AID - 10.1038/jhg.2010.90 [doi] PST - ppublish SO - J Hum Genet. 2010 Oct;55(10):691-6. doi: 10.1038/jhg.2010.90. Epub 2010 Aug 12. PMID- 20865042 OWN - NLM STAT- MEDLINE DCOM- 20110113 LR - 20211020 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 5 IP - 8 DP - 2010 Aug 26 TI - Detection of Mycobacterium leprae DNA from archaeological skeletal remains in Japan using whole genome amplification and polymerase chain reaction. PG - e12422 LID - e12422 [pii] LID - 10.1371/journal.pone.0012422 [doi] AB - BACKGROUND: Identification of pathogen DNA from archaeological human remains is a powerful tool in demonstrating that the infectious disease existed in the past. However, it is very difficult to detect trace amounts of DNA remnants attached to the human skeleton, especially from those buried in a humid atmosphere with a relatively high environmental temperature such as in Asia. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate Mycobacterium leprae DNA from archaeological skeletal remains in Japan by polymerase chain reaction, DNA sequencing and single nucleotide polymorphism (SNP) analysis. In addition, we have established a highly sensitive method of detecting DNA using a combination of whole genome amplification and polymerase chain reaction, or WGA-PCR, which provides superior sensitivity and specificity in detecting DNA from trace amounts of skeletal materials. CONCLUSION/SIGNIFICANCE: We have detected M. leprae DNA in archaeological skeletal remains for the first time in the Far East. Its SNP genotype corresponded to type 1; the first detected case worldwide of ancient M. leprae DNA. We also developed a highly sensitive method to detect ancient DNA by utilizing whole genome amplification. FAU - Suzuki, Koichi AU - Suzuki K AD - Laboratory of Molecular Diagnostics, Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan. koichis@nih.go.jp FAU - Takigawa, Wataru AU - Takigawa W FAU - Tanigawa, Kazunari AU - Tanigawa K FAU - Nakamura, Kazuaki AU - Nakamura K FAU - Ishido, Yuko AU - Ishido Y FAU - Kawashima, Akira AU - Kawashima A FAU - Wu, Huhehasi AU - Wu H FAU - Akama, Takeshi AU - Akama T FAU - Sue, Mariko AU - Sue M FAU - Yoshihara, Aya AU - Yoshihara A FAU - Mori, Shuichi AU - Mori S FAU - Ishii, Norihisa AU - Ishii N LA - eng PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100826 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Bacterial) SB - IM MH - *Archaeology MH - Base Sequence MH - *Cadaver MH - DNA, Bacterial/*genetics/isolation & purification MH - Genome, Bacterial MH - Humans MH - Japan MH - Molecular Sequence Data MH - Mycobacterium leprae/genetics/*isolation & purification MH - Polymerase Chain Reaction/*methods MH - Polymorphism, Single Nucleotide PMC - PMC2928730 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2010/09/25 06:00 MHDA- 2011/01/14 06:00 PMCR- 2010/08/26 CRDT- 2010/09/25 06:00 PHST- 2010/04/18 00:00 [received] PHST- 2010/08/04 00:00 [accepted] PHST- 2010/09/25 06:00 [entrez] PHST- 2010/09/25 06:00 [pubmed] PHST- 2011/01/14 06:00 [medline] PHST- 2010/08/26 00:00 [pmc-release] AID - e12422 [pii] AID - 10-PONE-RA-18056R1 [pii] AID - 10.1371/journal.pone.0012422 [doi] PST - epublish SO - PLoS One. 2010 Aug 26;5(8):e12422. doi: 10.1371/journal.pone.0012422. PMID- 20456521 OWN - NLM STAT- MEDLINE DCOM- 20110106 LR - 20240318 IS - 1469-7580 (Electronic) IS - 0021-8782 (Print) IS - 0021-8782 (Linking) VI - 217 IP - 1 DP - 2010 Jul TI - Auto-fluorescence emitted from the cell residues preserved in human tissues of medieval Korean mummies. PG - 67-75 LID - 10.1111/j.1469-7580.2010.01240.x [doi] AB - As a significant association has been established between residual ancient DNA (aDNA) and histological preservation, the morphological identification or confirmation of preserved cell residue in ancient tissues would greatly facilitate aDNA studies and enhance the definitiveness of their conclusions. However, morphological differentiation of cell residue from other tissue structures has always been difficult, even for experienced histologists, due to the severe degradation of cells over long burial durations. In the present study, using a fluorescence microscopy equipped with a specific type of filter set (excitation filter, 510-550 nm; dichroic mirror, 570 nm; emission filter, approximately 590 nm), we found that certain structures in well-preserved mummified tissues emitted auto-fluorescence. Those structures were actually cell residues (e.g. fragmented DNA), laser capture microdissection and Quantifiler kit analysis having shown that preservation of nuclear DNA correlates with auto-fluorescence emission in laser capture microdissection-captured areas. Detection of auto-fluorescence could be an effective means of identifying cell residues in ancient tissue, enabling selection of the well-preserved samples necessary in successful aDNA studies. FAU - Lim, Do-Seon AU - Lim DS AD - Department of Dental Hygiene, Eulji University, Sungnam, Korea. FAU - Oh, Chang Seok AU - Oh CS FAU - Lee, Sang Jun AU - Lee SJ FAU - Shin, Dong Hoon AU - Shin DH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100426 PL - England TA - J Anat JT - Journal of anatomy JID - 0137162 SB - IM MH - Cartilage/cytology MH - Cartilage, Articular/ultrastructure MH - Chondrocytes/ultrastructure MH - *Fluorescence MH - Humans MH - Kidney/cytology MH - Lung/cytology MH - Microdissection/methods MH - Microscopy, Confocal MH - Microscopy, Electron, Scanning MH - Microscopy, Fluorescence/methods MH - Mummies/*pathology MH - Paleopathology PMC - PMC2913013 EDAT- 2010/05/12 06:00 MHDA- 2011/01/07 06:00 PMCR- 2012/07/01 CRDT- 2010/05/12 06:00 PHST- 2010/05/12 06:00 [entrez] PHST- 2010/05/12 06:00 [pubmed] PHST- 2011/01/07 06:00 [medline] PHST- 2012/07/01 00:00 [pmc-release] AID - JOA1240 [pii] AID - 10.1111/j.1469-7580.2010.01240.x [doi] PST - ppublish SO - J Anat. 2010 Jul;217(1):67-75. doi: 10.1111/j.1469-7580.2010.01240.x. Epub 2010 Apr 26. PMID- 20514042 OWN - NLM STAT- MEDLINE DCOM- 20100902 LR - 20221207 IS - 1469-3178 (Electronic) IS - 1469-221X (Print) IS - 1469-221X (Linking) VI - 11 IP - 6 DP - 2010 Jun TI - History in a single hair. PG - 427-30 LID - 10.1038/embor.2010.70 [doi] AB - Museums are treasure troves of ancient DNA. Modern extraction and sequencing technology is key to putting the secrets of genetic history to use FAU - Wolinsky, Howard AU - Wolinsky H LA - eng PT - Historical Article PT - Journal Article PL - England TA - EMBO Rep JT - EMBO reports JID - 100963049 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Biological Evolution MH - DNA, Mitochondrial/*genetics/*isolation & purification MH - Extinction, Biological MH - Fossils MH - Genomics/methods MH - Geologic Sediments MH - Hair/*metabolism MH - History, Ancient MH - Humans MH - Inuit/genetics MH - Mammoths/genetics MH - *Museums MH - Paleontology/*methods MH - Sequence Analysis, DNA/economics/*methods PMC - PMC2892323 OAB - Modern extraction and sequencing technologies have given a huge boost to the emerging field of palaeogenomics. Howard Wolinsky explores how these advances help scientists to understand the function of ancient genes and their evolution. OABL- eng EDAT- 2010/06/02 06:00 MHDA- 2010/09/03 06:00 PMCR- 2011/06/01 CRDT- 2010/06/02 06:00 PHST- 2010/06/02 06:00 [entrez] PHST- 2010/06/02 06:00 [pubmed] PHST- 2010/09/03 06:00 [medline] PHST- 2011/06/01 00:00 [pmc-release] AID - embor201070 [pii] AID - 10.1038/embor.2010.70 [doi] PST - ppublish SO - EMBO Rep. 2010 Jun;11(6):427-30. doi: 10.1038/embor.2010.70. PMID- 20345871 OWN - NLM STAT- MEDLINE DCOM- 20101015 LR - 20111117 IS - 1744-313X (Electronic) IS - 1744-3121 (Linking) VI - 37 IP - 3 DP - 2010 Jun TI - Changes in frequency of IDDM-associated HLA DQB, CTLA4 and INS alleles. PG - 155-8 LID - 10.1111/j.1744-313X.2010.00896.x [doi] AB - The incidence of type 1 diabetes is increasing worldwide. In Poland, the number of cases tripled during the last two decades. The aim of this study was to test the hypothesis that the increase may be at least partly explained by a shift in predisposing alleles' frequencies - resulting from treating the otherwise lethal disease, generally better health care as well as selective pressure imposed by pathogens affecting humankind throughout history. The source of DNA was skeletal remains of 232 individuals excavated in four burial sites, dating back to 11th-14th centuries. With all necessary precautions required in ancient DNA analysis, frequencies of HLA DQB(57), CTLA4+49A/G and INS -23A/T alleles were assessed and compared with available data, characterising contemporary Polish population. Frequency of HLA DQB(57-Asp) protective allele is much higher in present-day population of Poland (50.6%) than in the group of 155 medieval specimens successfully typed for this polymorphism (28.4%, P < 0.001). Out of 86 medieval individuals typed for CTLA4+49A/G, 29.1% were homozygous for the predisposing G allele, which is significantly more than contemporarily - 7.6% (P < 0.001). No statistically significant difference was found in alleles and genotypes frequencies of INS-23A/T polymorphic site. Contrary to the initial assumptions, genetic predisposition towards type 1 diabetes, conferred by HLA DQB(57), CTLA4+49A/G and INS -23A/T alleles is much lower contemporarily than it was approximately 700 years before present. This suggests involvement of other than genetic factors in the fast growing incidence of the disease. FAU - Witas, H W AU - Witas HW AD - Department of Molecular Biology, Oncology, Medical University of Łódź, Łódź, Poland. FAU - Jedrychowska-Dańska, K AU - Jedrychowska-Dańska K FAU - Zawicki, P AU - Zawicki P LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100314 PL - England TA - Int J Immunogenet JT - International journal of immunogenetics JID - 101232337 RN - 0 (Antigens, CD) RN - 0 (CTLA-4 Antigen) RN - 0 (CTLA4 protein, human) RN - 0 (HLA-DQ Antigens) RN - 0 (HLA-DQ beta-Chains) RN - 0 (HLA-DQB1 antigen) RN - 0 (Insulin) RN - 9007-49-2 (DNA) SB - IM MH - Alleles MH - Antigens, CD/*genetics MH - CTLA-4 Antigen MH - DNA/genetics/isolation & purification MH - Diabetes Mellitus, Type 1/*genetics/history/immunology MH - Gene Frequency MH - Genotype MH - HLA-DQ Antigens/*genetics MH - HLA-DQ beta-Chains MH - History, Medieval MH - Humans MH - Insulin/*genetics MH - Poland EDAT- 2010/03/30 06:00 MHDA- 2010/10/16 06:00 CRDT- 2010/03/30 06:00 PHST- 2010/03/30 06:00 [entrez] PHST- 2010/03/30 06:00 [pubmed] PHST- 2010/10/16 06:00 [medline] AID - EJI896 [pii] AID - 10.1111/j.1744-313X.2010.00896.x [doi] PST - ppublish SO - Int J Immunogenet. 2010 Jun;37(3):155-8. doi: 10.1111/j.1744-313X.2010.00896.x. Epub 2010 Mar 14. PMID- 20229501 OWN - NLM STAT- MEDLINE DCOM- 20100915 LR - 20100525 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 142 IP - 2 DP - 2010 Jun TI - Technical note: PCR analysis of minimum target amount of ancient DNA. PG - 321-7 LID - 10.1002/ajpa.21268 [doi] AB - The study of ancient DNA plays an important role in archaeological and palaeontological research as well as in pathology and forensics. Here, we present a new tool for ancient DNA analysis, which overcomes contamination problems, DNA degradation, and the negative effects of PCR inhibitors while reducing the amount of starting target material in the picogram range. Ancient bone samples from four Egyptian mummies were examined by combining laser microdissection, conventional DNA extraction, and low-volume PCR. Initially, several bone particles (osteons) in the micrometer range were extracted by laser microdissection. Subsequently, ancient DNA amplification was performed to verify our extraction method. Amelogenin and beta-actin gene specific fragments were amplified via low-volume PCR in a total reaction volume of 1 microl. Results of microdissected mummy DNA samples were compared to mummy DNA, which was extracted using a standard DNA extraction method based on pulverization of bone material. Our results highlight the combination of laser microdissection and low-volume PCR as a promising new technique in ancient DNA analysis. CI - Copyright 2010 Wiley-Liss, Inc. FAU - Woide, Daniela AU - Woide D AD - Helmholtz Zentrum Munich, Institute of Radiation Protection, 85764 Neuherberg, Germany. FAU - Zink, Albert AU - Zink A FAU - Thalhammer, Stefan AU - Thalhammer S LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Actins) RN - 0 (Amelogenin) RN - 9007-49-2 (DNA) SB - IM MH - Actins/genetics MH - Amelogenin/genetics MH - DNA/analysis/*isolation & purification MH - Egypt MH - Electrophoresis, Polyacrylamide Gel MH - Haversian System/chemistry MH - Humans MH - Microdissection/methods MH - *Mummies MH - Polymerase Chain Reaction/*methods MH - Sequence Analysis, DNA/*methods EDAT- 2010/03/17 06:00 MHDA- 2010/09/16 06:00 CRDT- 2010/03/16 06:00 PHST- 2010/03/16 06:00 [entrez] PHST- 2010/03/17 06:00 [pubmed] PHST- 2010/09/16 06:00 [medline] AID - 10.1002/ajpa.21268 [doi] PST - ppublish SO - Am J Phys Anthropol. 2010 Jun;142(2):321-7. doi: 10.1002/ajpa.21268. PMID- 20498832 OWN - NLM STAT- MEDLINE DCOM- 20100907 LR - 20211020 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 5 IP - 5 DP - 2010 May 14 TI - The microcephalin ancestral allele in a Neanderthal individual. PG - e10648 LID - 10.1371/journal.pone.0010648 [doi] LID - e10648 AB - BACKGROUND: The high frequency (around 0.70 worldwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the first PCR amplification and high-throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. CONCLUSIONS/SIGNIFICANCE: The MCPH1 genotype of the Monti Lessini (MLS) Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA. FAU - Lari, Martina AU - Lari M AD - Dipartimento di Biologia Evoluzionistica, Laboratori di Antropologia, Università di Firenze, Firenze, Italy. FAU - Rizzi, Ermanno AU - Rizzi E FAU - Milani, Lucio AU - Milani L FAU - Corti, Giorgio AU - Corti G FAU - Balsamo, Carlotta AU - Balsamo C FAU - Vai, Stefania AU - Vai S FAU - Catalano, Giulio AU - Catalano G FAU - Pilli, Elena AU - Pilli E FAU - Longo, Laura AU - Longo L FAU - Condemi, Silvana AU - Condemi S FAU - Giunti, Paolo AU - Giunti P FAU - Hänni, Catherine AU - Hänni C FAU - De Bellis, Gianluca AU - De Bellis G FAU - Orlando, Ludovic AU - Orlando L FAU - Barbujani, Guido AU - Barbujani G FAU - Caramelli, David AU - Caramelli D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100514 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Cell Cycle Proteins) RN - 0 (Cytoskeletal Proteins) RN - 0 (DNA, Mitochondrial) RN - 0 (MCPH1 protein, human) RN - 0 (Nerve Tissue Proteins) SB - IM MH - *Alleles MH - Cell Cycle Proteins MH - Cytoskeletal Proteins MH - DNA, Mitochondrial/genetics MH - *Fossils MH - Genetic Loci/genetics MH - Humans MH - Nerve Tissue Proteins/*genetics MH - *Phylogeny MH - Sequence Analysis, DNA PMC - PMC2871044 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2010/05/26 06:00 MHDA- 2010/09/08 06:00 PMCR- 2010/05/14 CRDT- 2010/05/26 06:00 PHST- 2010/01/19 00:00 [received] PHST- 2010/04/23 00:00 [accepted] PHST- 2010/05/26 06:00 [entrez] PHST- 2010/05/26 06:00 [pubmed] PHST- 2010/09/08 06:00 [medline] PHST- 2010/05/14 00:00 [pmc-release] AID - 10-PONE-RA-15630R1 [pii] AID - 10.1371/journal.pone.0010648 [doi] PST - epublish SO - PLoS One. 2010 May 14;5(5):e10648. doi: 10.1371/journal.pone.0010648. PMID- 20463713 OWN - NLM STAT- MEDLINE DCOM- 20100615 LR - 20221207 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 465 IP - 7295 DP - 2010 May 13 TI - Ancient DNA set to rewrite human history. PG - 148-9 LID - 10.1038/465148a [doi] FAU - Dalton, Rex AU - Dalton R LA - eng PT - Historical Article PT - News PL - England TA - Nature JT - Nature JID - 0410462 SB - IM MH - Animals MH - Climate MH - *Emigration and Immigration MH - *Evolution, Molecular MH - Fossils MH - Genome, Human/genetics MH - Greenland MH - History, Ancient MH - Hominidae/*genetics MH - Humans MH - Inuit/genetics MH - *Phylogeny MH - Sequence Analysis, DNA EDAT- 2010/05/14 06:00 MHDA- 2010/06/16 06:00 CRDT- 2010/05/14 06:00 PHST- 2010/05/14 06:00 [entrez] PHST- 2010/05/14 06:00 [pubmed] PHST- 2010/06/16 06:00 [medline] AID - 465148a [pii] AID - 10.1038/465148a [doi] PST - ppublish SO - Nature. 2010 May 13;465(7295):148-9. doi: 10.1038/465148a. PMID- 20448179 OWN - NLM STAT- MEDLINE DCOM- 20100518 LR - 20211020 IS - 1095-9203 (Electronic) IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 328 IP - 5979 DP - 2010 May 7 TI - Targeted investigation of the Neandertal genome by array-based sequence capture. PG - 723-5 LID - 10.1126/science.1188046 [doi] AB - It is now possible to perform whole-genome shotgun sequencing as well as capture of specific genomic regions for extinct organisms. However, targeted resequencing of large parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of approximately 99.8% microbial DNA. Using this approach, we have sequenced approximately 14,000 protein-coding positions inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals. FAU - Burbano, Hernán A AU - Burbano HA AD - Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. FAU - Hodges, Emily AU - Hodges E FAU - Green, Richard E AU - Green RE FAU - Briggs, Adrian W AU - Briggs AW FAU - Krause, Johannes AU - Krause J FAU - Meyer, Matthias AU - Meyer M FAU - Good, Jeffrey M AU - Good JM FAU - Maricic, Tomislav AU - Maricic T FAU - Johnson, Philip L F AU - Johnson PL FAU - Xuan, Zhenyu AU - Xuan Z FAU - Rooks, Michelle AU - Rooks M FAU - Bhattacharjee, Arindam AU - Bhattacharjee A FAU - Brizuela, Leonardo AU - Brizuela L FAU - Albert, Frank W AU - Albert FW FAU - de la Rasilla, Marco AU - de la Rasilla M FAU - Fortea, Javier AU - Fortea J FAU - Rosas, Antonio AU - Rosas A FAU - Lachmann, Michael AU - Lachmann M FAU - Hannon, Gregory J AU - Hannon GJ FAU - Pääbo, Svante AU - Pääbo S LA - eng GR - P01 CA013106/CA/NCI NIH HHS/United States GR - P01 CA013106-38/CA/NCI NIH HHS/United States GR - P01 CA013106-39/CA/NCI NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Proteins) SB - IM CIN - Nat Rev Genet. 2010 Jul;11(7):456. doi: 10.1038/nrg2821. PMID: 20517343 MH - Amino Acid Substitution MH - Animals MH - Fossils MH - Genes MH - *Genome MH - *Genome, Human MH - Hominidae/*genetics MH - Humans MH - Nucleic Acid Hybridization MH - Oligonucleotide Array Sequence Analysis/*methods MH - Pan troglodytes/genetics MH - Proteins/chemistry/genetics MH - Sequence Alignment MH - Sequence Analysis, DNA/*methods PMC - PMC3140021 MID - NIHMS249667 EDAT- 2010/05/08 06:00 MHDA- 2010/05/19 06:00 PMCR- 2011/07/20 CRDT- 2010/05/08 06:00 PHST- 2010/05/08 06:00 [entrez] PHST- 2010/05/08 06:00 [pubmed] PHST- 2010/05/19 06:00 [medline] PHST- 2011/07/20 00:00 [pmc-release] AID - 328/5979/723 [pii] AID - 10.1126/science.1188046 [doi] PST - ppublish SO - Science. 2010 May 7;328(5979):723-5. doi: 10.1126/science.1188046. PMID- 20414896 OWN - NLM STAT- MEDLINE DCOM- 20100721 LR - 20100428 IS - 1521-1878 (Electronic) IS - 0265-9247 (Linking) VI - 32 IP - 5 DP - 2010 May TI - Analysis of ancient human genomes: using next generation sequencing, 20-fold coverage of the genome of a 4,000-year-old human from Greenland has been obtained. PG - 388-91 LID - 10.1002/bies.201000026 [doi] AB - High-capacity sequencing technologies have dramatically reduced both the cost and time required to generate complete human genome sequences. Besides expanding our knowledge about existing diversity, the nature of these technologies makes it possible to extend knowledge in yet another dimension: time. Recently, the complete genome sequence of a 4,000-year-old human from the Saqqaq culture of Greenland was determined to 20-fold coverage. These data make it possible to investigate the population affinities of this enigmatic culture and, by identifying several phenotypic traits of this individual, provide a limited glimpse into how these people may have looked. While undoubtedly a milestone in ancient DNA research, the cost to generate an ancient genome, even from such an exceptionally preserved specimen, remains out of reach for most. Nonetheless, recently developed DNA capture methods, already applied to Neanderthal and fossil human mitochondrial DNA, may soon make large-scale genome-wide analysis of ancient human diversity a reality, providing a fresh look at human population history. FAU - Shapiro, Beth AU - Shapiro B AD - Department of Biology, The Pennsylvania State University, University Park, PA, USA. FAU - Hofreiter, Michael AU - Hofreiter M LA - eng PT - Journal Article PL - United States TA - Bioessays JT - BioEssays : news and reviews in molecular, cellular and developmental biology JID - 8510851 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - DNA, Mitochondrial/genetics MH - Fossils MH - Genome, Human/*genetics MH - Greenland MH - Humans MH - Sequence Analysis, DNA/*methods EDAT- 2010/04/24 06:00 MHDA- 2010/07/22 06:00 CRDT- 2010/04/24 06:00 PHST- 2010/04/24 06:00 [entrez] PHST- 2010/04/24 06:00 [pubmed] PHST- 2010/07/22 06:00 [medline] AID - 10.1002/bies.201000026 [doi] PST - ppublish SO - Bioessays. 2010 May;32(5):388-91. doi: 10.1002/bies.201000026. PMID- 20404179 OWN - NLM STAT- MEDLINE DCOM- 20100602 LR - 20221207 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 107 IP - 17 DP - 2010 Apr 27 TI - Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. PG - 7686-91 LID - 10.1073/pnas.0912264107 [doi] AB - The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as "cryptic domestication," given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East. FAU - Larson, Greger AU - Larson G AD - State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China. greger.larson@durham.ac.uk FAU - Liu, Ranran AU - Liu R FAU - Zhao, Xingbo AU - Zhao X FAU - Yuan, Jing AU - Yuan J FAU - Fuller, Dorian AU - Fuller D FAU - Barton, Loukas AU - Barton L FAU - Dobney, Keith AU - Dobney K FAU - Fan, Qipeng AU - Fan Q FAU - Gu, Zhiliang AU - Gu Z FAU - Liu, Xiao-Hui AU - Liu XH FAU - Luo, Yunbing AU - Luo Y FAU - Lv, Peng AU - Lv P FAU - Andersson, Leif AU - Andersson L FAU - Li, Ning AU - Li N LA - eng SI - GENBANK/FJ601390 SI - GENBANK/FJ601391 SI - GENBANK/FJ601392 SI - GENBANK/FJ601393 SI - GENBANK/FJ601394 SI - GENBANK/FJ601395 SI - GENBANK/FJ601396 SI - GENBANK/FJ601397 SI - GENBANK/FJ601398 SI - GENBANK/FJ601399 SI - GENBANK/FJ601400 SI - GENBANK/FJ601401 SI - GENBANK/FJ601402 SI - GENBANK/FJ601403 SI - GENBANK/FJ601404 SI - GENBANK/FJ601405 SI - GENBANK/FJ601406 SI - GENBANK/FJ601407 SI - GENBANK/FJ601408 SI - GENBANK/FJ601409 SI - GENBANK/FJ601410 SI - GENBANK/FJ601411 SI - GENBANK/FJ601412 SI - GENBANK/FJ601413 SI - GENBANK/FJ601414 SI - GENBANK/FJ601415 SI - GENBANK/FJ601416 SI - GENBANK/FJ601417 SI - GENBANK/FJ601418 SI - GENBANK/FJ601419 SI - GENBANK/FJ601420 SI - GENBANK/FJ601421 SI - GENBANK/FJ601422 SI - GENBANK/FJ601423 SI - GENBANK/FJ601424 SI - GENBANK/FJ601425 SI - GENBANK/FJ601426 SI - GENBANK/FJ601427 SI - GENBANK/FJ601428 SI - GENBANK/FJ601429 SI - GENBANK/FJ601430 SI - GENBANK/FJ601431 SI - GENBANK/FJ601432 SI - GENBANK/FJ601433 SI - GENBANK/FJ601434 SI - GENBANK/FJ601435 SI - GENBANK/FJ601436 SI - GENBANK/FJ601437 SI - GENBANK/FJ601438 SI - GENBANK/FJ601439 SI - GENBANK/FJ601440 SI - GENBANK/FJ601441 SI - GENBANK/FJ601442 SI - GENBANK/FJ601443 SI - GENBANK/FJ601444 SI - GENBANK/FJ601445 SI - GENBANK/FJ601446 SI - GENBANK/FJ601447 SI - GENBANK/FJ601448 SI - GENBANK/FJ601449 SI - GENBANK/FJ601450 SI - GENBANK/FJ601451 SI - GENBANK/FJ601452 SI - GENBANK/FJ601453 SI - GENBANK/FJ601454 SI - GENBANK/FJ601455 SI - GENBANK/FJ601456 SI - GENBANK/FJ601457 SI - GENBANK/FJ601458 SI - GENBANK/FJ601459 SI - GENBANK/FJ601460 SI - GENBANK/FJ601461 SI - GENBANK/FJ601462 SI - GENBANK/FJ601463 SI - GENBANK/FJ601464 SI - GENBANK/FJ601465 SI - GENBANK/FJ601466 SI - GENBANK/FJ601467 SI - GENBANK/FJ601468 SI - GENBANK/FJ601469 SI - GENBANK/FJ601470 SI - GENBANK/FJ601471 SI - GENBANK/FJ601472 SI - GENBANK/FJ601473 SI - GENBANK/FJ601474 SI - GENBANK/FJ601475 SI - GENBANK/FJ601476 SI - GENBANK/FJ601477 SI - GENBANK/FJ601478 SI - GENBANK/FJ601479 SI - GENBANK/FJ601480 SI - GENBANK/FJ601481 SI - GENBANK/FJ601482 SI - GENBANK/FJ601483 SI - GENBANK/FJ601484 SI - GENBANK/FJ601485 SI - GENBANK/FJ601486 SI - GENBANK/FJ601487 SI - GENBANK/FJ601488 SI - GENBANK/FJ601489 SI - GENBANK/FJ601490 SI - GENBANK/FJ601491 SI - GENBANK/FJ601492 SI - GENBANK/FJ601493 SI - GENBANK/FJ601494 SI - GENBANK/FJ601495 SI - GENBANK/FJ601496 SI - GENBANK/FJ601497 SI - GENBANK/FJ601498 SI - GENBANK/FJ601499 SI - GENBANK/FJ601500 SI - GENBANK/FJ601501 SI - GENBANK/FJ601502 SI - GENBANK/FJ601503 SI - GENBANK/FJ601504 SI - GENBANK/FJ601505 SI - GENBANK/FJ601506 SI - GENBANK/FJ601507 SI - GENBANK/FJ601508 SI - GENBANK/FJ601509 SI - GENBANK/FJ601510 SI - GENBANK/FJ601511 SI - GENBANK/FJ601512 SI - GENBANK/FJ601513 SI - GENBANK/FJ601514 SI - GENBANK/FJ601515 SI - GENBANK/FJ601516 SI - GENBANK/FJ601517 SI - GENBANK/FJ601518 SI - GENBANK/FJ601519 SI - GENBANK/FJ601520 SI - GENBANK/FJ601521 SI - GENBANK/FJ601522 SI - GENBANK/FJ601523 SI - GENBANK/FJ601524 SI - GENBANK/FJ601525 SI - GENBANK/FJ601526 SI - GENBANK/FJ601527 SI - GENBANK/FJ601528 SI - GENBANK/FJ601529 SI - GENBANK/FJ601530 SI - GENBANK/FJ601531 SI - GENBANK/FJ601532 SI - GENBANK/FJ601533 SI - GENBANK/FJ601534 SI - GENBANK/FJ601535 SI - GENBANK/FJ601536 SI - GENBANK/FJ601537 SI - GENBANK/FJ601538 SI - GENBANK/FJ601539 SI - GENBANK/FJ601540 SI - GENBANK/FJ601541 SI - GENBANK/FJ601542 SI - GENBANK/FJ601543 SI - GENBANK/FJ601544 SI - GENBANK/FJ601545 SI - GENBANK/FJ601546 SI - GENBANK/FJ601547 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100419 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/*history MH - *Animal Migration MH - Animals MH - Base Sequence MH - Cluster Analysis MH - DNA, Mitochondrial/*genetics MH - Demography MH - *Evolution, Molecular MH - Asia, Eastern MH - *Fossils MH - Geography MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - *Phylogeny MH - Sequence Analysis, DNA MH - *Sus scrofa PMC - PMC2867865 COIS- The authors declare no conflict of interest. EDAT- 2010/04/21 06:00 MHDA- 2010/06/03 06:00 PMCR- 2010/04/19 CRDT- 2010/04/21 06:00 PHST- 2010/04/21 06:00 [entrez] PHST- 2010/04/21 06:00 [pubmed] PHST- 2010/06/03 06:00 [medline] PHST- 2010/04/19 00:00 [pmc-release] AID - 0912264107 [pii] AID - 200912264 [pii] AID - 10.1073/pnas.0912264107 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7686-91. doi: 10.1073/pnas.0912264107. Epub 2010 Apr 19. PMID- 20649402 OWN - NLM STAT- MEDLINE DCOM- 20110303 LR - 20110418 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 82 IP - 2 DP - 2010 Apr TI - Ancient DNA methodology: thoughts from Brian M. Kemp and David Glenn Smith on "Mitochondrial DNA of protohistoric remains of an Arikara population from South Dakota". PG - 227-38 LID - 10.3378/027.082.0207 [doi] FAU - Kemp, Brian M AU - Kemp BM FAU - Glenn Smith, David AU - Glenn Smith D LA - eng PT - Comment PT - Historical Article PT - Letter PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM CON - Hum Biol. 2010 Apr;82(2):157-78. doi: 10.3378/027.082.0203. PMID: 20649398 MH - Animals MH - DNA, Mitochondrial/*analysis MH - Gene Amplification MH - Genetic Variation MH - Genetics, Population MH - History, Ancient MH - Humans MH - Indians, North American/genetics/*history MH - Phylogeny MH - Polymerase Chain Reaction MH - South Dakota EDAT- 2010/07/24 06:00 MHDA- 2011/03/04 06:00 CRDT- 2010/07/24 06:00 PHST- 2010/07/24 06:00 [entrez] PHST- 2010/07/24 06:00 [pubmed] PHST- 2011/03/04 06:00 [medline] AID - 10.3378/027.082.0207 [doi] PST - ppublish SO - Hum Biol. 2010 Apr;82(2):227-38. doi: 10.3378/027.082.0207. PMID- 20649397 OWN - NLM STAT- MEDLINE DCOM- 20110303 LR - 20110418 IS - 1534-6617 (Electronic) IS - 0018-7143 (Linking) VI - 82 IP - 2 DP - 2010 Apr TI - Investigation of ancient DNA from Western Siberia and the Sargat culture. PG - 143-56 LID - 10.3378/027.082.0202 [doi] AB - Mitochondrial DNA from 14 archaeological samples at the Ural State University in Yekaterinburg, Russia, was extracted to test the feasibility of ancient DNA work on their collection. These samples come from a number of sites that fall into two groupings. Seven samples are from three sites, dating to the 8th-12th century AD, that belong to a northern group of what are thought to be Ugrians, who lived along the Ural Mountains in northwestern Siberia. The remaining seven samples are from two sites that belong to a southern group representing the Sargat culture, dating between roughly the 5th century BC and the 5th century AD, from southwestern Siberia near the Ural Mountains and the present-day Kazakhstan border. The samples are derived from several burial types, including kurgan burials. They also represent a number of different skeletal elements and a range of observed preservation. The northern sites repeatedly failed to amplify after multiple extraction and amplification attempts, but the samples from the southern sites were successfully extracted and amplified. The sequences obtained from the southern sites support the hypothesis that the Sargat culture was a potential zone of intermixture between native Ugrian and/or Siberian populations and steppe peoples from the south, possibly early Iranian or Indo-Iranian, which has been previously suggested by archaeological analysis. FAU - Bennett, Casey C AU - Bennett CC AD - Department of Anthropology, Indiana University, Bloomington, IN, USA. FAU - Kaestle, Frederika A AU - Kaestle FA LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM MH - *Culture MH - DNA, Mitochondrial/analysis/genetics/*history MH - Feasibility Studies MH - Female MH - Gene Amplification MH - Gene Flow MH - Genetic Variation MH - Genetics, Population/*methods MH - Haplotypes/*genetics MH - History, Ancient MH - Humans MH - Mutation MH - Prevalence MH - Siberia EDAT- 2010/07/24 06:00 MHDA- 2011/03/04 06:00 CRDT- 2010/07/24 06:00 PHST- 2010/07/24 06:00 [entrez] PHST- 2010/07/24 06:00 [pubmed] PHST- 2011/03/04 06:00 [medline] AID - 10.3378/027.082.0202 [doi] PST - ppublish SO - Hum Biol. 2010 Apr;82(2):143-56. doi: 10.3378/027.082.0202. PMID- 20186156 OWN - NLM STAT- MEDLINE DCOM- 20100823 LR - 20221207 IS - 1435-232X (Electronic) IS - 1434-5161 (Linking) VI - 55 IP - 4 DP - 2010 Apr TI - Ancient DNA from nomads in 2500-year-old archeological sites of Pengyang, China. PG - 215-8 LID - 10.1038/jhg.2010.8 [doi] AB - Six human remains (dating approximately 2500 years ago) were excavated from Pengyang, China, an area occupied by both ancient nomadic and farming people. The funerary objects found with these remains suggested they were nomads. To further confirm their ancestry, we analyzed both the maternal lineages and paternal lineages of the ancient DNA. From the mitochondrial DNA, six haplotypes were identified as three haplogroups: C, D4 and M10. The haplotype-sharing populations and phylogenetic analyses revealed that these individuals were closely associated with the ancient Xiongnu and modern northern Asians. Single-nucleotide polymorphism analysis of Y chromosomes from four male samples that were typed as haplogroup Q indicated that these people had originated in Siberia. These results show that these ancient people from Pengyang present a close genetic affinity to nomadic people, indicating that northern nomads had reached the Central Plain area of China nearly 2500 years ago. FAU - Zhao, Yong-Bin AU - Zhao YB AD - Laboratory of Ancient DNA, Research Center for Chinese Frontier Archaeology of Jilin University, Changchun, China. FAU - Li, Hong-Jie AU - Li HJ FAU - Cai, Da-Wei AU - Cai DW FAU - Li, Chun-Xiang AU - Li CX FAU - Zhang, Quan-Chao AU - Zhang QC FAU - Zhu, Hong AU - Zhu H FAU - Zhou, Hui AU - Zhou H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100226 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - China MH - DNA, Mitochondrial/classification/*genetics MH - Asia, Eastern/ethnology MH - Female MH - *Fossils MH - Haplotypes MH - Humans MH - Male MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Siberia/ethnology MH - *Transients and Migrants EDAT- 2010/02/27 06:00 MHDA- 2010/08/24 06:00 CRDT- 2010/02/27 06:00 PHST- 2010/02/27 06:00 [entrez] PHST- 2010/02/27 06:00 [pubmed] PHST- 2010/08/24 06:00 [medline] AID - jhg20108 [pii] AID - 10.1038/jhg.2010.8 [doi] PST - ppublish SO - J Hum Genet. 2010 Apr;55(4):215-8. doi: 10.1038/jhg.2010.8. Epub 2010 Feb 26. PMID- 20028723 OWN - NLM STAT- MEDLINE DCOM- 20100422 LR - 20211020 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 38 IP - 6 DP - 2010 Apr TI - Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. PG - e87 LID - 10.1093/nar/gkp1163 [doi] AB - DNA sequences determined from ancient organisms have high error rates, primarily due to uracil bases created by cytosine deamination. We use synthetic oligonucleotides, as well as DNA extracted from mammoth and Neandertal remains, to show that treatment with uracil-DNA-glycosylase and endonuclease VIII removes uracil residues from ancient DNA and repairs most of the resulting abasic sites, leaving undamaged parts of the DNA fragments intact. Neandertal DNA sequences determined with this protocol have greatly increased accuracy. In addition, our results demonstrate that Neandertal DNA retains in vivo patterns of CpG methylation, potentially allowing future studies of gene inactivation and imprinting in ancient organisms. FAU - Briggs, Adrian W AU - Briggs AW AD - Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. briggs@eva.mpg.de FAU - Stenzel, Udo AU - Stenzel U FAU - Meyer, Matthias AU - Meyer M FAU - Krause, Johannes AU - Krause J FAU - Kircher, Martin AU - Kircher M FAU - Pääbo, Svante AU - Pääbo S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091222 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Oligonucleotides) RN - 8J337D1HZY (Cytosine) RN - EC 3.1.25.1 (Deoxyribonuclease (Pyrimidine Dimer)) RN - EC 3.2.2.- (Uracil-DNA Glycosidase) SB - IM MH - Animals MH - CpG Islands MH - Cytosine/chemistry MH - *DNA Methylation MH - DNA Repair MH - Deamination MH - Deoxyribonuclease (Pyrimidine Dimer) MH - Hominidae/genetics MH - Humans MH - Mammoths/genetics MH - Oligonucleotides/chemistry MH - Sequence Analysis, DNA/*methods MH - Uracil-DNA Glycosidase PMC - PMC2847228 EDAT- 2009/12/24 06:00 MHDA- 2010/04/23 06:00 PMCR- 2009/12/22 CRDT- 2009/12/24 06:00 PHST- 2009/12/24 06:00 [entrez] PHST- 2009/12/24 06:00 [pubmed] PHST- 2010/04/23 06:00 [medline] PHST- 2009/12/22 00:00 [pmc-release] AID - gkp1163 [pii] AID - 10.1093/nar/gkp1163 [doi] PST - ppublish SO - Nucleic Acids Res. 2010 Apr;38(6):e87. doi: 10.1093/nar/gkp1163. Epub 2009 Dec 22. PMID- 19955482 OWN - NLM STAT- MEDLINE DCOM- 20100512 LR - 20100317 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 27 IP - 4 DP - 2010 Apr TI - Inferring genealogical processes from patterns of Bronze-Age and modern DNA variation in Sardinia. PG - 875-86 LID - 10.1093/molbev/msp292 [doi] AB - The ancient inhabitants of a region are often regarded as ancestral, and hence genetically related, to the modern dwellers (for instance, in studies of admixture), but so far, this assumption has not been tested empirically using ancient DNA data. We studied mitochondrial DNA (mtDNA) variation in Sardinia, across a time span of 2,500 years, comparing 23 Bronze-Age (nuragic) mtDNA sequences with those of 254 modern individuals from two regions, Ogliastra (a likely genetic isolate) and Gallura, and considering the possible impact of gene flow from mainland Italy. To understand the genealogical relationships between past and present populations, we developed seven explicit demographic models; we tested whether these models can account for the levels and patterns of genetic diversity in the data and which one does it best. Extensive simulation based on a serial coalescent algorithm allowed us to compare the posterior probability of each model and estimate the relevant evolutionary (mutation and migration rates) and demographic (effective population sizes, times since population splits) parameters, by approximate Bayesian computations. We then validated the analyses by investigating how well parameters estimated from the simulated data can reproduce the observed data set. We show that a direct genealogical continuity between Bronze-Age Sardinians and the current people of Ogliastra, but not Gallura, has a much higher probability than any alternative scenarios and that genetic diversity in Gallura evolved largely independently, owing in part to gene flow from the mainland. FAU - Ghirotto, Silvia AU - Ghirotto S AD - Dipartimento di Biologia ed Evoluzione, Università di Ferrara, Ferrara, Italy. FAU - Mona, Stefano AU - Mona S FAU - Benazzo, Andrea AU - Benazzo A FAU - Paparazzo, Francesco AU - Paparazzo F FAU - Caramelli, David AU - Caramelli D FAU - Barbujani, Guido AU - Barbujani G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091202 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration MH - Gene Flow MH - *Genealogy and Heraldry MH - Humans MH - Italy MH - Population Density EDAT- 2009/12/04 06:00 MHDA- 2010/05/13 06:00 CRDT- 2009/12/04 06:00 PHST- 2009/12/04 06:00 [entrez] PHST- 2009/12/04 06:00 [pubmed] PHST- 2010/05/13 06:00 [medline] AID - msp292 [pii] AID - 10.1093/molbev/msp292 [doi] PST - ppublish SO - Mol Biol Evol. 2010 Apr;27(4):875-86. doi: 10.1093/molbev/msp292. Epub 2009 Dec 2. PMID- 20339040 OWN - NLM STAT- MEDLINE DCOM- 20100413 LR - 20101118 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 327 IP - 5973 DP - 2010 Mar 26 TI - Human evolution. Ancient DNA from Siberia fingers a possible new human lineage. PG - 1566-7 LID - 10.1126/science.327.5973.1566-b [doi] FAU - Balter, Michael AU - Balter M LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - *Biological Evolution MH - DNA, Mitochondrial/chemistry/*genetics MH - Finger Phalanges MH - Genome, Mitochondrial MH - Hominidae/*classification/genetics MH - Humans MH - Sequence Analysis, DNA MH - Sequence Homology, Nucleic Acid MH - Siberia MH - Time EDAT- 2010/03/27 06:00 MHDA- 2010/04/14 06:00 CRDT- 2010/03/27 06:00 PHST- 2010/03/27 06:00 [entrez] PHST- 2010/03/27 06:00 [pubmed] PHST- 2010/04/14 06:00 [medline] AID - 327/5973/1566-b [pii] AID - 10.1126/science.327.5973.1566-b [doi] PST - ppublish SO - Science. 2010 Mar 26;327(5973):1566-7. doi: 10.1126/science.327.5973.1566-b. PMID- 20428686 OWN - NLM STAT- MEDLINE DCOM- 20100730 LR - 20190606 IS - 1678-8060 (Electronic) IS - 0074-0276 (Linking) VI - 105 IP - 2 DP - 2010 Mar TI - Paleoparasitological report on Ascaris aDNA from an ancient East Asian sample. PG - 225-8 LID - S0074-02762010000200020 [pii] AB - In this study, Ascaris DNA was extracted and sequenced from a medieval archaeological sample in Korea. While Ascaris eggs were confirmed to be of human origin by archaeological evidence, it was not possible to pinpoint the exact species due to close genetic relationships among them. Despite this shortcoming, this is the first Ascaris ancient DNA (aDNA) report from a medieval Asian country and thus will expand the scope of Ascaris aDNA research. FAU - Oh, Chang Seok AU - Oh CS AD - Institute of Forensic Medicine, Seoul National University College of Medicine, Chongno-Gu, Seoul, Korea. FAU - Seo, Min AU - Seo M FAU - Lim, Nam Jin AU - Lim NJ FAU - Lee, Sang Jun AU - Lee SJ FAU - Lee, Eun-Joo AU - Lee EJ FAU - Lee, Soong Deok AU - Lee SD FAU - Shin, Dong Hoon AU - Shin DH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Brazil TA - Mem Inst Oswaldo Cruz JT - Memorias do Instituto Oswaldo Cruz JID - 7502619 RN - 0 (DNA, Helminth) RN - 9035-37-4 (Cytochromes b) SB - IM MH - Animals MH - Ascaris lumbricoides/*genetics/isolation & purification MH - Cytochromes b/genetics MH - DNA, Helminth/*genetics/isolation & purification MH - Humans MH - Mummies/*parasitology MH - Polymerase Chain Reaction MH - Republic of Korea EDAT- 2010/04/30 06:00 MHDA- 2010/07/31 06:00 CRDT- 2010/04/30 06:00 PHST- 2009/08/10 00:00 [received] PHST- 2010/02/09 00:00 [accepted] PHST- 2010/04/30 06:00 [entrez] PHST- 2010/04/30 06:00 [pubmed] PHST- 2010/07/31 06:00 [medline] AID - S0074-02762010000200020 [pii] AID - 10.1590/s0074-02762010000200020 [doi] PST - ppublish SO - Mem Inst Oswaldo Cruz. 2010 Mar;105(2):225-8. doi: 10.1590/s0074-02762010000200020. PMID- 19918991 OWN - NLM STAT- MEDLINE DCOM- 20100503 LR - 20100208 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 141 IP - 3 DP - 2010 Mar TI - Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta, Argentina). PG - 452-62 LID - 10.1002/ajpa.21165 [doi] AB - Ancient DNA recovered from 21 individuals excavated from burial sites in the Pampa Grande (PG) region (Salta province) of North-Western Argentina (NWA) was analyzed using various genetic markers (mitochondrial DNA, autosomal STRs, and Y chromosomal STRs). The results were compared to ancient and modern DNA from various populations in the Andean and North Argentinean regions, with the aim of establishing their relationships with PG. The mitochondrial haplogroup frequencies described (11% A, 47% B, and 42% D) presented values comparable to those found for the ancient Andean populations from Peru and San Pedro de Atacama. On the other hand, mitochondrial and Y chromosomal haplotypes were specific to PG, as they did not match any other of the South American populations studied. The described genetic diversity indicates homogeneity in the genetic structure of the ancient Andean populations, which was probably facilitated by the intense exchange network in the Andean zone, in particular among Tiwanaku, San Pedro de Atacama, and NWA. The discovery of haplotypes unique to PG could be due to a loss of genetic diversity caused by recent events affecting the autochthonous populations (establishment of the Inca Empire in the region, colonization by the Europeans). FAU - Carnese, Fransisco R AU - Carnese FR AD - Universidad de Buenos Aires, Facultad de Filosofía y Letras, Instituto de Ciencias Antropológicas, Sección Antropología, Biológica, Buenos Aires 1406, Argentina. FAU - Mendisco, Fanny AU - Mendisco F FAU - Keyser, Christine AU - Keyser C FAU - Dejean, Cristina B AU - Dejean CB FAU - Dugoujon, Jean-Michel AU - Dugoujon JM FAU - Bravi, Claudio M AU - Bravi CM FAU - Ludes, Bertrand AU - Ludes B FAU - Crubézy, Eric AU - Crubézy E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) RN - 9007-49-2 (DNA) SB - IM MH - Argentina MH - Burial/methods MH - Chromosomes, Human, Y/*genetics MH - DNA/*genetics/isolation & purification MH - DNA, Mitochondrial/genetics MH - Gene Expression Profiling/methods MH - Genetic Markers MH - Genetic Variation MH - Genetics, Medical/methods MH - Humans MH - Male MH - Microsatellite Repeats/genetics MH - Museums MH - Paleontology/*methods MH - Polymerase Chain Reaction/methods MH - South America EDAT- 2009/11/18 06:00 MHDA- 2010/05/04 06:00 CRDT- 2009/11/18 06:00 PHST- 2009/11/18 06:00 [entrez] PHST- 2009/11/18 06:00 [pubmed] PHST- 2010/05/04 06:00 [medline] AID - 10.1002/ajpa.21165 [doi] PST - ppublish SO - Am J Phys Anthropol. 2010 Mar;141(3):452-62. doi: 10.1002/ajpa.21165. PMID- 20159872 OWN - NLM STAT- MEDLINE DCOM- 20100226 LR - 20171116 IS - 1538-3598 (Electronic) IS - 0098-7484 (Linking) VI - 303 IP - 7 DP - 2010 Feb 17 TI - Ancestry and pathology in King Tutankhamun's family. PG - 638-47 LID - 10.1001/jama.2010.121 [doi] AB - CONTEXT: The New Kingdom in ancient Egypt, comprising the 18th, 19th, and 20th dynasties, spanned the mid-16th to the early 11th centuries bc. The late 18th dynasty, which included the reigns of pharaohs Akhenaten and Tutankhamun, was an extraordinary time. The identification of a number of royal mummies from this era, the exact relationships between some members of the royal family, and possible illnesses and causes of death have been matters of debate. OBJECTIVES: To introduce a new approach to molecular and medical Egyptology, to determine familial relationships among 11 royal mummies of the New Kingdom, and to search for pathological features attributable to possible murder, consanguinity, inherited disorders, and infectious diseases. DESIGN: From September 2007 to October 2009, royal mummies underwent detailed anthropological, radiological, and genetic studies as part of the King Tutankhamun Family Project. Mummies distinct from Tutankhamun's immediate lineage served as the genetic and morphological reference. To authenticate DNA results, analytical steps were repeated and independently replicated in a second ancient DNA laboratory staffed by a separate group of personnel. Eleven royal mummies dating from circa 1410-1324 bc and suspected of being kindred of Tutankhamun and 5 royal mummies dating to an earlier period, circa 1550-1479 bc, were examined. MAIN OUTCOME MEASURES: Microsatellite-based haplotypes in the mummies, generational segregation of alleles within possible pedigree variants, and correlation of identified diseases with individual age, archeological evidence, and the written historical record. RESULTS: Genetic fingerprinting allowed the construction of a 5-generation pedigree of Tutankhamun's immediate lineage. The KV55 mummy and KV35YL were identified as the parents of Tutankhamun. No signs of gynecomastia and craniosynostoses (eg, Antley-Bixler syndrome) or Marfan syndrome were found, but an accumulation of malformations in Tutankhamun's family was evident. Several pathologies including Köhler disease II were diagnosed in Tutankhamun; none alone would have caused death. Genetic testing for STEVOR, AMA1, or MSP1 genes specific for Plasmodium falciparum revealed indications of malaria tropica in 4 mummies, including Tutankhamun's. These results suggest avascular bone necrosis in conjunction with the malarial infection as the most likely cause of death in Tutankhamun. Walking impairment and malarial disease sustained by Tutankhamun is supported by the discovery of canes and an afterlife pharmacy in his tomb. CONCLUSION: Using a multidisciplinary scientific approach, we showed the feasibility of gathering data on Pharaonic kinship and diseases and speculated about individual causes of death. FAU - Hawass, Zahi AU - Hawass Z AD - Supreme Council of Antiquities, Cairo, Egypt. FAU - Gad, Yehia Z AU - Gad YZ FAU - Ismail, Somaia AU - Ismail S FAU - Khairat, Rabab AU - Khairat R FAU - Fathalla, Dina AU - Fathalla D FAU - Hasan, Naglaa AU - Hasan N FAU - Ahmed, Amal AU - Ahmed A FAU - Elleithy, Hisham AU - Elleithy H FAU - Ball, Markus AU - Ball M FAU - Gaballah, Fawzi AU - Gaballah F FAU - Wasef, Sally AU - Wasef S FAU - Fateen, Mohamed AU - Fateen M FAU - Amer, Hany AU - Amer H FAU - Gostner, Paul AU - Gostner P FAU - Selim, Ashraf AU - Selim A FAU - Zink, Albert AU - Zink A FAU - Pusch, Carsten M AU - Pusch CM LA - eng PT - Biography PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - JAMA JT - JAMA JID - 7501160 SB - IM CIN - JAMA. 2010 Feb 17;303(7):667-8. doi: 10.1001/jama.2010.153. PMID: 20159878 CIN - JAMA. 2010 Jun 23;303(24):2471-2; author reply 2473-5. doi: 10.1001/jama.2010.819. PMID: 20571006 CIN - JAMA. 2010 Jun 23;303(24):2471; author reply 2473-5. doi: 10.1001/jama.2010.818. PMID: 20571007 CIN - JAMA. 2010 Jun 23;303(24):2472-3; author reply 2473-5. doi: 10.1001/jama.2010.821. PMID: 20571008 CIN - JAMA. 2010 Jun 23;303(24):2472; author reply 2473-5. doi: 10.1001/jama.2010.820. PMID: 20571009 CIN - JAMA. 2010 Jun 23;303(24):2473; author reply 2473-5. doi: 10.1001/jama.2010.822. PMID: 20571010 MH - Cause of Death MH - Clubfoot MH - Consanguinity MH - *DNA Fingerprinting MH - Egypt, Ancient MH - Female MH - History, Ancient MH - Humans MH - Malaria, Falciparum/genetics/*pathology MH - Male MH - Microsatellite Repeats MH - Mummies/*pathology MH - Osteonecrosis/*pathology MH - Pedigree PS - King Tutankhamun FPS - King Tutankhamun EDAT- 2010/02/18 06:00 MHDA- 2010/02/27 06:00 CRDT- 2010/02/18 06:00 PHST- 2010/02/18 06:00 [entrez] PHST- 2010/02/18 06:00 [pubmed] PHST- 2010/02/27 06:00 [medline] AID - 303/7/638 [pii] AID - 10.1001/jama.2010.121 [doi] PST - ppublish SO - JAMA. 2010 Feb 17;303(7):638-47. doi: 10.1001/jama.2010.121. PMID- 20133614 OWN - NLM STAT- MEDLINE DCOM- 20100510 LR - 20211020 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 107 IP - 7 DP - 2010 Feb 16 TI - Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication. PG - 2807-12 LID - 10.1073/pnas.0909724107 [doi] AB - Although the cultural and nutritive importance of the turkey (Meleagris gallopavo) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC-AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey (Meleagris gallopavo gallopavo) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices. FAU - Speller, Camilla F AU - Speller CF AD - Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada. FAU - Kemp, Brian M AU - Kemp BM FAU - Wyatt, Scott D AU - Wyatt SD FAU - Monroe, Cara AU - Monroe C FAU - Lipe, William D AU - Lipe WD FAU - Arndt, Ursula M AU - Arndt UM FAU - Yang, Dongya Y AU - Yang DY LA - eng SI - GENBANK/GQ303154 SI - GENBANK/GQ303155 SI - GENBANK/GQ303156 SI - GENBANK/GQ303157 SI - GENBANK/GQ303158 SI - GENBANK/GQ303159 SI - GENBANK/GQ303160 SI - GENBANK/GQ303161 SI - GENBANK/GQ303162 SI - GENBANK/GQ303163 SI - GENBANK/GQ303164 SI - GENBANK/GQ303165 SI - GENBANK/GQ303166 SI - GENBANK/GQ303167 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100201 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Animals, Domestic/*genetics MH - Base Sequence MH - Bone and Bones/chemistry MH - Breeding/*methods MH - Cluster Analysis MH - DNA Primers/genetics MH - DNA, Mitochondrial/*genetics MH - Demography MH - Feces/chemistry MH - *Fossils MH - Founder Effect MH - Geography MH - Humans MH - Molecular Sequence Data MH - *Phylogeny MH - Sequence Analysis, DNA MH - Southwestern United States MH - Species Specificity MH - Turkeys/*genetics PMC - PMC2840336 COIS- The authors declare no conflict of interest. EDAT- 2010/02/06 06:00 MHDA- 2010/05/11 06:00 PMCR- 2010/02/01 CRDT- 2010/02/06 06:00 PHST- 2010/02/06 06:00 [entrez] PHST- 2010/02/06 06:00 [pubmed] PHST- 2010/05/11 06:00 [medline] PHST- 2010/02/01 00:00 [pmc-release] AID - 0909724107 [pii] AID - 200909724 [pii] AID - 10.1073/pnas.0909724107 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2807-12. doi: 10.1073/pnas.0909724107. Epub 2010 Feb 1. PMID- 20045327 OWN - NLM STAT- MEDLINE DCOM- 20100506 LR - 20100210 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 20 IP - 3 DP - 2010 Feb 9 TI - A complete mtDNA genome of an early modern human from Kostenki, Russia. PG - 231-6 LID - 10.1016/j.cub.2009.11.068 [doi] AB - The recovery of DNA sequences from early modern humans (EMHs) could shed light on their interactions with archaic groups such as Neandertals and their relationships to current human populations. However, such experiments are highly problematic because present-day human DNA frequently contaminates bones [1, 2]. For example, in a recent study of mitochondrial (mt) DNA from Neolithic European skeletons, sequence variants were only taken as authentic if they were absent or rare in the present population, whereas others had to be discounted as possible contamination [3, 4]. This limits analysis to EMH individuals carrying rare sequences and thus yields a biased view of the ancient gene pool. Other approaches of identifying contaminating DNA, such as genotyping all individuals who have come into contact with a sample, restrict analyses to specimens where this is possible [5, 6] and do not exclude all possible sources of contamination. By studying mtDNA in Neandertal remains, where contamination and endogenous DNA can be distinguished by sequence, we show that fragmentation patterns and nucleotide misincorporations can be used to gauge authenticity of ancient DNA sequences. We use these features to determine a complete mtDNA sequence from a approximately 30,000-year-old EMH from the Kostenki 14 site in Russia. FAU - Krause, Johannes AU - Krause J AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. krause@eva.mpg.de FAU - Briggs, Adrian W AU - Briggs AW FAU - Kircher, Martin AU - Kircher M FAU - Maricic, Tomislav AU - Maricic T FAU - Zwyns, Nicolas AU - Zwyns N FAU - Derevianko, Anatoli AU - Derevianko A FAU - Pääbo, Svante AU - Pääbo S LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091231 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics/*history/isolation & purification MH - Evolution, Molecular MH - Fossils MH - *Genome, Human MH - *Genome, Mitochondrial MH - History, Ancient MH - Humans MH - Polymerase Chain Reaction MH - Russia EDAT- 2010/01/05 06:00 MHDA- 2010/05/07 06:00 CRDT- 2010/01/05 06:00 PHST- 2009/10/14 00:00 [received] PHST- 2009/11/23 00:00 [revised] PHST- 2009/11/23 00:00 [accepted] PHST- 2010/01/05 06:00 [entrez] PHST- 2010/01/05 06:00 [pubmed] PHST- 2010/05/07 06:00 [medline] AID - S0960-9822(09)02139-3 [pii] AID - 10.1016/j.cub.2009.11.068 [doi] PST - ppublish SO - Curr Biol. 2010 Feb 9;20(3):231-6. doi: 10.1016/j.cub.2009.11.068. Epub 2009 Dec 31. PMID- 20193133 OWN - NLM STAT- MEDLINE DCOM- 20100520 LR - 20190608 IS - 1976-670X (Electronic) IS - 1976-6696 (Linking) VI - 43 IP - 2 DP - 2010 Feb TI - Mitochondrial DNA analysis of ancient human bones excavated from Nukdo island, S.Korea. PG - 133-9 AB - We have performed analyses using ancient DNA extracted from 25 excavated human bones, estimating around the 1(st) century B.C. Ancient human bones were obtained from Nukdo Island, which is located off of the Korean peninsula of East Asia. We made concerted efforts to extract ancient DNA of high quality and to obtain reproducible PCR products, as this was a primary consideration for this extensive kind of undertaking. We performed PCR amplifications for several regions of the mitochondrial DNA, and could determine mitochondrial haplogroups for 21 ancient DNA samples. Genetic information from mitochondrial DNA belonged to super-haplogroup M, haplogroup D or its sub-haplogroups (D4 or D4b), which are distinctively found in East Asians, including Koreans or Japanese. The dendrogram and principal component analysis based on haplogroup frequencies revealed that the Nukdo population was close to those of the East Asians and clearly distinguished from populations shown in the other regions. Considering that Nukdo is geologically isolated in the southern part of them Korean peninsula and is a site of commercial importance with neighboring countries, these results may reflect genetic continuity for the habitation and migration of ethnic groups who had lived in a particular area in the past. Therefore, we suggest that phylogenetic analyses of ancient DNA have significant advantages for clarifying the origins and migrations of ethnic groups, or human races. FAU - Kim, Ae-Jin AU - Kim AJ AD - Medical & Bio-Material Research Center and Division of Life Sciences, College of Natural Sciences, Kangwon National University, Chuncheon 200-701, Korea. FAU - Kim, Kijeong AU - Kim K FAU - Choi, Jee-Hye AU - Choi JH FAU - Choi, Eun-Ha AU - Choi EH FAU - Jung, Yu-Jin AU - Jung YJ FAU - Min, Na Young AU - Min NY FAU - Lkhagvasuren, Gavaachimed AU - Lkhagvasuren G FAU - Rhee, Sangmyung AU - Rhee S FAU - Kim, Jae-Hyun AU - Kim JH FAU - Noh, Maengseok AU - Noh M FAU - Park, Ae Ja AU - Park AJ FAU - Kim, Kyung-Yong AU - Kim KY FAU - Kang, Yoonsung AU - Kang Y FAU - Lee, Kwang-Ho AU - Lee KH FAU - Kim, Keun-Cheol AU - Kim KC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Korea (South) TA - BMB Rep JT - BMB reports JID - 101465334 RN - 0 (DNA, Mitochondrial) SB - IM MH - Bone and Bones/chemistry MH - DNA, Mitochondrial/chemistry/*classification MH - Haplotypes MH - Humans MH - Phylogeny MH - Principal Component Analysis MH - Republic of Korea MH - Sequence Analysis, DNA EDAT- 2010/03/03 06:00 MHDA- 2010/05/21 06:00 CRDT- 2010/03/03 06:00 PHST- 2010/03/03 06:00 [entrez] PHST- 2010/03/03 06:00 [pubmed] PHST- 2010/05/21 06:00 [medline] AID - 10.5483/bmbrep.2010.43.2.133 [doi] PST - ppublish SO - BMB Rep. 2010 Feb;43(2):133-9. doi: 10.5483/bmbrep.2010.43.2.133. PMID- 19639639 OWN - NLM STAT- MEDLINE DCOM- 20100430 LR - 20100113 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 141 IP - 2 DP - 2010 Feb TI - Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis. PG - 208-21 LID - 10.1002/ajpa.21135 [doi] AB - Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021-16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups. CI - 2009 Wiley-Liss, Inc. FAU - Fehren-Schmitz, Lars AU - Fehren-Schmitz L AD - Johann-Friedrich-Blumenbach Department of Zoology and Anthropology, Historical Anthropology and Human Ecology, University of Goettingen, Germany. lfehren@gwdg.de FAU - Reindel, Markus AU - Reindel M FAU - Cagigao, Elsa Tomasto AU - Cagigao ET FAU - Hummel, Susanne AU - Hummel S FAU - Herrmann, Bernd AU - Herrmann B LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - Cluster Analysis MH - DNA Primers/genetics MH - DNA, Mitochondrial/*genetics MH - *Fossils MH - *Genetic Variation MH - Haplotypes/genetics MH - History, Ancient MH - History, Medieval MH - Humans MH - Molecular Sequence Data MH - Peru MH - Phylogeny MH - *Population Dynamics MH - Reverse Transcriptase Polymerase Chain Reaction MH - Sequence Analysis, DNA EDAT- 2009/07/30 09:00 MHDA- 2010/05/01 06:00 CRDT- 2009/07/30 09:00 PHST- 2009/07/30 09:00 [entrez] PHST- 2009/07/30 09:00 [pubmed] PHST- 2010/05/01 06:00 [medline] AID - 10.1002/ajpa.21135 [doi] PST - ppublish SO - Am J Phys Anthropol. 2010 Feb;141(2):208-21. doi: 10.1002/ajpa.21135. PMID- 19781880 OWN - NLM STAT- MEDLINE DCOM- 20100505 LR - 20220408 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 194 IP - 1-3 DP - 2010 Jan 30 TI - Efficiency evaluation of a DNA extraction and purification protocol on archival formalin-fixed and paraffin-embedded tissue. PG - e25-8 LID - 10.1016/j.forsciint.2009.09.004 [doi] AB - Formalin-fixed and paraffin-embedded tissue (FF-PET) is an invaluable resource for retrospective molecular genetic studies, but the extraction of high-quality genomic DNA from FF-PET is still a problematic issue. Despite the range of DNA extraction methods currently in use, the association of phenol-chloroform extraction and silica-based purification protocols, reported in ancient DNA studies on archaeological bones, has, to our knowledge, not been used for DNA extraction from FF-PET yet. The present study compared the efficiency of three DNA extraction and purification protocols from two different FF-PET substrates, heart and liver, by using quantitative PCR and multiplex amplification. We showed that the method, using phenol-chloroform and the QIAamp DNA mini Kit (Qiagen), was the most effective DNA extraction and purification method and that the DNA quantity extracted from liver is statistically more important than that extracted from heart. Autosomal STR typing by multiplex amplifications gave partial allelic profiles with only small size products (less than 300 bases) amplified, suggesting that DNA extracted from FF-PET was degraded. In conclusion, the protocol presented here, previously described in studies on ancient bones, should find application in different molecular studies involving FF-PET material. CI - 2009 Elsevier Ireland Ltd. All rights reserved. FAU - Farrugia, A AU - Farrugia A AD - Institute of Legal Medicine, EA4438, University of Strasbourg, Strasbourg, France. audrey.farrugia@unistra.fr FAU - Keyser, C AU - Keyser C FAU - Ludes, B AU - Ludes B LA - eng PT - Journal Article DEP - 20090924 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (Fixatives) RN - 0 (Solvents) RN - 1HG84L3525 (Formaldehyde) RN - 339NCG44TV (Phenol) RN - 7V31YC746X (Chloroform) RN - 9007-49-2 (DNA) SB - IM MH - Chloroform MH - DNA/*isolation & purification MH - DNA Degradation, Necrotic MH - DNA Fingerprinting MH - *Fixatives MH - Forensic Genetics/methods MH - *Formaldehyde MH - Humans MH - Liver/pathology MH - Myocardium/pathology MH - *Paraffin Embedding MH - Phenol MH - Polymerase Chain Reaction MH - Solvents MH - Tandem Repeat Sequences EDAT- 2009/09/29 06:00 MHDA- 2010/05/06 06:00 CRDT- 2009/09/29 06:00 PHST- 2009/02/09 00:00 [received] PHST- 2009/06/29 00:00 [revised] PHST- 2009/09/02 00:00 [accepted] PHST- 2009/09/29 06:00 [entrez] PHST- 2009/09/29 06:00 [pubmed] PHST- 2010/05/06 06:00 [medline] AID - S0379-0738(09)00366-1 [pii] AID - 10.1016/j.forsciint.2009.09.004 [doi] PST - ppublish SO - Forensic Sci Int. 2010 Jan 30;194(1-3):e25-8. doi: 10.1016/j.forsciint.2009.09.004. Epub 2009 Sep 24. PMID- 20100333 OWN - NLM STAT- MEDLINE DCOM- 20100315 LR - 20211020 IS - 1471-2148 (Electronic) IS - 1471-2148 (Linking) VI - 10 DP - 2010 Jan 25 TI - Human evolution in Siberia: from frozen bodies to ancient DNA. PG - 25 LID - 10.1186/1471-2148-10-25 [doi] AB - BACKGROUND: The Yakuts contrast strikingly with other populations from Siberia due to their cattle- and horse-breeding economy as well as their Turkic language. On the basis of ethnological and linguistic criteria as well as population genetic studies, it has been assumed that they originated from South Siberian populations. However, many questions regarding the origins of this intriguing population still need to be clarified (e.g. the precise origin of paternal lineages and the admixture rate with indigenous populations). This study attempts to better understand the origins of the Yakuts by performing genetic analyses on 58 mummified frozen bodies dated from the 15th to the 19th century, excavated from Yakutia (Eastern Siberia). RESULTS: High quality data were obtained for the autosomal STRs, Y-chromosomal STRs and SNPs and mtDNA due to exceptional sample preservation. A comparison with the same markers on seven museum specimens excavated 3 to 15 years ago showed significant differences in DNA quantity and quality. Direct access to ancient genetic data from these molecular markers combined with the archaeological evidence, demographical studies and comparisons with 166 contemporary individuals from the same location as the frozen bodies helped us to clarify the microevolution of this intriguing population. CONCLUSION: We were able to trace the origins of the male lineages to a small group of horse-riders from the Cis-Baïkal area. Furthermore, mtDNA data showed that intermarriages between the first settlers with Evenks women led to the establishment of genetic characteristics during the 15th century that are still observed today. FAU - Crubézy, Eric AU - Crubézy E AD - Laboratoire AMIS, FRE 2960 CNRS, Université de Toulouse, 37 allées Jules Guesde, 31073 Toulouse, France. crubezy.eric@free.fr FAU - Amory, Sylvain AU - Amory S FAU - Keyser, Christine AU - Keyser C FAU - Bouakaze, Caroline AU - Bouakaze C FAU - Bodner, Martin AU - Bodner M FAU - Gibert, Morgane AU - Gibert M FAU - Röck, Alexander AU - Röck A FAU - Parson, Walther AU - Parson W FAU - Alexeev, Anatoly AU - Alexeev A FAU - Ludes, Bertrand AU - Ludes B LA - eng GR - L 397/FWF_/Austrian Science Fund FWF/Austria PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100125 PL - England TA - BMC Evol Biol JT - BMC evolutionary biology JID - 100966975 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Biological Evolution MH - Cell Nucleus/genetics MH - Chromosomes, Human, Y/genetics MH - DNA/genetics MH - DNA, Mitochondrial/genetics MH - Female MH - *Genetics, Population MH - Humans MH - Male MH - Siberia PMC - PMC2829035 EDAT- 2010/01/27 06:00 MHDA- 2010/03/17 06:00 PMCR- 2010/01/25 CRDT- 2010/01/27 06:00 PHST- 2009/03/25 00:00 [received] PHST- 2010/01/25 00:00 [accepted] PHST- 2010/01/27 06:00 [entrez] PHST- 2010/01/27 06:00 [pubmed] PHST- 2010/03/17 06:00 [medline] PHST- 2010/01/25 00:00 [pmc-release] AID - 1471-2148-10-25 [pii] AID - 10.1186/1471-2148-10-25 [doi] PST - epublish SO - BMC Evol Biol. 2010 Jan 25;10:25. doi: 10.1186/1471-2148-10-25. PMID- 20072618 OWN - NLM STAT- MEDLINE DCOM- 20100520 LR - 20211020 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 5 IP - 1 DP - 2010 Jan 8 TI - Characterization of nucleotide misincorporation patterns in the iceman's mitochondrial DNA. PG - e8629 LID - 10.1371/journal.pone.0008629 [doi] LID - e8629 AB - BACKGROUND: The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation ("miscoding lesions") has been the object of extensive investigations. METHODOLOGY/PRINCIPAL FINDINGS: To improve our knowledge regarding the nature and incidence of ancient DNA nucleotide misincorporations, we have utilized 6,859 (629,975 bp) mitochondrial (mt) DNA sequences obtained from the 5,350-5,100-years-old, freeze-desiccated human mummy popularly known as the Tyrolean Iceman or Otzi. To generate the sequences, we have applied a mixed PCR/pyrosequencing procedure allowing one to obtain a particularly high sequence coverage. As a control, we have produced further 8,982 (805,155 bp) mtDNA sequences from a contemporary specimen using the same system and starting from the same template copy number of the ancient sample. From the analysis of the nucleotide misincorporation rate in ancient, modern, and putative contaminant sequences, we observed that the rate of misincorporation is significantly lower in modern and putative contaminant sequence datasets than in ancient sequences. In contrast, type 2 transitions represent the vast majority (85%) of the observed nucleotide misincorporations in ancient sequences. CONCLUSIONS/SIGNIFICANCE: This study provides a further contribution to the knowledge of nucleotide misincorporation patterns in DNA sequences obtained from freeze-preserved archeological specimens. In the Iceman system, ancient sequences can be clearly distinguished from contaminants on the basis of nucleotide misincorporation rates. This observation confirms a previous identification of the ancient mummy sequences made on a purely phylogenetical basis. The present investigation provides further indication that the majority of ancient DNA damage is reflected by type 2 (cytosine-->thymine/guanine-->adenine) transitions and that type 1 transitions are essentially PCR artifacts. FAU - Olivieri, Cristina AU - Olivieri C AD - Laboratorio di Archeo-Antropologia molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Camerino, Italy. FAU - Ermini, Luca AU - Ermini L FAU - Rizzi, Ermanno AU - Rizzi E FAU - Corti, Giorgio AU - Corti G FAU - Bonnal, Raoul AU - Bonnal R FAU - Luciani, Stefania AU - Luciani S FAU - Marota, Isolina AU - Marota I FAU - De Bellis, Gianluca AU - De Bellis G FAU - Rollo, Franco AU - Rollo F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100108 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) RN - 0 (Nucleotides) SB - IM MH - DNA, Mitochondrial/*genetics MH - *Fossils MH - *Freezing MH - Humans MH - Nucleotides/*metabolism MH - *Paleontology PMC - PMC2799664 COIS- Competing Interests: Research work was supported by an Eli Lilly donation. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials. EDAT- 2010/01/15 06:00 MHDA- 2010/05/21 06:00 PMCR- 2010/01/08 CRDT- 2010/01/15 06:00 PHST- 2009/08/20 00:00 [received] PHST- 2009/12/15 00:00 [accepted] PHST- 2010/01/15 06:00 [entrez] PHST- 2010/01/15 06:00 [pubmed] PHST- 2010/05/21 06:00 [medline] PHST- 2010/01/08 00:00 [pmc-release] AID - 09-PONE-RA-12402R2 [pii] AID - 10.1371/journal.pone.0008629 [doi] PST - epublish SO - PLoS One. 2010 Jan 8;5(1):e8629. doi: 10.1371/journal.pone.0008629. PMID- 19793751 OWN - NLM STAT- MEDLINE DCOM- 20100301 LR - 20211020 IS - 1471-2954 (Electronic) IS - 0962-8452 (Print) IS - 0962-8452 (Linking) VI - 277 IP - 1678 DP - 2010 Jan 7 TI - Tuberculosis in Dr Granville's mummy: a molecular re-examination of the earliest known Egyptian mummy to be scientifically examined and given a medical diagnosis. PG - 51-6 LID - 10.1098/rspb.2009.1484 [doi] AB - 'Dr Granville's mummy' was described to the Royal Society of London in 1825 and was the first ancient Egyptian mummy to be subjected to a scientific autopsy. The remains are those of a woman, Irtyersenu, aged about 50, from the necropolis of Thebes and dated to about 600 BC. Augustus Bozzi Granville (1783-1872), an eminent physician and obstetrician, described many organs still in situ and attributed the cause of death to a tumour of the ovary. However, subsequent histological investigations indicate that the tumour is a benign cystadenoma. Histology of the lungs demonstrated a potentially fatal pulmonary exudate and earlier studies attempted to associate this with particular disease conditions. Palaeopathology and ancient DNA analyses show that tuberculosis was widespread in ancient Egypt, so a systematic search for tuberculosis was made, using specific DNA and lipid biomarker analyses. Clear evidence for Mycobacterium tuberculosis complex DNA was obtained in lung tissue and gall bladder samples, based on nested PCR of the IS6110 locus. Lung and femurs were positive for specific M. tuberculosis complex cell-wall mycolic acids, demonstrated by high-performance liquid chromatography of pyrenebutyric acid-pentafluorobenzyl mycolates. Therefore, tuberculosis is likely to have been the major cause of death of Irtyersenu. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centre for Infectious Diseases and International Health, University College London, London W1T 4JF, UK. h.donoghue@ucl.ac.uk FAU - Lee, Oona Y-C AU - Lee OY FAU - Minnikin, David E AU - Minnikin DE FAU - Besra, Gurdyal S AU - Besra GS FAU - Taylor, John H AU - Taylor JH FAU - Spigelman, Mark AU - Spigelman M LA - eng GR - G0802079/MRC_/Medical Research Council/United Kingdom GR - WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090930 PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Bacterial) RN - 0 (Mycolic Acids) SB - IM MH - DNA, Bacterial/chemistry/genetics MH - Egypt MH - Female MH - Femur/microbiology MH - Humans MH - Lung/microbiology MH - Middle Aged MH - Mummies/*microbiology MH - Mycobacterium tuberculosis/genetics/*isolation & purification MH - Mycolic Acids/analysis MH - Polymerase Chain Reaction MH - Tuberculosis, Pulmonary/*diagnosis PMC - PMC2842630 EDAT- 2009/10/02 06:00 MHDA- 2010/03/02 06:00 PMCR- 2009/09/30 CRDT- 2009/10/02 06:00 PHST- 2009/10/02 06:00 [entrez] PHST- 2009/10/02 06:00 [pubmed] PHST- 2010/03/02 06:00 [medline] PHST- 2009/09/30 00:00 [pmc-release] AID - rspb.2009.1484 [pii] AID - rspb20091484 [pii] AID - 10.1098/rspb.2009.1484 [doi] PST - ppublish SO - Proc Biol Sci. 2010 Jan 7;277(1678):51-6. doi: 10.1098/rspb.2009.1484. Epub 2009 Sep 30. PMID- 20492755 OWN - NLM STAT- MEDLINE DCOM- 20101112 LR - 20220623 IS - 0015-5500 (Print) IS - 0015-5500 (Linking) VI - 56 IP - 2 DP - 2010 TI - DNA analysis of ancient skeletal remains. PG - 47-50 AB - Non-Governmental Organization Archaia (http://www.archaia.cz) carried out the rescue archaeological research at Knezeves near Prague in 1998. Most of dating objects in Knezeves come from the period of Late and Final Bronze Age. The approximately 3,000 years old set, which included 11 human remains from three settlement features, was collected for the study. First, gender was determined according to anthropological characteristics. Ancient DNA from bones was extracted by the phenol-chloroform procedure and N-phenacetylthiazolum bromide reagent. Polymerase chain reaction amplification of AMEL XY, part of amelogenin gene, with subsequent polyacrylamide gel electrophoresis and Short Tandem Repeats analysis followed. DNA profiles of skeletal remains were obtained by the fragmentation analysis of autosomal short tandem repeat markers. Genetic profiles showed us whether individuals from Knezeves were in mutual relationship (parent - descendant). The congruence of results in sex determination supported reliability of genetic methods, which are suitable for sex determination of fragmental and subadult skeletal remains. FAU - Eliásová, I AU - Eliásová I AD - Charles University in Prague, Faculty of Science, Department of Anthropology and Human Genetics, Prague, Czech Republic. i.eliasova@seznam.cz FAU - Mazura, I AU - Mazura I FAU - Smejtek, L AU - Smejtek L LA - eng PT - Historical Article PT - Journal Article PT - Retracted Publication PL - Czech Republic TA - Folia Biol (Praha) JT - Folia biologica JID - 0234640 RN - 9007-49-2 (DNA) SB - IM EIN - Folia Biol (Praha). 2013;59(1):51 RIN - Folia Biol (Praha). 2013;59(3):138. PMID: 23890482 MH - Archaeology/*methods MH - Base Sequence MH - Bone and Bones/*chemistry MH - DNA/*analysis MH - Female MH - History, Ancient MH - Humans MH - Male MH - Microsatellite Repeats MH - Polymerase Chain Reaction/methods MH - Sequence Analysis, DNA/*methods EDAT- 2010/05/25 06:00 MHDA- 2010/11/13 06:00 CRDT- 2010/05/25 06:00 PHST- 2010/05/25 06:00 [entrez] PHST- 2010/05/25 06:00 [pubmed] PHST- 2010/11/13 06:00 [medline] AID - file/6028/fb2010a0008.pdf [pii] PST - ppublish SO - Folia Biol (Praha). 2010;56(2):47-50. PMID- 20441577 OWN - NLM STAT- MEDLINE DCOM- 20100929 LR - 20211020 IS - 1474-760X (Electronic) IS - 1465-6906 (Print) IS - 1474-7596 (Linking) VI - 11 IP - 5 DP - 2010 TI - Computational challenges in the analysis of ancient DNA. PG - R47 LID - 10.1186/gb-2010-11-5-r47 [doi] AB - High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering. FAU - Prüfer, Kay AU - Prüfer K AD - Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. pruefer@eva.mpg.de FAU - Stenzel, Udo AU - Stenzel U FAU - Hofreiter, Michael AU - Hofreiter M FAU - Pääbo, Svante AU - Pääbo S FAU - Kelso, Janet AU - Kelso J FAU - Green, Richard E AU - Green RE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100506 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Sequence MH - Computational Biology/*methods MH - Computer Simulation MH - DNA/*analysis/*genetics MH - Databases, Nucleic Acid MH - *Extinction, Biological MH - Genetic Variation MH - Humans MH - Sequence Alignment MH - Sequence Analysis, DNA/*methods PMC - PMC2898072 EDAT- 2010/05/06 06:00 MHDA- 2010/09/30 06:00 PMCR- 2010/05/06 CRDT- 2010/05/06 06:00 PHST- 2009/10/16 00:00 [received] PHST- 2010/01/05 00:00 [revised] PHST- 2010/05/06 00:00 [accepted] PHST- 2010/05/06 06:00 [entrez] PHST- 2010/05/06 06:00 [pubmed] PHST- 2010/09/30 06:00 [medline] PHST- 2010/05/06 00:00 [pmc-release] AID - gb-2010-11-5-r47 [pii] AID - 10.1186/gb-2010-11-5-r47 [doi] PST - ppublish SO - Genome Biol. 2010;11(5):R47. doi: 10.1186/gb-2010-11-5-r47. Epub 2010 May 6. PMID- 19864251 OWN - NLM STAT- MEDLINE DCOM- 20100308 LR - 20211020 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 38 IP - 2 DP - 2010 Jan TI - Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX. PG - e7 LID - 10.1093/nar/gkp897 [doi] AB - The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples, the pervasive presence of highly PCR-amplifiable human DNA contaminants in the vast majority of samples can lead to the creation of recombinant hybrids and other non-authentic artefacts. The resulting PCR-generated sequences can then be difficult, if not impossible, to authenticate. In contrast, single primer extension (SPEX)-based approaches can genotype single nucleotide polymorphisms from ancient fragments of DNA as accurately as modern DNA. A single SPEX-type assay can amplify just one of the duplex DNA strands at target loci and generate a multi-fold depth-of-coverage, with non-authentic recombinant hybrids reduced to undetectable levels. Crucially, SPEX-type approaches can preferentially access genetic information from damaged and degraded endogenous ancient DNA templates over modern human DNA contaminants. The development of SPEX-type assays offers the potential for highly accurate, quantitative genotyping from ancient hominin samples. FAU - Brotherton, Paul AU - Brotherton P AD - Australian Centre for Ancient DNA, Darling Building, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, Adelaide, South Australia 5005, Australia. FAU - Sanchez, Juan J AU - Sanchez JJ FAU - Cooper, Alan AU - Cooper A FAU - Endicott, Phillip AU - Endicott P LA - eng GR - Wellcome Trust/United Kingdom PT - Comparative Study PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091027 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 SB - IM MH - Animals MH - Base Sequence MH - Genotype MH - Hominidae/*genetics MH - Humans MH - Molecular Sequence Data MH - Museums MH - Nucleic Acid Amplification Techniques/*methods MH - Polymerase Chain Reaction MH - *Polymorphism, Single Nucleotide MH - Reproducibility of Results MH - *Sequence Analysis, DNA PMC - PMC2811011 EDAT- 2009/10/30 06:00 MHDA- 2010/02/26 06:00 PMCR- 2009/10/27 CRDT- 2009/10/30 06:00 PHST- 2009/10/30 06:00 [entrez] PHST- 2009/10/30 06:00 [pubmed] PHST- 2010/02/26 06:00 [medline] PHST- 2009/10/27 00:00 [pmc-release] AID - gkp897 [pii] AID - 10.1093/nar/gkp897 [doi] PST - ppublish SO - Nucleic Acids Res. 2010 Jan;38(2):e7. doi: 10.1093/nar/gkp897. Epub 2009 Oct 27. PMID- 19788938 OWN - NLM STAT- MEDLINE DCOM- 20100204 LR - 20091130 IS - 1872-8278 (Electronic) IS - 1567-7249 (Linking) VI - 10 IP - 1 DP - 2010 Jan TI - Ancient mitogenomics. PG - 1-11 LID - 10.1016/j.mito.2009.09.005 [doi] AB - The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field. FAU - Ho, Simon Y W AU - Ho SY AD - Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT 0200, Australia. simon.ho@anu.edu.au FAU - Gilbert, M Thomas P AU - Gilbert MT LA - eng PT - Journal Article PT - Review DEP - 20090927 PL - Netherlands TA - Mitochondrion JT - Mitochondrion JID - 100968751 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - DNA, Mitochondrial/*analysis/genetics MH - *Fossils MH - Genomics/*methods MH - Humans MH - Phylogeny MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA RF - 90 EDAT- 2009/10/01 06:00 MHDA- 2010/02/05 06:00 CRDT- 2009/10/01 06:00 PHST- 2009/07/08 00:00 [received] PHST- 2009/09/21 00:00 [revised] PHST- 2009/09/23 00:00 [accepted] PHST- 2009/10/01 06:00 [entrez] PHST- 2009/10/01 06:00 [pubmed] PHST- 2010/02/05 06:00 [medline] AID - S1567-7249(09)00152-4 [pii] AID - 10.1016/j.mito.2009.09.005 [doi] PST - ppublish SO - Mitochondrion. 2010 Jan;10(1):1-11. doi: 10.1016/j.mito.2009.09.005. Epub 2009 Sep 27. PMID- 19781941 OWN - NLM STAT- MEDLINE DCOM- 20100212 LR - 20141120 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 19 IP - 20 DP - 2009 Nov 3 TI - Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians. PG - 1758-62 LID - 10.1016/j.cub.2009.09.017 [doi] AB - The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1-3]. Of particular interest is whether population replacement or cultural exchange was responsible [3-5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations. FAU - Malmström, Helena AU - Malmström H AD - Department of Evolutionary Biology, Uppsala University, Sweden. FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Thomas, Mark G AU - Thomas MG FAU - Brandström, Mikael AU - Brandström M FAU - Storå, Jan AU - Storå J FAU - Molnar, Petra AU - Molnar P FAU - Andersen, Pernille K AU - Andersen PK FAU - Bendixen, Christian AU - Bendixen C FAU - Holmlund, Gunilla AU - Holmlund G FAU - Götherström, Anders AU - Götherström A FAU - Willerslev, Eske AU - Willerslev E LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090924 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) SB - IM CIN - Curr Biol. 2009 Nov 3;19(20):R948-9. doi: 10.1016/j.cub.2009.09.054. PMID: 19889371 MH - Agriculture/*history MH - Anthropology, Physical MH - DNA, Mitochondrial/chemistry MH - Emigration and Immigration/*history MH - Genetic Variation MH - History, Ancient MH - Humans MH - Scandinavian and Nordic Countries EDAT- 2009/09/29 06:00 MHDA- 2010/02/13 06:00 CRDT- 2009/09/29 06:00 PHST- 2009/07/30 00:00 [received] PHST- 2009/09/01 00:00 [revised] PHST- 2009/09/08 00:00 [accepted] PHST- 2009/09/29 06:00 [entrez] PHST- 2009/09/29 06:00 [pubmed] PHST- 2010/02/13 06:00 [medline] AID - S0960-9822(09)01694-7 [pii] AID - 10.1016/j.cub.2009.09.017 [doi] PST - ppublish SO - Curr Biol. 2009 Nov 3;19(20):1758-62. doi: 10.1016/j.cub.2009.09.017. Epub 2009 Sep 24. PMID- 19847306 OWN - NLM STAT- MEDLINE DCOM- 20100312 LR - 20211020 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 4 IP - 10 DP - 2009 Oct 22 TI - Single nucleotide polymorphism analysis of European archaeological M. leprae DNA. PG - e7547 LID - 10.1371/journal.pone.0007547 [doi] LID - e7547 AB - BACKGROUND: Leprosy was common in Europe eight to twelve centuries ago but molecular confirmation of this has been lacking. We have extracted M. leprae ancient DNA (aDNA) from medieval bones and single nucleotide polymorphism (SNP) typed the DNA, this provides insight into the pattern of leprosy transmission in Europe and may assist in the understanding of M. leprae evolution. METHODS AND FINDINGS: Skeletons have been exhumed from 3 European countries (the United Kingdom, Denmark and Croatia) and are dated around the medieval period (476 to 1350 A.D.). we tested for the presence of 3 previously identified single nucleotide polymorphisms (SNPs) in 10 aDNA extractions. M. leprae aDNA was extracted from 6 of the 10 bone samples. SNP analysis of these 6 extractions were compared to previously analysed European SNP data using the same PCR assays and were found to be the same. Testing for the presence of SNPs in M. leprae DNA extracted from ancient bone samples is a novel approach to analysing European M. leprae DNA and the findings concur with the previously published data that European M. leprae strains fall in to one group (SNP group 3). CONCLUSIONS: These findings support the suggestion that the M. leprae genome is extremely stable and show that archaeological M. leprae DNA can be analysed to gain detailed information about the genotypic make-up of European leprosy, which may assist in the understanding of leprosy transmission worldwide. FAU - Watson, Claire L AU - Watson CL AD - Department of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom. claire.watson@lshtm.ac.uk FAU - Lockwood, Diana N J AU - Lockwood DN LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091022 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Bacterial) SB - IM MH - Archaeology/methods MH - Bacterial Typing Techniques/methods MH - Base Sequence MH - DNA Fingerprinting MH - DNA, Bacterial/*genetics MH - Europe MH - Genotype MH - Humans MH - Leprosy/*microbiology MH - Molecular Sequence Data MH - Mycobacterium leprae/*genetics MH - Polymerase Chain Reaction MH - Polymorphism, Restriction Fragment Length MH - *Polymorphism, Single Nucleotide PMC - PMC2761613 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2009/10/23 06:00 MHDA- 2010/03/13 06:00 PMCR- 2009/10/22 CRDT- 2009/10/23 06:00 PHST- 2009/02/17 00:00 [received] PHST- 2009/07/02 00:00 [accepted] PHST- 2009/10/23 06:00 [entrez] PHST- 2009/10/23 06:00 [pubmed] PHST- 2010/03/13 06:00 [medline] PHST- 2009/10/22 00:00 [pmc-release] AID - 09-PONE-RA-08742R1 [pii] AID - 10.1371/journal.pone.0007547 [doi] PST - epublish SO - PLoS One. 2009 Oct 22;4(10):e7547. doi: 10.1371/journal.pone.0007547. PMID- 19729623 OWN - NLM STAT- MEDLINE DCOM- 20090918 LR - 20090904 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 325 IP - 5945 DP - 2009 Sep 4 TI - Archaeology. Ancient DNA says Europe's first farmers came from afar. PG - 1189 LID - 10.1126/science.325_1189 [doi] FAU - Balter, Michael AU - Balter M LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM MH - Agriculture/*history MH - Archaeology MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration MH - Europe MH - History, Ancient MH - Humans MH - Sequence Analysis, DNA MH - Skull/*chemistry EDAT- 2009/09/05 06:00 MHDA- 2009/09/19 06:00 CRDT- 2009/09/05 06:00 PHST- 2009/09/05 06:00 [entrez] PHST- 2009/09/05 06:00 [pubmed] PHST- 2009/09/19 06:00 [medline] AID - 325/5945/1189 [pii] AID - 10.1126/science.325_1189 [doi] PST - ppublish SO - Science. 2009 Sep 4;325(5945):1189. doi: 10.1126/science.325_1189. PMID- 19661919 OWN - NLM STAT- MEDLINE DCOM- 20091022 LR - 20211020 IS - 1460-2075 (Electronic) IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 28 IP - 17 DP - 2009 Sep 2 TI - The Neandertal genome and ancient DNA authenticity. PG - 2494-502 LID - 10.1038/emboj.2009.222 [doi] AB - Recent advances in high-thoughput DNA sequencing have made genome-scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the authenticity of the DNA sequences retrieved. We discuss how these difficulties can be addressed, particularly with regard to analyses of the Neandertal genome. We argue that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination. Indirect measures, such as the extent of DNA fragmentation, nucleotide misincorporations, or comparison of derived allele frequencies in different fragment size classes, are unreliable. Fortunately, interim approaches based on mtDNA differences between Neandertals and current humans, detection of male contamination through Y chromosomal sequences, and repeated sequencing from the same fossil to detect autosomal contamination allow initial large-scale sequencing of Neandertal genomes. This will result in the discovery of fixed differences in the nuclear genome between Neandertals and current humans that can serve as future direct assays for contamination. For analyses of other fossil hominins, which may become possible in the future, we suggest a similar 'boot-strap' approach in which interim approaches are applied until sufficient data for more definitive direct assays are acquired. FAU - Green, Richard E AU - Green RE AD - Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Briggs, Adrian W AU - Briggs AW FAU - Krause, Johannes AU - Krause J FAU - Prüfer, Kay AU - Prüfer K FAU - Burbano, Hernán A AU - Burbano HA FAU - Siebauer, Michael AU - Siebauer M FAU - Lachmann, Michael AU - Lachmann M FAU - Pääbo, Svante AU - Pääbo S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20090806 PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Sequence MH - DNA/*chemistry MH - DNA, Mitochondrial/chemistry MH - Evolution, Molecular MH - Fossils MH - Genetic Variation MH - *Genome MH - Hominidae/*genetics MH - Humans MH - Phylogeny MH - Sequence Analysis, DNA PMC - PMC2725275 COIS- The authors declare that they have no conflict of interest. EDAT- 2009/08/08 09:00 MHDA- 2009/10/23 06:00 PMCR- 2009/09/02 CRDT- 2009/08/08 09:00 PHST- 2009/06/29 00:00 [received] PHST- 2009/07/10 00:00 [accepted] PHST- 2009/08/08 09:00 [entrez] PHST- 2009/08/08 09:00 [pubmed] PHST- 2009/10/23 06:00 [medline] PHST- 2009/09/02 00:00 [pmc-release] AID - emboj2009222 [pii] AID - 10.1038/emboj.2009.222 [doi] PST - ppublish SO - EMBO J. 2009 Sep 2;28(17):2494-502. doi: 10.1038/emboj.2009.222. Epub 2009 Aug 6. PMID- 19570745 OWN - NLM STAT- MEDLINE DCOM- 20091203 LR - 20221207 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 26 IP - 9 DP - 2009 Sep TI - Genealogical discontinuities among Etruscan, Medieval, and contemporary Tuscans. PG - 2157-66 LID - 10.1093/molbev/msp126 [doi] AB - The available mitochondrial DNA (mtDNA) data do not point to clear genetic relationships between current Tuscans and the Bronze-Age inhabitants of Tuscany, the Etruscans. To understand how and when such a genetic discontinuity may have arisen, we extracted and typed the mtDNAs of 27 medieval Tuscans from an initial sample of 61, spanning a period between the 10th and 15th century AD. We then tested by serial coalescent simulation various models describing the genealogical relationships among past and current inhabitants of Tuscany, the latter including three samples (from Murlo, Volterra, and Casentino) that were recently claimed to be of Etruscan descent. Etruscans and medieval Tuscans share three mitochondrial haplotypes but fall in distinct branches of the mitochondrial genealogy in the only model that proved compatible with the data. Under that model, contemporary people of Tuscany show clear genetic relationships with Medieval people, but not with the Etruscans, along the female lines. No evidence of excess mutation was found in the Etruscan DNAs by a Bayesian test, and so there is no reason to suspect that these results are biased by systematic contamination of the ancient sequences or laboratory artefacts. Extensive demographic changes before AD 1000 are thus the simplest explanation for the differences between the contemporary and the Bronze-Age mtDNAs of Tuscany. Accordingly, genealogical continuity between ancient and modern populations of the same area does not seem a safe general assumption, but rather a hypothesis that, when possible, should be tested using ancient DNA analysis. FAU - Guimaraes, Silvia AU - Guimaraes S AD - Dipartimento di Biologia Evoluzionistica, Laboratorio di Antropologia, Università di Firenze, Firenze, Italy. FAU - Ghirotto, Silvia AU - Ghirotto S FAU - Benazzo, Andrea AU - Benazzo A FAU - Milani, Lucio AU - Milani L FAU - Lari, Martina AU - Lari M FAU - Pilli, Elena AU - Pilli E FAU - Pecchioli, Elena AU - Pecchioli E FAU - Mallegni, Francesco AU - Mallegni F FAU - Lippi, Barbara AU - Lippi B FAU - Bertoldi, Francesca AU - Bertoldi F FAU - Gelichi, Sauro AU - Gelichi S FAU - Casoli, Antonella AU - Casoli A FAU - Belle, Elise M S AU - Belle EM FAU - Caramelli, David AU - Caramelli D FAU - Barbujani, Guido AU - Barbujani G LA - eng SI - GENBANK/FJ946288 SI - GENBANK/FJ946289 SI - GENBANK/FJ946290 SI - GENBANK/FJ946291 SI - GENBANK/FJ946292 SI - GENBANK/FJ946293 SI - GENBANK/FJ946294 SI - GENBANK/FJ946295 SI - GENBANK/FJ946296 SI - GENBANK/FJ946297 SI - GENBANK/FJ946298 SI - GENBANK/FJ946299 SI - GENBANK/FJ946300 SI - GENBANK/FJ946301 SI - GENBANK/FJ946302 SI - GENBANK/FJ946303 SI - GENBANK/FJ946304 SI - GENBANK/FJ946305 SI - GENBANK/FJ946306 SI - GENBANK/FJ946307 SI - GENBANK/FJ946308 SI - GENBANK/FJ946309 SI - GENBANK/FJ946310 SI - GENBANK/FJ946311 SI - GENBANK/FJ946312 SI - GENBANK/FJ946313 SI - GENBANK/FJ946314 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090701 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) SB - IM MH - Computer Simulation MH - Consensus Sequence MH - DNA, Mitochondrial/genetics MH - Demography MH - Female MH - Gene Regulatory Networks MH - *Genealogy and Heraldry MH - Genetic Variation MH - History, 15th Century MH - History, 21st Century MH - History, Medieval MH - Humans MH - Italy MH - Male MH - Models, Genetic MH - Molecular Sequence Data MH - *Phylogeny MH - Reproducibility of Results MH - Sample Size MH - White People/*genetics/*history EDAT- 2009/07/03 09:00 MHDA- 2009/12/16 06:00 CRDT- 2009/07/03 09:00 PHST- 2009/07/03 09:00 [entrez] PHST- 2009/07/03 09:00 [pubmed] PHST- 2009/12/16 06:00 [medline] AID - msp126 [pii] AID - 10.1093/molbev/msp126 [doi] PST - ppublish SO - Mol Biol Evol. 2009 Sep;26(9):2157-66. doi: 10.1093/molbev/msp126. Epub 2009 Jul 1. PMID- 19449030 OWN - NLM STAT- MEDLINE DCOM- 20090928 LR - 20221207 IS - 1432-1203 (Electronic) IS - 0340-6717 (Linking) VI - 126 IP - 3 DP - 2009 Sep TI - Ancient DNA provides new insights into the history of south Siberian Kurgan people. PG - 395-410 LID - 10.1007/s00439-009-0683-0 [doi] AB - To help unravel some of the early Eurasian steppe migration movements, we determined the Y-chromosomal and mitochondrial haplotypes and haplogroups of 26 ancient human specimens from the Krasnoyarsk area dated from between the middle of the second millennium BC. to the fourth century AD. In order to go further in the search of the geographic origin and physical traits of these south Siberian specimens, we also typed phenotype-informative single nucleotide polymorphisms. Our autosomal, Y-chromosomal and mitochondrial DNA analyses reveal that whereas few specimens seem to be related matrilineally or patrilineally, nearly all subjects belong to haplogroup R1a1-M17 which is thought to mark the eastward migration of the early Indo-Europeans. Our results also confirm that at the Bronze and Iron Ages, south Siberia was a region of overwhelmingly predominant European settlement, suggesting an eastward migration of Kurgan people across the Russo-Kazakh steppe. Finally, our data indicate that at the Bronze and Iron Age timeframe, south Siberians were blue (or green)-eyed, fair-skinned and light-haired people and that they might have played a role in the early development of the Tarim Basin civilization. To the best of our knowledge, no equivalent molecular analysis has been undertaken so far. FAU - Keyser, Christine AU - Keyser C AD - Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Université de Strasbourg, 11 rue Humann, 67085, Strasbourg Cedex, France. Christine.Keyser@iml-ulp.u-strasbg.fr FAU - Bouakaze, Caroline AU - Bouakaze C FAU - Crubézy, Eric AU - Crubézy E FAU - Nikolaev, Valery G AU - Nikolaev VG FAU - Montagnon, Daniel AU - Montagnon D FAU - Reis, Tatiana AU - Reis T FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Historical Article PT - Journal Article DEP - 20090516 PL - Germany TA - Hum Genet JT - Human genetics JID - 7613873 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/classification/*genetics MH - Chromosomes, Human, Y/*genetics MH - DNA, Mitochondrial/*genetics MH - Gene Pool MH - Geography MH - Haplotypes/*genetics MH - History, Ancient MH - Humans MH - Male MH - Pigmentation MH - Polymorphism, Single Nucleotide MH - Siberia MH - Tandem Repeat Sequences EDAT- 2009/05/19 09:00 MHDA- 2009/09/29 06:00 CRDT- 2009/05/19 09:00 PHST- 2009/02/06 00:00 [received] PHST- 2009/05/06 00:00 [accepted] PHST- 2009/05/19 09:00 [entrez] PHST- 2009/05/19 09:00 [pubmed] PHST- 2009/09/29 06:00 [medline] AID - 10.1007/s00439-009-0683-0 [doi] PST - ppublish SO - Hum Genet. 2009 Sep;126(3):395-410. doi: 10.1007/s00439-009-0683-0. Epub 2009 May 16. PMID- 19650893 OWN - NLM STAT- MEDLINE DCOM- 20090923 LR - 20221207 IS - 1471-2148 (Electronic) IS - 1471-2148 (Linking) VI - 9 DP - 2009 Aug 3 TI - Demographic history of Canary Islands male gene-pool: replacement of native lineages by European. PG - 181 LID - 10.1186/1471-2148-9-181 [doi] AB - BACKGROUND: The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th-18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times. RESULTS: Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th-18th centuries than today. CONCLUSION: The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts. FAU - Fregel, Rosa AU - Fregel R AD - Department of Genetics, University of La Laguna, Avda. Astrofísico Fco, Sánchez, La Laguna, 38271 Santa Cruz de Tenerife, Spain. rfregel@gmail.com FAU - Gomes, Verónica AU - Gomes V FAU - Gusmão, Leonor AU - Gusmão L FAU - González, Ana M AU - González AM FAU - Cabrera, Vicente M AU - Cabrera VM FAU - Amorim, António AU - Amorim A FAU - Larruga, Jose M AU - Larruga JM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090803 PL - England TA - BMC Evol Biol JT - BMC evolutionary biology JID - 100966975 RN - 0 (DNA, Mitochondrial) SB - IM MH - Black People/*genetics MH - Chromosomes, Human, Y/*genetics MH - DNA, Mitochondrial/genetics MH - Evolution, Molecular MH - Female MH - *Gene Pool MH - *Genetics, Population MH - Humans MH - Male MH - Polymorphism, Restriction Fragment Length MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA MH - Spain MH - White People/*genetics PMC - PMC2728732 EDAT- 2009/08/05 09:00 MHDA- 2009/09/24 06:00 PMCR- 2009/08/03 CRDT- 2009/08/05 09:00 PHST- 2009/01/16 00:00 [received] PHST- 2009/08/03 00:00 [accepted] PHST- 2009/08/05 09:00 [entrez] PHST- 2009/08/05 09:00 [pubmed] PHST- 2009/09/24 06:00 [medline] PHST- 2009/08/03 00:00 [pmc-release] AID - 1471-2148-9-181 [pii] AID - 10.1186/1471-2148-9-181 [doi] PST - epublish SO - BMC Evol Biol. 2009 Aug 3;9:181. doi: 10.1186/1471-2148-9-181. PMID- 19714206 OWN - NLM STAT- MEDLINE DCOM- 20091116 LR - 20240323 IS - 1553-7358 (Electronic) IS - 1553-734X (Print) IS - 1553-734X (Linking) VI - 5 IP - 8 DP - 2009 Aug TI - The origins of lactase persistence in Europe. PG - e1000491 LID - 10.1371/journal.pcbi.1000491 [doi] LID - e1000491 AB - Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (-13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the--13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and unlinked genetic markers in Europe and western Asia's geographic space. Using data on--13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the--13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe. FAU - Itan, Yuval AU - Itan Y AD - Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom. FAU - Powell, Adam AU - Powell A FAU - Beaumont, Mark A AU - Beaumont MA FAU - Burger, Joachim AU - Burger J FAU - Thomas, Mark G AU - Thomas MG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090828 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Genetic Markers) RN - 1406-16-2 (Vitamin D) RN - EC 3.2.1.108 (Lactase) RN - J2B2A4N98G (Lactose) SB - IM MH - Alleles MH - Bayes Theorem MH - Computational Biology/methods MH - Computer Simulation MH - Diet MH - Europe MH - Evolution, Molecular MH - Gene Frequency MH - Genetic Markers MH - Geography MH - Haplotypes MH - Humans MH - Lactase/*chemistry/genetics/physiology MH - Lactose/metabolism MH - *Polymorphism, Genetic MH - Vitamin D/metabolism PMC - PMC2722739 COIS- The authors have declared that no competing interests exist. EDAT- 2009/08/29 09:00 MHDA- 2009/11/17 06:00 PMCR- 2009/08/28 CRDT- 2009/08/29 09:00 PHST- 2009/02/05 00:00 [received] PHST- 2009/07/28 00:00 [accepted] PHST- 2009/08/29 09:00 [entrez] PHST- 2009/08/29 09:00 [pubmed] PHST- 2009/11/17 06:00 [medline] PHST- 2009/08/28 00:00 [pmc-release] AID - 09-PLCB-RA-0120R2 [pii] AID - 10.1371/journal.pcbi.1000491 [doi] PST - ppublish SO - PLoS Comput Biol. 2009 Aug;5(8):e1000491. doi: 10.1371/journal.pcbi.1000491. Epub 2009 Aug 28. PMID- 19608918 OWN - NLM STAT- MEDLINE DCOM- 20090729 LR - 20090717 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 325 IP - 5938 DP - 2009 Jul 17 TI - Targeted retrieval and analysis of five Neandertal mtDNA genomes. PG - 318-21 LID - 10.1126/science.1174462 [doi] AB - Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes. FAU - Briggs, Adrian W AU - Briggs AW AD - Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. briggs@eva.mpg.de FAU - Good, Jeffrey M AU - Good JM FAU - Green, Richard E AU - Green RE FAU - Krause, Johannes AU - Krause J FAU - Maricic, Tomislav AU - Maricic T FAU - Stenzel, Udo AU - Stenzel U FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C FAU - Rudan, Pavao AU - Rudan P FAU - Brajkovic, Dejana AU - Brajkovic D FAU - Kucan, Zeljko AU - Kucan Z FAU - Gusic, Ivan AU - Gusic I FAU - Schmitz, Ralf AU - Schmitz R FAU - Doronichev, Vladimir B AU - Doronichev VB FAU - Golovanova, Liubov V AU - Golovanova LV FAU - de la Rasilla, Marco AU - de la Rasilla M FAU - Fortea, Javier AU - Fortea J FAU - Rosas, Antonio AU - Rosas A FAU - Pääbo, Svante AU - Pääbo S LA - eng SI - GENBANK/FM865407 SI - GENBANK/FM865408 SI - GENBANK/FM865409 SI - GENBANK/FM865410 SI - GENBANK/FM865411 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM CIN - Science. 2009 Jul 17;325(5938):252. doi: 10.1126/science.325_252. PMID: 19608883 MH - Animals MH - Bayes Theorem MH - DNA Primers MH - DNA, Mitochondrial/analysis/*genetics/isolation & purification MH - Evolution, Molecular MH - Female MH - *Fossils MH - Gene Library MH - Genetic Variation MH - Genome, Human MH - *Genome, Mitochondrial MH - Geography MH - Hominidae/*genetics MH - Humans MH - Male MH - Molecular Sequence Data MH - Phylogeny MH - Population Density MH - *Sequence Analysis, DNA EDAT- 2009/07/18 09:00 MHDA- 2009/07/30 09:00 CRDT- 2009/07/18 09:00 PHST- 2009/07/18 09:00 [entrez] PHST- 2009/07/18 09:00 [pubmed] PHST- 2009/07/30 09:00 [medline] AID - 325/5938/318 [pii] AID - 10.1126/science.1174462 [doi] PST - ppublish SO - Science. 2009 Jul 17;325(5938):318-21. doi: 10.1126/science.1174462. PMID- 19608883 OWN - NLM STAT- MEDLINE DCOM- 20090729 LR - 20101118 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 325 IP - 5938 DP - 2009 Jul 17 TI - Ancient DNA. Sequencing Neandertal mitochondrial genomes by the half-dozen. PG - 252 LID - 10.1126/science.325_252 [doi] FAU - Pennisi, Elizabeth AU - Pennisi E LA - eng PT - Comment PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM CON - Science. 2009 Jul 17;325(5938):318-21. doi: 10.1126/science.1174462. PMID: 19608918 MH - Animals MH - Biological Evolution MH - Bone and Bones MH - DNA, Mitochondrial/genetics MH - Female MH - *Fossils MH - Gene Library MH - Genetic Variation MH - Genome, Human MH - *Genome, Mitochondrial MH - Hominidae/*genetics MH - Humans MH - Male MH - Population Density MH - *Sequence Analysis, DNA/economics EDAT- 2009/07/18 09:00 MHDA- 2009/07/30 09:00 CRDT- 2009/07/18 09:00 PHST- 2009/07/18 09:00 [entrez] PHST- 2009/07/18 09:00 [pubmed] PHST- 2009/07/30 09:00 [medline] AID - 325/5938/252 [pii] AID - 10.1126/science.325_252 [doi] PST - ppublish SO - Science. 2009 Jul 17;325(5938):252. doi: 10.1126/science.325_252. PMID- 19523150 OWN - NLM STAT- MEDLINE DCOM- 20090806 LR - 20090615 IS - 1469-1809 (Electronic) IS - 0003-4800 (Linking) VI - 73 IP - Pt 4 DP - 2009 Jul TI - Ancient DNA and family relationships in a Pompeian house. PG - 429-37 LID - 10.1111/j.1469-1809.2009.00520.x [doi] AB - Archaeological, anthropological and pathological data suggest that thirteen skeletons found in a house at the Pompeii archaeological site, dated to 79 A.D., belong to one family. To verify this and to identify the relationships between these individuals, we analyzed DNA extracted from bone specimens. Specifically, hypervariable segment 1 (HVS1) of the human mitochondrial DNA (mtDNA) control region was amplified in two overlapping polymerase chain reactions and the sequences were compared to the revised Cambridge Reference Sequence. As independent controls, other polymorphic sites in HVS1, HVS2 and in the coding region were analyzed. We also amplified some short tandem repeats of the thirteen specimens. This study revealed that six of the thirteen individuals are indeed closely related. FAU - Di Bernardo, Giovanni AU - Di Bernardo G AD - Department of Experimental Medicine, Biotechnology and Molecular Biology Section Antonino Cascino, 2nd University of Naples, Via Costantinopoli 16, Naples, Italy. FAU - Del Gaudio, Stefania AU - Del Gaudio S FAU - Galderisi, Umberto AU - Galderisi U FAU - Cascino, Antonino AU - Cascino A FAU - Cipollaro, Marilena AU - Cipollaro M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Ann Hum Genet JT - Annals of human genetics JID - 0416661 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Adolescent MH - Adult MH - Aged MH - Child MH - Child, Preschool MH - DNA/*genetics MH - DNA, Mitochondrial/genetics MH - Family MH - Female MH - Humans MH - Male MH - Middle Aged MH - *Paleontology MH - Pedigree MH - Skeleton MH - Young Adult EDAT- 2009/06/16 09:00 MHDA- 2009/08/07 09:00 CRDT- 2009/06/16 09:00 PHST- 2009/06/16 09:00 [entrez] PHST- 2009/06/16 09:00 [pubmed] PHST- 2009/08/07 09:00 [medline] AID - AHG520 [pii] AID - 10.1111/j.1469-1809.2009.00520.x [doi] PST - ppublish SO - Ann Hum Genet. 2009 Jul;73(Pt 4):429-37. doi: 10.1111/j.1469-1809.2009.00520.x. PMID- 19415315 OWN - NLM STAT- MEDLINE DCOM- 20090915 LR - 20211203 IS - 1437-1596 (Electronic) IS - 0937-9827 (Linking) VI - 123 IP - 4 DP - 2009 Jul TI - Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis. PG - 315-25 LID - 10.1007/s00414-009-0348-5 [doi] AB - In the present study, a multiplexed genotyping assay for ten single nucleotide polymorphisms (SNPs) located within six pigmentation candidate genes was developed on modern biological samples and applied to DNA retrieved from 25 archeological human remains from southern central Siberia dating from the Bronze and Iron Ages. SNP genotyping was successful for the majority of ancient samples and revealed that most probably had typical European pigment features, i.e., blue or green eye color, light hair color and skin type, and were likely of European individual ancestry. To our knowledge, this study reports for the first time the multiplexed typing of autosomal SNPs on aged and degraded DNA. By providing valuable information on pigment traits of an individual and allowing individual biogeographical ancestry estimation, autosomal SNP typing can improve ancient DNA studies and aid human identification in some forensic casework situations when used to complement conventional molecular markers. FAU - Bouakaze, Caroline AU - Bouakaze C AD - Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, 11 rue Humann, 67085 Strasbourg Cedex, France. caroline.bouakaze@ulp.u-strasbg.fr FAU - Keyser, Christine AU - Keyser C FAU - Crubézy, Eric AU - Crubézy E FAU - Montagnon, Daniel AU - Montagnon D FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Journal Article DEP - 20090505 PL - Germany TA - Int J Legal Med JT - International journal of legal medicine JID - 9101456 RN - 0 (Antigens, Neoplasm) RN - 0 (Antiporters) RN - 0 (Guanine Nucleotide Exchange Factors) RN - 0 (Membrane Transport Proteins) RN - 0 (OCA2 protein, human) RN - 0 (Receptor, Melanocortin, Type 1) RN - 0 (SLC24A5 protein, human) RN - 0 (SLC45A2 protein, human) RN - EC 2.3.2.27 (HERC2 protein, human) RN - EC 2.3.2.27 (Ubiquitin-Protein Ligases) RN - EC 5.3.- (Intramolecular Oxidoreductases) RN - EC 5.3.3.12 (dopachrome isomerase) SB - IM MH - Antigens, Neoplasm/genetics MH - Antiporters/genetics MH - DNA Degradation, Necrotic MH - DNA Fingerprinting MH - Eye Color/*genetics MH - Forensic Anthropology MH - Genotype MH - Guanine Nucleotide Exchange Factors/genetics MH - Hair Color/*genetics MH - Humans MH - Intramolecular Oxidoreductases/genetics MH - Membrane Transport Proteins/genetics MH - Polymerase Chain Reaction MH - *Polymorphism, Single Nucleotide MH - Racial Groups/*genetics MH - Receptor, Melanocortin, Type 1/genetics MH - Skin Pigmentation/*genetics MH - Ubiquitin-Protein Ligases EDAT- 2009/05/06 09:00 MHDA- 2009/09/16 06:00 CRDT- 2009/05/06 09:00 PHST- 2008/12/16 00:00 [received] PHST- 2009/04/07 00:00 [accepted] PHST- 2009/05/06 09:00 [entrez] PHST- 2009/05/06 09:00 [pubmed] PHST- 2009/09/16 06:00 [medline] AID - 10.1007/s00414-009-0348-5 [doi] PST - ppublish SO - Int J Legal Med. 2009 Jul;123(4):315-25. doi: 10.1007/s00414-009-0348-5. Epub 2009 May 5. PMID- 19545382 OWN - NLM STAT- MEDLINE DCOM- 20090804 LR - 20230516 IS - 1471-2156 (Electronic) IS - 1471-2156 (Linking) VI - 10 DP - 2009 Jun 19 TI - Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman. PG - 29 LID - 10.1186/1471-2156-10-29 [doi] AB - BACKGROUND: Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman. RESULTS: The multiplex assay developed for this study was able to confirm that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups. CONCLUSION: The new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of a priori risks would significantly improve the credibility of results. FAU - Endicott, Phillip AU - Endicott P AD - Museèe de l'Homme, 17 place du Trocadero, 75116 Paris, France. phillip.endicott@gmail.com FAU - Sanchez, Juan J AU - Sanchez JJ FAU - Pichler, Irene AU - Pichler I FAU - Brotherton, Paul AU - Brotherton P FAU - Brooks, Jerome AU - Brooks J FAU - Egarter-Vigl, Eduard AU - Egarter-Vigl E FAU - Cooper, Alan AU - Cooper A FAU - Pramstaller, Peter AU - Pramstaller P LA - eng GR - WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090619 PL - England TA - BMC Genet JT - BMC genetics JID - 100966978 RN - 0 (DNA, Mitochondrial) SB - IM MH - *Biological Evolution MH - Bone and Bones/chemistry MH - DNA, Mitochondrial/*genetics MH - Evolution, Molecular MH - Humans MH - Polymerase Chain Reaction/*methods MH - *Polymorphism, Genetic MH - Sensitivity and Specificity MH - Sequence Analysis, DNA/methods PMC - PMC2717998 EDAT- 2009/06/24 09:00 MHDA- 2009/08/06 09:00 PMCR- 2009/06/19 CRDT- 2009/06/24 09:00 PHST- 2008/11/17 00:00 [received] PHST- 2009/06/19 00:00 [accepted] PHST- 2009/06/24 09:00 [entrez] PHST- 2009/06/24 09:00 [pubmed] PHST- 2009/08/06 09:00 [medline] PHST- 2009/06/19 00:00 [pmc-release] AID - 1471-2156-10-29 [pii] AID - 10.1186/1471-2156-10-29 [doi] PST - epublish SO - BMC Genet. 2009 Jun 19;10:29. doi: 10.1186/1471-2156-10-29. PMID- 19454219 OWN - NLM STAT- MEDLINE DCOM- 20151223 LR - 20150626 IS - 1096-0309 (Electronic) IS - 0003-2697 (Linking) VI - 388 IP - 2 DP - 2009 May 15 TI - Simultaneous assessment of average fragment size and amount in minute samples of degraded DNA. PG - 345-7 LID - 10.1016/j.ab.2009.02.003 [doi] AB - There is currently no method allowing routine characterization of minute amounts of degraded DNA samples such as those encountered in forensic science, archived tissues, ancient DNA, extracellular or stool DNA, and processed food. Here we describe and directly validate such a method based, on the one hand, on a generalized DNA random fragmentation model and, on the other, on two quantitative polymerase chain reaction (PCR) experiments using two different target sizes. The model also makes it possible to determine the minimum sample amount, the minimum mass average fragment size, and the maximum degradation time necessary to obtain a positive PCR. FAU - Colotte, Marthe AU - Colotte M AD - Université de Bordeaux; Plate-forme génomique fonctionnelle 146 Rue Léo Saignat; 33076 Bordeaux cedex; France. FAU - Couallier, Vincent AU - Couallier V FAU - Tuffet, Sophie AU - Tuffet S FAU - Bonnet, Jacques AU - Bonnet J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Anal Biochem JT - Analytical biochemistry JID - 0370535 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*analysis/genetics/*metabolism MH - DNA Fragmentation MH - Forensic Genetics/methods MH - Humans MH - Polymerase Chain Reaction/*methods EDAT- 2009/05/21 09:00 MHDA- 2015/12/24 06:00 CRDT- 2009/05/21 09:00 PHST- 2009/05/21 09:00 [entrez] PHST- 2009/05/21 09:00 [pubmed] PHST- 2015/12/24 06:00 [medline] AID - S0003-2697(09)00102-X [pii] AID - 10.1016/j.ab.2009.02.003 [doi] PST - ppublish SO - Anal Biochem. 2009 May 15;388(2):345-7. doi: 10.1016/j.ab.2009.02.003. PMID- 19294688 OWN - NLM STAT- MEDLINE DCOM- 20090921 LR - 20090427 IS - 1522-2683 (Electronic) IS - 0173-0835 (Linking) VI - 30 IP - 8 DP - 2009 Apr TI - Improving the sensitivity of negative controls in ancient DNA extractions. PG - 1282-5 LID - 10.1002/elps.200800473 [doi] AB - Much attention has been paid on ancient DNA (aDNA) studies, and negative control was used as one of the stringent quality assurance criteria in order to detect potential contamination. However, the results of some aDNA studies showed the evidence of contamination despite their negative controls failed to do so. Using lambda DNA to mock extraneous contaminating DNA, our study showed that aDNA had a property of improving the efficiency of extraction including contaminating DNA, while negative controls had low sensitivity to detect contamination. To circumvent this problem, carrier DNA such as poly(dA) is suggested to be introduced into aDNA extraction. FAU - Xu, Zhi AU - Xu Z AD - State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, PR China. FAU - Zhang, Fan AU - Zhang F FAU - Xu, Bosong AU - Xu B FAU - Tan, Jingze AU - Tan J FAU - Li, Shilin AU - Li S FAU - Jin, Li AU - Jin L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Electrophoresis JT - Electrophoresis JID - 8204476 RN - 0 (DNA, Viral) RN - 24937-83-5 (Poly A) RN - 25191-20-2 (poly(dA)) RN - 9007-49-2 (DNA) SB - IM MH - Archaeology MH - Bacteriophage lambda/chemistry/genetics MH - Bone and Bones/chemistry MH - *DNA/chemistry/isolation & purification MH - DNA, Viral/chemistry MH - Drug Contamination MH - Humans MH - Poly A/*chemistry MH - Polymerase Chain Reaction MH - Sensitivity and Specificity MH - Sequence Analysis, DNA/*methods MH - Tooth/chemistry EDAT- 2009/03/19 09:00 MHDA- 2009/09/22 06:00 CRDT- 2009/03/19 09:00 PHST- 2009/03/19 09:00 [entrez] PHST- 2009/03/19 09:00 [pubmed] PHST- 2009/09/22 06:00 [medline] AID - 10.1002/elps.200800473 [doi] PST - ppublish SO - Electrophoresis. 2009 Apr;30(8):1282-5. doi: 10.1002/elps.200800473. PMID- 19215875 OWN - NLM STAT- MEDLINE DCOM- 20090429 LR - 20101118 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 3 IP - 2 DP - 2009 Mar TI - Novel methods of molecular sex identification from skeletal tissue using the amelogenin gene. PG - 74-9 LID - 10.1016/j.fsigen.2008.10.007 [doi] AB - Sex identification from skeletal material is of vital importance in order to reconstruct the demographic variables of an individual in forensic genetics and ancient DNA (aDNA) analysis. When the use of conventional methods of sex identification are impossible, molecular analysis of the X and Y chromosomes provides an expedient solution. Two novel systems of molecular sex identification suitable for skeletal material using the amelogenin gene are described, beginning in intron 2-3, spanning exon 3 and ending in intron 3-4. This area was optimal for sexing, as it includes 14 sex-specific polymorphic regions in addition to an indel (insertion or deletion of nucleotides). Once optimised and working with 100% efficiency on the controls, these procedures were applied to a collection of miscellaneous archaeological skeletons (ex situ) sourced from the Raymond Dart Collection of Human Skeletons (Dart Collection). This collection was used to optimise these techniques for skeletal remains derived from an archaeological context. These methods produced 46.66% sex results for the ex situ sample, which is within the normal range for aDNA studies. These new techniques are optimal for sex identification, with both the inherent control of isolating many sex-specific features and combined with the use of sensitive micro-fluidic electrophoresis. FAU - Gibbon, Victoria AU - Gibbon V AD - Department of Internal Medicine, University of the Witwatersrand, 7 York Rd, Johannesburg, 2193 Parktown, South Africa. gibbonv@gmail.com FAU - Paximadis, Maria AU - Paximadis M FAU - Strkalj, Goran AU - Strkalj G FAU - Ruff, Paul AU - Ruff P FAU - Penny, Clem AU - Penny C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081213 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (Amelogenin) SB - IM MH - Amelogenin/*genetics MH - Base Sequence MH - Bone and Bones/chemistry MH - Chromosomes, Human, X/chemistry MH - Chromosomes, Human, Y/chemistry MH - Forensic Genetics/methods MH - Humans MH - Molecular Sequence Data MH - Paleontology/methods MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Sequence Homology, Nucleic Acid MH - Sex Determination Analysis/*methods MH - Sex Determination by Skeleton/*methods EDAT- 2009/02/14 09:00 MHDA- 2009/04/30 09:00 CRDT- 2009/02/14 09:00 PHST- 2008/07/03 00:00 [received] PHST- 2008/09/22 00:00 [revised] PHST- 2008/10/15 00:00 [accepted] PHST- 2009/02/14 09:00 [entrez] PHST- 2009/02/14 09:00 [pubmed] PHST- 2009/04/30 09:00 [medline] AID - S1872-4973(08)00147-6 [pii] AID - 10.1016/j.fsigen.2008.10.007 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2009 Mar;3(2):74-9. doi: 10.1016/j.fsigen.2008.10.007. Epub 2008 Dec 13. PMID- 18951391 OWN - NLM STAT- MEDLINE DCOM- 20090520 LR - 20100502 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 138 IP - 3 DP - 2009 Mar TI - Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American. PG - 255-65 LID - 10.1002/ajpa.20923 [doi] AB - Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America. CI - (c) 2008 Wiley-Liss, Inc. FAU - Adachi, Noboru AU - Adachi N AD - Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimo-Kato, Chuo, Yamanashi, Japan. nadachi@yamanashi.ac.jp FAU - Shinoda, Ken-ichi AU - Shinoda K FAU - Umetsu, Kazuo AU - Umetsu K FAU - Matsumura, Hirofumi AU - Matsumura H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) RN - 0 (RNA, Transfer, Arg) RN - EC 1.6.99.3 (NADH Dehydrogenase) SB - IM EIN - Am J Phys Anthropol. 2010 Mar;141(3):504-5 MH - Asia MH - Bone and Bones/*anatomy & histology MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - Humans MH - Indians, North American/*genetics MH - Japan MH - NADH Dehydrogenase/genetics MH - Phylogeny MH - RNA, Transfer, Arg/genetics MH - Siberia MH - Skeleton EDAT- 2008/10/28 09:00 MHDA- 2009/05/21 09:00 CRDT- 2008/10/28 09:00 PHST- 2008/10/28 09:00 [pubmed] PHST- 2009/05/21 09:00 [medline] PHST- 2008/10/28 09:00 [entrez] AID - 10.1002/ajpa.20923 [doi] PST - ppublish SO - Am J Phys Anthropol. 2009 Mar;138(3):255-65. doi: 10.1002/ajpa.20923. PMID- 19352435 OWN - NLM STAT- MEDLINE DCOM- 20090706 LR - 20211020 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 4 IP - 4 DP - 2009 TI - Changes in dry state hemoglobin over time do not increase the potential for oxidative DNA damage in dried blood. PG - e5110 LID - 10.1371/journal.pone.0005110 [doi] LID - e5110 AB - BACKGROUND: Hemoglobin (Hb) is the iron-containing oxygen transport protein present in the red blood cells of vertebrates. Ancient DNA and forensic scientists are particularly interested in Hb reactions in the dry state because both regularly encounter aged, dried bloodstains. The DNA in such stains may be oxidatively damaged and, in theory, may be deteriorated by the presence of Hb. To understand the nature of the oxidative systems potentially available to degrade DNA in the presence of dried Hb, we need to determine what molecular species Hb forms over time. These species will determine what type of iron (i.e. Fe(2+)/Fe(3+)/Fe(4+)) is available to participate in further chemical reactions. The availability of "free" iron will affect the ability of the system to undergo Fenton-type reactions which generate the highly reactive hydroxyl radical (OH*). The OH* can directly damage DNA. METHODOLOGY/PRINCIPAL FINDINGS: Oxygenated Hb (oxyHb) converts over time to oxidized Hb (metHb), but this happens more quickly in the dry state than in the hydrated state, as shown by monitoring stabilized oxyHb. In addition, dry state oxyHb converts into at least one other unknown species other than metHb. Although "free" iron was detectable as both Fe(2+) and Fe(3+) in dry and hydrated oxyHb and metHb, the amount of ions detected did not increase over time. There was no evidence that Hb becomes more prone to generating OH* as it ages in either the hydrated or dry states. CONCLUSIONS: The Hb molecule in the dried state undergoes oxidative changes and releases reactive Fe(II) cations. These changes, however, do not appear to increase the ability of Hb to act as a more aggressive Fenton reagent over time. Nevertheless, the presence of Hb in the vicinity of DNA in dried bloodstains creates the opportunity for OH*-induced oxidative damage to the deoxyribose sugar and the DNA nucleobases. FAU - Marrone, April AU - Marrone A AD - Graduate Program in Chemistry, Department of Chemistry, University of Central Florida, Orlando, Florida, United States of America. FAU - Ballantyne, Jack AU - Ballantyne J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090408 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Hemoglobins) RN - 3352-57-6 (Hydroxyl Radical) RN - 9007-49-2 (DNA) SB - IM MH - DNA/*metabolism MH - *DNA Damage MH - Hemoglobins/*chemistry/metabolism MH - Humans MH - Hydroxyl Radical/metabolism MH - *Oxidative Stress PMC - PMC2662409 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2009/04/09 09:00 MHDA- 2009/07/07 09:00 PMCR- 2009/04/08 CRDT- 2009/04/09 09:00 PHST- 2009/02/03 00:00 [received] PHST- 2009/03/11 00:00 [accepted] PHST- 2009/04/09 09:00 [entrez] PHST- 2009/04/09 09:00 [pubmed] PHST- 2009/07/07 09:00 [medline] PHST- 2009/04/08 00:00 [pmc-release] AID - 09-PONE-RA-08489R1 [pii] AID - 10.1371/journal.pone.0005110 [doi] PST - ppublish SO - PLoS One. 2009;4(4):e5110. doi: 10.1371/journal.pone.0005110. Epub 2009 Apr 8. PMID- 19148284 OWN - NLM STAT- MEDLINE DCOM- 20090213 LR - 20211020 IS - 1553-7404 (Electronic) IS - 1553-7390 (Print) IS - 1553-7390 (Linking) VI - 5 IP - 1 DP - 2009 Jan TI - Sequences from first settlers reveal rapid evolution in Icelandic mtDNA pool. PG - e1000343 LID - 10.1371/journal.pgen.1000343 [doi] LID - e1000343 AB - A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA) control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples. FAU - Helgason, Agnar AU - Helgason A AD - deCODE Genetics, Reykjavik, Iceland. agnar@decode.is FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C FAU - Ghosh, Shyamali AU - Ghosh S FAU - Sigurethardóttir, Sigrún AU - Sigurethardóttir S FAU - Sampietro, Maria Lourdes AU - Sampietro ML FAU - Gigli, Elena AU - Gigli E FAU - Baker, Adam AU - Baker A FAU - Bertranpetit, Jaume AU - Bertranpetit J FAU - Arnadóttir, Lilja AU - Arnadóttir L FAU - Thornorsteinsdottir, Unnur AU - Thornorsteinsdottir U FAU - Stefánsson, Kári AU - Stefánsson K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090116 PL - United States TA - PLoS Genet JT - PLoS genetics JID - 101239074 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*chemistry MH - *Evolution, Molecular MH - *Gene Pool MH - *Genetics, Population MH - Geography MH - Humans MH - Iceland MH - Sequence Analysis, DNA PMC - PMC2613751 COIS- The authors have declared that no competing interests exist. EDAT- 2009/01/17 09:00 MHDA- 2009/02/14 09:00 PMCR- 2009/01/01 CRDT- 2009/01/17 09:00 PHST- 2008/09/10 00:00 [received] PHST- 2008/12/16 00:00 [accepted] PHST- 2009/01/17 09:00 [entrez] PHST- 2009/01/17 09:00 [pubmed] PHST- 2009/02/14 09:00 [medline] PHST- 2009/01/01 00:00 [pmc-release] AID - 08-PLGE-RA-1192R2 [pii] AID - 10.1371/journal.pgen.1000343 [doi] PST - ppublish SO - PLoS Genet. 2009 Jan;5(1):e1000343. doi: 10.1371/journal.pgen.1000343. Epub 2009 Jan 16. PMID- 19067027 OWN - NLM STAT- MEDLINE DCOM- 20090529 LR - 20211020 IS - 0022-2844 (Print) IS - 0022-2844 (Linking) VI - 68 IP - 1 DP - 2009 Jan TI - Postmortem miscoding lesions in sequence analysis of human ancient mitochondrial DNA. PG - 40-55 LID - 10.1007/s00239-008-9184-3 [doi] AB - Genetic miscoding lesions can cause inaccuracies during the interpretation of ancient DNA sequence data. In this study, genetic miscoding lesions were identified and assessed by cloning and direct sequencing of degraded, amplified mitochondrial DNA (mtDNA) extracted from human remains. Forty-two individuals, comprising nine collections from five geographic locations, were analyzed for the presence of DNA damage that can affect the generation of a correct mtDNA profile. In agreement with previous studies, high levels (56.5% of all damage sites) of proposed hydrolytic damage products were observed. Among these, type 2 transitions (cytosine --> thymine or guanine --> adenine), which are highly indicative of hydrolytic deamination, were observed in 50% of all misincorporations that occurred. In addition to hydrolytic damage products, oxidative damage products were also observed in this study and were responsible for approximately 43.5% of all misincorporations. This level of misincorporation is in contrast to previous studies characterizing miscoding lesions from the analysis of bone and teeth, where few to no oxidative damage products were observed. Of all the oxidative damage products found in this study, type 2 transversions (cytosine --> adenine/guanine --> thymine or cytosine --> guanine/guanine --> cytosine), which are commonly formed through the generation of 8-hydroxyguanine, accounted for 30.3% of all genetic miscoding lesions observed. This study identifies the previously unreported presence of oxidative DNA damage and proposes that damage to degraded DNA templates is highly specific in type, correlating with the geographic location and the taphonomic conditions of the depositional environment from which the remains are recovered. FAU - Lamers, Ryan AU - Lamers R AD - Department of Biology, Lakehead University, Thunder Bay, ON, Canada. FAU - Hayter, Shana AU - Hayter S FAU - Matheson, Carney D AU - Matheson CD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081206 PL - Germany TA - J Mol Evol JT - Journal of molecular evolution JID - 0360051 RN - 0 (DNA, Mitochondrial) RN - 5614-64-2 (8-hydroxyguanine) RN - 5Z93L87A1R (Guanine) RN - 8J337D1HZY (Cytosine) RN - JAC85A2161 (Adenine) RN - QR26YLT7LT (Thymine) SB - IM MH - Adenine/chemistry MH - Cytosine/chemistry MH - DNA Damage/*genetics MH - DNA, Mitochondrial/chemistry/*genetics MH - Guanine/analogs & derivatives/chemistry MH - Humans MH - Sequence Analysis MH - Thymine/chemistry EDAT- 2008/12/11 09:00 MHDA- 2009/05/30 09:00 CRDT- 2008/12/11 09:00 PHST- 2008/06/25 00:00 [received] PHST- 2008/11/11 00:00 [accepted] PHST- 2008/11/11 00:00 [revised] PHST- 2008/12/11 09:00 [pubmed] PHST- 2009/05/30 09:00 [medline] PHST- 2008/12/11 09:00 [entrez] AID - 10.1007/s00239-008-9184-3 [doi] PST - ppublish SO - J Mol Evol. 2009 Jan;68(1):40-55. doi: 10.1007/s00239-008-9184-3. Epub 2008 Dec 6. PMID- 18661472 OWN - NLM STAT- MEDLINE DCOM- 20090213 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 138 IP - 1 DP - 2009 Jan TI - Ancient DNA analysis of human remains from the Upper Capital City of Kublai Khan. PG - 23-9 LID - 10.1002/ajpa.20894 [doi] AB - Analysis of DNA from human archaeological remains is a powerful tool for reconstructing ancient events in human history. To help understand the origin of the inhabitants of Kublai Khan's Upper Capital in Inner Mongolia, we analyzed mitochondrial DNA (mtDNA) polymorphisms in 21 ancient individuals buried in the Zhenzishan cemetery of the Upper Capital. MtDNA coding and noncoding region polymorphisms identified in the ancient individuals were characteristic of the Asian mtDNA haplogroups A, B, N9a, C, D, Z, M7b, and M. Phylogenetic analysis of the ancient mtDNA sequences, and comparison with extant reference populations, revealed that the maternal lineages of the population buried in the Zhenzishan cemetery are of Asian origin and typical of present-day Han Chinese, despite the presence of typical European morphological features in several of the skeletons. FAU - Fu, Yuqin AU - Fu Y AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China. FAU - Xie, Chengzhi AU - Xie C FAU - Xu, Xuelian AU - Xu X FAU - Li, Chunxiang AU - Li C FAU - Zhang, Quanchao AU - Zhang Q FAU - Zhou, Hui AU - Zhou H FAU - Zhu, Hong AU - Zhu H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Adolescent MH - Adult MH - Archaeology/methods MH - Asian People/*genetics MH - Cemeteries MH - China MH - Climate MH - DNA/*genetics MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - Female MH - Genetics, Population MH - Humans MH - Male MH - Phylogeny MH - Polymerase Chain Reaction MH - Polymorphism, Genetic MH - Seasons MH - Tooth/anatomy & histology MH - Young Adult EDAT- 2008/07/29 09:00 MHDA- 2009/02/14 09:00 CRDT- 2008/07/29 09:00 PHST- 2008/07/29 09:00 [pubmed] PHST- 2009/02/14 09:00 [medline] PHST- 2008/07/29 09:00 [entrez] AID - 10.1002/ajpa.20894 [doi] PST - ppublish SO - Am J Phys Anthropol. 2009 Jan;138(1):23-9. doi: 10.1002/ajpa.20894. PMID- 18790087 OWN - NLM STAT- MEDLINE DCOM- 20090504 LR - 20221207 IS - 1567-1348 (Print) IS - 1567-1348 (Linking) VI - 8 IP - 6 DP - 2008 Dec TI - Is the European spatial distribution of the HIV-1-resistant CCR5-Delta32 allele formed by a breakdown of the pathocenosis due to the historical Roman expansion? PG - 864-74 LID - 10.1016/j.meegid.2008.08.007 [doi] AB - We studied the possible effects of the expansion of ancient Mediterranean civilizations during the five centuries before and after Christ on the European distribution of the mutant allele for the chemokine receptor gene CCR5 which has a 32-bp deletion (CCR5-Delta32). There is a strong evidence for the unitary origin of the CCR5-Delta32 mutation, this it is found principally in Europe and Western Asia, with generally a north-south downhill cline frequency. Homozygous carriers of this mutation show a resistance to HIV-1 infection and a slower progression towards AIDS. However, HIV has clearly emerged too recently to have been the selective force on CCR5. Our analyses showed strong negative correlations in Europe between the allele frequency and two historical parameters, i.e. the first colonization dates by the great ancient Mediterranean civilizations, and the distances from the Northern frontiers of the Roman Empire in its greatest expansion. Moreover, other studies have shown that the deletion frequencies in both German Bronze Age and Swedish Neolithic populations were similar to those found in the corresponding modern populations, and this deletion has been found in ancient DNA of around 7000 years ago, suggesting that in the past, the deletion frequency could have been relatively high in European populations. In addition, in West Nile virus pathogenesis, CCR5 plays an antimicrobial role showing that host genetic factors are highly pathogen-specific. Our results added to all these previous data suggest that the actual European allele frequency distribution might not be due to genes spreading, but to a negative selection resulting in the spread of pathogens principally during Roman expansion. Indeed, as gene flows from colonizers to European native populations were extremely low, the mutational changes might be associated with vulnerability to imported infections. To date, the nature of the parasites remains unknown; however, zoonoses could be incriminated. FAU - Faure, Eric AU - Faure E AD - LATP, CNRS-UMR 6632, Evolution biologique et modélisation, case 5, Université de Provence, Place Victor Hugo, 13331 Marseille Cedex 3, France. Eric.Faure@univ-provence.fr FAU - Royer-Carenzi, Manuela AU - Royer-Carenzi M LA - eng PT - Historical Article PT - Journal Article DEP - 20080827 PL - Netherlands TA - Infect Genet Evol JT - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JID - 101084138 RN - 0 (Receptors, CCR5) SB - IM CIN - Infect Genet Evol. 2009 Jul;9(4):387-9. doi: 10.1016/j.meegid.2009.01.001. PMID: 19472441 MH - Analysis of Variance MH - Demography MH - Evolution, Molecular MH - Gene Flow MH - *Gene Frequency MH - Geography MH - HIV Infections/*genetics/immunology MH - *HIV-1 MH - History, Ancient MH - Humans MH - Immunity, Innate/*genetics MH - Linear Models MH - *Mutation MH - Receptors, CCR5/*genetics MH - Roman World/history MH - Selection, Genetic MH - White People/*genetics/history EDAT- 2008/09/16 09:00 MHDA- 2009/05/05 09:00 CRDT- 2008/09/16 09:00 PHST- 2007/11/09 00:00 [received] PHST- 2008/04/30 00:00 [revised] PHST- 2008/08/20 00:00 [accepted] PHST- 2008/09/16 09:00 [pubmed] PHST- 2009/05/05 09:00 [medline] PHST- 2008/09/16 09:00 [entrez] AID - S1567-1348(08)00152-4 [pii] AID - 10.1016/j.meegid.2008.08.007 [doi] PST - ppublish SO - Infect Genet Evol. 2008 Dec;8(6):864-74. doi: 10.1016/j.meegid.2008.08.007. Epub 2008 Aug 27. PMID- 19015520 OWN - NLM STAT- MEDLINE DCOM- 20090107 LR - 20211020 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 105 IP - 47 DP - 2008 Nov 25 TI - Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age. PG - 18226-31 LID - 10.1073/pnas.0807592105 [doi] AB - In 2005 four outstanding multiple burials were discovered near Eulau, Germany. The 4,600-year-old graves contained groups of adults and children buried facing each other. Skeletal and artifactual evidence and the simultaneous interment of the individuals suggest the supposed families fell victim to a violent event. In a multidisciplinary approach, archaeological, anthropological, geochemical (radiogenic isotopes), and molecular genetic (ancient DNA) methods were applied to these unique burials. Using autosomal, mitochondrial, and Y-chromosomal markers, we identified genetic kinship among the individuals. A direct child-parent relationship was detected in one burial, providing the oldest molecular genetic evidence of a nuclear family. Strontium isotope analyses point to different origins for males and children versus females. By this approach, we gain insight into a Late Stone Age society, which appears to have been exogamous and patrilocal, and in which genetic kinship seems to be a focal point of social organization. FAU - Haak, Wolfgang AU - Haak W AD - Institut für Anthropologie, Johannes Gutenberg-Universität Mainz, Saarstrasse 21, D-55099 Mainz, Germany. wolfgang.haak@adelaide.edu.au FAU - Brandt, Guido AU - Brandt G FAU - de Jong, Hylke N AU - de Jong HN FAU - Meyer, Christian AU - Meyer C FAU - Ganslmeier, Robert AU - Ganslmeier R FAU - Heyd, Volker AU - Heyd V FAU - Hawkesworth, Chris AU - Hawkesworth C FAU - Pike, Alistair W G AU - Pike AW FAU - Meller, Harald AU - Meller H FAU - Alt, Kurt W AU - Alt KW LA - eng SI - GENBANK/FJ424615 SI - GENBANK/FJ424616 SI - GENBANK/FJ424617 SI - GENBANK/FJ424618 SI - GENBANK/FJ424619 SI - GENBANK/FJ424620 SI - GENBANK/FJ424621 SI - GENBANK/FJ424622 SI - GENBANK/FJ424623 SI - GENBANK/FJ424624 SI - GENBANK/FJ424625 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081117 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Strontium Isotopes) RN - 9007-49-2 (DNA) SB - IM MH - Adult MH - *Anthropology MH - *Bone and Bones MH - Child MH - DNA/*genetics MH - *Fossils MH - Funeral Rites MH - Germany MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - *Social Behavior MH - Strontium Isotopes/*analysis PMC - PMC2587582 COIS- The authors declare no conflict of interest. EDAT- 2008/11/19 09:00 MHDA- 2009/01/08 09:00 PMCR- 2009/05/25 CRDT- 2008/11/19 09:00 PHST- 2008/11/19 09:00 [pubmed] PHST- 2009/01/08 09:00 [medline] PHST- 2008/11/19 09:00 [entrez] PHST- 2009/05/25 00:00 [pmc-release] AID - 0807592105 [pii] AID - 5608 [pii] AID - 10.1073/pnas.0807592105 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18226-31. doi: 10.1073/pnas.0807592105. Epub 2008 Nov 17. PMID- 18618657 OWN - NLM STAT- MEDLINE DCOM- 20090122 LR - 20221207 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 137 IP - 3 DP - 2008 Nov TI - An ancient DNA test of a founder effect in Native American ABO blood group frequencies. PG - 342-7 LID - 10.1002/ajpa.20887 [doi] AB - Anthropologists have assumed that reduced genetic diversity in extant Native Americans is due to a founder effect that occurred during the initial peopling of the Americas. However, low diversity could also be the result of subsequent historical events, such as the population decline following European contact. In this study, we show that autosomal DNA from ancient Native American skeletal remains can be used to investigate the low level of ABO blood group diversity in the Americas. Extant Native Americans exhibit a high frequency of blood type O, which may reflect a founder effect, genetic drift associated with the historical population decline, or natural selection in response to the smallpox epidemics that occurred following European contact. To help distinguish between these possibilities, we determined the ABO genotypes of 15 precontact individuals from eastern North America. The precontact ABO frequencies were not significantly different from those observed in extant Native Americans from the same region, but they did differ significantly from the ABO frequencies in extant Siberian populations. Studies of other precontact populations are needed to better test the three hypotheses for low ABO blood group diversity in the Americas, but our findings are most consistent with the hypothesis of a founder effect during the initial settlement of this continent. FAU - Halverson, Melissa S AU - Halverson MS AD - Department of Anthropology, University of Texas, Austin, TX 78712, USA. FAU - Bolnick, Deborah A AU - Bolnick DA LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (ABO Blood-Group System) RN - 9007-49-2 (DNA) SB - IM MH - ABO Blood-Group System/*genetics MH - DNA/*chemistry MH - Disease Outbreaks MH - *Founder Effect MH - Genetic Drift MH - *Genetic Variation MH - Genotype MH - History, Ancient MH - Humans MH - Indians, North American/*genetics/history MH - Selection, Genetic MH - Sequence Analysis, DNA MH - White People/genetics EDAT- 2008/07/12 09:00 MHDA- 2009/01/23 09:00 CRDT- 2008/07/12 09:00 PHST- 2008/07/12 09:00 [pubmed] PHST- 2009/01/23 09:00 [medline] PHST- 2008/07/12 09:00 [entrez] AID - 10.1002/ajpa.20887 [doi] PST - ppublish SO - Am J Phys Anthropol. 2008 Nov;137(3):342-7. doi: 10.1002/ajpa.20887. PMID- 18925940 OWN - NLM STAT- MEDLINE DCOM- 20081201 LR - 20211203 IS - 1743-422X (Electronic) IS - 1743-422X (Linking) VI - 5 DP - 2008 Oct 16 TI - Could FIV zoonosis responsible of the breakdown of the pathocenosis which has reduced the European CCR5-Delta32 allele frequencies? PG - 119 LID - 10.1186/1743-422X-5-119 [doi] AB - BACKGROUND: In Europe, the north-south downhill cline frequency of the chemokine receptor CCR5 allele with a 32-bp deletion (CCR5-Delta32) raises interesting questions for evolutionary biologists. We had suggested first that, in the past, the European colonizers, principally Romans, might have been instrumental of a progressively decrease of the frequencies southwards. Indeed, statistical analyses suggested strong negative correlations between the allele frequency and historical parameters including the colonization dates by Mediterranean civilisations. The gene flows from colonizers to native populations were extremely low but colonizers are responsible of the spread of several diseases suggesting that the dissemination of parasites in naive populations could have induced a breakdown rupture of the fragile pathocenosis changing the balance among diseases. The new equilibrium state has been reached through a negative selection of the null allele. RESULTS: Most of the human diseases are zoonoses and cat might have been instrumental in the decrease of the allele frequency, because its diffusion through Europe was a gradual process, due principally to Romans; and that several cat zoonoses could be transmitted to man. The possible implication of a feline lentivirus (FIV) which does not use CCR5 as co-receptor is discussed. This virus can infect primate cells in vitro and induces clinical signs in macaque. Moreover, most of the historical regions with null or low frequency of CCR5-Delta32 allele coincide with historical range of the wild felid species which harbor species-specific FIVs. CONCLUSION: We proposed the hypothesis that the actual European CCR5 allelic frequencies are the result of a negative selection due to a disease spreading. A cat zoonosis, could be the most plausible hypothesis. Future studies could provide if CCR5 can play an antimicrobial role in FIV pathogenesis. Moreover, studies of ancient DNA could provide more evidences regarding the implications of zoonoses in the actual CCR5-Delta32 distribution. FAU - Faure, Eric AU - Faure E AD - LATP, CNRS-UMR 6632, IFR48 Infectiopole, Evolution biologique et modélisation, Université de Provence, Marseille, France. Eric.Faure@univ-provence.fr LA - eng PT - Journal Article DEP - 20081016 PL - England TA - Virol J JT - Virology journal JID - 101231645 RN - 0 (Receptors, CCR5) SB - IM MH - Animals MH - Cats MH - Ethnicity MH - Europe MH - *Gene Frequency MH - Genetics, Population MH - Humans MH - Immunodeficiency Virus, Feline/*growth & development MH - Lentivirus Infections/*transmission MH - Receptors, CCR5/*genetics MH - Selection, Genetic MH - *Sequence Deletion MH - Zoonoses/*transmission PMC - PMC2575341 EDAT- 2008/10/18 09:00 MHDA- 2008/12/17 09:00 PMCR- 2008/10/16 CRDT- 2008/10/18 09:00 PHST- 2008/08/26 00:00 [received] PHST- 2008/10/16 00:00 [accepted] PHST- 2008/10/18 09:00 [pubmed] PHST- 2008/12/17 09:00 [medline] PHST- 2008/10/18 09:00 [entrez] PHST- 2008/10/16 00:00 [pmc-release] AID - 1743-422X-5-119 [pii] AID - 10.1186/1743-422X-5-119 [doi] PST - epublish SO - Virol J. 2008 Oct 16;5:119. doi: 10.1186/1743-422X-5-119. PMID- 19092297 OWN - NLM STAT- MEDLINE DCOM- 20090227 LR - 20211020 IS - 1720-8386 (Electronic) IS - 0391-4097 (Linking) VI - 31 IP - 10 DP - 2008 Oct TI - The genetic ascertainment of multiple endocrine neoplasia type 1 syndrome by ancient DNA analysis. PG - 905-9 AB - Multiple endocrine neoplasia type 1 (MEN1) is a rare autosomal dominant inherited endocrine cancer syndrome characterised by parathyroid, pancreas, and anterior pituitary tumors. The disease responsible gene, MEN1, was identified in 1997 and localizes to chromosome 11q13 in a minimal 600 kb interval between PYGM and D11S449 loci. About 10-20% of MEN1 patients do not have any mutation in the coding region and/or in the exon-intron junctions of the MEN1 gene. In this case, familial haplotype analysis of the 11q13 region, in at least two generations of affected members, is the only possible genetic ascertainment of the disease. We performed a microsatellite haplotype analysis at 11q13 region in 8 living and 1 deceased member of a MEN1 Italian family without any detected germline mutation of the MEN1 gene. The application of forensic techniques for ancient DNA analysis made it possible to identify the familial disease-associated haplotype and demonstrated that MEN1 disease haplotype family history can be reconstructed even when one or more family members are deceased. Identification of MEN1 disease haplotype is helpful in the clinical management of patients and relatives in families without any mutation of the MEN1 gene. Genetic screening allows the identification of individuals who are at risk before the development of clinical symptoms, limiting invasive annual cancer surveillance only to genetically positive individuals and making it possible to avoid further clinical screenings in non-carriers. FAU - Marini, F AU - Marini F AD - Regional Center for Hereditary Endocrine Tumours, Department of Internal Medicine, University of Florence, Florence, Italy. FAU - Carbonell Sala, S AU - Carbonell Sala S FAU - Falchetti, A AU - Falchetti A FAU - Caramelli, D AU - Caramelli D FAU - Brandi, M L AU - Brandi ML LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Italy TA - J Endocrinol Invest JT - Journal of endocrinological investigation JID - 7806594 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Child MH - DNA, Mitochondrial/analysis MH - Female MH - Femur/chemistry MH - Forensic Anthropology/*methods MH - Haplotypes MH - Humans MH - Male MH - Microsatellite Repeats/genetics MH - Multiple Endocrine Neoplasia Type 1/*genetics MH - Pedigree EDAT- 2008/12/19 09:00 MHDA- 2009/02/28 09:00 CRDT- 2008/12/19 09:00 PHST- 2008/12/19 09:00 [entrez] PHST- 2008/12/19 09:00 [pubmed] PHST- 2009/02/28 09:00 [medline] AID - 5016 [pii] AID - 10.1007/BF03346440 [doi] PST - ppublish SO - J Endocrinol Invest. 2008 Oct;31(10):905-9. doi: 10.1007/BF03346440. PMID- 18833341 OWN - NLM STAT- MEDLINE DCOM- 20081212 LR - 20181113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 3 IP - 10 DP - 2008 Oct 1 TI - Mitochondrial DNA evidence for a diversified origin of workers building First Emperor of China. PG - e3275 LID - 10.1371/journal.pone.0003275 [doi] LID - e3275 AB - Variant studies on ancient DNA have attempted to reveal individual origin. Here, based on cloning sequencing and polymerase chain reaction-restriction fragment length polymorphisms, we analyzed polymorphisms in the first hypervariable region and coding regions of mitochondrial DNA of 19 human bone remains which were excavated from a tomb near the Terra Cotta Warriors and dated some 2,200 years before present. With the aim of shedding light on origins of these samples who were supposed to be workers building the mausoleum for the First Emperor of China, we compared them with 2,164 mtDNA profiles from 32 contemporary Chinese populations at both population and individual levels. Our results showed that mausoleum-building workers may be derived from very diverse sources of origin. FAU - Xu, Zhi AU - Xu Z AD - Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China. FAU - Zhang, Fan AU - Zhang F FAU - Xu, Bosong AU - Xu B FAU - Tan, Jingze AU - Tan J FAU - Li, Shilin AU - Li S FAU - Li, Chunxiang AU - Li C FAU - Zhou, Hui AU - Zhou H FAU - Zhu, Hong AU - Zhu H FAU - Zhang, Jun AU - Zhang J FAU - Duan, Qingbo AU - Duan Q FAU - Jin, Li AU - Jin L LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081001 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - China MH - Cloning, Molecular MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - *Occupations MH - Polymorphism, Restriction Fragment Length MH - Sequence Homology, Nucleic Acid PMC - PMC2557057 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2008/10/04 09:00 MHDA- 2008/12/17 09:00 PMCR- 2008/10/01 CRDT- 2008/10/04 09:00 PHST- 2008/06/23 00:00 [received] PHST- 2008/09/04 00:00 [accepted] PHST- 2008/10/04 09:00 [pubmed] PHST- 2008/12/17 09:00 [medline] PHST- 2008/10/04 09:00 [entrez] PHST- 2008/10/01 00:00 [pmc-release] AID - 08-PONE-RA-05215R1 [pii] AID - 10.1371/journal.pone.0003275 [doi] PST - epublish SO - PLoS One. 2008 Oct 1;3(10):e3275. doi: 10.1371/journal.pone.0003275. PMID- 18684136 OWN - NLM STAT- MEDLINE DCOM- 20090729 LR - 20090420 IS - 0962-1083 (Print) IS - 0962-1083 (Linking) VI - 17 IP - 19 DP - 2008 Oct TI - Ancient DNA applications for wildlife conservation. PG - 4186-96 LID - 10.1111/j.1365-294X.2008.03891.x [doi] AB - Ancient DNA analyses of historical, archaeological and paleontological remains can contribute important information for the conservation of populations and species that cannot be obtained any other way. In addition to ancient DNA analyses involving a single or few individuals, population level studies are now possible. Biases inherent in estimating population parameters and history from modern genetic diversity are exaggerated when populations are small or have been heavily impacted by recent events, as is common for many endangered species. Going directly back in time to study past populations removes many of the assumptions that undermine conclusions based only on recent populations. Accurate characterization of historic population size, levels of gene flow and relationships with other populations are fundamental to developing appropriate conservation and management plans. The incorporation of ancient DNA into conservation genetics holds a lot of potential, if it is employed responsibly. FAU - Leonard, Jennifer A AU - Leonard JA AD - Genetics Program, Smithsonian Institution, 3001 Connecticut Avenue NW, Washington, DC 20008-0551, USA. jennifer.leonard@ebc.uu.se LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Mol Ecol JT - Molecular ecology JID - 9214478 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Animals, Wild/*genetics MH - Birds/genetics MH - Breeding/methods/standards MH - Climate MH - *Conservation of Natural Resources MH - DNA/*genetics MH - Fishes/genetics MH - Gene Flow MH - Genetic Drift MH - *Genetic Variation MH - Greenhouse Effect MH - Humans MH - Mammals/genetics MH - Population Density MH - Social Responsibility EDAT- 2008/08/08 09:00 MHDA- 2009/07/30 09:00 CRDT- 2008/08/08 09:00 PHST- 2008/08/08 09:00 [pubmed] PHST- 2009/07/30 09:00 [medline] PHST- 2008/08/08 09:00 [entrez] AID - MEC3891 [pii] AID - 10.1111/j.1365-294X.2008.03891.x [doi] PST - ppublish SO - Mol Ecol. 2008 Oct;17(19):4186-96. doi: 10.1111/j.1365-294X.2008.03891.x. PMID- 18692462 OWN - NLM STAT- MEDLINE DCOM- 20080902 LR - 20080811 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 134 IP - 3 DP - 2008 Aug 8 TI - Genome sequences from extinct relatives. PG - 388-9 LID - 10.1016/j.cell.2008.07.026 [doi] AB - Next-generation sequencing methods use massively parallel detection of short sequencing reactions, making them ideal for the analysis of ancient DNA. In this issue, Green et al. (2008) exploit this feature to infer the complete mitochondrial genome sequence of one Neanderthal and place bounds on its time of common ancestry with modern humans. FAU - Clark, Andrew G AU - Clark AG AD - Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA. ac347@cornell.edu LA - eng PT - Comment PT - Journal Article PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Mitochondrial) SB - IM CON - Cell. 2008 Aug 8;134(3):416-26. doi: 10.1016/j.cell.2008.06.021. PMID: 18692465 MH - Animals MH - DNA, Mitochondrial/*genetics MH - *Fossils MH - Hominidae/*genetics MH - Humans MH - Sequence Analysis, DNA EDAT- 2008/08/12 09:00 MHDA- 2008/09/03 09:00 CRDT- 2008/08/12 09:00 PHST- 2008/08/12 09:00 [pubmed] PHST- 2008/09/03 09:00 [medline] PHST- 2008/08/12 09:00 [entrez] AID - S0092-8674(08)00946-X [pii] AID - 10.1016/j.cell.2008.07.026 [doi] PST - ppublish SO - Cell. 2008 Aug 8;134(3):388-9. doi: 10.1016/j.cell.2008.07.026. PMID- 18644108 OWN - NLM STAT- MEDLINE DCOM- 20081002 LR - 20231105 IS - 1471-2148 (Electronic) IS - 1471-2148 (Linking) VI - 8 DP - 2008 Jul 21 TI - Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba. PG - 213 LID - 10.1186/1471-2148-8-213 [doi] AB - BACKGROUND: Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. RESULTS: The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. CONCLUSION: While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times. FAU - Mendizabal, Isabel AU - Mendizabal I AD - Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain. isabel.mendizabal@upf.edu FAU - Sandoval, Karla AU - Sandoval K FAU - Berniell-Lee, Gemma AU - Berniell-Lee G FAU - Calafell, Francesc AU - Calafell F FAU - Salas, Antonio AU - Salas A FAU - Martínez-Fuentes, Antonio AU - Martínez-Fuentes A FAU - Comas, David AU - Comas D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080721 PL - England TA - BMC Evol Biol JT - BMC evolutionary biology JID - 100966975 RN - 0 (DNA, Mitochondrial) SB - IM MH - Chromosomes, Human, Y/*genetics MH - Cuba/ethnology MH - DNA, Mitochondrial/*genetics MH - Female MH - *Genetic Variation MH - Genetics, Population MH - Haplotypes MH - Humans MH - Male MH - *Phylogeny MH - Polymorphism, Single Nucleotide/genetics MH - Racial Groups/genetics PMC - PMC2492877 EDAT- 2008/07/23 09:00 MHDA- 2008/10/03 09:00 PMCR- 2008/07/21 CRDT- 2008/07/23 09:00 PHST- 2008/05/16 00:00 [received] PHST- 2008/07/21 00:00 [accepted] PHST- 2008/07/23 09:00 [pubmed] PHST- 2008/10/03 09:00 [medline] PHST- 2008/07/23 09:00 [entrez] PHST- 2008/07/21 00:00 [pmc-release] AID - 1471-2148-8-213 [pii] AID - 10.1186/1471-2148-8-213 [doi] PST - epublish SO - BMC Evol Biol. 2008 Jul 21;8:213. doi: 10.1186/1471-2148-8-213. PMID- 18501471 OWN - NLM STAT- MEDLINE DCOM- 20081218 LR - 20110503 IS - 0169-5347 (Print) IS - 0169-5347 (Linking) VI - 23 IP - 7 DP - 2008 Jul TI - New developments in ancient genomics. PG - 386-93 LID - 10.1016/j.tree.2008.04.002 [doi] AB - Ancient DNA research is on the crest of a 'third wave' of progress due to the introduction of a new generation of DNA sequencing technologies. Here we review the advantages and disadvantages of the four new DNA sequencers that are becoming available to researchers. These machines now allow the recovery of orders of magnitude more DNA sequence data, albeit as short sequence reads. Hence, the potential reassembly of complete ancient genomes seems imminent, and when used to screen libraries of ancient sequences, these methods are cost effective. This new wealth of data is also likely to herald investigations into the functional properties of extinct genes and gene complexes and will improve our understanding of the biological basis of extinct phenotypes. FAU - Millar, Craig D AU - Millar CD AD - Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand. FAU - Huynen, Leon AU - Huynen L FAU - Subramanian, Sankar AU - Subramanian S FAU - Mohandesan, Elmira AU - Mohandesan E FAU - Lambert, David M AU - Lambert DM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20080522 PL - England TA - Trends Ecol Evol JT - Trends in ecology & evolution JID - 8805125 SB - IM MH - Animals MH - *Biological Evolution MH - *Ecology MH - Genomics/economics/*methods MH - Humans MH - Phenotype MH - *Phylogeny MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA/economics/*methods RF - 75 EDAT- 2008/05/27 09:00 MHDA- 2008/12/19 09:00 CRDT- 2008/05/27 09:00 PHST- 2007/09/13 00:00 [received] PHST- 2008/03/27 00:00 [revised] PHST- 2008/04/04 00:00 [accepted] PHST- 2008/05/27 09:00 [pubmed] PHST- 2008/12/19 09:00 [medline] PHST- 2008/05/27 09:00 [entrez] AID - S0169-5347(08)00160-2 [pii] AID - 10.1016/j.tree.2008.04.002 [doi] PST - ppublish SO - Trends Ecol Evol. 2008 Jul;23(7):386-93. doi: 10.1016/j.tree.2008.04.002. Epub 2008 May 22. PMID- 18420593 OWN - NLM STAT- MEDLINE DCOM- 20080922 LR - 20080616 IS - 1537-1719 (Electronic) IS - 0737-4038 (Linking) VI - 25 IP - 7 DP - 2008 Jul TI - Bayesian inference of errors in ancient DNA caused by postmortem degradation. PG - 1503-11 LID - 10.1093/molbev/msn095 [doi] AB - Methods for extracting and amplifying sequences using ancient DNA (aDNA) can be prone to errors caused by postmortem modifications of the DNA strand. A new statistical method is developed for predicting errors in aDNA sequences caused by such processes. In addition to the canonical DNA substitution model parameters, a discrete Markov chain is used to describe nucleotide substitutions occurring via postmortem degradation of the aDNA sequences. A computer program, BYPASSR-degr, was developed implementing the method and was used in subsequent analyses of simulated data sets under the new model. Simulation studies show that the new method can be powerful and accurate in identifying damaged sites. The method is applied to analyze aDNA sequences of Etruscans, Adélie penguins, and horses. No significant signals of degradation were observed at any sites of the aDNA sequences we analyzed. FAU - Mateiu, Ligia M AU - Mateiu LM AD - Department of Forest Sciences/Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. FAU - Rannala, Bruce H AU - Rannala BH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080416 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 9007-49-2 (DNA) SB - IM MH - Algorithms MH - Animals MH - Base Sequence MH - *Bayes Theorem MH - DNA/*analysis/genetics MH - *DNA Damage MH - DNA Fragmentation MH - Fossils MH - Horses/genetics MH - Humans MH - Markov Chains MH - Mathematics MH - *Models, Genetic MH - *Models, Statistical MH - Molecular Sequence Data MH - Sequence Analysis, DNA/methods MH - Spheniscidae/genetics EDAT- 2008/04/19 09:00 MHDA- 2008/09/23 09:00 CRDT- 2008/04/19 09:00 PHST- 2008/04/19 09:00 [pubmed] PHST- 2008/09/23 09:00 [medline] PHST- 2008/04/19 09:00 [entrez] AID - msn095 [pii] AID - 10.1093/molbev/msn095 [doi] PST - ppublish SO - Mol Biol Evol. 2008 Jul;25(7):1503-11. doi: 10.1093/molbev/msn095. Epub 2008 Apr 16. PMID- 19083823 OWN - NLM STAT- MEDLINE DCOM- 20090227 LR - 20081222 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 2 IP - 3 DP - 2008 Jun TI - Case report: identification of skeletal remains using short-amplicon marker analysis of severely degraded DNA extracted from a decomposed and charred femur. PG - 212-8 LID - 10.1016/j.fsigen.2008.02.005 [doi] AB - Applying two extraction protocols to isolate DNA from a charred femur recovered after a major forest fire, a range of established and recently developed forensic marker sets that included mini-STRs and SNPs were used to type the sample and confirm identity by comparison to a claimed daughter of the deceased. Identification of the remains suggested that the individual had been dead for 10 years and the DNA was therefore likely to be severely degraded from the combined effects of decomposition and exposure to very high temperatures. We used new marker sets specifically developed to analyze degraded DNA comprising both reduced-length amplicon STR sets and autosomal SNP multiplexes, giving an opportunity to assess the ability of each approach to successfully type highly degraded material from a challenging case. The results also suggest a modified ancient DNA extraction procedure offers improved typing success from degraded skeletal material. FAU - Fondevila, M AU - Fondevila M AD - Institute of Legal Medicine, Genomic Medicine Group, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain. FAU - Phillips, C AU - Phillips C FAU - Naveran, N AU - Naveran N FAU - Fernandez, L AU - Fernandez L FAU - Cerezo, M AU - Cerezo M FAU - Salas, A AU - Salas A FAU - Carracedo, A AU - Carracedo A FAU - Lareu, M V AU - Lareu MV LA - eng PT - Case Reports PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080410 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) RN - 9007-49-2 (DNA) SB - IM MH - Alleles MH - Benchmarking MH - DNA/*analysis/genetics/isolation & purification MH - DNA Fingerprinting/*methods MH - DNA, Mitochondrial/genetics MH - Femur/*chemistry MH - Forensic Anthropology/*methods MH - Genetic Markers MH - Genotype MH - Humans MH - Likelihood Functions MH - Microsatellite Repeats MH - Nuclear Family MH - Polymerase Chain Reaction MH - Polymorphism, Single Nucleotide MH - Sensitivity and Specificity EDAT- 2008/12/17 09:00 MHDA- 2009/02/28 09:00 CRDT- 2008/12/17 09:00 PHST- 2007/10/30 00:00 [received] PHST- 2008/01/22 00:00 [revised] PHST- 2008/02/18 00:00 [accepted] PHST- 2008/12/17 09:00 [entrez] PHST- 2008/12/17 09:00 [pubmed] PHST- 2009/02/28 09:00 [medline] AID - S1872-4973(08)00037-9 [pii] AID - 10.1016/j.fsigen.2008.02.005 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2008 Jun;2(3):212-8. doi: 10.1016/j.fsigen.2008.02.005. Epub 2008 Apr 10. PMID- 18440082 OWN - NLM STAT- MEDLINE DCOM- 20080814 LR - 20080526 IS - 0167-7799 (Print) IS - 0167-7799 (Linking) VI - 26 IP - 6 DP - 2008 Jun TI - Engineered polymerases amplify the potential of ancient DNA. PG - 285-7 LID - 10.1016/j.tibtech.2008.03.005 [doi] AB - The generation of genomic data from mammoths and Neanderthals has reinvigorated discussion about whether extinct species could be brought back within the foreseeable future. However, post-mortem DNA decay rapidly reduces the number and quality of surviving DNA fragments, consequently increasing rates of sequencing error and forming a significant obstacle to accurate sequence reconstruction. Recent work has shown that it is possible to engineer a polymerase capable of using even highly damaged fragments as template sequences. FAU - Shapiro, Beth AU - Shapiro B AD - Department of Biology, 326 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16801, USA. beth.shapiro@psu.edu LA - eng PT - Journal Article PT - Review DEP - 20080424 PL - England TA - Trends Biotechnol JT - Trends in biotechnology JID - 8310903 RN - 9007-49-2 (DNA) RN - EC 2.7.7.7 (DNA-Directed DNA Polymerase) SB - IM MH - Animals MH - Biotechnology/*methods MH - DNA/*chemistry MH - DNA-Directed DNA Polymerase/*chemistry/*genetics MH - Fossils MH - *Genetic Techniques MH - Humans MH - Protein Engineering/*methods MH - Sequence Analysis, DNA/methods RF - 24 EDAT- 2008/04/29 09:00 MHDA- 2008/08/15 09:00 CRDT- 2008/04/29 09:00 PHST- 2007/12/14 00:00 [received] PHST- 2008/03/03 00:00 [revised] PHST- 2008/03/17 00:00 [accepted] PHST- 2008/04/29 09:00 [pubmed] PHST- 2008/08/15 09:00 [medline] PHST- 2008/04/29 09:00 [entrez] AID - S0167-7799(08)00106-6 [pii] AID - 10.1016/j.tibtech.2008.03.005 [doi] PST - ppublish SO - Trends Biotechnol. 2008 Jun;26(6):285-7. doi: 10.1016/j.tibtech.2008.03.005. Epub 2008 Apr 24. PMID- 18322457 OWN - NLM STAT- MEDLINE DCOM- 20080530 LR - 20111209 IS - 1365-2540 (Electronic) IS - 0018-067X (Linking) VI - 100 IP - 6 DP - 2008 Jun TI - Genetic evidence and the modern human origins debate. PG - 555-63 LID - 10.1038/hdy.2008.14 [doi] AB - A continued debate in anthropology concerns the evolutionary origin of 'anatomically modern humans' (Homo sapiens sapiens). Different models have been proposed to examine the related questions of (1) where and when anatomically modern humans first appeared and (2) the genetic and evolutionary relationship between modern humans and earlier human populations. Genetic data have been increasingly used to address these questions. Genetic data on living human populations have been used to reconstruct the evolutionary history of the human species by considering how global patterns of human variation could be produced given different evolutionary scenarios. Of particular interest are gene trees that reconstruct the time and place of the most recent common ancestor of humanity for a given haplotype and the analysis of regional differences in genetic diversity. Ancient DNA has also allowed a direct assessment of genetic variation in European Neandertals. Together with the fossil record, genetic data provide insight into the origin of modern humans. The evidence points to an African origin of modern humans dating back to 200,000 years followed by later expansions of moderns out of Africa across the Old World. What is less clear is what happened when these early modern humans met preexisting 'archaic human' populations outside of Africa. At present, it is difficult to distinguish between a model of total genetic replacement and a model that includes some degree of genetic mixture. FAU - Relethford, J H AU - Relethford JH AD - Department of Anthropology, State University of New York College at Oneonta, Oneonta, NY 13820, USA. relethjh@oneonta.edu LA - eng PT - Journal Article PT - Review DEP - 20080305 PL - England TA - Heredity (Edinb) JT - Heredity JID - 0373007 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Biological Evolution MH - DNA/genetics MH - Emigration and Immigration MH - Fossils MH - Genetic Variation MH - *Hominidae MH - Humans MH - Models, Genetic MH - Phylogeny RF - 45 EDAT- 2008/03/07 09:00 MHDA- 2008/05/31 09:00 CRDT- 2008/03/07 09:00 PHST- 2008/03/07 09:00 [pubmed] PHST- 2008/05/31 09:00 [medline] PHST- 2008/03/07 09:00 [entrez] AID - hdy200814 [pii] AID - 10.1038/hdy.2008.14 [doi] PST - ppublish SO - Heredity (Edinb). 2008 Jun;100(6):555-63. doi: 10.1038/hdy.2008.14. Epub 2008 Mar 5. PMID- 18511664 OWN - NLM STAT- MEDLINE DCOM- 20080627 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 320 IP - 5880 DP - 2008 May 30 TI - Genetics. Ancient DNA from frozen hair may untangle Eskimo roots. PG - 1146-7 LID - 10.1126/science.320.5880.1146b [doi] FAU - Balter, Michael AU - Balter M LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - Asian People/genetics MH - *DNA, Mitochondrial MH - Emigration and Immigration MH - Freezing MH - Genetic Markers MH - Greenland MH - Hair/*chemistry MH - History, Ancient MH - Humans MH - Inuit/*genetics MH - Male EDAT- 2008/05/31 09:00 MHDA- 2008/06/28 09:00 CRDT- 2008/05/31 09:00 PHST- 2008/05/31 09:00 [pubmed] PHST- 2008/06/28 09:00 [medline] PHST- 2008/05/31 09:00 [entrez] AID - 320/5880/1146b [pii] AID - 10.1126/science.320.5880.1146b [doi] PST - ppublish SO - Science. 2008 May 30;320(5880):1146-7. doi: 10.1126/science.320.5880.1146b. PMID- 18509537 OWN - NLM STAT- MEDLINE DCOM- 20080902 LR - 20211020 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 3 IP - 5 DP - 2008 May 28 TI - Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years. PG - e2214 LID - 10.1371/journal.pone.0002214 [doi] LID - e2214 AB - BACKGROUND: Given the relative abundance of modern human DNA and the inherent impossibility for incontestable proof of authenticity, results obtained on ancient human DNA have often been questioned. The widely accepted rules regarding ancient DNA work mainly affect laboratory procedures, however, pre-laboratory contamination occurring during excavation and archaeological-/anthropological handling of human remains as well as rapid degradation of authentic DNA after excavation are major obstacles. METHODOLOGY/PRINCIPAL FINDINGS: We avoided some of these obstacles by analyzing DNA from ten Viking Age subjects that at the time of sampling were untouched by humans for 1,000 years. We removed teeth from the subjects prior to handling by archaeologists and anthropologists using protective equipment. An additional tooth was removed after standard archaeological and anthropological handling. All pre-PCR work was carried out in a "clean- laboratory" dedicated solely to ancient DNA work. Mitochondrial DNA was extracted and overlapping fragments spanning the HVR-1 region as well as diagnostic sites in the coding region were PCR amplified, cloned and sequenced. Consistent results were obtained with the "unhandled" teeth and there was no indication of contamination, while the latter was the case with half of the "handled" teeth. The results allowed the unequivocal assignment of a specific haplotype to each of the subjects, all haplotypes being compatible in their character states with a phylogenetic tree drawn from present day European populations. Several of the haplotypes are either infrequent or have not been observed in modern Scandinavians. The observation of haplogroup I in the present study (<2% in modern Scandinavians) supports our previous findings of a pronounced frequency of this haplogroup in Viking and Iron Age Danes. CONCLUSION: The present work provides further evidence that retrieval of ancient human DNA is a possible task provided adequate precautions are taken and well-considered sampling is applied. FAU - Melchior, Linea AU - Melchior L AD - Research Laboratory, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark. FAU - Kivisild, Toomas AU - Kivisild T FAU - Lynnerup, Niels AU - Lynnerup N FAU - Dissing, Jørgen AU - Dissing J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080528 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology MH - Base Sequence MH - *Bone and Bones MH - DNA, Mitochondrial/*genetics MH - Denmark MH - *Fossils MH - Haplotypes MH - Humans MH - Molecular Sequence Data MH - Polymerase Chain Reaction MH - Sequence Homology, Amino Acid PMC - PMC2386972 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2008/05/30 09:00 MHDA- 2008/09/03 09:00 PMCR- 2008/05/28 CRDT- 2008/05/30 09:00 PHST- 2008/02/07 00:00 [received] PHST- 2008/04/02 00:00 [accepted] PHST- 2008/05/30 09:00 [pubmed] PHST- 2008/09/03 09:00 [medline] PHST- 2008/05/30 09:00 [entrez] PHST- 2008/05/28 00:00 [pmc-release] AID - 08-PONE-RA-03549R1 [pii] AID - 10.1371/journal.pone.0002214 [doi] PST - epublish SO - PLoS One. 2008 May 28;3(5):e2214. doi: 10.1371/journal.pone.0002214. PMID- 18509458 OWN - NLM STAT- MEDLINE DCOM- 20080902 LR - 20211020 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 3 IP - 5 DP - 2008 May 28 TI - Cryptic contamination and phylogenetic nonsense. PG - e2316 LID - 10.1371/journal.pone.0002316 [doi] LID - e2316 AB - Ancient human DNA has been treated cautiously ever since the problems related to this type of material were exposed in the early 1990s, but as sequential genetic data from ancient specimens have been key components in several evolutionary and ecological studies, interest in ancient human DNA is on the increase again. It is especially tempting to approach archaeological and anthropological questions through this type of material, but DNA from ancient human tissue is notoriously complicated to work with due to the risk of contamination with modern human DNA. Various ways of authenticating results based on ancient human DNA have been developed to circumvent the problems. One commonly used method is to predict what the contamination is expected to look like and then test whether the ancient human DNA fulfils this prediction. If it does, the results are rejected as contamination, while if it does not, they are often considered authentic. We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists. We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material. FAU - Linderholm, Anna AU - Linderholm A AD - Archaeological Research laboratory, Stockholm University, Stockholm, Sweden. anna.linderholm@arklab.su.se FAU - Malmström, Helena AU - Malmström H FAU - Lidén, Kerstin AU - Lidén K FAU - Holmlund, Gunilla AU - Holmlund G FAU - Götherström, Anders AU - Götherström A LA - eng PT - Journal Article DEP - 20080528 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA Primers) RN - 9007-49-2 (DNA) SB - IM MH - Anthropology MH - Archaeology MH - Base Sequence MH - DNA/*genetics MH - DNA Primers MH - Humans MH - *Phylogeny MH - Polymerase Chain Reaction PMC - PMC2384008 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2008/05/30 09:00 MHDA- 2008/09/03 09:00 PMCR- 2008/05/28 CRDT- 2008/05/30 09:00 PHST- 2008/03/31 00:00 [received] PHST- 2008/04/22 00:00 [accepted] PHST- 2008/05/30 09:00 [pubmed] PHST- 2008/09/03 09:00 [medline] PHST- 2008/05/30 09:00 [entrez] PHST- 2008/05/28 00:00 [pmc-release] AID - 08-PONE-RA-04106R1 [pii] AID - 10.1371/journal.pone.0002316 [doi] PST - epublish SO - PLoS One. 2008 May 28;3(5):e2316. doi: 10.1371/journal.pone.0002316. PMID- 18702302 OWN - NLM STAT- MEDLINE DCOM- 20080923 LR - 20221207 IS - 0026-8984 (Print) IS - 0026-8984 (Linking) VI - 42 IP - 3 DP - 2008 May-Jun TI - [Phylogenetic analysis of ancient mitochondrial DNA lineages of human remains found in Yakutia]. PG - 445-53 AB - Molecular genetic analysis of ancient human remains are mostly based on mitochondrial DNA due to its better preservation in human skeletons in comparison with nuclear DNA. We investigated mtDNA extracted from human skeletons found in graves in Yakutia to determine their haplotypes and to compare them with lineages of modern populations. Ancient DNA was extracted from fragments of three skeletons of Yakut graves at At-Dabaan, Ojuluun and Jaraama sites (dating XVIII century) and two skeletons of Neolithic graves at Kerdugen site found in central Yakutia (Churapchinsky, Kangalassky and Megino-Kangalassky districts of Yakutia). Five different haplotypes belonging to specific Asian haplogroups were identified. Lineages of mtDNA of Yakut graves belong to haplo-groups C4a, D5a2 and B5b. Our results indicate the continuity of mitochondrial lineages in the Yakut gene pool during the last 300 years. Haplotypes of two humans from Kerdugen site graves belong to haplogroups A4 and G2a/D. We compared these haplotypes with that of 40,000 Eurasian individuals, 900 of them from Yakutia. No exact matches were found in Paleoasian populations of Chukchi, Eskimos, Koryaks and Itelmen. Phylogenetically close haplotypes (+/- 1 mutation) were found in populations of Yakuts and Evenks, as well as in some populations of China, Southern and Western Siberia. FAU - Fedorova, S A AU - Fedorova SA FAU - Stepanov, A D AU - Stepanov AD FAU - Adoian, M AU - Adoian M FAU - Parik, J AU - Parik J FAU - Argunov, V A AU - Argunov VA FAU - Ozawa, T AU - Ozawa T FAU - Khusnutdinova, E K AU - Khusnutdinova EK FAU - Villems, R AU - Villems R LA - rus PT - Journal Article PL - Russia (Federation) TA - Mol Biol (Mosk) JT - Molekuliarnaia biologiia JID - 0105454 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/ethnology/*genetics MH - DNA, Mitochondrial/*genetics MH - Haplotypes/genetics MH - Humans MH - Paleontology MH - *Phylogeny MH - Siberia EDAT- 2008/08/16 09:00 MHDA- 2008/09/24 09:00 CRDT- 2008/08/16 09:00 PHST- 2008/08/16 09:00 [pubmed] PHST- 2008/09/24 09:00 [medline] PHST- 2008/08/16 09:00 [entrez] PST - ppublish SO - Mol Biol (Mosk). 2008 May-Jun;42(3):445-53. PMID- 18493066 OWN - NLM STAT- MEDLINE DCOM- 20080922 LR - 20211020 IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 179 IP - 1 DP - 2008 May TI - Estimation of 2Nes from temporal allele frequency data. PG - 497-502 LID - 10.1534/genetics.107.085019 [doi] AB - We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-delta 32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is approximately 0.43. FAU - Bollback, Jonathan P AU - Bollback JP AD - Department of Biology and Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark. j.p.bollback@ed.ac.uk FAU - York, Thomas L AU - York TL FAU - Nielsen, Rasmus AU - Nielsen R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Genetics JT - Genetics JID - 0374636 RN - 0 (Receptors, CCR5) SB - IM MH - *Gene Frequency MH - *Genetics, Population MH - Humans MH - Levivirus/genetics MH - *Models, Genetic MH - Mutation/genetics MH - *Population Density MH - Receptors, CCR5/genetics MH - Selection, Genetic PMC - PMC2390626 EDAT- 2008/05/22 09:00 MHDA- 2008/09/23 09:00 PMCR- 2008/08/01 CRDT- 2008/05/22 09:00 PHST- 2008/05/22 09:00 [pubmed] PHST- 2008/09/23 09:00 [medline] PHST- 2008/05/22 09:00 [entrez] PHST- 2008/08/01 00:00 [pmc-release] AID - 179/1/497 [pii] AID - gen1791497 [pii] AID - 10.1534/genetics.107.085019 [doi] PST - ppublish SO - Genetics. 2008 May;179(1):497-502. doi: 10.1534/genetics.107.085019. PMID- 18257014 OWN - NLM STAT- MEDLINE DCOM- 20080417 LR - 20080410 IS - 1096-8644 (Electronic) IS - 0002-9483 (Linking) VI - 136 IP - 1 DP - 2008 May TI - Technical note: improved ancient DNA purification for PCR using ion-exchange columns. PG - 114-21 LID - 10.1002/ajpa.20782 [doi] AB - A novel method of ancient DNA (aDNA) purification was developed using ion-exchange columns to improve PCR-amplifiable DNA extraction from ancient bone samples. Thirteen PCR-resistant ancient bone samples aged 500-3,300 years were tested to extract aDNA using a recently reported, silica-based aDNA extraction method and an ion-exchange column method for the further purification. The PCR success rates of the aDNA extracts were evaluated for the amplification ability of the fragments of mitochondrial DNA, a high-copy DNA, and amelogenin, a low-copy DNA. The results demonstrate that the further purification of silica-based aDNA extracts using ion-exchange columns considerably improved PCR amplification. We suggest that the ion-exchange column-based method will be useful for the improvement of PCR-amplifiable aDNA extraction, particularly from the poorly preserved, PCR-resistant, ancient samples. CI - (c) 2008 Wiley-Liss, Inc. FAU - Kim, Kijeong AU - Kim K AD - Institute for Medical Sciences, Chung-Ang University, Seoul 156-756, South Korea. FAU - Kim, Kyung-Yong AU - Kim KY FAU - Jeon, Eunhee AU - Jeon E FAU - Togloom, Ariunaa AU - Togloom A FAU - Cho, Youn-Ock AU - Cho YO FAU - Lee, Min-Soo AU - Lee MS FAU - Lkhagvasuren, Gavaachimed AU - Lkhagvasuren G FAU - Choi, Jee-Hye AU - Choi JH FAU - Tumen, Dashtseveg AU - Tumen D FAU - Ja Park, Ae AU - Ja Park A FAU - Kim, Keun-Cheol AU - Kim KC FAU - Park, Ki-Won AU - Park KW FAU - Kim, Jae-Hyun AU - Kim JH FAU - Noh, Maengseok AU - Noh M FAU - Yoo, Kwon-Jong AU - Yoo KJ FAU - Lee, Kwang-Ho AU - Lee KH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 9007-49-2 (DNA) SB - IM MH - Bone and Bones MH - Chromatography, Ion Exchange MH - DNA/*isolation & purification MH - Forensic Anthropology/*methods MH - Humans MH - Polymerase Chain Reaction/*methods EDAT- 2008/02/08 09:00 MHDA- 2008/04/18 09:00 CRDT- 2008/02/08 09:00 PHST- 2008/02/08 09:00 [pubmed] PHST- 2008/04/18 09:00 [medline] PHST- 2008/02/08 09:00 [entrez] AID - 10.1002/ajpa.20782 [doi] PST - ppublish SO - Am J Phys Anthropol. 2008 May;136(1):114-21. doi: 10.1002/ajpa.20782. PMID- 18318449 OWN - NLM STAT- MEDLINE DCOM- 20080731 LR - 20080408 IS - 0173-0835 (Print) IS - 0173-0835 (Linking) VI - 29 IP - 7 DP - 2008 Apr TI - Interaction of humic acids with human DNA: proposed mechanisms and kinetics. PG - 1467-72 LID - 10.1002/elps.200700699 [doi] AB - Human DNA quantification by quantitative real-time PCR (QRT-PCR) has gained great importance in forensic DNA and ancient DNA studies. However, in such samples, DNA quantification is impaired by the frequently present humic acid (HA). We have previously shown that the addition of synthetic HA inhibits QRT-PCR. In this study we investigated the possible mechanisms of HA interaction with human DNA, and kinetics of QRT-PCR inhibition. In QRT-PCR with pure human DNA and no HA added, VMAX was 40. With DNA sample containing 4 microg/mL of HA, VMAX was 30.30 while the addition of extra Taq polymerase to the same sample changed VMAX into 38.91, amplifying between 80 and 90% of input DNA. The KM/VMAX ratio in all the samples remained constant, indicating that the mechanism of HA inhibition of QRT-PCR is uncompetitive by nature. Moreover, HA shifts the human DNA melting temperature point (Tm) from 75 to 87 degrees C and inhibits DNase I-mediated DNA cleavage, most probably affecting the enzyme's activity. FAU - Sutlovic, Davorka AU - Sutlovic D AD - Department of Pathology and Forensic Medicine, Split University Hospital and School of Medicine, Split, Croatia. dsutlov@kbsplit.hr FAU - Gamulin, Stjepan AU - Gamulin S FAU - Definis-Gojanovic, Marija AU - Definis-Gojanovic M FAU - Gugic, Dijana AU - Gugic D FAU - Andjelinovic, Simun AU - Andjelinovic S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Electrophoresis JT - Electrophoresis JID - 8204476 RN - 0 (Humic Substances) RN - 9007-49-2 (DNA) SB - IM MH - DNA/*chemistry MH - Electrophoresis, Agar Gel MH - Humans MH - *Humic Substances MH - Reverse Transcriptase Polymerase Chain Reaction MH - Spectrophotometry, Ultraviolet EDAT- 2008/03/06 09:00 MHDA- 2008/08/01 09:00 CRDT- 2008/03/06 09:00 PHST- 2008/03/06 09:00 [pubmed] PHST- 2008/08/01 09:00 [medline] PHST- 2008/03/06 09:00 [entrez] AID - 10.1002/elps.200700699 [doi] PST - ppublish SO - Electrophoresis. 2008 Apr;29(7):1467-72. doi: 10.1002/elps.200700699. PMID- 18162443 OWN - NLM STAT- MEDLINE DCOM- 20080703 LR - 20081121 IS - 1567-1348 (Print) IS - 1567-1348 (Linking) VI - 8 IP - 2 DP - 2008 Mar TI - HIV-1 protecting CCR5-Delta32 allele in medieval Poland. PG - 146-51 AB - CCR5-Delta32 is the mutation in the chemokine receptor CCR5 that gives its homozygous carriers nearly complete protections from HIV-1 infection. Restricted almost exclusively to Europe, the mutation is thought to have originated in the continent and risen in frequency to the present-day value of approximately 10% due to a selective advantage it gave its carriers. The mutation bearing allele was initially calculated to be approximately 1000 years old and pandemic diseases, such as Bubonic Plague or smallpox were postulated to have selected it. However, new reports appear, that question these hypotheses. Data from ancient DNA (aDNA) studies prove the mutation to be much older, as suggested by calculations based on newer genetic maps. In order to investigate if the plagues of the last millennium selected the allele, and add to the discussion on CCR5-Delta32 origin and age, we searched for the mutation in aDNA isolated from individuals whose skeletal remains were collected at archaeological sites in Poland, dated back to 11-14th centuries. The calculated mean frequency of the allele in medieval Poland (5.06% as compared to contemporary 10.26%), implies its longer than previously believed presence in European populations, and suggests that historic pandemics had little effect on its present-day frequency. FAU - Zawicki, Przemysław AU - Zawicki P AD - Department of Molecular Biology, Chair of Oncology, Medical University of Łódź, Łódź, Poland. zawickip@wp.pl FAU - Witas, Henryk W AU - Witas HW LA - eng PT - Comparative Study PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071119 PL - Netherlands TA - Infect Genet Evol JT - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JID - 101084138 RN - 0 (Mutant Proteins) RN - 0 (Receptors, CCR5) SB - IM MH - Acquired Immunodeficiency Syndrome/*genetics/history MH - Alleles MH - Base Sequence MH - Gene Frequency MH - Genetic Predisposition to Disease MH - *HIV-1 MH - Heterozygote MH - *History, Medieval MH - Humans MH - Immunity, Innate/*genetics MH - Molecular Sequence Data MH - Mutant Proteins/physiology MH - Poland MH - Receptors, CCR5/*genetics/*history EDAT- 2007/12/29 09:00 MHDA- 2008/07/04 09:00 CRDT- 2007/12/29 09:00 PHST- 2007/08/23 00:00 [received] PHST- 2007/10/24 00:00 [revised] PHST- 2007/11/13 00:00 [accepted] PHST- 2007/12/29 09:00 [pubmed] PHST- 2008/07/04 09:00 [medline] PHST- 2007/12/29 09:00 [entrez] AID - S1567-1348(07)00173-6 [pii] AID - 10.1016/j.meegid.2007.11.003 [doi] PST - ppublish SO - Infect Genet Evol. 2008 Mar;8(2):146-51. doi: 10.1016/j.meegid.2007.11.003. Epub 2007 Nov 19. PMID- 18327505 OWN - NLM STAT- MEDLINE DCOM- 20081014 LR - 20190606 IS - 0074-0276 (Print) IS - 0074-0276 (Linking) VI - 103 IP - 1 DP - 2008 Feb TI - Molecular paleoparasitological diagnosis of Ascaris sp. from coprolites: new scenery of ascariasis in pre-Colombian South America times. PG - 106-8 AB - Paleoparasitological studies using microscopy showed that Ascarisand Trichuris trichiura are the human intestinal parasites most found in archaeological sites. However, in pre-Columbian South American archaeological sites, Ascaris is rare. In this work we standardized a molecular methodology for Ascaris diagnosis directly from ancient DNA retrieved from coprolites. Using cythochrome b gene (142 bp) target, ancient DNA sequences were retrieved from South American samples, negative by microscopy. Moreover, the methodology applied was sensitive enough to detect ancient DNA extracted from 30 Ascaris eggs from an European coprolite. These results revealed a new scenery for the paleodistribution of Ascaris in South America. FAU - Leles, Daniela AU - Leles D AD - Escola Nacional de Saúde Pública, FiocruzRio de Janeiro, Brasil. FAU - Araújo, Adauto AU - Araújo A FAU - Ferreira, Luiz Fernando AU - Ferreira LF FAU - Vicente, Ana Carolina Paulo AU - Vicente AC FAU - Iñiguez, Alena Mayo AU - Iñiguez AM LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080131 PL - Brazil TA - Mem Inst Oswaldo Cruz JT - Memorias do Instituto Oswaldo Cruz JID - 7502619 RN - 0 (DNA, Helminth) RN - 9035-37-4 (Cytochromes b) SB - IM MH - Animals MH - *Ascariasis/diagnosis/history MH - Ascaris/*genetics/isolation & purification MH - Cytochromes b/chemistry/*genetics MH - DNA, Helminth/chemistry/genetics/*isolation & purification MH - Feces/*parasitology MH - History, Ancient MH - Humans MH - Paleopathology/*methods MH - Polymerase Chain Reaction MH - Sensitivity and Specificity MH - Sequence Analysis, DNA MH - South America EDAT- 2008/03/11 09:00 MHDA- 2008/10/15 09:00 CRDT- 2008/03/11 09:00 PHST- 2007/09/05 00:00 [received] PHST- 2007/12/27 00:00 [accepted] PHST- 2008/03/11 09:00 [pubmed] PHST- 2008/10/15 09:00 [medline] PHST- 2008/03/11 09:00 [entrez] AID - S0074-02762008005000004 [pii] AID - 10.1590/s0074-02762008005000004 [doi] PST - ppublish SO - Mem Inst Oswaldo Cruz. 2008 Feb;103(1):106-8. doi: 10.1590/s0074-02762008005000004. Epub 2008 Jan 31. PMID- 19002248 OWN - NLM STAT- MEDLINE DCOM- 20081212 LR - 20220316 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 3 IP - 11 DP - 2008 TI - Phylotyping and functional analysis of two ancient human microbiomes. PG - e3703 LID - 10.1371/journal.pone.0003703 [doi] LID - e3703 AB - BACKGROUND: The Human Microbiome Project (HMP) is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas. METHODOLOGY/PRINCIPAL FINDINGS: We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases. CONCLUSIONS/SIGNIFICANCE: We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today. FAU - Tito, Raúl Y AU - Tito RY AD - Department of Anthropology, University of Oklahoma, Norman, OK, USA. FAU - Macmil, Simone AU - Macmil S FAU - Wiley, Graham AU - Wiley G FAU - Najar, Fares AU - Najar F FAU - Cleeland, Lauren AU - Cleeland L FAU - Qu, Chunmei AU - Qu C FAU - Wang, Ping AU - Wang P FAU - Romagne, Frederic AU - Romagne F FAU - Leonard, Sylvain AU - Leonard S FAU - Ruiz, Agustín Jiménez AU - Ruiz AJ FAU - Reinhard, Karl AU - Reinhard K FAU - Roe, Bruce A AU - Roe BA FAU - Lewis, Cecil M Jr AU - Lewis CM Jr LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081111 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Bacterial) SB - IM MH - Bacteria/classification/isolation & purification MH - DNA, Bacterial/analysis MH - Evolution, Molecular MH - Gastrointestinal Tract/*microbiology MH - Genome, Bacterial MH - Geography MH - Humans MH - Metagenome/*genetics MH - Mexico MH - *Phylogeny PMC - PMC2577302 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2008/11/13 09:00 MHDA- 2008/12/17 09:00 PMCR- 2008/11/11 CRDT- 2008/11/13 09:00 PHST- 2008/10/22 00:00 [received] PHST- 2008/10/23 00:00 [accepted] PHST- 2008/11/13 09:00 [pubmed] PHST- 2008/12/17 09:00 [medline] PHST- 2008/11/13 09:00 [entrez] PHST- 2008/11/11 00:00 [pmc-release] AID - 08-PONE-RA-06969 [pii] AID - 10.1371/journal.pone.0003703 [doi] PST - ppublish SO - PLoS One. 2008;3(11):e3703. doi: 10.1371/journal.pone.0003703. Epub 2008 Nov 11. PMID- 18776392 OWN - NLM STAT- MEDLINE DCOM- 20101116 LR - 20221207 IS - 1746-8272 (Electronic) IS - 0261-3166 (Linking) IP - 52 DP - 2008 TI - Translesion synthesis across the (6-4) photoproduct and its Dewar valence isomer by the Y-family and engineered DNA polymerases. PG - 339-40 LID - 10.1093/nass/nrn171 [doi] AB - We analyzed the translesion synthesis across the UV-induced lesions, the (6-4) photoproduct and its Dewar valence isomer, by using human DNA polymerases eta and iota in vitro. The primer extension experiments revealed that pol eta tended to incorporate dG opposite the 3' component of both lesions, but the incorporation efficiency for the Dewar isomer was higher than that for the (6-4) photoproduct. On the other hand, pol iota was likely to incorporate dA opposite the 3' components of the (6-4) photoproduct and its Dewar isomer with a similar efficiency. Elongation after the incorporation opposite the UV lesions was not observed for these Y-family polymerases. We further analyzed the bypass ability of an engineered polymerase developed from Thermus DNA polymerase for the amplification of ancient DNA. This polymerase could bypass the Dewar isomer more efficiently than the (6-4) photoproduct. FAU - Yamamoto, Junpei AU - Yamamoto J AD - Division of Chemisty, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 563-8531, Japan. FAU - Loakes, David AU - Loakes D FAU - Masutani, Chikahide AU - Masutani C FAU - Simmyo, Shizu AU - Simmyo S FAU - Urabe, Kumiko AU - Urabe K FAU - Hanaoka, Fumio AU - Hanaoka F FAU - Holliger, Philipp AU - Holliger P FAU - Iwai, Shigenori AU - Iwai S LA - eng GR - MC_U105178804/MRC_/Medical Research Council/United Kingdom PT - Journal Article PL - England TA - Nucleic Acids Symp Ser (Oxf) JT - Nucleic acids symposium series (2004) JID - 101259965 RN - 0 (Pyrimidine Dimers) RN - 0 (pyrimidine-pyrimidone dimer) RN - 9007-49-2 (DNA) RN - EC 2.7.7.7 (DNA-Directed DNA Polymerase) RN - EC 2.7.7.7 (Rad30 protein) RN - EC 2.7.7.7 (DNA Polymerase iota) SB - IM MH - DNA/biosynthesis/chemistry MH - DNA-Directed DNA Polymerase/genetics/*metabolism MH - Humans MH - Isomerism MH - Mutation MH - Protein Engineering MH - Pyrimidine Dimers/*chemistry MH - Thermus/enzymology MH - DNA Polymerase iota EDAT- 2008/09/09 09:00 MHDA- 2010/11/17 06:00 CRDT- 2008/09/09 09:00 PHST- 2008/09/09 09:00 [pubmed] PHST- 2010/11/17 06:00 [medline] PHST- 2008/09/09 09:00 [entrez] AID - nrn171 [pii] AID - 10.1093/nass/nrn171 [doi] PST - ppublish SO - Nucleic Acids Symp Ser (Oxf). 2008;(52):339-40. doi: 10.1093/nass/nrn171. PMID- 18576944 OWN - NLM STAT- MEDLINE DCOM- 20081204 LR - 20220409 IS - 1527-8204 (Print) IS - 1527-8204 (Linking) VI - 9 DP - 2008 TI - Next-generation DNA sequencing methods. PG - 387-402 LID - 10.1146/annurev.genom.9.081307.164359 [doi] AB - Recent scientific discoveries that resulted from the application of next-generation DNA sequencing technologies highlight the striking impact of these massively parallel platforms on genetics. These new methods have expanded previously focused readouts from a variety of DNA preparation protocols to a genome-wide scale and have fine-tuned their resolution to single base precision. The sequencing of RNA also has transitioned and now includes full-length cDNA analyses, serial analysis of gene expression (SAGE)-based methods, and noncoding RNA discovery. Next-generation sequencing has also enabled novel applications such as the sequencing of ancient DNA samples, and has substantially widened the scope of metagenomic analysis of environmentally derived samples. Taken together, an astounding potential exists for these technologies to bring enormous change in genetic and biological research and to enhance our fundamental biological knowledge. FAU - Mardis, Elaine R AU - Mardis ER AD - Department of Genetics and Molecular Microbiology and Genome Sequencing Center, Washington University School of Medicine, St. Louis MO 63108, USA. emardis@wustl.edu LA - eng PT - Journal Article PT - Review PL - United States TA - Annu Rev Genomics Hum Genet JT - Annual review of genomics and human genetics JID - 100911346 RN - 0 (RNA, Untranslated) SB - IM MH - Chromatin Immunoprecipitation/methods MH - Fossils MH - Gene Expression Profiling/methods MH - Genome, Human MH - Genomics/methods MH - Humans MH - RNA, Untranslated/genetics MH - Sequence Analysis, DNA/instrumentation/*methods/trends RF - 55 EDAT- 2008/06/26 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/06/26 09:00 PHST- 2008/06/26 09:00 [pubmed] PHST- 2008/12/17 09:00 [medline] PHST- 2008/06/26 09:00 [entrez] AID - 10.1146/annurev.genom.9.081307.164359 [doi] PST - ppublish SO - Annu Rev Genomics Hum Genet. 2008;9:387-402. doi: 10.1146/annurev.genom.9.081307.164359. PMID- 18084031 OWN - NLM STAT- MEDLINE DCOM- 20080215 LR - 20211020 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 36 IP - 1 DP - 2008 Jan TI - From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. PG - e5 AB - Current efforts to recover the Neandertal and mammoth genomes by 454 DNA sequencing demonstrate the sensitivity of this technology. However, routine 454 sequencing applications still require microgram quantities of initial material. This is due to a lack of effective methods for quantifying 454 sequencing libraries, necessitating expensive and labour-intensive procedures when sequencing ancient DNA and other poor DNA samples. Here we report a 454 sequencing library quantification method based on quantitative PCR that effectively eliminates these limitations. We estimated both the molecule numbers and the fragment size distributions in sequencing libraries derived from Neandertal DNA extracts, SAGE ditags and bonobo genomic DNA, obtaining optimal sequencing yields without performing any titration runs. Using this method, 454 sequencing can routinely be performed from as little as 50 pg of initial material without titration runs, thereby drastically reducing costs while increasing the scope of sample throughput and protocol development on the 454 platform. The method should also apply to Illumina/Solexa and ABI/SOLiD sequencing, and should therefore help to widen the accessibility of all three platforms. FAU - Meyer, Matthias AU - Meyer M AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. mmeyer@eva.mpg.de FAU - Briggs, Adrian W AU - Briggs AW FAU - Maricic, Tomislav AU - Maricic T FAU - Höber, Barbara AU - Höber B FAU - Höffner, Barbara AU - Höffner B FAU - Krause, Johannes AU - Krause J FAU - Weihmann, Antje AU - Weihmann A FAU - Pääbo, Svante AU - Pääbo S FAU - Hofreiter, Michael AU - Hofreiter M LA - eng PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071215 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 SB - IM MH - Animals MH - Fossils MH - Gene Library MH - Hominidae/genetics MH - Humans MH - Pan paniscus/genetics MH - Polymerase Chain Reaction/*methods MH - Sequence Analysis, DNA/*methods PMC - PMC2248761 EDAT- 2007/12/18 09:00 MHDA- 2008/02/19 09:00 PMCR- 2007/12/15 CRDT- 2007/12/18 09:00 PHST- 2007/12/18 09:00 [pubmed] PHST- 2008/02/19 09:00 [medline] PHST- 2007/12/18 09:00 [entrez] PHST- 2007/12/15 00:00 [pmc-release] AID - gkm1095 [pii] AID - 10.1093/nar/gkm1095 [doi] PST - ppublish SO - Nucleic Acids Res. 2008 Jan;36(1):e5. doi: 10.1093/nar/gkm1095. Epub 2007 Dec 15. PMID- 17955361 OWN - NLM STAT- MEDLINE DCOM- 20080212 LR - 20071207 IS - 0006-2928 (Print) IS - 0006-2928 (Linking) VI - 45 IP - 11-12 DP - 2007 Dec TI - Encoding PCR products with batch-stamps and barcodes. PG - 761-7 AB - Polymerase chain reaction (PCR) has become the mainstay of DNA sequence analysis. Yet there is always uncertainty concerning the source of the template DNA that gave rise to a particular PCR product. The risks of contamination, biased amplification, and product redundancy are especially high when limited amounts of template DNA are used. We have developed and applied molecular encoding principles to solve this source-uncertainty problem for DNA sequences generated by standard PCR. Batch-stamps specify the date and sample identity, and barcodes detect template redundancy. Our approach thus enables classification of each PCR-derived sequence as valid, contaminant, or redundant, and provides a measure of sequence diversity. We recommend that batch-stamps and barcodes be used when amplifying irreplaceable DNAs and cDNAs available for forensic, clinical, single cell, and ancient DNA analyses. FAU - McCloskey, Megan L AU - McCloskey ML AD - Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-0002, USA. FAU - Stöger, Reinhard AU - Stöger R FAU - Hansen, R Scott AU - Hansen RS FAU - Laird, Charles D AU - Laird CD LA - eng GR - GM 53805/GM/NIGMS NIH HHS/United States GR - HD 02274/HD/NICHD NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20071023 PL - United States TA - Biochem Genet JT - Biochemical genetics JID - 0126611 RN - 0 (FMR1 protein, human) RN - 0 (Oligonucleotides) RN - 139135-51-6 (Fragile X Mental Retardation Protein) SB - IM MH - Fragile X Mental Retardation Protein/*genetics MH - Humans MH - Oligonucleotides/chemistry/*genetics MH - *Polymerase Chain Reaction/methods MH - Quantitative Trait Loci/*genetics MH - Sensitivity and Specificity EDAT- 2007/10/24 09:00 MHDA- 2008/02/13 09:00 CRDT- 2007/10/24 09:00 PHST- 2007/01/31 00:00 [received] PHST- 2007/05/29 00:00 [accepted] PHST- 2007/10/24 09:00 [pubmed] PHST- 2008/02/13 09:00 [medline] PHST- 2007/10/24 09:00 [entrez] AID - 10.1007/s10528-007-9114-x [doi] PST - ppublish SO - Biochem Genet. 2007 Dec;45(11-12):761-7. doi: 10.1007/s10528-007-9114-x. Epub 2007 Oct 23. PMID- 17320326 OWN - NLM STAT- MEDLINE DCOM- 20071018 LR - 20101118 IS - 1872-6283 (Electronic) IS - 0379-0738 (Linking) VI - 173 IP - 1 DP - 2007 Nov 15 TI - Genetic analysis of the skeletal remains attributed to Francesco Petrarca. PG - 36-40 AB - We report on the mitochondrial DNA (mtDNA) analysis of the supposed remains of Francesco Petrarca exhumed in November 2003, from the S. Maria Assunta church, in Arquà Padua (Italy) where he died in 1374. The optimal preservation of the remains allowed the retrieval of sufficient mtDNA for genetic analysis. DNA was extracted from a rib and a tooth and mtDNA sequences were determined in multiple clones using the strictest criteria currently available for validation of ancient DNA sequences, including independent replication. MtDNA sequences from the tooth and rib were not identical, suggesting that they belonged to different individuals. Indeed, molecular gender determination showed that the postcranial remains belonged to a male while the skull belonged to a female. Historical records indicated that the remains were violated in 1630, possibly by thieves. These results are consistent with morphological investigations and confirm the importance of integrating molecular and morphological approaches in investigating historical remains. FAU - Caramelli, David AU - Caramelli D AD - Dipartimento di Biologia Animale e Genetica, Laboratorio di Antropologia, Università di Firenze, via del Proconsolo 12, 50122 Firenze, Italy. david.caramelli@unifi.it FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C FAU - Capelli, Cristian AU - Capelli C FAU - Lari, Martina AU - Lari M FAU - Sampietro, María Lourdes AU - Sampietro ML FAU - Gigli, Elena AU - Gigli E FAU - Milani, Lucio AU - Milani L FAU - Pilli, Elena AU - Pilli E FAU - Guimaraes, Silvia AU - Guimaraes S FAU - Chiarelli, Brunetto AU - Chiarelli B FAU - Marin, Vito Terribile Wien AU - Marin VT FAU - Casoli, Antonella AU - Casoli A FAU - Stanyon, Roscoe AU - Stanyon R FAU - Bertranpetit, Jaume AU - Bertranpetit J FAU - Barbujani, Guido AU - Barbujani G LA - eng PT - Historical Article PT - Journal Article DEP - 20070222 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (DNA, Mitochondrial) SB - IM MH - *DNA Fingerprinting MH - DNA, Mitochondrial/*analysis MH - Exhumation MH - *Famous Persons MH - History, Ancient MH - Humans MH - Italy MH - Male MH - Molar MH - Polymerase Chain Reaction MH - Ribs MH - Sequence Analysis, DNA MH - Sex Determination Analysis EDAT- 2007/02/27 09:00 MHDA- 2007/10/19 09:00 CRDT- 2007/02/27 09:00 PHST- 2006/11/10 00:00 [received] PHST- 2007/01/20 00:00 [accepted] PHST- 2007/02/27 09:00 [pubmed] PHST- 2007/10/19 09:00 [medline] PHST- 2007/02/27 09:00 [entrez] AID - S0379-0738(07)00054-0 [pii] AID - 10.1016/j.forsciint.2007.01.020 [doi] PST - ppublish SO - Forensic Sci Int. 2007 Nov 15;173(1):36-40. doi: 10.1016/j.forsciint.2007.01.020. Epub 2007 Feb 22. PMID- 18225581 OWN - NLM STAT- MEDLINE DCOM- 20080212 LR - 20080129 IS - 0250-7005 (Print) IS - 0250-7005 (Linking) VI - 27 IP - 6B DP - 2007 Nov-Dec TI - Detection and analysis of cancer genes amplified from bone material of a Scythian royal burial in Arzhan near Tuva, Siberia. PG - 4117-9 AB - Molecular paleopathology has become an emerging field that helps to characterize molecular markers of past disease. Especially highly sensitive genetic techniques such as PCR are an important means of unraveling changes in ancient DNA extracted from bone tissue, teeth and mummified soft tissue. In the present study, excavated bone material from the skeleton of a Scythian sovereign, morphologically and immunohistochemically suspicious of a metastatic prostate carcinoma, was analyzed by PCR for amplifiable human gene sequences. Short sequences of the human GADD153 DNA repair gene and p53 tumor suppressor gene were detectable which revealed the absence of mutations according to the data of automatic sequencing. Using bisulfite-treated DNA from the bone, methylation-specific PCR detected hypermethylated promoter sequences of the p14ARF tumor suppressor gene. In summary, these data show that it is possible: a) to amply short human DNA stretches from 2,500-year-old bone material, b) to detect tumorigenetically important genes within this DNA, c) to detect epigenetically modified DNA in ancient bone material. The finding of hypermethylated p14ARF sequences merits attention because this may indicate an intraosseal neoplastic process and may corroborate the hypothesis of prostate cancer. FAU - Schlott, Thilo AU - Schlott T AD - Department of Pathology, Georg August Universitaet, Goettingen, Germany. thiloschlott@web.de FAU - Eiffert, Helmut AU - Eiffert H FAU - Schmidt-Schultz, Tyede AU - Schmidt-Schultz T FAU - Gebhardt, Melanie AU - Gebhardt M FAU - Parzinger, Hermann AU - Parzinger H FAU - Schultz, Michael AU - Schultz M LA - eng PT - Journal Article PL - Greece TA - Anticancer Res JT - Anticancer research JID - 8102988 RN - 0 (DDIT3 protein, human) RN - 0 (DNA, Neoplasm) RN - 0 (Tumor Suppressor Protein p14ARF) RN - 147336-12-7 (Transcription Factor CHOP) SB - IM MH - Anthropology, Physical/methods MH - Bone and Bones/*chemistry MH - DNA Repair MH - DNA, Neoplasm/analysis/*genetics MH - Gene Amplification MH - *Genes, p53 MH - Humans MH - Male MH - Prostatic Neoplasms/*genetics MH - Sequence Analysis, DNA/methods MH - Siberia MH - Transcription Factor CHOP/*genetics MH - Tumor Suppressor Protein p14ARF/*genetics EDAT- 2008/01/30 09:00 MHDA- 2008/02/13 09:00 CRDT- 2008/01/30 09:00 PHST- 2008/01/30 09:00 [pubmed] PHST- 2008/02/13 09:00 [medline] PHST- 2008/01/30 09:00 [entrez] PST - ppublish SO - Anticancer Res. 2007 Nov-Dec;27(6B):4117-9. PMID- 17657509 OWN - NLM STAT- MEDLINE DCOM- 20080402 LR - 20221207 IS - 0340-6717 (Print) IS - 0340-6717 (Linking) VI - 122 IP - 3-4 DP - 2007 Nov TI - Y chromosomes of prehistoric people along the Yangtze River. PG - 383-8 AB - The ability to extract mitochondrial and nuclear DNA from ancient remains has enabled the study of ancient DNA, a legitimate field for over 20 years now. Recently, Y chromosome genotyping has begun to be applied to ancient DNA. The Y chromosome haplogroup in East Asia has since caught the attention of molecular anthropologists, as it is one of the most ethnic-related genetic markers of the region. In this paper, the Y chromosome haplogroup of DNA from ancient East Asians was examined, in order to genetically link them to modern populations. Fifty-six human remains were sampled from five archaeological sites, primarily along the Yangtze River. Strict criteria were followed to eliminate potential contamination. Five SNPs from the Y chromosome were successfully amplified from most of the samples, with at least 62.5% of the samples belonging to the O haplogroup, similar to the frequency for modern East Asian populations. A high frequency of O1 was found in Liangzhu Culture sites around the mouth of the Yangtze River, linking this culture to modern Austronesian and Daic populations. A rare haplogroup, O3d, was found at the Daxi site in the middle reaches of the Yangtze River, indicating that the Daxi people might be the ancestors of modern Hmong-Mien populations, which show only small traces of O3d today. Noticeable genetic segregation was observed among the prehistoric cultures, demonstrating the genetic foundation of the multiple origins of the Chinese Civilization. FAU - Li, Hui AU - Li H AD - MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China. H.Li@yale.edu FAU - Huang, Ying AU - Huang Y FAU - Mustavich, Laura F AU - Mustavich LF FAU - Zhang, Fan AU - Zhang F FAU - Tan, Jing-Ze AU - Tan JZ FAU - Wang, Ling-E AU - Wang LE FAU - Qian, Ji AU - Qian J FAU - Gao, Meng-He AU - Gao MH FAU - Jin, Li AU - Jin L LA - eng PT - Historical Article PT - Journal Article DEP - 20070727 PL - Germany TA - Hum Genet JT - Human genetics JID - 7613873 RN - 0 (Genetic Markers) RN - 9007-49-2 (DNA) SB - IM MH - Asian People/*genetics MH - China MH - Chromosomes, Human, Y/*genetics MH - DNA/genetics/history/isolation & purification MH - Evolution, Molecular MH - Fossils MH - Fresh Water MH - Genetic Markers MH - Genetic Variation MH - Haplotypes MH - History, Ancient MH - Humans MH - Male MH - Polymorphism, Single Nucleotide EDAT- 2007/07/28 09:00 MHDA- 2008/04/03 09:00 CRDT- 2007/07/28 09:00 PHST- 2007/06/15 00:00 [received] PHST- 2007/07/16 00:00 [accepted] PHST- 2007/07/28 09:00 [pubmed] PHST- 2008/04/03 09:00 [medline] PHST- 2007/07/28 09:00 [entrez] AID - 10.1007/s00439-007-0407-2 [doi] PST - ppublish SO - Hum Genet. 2007 Nov;122(3-4):383-8. doi: 10.1007/s00439-007-0407-2. Epub 2007 Jul 27. PMID- 17534642 OWN - NLM STAT- MEDLINE DCOM- 20080319 LR - 20221207 IS - 0937-9827 (Print) IS - 0937-9827 (Linking) VI - 121 IP - 6 DP - 2007 Nov TI - First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA. PG - 493-9 AB - In the present study, a set of 13 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) selected for the identification of the most frequent Asian Y-haplogroups was included in an allele-specific primer extension assay. Single nucleotide polymorphism (SNP) genotyping was accomplished by co-amplification of these 13 DNA fragments within 2 multiplex PCRs followed by detection with 1 minisequencing reaction using the SNaPshottrade mark Multiplex kit and analysis of extension products by capillary electrophoresis. First developed on modern samples, the assay was optimized for the analysis of 11 ancient DNA (aDNA) samples from the Krasnoyarsk region (southern Siberia) that were dated from 5,500-1,800 years before present (YBP). SNP typing was successful for most of them, which were all assigned to Y-haplogroup R1a1 except one. These results show that SNPs are well-suited for the analysis of aged and degraded DNA samples. Moreover, we found that the SNaPshot minisequencing methodology is a convenient, robust, and efficient method for SNP typing. To our knowledge, this study reports the first successful investigation of Y-SNPs on aDNA samples. The potential use of Y-SNPs in both evolutionary and forensic fields is also discussed. FAU - Bouakaze, C AU - Bouakaze C AD - Institute of Legal Medicine, EA3428, Strasbourg, France. caroline.bouakaze@ulp.u-strasbg.fr FAU - Keyser, C AU - Keyser C FAU - Amory, S AU - Amory S FAU - Crubézy, E AU - Crubézy E FAU - Ludes, B AU - Ludes B LA - eng PT - Journal Article DEP - 20070530 PL - Germany TA - Int J Legal Med JT - International journal of legal medicine JID - 9101456 SB - IM MH - Alleles MH - Asian People/*genetics MH - Bone and Bones/metabolism MH - Chromosomes, Human, Y/*genetics MH - Evolution, Molecular MH - Female MH - *Haplotypes MH - Humans MH - Male MH - Paleontology/*methods MH - Polymerase Chain Reaction/methods MH - Polymorphism, Single Nucleotide/*genetics MH - *Postmortem Changes MH - Sequence Analysis, DNA MH - Siberia EDAT- 2007/05/31 09:00 MHDA- 2008/03/20 09:00 CRDT- 2007/05/31 09:00 PHST- 2006/10/31 00:00 [received] PHST- 2007/05/07 00:00 [accepted] PHST- 2007/05/31 09:00 [pubmed] PHST- 2008/03/20 09:00 [medline] PHST- 2007/05/31 09:00 [entrez] AID - 10.1007/s00414-007-0177-3 [doi] PST - ppublish SO - Int J Legal Med. 2007 Nov;121(6):493-9. doi: 10.1007/s00414-007-0177-3. Epub 2007 May 30. PMID- 17962526 OWN - NLM STAT- MEDLINE DCOM- 20071109 LR - 20071026 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 318 IP - 5850 DP - 2007 Oct 26 TI - Genetics. Ancient DNA reveals Neandertals with red hair, fair complexions. PG - 546-7 FAU - Culotta, Elizabeth AU - Culotta E LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (FOXP2 protein, human) RN - 0 (Forkhead Transcription Factors) RN - 0 (Receptor, Melanocortin, Type 1) SB - IM MH - Animals MH - Forkhead Transcription Factors/genetics MH - Hair Color/*genetics MH - Hominidae/*genetics MH - Humans MH - Point Mutation MH - Polymerase Chain Reaction MH - Receptor, Melanocortin, Type 1/*genetics/metabolism MH - Skin Pigmentation/*genetics EDAT- 2007/10/27 09:00 MHDA- 2007/11/10 09:00 CRDT- 2007/10/27 09:00 PHST- 2007/10/27 09:00 [pubmed] PHST- 2007/11/10 09:00 [medline] PHST- 2007/10/27 09:00 [entrez] AID - 318/5850/546 [pii] AID - 10.1126/science.318.5850.546 [doi] PST - ppublish SO - Science. 2007 Oct 26;318(5850):546-7. doi: 10.1126/science.318.5850.546. PMID- 17715061 OWN - NLM STAT- MEDLINE DCOM- 20071101 LR - 20231105 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 104 IP - 37 DP - 2007 Sep 11 TI - Patterns of damage in genomic DNA sequences from a Neandertal. PG - 14616-21 AB - High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms. FAU - Briggs, Adrian W AU - Briggs AW AD - Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. briggs@eva.mpg.de FAU - Stenzel, Udo AU - Stenzel U FAU - Johnson, Philip L F AU - Johnson PL FAU - Green, Richard E AU - Green RE FAU - Kelso, Janet AU - Kelso J FAU - Prüfer, Kay AU - Prüfer K FAU - Meyer, Matthias AU - Meyer M FAU - Krause, Johannes AU - Krause J FAU - Ronan, Michael T AU - Ronan MT FAU - Lachmann, Michael AU - Lachmann M FAU - Pääbo, Svante AU - Pääbo S LA - eng SI - GENBANK/CAAN02000001 SI - GENBANK/CAAN02000002 SI - GENBANK/CAAN02000003 SI - GENBANK/CAAN02000004 SI - GENBANK/CAAN02000005 SI - GENBANK/CAAN02000006 SI - GENBANK/CAAN02000007 SI - GENBANK/CAAN02000008 SI - GENBANK/CAAN02000009 SI - GENBANK/CAAN02000010 SI - GENBANK/CAAN02000011 SI - GENBANK/CAAN02000012 SI - GENBANK/CAAN02000013 SI - GENBANK/CAAN02000014 SI - GENBANK/CAAN02000015 SI - GENBANK/CAAN02000016 SI - GENBANK/CAAN02000017 SI - GENBANK/CAAN02000018 SI - GENBANK/CAAN02000019 SI - 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GENBANK/CAAN02000995 SI - GENBANK/CAAN02000996 SI - GENBANK/CAAN02000997 SI - GENBANK/CAAN02000998 SI - GENBANK/CAAN02000999 SI - GENBANK/CAAN02001000 GR - R01 GM040282/GM/NIGMS NIH HHS/United States GR - R01-GM40282/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070821 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 8J337D1HZY (Cytosine) RN - 9007-49-2 (DNA) RN - EC 2.7.7.7 (DNA-Directed DNA Polymerase) SB - IM MH - Bacteriophage T4/enzymology MH - Base Sequence MH - Computer Simulation MH - Cytosine/metabolism MH - DNA/genetics/history MH - *DNA Damage MH - DNA-Directed DNA Polymerase/metabolism MH - Deamination MH - *Genome MH - Genomic Library MH - History, Ancient MH - Humans MH - Likelihood Functions MH - Models, Biological MH - Molecular Sequence Data MH - Paleontology/*methods MH - Polymerase Chain Reaction MH - Reference Standards MH - *Sequence Analysis, DNA MH - Templates, Genetic PMC - PMC1976210 COIS- The authors declare no conflict of interest. EDAT- 2007/08/24 09:00 MHDA- 2007/11/02 09:00 PMCR- 2008/03/11 CRDT- 2007/08/24 09:00 PHST- 2007/08/24 09:00 [pubmed] PHST- 2007/11/02 09:00 [medline] PHST- 2007/08/24 09:00 [entrez] PHST- 2008/03/11 00:00 [pmc-release] AID - 0704665104 [pii] AID - 6911 [pii] AID - 10.1073/pnas.0704665104 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14616-21. doi: 10.1073/pnas.0704665104. Epub 2007 Aug 21. PMID- 17506489 OWN - NLM STAT- MEDLINE DCOM- 20070905 LR - 20221207 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 133 IP - 4 DP - 2007 Aug TI - Tracing the genetic history of the Chinese people: mitochondrial DNA analysis of aneolithic population from the Lajia site. PG - 1128-36 AB - Ancient DNA analysis was conducted on the dental remains of specimens from the Lajia site, dating back 3,800-4,000 years. The Lajia site is located in Minhe county, Qinghai province, in northwestern China. Archaeological studies link Lajia to the late period of the Qijia culture, one of the most important Neolithic civilizations of the upper Yellow River region, the cradle of Chinese civilization. Excavations at the site revealed that the inhabitants died in their houses as the result of a sudden flood. The Lajia site provides a rare chance to study the putative families, all of whom died at the same instant. Possible maternal familial relationships were investigated through mitochondrial DNA (mtDNA) sequence analysis. Twelve sequences from individuals found in one house were assigned to only five haplotypes, consistent with a possible close kinship. Results from analyses of RFLP typing and HVI motifs suggest that the Lajia people belonged to the haplogroups B, C, D, M*, and M10. This study, combined with archaeological and anthropological investigations, provides a better understanding of the genetic history of the Chinese people. CI - (c) 2007 Wiley-Liss, Inc. FAU - Gao, Shi-Zhu AU - Gao SZ AD - Laboratory of Ancient DNA, Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China. FAU - Yang, Yi-Dai AU - Yang YD FAU - Xu, Yue AU - Xu Y FAU - Zhang, Quan-Chao AU - Zhang QC FAU - Zhu, Hong AU - Zhu H FAU - Zhou, Hui AU - Zhou H LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/genetics/*history MH - China MH - DNA, Mitochondrial/*chemistry/classification MH - Female MH - Haplotypes MH - History, Ancient MH - Humans MH - Male MH - Phylogeny MH - Polymorphism, Restriction Fragment Length MH - Sequence Analysis, DNA EDAT- 2007/05/18 09:00 MHDA- 2007/09/06 09:00 CRDT- 2007/05/18 09:00 PHST- 2007/05/18 09:00 [pubmed] PHST- 2007/09/06 09:00 [medline] PHST- 2007/05/18 09:00 [entrez] AID - 10.1002/ajpa.20623 [doi] PST - ppublish SO - Am J Phys Anthropol. 2007 Aug;133(4):1128-36. doi: 10.1002/ajpa.20623. PMID- 17456455 OWN - NLM STAT- MEDLINE DCOM- 20080117 LR - 20221207 IS - 0962-8452 (Print) IS - 1471-2954 (Electronic) IS - 0962-8452 (Linking) VI - 274 IP - 1618 DP - 2007 Jul 7 TI - Evidence of ancient DNA reveals the first European lineage in Iron Age Central China. PG - 1597-601 AB - Various studies on ancient DNA have attempted to reconstruct population movement in Asia, with much interest focused on determining the arrival of European lineages in ancient East Asia. Here, we discuss our analysis of the mitochondrial DNA of human remains excavated from the Yu Hong tomb in Taiyuan, China, dated 1400 years ago. The burial style of this tomb is characteristic of Central Asia at that time. Our analysis shows that Yu Hong belonged to the haplogroup U5, one of the oldest western Eurasian-specific haplogroups, while his wife can be classified as haplogroup G, the type prevalent in East Asia. Our findings show that this man with European lineage arrived in Taiyuan approximately 1400 years ago, and most probably married a local woman. Haplogroup U5 was the first west Eurasian-specific lineage to be found in the central part of ancient China, and Taiyuan may be the easternmost location of the discovered remains of European lineage in ancient China. FAU - Xie, C Z AU - Xie CZ AD - Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, PR China. FAU - Li, C X AU - Li CX FAU - Cui, Y Q AU - Cui YQ FAU - Zhang, Q C AU - Zhang QC FAU - Fu, Y Q AU - Fu YQ FAU - Zhu, H AU - Zhu H FAU - Zhou, H AU - Zhou H LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - China MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration/*history MH - Female MH - Femur/anatomy & histology/*chemistry MH - *Fossils MH - Haplotypes/genetics MH - History, Medieval MH - Humans MH - Male MH - Molecular Sequence Data MH - Sequence Analysis, DNA MH - Tooth/anatomy & histology/*chemistry MH - White People/genetics PMC - PMC2169275 EDAT- 2007/04/26 09:00 MHDA- 2008/01/18 09:00 PMCR- 2008/07/07 CRDT- 2007/04/26 09:00 PHST- 2007/04/26 09:00 [pubmed] PHST- 2008/01/18 09:00 [medline] PHST- 2007/04/26 09:00 [entrez] PHST- 2008/07/07 00:00 [pmc-release] AID - F72136W63154M126 [pii] AID - rspb20070219 [pii] AID - 10.1098/rspb.2007.0219 [doi] PST - ppublish SO - Proc Biol Sci. 2007 Jul 7;274(1618):1597-601. doi: 10.1098/rspb.2007.0219. PMID- 17610332 OWN - NLM STAT- MEDLINE DCOM- 20070830 LR - 20181113 IS - 1673-1581 (Print) IS - 1673-1581 (Linking) VI - 8 IP - 7 DP - 2007 Jul TI - Extremely high frequency of autoimmune-predisposing alleles in medieval specimens. PG - 512-4 AB - The precise etiology and reasons for the increase in incidence of autoimmune disorders still remain unclear, and although both genetic and environmental factors have been proven to shape individual predisposition, it is not known which of the factors, if not both, is responsible for the boom observed during the last decades. In order to establish whether a higher frequency of autoimmune-predisposing alleles may explain this increase we took advantage of ancient DNA methodology to establish the genetic predisposition, conferred by cytotoxic T lymphocyte associated antigen-4 (CTLA4) +49A/G and human leukocyte antigens (HLA) DQB1(57), in population inhabiting Poland in the Middle Ages. After successful typing of 42 individuals from a 12th approximately 14th's century archeological burial site, we found that frequencies of the predisposing alleles in the medieval population were higher than they are at present, suggesting thus that the recently observed incidence increase results most probably from factors of other than genetic nature. FAU - Witas, H W AU - Witas HW AD - Department of Molecular Biology, Medical University of Lodz, Sporna 36/50, PL-91738 Lodz, Poland. witas@usk4.umed.lodz.pl FAU - Jedrychowska-Dańska, K AU - Jedrychowska-Dańska K FAU - Zawicki, P AU - Zawicki P LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - China TA - J Zhejiang Univ Sci B JT - Journal of Zhejiang University. Science. B JID - 101236535 RN - 0 (Antigens, CD) RN - 0 (Antigens, Differentiation) RN - 0 (CTLA-4 Antigen) RN - 0 (CTLA4 protein, human) RN - 0 (HLA-DQ Antigens) RN - 0 (HLA-DQ beta-Chains) RN - 0 (HLA-DQB1 antigen) RN - 9007-49-2 (DNA) SB - IM MH - Alleles MH - Antigens, CD/genetics MH - Antigens, Differentiation/genetics MH - Autoimmune Diseases/genetics/*history/immunology MH - CTLA-4 Antigen MH - DNA/genetics/isolation & purification MH - Gene Frequency MH - Genotype MH - HLA-DQ Antigens/genetics MH - HLA-DQ beta-Chains MH - History, Medieval MH - Humans MH - Poland MH - Tooth/chemistry PMC - PMC1906598 EDAT- 2007/07/05 09:00 MHDA- 2007/08/31 09:00 PMCR- 2007/07/01 CRDT- 2007/07/05 09:00 PHST- 2007/07/05 09:00 [pubmed] PHST- 2007/08/31 09:00 [medline] PHST- 2007/07/05 09:00 [entrez] PHST- 2007/07/01 00:00 [pmc-release] AID - 10.1631/jzus.2007.B0512 [doi] PST - ppublish SO - J Zhejiang Univ Sci B. 2007 Jul;8(7):512-4. doi: 10.1631/jzus.2007.B0512. PMID- 17593420 OWN - NLM STAT- MEDLINE DCOM- 20080320 LR - 20181113 IS - 0022-2844 (Print) IS - 0022-2844 (Linking) VI - 65 IP - 1 DP - 2007 Jul TI - A statistical approach to identify ancient template DNA. PG - 92-102 AB - One of the key problems in the study of ancient DNA is that of authenticating sequences obtained from PCR amplifications of highly degraded samples. Contamination of ancient samples and postmortem damage to endogenous DNA templates are the major obstacles facing researchers in this task. In particular, the authentication of sequences obtained from ancient human remains is thought by many to be rather challenging. We propose a novel approach, based on the c statistic, that can be employed to help identify the sequence motif of an endogenous template, based on a sample of sequences that reflect the nucleotide composition of individual template molecules obtained from ancient tissues (such as cloned products from a PCR amplification). The c statistic exploits as information the most common form of postmortem damage observed among clone sequences in ancient DNA studies, namely, lesion-induced substitutions caused by cytosine deamination events. Analyses of simulated sets of templates with miscoding lesions and real sets of clone sequences from the literature indicate that the c-based approach is highly effective in identifying endogenous sequence motifs, even when they are not present among the sampled clones. The proposed approach is likely to be of general use to researchers working with DNA from ancient tissues, particularly from human remains, where authentication of results has been most challenging. FAU - Helgason, Agnar AU - Helgason A AD - deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland. agnar@decode.is FAU - Pálsson, Snaebjörn AU - Pálsson S FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C FAU - Ghosh, Shyamali AU - Ghosh S FAU - Sigurdardóttir, Sigrún AU - Sigurdardóttir S FAU - Baker, Adam AU - Baker A FAU - Hrafnkelsson, Birgir AU - Hrafnkelsson B FAU - Arnadóttir, Lilja AU - Arnadóttir L FAU - Thorsteinsdóttir, Unnur AU - Thorsteinsdóttir U FAU - Stefánsson, Kári AU - Stefánsson K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070625 PL - Germany TA - J Mol Evol JT - Journal of molecular evolution JID - 0360051 RN - 9007-49-2 (DNA) SB - IM MH - DNA/*analysis/metabolism MH - *DNA Damage MH - Data Interpretation, Statistical MH - Humans MH - Mitochondria/*genetics/metabolism MH - *Models, Statistical MH - *Postmortem Changes EDAT- 2007/06/27 09:00 MHDA- 2008/03/21 09:00 CRDT- 2007/06/27 09:00 PHST- 2006/11/24 00:00 [received] PHST- 2007/04/03 00:00 [accepted] PHST- 2007/06/27 09:00 [pubmed] PHST- 2008/03/21 09:00 [medline] PHST- 2007/06/27 09:00 [entrez] AID - 10.1007/s00239-006-0259-8 [doi] PST - ppublish SO - J Mol Evol. 2007 Jul;65(1):92-102. doi: 10.1007/s00239-006-0259-8. Epub 2007 Jun 25. PMID- 19083754 OWN - NLM STAT- MEDLINE DCOM- 20090227 LR - 20191210 IS - 1878-0326 (Electronic) IS - 1872-4973 (Linking) VI - 1 IP - 2 DP - 2007 Jun TI - High efficiency DNA extraction from bone by total demineralization. PG - 191-5 LID - 10.1016/j.fsigen.2007.02.006 [doi] AB - In historical cases, missing persons' identification, mass disasters, and ancient DNA investigations, bone and teeth samples are often the only, and almost always the best, biological material available for DNA typing. This is because of the physical and chemical barrier that the protein:mineral matrix of bone poses to environmental deterioration and biological attack. Most bone extraction protocols utilized in the forensic community involve an incubation period of bone powder in extraction buffer for proteinase digestion, followed by the collection of the supernatant, and the disposal of large quantities of undissolved bone powder. Here we present an extremely efficient protocol for recovery of DNA by complete demineralization, resulting in full physical dissolution of the bone sample. This is performed in a manner that retains and concentrates all the reagent volume, for complete DNA recovery. For our study, we selected 14 challenging bone samples. The bones were extracted side-by-side with our new demineralization protocol and the standard extraction protocol in use at AFDIL. A real-time quantification assay based on the amplification of a 143 bp mtDNA fragment showed that this new demineralization protocol significantly enhances the quantity of DNA that can be extracted and amplified from degraded skeletal remains. We have used this technique to successfully recover authentic DNA sequences from extremely challenging samples that failed repeatedly using the standard protocol. FAU - Loreille, Odile M AU - Loreille OM AD - Armed Forces DNA Identification Laboratory, 1413 Research Blvd., Bldg. 101, Rockville, MD 20850, United States. odile.loreille@afip.osd.mil FAU - Diegoli, Toni M AU - Diegoli TM FAU - Irwin, Jodi A AU - Irwin JA FAU - Coble, Michael D AU - Coble MD FAU - Parsons, Thomas J AU - Parsons TJ LA - eng PT - Comparative Study PT - Evaluation Study PT - Journal Article DEP - 20070312 PL - Netherlands TA - Forensic Sci Int Genet JT - Forensic science international. Genetics JID - 101317016 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Bone Demineralization Technique/*methods MH - Bone and Bones/*chemistry MH - DNA/*genetics/*isolation & purification MH - DNA, Mitochondrial/genetics/isolation & purification MH - Forensic Genetics/*methods MH - Humans MH - Microsatellite Repeats MH - Tooth/chemistry EDAT- 2007/06/01 00:00 MHDA- 2009/02/28 09:00 CRDT- 2008/12/17 09:00 PHST- 2007/01/24 00:00 [received] PHST- 2007/02/03 00:00 [accepted] PHST- 2008/12/17 09:00 [entrez] PHST- 2007/06/01 00:00 [pubmed] PHST- 2009/02/28 09:00 [medline] AID - S1872-4973(07)00063-4 [pii] AID - 10.1016/j.fsigen.2007.02.006 [doi] PST - ppublish SO - Forensic Sci Int Genet. 2007 Jun;1(2):191-5. doi: 10.1016/j.fsigen.2007.02.006. Epub 2007 Mar 12. PMID- 17626351 OWN - NLM STAT- MEDLINE DCOM- 20070726 LR - 20070713 IS - 0022-3395 (Print) IS - 0022-3395 (Linking) VI - 93 IP - 3 DP - 2007 Jun TI - Paleoparasitological report on the stool from a Medieval child mummy in Yangju, Korea. PG - 589-92 AB - Previous studies have successfully shown evidence for parasitic infections in human remains from various archaeological sites. However, in the case of Korea, since there have been very few paleoparasitological reports published, pre-20th century parasitic infection patterns remain obscure. Therefore, in order to partly fill this gap, we are reporting on a case of paleoparasitic infection from the feces of a 15th century child mummy from Yangju, Korea. In the course of the present study, we found the eggs of Clonorchis sinensis, Ascaris lumbricoides, and Trichuris trichiura in the feces of the mummy. Trichuris trichiura eggs were found in far greater numbers than other parasite eggs; in fact, intact bipolar plugs were clearly observed and even the larvae were still visible in some eggs. The eggs of C. sinensis and A. lumbricoides were also well preserved, though not in as great a number. Since we could find a number of well-preserved larvae-containing eggs, we are encouraged that successful extraction, amplification, and sequence determination of ancient DNA from the paleoparasite eggs might be possible in future studies. With additional paleoparasitological investigation using feces from Korean mummies, we hope that a history of parasite infection in Korea will be reconstructed. FAU - Seo, Min AU - Seo M AD - Department of Parasitology, Dankook University College of Medicine, Chonan 330-714, Korea. FAU - Guk, Sang-Mee AU - Guk SM FAU - Kim, Jaehyup AU - Kim J FAU - Chai, Jong-Yil AU - Chai JY FAU - Bok, Gi Dae AU - Bok GD FAU - Park, Sung Sil AU - Park SS FAU - Oh, Chang Seok AU - Oh CS FAU - Kim, Myeung Ju AU - Kim MJ FAU - Yil, Yang Su AU - Yil YS FAU - Shin, Myung Ho AU - Shin MH FAU - Kang, In Uk AU - Kang IU FAU - Shin, Dong Hoon AU - Shin DH LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Parasitol JT - The Journal of parasitology JID - 7803124 SB - IM MH - Animals MH - Ascariasis/history MH - Ascaris lumbricoides/isolation & purification MH - Clonorchiasis/history MH - Clonorchis sinensis/isolation & purification MH - Feces/parasitology MH - Helminthiasis/*history MH - History, 15th Century MH - Humans MH - Mummies/*parasitology MH - Trichuriasis/history MH - Trichuris/isolation & purification EDAT- 2007/07/14 09:00 MHDA- 2007/07/27 09:00 CRDT- 2007/07/14 09:00 PHST- 2007/07/14 09:00 [pubmed] PHST- 2007/07/27 09:00 [medline] PHST- 2007/07/14 09:00 [entrez] AID - 10.1645/GE-905R3.1 [doi] PST - ppublish SO - J Parasitol. 2007 Jun;93(3):589-92. doi: 10.1645/GE-905R3.1. PMID- 17510332 OWN - NLM STAT- MEDLINE DCOM- 20070606 LR - 20101118 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 316 IP - 5827 DP - 2007 May 18 TI - Ancient DNA. No sex please, we're Neandertals. PG - 967 FAU - Pennisi, Elizabeth AU - Pennisi E LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Biological Evolution MH - DNA/*genetics MH - DNA, Mitochondrial/genetics MH - Databases, Nucleic Acid MH - *Fossils MH - Gene Flow MH - Genome MH - Genome, Human MH - Hominidae/*genetics MH - Humans MH - *Hybridization, Genetic MH - Polymorphism, Single Nucleotide MH - *Sexual Behavior EDAT- 2007/05/19 09:00 MHDA- 2007/06/07 09:00 CRDT- 2007/05/19 09:00 PHST- 2007/05/19 09:00 [pubmed] PHST- 2007/06/07 09:00 [medline] PHST- 2007/05/19 09:00 [entrez] AID - 316/5827/967a [pii] AID - 10.1126/science.316.5827.967a [doi] PST - ppublish SO - Science. 2007 May 18;316(5827):967. doi: 10.1126/science.316.5827.967a. PMID- 17389894 OWN - NLM STAT- MEDLINE DCOM- 20070525 LR - 20111209 IS - 0018-067X (Print) IS - 0018-067X (Linking) VI - 98 IP - 4 DP - 2007 Apr TI - Ancient DNA closes on human uniqueness: the base nature of Neanderthals. PG - 187-8 FAU - Foley, R A AU - Foley RA FAU - Lahr, M Mirazón AU - Lahr MM LA - eng PT - News PL - England TA - Heredity (Edinb) JT - Heredity JID - 0373007 RN - 9007-49-2 (DNA) SB - IM MH - Africa MH - Animals MH - DNA/*genetics/isolation & purification MH - Evolution, Molecular MH - Hominidae/*genetics MH - Humans EDAT- 2007/03/29 09:00 MHDA- 2007/05/26 09:00 CRDT- 2007/03/29 09:00 PHST- 2007/03/29 09:00 [pubmed] PHST- 2007/05/26 09:00 [medline] PHST- 2007/03/29 09:00 [entrez] AID - 6800953 [pii] AID - 10.1038/sj.hdy.6800953 [doi] PST - ppublish SO - Heredity (Edinb). 2007 Apr;98(4):187-8. doi: 10.1038/sj.hdy.6800953. PMID- 17379733 OWN - NLM STAT- MEDLINE DCOM- 20071128 LR - 20220330 IS - 1350-0872 (Print) IS - 1350-0872 (Linking) VI - 153 IP - Pt 4 DP - 2007 Apr TI - First report of Mycobacterium bovis DNA in human remains from the Iron Age. PG - 1243-1249 LID - 10.1099/mic.0.2006/002154-0 [doi] AB - Tuberculosis has plagued humankind since prehistoric times, as is evident from characteristic lesions on human skeletons dating back to the Neolithic period. The disease in man is due predominantly to infection with either Mycobacterium tuberculosis or Mycobacterium bovis, both members of the M. tuberculosis (MTB) complex. A number of studies have shown that when conditions permit, surviving mycobacterial DNA may be amplified from bone by PCR. Such ancient DNA (aDNA) analyses are subject to stringent tests of authenticity and, when feasible, are invariably limited by DNA fragmentation. Using PCRs based on single-nucleotide polymorphic loci and regions of difference (RDs) in the MTB complex, a study was made of five Iron Age individuals with spinal lesions recovered from the cemetery of Aymyrlyg, South Siberia. A sensitive screening PCR for MTB complex mycobacteria was positive in four out of the five cases. Genotyping evidence indicated that all four cases were due to infection with M. bovis rather than M. tuberculosis and the data were consistent with the proposed phylogenetic model of the MTB complex. This is believed to be the first report of M. bovis causing Pott's disease in archaeological human remains. The study shows that genotyping of ancestral strains of MTB complex mycobacteria from contexts of known date provides information which allows the phylogeny of the model to be tested. Moreover, it shows that loss of DNA from RD4, which defines classic M. bovis, had already occurred from the genome over 2000 years before the present. FAU - Taylor, G Michael AU - Taylor GM AD - Centre for Molecular Microbiology and Infectious Diseases, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK. FAU - Murphy, Eileen AU - Murphy E AD - School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, Belfast BT7 1NN, UK. FAU - Hopkins, Richard AU - Hopkins R AD - Centre for Molecular Microbiology and Infectious Diseases, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK. FAU - Rutland, Paul AU - Rutland P AD - Department of Genetics, Institute of Child Health, University College London, London WC1N 1EH, UK. FAU - Chistov, Yuri AU - Chistov Y AD - Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), 3 University Embankment, St Petersburg 199034, Russia. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Microbiology (Reading) JT - Microbiology (Reading, England) JID - 9430468 RN - 0 (DNA, Bacterial) SB - IM MH - Animals MH - Cattle MH - DNA, Bacterial/history/*isolation & purification MH - Female MH - History, Ancient MH - Humans MH - Male MH - Mycobacterium bovis/*genetics/isolation & purification MH - Polymerase Chain Reaction MH - Siberia MH - Spine/*microbiology/pathology MH - Tuberculosis, Spinal/*history/microbiology/pathology EDAT- 2007/03/24 09:00 MHDA- 2007/12/06 09:00 CRDT- 2007/03/24 09:00 PHST- 2007/03/24 09:00 [pubmed] PHST- 2007/12/06 09:00 [medline] PHST- 2007/03/24 09:00 [entrez] AID - 10.1099/mic.0.2006/002154-0 [doi] PST - ppublish SO - Microbiology (Reading). 2007 Apr;153(Pt 4):1243-1249. doi: 10.1099/mic.0.2006/002154-0. PMID- 17255122 OWN - NLM STAT- MEDLINE DCOM- 20070820 LR - 20070329 IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 24 IP - 4 DP - 2007 Apr TI - More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA. PG - 998-1004 AB - Authentication of ancient human DNA results is an exceedingly difficult challenge due to the presence of modern contaminant DNA sequences. Nevertheless, the field of ancient human genetics generates huge scientific and public interest, and thus researchers are rarely discouraged by problems concerning the authenticity of such data. Although several methods have been developed to the purpose of authenticating ancient DNA (aDNA) results, while they are useful in faunal research, most of the methods have proven complicated to apply to ancient human DNA. Here, we investigate in detail the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing so, we also produce data that describes the efficiency of bleach incubation of bone powder and its relative detrimental effects on contaminant and authentic ancient DNA. We note that bleach treatment is significantly more detrimental to contaminant than to authentic aDNA in the bleached bone powder. Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination. This asymmetrical behavior of authentic and contaminant DNA can be used to identify authentic haplotypes in human aDNA studies. FAU - Malmström, Helena AU - Malmström H AD - Evolutionary Biology, Uppsala University, Uppsala, Sweden. FAU - Svensson, Emma M AU - Svensson EM FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Willerslev, Eske AU - Willerslev E FAU - Götherström, Anders AU - Götherström A FAU - Holmlund, Gunilla AU - Holmlund G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070125 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Bone and Bones/metabolism MH - Cattle MH - DNA/*analysis/genetics MH - DNA, Mitochondrial/analysis/genetics MH - Dogs MH - Fossils MH - *Haplotypes MH - Humans MH - Polymerase Chain Reaction/methods MH - Specimen Handling/methods MH - Tooth/metabolism EDAT- 2007/01/27 09:00 MHDA- 2007/08/21 09:00 CRDT- 2007/01/27 09:00 PHST- 2007/01/27 09:00 [pubmed] PHST- 2007/08/21 09:00 [medline] PHST- 2007/01/27 09:00 [entrez] AID - msm015 [pii] AID - 10.1093/molbev/msm015 [doi] PST - ppublish SO - Mol Biol Evol. 2007 Apr;24(4):998-1004. doi: 10.1093/molbev/msm015. Epub 2007 Jan 25. PMID- 17205549 OWN - NLM STAT- MEDLINE DCOM- 20070516 LR - 20101118 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 132 IP - 4 DP - 2007 Apr TI - A preliminary analysis of the DNA and diet of the extinct Beothuk: a systematic approach to ancient human DNA. PG - 594-604 AB - We have used a systematic protocol for extracting, quantitating, sexing and validating ancient human mitochondrial and nuclear DNA of one male and one female Beothuk, a Native American population from Newfoundland, which became extinct approximately 180 years ago. They carried mtDNA haplotypes, which fall within haplogroups X and C, consistent with Northeastern Native populations today. In addition we have sexed the male using a novel-sexing assay and confirmed the authenticity of his Y chromosome with the presence of the Native American specific Y-QM3 single nucleotide polymorphism (SNP). This is the first ancient nuclear SNP typed from a Native population in the Americas. In addition, using the same teeth we conducted a stable isotopes analysis of collagen and dentine to show that both individuals relied on marine sources (fresh and salt water fish, seals) with no hierarchy seen between them, and that their water sources were pooled or stored water. Both mtDNA sequence data and Y SNP data hint at possible gene flow or a common ancestral population for both the Beothuk and the current day Mikmaq, but more importantly the data do not lend credence to the proposed idea that the Beothuk (specifically, Nonosabasut) were of admixed (European-Native American) descent. We also analyzed patterns of DNA damage in the clones of authentic mtDNA sequences; there is no tendency for DNA damage to occur preferentially at previously defined mutational hotspots, suggesting that such mutational hotspots are not hypervariable because they are more prone to damage. FAU - Kuch, Melanie AU - Kuch M AD - McMaster Ancient DNA Center, McMaster University, Hamilton, ON L8S 4L9, Canada. FAU - Gröcke, Darren R AU - Gröcke DR FAU - Knyf, Martin C AU - Knyf MC FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Younghusband, Ban AU - Younghusband B FAU - Young, Terry AU - Young T FAU - Marshall, Ingeborg AU - Marshall I FAU - Willerslev, Eske AU - Willerslev E FAU - Stoneking, Mark AU - Stoneking M FAU - Poinar, Hendrik AU - Poinar H LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) RN - 9007-34-5 (Collagen) SB - IM MH - Base Sequence MH - Chromosomes, Human, Y/*genetics MH - Collagen/chemistry MH - DNA Damage/genetics MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - Dentin/chemistry MH - *Diet MH - Female MH - *Genetics, Population MH - Haplotypes/genetics MH - Humans MH - Indians, North American/*genetics MH - Isotope Labeling MH - Male MH - Molecular Sequence Data MH - Newfoundland and Labrador MH - Polymorphism, Single Nucleotide/genetics MH - Sequence Analysis, DNA MH - Sex Determination Analysis/methods EDAT- 2007/01/06 09:00 MHDA- 2007/05/17 09:00 CRDT- 2007/01/06 09:00 PHST- 2007/01/06 09:00 [pubmed] PHST- 2007/05/17 09:00 [medline] PHST- 2007/01/06 09:00 [entrez] AID - 10.1002/ajpa.20536 [doi] PST - ppublish SO - Am J Phys Anthropol. 2007 Apr;132(4):594-604. doi: 10.1002/ajpa.20536. PMID- 17360422 OWN - NLM STAT- MEDLINE DCOM- 20070424 LR - 20221207 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 104 IP - 10 DP - 2007 Mar 6 TI - Absence of the lactase-persistence-associated allele in early Neolithic Europeans. PG - 3736-41 AB - Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk. Some have argued for the "culture-historical hypothesis," whereby LP alleles were rare until the advent of dairying early in the Neolithic but then rose rapidly in frequency under natural selection. Others favor the "reverse cause hypothesis," whereby dairying was adopted in populations with preadaptive high LP allele frequencies. Analysis based on the conservation of lactase gene haplotypes indicates a recent origin and high selection coefficients for LP, although it has not been possible to say whether early Neolithic European populations were lactase persistent at appreciable frequencies. We developed a stepwise strategy for obtaining reliable nuclear ancient DNA from ancient skeletons, based on (i) the selection of skeletons from archaeological sites that showed excellent biomolecular preservation, (ii) obtaining highly reproducible human mitochondrial DNA sequences, and (iii) reliable short tandem repeat (STR) genotypes from the same specimens. By applying this experimental strategy, we have obtained high-confidence LP-associated genotypes from eight Neolithic and one Mesolithic human remains, using a range of strict criteria for ancient DNA work. We did not observe the allele most commonly associated with LP in Europeans, thus providing evidence for the culture-historical hypothesis, and indicating that LP was rare in early European farmers. FAU - Burger, J AU - Burger J AD - Johannes Gutenberg University, Institute of Anthropology, Saarstrasse 21, D-55099 Mainz, Germany. jburger@uni-mainz.de FAU - Kirchner, M AU - Kirchner M FAU - Bramanti, B AU - Bramanti B FAU - Haak, W AU - Haak W FAU - Thomas, M G AU - Thomas MG LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070228 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) RN - EC 3.2.1.108 (Lactase) RN - J2B2A4N98G (Lactose) SB - IM MH - *Alleles MH - Bone and Bones/metabolism MH - DNA, Mitochondrial/genetics MH - Emigration and Immigration MH - Europe MH - Genetics, Population MH - History, Ancient MH - Humans MH - Lactase/*genetics MH - Lactose/metabolism MH - Lactose Intolerance/*genetics MH - Polymorphism, Single Nucleotide MH - Tandem Repeat Sequences MH - Tooth/metabolism MH - White People/*genetics/history PMC - PMC1820653 COIS- The authors declare no conflict of interest. EDAT- 2007/03/16 09:00 MHDA- 2007/04/25 09:00 PMCR- 2007/09/06 CRDT- 2007/03/16 09:00 PHST- 2007/03/16 09:00 [pubmed] PHST- 2007/04/25 09:00 [medline] PHST- 2007/03/16 09:00 [entrez] PHST- 2007/09/06 00:00 [pmc-release] AID - 0607187104 [pii] AID - 5218 [pii] AID - 10.1073/pnas.0607187104 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3736-41. doi: 10.1073/pnas.0607187104. Epub 2007 Feb 28. PMID- 16839727 OWN - NLM STAT- MEDLINE DCOM- 20070503 LR - 20070223 IS - 0379-0738 (Print) IS - 0379-0738 (Linking) VI - 166 IP - 2-3 DP - 2007 Mar 2 TI - STR typing of ancient DNA extracted from hair shafts of Siberian mummies. PG - 218-29 AB - The aim of this study was to determine if ancient hair shafts could be suitable for nuclear DNA analysis and to develop an efficient and straightforward protocol for DNA extraction and STR typing of ancient specimens. The developed method was validated on modern and forensic samples and then successfully applied on ancient hairs collected from Siberian mummies dating from the 16th to the early 19th centuries. In parallel extractions including or excluding a washing step were performed at least two times for each sample in order to evaluate the influence on the quantity of nuclear DNA yielded and on the typing efficiency. Twelve ancient individuals were analyzed through our approach and full and reliable profiles were obtained for four of them. These profiles were validated by comparison with those obtained from bone and teeth DNA extracted from the same ancient specimens. The present study demonstrates that the washing step cannot be considered as deleterious for DNA retrieval since the same results were obtained by the two approaches. This finding challenges the hypothesis that recoverable nuclear DNA is only found on the outer surface of hair shafts and provides evidence that nuclear DNA can be successfully extracted from ancient hair shafts. The method described here constitutes a promising way for non-invasive investigations in ancient DNA analysis for precious or historical samples as well as forensic casework analyses. FAU - Amory, S AU - Amory S AD - Laboratory of Molecular Anthropology, Institute of Legal Medicine of Strasbourg, 11 rue Humann, 67085 Strasbourg Cedex, France. sylvain.amory@iml-ulp.u-strabg.fr FAU - Keyser, C AU - Keyser C FAU - Crubézy, E AU - Crubézy E FAU - Ludes, B AU - Ludes B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060712 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 9007-49-2 (DNA) SB - IM MH - Bone and Bones/chemistry MH - Chromosomes, Human, Y MH - DNA/*isolation & purification MH - DNA Fingerprinting/*methods MH - Female MH - Genotype MH - Hair/*chemistry MH - Humans MH - Male MH - *Mummies MH - Polymerase Chain Reaction MH - Siberia MH - *Tandem Repeat Sequences MH - Tooth/chemistry EDAT- 2006/07/15 09:00 MHDA- 2007/05/04 09:00 CRDT- 2006/07/15 09:00 PHST- 2006/05/05 00:00 [received] PHST- 2006/05/22 00:00 [revised] PHST- 2006/05/24 00:00 [accepted] PHST- 2006/07/15 09:00 [pubmed] PHST- 2007/05/04 09:00 [medline] PHST- 2006/07/15 09:00 [entrez] AID - S0379-0738(06)00342-2 [pii] AID - 10.1016/j.forsciint.2006.05.042 [doi] PST - ppublish SO - Forensic Sci Int. 2007 Mar 2;166(2-3):218-29. doi: 10.1016/j.forsciint.2006.05.042. Epub 2006 Jul 12. PMID- 16687224 OWN - NLM STAT- MEDLINE DCOM- 20070403 LR - 20221207 IS - 0379-0738 (Print) IS - 0379-0738 (Linking) VI - 166 IP - 1 DP - 2007 Feb 14 TI - The last Viking King: a royal maternity case solved by ancient DNA analysis. PG - 21-7 AB - The last of the Danish Viking Kings, Sven Estridsen, died in a.d. 1074 and is entombed in Roskilde Cathedral with other Danish kings and queens. Sven's mother, Estrid, is entombed in a pillar across the chancel. However, while there is no reasonable doubt about the identity of Sven, there have been doubts among historians whether the woman entombed was indeed Estrid. To shed light on this problem, we have extracted and analysed mitochondrial DNA (mtDNA) from pulp of teeth from each of the two royals. Four overlapping DNA-fragments covering about 400bp of hypervariable region 1 (HVR-1) of the D-loop were PCR amplified, cloned and a number of clones with each segment were sequenced. Also a segment containing the H/non-H specific nucleotide 7028 was sequenced. Consensus sequences were determined and D-loop results were replicated in an independent laboratory. This allowed the assignment of King Sven Estridsen to haplogroup H; Estrid's sequence differed from that of Sven at two positions in HVR-1, 16093T-->C and 16304T-->C, indicating that she belongs to subgroup H5a. Given the maternal inheritance of mtDNA, offspring will have the same mtDNA sequence as their mother with the exception of rare cases where the sequence has been altered by a germ line mutation. Therefore, the observation of two sequence differences makes it highly unlikely that the entombed woman was the mother of Sven. In addition, physical examination of the skeleton and the teeth strongly indicated that this woman was much younger (approximately 35 years) at the time of death than the 70 years history records tell. Although the entombed woman cannot be the Estrid, she may well be one of Sven's two daughters-in-law who were also called Estrid and who both became queens. FAU - Dissing, Jørgen AU - Dissing J AD - Research Laboratory, Institute of Forensic Medicine, University of Copenhagen, Frederik V Vej 11, DK-2100 Copenhagen, Denmark. joergen.dissing@forensic.ku.dk FAU - Binladen, Jonas AU - Binladen J FAU - Hansen, Anders AU - Hansen A FAU - Sejrsen, Birgitte AU - Sejrsen B FAU - Willerslev, Eske AU - Willerslev E FAU - Lynnerup, Niels AU - Lynnerup N LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060509 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - DNA, Mitochondrial/analysis/*history MH - Denmark MH - Female MH - Forensic Medicine MH - History, Ancient MH - Humans MH - Male MH - Molecular Sequence Data MH - Mothers MH - Polymerase Chain Reaction MH - Tooth/chemistry MH - White People/*genetics EDAT- 2006/05/12 09:00 MHDA- 2007/04/04 09:00 CRDT- 2006/05/12 09:00 PHST- 2006/03/06 00:00 [received] PHST- 2006/03/25 00:00 [revised] PHST- 2006/03/26 00:00 [accepted] PHST- 2006/05/12 09:00 [pubmed] PHST- 2007/04/04 09:00 [medline] PHST- 2006/05/12 09:00 [entrez] AID - S0379-0738(06)00170-8 [pii] AID - 10.1016/j.forsciint.2006.03.020 [doi] PST - ppublish SO - Forensic Sci Int. 2007 Feb 14;166(1):21-7. doi: 10.1016/j.forsciint.2006.03.020. Epub 2006 May 9. PMID- 17167798 OWN - NLM STAT- MEDLINE DCOM- 20070302 LR - 20200930 IS - 1552-4825 (Print) IS - 1552-4825 (Linking) VI - 143A IP - 2 DP - 2007 Jan 15 TI - Nuchal cystic hygroma in five fetuses from 1819 to 1826 in the Meckel-anatomical collections at the University of Halle, Germany. PG - 119-28 AB - The Anatomical collection of the Department of Anatomy and Cell Biology, Medical School of the University of Halle, Germany, comprises more than 8,000 specimens. Around 600 of them show congenital anomalies. The collection of abnormal human and animal fetuses began as the private collection of Johann Friedrich Meckel the Elder (1724-1774), his son Philipp Friedrich Theodor Meckel (1755-1803) and his grandson Johann Friedrich Meckel the Younger (1781-1833). Meckel the Younger founded the systematic science of developmental pathology. Radiographical techniques, computer tomographic (CT) methods, magnetic resonance imaging (MRI), and comparative genomic hybridization (CGH) were used to diagnose abnormal human fetuses in the Meckel-anatomical collections. Cystic hygroma colli was found in five of the human fetuses originally described by JF Meckel the Younger in 1826 and one of his students in 1819 [Hencke, 1819]. CGH analyses were used to test whether the observed cystic hygroma colli could be caused by chromosomal aneuploidies. CGH-ratio profiles of all chromosomes were apparently normal. PCR-based sex determination tests on ancient DNA were used to determine the fetal gonosomal constitution. It is likely that the Meckel specimens are among the oldest fetuses in which Ullrich-Turner "phenotype" has been diagnosed. CI - (c) 2006 Wiley-Liss, Inc FAU - Göbbel, Luminita AU - Göbbel L AD - Department of Anatomy and Cell Biology, Martin-Luther University Halle-Wittenberg, Halle/Saale, Germany. luminita.goebbel@medizin.uni-halle.de FAU - Schultka, Rüdiger AU - Schultka R FAU - Klunker, Rudyard AU - Klunker R FAU - Stock, Karsten AU - Stock K FAU - Helm, Jürgen AU - Helm J FAU - Olsson, Lennart AU - Olsson L FAU - Opitz, John M AU - Opitz JM FAU - Gerlach, Antje AU - Gerlach A FAU - Tönnies, Holger AU - Tönnies H LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Med Genet A JT - American journal of medical genetics. Part A JID - 101235741 RN - 9007-49-2 (DNA) SB - IM MH - DNA/analysis/genetics MH - Developmental Biology MH - Female MH - Fetal Diseases/genetics/*pathology MH - Fetus/abnormalities MH - Germany MH - History, 19th Century MH - Humans MH - Lymphangioma, Cystic/genetics/*pathology MH - Male MH - Museums MH - Neck/pathology MH - Nucleic Acid Hybridization MH - Skull/pathology EDAT- 2006/12/15 09:00 MHDA- 2007/03/03 09:00 CRDT- 2006/12/15 09:00 PHST- 2006/12/15 09:00 [pubmed] PHST- 2007/03/03 09:00 [medline] PHST- 2006/12/15 09:00 [entrez] AID - 10.1002/ajmg.a.31488 [doi] PST - ppublish SO - Am J Med Genet A. 2007 Jan 15;143A(2):119-28. doi: 10.1002/ajmg.a.31488. PMID- 17966429 OWN - NLM STAT- MEDLINE DCOM- 20071207 LR - 20161109 IS - 0065-2598 (Print) IS - 0065-2598 (Linking) VI - 603 DP - 2007 TI - Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA. PG - 327-38 AB - The precise nature of the pathogen having caused early plague pandemics is uncertain. Although Yersinia pestis is a likely candidate for all three plague pandemics, the very rare direct evidence that can be deduced from ancient DNA (aDNA) analysis is controversial. Moreover, which of the three biovars, Antiqua, Medievalis or Orientalis, was associated with these pandemics is still debated. There is a need for phylogenetic analysis performed on Y. pestis strains isolated from countries from which plague probably arose and is still endemic. In addition there exist technical difficulties inherent to aDNA investigations and a lack of appropriate genetic targets. The recently described CRISPRs (clustered regularly interspaced short palindromic repeats) may represent such a target. CRISPR loci consist of a succession of highly conserved regions separated by specific "spacers" usually of viral origin. To be of use, data describing the mechanisms of evolution and diversity of CRISPRs in Y. pestis, its closest neighbors, and other species which might contaminate ancient DNA, are necessary. The investigation of closely related Y. pestis isolates has revealed recent mutation events in which elements constituting CRISPRs were acquired or lost, providing essential insight on their evolution. Rules deduced represent the basis for subsequent interpretation. In the present study, the CRISPR loci from representative Y. pestis and Yersinia pseudotuberculosis strains were investigated by PCR amplification and sequence analysis. The investigation of this wider panel of strains, including other subspecies or ecotypes within Y. pestis and also Y. pseudotuberculosis strains provides a database of the existing CRISPR spacers and helps predict the expected CRISPR structure of the Y. pestis ancestor. This knowledge will open the way to the development of a spoligotyping assay, in which spacers can be amplified even from highly degraded DNA samples. The data obtained show that CRISPR analysis can provide a very powerful typing tool, adapted to the systematic, large-scale genotyping of Y. pestis isolates, and the creation of international typing databases. In addition, CRISPRs do constitute a very promising new tool and genetic target to investigate ancient DNA. The corresponding genetic targets are small (<70bp), present in multiple copies (usually more than 10), highly conserved and specific. In addition, the assay can be run in any laboratory. Interpretation of the data is not dependent on accurate sequence data. FAU - Vergnaud, Gilles AU - Vergnaud G AD - Université Paris-Sud, Institut de Génétique et Microbiologie, Orsay, France. gilles.vergnaud@igmors.u-psud.fr FAU - Li, Yanjun AU - Li Y FAU - Gorgé, Olivier AU - Gorgé O FAU - Cui, Yujun AU - Cui Y FAU - Song, Yajun AU - Song Y FAU - Zhou, Dongsheng AU - Zhou D FAU - Grissa, Ibtissem AU - Grissa I FAU - Dentovskaya, Svetlana V AU - Dentovskaya SV FAU - Platonov, Mikhail E AU - Platonov ME FAU - Rakin, Alexander AU - Rakin A FAU - Balakhonov, Sergey V AU - Balakhonov SV FAU - Neubauer, Heinrich AU - Neubauer H FAU - Pourcel, Christine AU - Pourcel C FAU - Anisimov, Andrey P AU - Anisimov AP FAU - Yang, Ruifu AU - Yang R LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Adv Exp Med Biol JT - Advances in experimental medicine and biology JID - 0121103 RN - 0 (DNA, Bacterial) SB - IM MH - Base Sequence MH - DNA, Bacterial/*genetics/*history MH - Disease Outbreaks/history MH - Evolution, Molecular MH - Genes, Bacterial MH - History, Ancient MH - Humans MH - Interspersed Repetitive Sequences MH - Molecular Sequence Data MH - Phylogeny MH - Plague/epidemiology/*history/microbiology MH - Species Specificity MH - Yersinia pestis/classification/*genetics/pathogenicity MH - Yersinia pseudotuberculosis/classification/genetics EDAT- 2007/10/31 09:00 MHDA- 2007/12/08 09:00 CRDT- 2007/10/31 09:00 PHST- 2007/10/31 09:00 [pubmed] PHST- 2007/12/08 09:00 [medline] PHST- 2007/10/31 09:00 [entrez] AID - 10.1007/978-0-387-72124-8_30 [doi] PST - ppublish SO - Adv Exp Med Biol. 2007;603:327-38. doi: 10.1007/978-0-387-72124-8_30. PMID- 17715147 OWN - NLM STAT- MEDLINE DCOM- 20071105 LR - 20230507 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 35 IP - 17 DP - 2007 TI - Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions. PG - 5717-28 AB - Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy. FAU - Brotherton, Paul AU - Brotherton P AD - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia. paul.brotherton@virgin.net FAU - Endicott, Phillip AU - Endicott P FAU - Sanchez, Juan J AU - Sanchez JJ FAU - Beaumont, Mark AU - Beaumont M FAU - Barnett, Ross AU - Barnett R FAU - Austin, Jeremy AU - Austin J FAU - Cooper, Alan AU - Cooper A LA - eng GR - WT_/Wellcome Trust/United Kingdom PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070822 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA Primers) RN - 56HH86ZVCT (Uracil) RN - 5Z93L87A1R (Guanine) RN - 8J337D1HZY (Cytosine) RN - 9007-49-2 (DNA) RN - EC 2.7.7.- (Taq Polymerase) RN - K72T3FS567 (Adenosine) SB - IM MH - Adenosine/chemistry MH - Animals MH - Cytosine/chemistry MH - DNA/chemistry MH - *DNA Damage MH - DNA Fragmentation MH - DNA Primers MH - *Fossils MH - Guanine/chemistry MH - Humans MH - Nucleic Acid Amplification Techniques/*methods MH - Polymerase Chain Reaction MH - *Sequence Analysis, DNA MH - Taq Polymerase MH - Templates, Genetic MH - Uracil/chemistry PMC - PMC2034480 EDAT- 2007/08/24 09:00 MHDA- 2007/11/06 09:00 PMCR- 2007/08/22 CRDT- 2007/08/24 09:00 PHST- 2007/08/24 09:00 [pubmed] PHST- 2007/11/06 09:00 [medline] PHST- 2007/08/24 09:00 [entrez] PHST- 2007/08/22 00:00 [pmc-release] AID - gkm588 [pii] AID - 10.1093/nar/gkm588 [doi] PST - ppublish SO - Nucleic Acids Res. 2007;35(17):5717-28. doi: 10.1093/nar/gkm588. Epub 2007 Aug 22. PMID- 17568987 OWN - NLM STAT- MEDLINE DCOM- 20070831 LR - 20200225 IS - 1434-5161 (Print) IS - 1434-5161 (Linking) VI - 52 IP - 7 DP - 2007 TI - Origins and genetic features of the Okhotsk people, revealed by ancient mitochondrial DNA analysis. PG - 618-627 LID - 10.1007/s10038-007-0164-z [doi] AB - In order to investigate the phylogenetic status of the Okhotsk people that were distributed in northern and eastern Hokkaido as well as southern Sakhalin during the fifth to the thirteenth centuries, DNA was carefully extracted from human bone and tooth remains excavated from archaeological sites. The hypervariable region 1 sequences of the mitochondrial DNA (mtDNA) control region were successfully amplified and 16 mtDNA haplotypes were identified from 37 individuals of the Okhotsk people. Of the 16 haplotypes found, 6 were unique to the Okhotsk people, whereas the other 10 were shared by northeastern Asian people that are currently distributed around Sakhalin and downstream of the Amur River. The phylogenetic relationships inferred from mtDNA sequences showed that the Okhotsk people were more closely related to the Nivkhi and Ulchi people among populations of northeastern Asia. In addition, the Okhotsk people had a relatively closer genetic affinity with the Ainu people of Hokkaido, and were likely intermediates of gene flow from the northeastern Asian people to the Ainu people. These findings support the hypothesis that the Okhotsk culture joined the Satsumon culture (direct descendants of the Jomon people) resulting in the Ainu culture, as suggested by previous archaeological and anthropological studies. FAU - Sato, Takehiro AU - Sato T AD - Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan. FAU - Amano, Tetsuya AU - Amano T AD - Hokkaido University Museum, Sapporo, 060-0810, Japan. FAU - Ono, Hiroko AU - Ono H AD - Hokkaido University Museum, Sapporo, 060-0810, Japan. FAU - Ishida, Hajime AU - Ishida H AD - Faculty of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan. FAU - Kodera, Haruto AU - Kodera H AD - School of Dental Medicine, Tsurumi University, Yokohama, 230-8501, Japan. FAU - Matsumura, Hirofumi AU - Matsumura H AD - Sapporo Medical University, Sapporo, 060-8556, Japan. FAU - Yoneda, Minoru AU - Yoneda M AD - Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, 277-8562, Japan. FAU - Masuda, Ryuichi AU - Masuda R AD - Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan. masudary@ees.hokudai.ac.jp. AD - Creative Research Initiative "Sousei", Hokkaido University, Sapporo, 060-0810, Japan. masudary@ees.hokudai.ac.jp. LA - eng SI - GENBANK/AB292314 SI - GENBANK/AB292315 SI - GENBANK/AB292316 SI - GENBANK/AB292317 SI - GENBANK/AB292318 SI - GENBANK/AB292319 SI - GENBANK/AB292320 SI - GENBANK/AB292321 SI - GENBANK/AB292322 SI - GENBANK/AB292323 SI - GENBANK/AB292324 SI - GENBANK/AB292325 SI - GENBANK/AB292326 SI - GENBANK/AB292327 SI - GENBANK/AB292328 SI - GENBANK/AB292329 SI - GENBANK/AB292330 SI - GENBANK/AB292331 SI - GENBANK/AB292332 SI - GENBANK/AB292333 SI - GENBANK/AB292334 SI - GENBANK/AB292335 SI - GENBANK/AB292336 SI - GENBANK/AB292337 SI - GENBANK/AB292338 SI - GENBANK/AB292339 SI - GENBANK/AB292340 SI - GENBANK/AB292341 SI - GENBANK/AB292342 SI - GENBANK/AB292343 SI - GENBANK/AB292344 SI - GENBANK/AB292345 SI - GENBANK/AB292346 SI - GENBANK/AB292347 SI - GENBANK/AB292348 SI - GENBANK/AB292349 SI - GENBANK/AB292350 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070614 PL - England TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - Evolution, Molecular MH - *Fossils MH - Haplotypes MH - Humans MH - Japan/ethnology MH - Korea/ethnology MH - Molecular Sequence Data MH - Phylogeny EDAT- 2007/06/15 09:00 MHDA- 2007/09/01 09:00 CRDT- 2007/06/15 09:00 PHST- 2007/03/27 00:00 [received] PHST- 2007/05/11 00:00 [accepted] PHST- 2007/06/15 09:00 [pubmed] PHST- 2007/09/01 09:00 [medline] PHST- 2007/06/15 09:00 [entrez] AID - 10.1007/s10038-007-0164-z [pii] AID - 10.1007/s10038-007-0164-z [doi] PST - ppublish SO - J Hum Genet. 2007;52(7):618-627. doi: 10.1007/s10038-007-0164-z. Epub 2007 Jun 14. PMID- 17146600 OWN - NLM STAT- MEDLINE DCOM- 20070329 LR - 20181113 IS - 0022-2844 (Print) IS - 0022-2844 (Linking) VI - 64 IP - 1 DP - 2007 Jan TI - Evaluating Neanderthal genetics and phylogeny. PG - 50-60 AB - The retrieval of Neanderthal (Homo neanderthalsensis) mitochondrial DNA is thought to be among the most significant ancient DNA contributions to date, allowing conflicting hypotheses on modern human (Homo sapiens) evolution to be tested directly. Recently, however, both the authenticity of the Neanderthal sequences and their phylogenetic position outside contemporary human diversity have been questioned. Using Bayesian inference and the largest dataset to date, we find strong support for a monophyletic Neanderthal clade outside the diversity of contemporary humans, in agreement with the expectations of the Out-of-Africa replacement model of modern human origin. From average pairwise sequence differences, we obtain support for claims that the first published Neanderthal sequence may include errors due to postmortem damage in the template molecules for PCR. In contrast, we find that recent results implying that the Neanderthal sequences are products of PCR artifacts are not well supported, suffering from inadequate experimental design and a presumably high percentage (>68%) of chimeric sequences due to "jumping PCR" events. FAU - Hebsgaard, Martin B AU - Hebsgaard MB AD - Centré for Ancient Genetics, Niels Bohr Institute and Biological Institute, University of Copenhagen, Juliane Maries vej 30, Copenhagen DK-2100, Denmark. FAU - Wiuf, Carsten AU - Wiuf C FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Glenner, Henrik AU - Glenner H FAU - Willerslev, Eske AU - Willerslev E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20061201 PL - Germany TA - J Mol Evol JT - Journal of molecular evolution JID - 0360051 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Artifacts MH - Bayes Theorem MH - *DNA, Mitochondrial MH - Hominidae/genetics/*physiology MH - Humans MH - *Phylogeny MH - Polymerase Chain Reaction EDAT- 2006/12/06 09:00 MHDA- 2007/03/30 09:00 CRDT- 2006/12/06 09:00 PHST- 2006/01/25 00:00 [received] PHST- 2006/08/29 00:00 [accepted] PHST- 2006/12/06 09:00 [pubmed] PHST- 2007/03/30 09:00 [medline] PHST- 2006/12/06 09:00 [entrez] AID - 10.1007/s00239-006-0017-y [doi] PST - ppublish SO - J Mol Evol. 2007 Jan;64(1):50-60. doi: 10.1007/s00239-006-0017-y. Epub 2006 Dec 1. PMID- 17218991 OWN - NLM STAT- MEDLINE DCOM- 20100316 LR - 20221207 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 1 IP - 1 DP - 2006 Dec 20 TI - Multiplexed SNP typing of ancient DNA clarifies the origin of Andaman mtDNA haplogroups amongst South Asian tribal populations. PG - e81 LID - e81 AB - The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately, significantly reducing the amount of errors appearing in published data sets. To show the sensitivity of this technique for screening mtDNA genomic sequence data, 20 historic samples of the enigmatic Andaman Islanders and 12 modern samples from three Indian tribal populations (Chenchu, Lambadi and Lodha) were genotyped for 20 coding region sites after provisional haplogroup assignment with control region sequences. The genotype data from the historic samples significantly revise the topologies for the Andaman M31 and M32 mtDNA lineages by rectifying conflicts in published data sets. The new Indian data extend the distribution of the M31a lineage to South Asia, challenging previous interpretations of mtDNA phylogeography. This genetic connection between the ancestors of the Andamanese and South Asian tribal groups approximately 30 kya has important implications for the debate concerning migration routes and settlement patterns of humans leaving Africa during the late Pleistocene, and indicates the need for more detailed genotyping strategies. The methodology serves as a low-cost, high-throughput model for the production and authentication of data from modern or ancient DNA, and demonstrates the value of museum collections as important records of human genetic diversity. FAU - Endicott, Phillip AU - Endicott P AD - Department of Zoology, University of Oxford Oxford, United Kingdom. phillip.endicott@zoo.ox.ac.uk FAU - Metspalu, Mait AU - Metspalu M FAU - Stringer, Chris AU - Stringer C FAU - Macaulay, Vincent AU - Macaulay V FAU - Cooper, Alan AU - Cooper A FAU - Sanchez, Juan J AU - Sanchez JJ LA - eng PT - Historical Article PT - Journal Article DEP - 20061220 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/*genetics/history MH - DNA, Mitochondrial/*genetics MH - Genetics, Population MH - History, 19th Century MH - History, Ancient MH - Humans MH - India MH - Phylogeny MH - Polymerase Chain Reaction MH - *Polymorphism, Single Nucleotide PMC - PMC1766372 COIS- Competing Interests: Competing Interests: The authors have declared that no competing interests exist. EDAT- 2007/01/16 09:00 MHDA- 2007/01/16 09:01 PMCR- 2006/12/20 CRDT- 2007/01/16 09:00 PHST- 2006/09/29 00:00 [received] PHST- 2006/10/30 00:00 [accepted] PHST- 2007/01/16 09:00 [pubmed] PHST- 2007/01/16 09:01 [medline] PHST- 2007/01/16 09:00 [entrez] PHST- 2006/12/20 00:00 [pmc-release] AID - 06-PONE-RA-00170 [pii] AID - 10.1371/journal.pone.0000081 [doi] PST - epublish SO - PLoS One. 2006 Dec 20;1(1):e81. doi: 10.1371/journal.pone.0000081. PMID- 17120261 OWN - NLM STAT- MEDLINE DCOM- 20070309 LR - 20191210 IS - 0173-0835 (Print) IS - 0173-0835 (Linking) VI - 27 IP - 24 DP - 2006 Dec TI - Usefulness of microchip electrophoresis for the analysis of mitochondrial DNA in forensic and ancient DNA studies. PG - 5101-9 AB - We evaluate the usefulness of a commercially available microchip CE (MCE) device in different genetic identification studies performed with mitochondrial DNA (mtDNA) targets, including the haplotype analysis of HVR1 and HVR2 and the study of interspecies diversity of cytochrome b (Cyt b) and 16S ribosomal RNA (16S rRNA) mitochondrial genes in forensic and ancient DNA samples. The MCE commercial system tested in this study proved to be a fast and sensitive detection method of length heteroplasmy in cytosine stretches produced by 16 189T>C transitions in HVR1 and by 309.1 and 309.2 C-insertions in HVR2. Moreover, the quantitative analysis of PCR amplicons performed by LIF allowed normalizing the amplicon input in the sequencing reactions, improving the overall quality of sequence data. These quantitative data in combination with the quantification of genomic mtDNA by real-time PCR has been successfully used to evaluate the PCR efficiency and detection limit of full sequencing methods of different mtDNA targets. The quantification of amplicons also provided a method for the rapid evaluation of PCR efficiency of multiplex-PCR versus singleplex-PCR to amplify short HV1 amplicons (around 100 bp) from severely degraded ancient DNA samples. The combination of human-specific (Cyt b) and universal (16S rRNA) mtDNA primer sets in a single PCR reaction followed by MCE detection offers a very rapid and simple screening test to differentiate between human and nonhuman hair forensic samples. This method was also very efficient with degraded DNA templates from forensic hair and bone samples, because of its applicability to detect small amplicon sizes. Future possibilities of MCE in forensic DNA typing, including nuclear STRs and SNP profiling are suggested. FAU - Alonso, Antonio AU - Alonso A AD - Instituto Nacional de Toxicología y Ciencias Forenses, Servicio de Biología, Madrid, Spain. a.alonso@mju.es FAU - Albarran, Cristina AU - Albarran C FAU - Martín, Pablo AU - Martín P FAU - García, Pilar AU - García P FAU - Capilla, Javier AU - Capilla J FAU - García, Oscar AU - García O FAU - de la Rua, Concepción AU - de la Rua C FAU - Izaguirre, Neskuts AU - Izaguirre N FAU - Pereira, Filipe AU - Pereira F FAU - Pereira, Luisa AU - Pereira L FAU - Amorim, António AU - Amorim A FAU - Sancho, Manuel AU - Sancho M LA - eng PT - Evaluation Study PT - Journal Article PL - Germany TA - Electrophoresis JT - Electrophoresis JID - 8204476 RN - 0 (DNA, Mitochondrial) RN - 0 (RNA, Ribosomal, 16S) RN - 0 (Receptors, Vasoactive Intestinal Peptide, Type II) RN - 0 (Receptors, Vasoactive Intestinal Polypeptide, Type I) RN - 0 (VIPR2 protein, human) RN - 9035-37-4 (Cytochromes b) SB - IM MH - Animals MH - Bone and Bones/chemistry MH - Cattle MH - Cytochromes b/genetics MH - DNA Fingerprinting/*methods MH - DNA, Mitochondrial/*analysis/genetics MH - Dogs MH - Electrophoresis, Microchip/*methods MH - Forensic Anthropology/*methods MH - Forensic Genetics/*methods MH - Hair/chemistry MH - Haplotypes MH - Humans MH - Mice MH - RNA, Ribosomal, 16S/genetics MH - Rats MH - Receptors, Vasoactive Intestinal Peptide, Type II/genetics MH - Receptors, Vasoactive Intestinal Polypeptide, Type I/genetics MH - Sequence Analysis, DNA EDAT- 2006/11/23 09:00 MHDA- 2007/03/10 09:00 CRDT- 2006/11/23 09:00 PHST- 2006/11/23 09:00 [pubmed] PHST- 2007/03/10 09:00 [medline] PHST- 2006/11/23 09:00 [entrez] AID - 10.1002/elps.200600331 [doi] PST - ppublish SO - Electrophoresis. 2006 Dec;27(24):5101-9. doi: 10.1002/elps.200600331. PMID- 17110569 OWN - NLM STAT- MEDLINE DCOM- 20061129 LR - 20240415 IS - 1095-9203 (Electronic) IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 314 IP - 5802 DP - 2006 Nov 17 TI - Sequencing and analysis of Neanderthal genomic DNA. PG - 1113-8 AB - Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. These results enabled us to calculate the human-Neanderthal divergence time based on multiple randomly distributed autosomal loci. Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor approximately 706,000 years ago, and that the human and Neanderthal ancestral populations split approximately 370,000 years ago, before the emergence of anatomically modern humans. Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics. FAU - Noonan, James P AU - Noonan JP AD - U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA. FAU - Coop, Graham AU - Coop G FAU - Kudaravalli, Sridhar AU - Kudaravalli S FAU - Smith, Doug AU - Smith D FAU - Krause, Johannes AU - Krause J FAU - Alessi, Joe AU - Alessi J FAU - Chen, Feng AU - Chen F FAU - Platt, Darren AU - Platt D FAU - Pääbo, Svante AU - Pääbo S FAU - Pritchard, Jonathan K AU - Pritchard JK FAU - Rubin, Edward M AU - Rubin EM LA - eng SI - GENBANK/DX935178 SI - GENBANK/DX935179 SI - GENBANK/DX935180 SI - GENBANK/DX935181 SI - GENBANK/DX935182 SI - GENBANK/DX935183 SI - GENBANK/DX935184 SI - GENBANK/DX935185 SI - GENBANK/DX935186 SI - GENBANK/DX935187 SI - GENBANK/DX935188 SI - GENBANK/DX935189 SI - GENBANK/DX935190 SI - GENBANK/DX935191 SI - GENBANK/DX935192 SI - GENBANK/DX935193 SI - GENBANK/DX935194 SI - GENBANK/DX935195 SI - GENBANK/DX935196 SI - GENBANK/DX935197 SI - GENBANK/DX935198 SI - GENBANK/DX935199 SI - GENBANK/DX935200 SI - GENBANK/DX935201 SI - GENBANK/DX935202 SI - GENBANK/DX935203 SI - GENBANK/DX935204 SI - GENBANK/DX935205 SI - GENBANK/DX935206 SI - GENBANK/DX935207 SI - GENBANK/DX935208 SI - GENBANK/DX935209 SI - GENBANK/DX935210 SI - GENBANK/DX935211 SI - GENBANK/DX935212 SI - GENBANK/DX935213 SI - GENBANK/DX935214 SI - GENBANK/DX935215 SI - GENBANK/DX935216 SI - GENBANK/DX935217 SI - GENBANK/DX935218 SI - GENBANK/DX935219 SI - GENBANK/DX935220 SI - GENBANK/DX935221 SI - GENBANK/DX935222 SI - GENBANK/DX935223 SI - GENBANK/DX935224 SI - GENBANK/DX935225 SI - GENBANK/DX935226 SI - GENBANK/DX935227 SI - GENBANK/DX935228 SI - GENBANK/DX935229 SI - GENBANK/DX935230 SI - GENBANK/DX935231 SI - GENBANK/DX935232 SI - GENBANK/DX935233 SI - GENBANK/DX935234 SI - GENBANK/DX935235 SI - GENBANK/DX935236 SI - GENBANK/DX935237 SI - GENBANK/DX935238 SI - GENBANK/DX935239 SI - GENBANK/DX935240 SI - GENBANK/DX935241 SI - GENBANK/DX935242 SI - GENBANK/DX935243 SI - GENBANK/DX935244 SI - GENBANK/DX935245 SI - GENBANK/DX935246 SI - GENBANK/DX935247 SI - GENBANK/DX935248 SI - GENBANK/DX935249 SI - GENBANK/DX935250 SI - GENBANK/DX935251 SI - GENBANK/DX935252 SI - 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GENBANK/DX936173 SI - GENBANK/DX936174 SI - GENBANK/DX936175 SI - GENBANK/DX936176 SI - GENBANK/DX936177 GR - HL066681/HL/NHLBI NIH HHS/United States GR - F32 GM074367/GM/NIGMS NIH HHS/United States GR - R01 HG002772-1/HG/NHGRI NIH HHS/United States GR - R01 HG002772-01/HG/NHGRI NIH HHS/United States GR - 1-F32-GM074367/GM/NIGMS NIH HHS/United States GR - R01 HG002772/HG/NHGRI NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM CIN - Science. 2006 Nov 17;314(5802):1068-71. doi: 10.1126/science.314.5802.1068. PMID: 17110549 CIN - Science. 2007 Mar 23;315(5819):1664; author reply 1664. doi: 10.1126/science.315.5819.1664. PMID: 17379790 MH - Animals MH - *Biological Evolution MH - Bone and Bones MH - Cell Nucleus MH - DNA/*genetics/isolation & purification MH - DNA, Mitochondrial MH - *Fossils MH - Gene Pool MH - Genome MH - Genome, Human MH - Genomic Library MH - History, Ancient MH - Hominidae/*genetics MH - Humans MH - Male MH - Molecular Sequence Data MH - Pan troglodytes/genetics MH - Polymerase Chain Reaction MH - Sequence Alignment MH - *Sequence Analysis, DNA/methods MH - Time PMC - PMC2583069 MID - NIHMS72167 EDAT- 2006/11/18 09:00 MHDA- 2006/12/09 09:00 PMCR- 2008/11/14 CRDT- 2006/11/18 09:00 PHST- 2006/11/18 09:00 [pubmed] PHST- 2006/12/09 09:00 [medline] PHST- 2006/11/18 09:00 [entrez] PHST- 2008/11/14 00:00 [pmc-release] AID - 314/5802/1113 [pii] AID - 10.1126/science.1131412 [doi] PST - ppublish SO - Science. 2006 Nov 17;314(5802):1113-8. doi: 10.1126/science.1131412. PMID- 16950265 OWN - NLM STAT- MEDLINE DCOM- 20070823 LR - 20061009 IS - 0020-7519 (Print) IS - 0020-7519 (Linking) VI - 36 IP - 13 DP - 2006 Nov TI - SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in pre-Columbian human coprolites. PG - 1419-25 AB - Enterobius vermicularis, pinworm, is one of the most common helminths worldwide, infecting nearly a billion people at all socio-economic levels. In prehistoric populations the paleoparasitological findings show a pinworm homogeneous distribution among hunter-gatherers in North America, intensified with the advent of agriculture. This same increase also occurred in the transition from nomad hunter-gatherers to sedentary farmers in South America, although E. vermicularis infection encompasses only the ancient Andean peoples, with no record among the pre-Colombian populations in the South American lowlands. However, the outline of pinworm paleoepidemiology has been supported by microscopic finding of eggs recovered from coprolites. Since molecular techniques are precise and sensitive in detecting pathogen ancient DNA (aDNA), and also could provide insights into the parasite evolutionary history, in this work we have performed a molecular paleoparasitological study of E. vermicularis. aDNA was recovered and pinworm 5S rRNA spacer sequences were determined from pre-Columbian coprolites (4110 BC-AD 900) from four different North and South American archaeological sites. The sequence analysis confirmed E. vermicularis identity and revealed a similarity among ancient and modern sequences. Moreover, polymorphisms were identified at the relative positions 160, 173 and 180, in independent coprolite samples from Tulán, San Pedro de Atacama, Chile (1080-950 BC). We also verified the presence of peculiarities (Splicing leader (SL1) RNA sequence, spliced donor site, the Sm antigen biding site, and RNA secondary structure) which characterise the SL1 RNA gene. The analysis shows that the SL1 RNA gene of contemporary pinworms was present in pre-Columbian E. vermicularis by 6110 years ago. We were successful in detecting E. vermicularis aDNA even in coprolites without direct microscopic evidence of the eggs, improving the diagnosis of helminth infections in the past and further pinworm paleoepidemiological studies. FAU - Iñiguez, Alena Mayo AU - Iñiguez AM AD - Intituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Manguinhos 21045-900 Rio de Janeiro, RJ, Brazil. alena@ioc.fiocruz.br FAU - Reinhard, Karl AU - Reinhard K FAU - Carvalho Gonçalves, Marcelo Luiz AU - Carvalho Gonçalves ML FAU - Ferreira, Luiz Fernando AU - Ferreira LF FAU - Araújo, Adauto AU - Araújo A FAU - Paulo Vicente, Ana Carolina AU - Paulo Vicente AC LA - eng SI - GENBANK/AY234771 SI - GENBANK/AY234772 SI - GENBANK/AY234773 SI - GENBANK/AY234774 SI - GENBANK/AY234775 SI - GENBANK/AY234776 SI - GENBANK/AY234777 SI - GENBANK/AY234778 SI - GENBANK/AY234779 SI - GENBANK/AY234780 SI - GENBANK/AY234781 SI - GENBANK/AY234782 SI - GENBANK/AY234783 SI - GENBANK/AY234784 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060810 PL - England TA - Int J Parasitol JT - International journal for parasitology JID - 0314024 RN - 0 (DNA, Helminth) RN - 0 (RNA, Helminth) RN - 0 (RNA, Spliced Leader) SB - IM MH - Animals MH - Base Sequence MH - DNA, Helminth/genetics MH - Enterobiasis/*history/parasitology MH - Enterobius/classification/genetics/*isolation & purification MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - Paleopathology/*methods MH - Polymerase Chain Reaction/methods MH - RNA, Helminth/*genetics MH - RNA, Spliced Leader/*genetics MH - Sequence Analysis, DNA/methods EDAT- 2006/09/05 09:00 MHDA- 2007/08/24 09:00 CRDT- 2006/09/05 09:00 PHST- 2006/05/10 00:00 [received] PHST- 2006/07/14 00:00 [revised] PHST- 2006/07/17 00:00 [accepted] PHST- 2006/09/05 09:00 [pubmed] PHST- 2007/08/24 09:00 [medline] PHST- 2006/09/05 09:00 [entrez] AID - S0020-7519(06)00262-1 [pii] AID - 10.1016/j.ijpara.2006.07.005 [doi] PST - ppublish SO - Int J Parasitol. 2006 Nov;36(13):1419-25. doi: 10.1016/j.ijpara.2006.07.005. Epub 2006 Aug 10. PMID- 16596603 OWN - NLM STAT- MEDLINE DCOM- 20061122 LR - 20171116 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 131 IP - 3 DP - 2006 Nov TI - Brief communication: identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNA. PG - 428-31 AB - We present a method to distinguish authentic ancient DNA from contaminating DNA in a human bone. This is achieved by taking account of the spatial distribution of the various sequence families within the bone and the extent of degradation of the template DNAs, as revealed by the error content of the sequences. To demonstrate the veracity of the method, we handled two ancient human tibiae in order to contaminate them with modern DNA, and then subjected segments of the bones to various decontaminating treatments, including removal of the outer 1-2 mm, before extracting DNA, cloning, and obtaining a total of 107 mitochondrial DNA sequences. Sequences resulting from the deliberate contamination were located exclusively in the outer 1-2 mm of the bones, and only one of these 27 sequences contained an error that could be ascribed to DNA degradation. A second, much smaller set of relatively error-free sequences, which we ascribe to contamination during excavation or curation, was also located exclusively in the outer 1-2 mm. In contrast, a family of 72 sequences, displaying extensive degradation products but identifiable as haplogroup U5a1a, was distributed throughout one of the bones and represents the authentic ancient DNA content of this specimen. CI - (c) 2006 Wiley-Liss, Inc. FAU - Bouwman, Abigail S AU - Bouwman AS AD - Faculty of Life Sciences, University of Manchester, Manchester M60 1QD, United Kingdom. FAU - Chilvers, Elizabeth R AU - Chilvers ER FAU - Brown, Keri A AU - Brown KA FAU - Brown, Terence A AU - Brown TA LA - eng GR - Wellcome Trust/United Kingdom PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA Primers) RN - 9007-49-2 (DNA) SB - IM MH - Bone and Bones/*chemistry MH - DNA/*isolation & purification MH - DNA Primers MH - England MH - Fossils MH - Greece, Ancient MH - History, Ancient MH - Humans MH - Tibia/chemistry EDAT- 2006/04/06 09:00 MHDA- 2006/12/09 09:00 CRDT- 2006/04/06 09:00 PHST- 2006/04/06 09:00 [pubmed] PHST- 2006/12/09 09:00 [medline] PHST- 2006/04/06 09:00 [entrez] AID - 10.1002/ajpa.20411 [doi] PST - ppublish SO - Am J Phys Anthropol. 2006 Nov;131(3):428-31. doi: 10.1002/ajpa.20411. PMID- 16596591 OWN - NLM STAT- MEDLINE DCOM- 20061024 LR - 20061115 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 131 IP - 2 DP - 2006 Oct TI - Population origins in Mongolia: genetic structure analysis of ancient and modern DNA. PG - 272-81 AB - In the present study, nuclear (autosomal and Y-chromosome short tandem repeats) and mitochondrial (hypervariable region I) ancient DNA data previously obtained from a 2,300-year-old Xiongnu population of the Egyin Gol Valley (south of Lake Baikal in northern Mongolia) (Keyser-Tracqui et al. 2003 Am. J. Hum. Genet. 73:247-260) were compared with data from two contemporary Mongolian populations: one from the same location (Egyin Gol Valley plus a perimeter of less than 100 km around the valley), and one from the whole of Mongolia. The principal objective of this comparative analysis was to assess the likelihood that genetic continuity exists between ancient and present-day Mongolian populations. Since the ancient Xiongnu sample might have been composed of some of the ancestors of the present-day Yakuts, data from a present-day Yakut population, as well as published data from Turkish populations, were also included in the comparative analysis. The main result of our study was the genetic similarity observed among Mongolian samples from different periods and geographic areas. This result supports the hypothesis that the succession over time of different Turkic and Mongolian tribes in the current territory of Mongolia resulted in cultural rather than genetic exchanges. Furthermore, it appears that the Yakuts probably did not find their origin among the Xiongnu tribes, as we previously hypothesized. FAU - Keyser-Tracqui, Christine AU - Keyser-Tracqui C AD - Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, 67085 Strasbourg, France. ckeyser@mageos.com FAU - Crubézy, Eric AU - Crubézy E FAU - Pamzsav, Horolma AU - Pamzsav H FAU - Varga, Tibor AU - Varga T FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Comparative Study PT - Historical Article PT - Journal Article PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Chromosomes, Human, Y/chemistry MH - DNA, Mitochondrial/analysis/*history MH - Female MH - Genealogy and Heraldry MH - *Genetics, Population MH - History, 21st Century MH - History, Ancient MH - Humans MH - Male MH - Mongolia MH - Tandem Repeat Sequences EDAT- 2006/04/06 09:00 MHDA- 2006/10/25 09:00 CRDT- 2006/04/06 09:00 PHST- 2006/04/06 09:00 [pubmed] PHST- 2006/10/25 09:00 [medline] PHST- 2006/04/06 09:00 [entrez] AID - 10.1002/ajpa.20429 [doi] PST - ppublish SO - Am J Phys Anthropol. 2006 Oct;131(2):272-81. doi: 10.1002/ajpa.20429. PMID- 16917897 OWN - NLM STAT- MEDLINE DCOM- 20061221 LR - 20221207 IS - 1042-0533 (Print) IS - 1042-0533 (Linking) VI - 18 IP - 5 DP - 2006 Sep-Oct TI - Ancient mitochondrial DNA from Malaysian hair samples: some indications of Southeast Asian population movements. PG - 654-67 AB - The late Pleistocene and early Holocene population history of Southeast Asia is not well-known. Our study provides new data on mitochondrial DNA (mtDNA) lineages of the aboriginal inhabitants of the Malay Peninsula, and through an extensive comparison to the known mtDNA diversity in Southeast and East Asia, provides some new insights into the origins and historical geography of certain mtDNA lineages in the region. We extracted DNA from hair samples (dating back 100 years) preserved in the Duckworth Collection and belonging to two Peninsular Malaysian individuals identified as "Negrito." Ancient DNA was analyzed by sequencing hypervariable region I (HVS-I) of the mtDNA control region and the mtDNA region V length polymorphism. The results show that the maternal lineages of these individuals belong to a recently defined haplogroup B sub-branch called B4c2. A comparison of mitochondrial haplotypes and haplogroups with those of 10,349 East Asian individuals indicates their very restricted geographical distribution (southwestern China, Southeast Asia Peninsula, and Indonesia). Recalculation of the B4c2 age across all of East Asia ( approximately 13,000 years) and in different subregions/populations suggests its rapid diffusion in Southeast Asia between the end of the Last Glacial Maximum and the Neolithic expansion of the Holocene. FAU - Ricaut, François-X AU - Ricaut FX AD - Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge CB2 1QH, United Kingdom. fx.ricaut@infonie.fr FAU - Bellatti, M AU - Bellatti M FAU - Lahr, Marta Mirazon AU - Lahr MM LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Hum Biol JT - American journal of human biology : the official journal of the Human Biology Council JID - 8915029 RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - Asia, Southeastern MH - Asian People/*genetics/history MH - DNA, Mitochondrial/*genetics MH - *Genetic Variation MH - History, Ancient MH - Humans MH - *Phylogeny EDAT- 2006/08/19 09:00 MHDA- 2006/12/22 09:00 CRDT- 2006/08/19 09:00 PHST- 2006/08/19 09:00 [pubmed] PHST- 2006/12/22 09:00 [medline] PHST- 2006/08/19 09:00 [entrez] AID - 10.1002/ajhb.20535 [doi] PST - ppublish SO - Am J Hum Biol. 2006 Sep-Oct;18(5):654-67. doi: 10.1002/ajhb.20535. PMID- 16809622 OWN - NLM STAT- MEDLINE DCOM- 20061211 LR - 20060803 IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 23 IP - 9 DP - 2006 Sep TI - Tracking down human contamination in ancient human teeth. PG - 1801-7 AB - DNA contamination arising from the manipulation of ancient calcified tissue samples is a poorly understood, yet fundamental, problem that affects the reliability of ancient DNA (aDNA) studies. We have typed the mitochondrial DNA hypervariable region I of the only 6 people involved in the excavation, washing, and subsequent anthropological and genetic study of 23 Neolithic remains excavated from Granollers (Barcelona, Spain) and searched for their presence among the 572 clones generated during the aDNA analyses of teeth from these samples. Of the cloned sequences, 17.13% could be unambiguously identified as contaminants, with those derived from the people involved in the retrieval and washing of the remains present in higher frequencies than those of the anthropologist and genetic researchers. This finding confirms, for the first time, previous hypotheses that teeth samples are most susceptible to contamination at their initial excavation. More worrying, the cloned contaminant sequences exhibit substitutions that can be attributed to DNA damage after the contamination event, and we demonstrate that the level of such damage increases with time: contaminants that are >10 years old have approximately 5 times more damage than those that are recent. Furthermore, we demonstrate that in this data set, the damage rate of the old contaminant sequences is indistinguishable from that of the endogenous DNA sequences. As such, the commonly used argument that miscoding lesions observed among cloned aDNA sequences can be used to support data authenticity is misleading in scenarios where the presence of old contaminant sequences is possible. We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results are accurate. FAU - Sampietro, María Lourdes AU - Sampietro ML AD - Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain. FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Lao, Oscar AU - Lao O FAU - Caramelli, David AU - Caramelli D FAU - Lari, Martina AU - Lari M FAU - Bertranpetit, Jaume AU - Bertranpetit J FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060629 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*analysis MH - *Haplotypes MH - History, Ancient MH - Humans MH - Paleodontology/*standards MH - *Specimen Handling MH - Tooth/*chemistry/pathology EDAT- 2006/07/01 09:00 MHDA- 2006/12/12 09:00 CRDT- 2006/07/01 09:00 PHST- 2006/07/01 09:00 [pubmed] PHST- 2006/12/12 09:00 [medline] PHST- 2006/07/01 09:00 [entrez] AID - msl047 [pii] AID - 10.1093/molbev/msl047 [doi] PST - ppublish SO - Mol Biol Evol. 2006 Sep;23(9):1801-7. doi: 10.1093/molbev/msl047. Epub 2006 Jun 29. PMID- 16485299 OWN - NLM STAT- MEDLINE DCOM- 20061109 LR - 20061115 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 131 IP - 1 DP - 2006 Sep TI - Mitochondrial DNA analysis of ancient Peruvian highlanders. PG - 98-107 AB - Ancient DNA recovered from 57 individuals excavated by Hiram Bingham at the rural communities of Paucarcancha, Patallacta, and Huata near the famed Inca royal estate and ritual site of Machu Picchu was analyzed by polymerase chain reaction, and the results were compared with ancient and modern DNA from various Central Andean areas to test their hypothesized indigenous highland origins. The control and coding regions of the mitochondrial DNA (mtDNA) of 35 individuals in this group were sequenced, and the haplogroups of each individual were determined. The frequency data for the haplogroups of these samples show clear proximity to those of modern Quechua and Aymara populations in the Peruvian and Bolivian highlands, and contrast with those of pre-Hispanic individuals of the north coast of Peru that we defined previously. Our study suggests a strong genetic affinity between sampled late pre-Hispanic individuals and modern Andean highlanders. A previous analysis of the Machu Picchu osteological collection suggests that the residents there were a mixed group of natives from various coastal and highland regions relocated by the Inca state for varied purposes. Overall, our study indicates that the sampled individuals from Paucarcancha and Patallacta were indigenous highlanders who provided supportive roles for nearby Machu Picchu. CI - 2006 Wiley-Liss, Inc. FAU - Shinoda, Ken-ichi AU - Shinoda K AD - Department of Anthropology, National Science Museum, Tokyo 169-0073, Japan. shinoda@kahaku.go.jp FAU - Adachi, Noboru AU - Adachi N FAU - Guillen, Sonia AU - Guillen S FAU - Shimada, Izumi AU - Shimada I LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*chemistry/classification MH - *Fossils MH - Haplotypes MH - Humans MH - Peru MH - Phylogeny MH - Polymerase Chain Reaction MH - Polymorphism, Genetic MH - Sequence Analysis, DNA EDAT- 2006/02/18 09:00 MHDA- 2006/11/11 09:00 CRDT- 2006/02/18 09:00 PHST- 2006/02/18 09:00 [pubmed] PHST- 2006/11/11 09:00 [medline] PHST- 2006/02/18 09:00 [entrez] AID - 10.1002/ajpa.20408 [doi] PST - ppublish SO - Am J Phys Anthropol. 2006 Sep;131(1):98-107. doi: 10.1002/ajpa.20408. PMID- 17278619 OWN - NLM STAT- MEDLINE DCOM- 20070315 LR - 20221207 IS - 0018-7143 (Print) IS - 0018-7143 (Linking) VI - 78 IP - 4 DP - 2006 Aug TI - Reanalysis of Eurasian population history: ancient DNA evidence of population affinities. PG - 413-40 AB - Mitochondrial hypervariable region I genetic data from ancient populations at two sites in Asia-Linzi in Shandong (northern China) and Egyin Gol in Mongolia-were reanalyzed to detect population affinities. Data from 51 modern populations were used to generate distance measures (Fst's) to the two ancient populations. The tests first analyzed relationships at the regional level and then compiled the top regional matches for an overall comparison to the two probe populations. The reanalysis showed that the Egyin Gol and Linzi populations have clear distinctions in genetic affinity. The Egyin Gol population as a whole appears to bear close affinities with modern populations of northern East Asia. The Linzi population seems to have some genetic affinities with the West, as suggested by the original analysis, although the original attribution of "European-like" seems to be misleading. We suggest that the Linzi individuals are potentially related to early Iranians, who are thought to have been widespread in parts of Central Eurasia and the steppe regions in the first millennium B.C., although some significant admixture between a number of populations of varying origin cannot be ruled out. We also examine the effect of sequence length on this type of genetic data analysis and discuss the results of previous studies on the Linzi sample. FAU - Bennett, Casey C AU - Bennett CC AD - Department of Anthropology, Indiana University, Bloomington, IN, USA. FAU - Kaestle, Frederika A AU - Kaestle FA LA - eng PT - Comparative Study PT - Journal Article PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/*genetics MH - China MH - DNA, Mitochondrial/*analysis MH - *Genetics, Population MH - Humans MH - Mongolia EDAT- 2007/02/07 09:00 MHDA- 2007/03/16 09:00 CRDT- 2007/02/07 09:00 PHST- 2007/02/07 09:00 [pubmed] PHST- 2007/03/16 09:00 [medline] PHST- 2007/02/07 09:00 [entrez] AID - 10.1353/hub.2006.0052 [doi] PST - ppublish SO - Hum Biol. 2006 Aug;78(4):413-40. doi: 10.1353/hub.2006.0052. PMID- 16425179 OWN - NLM STAT- MEDLINE DCOM- 20071213 LR - 20221207 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 130 IP - 3 DP - 2006 Jul TI - Insights into the "isolation" of the Basques: mtDNA lineages from the historical site of Aldaieta (6th-7th centuries AD). PG - 394-404 AB - We analyzed the hypervariable region I (HVR-I) sequence variability of the mitochondrial DNA (mtDNA) of individuals buried at Aldaieta (6th-7th centuries AD) in order to find out more about the biosocial implications of this cemetery. The results, fully authenticated by means of diverse criteria (analysis of duplicates, replication in an independent laboratory, quantification of target DNA, and sequencing and cloning of polymerase chain reaction products), suggest that Aldaieta largely consists of autochthonous individuals who shared common funereal customs with the late Ancient North Pyrenean cemeteries of Western Europe (the Reihengräberfelder), a cultural influence possibly accompanied by a certain genetic flow. Furthermore, the distribution of mtDNA lineages in the cemetery highlighted the existence of a significant number of family relationships, supporting the belief that it was a stable settlement and not a group that had haphazardly settled in the area. Finally, this paper stresses the importance of ancient DNA data for reconstructing the biological history of human populations, rendering it possible to verify certain hypotheses based solely on current population data. The presence at Aldaieta of an mtDNA lineage originating in Northwest Africa testifies to the existence of contact between the Iberian Peninsula and Northwest Africa prior to the Moorish occupation. Both this latter discovery and the high frequency of haplogroup J at the Aldaieta cemetery raise questions about the generally accepted belief that, since ancient times, the influence of other human groups has been very scarce in the Basque Country. FAU - Alzualde, Ainhoa AU - Alzualde A AD - Genetika, Antropologia Fisikoa, eta Animali Fisiologia Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea, 48080 Bilbo, Spain. FAU - Izagirre, Neskuts AU - Izagirre N FAU - Alonso, Santos AU - Alonso S FAU - Alonso, Antonio AU - Alonso A FAU - Albarrán, Cristina AU - Albarrán C FAU - Azkarate, Agustin AU - Azkarate A FAU - de la Rúa, Concepción AU - de la Rúa C LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Complementarity Determining Regions) RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - Complementarity Determining Regions/chemistry MH - DNA, Mitochondrial/*chemistry MH - *Genetic Variation MH - Genetics, Population MH - Haplotypes/*genetics MH - History, Medieval MH - Humans MH - Molecular Sequence Data MH - Polymerase Chain Reaction MH - Polymorphism, Genetic MH - Spain MH - Tooth/chemistry MH - White People/genetics/*history EDAT- 2006/01/21 09:00 MHDA- 2007/12/14 09:00 CRDT- 2006/01/21 09:00 PHST- 2006/01/21 09:00 [pubmed] PHST- 2007/12/14 09:00 [medline] PHST- 2006/01/21 09:00 [entrez] AID - 10.1002/ajpa.20375 [doi] PST - ppublish SO - Am J Phys Anthropol. 2006 Jul;130(3):394-404. doi: 10.1002/ajpa.20375. PMID- 16809513 OWN - NLM STAT- MEDLINE DCOM- 20060714 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 312 IP - 5782 DP - 2006 Jun 30 TI - Comment on "Ancient DNA from the first European farmers in 7500-year-old Neolithic sites". PG - 1875; author reply 1875 AB - On the basis of analysis of ancient DNA from early European farmers, Haak et al. (Reports, 11 November 2005, p. 1016) argued for the Paleolithic ancestry of modern Europeans. We stress that the study is more limited in scope than the authors claim, in part because not all of the skeletal samples date to the time of the Neolithic transition in a given area of Europe. FAU - Ammerman, Albert J AU - Ammerman AJ AD - Department of Classics, Colgate University, Hamilton, New York, USA. Aammerman@mail.colgate.edu FAU - Pinhasi, Ron AU - Pinhasi R FAU - Bánffy, Eszter AU - Bánffy E LA - eng PT - Comment PT - Historical Article PT - Journal Article PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM CON - Science. 2005 Nov 11;310(5750):1016-8. doi: 10.1126/science.1118725. PMID: 16284177 MH - Agriculture/*history MH - Culture MH - DNA, Mitochondrial/*genetics/history MH - Europe MH - Female MH - History, Ancient MH - Humans MH - Male MH - Sample Size MH - White People/*genetics/history EDAT- 2006/07/01 09:00 MHDA- 2006/07/15 09:00 CRDT- 2006/07/01 09:00 PHST- 2006/07/01 09:00 [pubmed] PHST- 2006/07/15 09:00 [medline] PHST- 2006/07/01 09:00 [entrez] AID - 312/5782/1875a [pii] AID - 10.1126/science.1123984 [doi] PST - ppublish SO - Science. 2006 Jun 30;312(5782):1875; author reply 1875. doi: 10.1126/science.1123984. PMID- 16856347 OWN - NLM STAT- MEDLINE DCOM- 20100406 LR - 20101118 IS - 1004-5619 (Print) IS - 1004-5619 (Linking) VI - 22 IP - 3 DP - 2006 Jun TI - [Homologous amelogenin gene test of archaeological samples]. PG - 213-6 AB - OBJECTIVE: Based on the sequence differences of Amelogenin homologous gene in the X and Y chromosomes, a pair of specific primers was designed to identify the sex of archaeological samples. METHODS: Ancient DNA fragments were extracted from the bones and teeth of sacrificial slaves with an improved method that combines phenol-chloroform extraction, silicon dioxide adsorption with ultrafiltration concentration. The polyacrylamide gel electrophoresis (PAGE) was used to detect PCR products. RESULTS: Seven in sixteen samples from eight graves showed positive results and the targeted segments were visible: a male with two bands of 106bp (Amel-X) and 112 bp (Amel-Y), while a female with only one band of 106 bp (Amel-X). Ancient DNA analyzing results from tooth samples are more marked than that from bones. CONCLUSION: The improved extraction method is more effective for ancient DNA extraction, which reduced the PCR inhibitors and lowered experimental costs. The sex determination technology based on Amelogenin homologous gene is an important and feasible method in the molecular archaeological research. FAU - Zhang, Hu-Qin AU - Zhang HQ AD - The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China. huqzhang@mail.xjtu.edu.cn FAU - Yang, Zhou-Qi AU - Yang ZQ FAU - Liu, Fang-E AU - Liu FE FAU - Zhang, Jin AU - Zhang J FAU - Zhao, Wen-Ming AU - Zhao WM LA - chi PT - English Abstract PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - China TA - Fa Yi Xue Za Zhi JT - Fa yi xue za zhi JID - 9426151 RN - 0 (Amelogenin) RN - 0 (DNA Primers) RN - 0 (Dental Enamel Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Alleles MH - Amelogenin/*genetics MH - Archaeology MH - Bone and Bones/*chemistry/metabolism MH - Chromosomes, Human, X MH - Chromosomes, Human, Y MH - DNA/*analysis/genetics/isolation & purification MH - DNA Primers MH - Dental Enamel Proteins/*genetics MH - Female MH - Gene Amplification MH - Humans MH - Male MH - Molecular Sequence Data MH - Polymerase Chain Reaction/methods MH - Sequence Analysis, DNA MH - Sex Determination Analysis/*methods MH - Tooth/*chemistry/metabolism EDAT- 2006/07/22 09:00 MHDA- 2010/04/07 06:00 CRDT- 2006/07/22 09:00 PHST- 2006/07/22 09:00 [pubmed] PHST- 2010/04/07 06:00 [medline] PHST- 2006/07/22 09:00 [entrez] PST - ppublish SO - Fa Yi Xue Za Zhi. 2006 Jun;22(3):213-6. PMID- 16702560 OWN - NLM STAT- MEDLINE DCOM- 20060705 LR - 20181113 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 103 IP - 21 DP - 2006 May 23 TI - Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans. PG - 8012-7 AB - The Etruscans, the only preclassical European population that has been genetically characterized so far, share only two haplotypes with their modern geographic counterparts, the Tuscans, who, nonetheless, appear to be their closest relatives. We modeled 10 demographic scenarios spanning the last 2,500 years and tested by serial coalescent simulation whether any are consistent with the patterns of genetic diversity observed within and between the Etruscan and the modern Tuscan populations. Models in which the Etruscans are the direct ancestors of modern Tuscans appear compatible with the observed data only when they also include a very high mutation rate and an ancient founder effect. A better fit was obtained when the ancient and the modern samples were extracted from two independently evolving populations, connected by little migration. Simulated and observed parameters were also similar for a scenario in which the ancient samples came from a subset, e.g., a social elite, genetically differentiated from the bulk of the Etruscan population. In principle, these results may be biased by factors such as gross and systematic errors in the ancient DNA sequences and failure to sample suitable modern individuals. If neither proves to be the case, this study strongly suggests that either the mitochondrial mutation rate is much higher than currently believed or the Etruscans left very few modern mitochondrial descendants. FAU - Belle, Elise M S AU - Belle EM AD - Dipartimento di Biologia, Università di Ferrara, Via Borsari, 46, 44100 Ferrara, Italy. FAU - Ramakrishnan, Uma AU - Ramakrishnan U FAU - Mountain, Joanna L AU - Mountain JL FAU - Barbujani, Guido AU - Barbujani G LA - eng GR - P01 GM028428/GM/NIGMS NIH HHS/United States GR - GM028428/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20060515 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM MH - Biological Evolution MH - DNA, Mitochondrial/genetics MH - *Evolution, Molecular MH - Founder Effect MH - Genetic Variation MH - Genetics, Population MH - Haplotypes MH - Humans MH - Italy MH - Likelihood Functions MH - Mutation MH - Phylogeny MH - Time Factors PMC - PMC1472421 COIS- Conflict of interest statement: No conflicts declared. EDAT- 2006/05/17 09:00 MHDA- 2006/07/06 09:00 PMCR- 2006/11/23 CRDT- 2006/05/17 09:00 PHST- 2006/05/17 09:00 [pubmed] PHST- 2006/07/06 09:00 [medline] PHST- 2006/05/17 09:00 [entrez] PHST- 2006/11/23 00:00 [pmc-release] AID - 0509718103 [pii] AID - 2261 [pii] AID - 10.1073/pnas.0509718103 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2006 May 23;103(21):8012-7. doi: 10.1073/pnas.0509718103. Epub 2006 May 15. PMID- 16342258 OWN - NLM STAT- MEDLINE DCOM- 20070508 LR - 20060320 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 129 IP - 4 DP - 2006 Apr TI - Molecular characterization of a pre-Columbian mummy and in situ coprolite. PG - 620-9 AB - The history of Homo sapiens dispersal around the world and inherent interpopulation contacts and conflicts has given rise to several transitions in his relationships with the natural world, with the final result of changes in the patterns of infectious disease (McMichael [2001] Ecosystem Health 7:107-115). Of particular interest, in this context, is the contact between Amerindians and Europeans that started at the end of the 15th century, and the resulting exchange of microbes. We successfully recovered ancient DNA from a pre-Columbian mummy from Cuzco (Peru), radiocarbon-dated to 980-1170 AD, for which consistent mtDNA amplifications and sequences were obtained. The analysis of mtDNA revealed that the mummy's haplogroup was characteristic of Native American populations. We also investigated a sample of feces directly isolated from the intestines of the mummy, using a polymerase chain reaction system designed to detect the broadest spectrum of bacterial DNAs. The analysis of results, following a criterion of "paleoecological consistency" (Rollo and Marota [1998] Philos. Trans. R. Soc. Lond. [Biol.] 354: 111-119), demonstrated that some vestiges of the original microbial flora of the feces were preserved. In particular, we were able to identify the DNA of Haemophylus parainfluenzae, thus suggesting that this recently recognized pathogen was present in precontact Native Americans. CI - Copyright 2006 Wiley-Liss, Inc. FAU - Luciani, Stefania AU - Luciani S AD - Laboratorio di Archeo-Antropologia Molecolare/DNA Antico, UNICAM, I-62032 Camerino, Italy. FAU - Fornaciari, Gino AU - Fornaciari G FAU - Rickards, Olga AU - Rickards O FAU - Labarga, Cristina Martínez AU - Labarga CM FAU - Rollo, Franco AU - Rollo F LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Bacterial) RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - DNA, Bacterial/*analysis/genetics/history MH - DNA, Mitochondrial/analysis/chemistry/history MH - Feces/*microbiology MH - Haemophilus Infections/*history/microbiology MH - Haemophilus parainfluenzae/*genetics/isolation & purification MH - Haplotypes MH - History, Medieval MH - Humans MH - Indians, South American/classification/*genetics/*history MH - Molecular Sequence Data MH - Mummies/*microbiology MH - Peru MH - Phylogeny MH - Polymerase Chain Reaction MH - Sequence Alignment MH - Sequence Analysis, DNA/methods EDAT- 2005/12/13 09:00 MHDA- 2007/05/09 09:00 CRDT- 2005/12/13 09:00 PHST- 2005/12/13 09:00 [pubmed] PHST- 2007/05/09 09:00 [medline] PHST- 2005/12/13 09:00 [entrez] AID - 10.1002/ajpa.20314 [doi] PST - ppublish SO - Am J Phys Anthropol. 2006 Apr;129(4):620-9. doi: 10.1002/ajpa.20314. PMID- 16608680 OWN - NLM STAT- MEDLINE DCOM- 20060511 LR - 20240315 IS - 0962-8452 (Print) IS - 1471-2954 (Electronic) IS - 0962-8452 (Linking) VI - 273 IP - 1587 DP - 2006 Mar 22 TI - Comment. Pathogenic microbial ancient DNA: a problem or an opportunity? PG - 641-2; discussion 643 FAU - Donoghue, Helen D AU - Donoghue HD AD - Department of Infection, University College London Centre for Infectious Diseases and International Health 46, Cleveland Street, London W1T 4JF, UK. h.donoghue@ucl.ac.uk FAU - Spigelman, Mark AU - Spigelman M LA - eng PT - Comment PT - Journal Article PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA, Bacterial) SB - IM CON - Proc Biol Sci. 2005 Jan 7;272(1558):3-16. doi: 10.1098/rspb.2004.2813. PMID: 15875564 MH - DNA, Bacterial/chemistry/*genetics MH - *Evolution, Molecular MH - Humans MH - *Paleontology MH - Sequence Analysis, DNA MH - Specimen Handling PMC - PMC1560079 EDAT- 2006/04/13 09:00 MHDA- 2006/05/12 09:00 PMCR- 2007/03/22 CRDT- 2006/04/13 09:00 PHST- 2006/04/13 09:00 [pubmed] PHST- 2006/05/12 09:00 [medline] PHST- 2006/04/13 09:00 [entrez] PHST- 2007/03/22 00:00 [pmc-release] AID - 7317042183142354 [pii] AID - rspb20053261 [pii] AID - 10.1098/rspb.2005.3261 [doi] PST - ppublish SO - Proc Biol Sci. 2006 Mar 22;273(1587):641-2; discussion 643. doi: 10.1098/rspb.2005.3261. PMID- 16649656 OWN - NLM STAT- MEDLINE DCOM- 20060606 LR - 20061115 IS - 0016-6758 (Print) IS - 0016-6758 (Linking) VI - 42 IP - 3 DP - 2006 Mar TI - [Ancient DNA]. PG - 293-309 AB - The review is devoted to molecular genetic studies of ancient DNA. The problems of DNA preservation and modification after cell death, as well as techniques of working with ancient DNA, including its retrieval, removal of inhibitors, PCR amplification, and phylogenetic analysis, are discussed in detail. The possibilities are considered of using ancient DNA in resolving issues of systematics and evolution of various animal taxa, population genetics of humans and rare species, taxonomic identification and paleontological reconstructions, geographic origin of populations, microbiological analysis of paleontological and archeological finds, as well as some humanitarian aspects of its use. FAU - Chelomina, G N AU - Chelomina GN LA - rus PT - English Abstract PT - Journal Article PT - Review PL - Russia (Federation) TA - Genetika JT - Genetika JID - 0047354 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/chemistry/*classification/*genetics MH - *Evolution, Molecular MH - *Fossils MH - Humans MH - *Phylogeny RF - 133 EDAT- 2006/05/03 09:00 MHDA- 2006/06/07 09:00 CRDT- 2006/05/03 09:00 PHST- 2006/05/03 09:00 [pubmed] PHST- 2006/06/07 09:00 [medline] PHST- 2006/05/03 09:00 [entrez] PST - ppublish SO - Genetika. 2006 Mar;42(3):293-309. PMID- 16623087 OWN - NLM STAT- MEDLINE DCOM- 20060523 LR - 20061115 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 64 IP - 1 DP - 2006 Mar TI - Sequence of deltaF508 CFTR allele identified at present is lacking in medieval specimens from Central Poland. Preliminary results. PG - 41-9 AB - deltaF508 is the most common (70%) among over 1000 mutations of the gene encoding ATP-regulated chloride channel, namely CFTR--cystic fibrosis transmembrane regulator. The time which passed from the calculated mutation event was anticipated on the basis of the frequency of contemporary haplotypes, but not on its direct identification. The presence of three base pairs deletion in the ancient DNA (aDNA) isolated from skeletal remains of the Middle Ages origin was investigated. Teeth excavated in the area of three sites located in Central Poland were processed for a DNA. 6 out of 82 samples did not produce amplificable fragments of DNA. Although the number of specimens analyzed was sufficient to confirm the presence of the rare mutation, the deltaF508 CFTR sequence was not found in the remains of individuals living back 35 - 45 generations. The absence of the mutated allele in the particular geographic region cannot state for the status of mutated allele throughout the country, especially at times when migrations were limited and movements of people were more area restricted than at present days. FAU - Witas, Henryk W AU - Witas HW AD - Department of Molecular Biology, Institute of Pediatrics, Medical University of Lódź, Lódź, Poland. witas@alef.am.lodz.pl FAU - Jatczak, Izabela AU - Jatczak I FAU - Jedrychowska-Dańska, Krystyna AU - Jedrychowska-Dańska K FAU - Zadzińska, Elzbieta AU - Zadzińska E FAU - Wrzesińska, Anna AU - Wrzesińska A FAU - Wrzesiński, Jacek AU - Wrzesiński J FAU - Nadolski, Jerzy AU - Nadolski J LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 126880-72-6 (Cystic Fibrosis Transmembrane Conductance Regulator) SB - IM MH - Adult MH - Child MH - Cystic Fibrosis/*epidemiology/*genetics/history MH - Cystic Fibrosis Transmembrane Conductance Regulator/*genetics MH - Female MH - Gene Frequency MH - Genetic Predisposition to Disease/*epidemiology/*genetics/history MH - History, Medieval MH - Humans MH - Incidence MH - Male MH - Pilot Projects MH - Poland/epidemiology MH - Sequence Analysis, DNA EDAT- 2006/04/21 09:00 MHDA- 2006/05/24 09:00 CRDT- 2006/04/21 09:00 PHST- 2006/04/21 09:00 [pubmed] PHST- 2006/05/24 09:00 [medline] PHST- 2006/04/21 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2006 Mar;64(1):41-9. PMID- 16323184 OWN - NLM STAT- MEDLINE DCOM- 20060922 LR - 20081121 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 129 IP - 3 DP - 2006 Mar TI - Population affinities of Neolithic Siberians: a snapshot from prehistoric Lake Baikal. PG - 349-61 AB - Archaeological evidence supports the inhabitation of the Lake Baikal region since the Paleolithic. Both metric and nonmetric osteological studies suggest that Neolithic Cis-Baikal populations are the ancestors of contemporary inhabitants of the region. To date, ancient DNA data have not been used to corroborate this biological continuity hypothesis. This study presents a temporal snapshot of the Cis-Baikal Neolithic by examining mtDNA diversity in two cemetery populations situated on the Angara River downstream of Lake Baikal. The 800 years separating the use of the two cemeteries is thought to represent a biocultural hiatus in the Cis-Baikal region, one that ended when a new group migrated into the area. To assess the likelihood that genetic continuity exists between these two Neolithic groups, we examined both mtDNA coding region and hypervariable region I (HVI) polymorphisms from skeletal remains excavated from both cemeteries (Lokomotiv and Ust'-Ida). The mtDNA haplogroup distributions of the two cemetery populations differ significantly, suggesting that they were biologically distinct groups. When the biological distance between these Neolithic groups is compared with modern Siberian and other East Eurasian groups, the posthiatus group (Serovo-Glazkovo) generally aligns with contemporary Siberians, while the prehiatus (Kitoi) individuals are significantly different from all but modern Kets and Shorians living in the Yenisey and Ob River basins to the west of Lake Baikal. These results suggest that the Lake Baikal region experienced a significant depopulation event during the sixth millennium BP, and was reoccupied by a new immigrant population some 800 years later. CI - (c) 2005 Wiley-Liss, Inc. FAU - Mooder, K P AU - Mooder KP AD - Human Identification Laboratory for Archaeology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada. km22@u.washington.edu FAU - Schurr, T G AU - Schurr TG FAU - Bamforth, F J AU - Bamforth FJ FAU - Bazaliiski, V I AU - Bazaliiski VI FAU - Savel'ev, N A AU - Savel'ev NA LA - eng PT - Comparative Study PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - DNA Primers MH - DNA, Mitochondrial/*genetics/*history MH - *Genetic Variation MH - *Genetics, Population MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Polymorphism, Single Nucleotide MH - *Population Dynamics MH - Principal Component Analysis MH - Siberia EDAT- 2005/12/03 09:00 MHDA- 2006/09/23 09:00 CRDT- 2005/12/03 09:00 PHST- 2005/12/03 09:00 [pubmed] PHST- 2006/09/23 09:00 [medline] PHST- 2005/12/03 09:00 [entrez] AID - 10.1002/ajpa.20247 [doi] PST - ppublish SO - Am J Phys Anthropol. 2006 Mar;129(3):349-61. doi: 10.1002/ajpa.20247. PMID- 16488882 OWN - NLM STAT- MEDLINE DCOM- 20060228 LR - 20201209 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 34 IP - 4 DP - 2006 TI - Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs. PG - 1102-11 AB - For many years, Taq polymerase has served as the stalwart enzyme in the PCR amplification of DNA. However, a major limitation of Taq is its inability to amplify damaged DNA, thereby restricting its usefulness in forensic applications. In contrast, Y-family DNA polymerases, such as Dpo4 from Sulfolobus solfataricus, can traverse a wide variety of DNA lesions. Here, we report the identification and characterization of five novel thermostable Dpo4-like enzymes from Acidianus infernus, Sulfolobus shibatae, Sulfolobus tengchongensis, Stygiolobus azoricus and Sulfurisphaera ohwakuensis, as well as two recombinant chimeras that have enhanced enzymatic properties compared with the naturally occurring polymerases. The Dpo4-like polymerases are moderately processive, can substitute for Taq in PCR and can bypass DNA lesions that normally block Taq. Such properties make the Dpo4-like enzymes ideally suited for the PCR amplification of damaged DNA samples. Indeed, by using a blend of Taq and Dpo4-like enzymes, we obtained a PCR amplicon from ultraviolet-irradiated DNA that was largely unamplifyable with Taq alone. The inclusion of thermostable Dpo4-like polymerases in PCRs, therefore, augments the recovery and analysis of lesion-containing DNA samples, such as those commonly found in forensic or ancient DNA molecular applications. FAU - McDonald, John P AU - McDonald JP AD - Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2725, USA. FAU - Hall, Ashley AU - Hall A FAU - Gasparutto, Didier AU - Gasparutto D FAU - Cadet, Jean AU - Cadet J FAU - Ballantyne, Jack AU - Ballantyne J FAU - Woodgate, Roger AU - Woodgate R LA - eng SI - GENBANK/DQ124669 SI - GENBANK/DQ124670 SI - GENBANK/DQ124671 SI - GENBANK/DQ124672 SI - GENBANK/DQ124673 SI - GENBANK/DQ124674 SI - GENBANK/DQ124675 GR - Intramural NIH HHS/United States PT - Evaluation Study PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20060218 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Archaeal Proteins) RN - 9007-49-2 (DNA) RN - EC 2.7.7.7 (DNA Polymerase beta) SB - IM MH - Archaea/*enzymology MH - Archaeal Proteins/classification/genetics/metabolism MH - Base Sequence MH - Cloning, Molecular MH - DNA/*biosynthesis MH - DNA Damage MH - DNA Fingerprinting MH - DNA Polymerase beta/classification/genetics/*metabolism MH - Enzyme Stability MH - Genes, Archaeal MH - Humans MH - K562 Cells MH - Molecular Sequence Data MH - Paleontology MH - Phylogeny MH - *Polymerase Chain Reaction MH - Sulfolobaceae/genetics MH - *Temperature MH - Templates, Genetic PMC - PMC1373694 EDAT- 2006/02/21 09:00 MHDA- 2006/03/01 09:00 PMCR- 2006/02/18 CRDT- 2006/02/21 09:00 PHST- 2006/02/21 09:00 [pubmed] PHST- 2006/03/01 09:00 [medline] PHST- 2006/02/21 09:00 [entrez] PHST- 2006/02/18 00:00 [pmc-release] AID - 34/4/1102 [pii] AID - 10.1093/nar/gkj512 [doi] PST - epublish SO - Nucleic Acids Res. 2006 Feb 18;34(4):1102-11. doi: 10.1093/nar/gkj512. Print 2006. PMID- 16452924 OWN - NLM STAT- MEDLINE DCOM- 20060420 LR - 20200930 IS - 1469-221X (Print) IS - 1469-3178 (Electronic) IS - 1469-221X (Linking) VI - 7 IP - 2 DP - 2006 Feb TI - Ancient DNA research goes nuclear. A new technique to extract sequence data from nuclear DNA may reveal exciting new insights into evolution and phylogeny. PG - 136-9 AB - A new technique to extract sequence data from nuclear DNA may reveal exciting new insights into evolution and phylogeny FAU - Hunter, Philip AU - Hunter P LA - eng PT - Comparative Study PT - Journal Article PL - England TA - EMBO Rep JT - EMBO reports JID - 100963049 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Sequence MH - Cell Nucleus/*chemistry MH - DNA/*analysis MH - *Evolution, Molecular MH - *Fossils MH - Humans MH - Molecular Sequence Data MH - *Phylogeny MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA PMC - PMC1369262 EDAT- 2006/02/03 09:00 MHDA- 2006/04/21 09:00 PMCR- 2007/02/01 CRDT- 2006/02/03 09:00 PHST- 2006/02/03 09:00 [pubmed] PHST- 2006/04/21 09:00 [medline] PHST- 2006/02/03 09:00 [entrez] PHST- 2007/02/01 00:00 [pmc-release] AID - 7400634 [pii] AID - 10.1038/sj.embor.7400634 [doi] PST - ppublish SO - EMBO Rep. 2006 Feb;7(2):136-9. doi: 10.1038/sj.embor.7400634. PMID- 15913935 OWN - NLM STAT- MEDLINE DCOM- 20060323 LR - 20070813 IS - 0379-0738 (Print) IS - 0379-0738 (Linking) VI - 156 IP - 2-3 DP - 2006 Jan 27 TI - Resistance of degraded hair shafts to contaminant DNA. PG - 208-12 AB - We have investigated the susceptibility of degraded human hair shaft samples to contamination by exogenous sources of DNA, including blood, saliva, skin cells, and purified DNA. The results indicate that on the whole hair shafts are either largely resistant to penetration by contaminant DNA, or extremely easy to successfully decontaminate. This pertains to samples that are both morphologically and biochemically degraded. We suggest that this resistance to the incorporation of contaminant DNA relates to the hydrophobic and impermeable nature of the keratin structures forming the hair shaft. Therefore, hair samples represent an important and underestimated source of DNA in both forensic and ancient DNA studies. FAU - Gilbert, M Thomas P AU - Gilbert MT AD - Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3PS, UK. mtpgilbert@spymac.com FAU - Menez, Laura AU - Menez L FAU - Janaway, Robert C AU - Janaway RC FAU - Tobin, Desmond J AU - Tobin DJ FAU - Cooper, Alan AU - Cooper A FAU - Wilson, Andrew S AU - Wilson AS LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050426 PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (DNA Primers) RN - 9007-49-2 (DNA) SB - IM MH - Blood MH - Cloning, Molecular MH - DNA/*analysis MH - DNA Fingerprinting MH - DNA Primers MH - Hair/*chemistry MH - Humans MH - Saliva EDAT- 2005/05/26 09:00 MHDA- 2006/03/24 09:00 CRDT- 2005/05/26 09:00 PHST- 2004/09/24 00:00 [received] PHST- 2005/02/15 00:00 [revised] PHST- 2005/02/17 00:00 [accepted] PHST- 2005/05/26 09:00 [pubmed] PHST- 2006/03/24 09:00 [medline] PHST- 2005/05/26 09:00 [entrez] AID - S0379-0738(05)00136-2 [pii] AID - 10.1016/j.forsciint.2005.02.021 [doi] PST - ppublish SO - Forensic Sci Int. 2006 Jan 27;156(2-3):208-12. doi: 10.1016/j.forsciint.2005.02.021. Epub 2005 Apr 26. PMID- 18175619 OWN - NLM STAT- MEDLINE DCOM- 20080207 LR - 20170330 IS - 0394-9001 (Print) IS - 0394-9001 (Linking) VI - 18 IP - 3 DP - 2006 TI - Studies on the preservation of the intestinal microbiota's DNA in human mummies from cold environments. PG - 725-40 AB - Analysis of ancient microorganism DNA represents one of the newest and most promising branches of molecular archaeology. In particular, microbial DNA associated with human remains can provide direct evidence of the occurrence and frequency of infectious diseases in historic times. Human mummies represent very interesting subjects for palaeomicrobiological investigations as they retain soft tissues. Recently reports on the identification of ancient bacterial pathogens in human mummies by DNA analysis are steadily becoming more numerous. However, despite this favourable trend, the analysis of ancient microbial DNA is still a contentious issue. As a model system, we studied the preservation of the intestinal microbiota's DNA in two naturally freeze-dried human mummies found on the Alps. This kind of mummy is an ideal subject for ancient DNA investigations. The first is a male body historically dated 1918 A.D. while the second is the famous Tyrolean Iceman (3.350-3.100 BC). FAU - Rollo, Franco AU - Rollo F AD - Laboratorio di Archeo-Antropologia molecolare/DNA antico, c/o Dipartimento di Biologia MCA, UNICAM, 62032 Camerino, Italy. francougo.rollo@unicam.it FAU - Ermini, Luca AU - Ermini L FAU - Luciani, Stefania AU - Luciani S FAU - Marota, Isolina AU - Marota I FAU - Olivieri, Cristina AU - Olivieri C LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Italy TA - Med Secoli JT - Medicina nei secoli JID - 0176472 RN - 0 (DNA, Bacterial) MH - Cold Climate MH - DNA, Bacterial/analysis/*history MH - History, Ancient MH - Humans MH - Intestines/*microbiology MH - Male MH - Molecular Biology/*methods MH - Mummies/*history MH - Paleopathology/methods EDAT- 2008/01/08 09:00 MHDA- 2008/02/08 09:00 CRDT- 2008/01/08 09:00 PHST- 2008/01/08 09:00 [pubmed] PHST- 2008/02/08 09:00 [medline] PHST- 2008/01/08 09:00 [entrez] PST - ppublish SO - Med Secoli. 2006;18(3):725-40. PMID- 18175618 OWN - NLM STAT- MEDLINE DCOM- 20080207 LR - 20170330 IS - 0394-9001 (Print) IS - 0394-9001 (Linking) VI - 18 IP - 3 DP - 2006 TI - Authenticity in ancient DNA studies. PG - 701-23 AB - Ancient DNA studies represent a powerful tool that can be used to obtain genetic insights into the past. However, despite the publication of large numbers of apparently successful ancient DNA studies, a number of problems exist with the field that are often ignored. Therefore, questions exist as to how reliable the conclusions of many of the published studies are. In this paper we outline first the problems associated with aDNA studies, and secondly present potential guidelines designed so as to enable non-specialist readers the opportunity to critically assess the quality of aDNA publications. FAU - Gilbert, M Thomas P AU - Gilbert MT AD - Center for Ancient Genetics, Niels Bohr and Biological Institutes, University of Copenhagen. mtpg@gmail.com FAU - Willerslev, Eske AU - Willerslev E LA - eng PT - Historical Article PT - Journal Article PL - Italy TA - Med Secoli JT - Medicina nei secoli JID - 0176472 RN - 9007-49-2 (DNA) MH - DNA/*analysis/classification/history MH - *Fossils MH - History, Ancient MH - Humans MH - Reproducibility of Results MH - Specimen Handling/history/methods EDAT- 2008/01/08 09:00 MHDA- 2008/02/08 09:00 CRDT- 2008/01/08 09:00 PHST- 2008/01/08 09:00 [pubmed] PHST- 2008/02/08 09:00 [medline] PHST- 2008/01/08 09:00 [entrez] PST - ppublish SO - Med Secoli. 2006;18(3):701-23. PMID- 16284177 OWN - NLM STAT- MEDLINE DCOM- 20051206 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 310 IP - 5750 DP - 2005 Nov 11 TI - Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. PG - 1016-8 AB - The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans. FAU - Haak, Wolfgang AU - Haak W AD - Institut für Anthropologie, Johannes Gutenberg Universität Mainz, Saarstrasse 21, D-55099 Mainz, Germany. haakw@uni-mainz.de FAU - Forster, Peter AU - Forster P FAU - Bramanti, Barbara AU - Bramanti B FAU - Matsumura, Shuichi AU - Matsumura S FAU - Brandt, Guido AU - Brandt G FAU - Tänzer, Marc AU - Tänzer M FAU - Villems, Richard AU - Villems R FAU - Renfrew, Colin AU - Renfrew C FAU - Gronenborn, Detlef AU - Gronenborn D FAU - Alt, Kurt Werner AU - Alt KW FAU - Burger, Joachim AU - Burger J LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM CIN - Science. 2005 Nov 11;310(5750):964-5. doi: 10.1126/science.310.5750.964. PMID: 16284157 CIN - Science. 2006 Jun 30;312(5782):1875; author reply 1875. doi: 10.1126/science.1123984. PMID: 16809513 MH - Agriculture/*history MH - Austria MH - Base Sequence MH - Computer Simulation MH - Cultural Evolution MH - DNA, Mitochondrial/chemistry/classification/*genetics/history MH - Emigration and Immigration MH - Europe MH - Female MH - Gene Frequency MH - Genetic Drift MH - Genetics, Population MH - Germany MH - Haplotypes MH - History, Ancient MH - Humans MH - Hungary MH - Male MH - Molecular Sequence Data MH - Population Dynamics MH - White People/*genetics/history EDAT- 2005/11/15 09:00 MHDA- 2005/12/13 09:00 CRDT- 2005/11/15 09:00 PHST- 2005/11/15 09:00 [pubmed] PHST- 2005/12/13 09:00 [medline] PHST- 2005/11/15 09:00 [entrez] AID - 310/5750/1016 [pii] AID - 10.1126/science.1118725 [doi] PST - ppublish SO - Science. 2005 Nov 11;310(5750):1016-8. doi: 10.1126/science.1118725. PMID- 16284157 OWN - NLM STAT- MEDLINE DCOM- 20051206 LR - 20221207 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 310 IP - 5750 DP - 2005 Nov 11 TI - Evolution. Ancient DNA yields clues to the puzzle of European origins. PG - 964-5 FAU - Balter, Michael AU - Balter M LA - eng PT - Comment PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM CON - Science. 2005 Nov 11;310(5750):1016-8. doi: 10.1126/science.1118725. PMID: 16284177 MH - Agriculture/*history MH - Chromosomes, Human, Y/genetics MH - Cultural Evolution MH - DNA, Mitochondrial/*analysis/genetics/history MH - Emigration and Immigration MH - Europe MH - Female MH - Genetics, Population MH - Haplotypes MH - History, Ancient MH - Humans MH - Male MH - Population Dynamics MH - White People/*genetics/history EDAT- 2005/11/15 09:00 MHDA- 2005/12/13 09:00 CRDT- 2005/11/15 09:00 PHST- 2005/11/15 09:00 [pubmed] PHST- 2005/12/13 09:00 [medline] PHST- 2005/11/15 09:00 [entrez] AID - 310/5750/964 [pii] AID - 10.1126/science.310.5750.964 [doi] PST - ppublish SO - Science. 2005 Nov 11;310(5750):964-5. doi: 10.1126/science.310.5750.964. PMID- 16182949 OWN - NLM STAT- MEDLINE DCOM- 20051110 LR - 20131121 IS - 0379-0738 (Print) IS - 0379-0738 (Linking) VI - 154 IP - 1 DP - 2005 Nov 10 TI - Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. PG - 53-61 AB - The extraction of DNA from archaeological or forensic skeletal remains can provide quite powerful data for analysis, but is plagued by a unique set of methodological problems. One of the most important methodological problems to overcome in such analyses is the presence of modern contamination on the surfaces of bones and teeth, which can lead to false positives and erroneous results unless it is removed before DNA extraction is initiated. Ancient DNA (aDNA) researchers and forensic scientists have employed a number of techniques to minimize such contamination. One such technique is the use of bleach (sodium hypochlorite--NaOCl) to "destroy" contaminating DNA. However, a consensus on the optimum concentration of sodium hypochlorite to be used and the amount of time the bone or tooth should be exposed to it has not emerged. The present study systematically approaches the issue by introducing contamination to ancient bones (from approximately 500 BP) and determining which of several sodium hypochlorite treatments best eliminates surface contamination. The elimination of surface contamination from bone requires immersion in at least 3.0% (w/v) sodium hypochlorite (approximately equal parts of commercial bleach and water) for at least 15 min. Endogenous DNA proved to be quite stable to even extreme sodium hypochlorite treatments (6% for 21 h), suggesting that DNA adsorbs to hydroxyapatite in the bone and that this process facilitates the preservation of DNA in ancient skeletal remains. FAU - Kemp, Brian M AU - Kemp BM AD - Department of Anthropology, University of California, Davis, CA 95616, USA. bmkemp@ucdavis.edu FAU - Smith, David Glenn AU - Smith DG LA - eng GR - RR00169/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (Disinfectants) RN - 9007-49-2 (DNA) RN - DY38VHM5OD (Sodium Hypochlorite) SB - IM MH - DNA/chemistry/*isolation & purification MH - Disinfectants/*administration & dosage MH - Forensic Anthropology/*methods MH - Fossils MH - Humans MH - Immersion MH - Polymerase Chain Reaction MH - Ribs/*chemistry MH - Sodium Hypochlorite/*administration & dosage MH - Time Factors MH - Tooth/chemistry EDAT- 2005/09/27 09:00 MHDA- 2005/11/11 09:00 CRDT- 2005/09/27 09:00 PHST- 2004/09/27 00:00 [received] PHST- 2004/11/24 00:00 [revised] PHST- 2004/11/26 00:00 [accepted] PHST- 2005/09/27 09:00 [pubmed] PHST- 2005/11/11 09:00 [medline] PHST- 2005/09/27 09:00 [entrez] AID - S0379-0738(04)00822-9 [pii] AID - 10.1016/j.forsciint.2004.11.017 [doi] PST - ppublish SO - Forensic Sci Int. 2005 Nov 10;154(1):53-61. doi: 10.1016/j.forsciint.2004.11.017. PMID- 16318358 OWN - NLM STAT- MEDLINE DCOM- 20060127 LR - 20051201 IS - 0039-9450 (Print) IS - 0039-9450 (Linking) VI - 50 IP - 14 Suppl DP - 2005 Nov TI - [PCR as a double-edged sword: ancient DNA and forensic science]. PG - 1912-6 FAU - Yonekawa, Hiromichi AU - Yonekawa H AD - yonekawa@rinshoken.or.jp LA - jpn PT - Journal Article PT - Review PL - Japan TA - Tanpakushitsu Kakusan Koso JT - Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme JID - 0413762 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*genetics MH - DNA, Mitochondrial/genetics MH - Evolution, Molecular MH - *Forensic Sciences MH - Humans MH - Paleontology MH - *Polymerase Chain Reaction RF - 26 EDAT- 2005/12/02 09:00 MHDA- 2006/01/28 09:00 CRDT- 2005/12/02 09:00 PHST- 2005/12/02 09:00 [pubmed] PHST- 2006/01/28 09:00 [medline] PHST- 2005/12/02 09:00 [entrez] PST - ppublish SO - Tanpakushitsu Kakusan Koso. 2005 Nov;50(14 Suppl):1912-6. PMID- 16596944 OWN - NLM STAT- MEDLINE DCOM- 20060526 LR - 20221207 IS - 0018-7143 (Print) IS - 0018-7143 (Linking) VI - 77 IP - 5 DP - 2005 Oct TI - Mitochondrial DNA of ancient Cumanians: culturally Asian steppe nomadic immigrants with substantially more western Eurasian mitochondrial DNA lineages. PG - 639-62 AB - The Cumanians were originally Asian pastoral nomads who in the 13th century migrated to Hungary. We have examined mitochondrial DNA from members of the earliest Cumanian population in Hungary from two archeologically well-documented excavations and from 74 modern Hungarians from different rural locations in Hungary. Haplogroups were defined based on HVS I sequences and examinations of haplogroup-associated polymorphic sites of the protein coding region and of HVS II. To exclude contamination, some ancient DNA samples were cloned. A database was created from previously published mtDNA HVS I sequences (representing 2,615 individuals from different Asian and European populations) and 74 modem Hungarian sequences from the present study. This database was used to determine the relationships between the ancient Cumanians, modern Hungarians, and Eurasian populations and to estimate the genetic distances between these populations. We attempted to deduce the genetic trace of the migration of Cumanians. This study is the first ancient DNA characterization of an eastern pastoral nomad population that migrated into Europe. The results indicate that, while still possessing a Central Asian steppe culture, the Cumanians received a large admixture of maternal genes from more westerly populations before arriving in Hungary. A similar dilution of genetic, but not cultural, factors may have accompanied the settlement of other Asian nomads in Europe. FAU - Bogácsi-Szabó, Erika AU - Bogácsi-Szabó E AD - Institute of Genetics, Biological Research Center of Hungarian Academy of Sciences, PO Box 521, H-6701 Szeged, Hungary. FAU - Kalmár, Tibor AU - Kalmár T FAU - Csányi, Bernadett AU - Csányi B FAU - Tömöry, Gyöngyvér AU - Tömöry G FAU - Czibula, Agnes AU - Czibula A FAU - Priskin, Katalin AU - Priskin K FAU - Horváth, Ferenc AU - Horváth F FAU - Downes, Christopher Stephen AU - Downes CS FAU - Raskó, István AU - Raskó I LA - eng SI - GENBANK/AY268482 SI - GENBANK/AY268483 SI - GENBANK/AY268484 SI - GENBANK/AY268485 SI - GENBANK/AY268486 SI - GENBANK/AY268487 SI - GENBANK/AY268488 SI - GENBANK/AY268489 SI - GENBANK/AY268490 SI - GENBANK/AY268491 SI - GENBANK/AY268492 PT - Comparative Study PT - Journal Article PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (Complementarity Determining Regions) RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People/*genetics MH - Complementarity Determining Regions/genetics MH - DNA, Mitochondrial/*genetics MH - Electrophoresis, Polyacrylamide Gel MH - Forensic Anthropology MH - *Genetic Variation MH - Genetics, Population/*methods MH - Geography MH - Haplotypes/genetics MH - Humans MH - Hungary MH - Molecular Sequence Data MH - *Population Dynamics MH - *Transients and Migrants MH - White People/*genetics EDAT- 2006/04/07 09:00 MHDA- 2006/05/27 09:00 CRDT- 2006/04/07 09:00 PHST- 2006/04/07 09:00 [pubmed] PHST- 2006/05/27 09:00 [medline] PHST- 2006/04/07 09:00 [entrez] PST - ppublish SO - Hum Biol. 2005 Oct;77(5):639-62. PMID- 16077732 OWN - NLM STAT- MEDLINE DCOM- 20051108 LR - 20050926 IS - 1018-4813 (Print) IS - 1018-4813 (Linking) VI - 13 IP - 10 DP - 2005 Oct TI - Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity. PG - 1106-12 AB - Research into ancient mitochondrial DNA is plagued by contamination, post mortem damage, and other artefacts. The stringent set of controls suggested by Cooper and Poinar a few years ago are, however, rarely followed in practice, and even when applied carefully, these criteria need not be sufficient to guarantee authenticity. The fairly relaxed prerequisites now common for ancient population studies have opened the door for all kinds of contamination and sequencing errors to enter ancient mtDNA data. To reject or question authenticity of particular sequencing results a posteriori, one can follow similar strategies of focused database comparisons that have proven to be effective and successful in the case of flawed modern mtDNA data. FAU - Bandelt, Hans-Jürgen AU - Bandelt HJ AD - Fachbereich Mathematik, Universität Hamburg, Hamburg, Germany. bandelt@math.uni-hamburg.de LA - eng PT - Historical Article PT - Journal Article PL - England TA - Eur J Hum Genet JT - European journal of human genetics : EJHG JID - 9302235 RN - 0 (DNA, Mitochondrial) SB - IM MH - Artifacts MH - DNA Fingerprinting MH - DNA, Mitochondrial/*genetics MH - History, Ancient MH - Humans MH - *Mosaicism MH - Phylogeny MH - Quality Control EDAT- 2005/08/04 09:00 MHDA- 2005/11/09 09:00 CRDT- 2005/08/04 09:00 PHST- 2005/08/04 09:00 [pubmed] PHST- 2005/11/09 09:00 [medline] PHST- 2005/08/04 09:00 [entrez] AID - 5201476 [pii] AID - 10.1038/sj.ejhg.5201476 [doi] PST - ppublish SO - Eur J Hum Genet. 2005 Oct;13(10):1106-12. doi: 10.1038/sj.ejhg.5201476. PMID- 15958782 OWN - NLM STAT- MEDLINE DCOM- 20060216 LR - 20061115 IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 22 IP - 10 DP - 2005 Oct TI - Extensive human DNA contamination in extracts from ancient dog bones and teeth. PG - 2040-7 AB - Ancient DNA (aDNA) sequences, especially those of human origin, are notoriously difficult to analyze due to molecular damage and exogenous DNA contamination. Relatively few systematic studies have focused on this problem. Here we investigate the extent and origin of human DNA contamination in the most frequently used sources for aDNA studies, that is, bones and teeth from museum collections. To distinguish contaminant DNA from authentic DNA we extracted DNA from dog (Canis familiaris) specimens. We monitored the presence of a 148-bp human-specific and a 152-bp dog-specific mitochondrial DNA (mtDNA) fragment in DNA extracts as well as in negative controls. The total number of human and dog template molecules were quantified using real-time polymerase chain reaction (PCR), and the sequences were characterized by amplicon cloning and sequencing. Although standard precautions to avoid contamination were taken, we found that all samples from the 29 dog specimens contained human DNA, often at levels exceeding the amount of authentic ancient dog DNA. The level of contaminating human DNA was also significantly higher in the dog extracts than in the negative controls, and an experimental setup indicated that this was not caused by the carrier effect. This suggests that the contaminating human DNA mainly originated from the dog bones rather than from laboratory procedures. When cloned, fragments within a contaminated PCR product generally displayed several different sequences, although one haplotype was often found in majority. This leads us to believe that recognized criteria for authenticating aDNA cannot separate contamination from ancient human DNA the way they are presently used. FAU - Malmström, Helena AU - Malmström H AD - Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. helena.malmstrom@ebc.uu.se FAU - Storå, Jan AU - Storå J FAU - Dalén, Love AU - Dalén L FAU - Holmlund, Gunilla AU - Holmlund G FAU - Götherström, Anders AU - Götherström A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050615 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA Primers) RN - 0 (DNA Probes) RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Sequence MH - Bone and Bones/*chemistry MH - DNA/*genetics/isolation & purification MH - DNA Primers MH - DNA Probes MH - DNA, Mitochondrial/genetics MH - Dogs/*genetics MH - Drug Contamination MH - Humans MH - Polymerase Chain Reaction MH - Species Specificity MH - Templates, Genetic MH - Tooth/*chemistry EDAT- 2005/06/17 09:00 MHDA- 2006/02/17 09:00 CRDT- 2005/06/17 09:00 PHST- 2005/06/17 09:00 [pubmed] PHST- 2006/02/17 09:00 [medline] PHST- 2005/06/17 09:00 [entrez] AID - msi195 [pii] AID - 10.1093/molbev/msi195 [doi] PST - ppublish SO - Mol Biol Evol. 2005 Oct;22(10):2040-7. doi: 10.1093/molbev/msi195. Epub 2005 Jun 15. PMID- 16162675 OWN - NLM STAT- MEDLINE DCOM- 20051121 LR - 20181113 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 102 IP - 39 DP - 2005 Sep 27 TI - Relatively well preserved DNA is present in the crystal aggregates of fossil bones. PG - 13783-8 AB - DNA from fossil human bones could provide invaluable information about population migrations, genetic relations between different groups and the spread of diseases. The use of ancient DNA from bones to study the genetics of past populations is, however, very often compromised by the altered and degraded state of preservation of the extracted material. The universally observed postmortem degradation, together with the real possibility of contamination with modern human DNA, makes the acquisition of reliable data, from humans in particular, very difficult. We demonstrate that relatively well preserved DNA is occluded within clusters of intergrown bone crystals that are resistant to disaggregation by the strong oxidant NaOCl. We obtained reproducible authentic sequences from both modern and ancient animal bones, including humans, from DNA extracts of crystal aggregates. The treatment with NaOCl also minimizes the possibility of modern DNA contamination. We thus demonstrate the presence of a privileged niche within fossil bone, which contains DNA in a better state of preservation than the DNA present in the total bone. This counterintuitive approach to extracting relatively well preserved DNA from bones significantly improves the chances of obtaining authentic ancient DNA sequences, especially from human bones. FAU - Salamon, Michal AU - Salamon M AD - Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel. michal.kaufman@weizmann.ac.il FAU - Tuross, Noreen AU - Tuross N FAU - Arensburg, Baruch AU - Arensburg B FAU - Weiner, Steve AU - Weiner S LA - eng SI - GENBANK/DQ020115 SI - GENBANK/DQ020116 SI - GENBANK/DQ020117 SI - GENBANK/DQ020118 SI - GENBANK/DQ020119 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050914 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 9007-49-2 (DNA) SB - IM MH - Base Sequence MH - Biodegradation, Environmental MH - Bone and Bones/*chemistry MH - Crystallization MH - DNA/*analysis/metabolism MH - *Fossils MH - Genetics, Population MH - Humans MH - Molecular Sequence Data MH - Paleontology MH - Sequence Analysis, DNA PMC - PMC1236542 EDAT- 2005/09/16 09:00 MHDA- 2005/12/13 09:00 PMCR- 2006/03/27 CRDT- 2005/09/16 09:00 PHST- 2005/09/16 09:00 [pubmed] PHST- 2005/12/13 09:00 [medline] PHST- 2005/09/16 09:00 [entrez] PHST- 2006/03/27 00:00 [pmc-release] AID - 0503718102 [pii] AID - 010213783 [pii] AID - 10.1073/pnas.0503718102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13783-8. doi: 10.1073/pnas.0503718102. Epub 2005 Sep 14. PMID- 16138912 OWN - NLM STAT- MEDLINE DCOM- 20051212 LR - 20081121 IS - 0003-4800 (Print) IS - 0003-4800 (Linking) VI - 69 IP - Pt 5 DP - 2005 Sep TI - The genetics of the pre-Roman Iberian Peninsula: a mtDNA study of ancient Iberians. PG - 535-48 AB - The Iberians developed a surprisingly sophisticated culture in the Mediterranean coast of the Iberian Peninsula from the 6th century BC until their conquest by the Romans in the 2nd century BC. They spoke and wrote a non-Indo-European language that still cannot be understood; their origins and relationships with other non-Indo-European peoples, like the Etruscans, are unclear, since their funerary practices were based on the cremation of bodies, and therefore anthropology has been unable to approach the study of this people. We have retrieved mitochondrial DNA (mtDNA) from a few of the scarce skeletal remains that have been preserved, some of them belonging to ritualistically executed individuals. The most stringent authentication criteria proposed for ancient DNA, such as independent replication, amino-acid analysis, quantitation of template molecules, multiple extractions and cloning of PCR products, have been followed to obtain reliable sequences from the mtDNA hypervariable region 1 (HVR1), as well as some haplogroup diagnostic SNPs. Phylogeographic analyses show that the haplogroup composition of the ancient Iberians was very similar to that found in modern Iberian Peninsula populations, suggesting a long-term genetic continuity since pre-Roman times. Nonetheless, there is less genetic diversity in the ancient Iberians than is found among modern populations, a fact that could reflect the small population size at the origin of the population sampled, and the heterogenic tribal structure of the Iberian society. Moreover, the Iberians were not especially closely related to the Etruscans, which points to considerable genetic heterogeneity in Pre-Roman Western Europe. FAU - Sampietro, M L AU - Sampietro ML AD - Unitat de Biologia Evolutiva, Department Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain. FAU - Caramelli, D AU - Caramelli D FAU - Lao, O AU - Lao O FAU - Calafell, F AU - Calafell F FAU - Comas, D AU - Comas D FAU - Lari, M AU - Lari M FAU - Agustí, B AU - Agustí B FAU - Bertranpetit, J AU - Bertranpetit J FAU - Lalueza-Fox, C AU - Lalueza-Fox C LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Ann Hum Genet JT - Annals of human genetics JID - 0416661 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Adult MH - Bone and Bones/metabolism MH - DNA/metabolism MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - Fossils MH - Genetic Variation MH - Genetics, Population MH - Geography MH - Haplotypes MH - *History, Ancient MH - Humans MH - Male MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA MH - Skeleton MH - Spain EDAT- 2005/09/06 09:00 MHDA- 2005/12/15 09:00 CRDT- 2005/09/06 09:00 PHST- 2005/09/06 09:00 [pubmed] PHST- 2005/12/15 09:00 [medline] PHST- 2005/09/06 09:00 [entrez] AID - AHG194 [pii] AID - 10.1111/j.1529-8817.2005.00194.x [doi] PST - ppublish SO - Ann Hum Genet. 2005 Sep;69(Pt 5):535-48. doi: 10.1111/j.1529-8817.2005.00194.x. PMID- 15714514 OWN - NLM STAT- MEDLINE DCOM- 20051021 LR - 20171116 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 128 IP - 1 DP - 2005 Sep TI - Long-term survival of ancient DNA in Egypt: response to Zink and Nerlich (2003). PG - 110-4; discussion 115-8 FAU - Gilbert, M Thomas P AU - Gilbert MT AD - Department of Zoology, Oxford University, Oxford, OX1 3PS United Kingdom. FAU - Barnes, Ian AU - Barnes I FAU - Collins, Matthew J AU - Collins MJ FAU - Smith, Colin AU - Smith C FAU - Eklund, Julie AU - Eklund J FAU - Goudsmit, Jaap AU - Goudsmit J FAU - Poinar, Hendrik AU - Poinar H FAU - Cooper, Alan AU - Cooper A LA - eng GR - Wellcome Trust/United Kingdom PT - Comment PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 9007-49-2 (DNA) SB - IM CON - Am J Phys Anthropol. 2003 Jun;121(2):109-11. doi: 10.1002/ajpa.10213. PMID: 12740953 MH - Archaeology/*methods MH - DNA/*history MH - Egypt, Ancient MH - Embalming/history/methods MH - History, Ancient MH - Humans MH - Humidity MH - Nucleic Acid Amplification Techniques MH - Temperature MH - Time Factors EDAT- 2005/02/17 09:00 MHDA- 2005/10/22 09:00 CRDT- 2005/02/17 09:00 PHST- 2005/02/17 09:00 [pubmed] PHST- 2005/10/22 09:00 [medline] PHST- 2005/02/17 09:00 [entrez] AID - 10.1002/ajpa.20045 [doi] PST - ppublish SO - Am J Phys Anthropol. 2005 Sep;128(1):110-4; discussion 115-8. doi: 10.1002/ajpa.20045. PMID- 16030148 OWN - NLM STAT- MEDLINE DCOM- 20051229 LR - 20181113 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 102 IP - 30 DP - 2005 Jul 26 TI - Progressive proximal expansion of the primate X chromosome centromere. PG - 10563-8 AB - Previous studies of the pericentromeric region of the human X chromosome short arm (Xp) revealed an age gradient from ancient DNA that contains expressed genes to recent human-specific DNA at the functional centromere. We analyzed the finished sequence of this human genomic region to investigate its evolutionary history. Phylogenetic analysis of >1,500 alpha-satellite monomers from the region revealed the presence of five physical domains, each containing monomers from a distinct phylogenetic clade. The most distal domain contains long interspersed nucleotide element repeats that were active >35 million years ago, whereas the four proximal domains contain more recently active long interspersed nucleotide element repeats. An out-of-register, unequal recombination (i.e., crossover) detected at the edge of the X chromosome-specific alpha-satellite array (DXZ1) may reflect the most recent of a series of punctuating events during evolution that resulted in a proximal physical expansion of the X centromere. The first 18 kb of this array has 97-99% pairwise identity among all 2-kb repeat units. To perform more detailed evolutionary comparisons, we sequenced the junction between the ancient DNA of Xp and the primate-specific alpha satellite in chimpanzee, gorilla, orangutan, vervet, macaque, and baboon. The striking conservation found in all cases supports the ancestral nature of the alpha satellite at this location. These studies demonstrate that the primate X centromere appears to have evolved through repeated expansion events occurring within the central, active region of centromeric DNA, with the newly added sequences then conferring centromere function. FAU - Schueler, Mary G AU - Schueler MG AD - Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Dunn, John M AU - Dunn JM FAU - Bird, Christine P AU - Bird CP FAU - Ross, Mark T AU - Ross MT FAU - Viggiano, Luigi AU - Viggiano L CN - NISC Comparative Sequencing Program FAU - Rocchi, Mariano AU - Rocchi M FAU - Willard, Huntington F AU - Willard HF FAU - Green, Eric D AU - Green ED LA - eng SI - GENBANK/AC134314 SI - GENBANK/AC140661 SI - GENBANK/AC147591 SI - GENBANK/AC147690 SI - GENBANK/AC147693 SI - GENBANK/AC147722 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050719 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 SB - IM MH - Animals MH - Base Sequence MH - Centromere/*genetics MH - Chromosomes, Human, X/*genetics MH - Cluster Analysis MH - Conserved Sequence/genetics MH - DNA Repeat Expansion/*genetics MH - *Evolution, Molecular MH - Humans MH - Interspersed Repetitive Sequences/genetics MH - Molecular Sequence Data MH - *Phylogeny MH - Primates/*genetics MH - Sequence Analysis, DNA PMC - PMC1180780 EDAT- 2005/07/21 09:00 MHDA- 2005/12/31 09:00 PMCR- 2006/01/26 CRDT- 2005/07/21 09:00 PHST- 2005/07/21 09:00 [pubmed] PHST- 2005/12/31 09:00 [medline] PHST- 2005/07/21 09:00 [entrez] PHST- 2006/01/26 00:00 [pmc-release] AID - 0503346102 [pii] AID - 010210563 [pii] AID - 10.1073/pnas.0503346102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10563-8. doi: 10.1073/pnas.0503346102. Epub 2005 Jul 19. PMID- 15935940 OWN - NLM STAT- MEDLINE DCOM- 20050912 LR - 20061115 IS - 0379-0738 (Print) IS - 0379-0738 (Linking) VI - 151 IP - 1 DP - 2005 Jun 30 TI - STR-genotyping from human medieval tooth and bone samples. PG - 31-5 AB - We extracted the DNA contained in samples of bones and teeth from 10 skeletons excavated from the Gravette site (400-1000 AD, south of France). Ancient DNA was analysed by autosomal short tandem repeats (STRs). The DNA present in these ancient remains appeared very degraded, but nevertheless, better conserved in tooth than in bone samples. Moreover, we showed that the DNA extracted from ancient dental pulp was not exempt from polymerase chain reaction (PCR) inhibitors, which could result from extreme DNA fragmentation. An adapted protocol with a supplementary step of purification removed this inhibition. FAU - Ricaut, François-Xavier AU - Ricaut FX AD - Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, 11 rue Humann, 67085 Strasbourg Cedex, France. fx.ricaut@infonie.fr FAU - Keyser-Tracqui, Christine AU - Keyser-Tracqui C FAU - Crubézy, Eric AU - Crubézy E FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (Amelogenin) RN - 0 (Dental Enamel Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Adult MH - Amelogenin MH - Bone and Bones/*pathology MH - Child MH - DNA/*analysis/chemistry MH - DNA Fingerprinting/*methods MH - Dental Enamel Proteins/*genetics MH - Female MH - Forensic Anthropology MH - Genotype MH - History, Medieval MH - Humans MH - Male MH - Paleontology MH - Polymerase Chain Reaction MH - *Tandem Repeat Sequences MH - Tooth Germ/pathology EDAT- 2005/06/07 09:00 MHDA- 2005/09/13 09:00 CRDT- 2005/06/07 09:00 PHST- 2004/04/10 00:00 [received] PHST- 2004/06/15 00:00 [revised] PHST- 2004/07/06 00:00 [accepted] PHST- 2005/06/07 09:00 [pubmed] PHST- 2005/09/13 09:00 [medline] PHST- 2005/06/07 09:00 [entrez] AID - S0379-0738(04)00420-7 [pii] AID - 10.1016/j.forsciint.2004.07.001 [doi] PST - ppublish SO - Forensic Sci Int. 2005 Jun 30;151(1):31-5. doi: 10.1016/j.forsciint.2004.07.001. PMID- 15960847 OWN - NLM STAT- MEDLINE DCOM- 20060612 LR - 20181113 IS - 1471-2156 (Electronic) IS - 1471-2156 (Linking) VI - 6 DP - 2005 Jun 16 TI - Tree measures and the number of segregating sites in time-structured population samples. PG - 35 AB - BACKGROUND: Time-structured genetic samples are a valuable source of information in population genetics because they provide several correlated observations of the underlying evolutionary processes. In this paper we study basic properties of the genetic variation in time-structured samples as reflected in the genealogies relating individuals and the number of segregating sites observed. Our emphasis is on "measurably evolving populations" i.e. populations from which it is possible to obtain time-structured samples that span a significant interval of evolutionary time. RESULTS: We use results from the coalescent process to derive properties of time-structured samples. In the first section we extend existing results to attain measures on coalescent trees relating time-structured samples. These include the expected time to a most recent common ancestor, the expected total branch length and the expected length of branches subtending only ancient individuals. The effect of different sampling schemes on the latter measure is studied. In the second section we study the special case where the full sample consists of a group of contemporary extant samples and a group of contemporary ancient samples. As regards this case, we present results and applications concerning the probability distribution of the number of segregating sites where a mutation is unique to the ancient individuals and the number of segregating sites where a mutation is shared between ancient and extant individuals. CONCLUSION: The methodology and results presented here is of use to the design and interpretation of ancient DNA experiments. Furthermore, the results may be useful in further development of statistical tests of e.g. population dynamics and selection, which include temporal information. FAU - Forsberg, Roald AU - Forsberg R AD - Bioinformatics Research Center, Department of Genetics and Ecology, University of Aarhus, Arhus, Denmark. roald@birc.au.dk FAU - Drummond, Alexei J AU - Drummond AJ FAU - Hein, Jotun AU - Hein J LA - eng GR - 1-R01-GM60729-01/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050616 PL - England TA - BMC Genet JT - BMC genetics JID - 100966978 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - *Biological Evolution MH - DNA, Mitochondrial/genetics MH - Humans MH - *Models, Genetic MH - *Mutation MH - Pedigree MH - Probability MH - Time PMC - PMC1185533 EDAT- 2005/06/18 09:00 MHDA- 2006/06/13 09:00 PMCR- 2005/06/16 CRDT- 2005/06/18 09:00 PHST- 2004/10/19 00:00 [received] PHST- 2005/06/16 00:00 [accepted] PHST- 2005/06/18 09:00 [pubmed] PHST- 2006/06/13 09:00 [medline] PHST- 2005/06/18 09:00 [entrez] PHST- 2005/06/16 00:00 [pmc-release] AID - 1471-2156-6-35 [pii] AID - 10.1186/1471-2156-6-35 [doi] PST - epublish SO - BMC Genet. 2005 Jun 16;6:35. doi: 10.1186/1471-2156-6-35. PMID- 15878988 OWN - NLM STAT- MEDLINE DCOM- 20050713 LR - 20231105 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 102 IP - 20 DP - 2005 May 17 TI - A late Neandertal femur from Les Rochers-de-Villeneuve, France. PG - 7085-90 AB - In 2002, a Neandertal partial femoral diaphysis was discovered at Les Rochers-de-Villeneuve (Vienne, France). Radiocarbon dated to approximately 40,700 14C years before present, this specimen is one of the most recent Middle Paleolithic Neandertals. The diaphysis derives from an archeological level indicating alternating human and carnivore (mostly hyena) occupation of the cave, reinforcing the close proximity and probable competition of Middle Paleolithic humans with large carnivores for resources and space. Morphological aspects of the diaphysis and ancient DNA extracted from it indicate that it is aligned with the Neandertals and is distinct from early modern humans. However, its midshaft cortical bone distribution places it between other Middle Paleolithic Neandertals and the Châtelperronian Neandertal from La Roche-à-Pierrot, supporting a pattern of changing mobility patterns among late Middle Paleolithic Neandertals on the eve of modern human dispersals into Europe. FAU - Beauval, Cédric AU - Beauval C AD - Institut de Préhistoire et de Géologie du Quaternaire and Laboratoire d'Anthropologie des Populations du Passé, Unité Mixte de Recherche, Université de Bordeaux, Talence, France. c.beauval@ipgq.u-bordeaux1.fr FAU - Maureille, Bruno AU - Maureille B FAU - Lacrampe-Cuyaubère, François AU - Lacrampe-Cuyaubère F FAU - Serre, David AU - Serre D FAU - Peressinotto, David AU - Peressinotto D FAU - Bordes, Jean-Guillaume AU - Bordes JG FAU - Cochard, David AU - Cochard D FAU - Couchoud, Isabelle AU - Couchoud I FAU - Dubrasquet, David AU - Dubrasquet D FAU - Laroulandie, Véronique AU - Laroulandie V FAU - Lenoble, Arnaud AU - Lenoble A FAU - Mallye, Jean-Baptiste AU - Mallye JB FAU - Pasty, Sylvain AU - Pasty S FAU - Primault, Jérôme AU - Primault J FAU - Rohland, Nadin AU - Rohland N FAU - Pääbo, Svante AU - Pääbo S FAU - Trinkaus, Erik AU - Trinkaus E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050506 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Carbon Radioisotopes) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Base Sequence MH - Carbon Radioisotopes MH - DNA, Mitochondrial/*genetics MH - Femur/*anatomy & histology MH - *Fossils MH - France MH - Hominidae/*anatomy & histology/genetics MH - Humans MH - Molecular Sequence Data MH - Sequence Alignment MH - Sequence Analysis, DNA PMC - PMC1129143 EDAT- 2005/05/10 09:00 MHDA- 2005/07/14 09:00 PMCR- 2005/11/17 CRDT- 2005/05/10 09:00 PHST- 2005/05/10 09:00 [pubmed] PHST- 2005/07/14 09:00 [medline] PHST- 2005/05/10 09:00 [entrez] PHST- 2005/11/17 00:00 [pmc-release] AID - 0502656102 [pii] AID - 01027085 [pii] AID - 10.1073/pnas.0502656102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 May 17;102(20):7085-90. doi: 10.1073/pnas.0502656102. Epub 2005 May 6. PMID- 15870386 OWN - NLM STAT- MEDLINE DCOM- 20050524 LR - 20191210 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 33 IP - 8 DP - 2005 TI - How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence? PG - 2549-56 AB - Forensic and ancient DNA (aDNA) extracts are mixtures of endogenous aDNA, existing in more or less damaged state, and contaminant DNA. To obtain the true aDNA sequence, it is not sufficient to generate a single direct sequence of the mixture, even where the authentic aDNA is the most abundant (e.g. 25% or more) in the component mixture. Only bacterial cloning can elucidate the components of this mixture. We calculate the number of clones that need to be sampled (for various mixture ratios) in order to be confident (at various levels of confidence) to have identified the major component. We demonstrate that to be >95% confident of identifying the most abundant sequence present at 70% in the ancient sample, 20 clones must be sampled. We make recommendations and offer a free-access web-based program, which constructs the most reliable consensus sequence from the user's input clone sequences and analyses the confidence limits for each nucleotide position and for the whole consensus sequence. Accepted authentication methods must be employed in order to assess the authenticity and endogeneity of the resulting consensus sequences (e.g. quantification and replication by another laboratory, blind testing, amelogenin sex versus morphological sex, the effective use of controls, etc.) and determine whether they are indeed aDNA. FAU - Bower, Mim A AU - Bower MA AD - Archaeogenetics Laboratory, McDonald Institute for Archaeological Research, University of Cambridge Downing Street, Cambridge CB2 3ER, UK. mab1004@cam.ac.uk FAU - Spencer, Matthew AU - Spencer M FAU - Matsumura, Shuichi AU - Matsumura S FAU - Nisbet, R Ellen R AU - Nisbet RE FAU - Howe, Christopher J AU - Howe CJ LA - eng PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050503 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 SB - IM MH - Cloning, Molecular MH - *Consensus Sequence MH - DNA Fingerprinting/*methods MH - *Fossils MH - Humans MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA/methods MH - Software MH - Templates, Genetic PMC - PMC1088305 EDAT- 2005/05/05 09:00 MHDA- 2005/05/25 09:00 PMCR- 2005/05/03 CRDT- 2005/05/05 09:00 PHST- 2005/05/05 09:00 [pubmed] PHST- 2005/05/25 09:00 [medline] PHST- 2005/05/05 09:00 [entrez] PHST- 2005/05/03 00:00 [pmc-release] AID - 33/8/2549 [pii] AID - 10.1093/nar/gki550 [doi] PST - epublish SO - Nucleic Acids Res. 2005 May 3;33(8):2549-56. doi: 10.1093/nar/gki550. Print 2005. PMID- 15742001 OWN - NLM STAT- MEDLINE DCOM- 20050804 LR - 20111209 IS - 0018-067X (Print) IS - 0018-067X (Linking) VI - 94 IP - 5 DP - 2005 May TI - What ancient DNA tells us. PG - 463-4 FAU - Hedrick, P AU - Hedrick P FAU - Waits, L AU - Waits L LA - eng PT - News PL - England TA - Heredity (Edinb) JT - Heredity JID - 0373007 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - *Biological Evolution MH - DNA, Mitochondrial/*genetics MH - *Fossils MH - *Geography MH - Humans MH - Species Specificity EDAT- 2005/03/03 09:00 MHDA- 2005/08/05 09:00 CRDT- 2005/03/03 09:00 PHST- 2005/03/03 09:00 [pubmed] PHST- 2005/08/05 09:00 [medline] PHST- 2005/03/03 09:00 [entrez] AID - 6800647 [pii] AID - 10.1038/sj.hdy.6800647 [doi] PST - ppublish SO - Heredity (Edinb). 2005 May;94(5):463-4. doi: 10.1038/sj.hdy.6800647. PMID- 15756672 OWN - NLM STAT- MEDLINE DCOM- 20050421 LR - 20061115 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 126 IP - 4 DP - 2005 Apr TI - Ancient DNA analysis of human neolithic remains found in northeastern Siberia. PG - 458-62 AB - We successfully extracted DNA from a bone sample of a Neolithic skeleton (dated 3,600 +/- 60 years BP) excavated in northeastern Yakutia (east Siberia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by sequencing of the hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The STR profile, the mitochondrial haplotype, and the haplogroup determined were compared with those of modern Eurasian and Native American populations. The results showed the affinity of this ancient skeleton with both east Siberian/Asian and Native American populations. FAU - Ricaut, François-Xavier AU - Ricaut FX AD - Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, 67085 Strasbourg, France. fx.ricaut@infonie.fr FAU - Fedoseeva, A AU - Fedoseeva A FAU - Keyser-Tracqui, Christine AU - Keyser-Tracqui C FAU - Crubézy, Eric AU - Crubézy E FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Base Sequence MH - Bone and Bones/*chemistry MH - DNA/*genetics MH - DNA Primers MH - DNA, Mitochondrial/genetics MH - *Fossils MH - Gene Frequency MH - Geography MH - Haplotypes/genetics MH - Humans MH - Polymorphism, Genetic MH - Population Dynamics MH - Sequence Analysis, DNA MH - Siberia MH - Tandem Repeat Sequences/genetics EDAT- 2005/03/10 09:00 MHDA- 2005/04/22 09:00 CRDT- 2005/03/10 09:00 PHST- 2005/03/10 09:00 [pubmed] PHST- 2005/04/22 09:00 [medline] PHST- 2005/03/10 09:00 [entrez] AID - 10.1002/ajpa.20257 [doi] PST - ppublish SO - Am J Phys Anthropol. 2005 Apr;126(4):458-62. doi: 10.1002/ajpa.20257. PMID- 15750025 OWN - NLM STAT- MEDLINE DCOM- 20050422 LR - 20071115 IS - 0022-1554 (Print) IS - 0022-1554 (Linking) VI - 53 IP - 3 DP - 2005 Mar TI - First systematic CGH-based analyses of ancient DNA samples of malformed fetuses preserved in the Meckel Anatomical Collection in Halle/Saale (Germany). PG - 381-4 AB - We present the first data on our comparative genomic hybridization (CGH)-based strategy for the analysis of ancient DNA (aDNA) samples extracted from fetuses preserved in the Meckel Anatomical Collection in Halle, Germany. The collection contains numerous differently fixed ancient samples of fetal malformations collected from the middle of the 18th to the early 19th century. The main objective of this study is to establish a "standard" aDNA extraction and amplification protocol as a prerequisite for successful CGH analyses to detect or exclude chromosomal imbalances possibly causative for the malformations described for the fetuses. FAU - Tönnies, H AU - Tönnies H AD - Institut für Humangenetik, Campus Virchow Klinikum, Charité, Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. holger.toennies@charite.de FAU - Gerlach, A AU - Gerlach A FAU - Klunker, R AU - Klunker R FAU - Schultka, R AU - Schultka R FAU - Göbbel, L AU - Göbbel L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Histochem Cytochem JT - The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society JID - 9815334 RN - 9007-49-2 (DNA) SB - IM MH - Congenital Abnormalities/genetics MH - DNA/*analysis/isolation & purification MH - Female MH - Fetus/*abnormalities MH - Humans MH - In Situ Hybridization, Fluorescence MH - Karyotyping MH - Male MH - Museums MH - Nucleic Acid Hybridization MH - Specimen Handling EDAT- 2005/03/08 09:00 MHDA- 2005/04/23 09:00 CRDT- 2005/03/08 09:00 PHST- 2005/03/08 09:00 [pubmed] PHST- 2005/04/23 09:00 [medline] PHST- 2005/03/08 09:00 [entrez] AID - 53/3/381 [pii] AID - 10.1369/jhc.4B6427.2005 [doi] PST - ppublish SO - J Histochem Cytochem. 2005 Mar;53(3):381-4. doi: 10.1369/jhc.4B6427.2005. PMID- 15719062 OWN - NLM STAT- MEDLINE DCOM- 20060307 LR - 20181113 IS - 1545-7885 (Electronic) IS - 1544-9173 (Print) IS - 1544-9173 (Linking) VI - 3 IP - 2 DP - 2005 Feb TI - Ancient DNA comes of age. PG - e56 LID - e56 AB - Ancient DNA enables researchers to study the genetics of populations in the past; despite difficulties in its extraction, aDNA reveals that evolution is even more complex than we had imagined FAU - Nicholls, Henry AU - Nicholls H AD - henry.nicholls@absw.org.uk LA - eng PT - Journal Article PL - United States TA - PLoS Biol JT - PLoS biology JID - 101183755 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*genetics/*standards MH - DNA Repair/genetics MH - *Evolution, Molecular MH - *Fossils MH - Humans/genetics MH - Paleontology/*methods/standards MH - Time PMC - PMC548952 EDAT- 2005/02/19 09:00 MHDA- 2006/03/08 09:00 PMCR- 2005/02/15 CRDT- 2005/02/19 09:00 PHST- 2005/02/19 09:00 [pubmed] PHST- 2006/03/08 09:00 [medline] PHST- 2005/02/19 09:00 [entrez] PHST- 2005/02/15 00:00 [pmc-release] AID - 10.1371/journal.pbio.0030056 [doi] PST - ppublish SO - PLoS Biol. 2005 Feb;3(2):e56. doi: 10.1371/journal.pbio.0030056. PMID- 15699220 OWN - NLM STAT- MEDLINE DCOM- 20050308 LR - 20230318 IS - 0002-9165 (Print) IS - 0002-9165 (Linking) VI - 81 IP - 2 DP - 2005 Feb TI - Origins and evolution of the Western diet: health implications for the 21st century. PG - 341-54 AB - There is growing awareness that the profound changes in the environment (eg, in diet and other lifestyle conditions) that began with the introduction of agriculture and animal husbandry approximately 10000 y ago occurred too recently on an evolutionary time scale for the human genome to adjust. In conjunction with this discordance between our ancient, genetically determined biology and the nutritional, cultural, and activity patterns of contemporary Western populations, many of the so-called diseases of civilization have emerged. In particular, food staples and food-processing procedures introduced during the Neolithic and Industrial Periods have fundamentally altered 7 crucial nutritional characteristics of ancestral hominin diets: 1) glycemic load, 2) fatty acid composition, 3) macronutrient composition, 4) micronutrient density, 5) acid-base balance, 6) sodium-potassium ratio, and 7) fiber content. The evolutionary collision of our ancient genome with the nutritional qualities of recently introduced foods may underlie many of the chronic diseases of Western civilization. FAU - Cordain, Loren AU - Cordain L AD - Department of Health and Exercise Science, Colorado State University, Fort Collins, CO 80523, USA. cordain@cahs.colostate.edu FAU - Eaton, S Boyd AU - Eaton SB FAU - Sebastian, Anthony AU - Sebastian A FAU - Mann, Neil AU - Mann N FAU - Lindeberg, Staffan AU - Lindeberg S FAU - Watkins, Bruce A AU - Watkins BA FAU - O'Keefe, James H AU - O'Keefe JH FAU - Brand-Miller, Janette AU - Brand-Miller J LA - eng PT - Journal Article PT - Review PL - United States TA - Am J Clin Nutr JT - The American journal of clinical nutrition JID - 0376027 RN - 0 (Dietary Fiber) RN - 0 (Fatty Acids) RN - 0 (Potassium, Dietary) RN - 0 (Sodium, Dietary) SB - IM CIN - Am J Clin Nutr. 2005 Aug;82(2):483; author reply 483-4. doi: 10.1093/ajcn/82.2.483. PMID: 16087997 MH - Acid-Base Equilibrium MH - Agriculture/*methods MH - *Biological Evolution MH - Chronic Disease/epidemiology MH - Diet/*trends MH - Dietary Fiber/administration & dosage MH - Fatty Acids/administration & dosage/analysis MH - Food Analysis MH - Food Handling/methods MH - Glycemic Index MH - Humans MH - Potassium, Dietary/administration & dosage MH - Sodium, Dietary/administration & dosage MH - United States RF - 172 EDAT- 2005/02/09 09:00 MHDA- 2005/03/09 09:00 CRDT- 2005/02/09 09:00 PHST- 2005/02/09 09:00 [pubmed] PHST- 2005/03/09 09:00 [medline] PHST- 2005/02/09 09:00 [entrez] AID - S0002-9165(23)27546-2 [pii] AID - 10.1093/ajcn.81.2.341 [doi] PST - ppublish SO - Am J Clin Nutr. 2005 Feb;81(2):341-54. doi: 10.1093/ajcn.81.2.341. PMID- 15389521 OWN - NLM STAT- MEDLINE DCOM- 20050218 LR - 20051116 IS - 0021-9541 (Print) IS - 0021-9541 (Linking) VI - 202 IP - 2 DP - 2005 Feb TI - Ancient DNA as a multidisciplinary experience. PG - 315-22 AB - Investigation into DNA from archeological remains offers an inestimable tool for unraveling the history of humankind. However, a series of basic and technical difficulties renders the analysis of ancient DNA (aDNA) molecules troublesome, depending either on their own peculiar characteristics or on the complexity of processes affecting the bone matrix over time, all compromising the preservation of ancient DNA. This review underlines the contribution of many different disciplines, in particular molecular biology and genetics, to overcome these obstacles. The role of each expertise is illustrated to appropriately address the questions arising in aDNA investigations. CI - 2004 Wiley-Liss, Inc. FAU - Cipollaro, M AU - Cipollaro M AD - Dipartimento di Medicina Sperimentale, Sezione di Biotecnologie e Biologia Molecolare, 2nd University of Naples, Naples, Italy. marilena.cipollaro@unina2.it FAU - Galderisi, U AU - Galderisi U FAU - Di Bernardo, G AU - Di Bernardo G LA - eng PT - Journal Article PT - Review PL - United States TA - J Cell Physiol JT - Journal of cellular physiology JID - 0050222 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Archaeology MH - *DNA/isolation & purification MH - DNA Damage MH - DNA Repair MH - DNA, Mitochondrial/genetics MH - *Fossils MH - Gene Amplification MH - *Genetics MH - Humans MH - *Interdisciplinary Communication MH - *Molecular Biology MH - Phylogeny MH - Science RF - 78 EDAT- 2004/09/25 05:00 MHDA- 2005/02/19 09:00 CRDT- 2004/09/25 05:00 PHST- 2004/09/25 05:00 [pubmed] PHST- 2005/02/19 09:00 [medline] PHST- 2004/09/25 05:00 [entrez] AID - 10.1002/jcp.20116 [doi] PST - ppublish SO - J Cell Physiol. 2005 Feb;202(2):315-22. doi: 10.1002/jcp.20116. PMID- 16285089 OWN - NLM STAT- MEDLINE DCOM- 20070529 LR - 20170330 IS - 0394-9001 (Print) IS - 0394-9001 (Linking) VI - 17 IP - 1 DP - 2005 TI - [Molecular paleopathology: a novel perspective for biomedical history]. PG - 181-91 AB - Molecular paleopathology is an emerging field that is devoted to the detection, indentification and characterization of the molecular signatures in past diseases. When studied with modern molecular techniques, ancient human remains may yield direct informations on the diseases of ancient populations as well as the history of human diseases. Data concerning specific diseases of infectious, neoplastic and genetic origin can be obtained by molecular investigations of skeletal and mummified human remains. In particular, ancient DNA extracted from bone tissue, teeth and mummified soft tissue can be deeply analyzed by using PCR-based molecular techniques. Additionally, DNA of ancient pathogens, including bacteria, viruses and parasites, can be isolated from human remains and molecular diagnosis of infectious diseases can be made. Thus, molecular data, complemented by morphological and biochemical analyses, could help to reconstruct the epidemiology of past diseases and epidemics. FAU - Ottini, Laura AU - Ottini L AD - Dipartmento di Medicina Sperimentale e Patologia, Sezione di Storia della Medicina, Università "La Sapienza", Roma. FAU - Lupi, Ramona AU - Lupi R FAU - Falchetti, Mario AU - Falchetti M FAU - Fornaciari, Gino AU - Fornaciari G FAU - Mariani-Costantini, Renato AU - Mariani-Costantini R FAU - Angeletti, Luciana Rita AU - Angeletti LR LA - ita PT - English Abstract PT - Historical Article PT - Journal Article TT - La paleopatologia moleceolare: il futuro per indagare il passato. PL - Italy TA - Med Secoli JT - Medicina nei secoli JID - 0176472 MH - Communicable Diseases/*history/microbiology MH - Genetic Diseases, Inborn/history MH - History, Ancient MH - Humans MH - Molecular Biology/*history MH - Neoplasms/genetics/*history MH - Paleopathology/*history EDAT- 2005/11/16 09:00 MHDA- 2007/05/30 09:00 CRDT- 2005/11/16 09:00 PHST- 2005/11/16 09:00 [pubmed] PHST- 2007/05/30 09:00 [medline] PHST- 2005/11/16 09:00 [entrez] PST - ppublish SO - Med Secoli. 2005;17(1):181-91. PMID- 16124858 OWN - NLM STAT- MEDLINE DCOM- 20051212 LR - 20220321 IS - 1527-8204 (Print) IS - 1527-8204 (Linking) VI - 6 DP - 2005 TI - Mitochondrial DNA and human evolution. PG - 165-83 AB - Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history. FAU - Pakendorf, Brigitte AU - Pakendorf B AD - Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. pakendorf@eva.mpg.de FAU - Stoneking, Mark AU - Stoneking M LA - eng PT - Journal Article PT - Review PL - United States TA - Annu Rev Genomics Hum Genet JT - Annual review of genomics and human genetics JID - 100911346 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - *Evolution, Molecular MH - Female MH - Gene Dosage MH - Genetic Variation MH - Genetics, Population MH - Genome, Human MH - Humans MH - Male MH - Mutation MH - Recombination, Genetic RF - 184 EDAT- 2005/08/30 09:00 MHDA- 2005/12/15 09:00 CRDT- 2005/08/30 09:00 PHST- 2005/08/30 09:00 [pubmed] PHST- 2005/12/15 09:00 [medline] PHST- 2005/08/30 09:00 [entrez] AID - 10.1146/annurev.genom.6.080604.162249 [doi] PST - ppublish SO - Annu Rev Genomics Hum Genet. 2005;6:165-83. doi: 10.1146/annurev.genom.6.080604.162249. PMID- 15865963 OWN - NLM STAT- MEDLINE DCOM- 20050808 LR - 20141120 IS - 0076-6879 (Print) IS - 0076-6879 (Linking) VI - 395 DP - 2005 TI - Isolation and analysis of DNA from archaeological, clinical, and natural history specimens. PG - 87-103 AB - The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. Novel methods exist for the isolation, purification, and analysis of aDNA because these DNA templates are likely to be damaged, fragmented and?or associated with non-nucleic acid material. However, contamination of ancient specimens and DNA extracts with modern DNA is more widespread than is generally acknowledged and remains a significant problem in aDNA analysis. Studies of human aDNA are uniquely sensitive to contamination due to the continual presence of potential contamination sources. Meticulous authentication of results and careful selection of polymorphic markers capable of distinguishing between aDNA and probable DNA contaminants are critical to a successful aDNA study. FAU - Mulligan, Connie J AU - Mulligan CJ AD - Department of Anthropology, University of Florida, Gainesville, Florida 32611, USA. LA - eng PT - Journal Article PL - United States TA - Methods Enzymol JT - Methods in enzymology JID - 0212271 RN - 0 (Enzyme Inhibitors) RN - 0 (Nucleic Acid Synthesis Inhibitors) RN - 9007-49-2 (DNA) SB - IM MH - Archaeology MH - Bone and Bones/chemistry MH - Connective Tissue/chemistry MH - DNA/genetics/*isolation & purification MH - DNA Damage MH - DNA Fragmentation MH - Drug Contamination MH - Enzyme Inhibitors/isolation & purification MH - *Fossils MH - Humans MH - Methods MH - Nucleic Acid Synthesis Inhibitors MH - Polymerase Chain Reaction MH - Tooth/chemistry EDAT- 2005/05/04 09:00 MHDA- 2005/08/09 09:00 CRDT- 2005/05/04 09:00 PHST- 2005/05/04 09:00 [pubmed] PHST- 2005/08/09 09:00 [medline] PHST- 2005/05/04 09:00 [entrez] AID - S0076687905950076 [pii] AID - 10.1016/S0076-6879(05)95007-6 [doi] PST - ppublish SO - Methods Enzymol. 2005;395:87-103. doi: 10.1016/S0076-6879(05)95007-6. PMID- 15570114 OWN - NLM STAT- MEDLINE DCOM- 20050421 LR - 20190902 IS - 1064-3745 (Print) IS - 1064-3745 (Linking) VI - 297 DP - 2005 TI - Protocols for ancient DNA typing. PG - 265-78 AB - Molecular analysis of fossil and archaeological remains has been established as a powerful tool in providing new insight in phylogenetic investigations. The overlapping set of molecular modifications and degradation that forensic samples share with archaeological specimen suggests the application of similar technical approaches to the respective biological material. Polymerase chain reaction is the molecular technique of choice for the retrieval of specimen deoxyribonucleic acid (DNA) molecules. Because of intrinsic sensitivity, potential contaminations from exogenous DNA sources must be monitored through the entire process by the introduction of multiple blank controls. Cloning and sequencing of polymerase chain reaction products often is the only way to discriminate between contaminations and endogenous sequences as well as to identify variable positions from nucleotide modifications/DNA polymerase errors. Phylogenetic analysis and investigations of the pattern of substitutions are an additional and necessary step to validate the retrieved sequence. Comparison with available related samples (modern or extinct) is critical to correctly validate the results and to avoid artifactual data. FAU - Capelli, Cristian AU - Capelli C AD - Institute of Legal Medicine, Catholic University of Rome, Rome, Italy. FAU - Tschentscher, Frank AU - Tschentscher F LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 9007-49-2 (DNA) SB - IM MH - Archaeology MH - Cloning, Molecular MH - DNA/classification/*genetics MH - Fossils MH - Humans MH - Phylogeny MH - Polymerase Chain Reaction/methods EDAT- 2004/12/01 09:00 MHDA- 2005/04/22 09:00 CRDT- 2004/12/01 09:00 PHST- 2004/12/01 09:00 [pubmed] PHST- 2005/04/22 09:00 [medline] PHST- 2004/12/01 09:00 [entrez] AID - 1-59259-867-6:265 [pii] AID - 10.1385/1-59259-867-6:265 [doi] PST - ppublish SO - Methods Mol Biol. 2005;297:265-78. doi: 10.1385/1-59259-867-6:265. PMID- 15570113 OWN - NLM STAT- MEDLINE DCOM- 20050421 LR - 20190902 IS - 1064-3745 (Print) IS - 1064-3745 (Linking) VI - 297 DP - 2005 TI - Methods for the study of ancient DNA. PG - 253-64 AB - Whereas the analysis of ancient DNA (aDNA) has become an increasingly popular mode of investigation in both archaeological and evolutionary studies, this approach is complicated by the degraded nature of ancient nucleic acids, the presence of enzymatic inhibitors in aDNA extracts, as well as the risk of contamination during either excavation or manipulation of samples. Despite these difficulties, numerous methods have been developed to optimize the recovery, study, and authentication of aDNA. In this article, we describe the procedures used in our laboratory to extract and amplify informative DNA segments from prehistoric or protohistoric human samples, as well as the precautions and strategies implemented to avoid or at least detect contaminations. FAU - Keyser-Tracqui, Christine AU - Keyser-Tracqui C AD - Laboratoire d'Anthropologie Moléculaire, Institut de Médicine Légale, Strasbourg, France. FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (Genetic Markers) RN - 9007-49-2 (DNA) SB - IM MH - Archaeology MH - DNA/*genetics/isolation & purification MH - *Forensic Medicine MH - Fossils MH - Genetic Markers MH - Humans MH - Polymerase Chain Reaction EDAT- 2004/12/01 09:00 MHDA- 2005/04/22 09:00 CRDT- 2004/12/01 09:00 PHST- 2004/12/01 09:00 [pubmed] PHST- 2005/04/22 09:00 [medline] PHST- 2004/12/01 09:00 [entrez] AID - 1-59259-867-6:253 [pii] AID - 10.1385/1-59259-867-6:253 [doi] PST - ppublish SO - Methods Mol Biol. 2005;297:253-64. doi: 10.1385/1-59259-867-6:253. PMID- 15539371 OWN - NLM STAT- MEDLINE DCOM- 20050104 LR - 20130424 IS - 1364-503X (Print) IS - 1364-503X (Linking) VI - 362 IP - 1825 DP - 2004 Dec 15 TI - Studying the effect of environmental change on biotic evolution: past genetic contributions, current work and future directions. PG - 2795-820 AB - Evolutionary geneticists currently face a major scientific opportunity when integrating across the rapidly increasing amount of genetic data and existing biological scenarios based on ecology, fossils or climate models. Although genetic data acquisition and analysis have improved tremendously, several limitations remain. Here, we discuss the feedback between history and genetic variation in the face of environmental change with increasing taxonomic and temporal scale, as well as the major challenges that lie ahead. In particular, we focus on recent developments in two promising genetic methods, those of 'phylochronology' and 'molecular clocks'. With the advent of ancient DNA techniques, we can now directly sample the recent past. We illustrate this amazing and largely untapped utility of ancient DNA extracted from accurately dated localities with documented environmental changes. Innovative statistical analyses of these genetic data expose the direct effect of recent environmental change on genetic endurance, or maintenance of genetic variation. The 'molecular clock' (assumption of a linear relationship between genetic distance and evolutionary time) has been used extensively in phylogenetic studies to infer time and correlation between lineage divergence time and concurrent environmental change. Several studies at both population and species scale support a persuasive relationship between particular perturbation events and time of biotic divergence. However, we are still a way from gleaning an overall pattern to this relationship, which is a prerequisite to ultimately understanding the mechanisms by which past environments have shaped the evolutionary trajectory. Current obstacles include as-yet undecided reasons behind the frequent discrepancy between molecular and fossil time estimates, and the frequent lack of consideration of extensive confidence intervals around time estimates. We suggest that use and interpretation of both ancient DNA and molecular clocks is most effective when results are synthesized with palaeontological (fossil) and ecological (life history) information. FAU - van Tuinen, Marcel AU - van Tuinen M AD - Department of Biological Sciences, Gilbert Hall, Stanford University, Stanford, CA 94305-5020, USA. mvtuinen@stanford.edu FAU - Ramakrishnan, Uma AU - Ramakrishnan U FAU - Hadly, Elizabeth A AU - Hadly EA LA - eng PT - Journal Article PT - Review PL - England TA - Philos Trans A Math Phys Eng Sci JT - Philosophical transactions. Series A, Mathematical, physical, and engineering sciences JID - 101133385 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/analysis/*genetics MH - *Environment MH - *Evolution, Molecular MH - Gene Expression Profiling/*methods/trends MH - Gene Expression Regulation/*genetics MH - Genetic Variation/genetics MH - Genetics, Population/*methods/trends MH - Humans MH - Models, Genetic MH - Paleontology/*methods/trends MH - Phylogeny RF - 80 EDAT- 2004/11/13 09:00 MHDA- 2005/01/05 09:00 CRDT- 2004/11/13 09:00 PHST- 2004/11/13 09:00 [pubmed] PHST- 2005/01/05 09:00 [medline] PHST- 2004/11/13 09:00 [entrez] AID - NGGF6UX5B93VU4L8 [pii] AID - 10.1098/rsta.2004.1465 [doi] PST - ppublish SO - Philos Trans A Math Phys Eng Sci. 2004 Dec 15;362(1825):2795-820. doi: 10.1098/rsta.2004.1465. PMID- 15648848 OWN - NLM STAT- MEDLINE DCOM- 20050421 LR - 20050114 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 62 IP - 4 DP - 2004 Dec TI - ABO genotyping by PCR-RFLP and cloning and sequencing. PG - 397-410 AB - A refined PCR-RFLP based method was established to genotype ABO blood groups. The main objective of this study was to make the techniques also suitable for working with degraded DNA. Specific primer design was carried out to choose fragments shorter than 200 bp as necessary in forensic and archaeological applications. Four fragments of exon 6 and 7 of the ABO gene were amplified and digested by in total 7 restriction endonucleases. Particular attention was paid to the base changes at nucleotide positions 261(delG), 297, 526, 703, 721, 771, 796 and 1060(delC) in order to distinguish the six common alleles A101, A201, B, O01, O02 and O03. Furthermore, this method also enables determination of seven of the less frequent alleles: A104, A204, Ax02, Ax03, O05, O06 and O07. The method was applied successfully to a series of blood samples with known phenotypes and genotypes as well as DNA extracted from a thirty year old blood stain and an ancient tooth sample. However, working with ancient DNA requires additional cloning and sequencing of the RFLP-typing results due to DNA post mortem damages such as deaminations, which could lead to false typing results. FAU - Haak, Wolfgang AU - Haak W AD - Institute of Anthropology, Molecular Archaeology Group, Johannes Gutenberg University Mainz. FAU - Burger, Joachim AU - Burger J FAU - Alt, Kurt Werner AU - Alt KW LA - eng PT - Historical Article PT - Journal Article PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (ABO Blood-Group System) RN - 0 (DNA Transposable Elements) SB - IM MH - ABO Blood-Group System/*genetics MH - Alleles MH - Archaeology MH - Blood Stains MH - Chromosome Deletion MH - *Cloning, Molecular MH - DNA Transposable Elements MH - Forensic Medicine MH - History, Ancient MH - Humans MH - Phenotype MH - *Polymerase Chain Reaction MH - *Polymorphism, Restriction Fragment Length MH - Postmortem Changes MH - Reproducibility of Results MH - *Sequence Analysis, DNA MH - Tooth/pathology EDAT- 2005/01/15 09:00 MHDA- 2005/04/22 09:00 CRDT- 2005/01/15 09:00 PHST- 2005/01/15 09:00 [pubmed] PHST- 2005/04/22 09:00 [medline] PHST- 2005/01/15 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2004 Dec;62(4):397-410. PMID- 15648845 OWN - NLM STAT- MEDLINE DCOM- 20050421 LR - 20101118 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 62 IP - 4 DP - 2004 Dec TI - Design of a multiplex PCR for genotyping 16 short tandem repeats in degraded DNA samples. PG - 369-78 AB - The molecular genotyping of individuals and reconstruction of kinship through short and high polymorphic DNA markers, so-called short tandem repeats (STR), has become an important and efficient method in anthropology and forensic science. The here introduced experimental design describes a multiplex PCR capable of simultaneously amplifying 16 STRs and the sex determinant locus amelogenin in a short fragment lengths range from 84 bp to 275 bp. Thus, the design depends predominantly on the routines for DNA typing of historical samples with highly degraded ancient DNA. It is shown, that the newly designed multiplex PCR is suitable for successful typing of both forensic and historical material. FAU - Schilz, Felix AU - Schilz F AD - Historical Anthropology and Human Ecology, Institute of Zoology and Anthropology, University of Göttingen. fschilz@gwdg.de FAU - Hummel, Susanne AU - Hummel S FAU - Herrmann, Bernd AU - Herrmann B LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (Amelogenin) RN - 0 (Dental Enamel Proteins) RN - 0 (Genetic Markers) SB - IM MH - Alleles MH - Amelogenin MH - Anthropology/methods MH - Burial MH - Chromosome Mapping MH - Chromosomes, Human, X/genetics MH - Chromosomes, Human, Y/genetics MH - DNA Fingerprinting/methods MH - Dental Enamel Proteins/*genetics MH - Europe MH - Genetic Markers/*genetics MH - *Genotype MH - History, Ancient MH - Humans MH - Paleopathology MH - Polymerase Chain Reaction/*methods MH - Reproducibility of Results MH - Sex Determination Processes MH - Tandem Repeat Sequences/*genetics EDAT- 2005/01/15 09:00 MHDA- 2005/04/22 09:00 CRDT- 2005/01/15 09:00 PHST- 2005/01/15 09:00 [pubmed] PHST- 2005/04/22 09:00 [medline] PHST- 2005/01/15 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2004 Dec;62(4):369-78. PMID- 15567864 OWN - NLM STAT- MEDLINE DCOM- 20041221 LR - 20090209 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 306 IP - 5701 DP - 2004 Nov 26 TI - Rise and fall of the Beringian steppe bison. PG - 1561-5 AB - The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later. FAU - Shapiro, Beth AU - Shapiro B AD - Henry Wellcome Ancient Biomolecules Centre, Oxford University, South Parks Road, Oxford OX13PS, UK. FAU - Drummond, Alexei J AU - Drummond AJ FAU - Rambaut, Andrew AU - Rambaut A FAU - Wilson, Michael C AU - Wilson MC FAU - Matheus, Paul E AU - Matheus PE FAU - Sher, Andrei V AU - Sher AV FAU - Pybus, Oliver G AU - Pybus OG FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Barnes, Ian AU - Barnes I FAU - Binladen, Jonas AU - Binladen J FAU - Willerslev, Eske AU - Willerslev E FAU - Hansen, Anders J AU - Hansen AJ FAU - Baryshnikov, Gennady F AU - Baryshnikov GF FAU - Burns, James A AU - Burns JA FAU - Davydov, Sergei AU - Davydov S FAU - Driver, Jonathan C AU - Driver JC FAU - Froese, Duane G AU - Froese DG FAU - Harington, C Richard AU - Harington CR FAU - Keddie, Grant AU - Keddie G FAU - Kosintsev, Pavel AU - Kosintsev P FAU - Kunz, Michael L AU - Kunz ML FAU - Martin, Larry D AU - Martin LD FAU - Stephenson, Robert O AU - Stephenson RO FAU - Storer, John AU - Storer J FAU - Tedford, Richard AU - Tedford R FAU - Zimov, Sergei AU - Zimov S FAU - Cooper, Alan AU - Cooper A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM CIN - Science. 2004 Nov 26;306(5701):1454. doi: 10.1126/science.306.5701.1454. PMID: 15567821 MH - Alaska MH - Animals MH - Bayes Theorem MH - *Bison/classification/genetics MH - Canada MH - China MH - *Climate MH - DNA, Mitochondrial/genetics MH - Environment MH - *Fossils MH - Genetic Variation MH - Genetics, Population MH - Human Activities MH - Humans MH - North America MH - Phylogeny MH - Population Dynamics MH - Sequence Analysis, DNA MH - Time EDAT- 2004/11/30 09:00 MHDA- 2004/12/22 09:00 CRDT- 2004/11/30 09:00 PHST- 2004/11/30 09:00 [pubmed] PHST- 2004/12/22 09:00 [medline] PHST- 2004/11/30 09:00 [entrez] AID - 306/5701/1561 [pii] AID - 10.1126/science.1101074 [doi] PST - ppublish SO - Science. 2004 Nov 26;306(5701):1561-5. doi: 10.1126/science.1101074. PMID- 15254256 OWN - NLM STAT- MEDLINE DCOM- 20050505 LR - 20120605 IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 21 IP - 11 DP - 2004 Nov TI - PCR-induced sequence alterations hamper the typing of prehistoric bone samples for diagnostic achondroplasia mutations. PG - 2005-11 AB - Achondroplasia (ACH) is a skeletal disorder (MIM100800) with an autosomal dominant Mendelian inheritance and complete penetrance. Here we report the screening of ancient bone samples for diagnostic ACH mutations. The diagnostic G-->A transition in the FGFR3 gene at cDNA position 1138 was detected in cloned polymerase chain reaction (PCR) products obtained from the dry mummy of the Semerchet tomb, Egypt (first dynasty, approximately 4,890-5,050 BP [before present]), and from an individual from Kirchheim, Germany (Merovingian period, approximately 1,300-1,500 BP), both of which had short stature. However, these mutations were also reproducibly observed in four ancient control samples from phenotypically healthy individuals (false-positives), rendering the reliable molecular typing of ancient bones for ACH impossible. The treatment of a false-positive DNA extract with uracil N-glycosylase (UNG) to minimize type 2 transitions (G-->A/C-->T) did not reduce the frequency of the false-positive diagnostic ACH mutations. Recently, it was suggested that ancient DNA extracts may induce mutations under PCR. Contemporary human template DNA from a phenotypically healthy individual was therefore spiked with an ancient DNA extract from a cave bear. Again, sequences with the diagnostic G-->A transition in the FGFR3 gene were observed, and it is likely that the false-positive G-->A transitions result from errors introduced during the PCR reaction. Amplifications in the presence of MnCl(2) indicate that position 1138 of the FGFR3 gene is particularly sensitive for mutations. Our data are in line with previously published results on the occurrence of nonrandom mutations in PCR products of contemporary human mitochondrial HVRI template DNA spiked with ancient DNA extracts. FAU - Pusch, C M AU - Pusch CM AD - Institute of Anthropology and Human Genetics, Division of Molecular Genetics, University of Tübingen, Tübingen, Germany. FAU - Broghammer, M AU - Broghammer M FAU - Nicholson, G J AU - Nicholson GJ FAU - Nerlich, A G AU - Nerlich AG FAU - Zink, A AU - Zink A FAU - Kennerknecht, I AU - Kennerknecht I FAU - Bachmann, L AU - Bachmann L FAU - Blin, N AU - Blin N LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040714 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Complementary) RN - 0 (DNA, Mitochondrial) RN - 0 (Receptors, Fibroblast Growth Factor) RN - 9007-49-2 (DNA) RN - EC 2.7.10.1 (FGFR3 protein, human) RN - EC 2.7.10.1 (Protein-Tyrosine Kinases) RN - EC 2.7.10.1 (Receptor, Fibroblast Growth Factor, Type 3) RN - EC 3.2.2.- (DNA Glycosylases) RN - EC 3.2.2.- (Uracil-DNA Glycosidase) SB - IM MH - Achondroplasia/*genetics MH - Biological Evolution MH - Cloning, Molecular MH - DNA/metabolism MH - DNA Glycosylases MH - DNA, Complementary/metabolism MH - DNA, Mitochondrial/genetics MH - Egypt MH - *Evolution, Molecular MH - Germany MH - Humans MH - Mummies MH - *Mutation MH - Paleopathology/*methods MH - Phenotype MH - Point Mutation MH - Polymerase Chain Reaction/*methods MH - Protein-Tyrosine Kinases/genetics MH - Receptor, Fibroblast Growth Factor, Type 3 MH - Receptors, Fibroblast Growth Factor/genetics MH - Reproducibility of Results MH - Sequence Analysis, DNA MH - Specimen Handling MH - Uracil-DNA Glycosidase EDAT- 2004/07/16 05:00 MHDA- 2005/05/06 09:00 CRDT- 2004/07/16 05:00 PHST- 2004/07/16 05:00 [pubmed] PHST- 2005/05/06 09:00 [medline] PHST- 2004/07/16 05:00 [entrez] AID - msh208 [pii] AID - 10.1093/molbev/msh208 [doi] PST - ppublish SO - Mol Biol Evol. 2004 Nov;21(11):2005-11. doi: 10.1093/molbev/msh208. Epub 2004 Jul 14. PMID- 15459281 OWN - NLM STAT- MEDLINE DCOM- 20041005 LR - 20191210 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 32 IP - 17 DP - 2004 Sep 30 TI - Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR. PG - e135 AB - PCR amplification of limited amounts of DNA template carries an increased risk of product redundancy and contamination. We use molecular barcoding to label each genomic DNA template with an individual sequence tag prior to PCR amplification. In addition, we include molecular 'batch-stamps' that effectively label each genomic template with a sample ID and analysis date. This highly sensitive method identifies redundant and contaminant sequences and serves as a reliable method for positive identification of desired sequences; we can therefore capture accurately the genomic template diversity in the sample analyzed. Although our application described here involves the use of hairpin-bisulfite PCR for amplification of double-stranded DNA, the method can readily be adapted to single-strand PCR. Useful applications will include analyses of limited template DNA for biomedical, ancient DNA and forensic purposes. FAU - Miner, Brooks E AU - Miner BE AD - Department of Biology, University of Washington, Seattle, WA 98195, USA. miner@u.washington.edu FAU - Stöger, Reinhard J AU - Stöger RJ FAU - Burden, Alice F AU - Burden AF FAU - Laird, Charles D AU - Laird CD FAU - Hansen, R Scott AU - Hansen RS LA - eng GR - R01 GM053805/GM/NIGMS NIH HHS/United States GR - P30 HD002274/HD/NICHD NIH HHS/United States GR - HD 02274/HD/NICHD NIH HHS/United States GR - R01 HD016659/HD/NICHD NIH HHS/United States GR - HD 16659/HD/NICHD NIH HHS/United States GR - GM 53805/GM/NIGMS NIH HHS/United States PT - Evaluation Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040930 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (FMR1 protein, human) RN - 0 (Nerve Tissue Proteins) RN - 0 (RNA-Binding Proteins) RN - 0 (Sulfites) RN - 139135-51-6 (Fragile X Mental Retardation Protein) SB - IM MH - Base Sequence MH - Fragile X Mental Retardation Protein MH - Genome, Human MH - Humans MH - Male MH - Molecular Sequence Data MH - Nerve Tissue Proteins/genetics MH - Polymerase Chain Reaction/*methods MH - Promoter Regions, Genetic MH - RNA-Binding Proteins/genetics MH - Sequence Analysis, DNA/*methods MH - Sulfites/*chemistry MH - Templates, Genetic PMC - PMC521679 EDAT- 2004/10/02 05:00 MHDA- 2004/10/06 09:00 PMCR- 2004/09/30 CRDT- 2004/10/02 05:00 PHST- 2004/10/02 05:00 [pubmed] PHST- 2004/10/06 09:00 [medline] PHST- 2004/10/02 05:00 [entrez] PHST- 2004/09/30 00:00 [pmc-release] AID - 32/17/e135 [pii] AID - gnh132 [pii] AID - 10.1093/nar/gnh132 [doi] PST - epublish SO - Nucleic Acids Res. 2004 Sep 30;32(17):e135. doi: 10.1093/nar/gnh132. PMID- 15336226 OWN - NLM STAT- MEDLINE DCOM- 20040930 LR - 20140815 IS - 1473-3099 (Print) IS - 1473-3099 (Linking) VI - 4 IP - 9 DP - 2004 Sep TI - Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA. PG - 584-92 AB - During the past 10 years palaeomicrobiology, a new scientific discipline, has developed. The study of ancient pathogens by direct detection of their DNA has answered several historical questions and shown changes to pathogens over time. However, ancient DNA (aDNA) continues to be controversial and great care is needed to provide valid data. Here we review the most successful application of the technology, which is the study of tuberculosis. This has provided direct support for the current theory of Mycobacterium tuberculosis evolution, and suggests areas of investigation for the interaction of M tuberculosis with its host. FAU - Donoghue, Helen D AU - Donoghue HD AD - Centre for Infectious Diseases and International Health, University College London, London, UK. FAU - Spigelman, Mark AU - Spigelman M FAU - Greenblatt, Charles L AU - Greenblatt CL FAU - Lev-Maor, Galit AU - Lev-Maor G FAU - Bar-Gal, Gila Kahila AU - Bar-Gal GK FAU - Matheson, Carney AU - Matheson C FAU - Vernon, Kim AU - Vernon K FAU - Nerlich, Andreas G AU - Nerlich AG FAU - Zink, Albert R AU - Zink AR LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Lancet Infect Dis JT - The Lancet. Infectious diseases JID - 101130150 RN - 0 (DNA, Bacterial) SB - IM MH - Animals MH - Biological Evolution MH - Communicable Diseases/history/microbiology MH - DNA, Bacterial/analysis/*history MH - History, Ancient MH - Humans MH - Mummies MH - Mycobacterium tuberculosis/*genetics MH - Paleopathology MH - Tuberculosis/*history/microbiology EDAT- 2004/09/01 05:00 MHDA- 2004/10/01 05:00 CRDT- 2004/09/01 05:00 PHST- 2004/09/01 05:00 [pubmed] PHST- 2004/10/01 05:00 [medline] PHST- 2004/09/01 05:00 [entrez] AID - S1473309904011338 [pii] AID - 10.1016/S1473-3099(04)01133-8 [doi] PST - ppublish SO - Lancet Infect Dis. 2004 Sep;4(9):584-92. doi: 10.1016/S1473-3099(04)01133-8. PMID- 15199524 OWN - NLM STAT- MEDLINE DCOM- 20040920 LR - 20200824 IS - 0002-9297 (Print) IS - 1537-6605 (Electronic) IS - 0002-9297 (Linking) VI - 75 IP - 2 DP - 2004 Aug TI - Authenticity of ancient-DNA results: a statistical approach. PG - 240-50 AB - Although there have been several papers recommending appropriate experimental designs for ancient-DNA studies, there have been few attempts at statistical analysis. We assume that we cannot decide whether a result is authentic simply by examining the sequence (e.g., when working with humans and domestic animals). We use a maximum-likelihood approach to estimate the probability that a positive result from a sample is (either partly or entirely) an amplification of DNA that was present in the sample before the experiment began. Our method is useful in two situations. First, we can decide in advance how many samples will be needed to achieve a given level of confidence. For example, to be almost certain (95% confidence interval 0.96-1.00, maximum-likelihood estimate 1.00) that a positive result comes, at least in part, from DNA present before the experiment began, we need to analyze at least five samples and controls, even if all samples and no negative controls yield positive results. Second, we can decide how much confidence to place in results that have been obtained already, whether or not there are positive results from some controls. For example, the risk that at least one negative control yields a positive result increases with the size of the experiment, but the effects of occasional contamination are less severe in large experiments. FAU - Spencer, Matthew AU - Spencer M AD - Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom. matts@mathstat.dal.ca FAU - Howe, Christopher J AU - Howe CJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040615 PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 SB - IM MH - *Data Interpretation, Statistical MH - Humans MH - Likelihood Functions MH - *Sequence Analysis, DNA MH - Time Factors PMC - PMC1216058 EDAT- 2004/06/17 05:00 MHDA- 2004/09/21 05:00 PMCR- 2005/02/01 CRDT- 2004/06/17 05:00 PHST- 2004/01/29 00:00 [received] PHST- 2004/05/21 00:00 [accepted] PHST- 2004/06/17 05:00 [pubmed] PHST- 2004/09/21 05:00 [medline] PHST- 2004/06/17 05:00 [entrez] PHST- 2005/02/01 00:00 [pmc-release] AID - S0002-9297(07)62406-9 [pii] AID - 40994 [pii] AID - 10.1086/422826 [doi] PST - ppublish SO - Am J Hum Genet. 2004 Aug;75(2):240-50. doi: 10.1086/422826. Epub 2004 Jun 15. PMID- 15084676 OWN - NLM STAT- MEDLINE DCOM- 20050214 LR - 20040712 IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 21 IP - 8 DP - 2004 Aug TI - Mutations induced by ancient DNA extracts? PG - 1463-7 AB - We have investigated whether some factor in ancient DNA extracts induces site-specific mutations in modern DNA. We find no evidence for higher mutation rates when extracts from three different Pleistocene mammals are added to modern DNA than when water or extraction blanks are added. We also fail to find evidence that any such factor affects ancient DNA sequences determined from the same extracts. This as well as the patterns of nucleotide substitutions seen in DNA sequences determined from hundreds of other specimens leads us to doubt that a previously unknown mutagenic factor can be a general feature of extracts from old tissues. FAU - Serre, D AU - Serre D FAU - Hofreiter, M AU - Hofreiter M FAU - Pääbo, S AU - Pääbo S LA - eng PT - Letter DEP - 20040414 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Sequence MH - DNA/*genetics MH - DNA, Mitochondrial/*genetics MH - *Fossils MH - Humans MH - Molecular Sequence Data MH - Mutation/*genetics MH - Plants/genetics MH - Sequence Analysis, DNA/*methods EDAT- 2004/04/16 05:00 MHDA- 2005/02/16 09:00 CRDT- 2004/04/16 05:00 PHST- 2004/04/16 05:00 [pubmed] PHST- 2005/02/16 09:00 [medline] PHST- 2004/04/16 05:00 [entrez] AID - msh139 [pii] AID - 10.1093/molbev/msh139 [doi] PST - ppublish SO - Mol Biol Evol. 2004 Aug;21(8):1463-7. doi: 10.1093/molbev/msh139. Epub 2004 Apr 14. PMID- 15456130 OWN - NLM STAT- MEDLINE DCOM- 20050322 LR - 20061115 IS - 0026-8984 (Print) IS - 0026-8984 (Linking) VI - 38 IP - 4 DP - 2004 Jul-Aug TI - [Polymorphism of mitochondrial genome noncoding regions in the three Kazakh populations inhabited different areas of Kazakhstan and in the samples of DNA from ancient people of Kazakhstan Altai]. PG - 592-601 AB - Polymorphism of major noncoding region of mitochondrial DNA (mtDNA D-loop, 528 bp in length) from the three modem kazakh populations and from DNA samples of ancient people inhabited modern Kazakhstani Altai were studied. PCR and RFLP analysis of 13 sites of restriction--BamHI, EcoRV, Sau3AI (1 restriction site), KpnI (2 sites), HaeIII (3 sites), RsaI (5 restriction sites), were carried out. The distribution of each site frequencies was determined. Nucleotide diversity (h) and genetic distance between different kazakh population and other populations of world were estimated. The same RFLP analysis of the mitochondrial DNA control region was carried out for the paleogenomic samples. It was shown that two samples of ancient mitochondrial DNA were monomorphous throughout all analyzed restriction sites. FAU - Aĭtkhozhina, N A AU - Aĭtkhozhina NA FAU - Dzisiuk, N V AU - Dzisiuk NV FAU - Liudvikova, E K AU - Liudvikova EK LA - rus PT - English Abstract PT - Journal Article TT - Polimorfizm nekodiruiushcheĭ oblasti mitokhondrial'nogo genoma tre populiatsiĭ kazakhov, prozhivaiushchikh na razlichnykh territoriiakh kazakhstana, i obratsov DNK drevnikh predstaviteleĭ kazakhstanskogo altaia. PL - Russia (Federation) TA - Mol Biol (Mosk) JT - Molekuliarnaia biologiia JID - 0105454 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - *Genetics, Population MH - *Genome, Human MH - Humans MH - Polymerase Chain Reaction MH - *Polymorphism, Genetic MH - Polymorphism, Restriction Fragment Length MH - Russia EDAT- 2004/10/01 05:00 MHDA- 2005/03/23 09:00 CRDT- 2004/10/01 05:00 PHST- 2004/10/01 05:00 [pubmed] PHST- 2005/03/23 09:00 [medline] PHST- 2004/10/01 05:00 [entrez] PST - ppublish SO - Mol Biol (Mosk). 2004 Jul-Aug;38(4):592-601. PMID- 15203015 OWN - NLM STAT- MEDLINE DCOM- 20040813 LR - 20170225 IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 14 IP - 12 DP - 2004 Jun 22 TI - Ancient mitochondrial DNA from hair. PG - R463-4 FAU - Gilbert, M Thomas P AU - Gilbert MT FAU - Wilson, Andrew S AU - Wilson AS FAU - Bunce, Michael AU - Bunce M FAU - Hansen, Anders J AU - Hansen AJ FAU - Willerslev, Eske AU - Willerslev E FAU - Shapiro, Beth AU - Shapiro B FAU - Higham, Thomas F G AU - Higham TF FAU - Richards, Michael P AU - Richards MP FAU - O'Connell, Tamsin C AU - O'Connell TC FAU - Tobin, Desmond J AU - Tobin DJ FAU - Janaway, Robert C AU - Janaway RC FAU - Cooper, Alan AU - Cooper A LA - eng PT - Comparative Study PT - Letter PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) RN - 0 (DNA, Ribosomal) SB - IM MH - Animals MH - DNA, Mitochondrial/*genetics MH - DNA, Ribosomal/genetics MH - *Fossils MH - Hair/*chemistry MH - Humans MH - Mammals/*genetics MH - Sequence Analysis, DNA MH - Specimen Handling/methods EDAT- 2004/06/19 05:00 MHDA- 2004/08/17 10:00 CRDT- 2004/06/19 05:00 PHST- 2004/06/19 05:00 [pubmed] PHST- 2004/08/17 10:00 [medline] PHST- 2004/06/19 05:00 [entrez] AID - S0960-9822(04)00411-7 [pii] AID - 10.1016/j.cub.2004.06.008 [doi] PST - ppublish SO - Curr Biol. 2004 Jun 22;14(12):R463-4. doi: 10.1016/j.cub.2004.06.008. PMID- 15182692 OWN - NLM STAT- MEDLINE DCOM- 20040902 LR - 20170225 IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 14 IP - 11 DP - 2004 Jun 8 TI - Ancient DNA: would the real Neandertal please stand up? PG - R431-3 AB - Mitochondrial DNA sequences recovered from eight Neandertal specimens cannot be detected in either early fossil Europeans or in modern populations. This indicates that, if Neandertals made any genetic contribution at all to modern humans, it must have been limited, though the extent of the contribution cannot be resolved at present. CI - Copyright 2004 Elsevier Ltd. FAU - Cooper, Alan AU - Cooper A AD - Henry Wellcome Ancient Biomolecules Centre and Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. FAU - Drummond, Alexei J AU - Drummond AJ FAU - Willerslev, Eske AU - Willerslev E LA - eng PT - Journal Article PT - Review PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - DNA, Mitochondrial/*genetics MH - *Fossils MH - Hominidae/*genetics MH - Humans MH - *Models, Genetic MH - Time Factors RF - 17 EDAT- 2004/06/09 05:00 MHDA- 2004/09/03 05:00 CRDT- 2004/06/09 05:00 PHST- 2004/06/09 05:00 [pubmed] PHST- 2004/09/03 05:00 [medline] PHST- 2004/06/09 05:00 [entrez] AID - S0960-9822(04)00364-1 [pii] AID - 10.1016/j.cub.2004.05.037 [doi] PST - ppublish SO - Curr Biol. 2004 Jun 8;14(11):R431-3. doi: 10.1016/j.cub.2004.05.037. PMID- 15255049 OWN - NLM STAT- MEDLINE DCOM- 20040816 LR - 20220316 IS - 0962-8452 (Print) IS - 1471-2954 (Electronic) IS - 0962-8452 (Linking) VI - 271 IP - 1542 DP - 2004 May 7 TI - Unravelling migrations in the steppe: mitochondrial DNA sequences from ancient central Asians. PG - 941-7 AB - This study helps to clarify the debate on the Western and Eastern genetic influences in Central Asia. Thirty-six skeletal remains from Kazakhstan (Central Asia), excavated from different sites dating between the fifteenth century BC to the fifth century AD, have been analysed for the hypervariable control region (HVR-I) and haplogroup diagnostic single nucleotide polymorphisms (SNPs) of the mitochondrial DNA genome. Standard authentication criteria for ancient DNA studies, including multiple extractions, cloning of PCR products and independent replication, have been followed. The distribution of east and west Eurasian lineages through time in the region is concordant with the available archaeological information: prior to the thirteenth-seventh century BC, all Kazakh samples belong to European lineages; while later an arrival of east Eurasian sequences that coexisted with the previous west Eurasian genetic substratum can be detected. The presence of an ancient genetic substratum of European origin in West Asia may be related to the discovery of ancient mummies with European features in Xinjiang and to the existence of an extinct Indo-European language, Tocharian. This study demonstrates the usefulness of the ancient DNA in unravelling complex patterns of past human migrations so as to help decipher the origin of present-day admixed populations. FAU - Lalueza-Fox, C AU - Lalueza-Fox C AD - Unitat d'Antropologia, Departimenti Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain. carles.lalueza@upf.edu FAU - Sampietro, M L AU - Sampietro ML FAU - Gilbert, M T P AU - Gilbert MT FAU - Castri, L AU - Castri L FAU - Facchini, F AU - Facchini F FAU - Pettener, D AU - Pettener D FAU - Bertranpetit, J AU - Bertranpetit J LA - eng PT - Comparative Study PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Proc Biol Sci JT - Proceedings. Biological sciences JID - 101245157 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration/*history MH - *Fossils MH - Geography MH - Haplotypes/genetics MH - *History, Ancient MH - Humans MH - Kazakhstan MH - Polymorphism, Restriction Fragment Length MH - Polymorphism, Single Nucleotide/genetics MH - Population Dynamics MH - Sequence Analysis, DNA PMC - PMC1691686 EDAT- 2004/07/17 05:00 MHDA- 2004/08/18 05:00 PMCR- 2006/05/07 CRDT- 2004/07/17 05:00 PHST- 2004/07/17 05:00 [pubmed] PHST- 2004/08/18 05:00 [medline] PHST- 2004/07/17 05:00 [entrez] PHST- 2006/05/07 00:00 [pmc-release] AID - 10.1098/rspb.2004.2698 [doi] PST - ppublish SO - Proc Biol Sci. 2004 May 7;271(1542):941-7. doi: 10.1098/rspb.2004.2698. PMID- 15014140 OWN - NLM STAT- MEDLINE DCOM- 20041210 LR - 20101118 IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 21 IP - 5 DP - 2004 May TI - Spiking of contemporary human template DNA with ancient DNA extracts induces mutations under PCR and generates nonauthentic mitochondrial sequences. PG - 957-64 AB - Proof of authenticity is the greatest challenge in palaeogenetic research, and many safeguards have become standard routine in laboratories specialized on ancient DNA research. Here we describe an as-yet unknown source of artifacts that will require special attention in the future. We show that ancient DNA extracts on their own can have an inhibitory and mutagenic effect under PCR. We have spiked PCR reactions including known human test DNA with 14 selected ancient DNA extracts from human and nonhuman sources. We find that the ancient DNA extracts inhibit the amplification of large fragments to different degrees, suggesting that the usual control against contaminations, i.e., the absence of long amplifiable fragments, is not sufficient. But even more important, we find that the extracts induce mutations in a nonrandom fashion. We have amplified a 148-bp stretch of the mitochondrial HVRI from contemporary human template DNA in spiked PCR reactions. Subsequent analysis of 547 sequences from cloned amplicons revealed that the vast majority (76.97%) differed from the correct sequence by single nucleotide substitutions and/or indels. In total, 34 positions of a 103-bp alignment are affected, and most mutations occur repeatedly in independent PCR amplifications. Several of the induced mutations occur at positions that have previously been detected in studies of ancient hominid sequences, including the Neandertal sequences. Our data imply that PCR-induced mutations are likely to be an intrinsic and general problem of PCR amplifications of ancient templates. Therefore, ancient DNA sequences should be considered with caution, at least as long as the molecular basis for the extract-induced mutations is not understood. FAU - Pusch, Carsten M AU - Pusch CM AD - Institute of Anthropology and Human Genetics, Division of Molecular Genetics, University of Tübingen, Tübingen, Germany. FAU - Bachmann, Lutz AU - Bachmann L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040310 PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Base Sequence MH - Biological Evolution MH - Cloning, Molecular MH - DNA/genetics MH - DNA Mutational Analysis/*methods MH - DNA, Mitochondrial/*genetics MH - *Evolution, Molecular MH - *Genome, Human MH - Humans MH - Molecular Sequence Data MH - *Mutation MH - Plasmids/metabolism MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA EDAT- 2004/03/12 05:00 MHDA- 2004/12/16 09:00 CRDT- 2004/03/12 05:00 PHST- 2004/03/12 05:00 [pubmed] PHST- 2004/12/16 09:00 [medline] PHST- 2004/03/12 05:00 [entrez] AID - msh107 [pii] AID - 10.1093/molbev/msh107 [doi] PST - ppublish SO - Mol Biol Evol. 2004 May;21(5):957-64. doi: 10.1093/molbev/msh107. Epub 2004 Mar 10. PMID- 15022363 OWN - NLM STAT- MEDLINE DCOM- 20040726 LR - 20221207 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 123 IP - 4 DP - 2004 Apr TI - Genetic analysis and ethnic affinities from two Scytho-Siberian skeletons. PG - 351-60 AB - We extracted DNA from two skeletons belonging to the Sytho-Siberian population, which were excavated from the Sebÿstei site (dating back 2,500 years) in the Altai Republic (Central Asia). Ancient DNA was analyzed by autosomal short tandem repeats (STRs) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these two skeletons were not close relatives. Moreover, their haplogroups were characteristic of Asian populations. Comparison with the haplogroup of 3,523 Asian and American individuals linked one skeleton with a putative ancestral paleo-Asiatic population and the other with Chinese populations. It appears that the genetic study of ancient populations of Central Asia brings important elements to the understanding of human population movements in Asia. CI - Copyright 2003 Wiley-Liss, Inc. FAU - Ricaut, François-Xavier AU - Ricaut FX AD - Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, 67085 Strasbourg, France. fx.ricault@infonie.fr FAU - Keyser-Tracqui, Christine AU - Keyser-Tracqui C FAU - Cammaert, Laurence AU - Cammaert L FAU - Crubézy, Eric AU - Crubézy E FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Adult MH - Asia/ethnology MH - Asian People/*genetics MH - Child, Preschool MH - DNA, Mitochondrial/analysis/genetics MH - Ethnicity/*genetics MH - *Fossils MH - Genetic Variation/*genetics MH - Humans MH - Male MH - Paleontology/methods MH - Polymorphism, Genetic/genetics MH - *Skeleton MH - Tandem Repeat Sequences/genetics EDAT- 2004/03/17 05:00 MHDA- 2004/07/28 05:00 CRDT- 2004/03/17 05:00 PHST- 2004/03/17 05:00 [pubmed] PHST- 2004/07/28 05:00 [medline] PHST- 2004/03/17 05:00 [entrez] AID - 10.1002/ajpa.10323 [doi] PST - ppublish SO - Am J Phys Anthropol. 2004 Apr;123(4):351-60. doi: 10.1002/ajpa.10323. PMID- 15015132 OWN - NLM STAT- MEDLINE DCOM- 20040510 LR - 20211203 IS - 0002-9297 (Print) IS - 1537-6605 (Electronic) IS - 0002-9297 (Linking) VI - 74 IP - 4 DP - 2004 Apr TI - The Etruscans: a population-genetic study. PG - 694-704 AB - The origins of the Etruscans, a non-Indo-European population of preclassical Italy, are unclear. There is broad agreement that their culture developed locally, but the Etruscans' evolutionary and migrational relationships are largely unknown. In this study, we determined mitochondrial DNA sequences in multiple clones derived from bone samples of 80 Etruscans who lived between the 7th and the 3rd centuries b.c. In the first phase of the study, we eliminated all specimens for which any of nine tests for validation of ancient DNA data raised the suspicion that either degradation or contamination by modern DNA might have occurred. On the basis of data from the remaining 30 individuals, the Etruscans appeared as genetically variable as modern populations. No significant heterogeneity emerged among archaeological sites or time periods, suggesting that different Etruscan communities shared not only a culture but also a mitochondrial gene pool. Genetic distances and sequence comparisons show closer evolutionary relationships with the eastern Mediterranean shores for the Etruscans than for modern Italian populations. All mitochondrial lineages observed among the Etruscans appear typically European or West Asian, but only a few haplotypes were found to have an exact match in a modern mitochondrial database, raising new questions about the Etruscans' fate after their assimilation into the Roman state. FAU - Vernesi, Cristiano AU - Vernesi C AD - Dipartimento di Biologia, Universita di Ferrara, Ferrara, Italy. FAU - Caramelli, David AU - Caramelli D FAU - Dupanloup, Isabelle AU - Dupanloup I FAU - Bertorelle, Giorgio AU - Bertorelle G FAU - Lari, Martina AU - Lari M FAU - Cappellini, Enrico AU - Cappellini E FAU - Moggi-Cecchi, Jacopo AU - Moggi-Cecchi J FAU - Chiarelli, Brunetto AU - Chiarelli B FAU - Castrì, Loredana AU - Castrì L FAU - Casoli, Antonella AU - Casoli A FAU - Mallegni, Francesco AU - Mallegni F FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C FAU - Barbujani, Guido AU - Barbujani G LA - eng SI - GENBANK/AY530759 SI - GENBANK/AY530760 SI - GENBANK/AY530761 SI - GENBANK/AY530762 SI - GENBANK/AY530763 SI - GENBANK/AY530764 SI - GENBANK/AY530765 SI - GENBANK/AY530766 SI - GENBANK/AY530767 SI - GENBANK/AY530768 SI - GENBANK/AY530769 SI - GENBANK/AY530770 SI - GENBANK/AY530771 SI - GENBANK/AY530772 SI - GENBANK/AY530773 SI - GENBANK/AY530774 SI - GENBANK/AY530775 SI - GENBANK/AY530776 SI - GENBANK/AY530777 SI - GENBANK/AY530778 SI - GENBANK/AY530779 SI - GENBANK/AY530780 SI - GENBANK/AY530781 SI - RefSeq/NC_001567 PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040310 PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Mitochondrial) SB - IM CIN - Am J Hum Genet. 2004 Nov;75(5):919-20; author reply 923-7. doi: 10.1086/425180. PMID: 15457405 CIN - Am J Hum Genet. 2004 Nov;75(5):920-3; author reply 923-7. doi: 10.1086/425220. PMID: 15457406 MH - Bone and Bones/metabolism MH - DNA, Mitochondrial/*analysis/*genetics/isolation & purification MH - Ethnicity/*genetics MH - Europe/ethnology MH - Evolution, Molecular MH - *Fossils MH - Genetic Variation/genetics MH - Genetics, Population MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Italy/ethnology MH - Molecular Sequence Data MH - *Phylogeny MH - Reproducibility of Results MH - Roman World PMC - PMC1181945 EDAT- 2004/03/12 05:00 MHDA- 2004/05/11 05:00 PMCR- 2004/10/01 CRDT- 2004/03/12 05:00 PHST- 2003/12/05 00:00 [received] PHST- 2004/01/28 00:00 [accepted] PHST- 2004/03/12 05:00 [pubmed] PHST- 2004/05/11 05:00 [medline] PHST- 2004/03/12 05:00 [entrez] PHST- 2004/10/01 00:00 [pmc-release] AID - S0002-9297(07)61894-1 [pii] AID - 40826 [pii] AID - 10.1086/383284 [doi] PST - ppublish SO - Am J Hum Genet. 2004 Apr;74(4):694-704. doi: 10.1086/383284. Epub 2004 Mar 10. PMID- 14766912 OWN - NLM STAT- MEDLINE DCOM- 20040409 LR - 20200826 IS - 1350-0872 (Print) IS - 1350-0872 (Linking) VI - 150 IP - Pt 2 DP - 2004 Feb TI - Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims. PG - 341-354 LID - 10.1099/mic.0.26594-0 [doi] AB - This study reports the results of a collaborative study undertaken by two independent research groups to (a) confirm recent PCR-based detection of Yersinia pestis DNA in human teeth from medieval plague victims in France, and (b) to extend these observations over five different European burial sites believed to contain plague victims dating from the late 13th to 17th centuries. Several different sets of primers were used, including those previously documented to yield positive results on ancient DNA extracts. No Y. pestis DNA could be amplified from DNA extracted from 108 teeth belonging to 61 individuals, despite the amplification of numerous other bacterial DNA sequences. Several methods of extracting dentine prior to the DNA extraction were also compared. PCR for bacterial 16S rDNA indicated the presence of multiple bacterial species in 23 out of 27 teeth DNA extracts where dentine was extracted using previously described methods. In comparison, positive results were obtained from only five out of 44 teeth DNA extracts for which a novel contamination-minimizing embedding technique was used. Therefore, high levels of environmental bacterial DNA are present in DNA extracts where previously described methods of tooth manipulation are used. To conclude, the absence of Y. pestis-specific DNA in an exhaustive search using specimens from multiple putative European plague burial sites does not allow us to confirm the identification of Y. pestis as the aetiological agent of the Black Death and subsequent plagues. In addition, the utility of the published tooth-based ancient DNA technique used to diagnose fatal bacteraemias in historical epidemics still awaits independent corroboration. FAU - Gilbert, M Thomas P AU - Gilbert MTP AD - Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. FAU - Cuccui, Jon AU - Cuccui J AD - Centre for Infection, Institute of Cell and Molecular Science, Barts and The London, Queen Mary's School of Medicine and Dentistry, 64 Turner St, London E1 2AD, UK. FAU - White, William AU - White W AD - Museum of London, 46 Eagle Wharf Road, London N1 7ED, UK. FAU - Lynnerup, Niels AU - Lynnerup N AD - Laboratory of Biological Anthropology, Institute of Forensic Pathology, University of Copenhagen, 1017, Copenhagen, Denmark. FAU - Titball, Richard W AU - Titball RW AD - Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK. FAU - Cooper, Alan AU - Cooper A AD - Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. FAU - Prentice, Michael B AU - Prentice MB AD - Centre for Infection, Institute of Cell and Molecular Science, Barts and The London, Queen Mary's School of Medicine and Dentistry, 64 Turner St, London E1 2AD, UK. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Microbiology (Reading) JT - Microbiology (Reading, England) JID - 9430468 RN - 0 (DNA Primers) RN - 0 (DNA, Bacterial) SB - IM CIN - Microbiology (Reading). 2004 Feb;150(Pt 2):263-264. doi: 10.1099/mic.0.26885-0. PMID: 14766902 MH - Base Sequence MH - DNA Primers MH - DNA, Bacterial/genetics/*isolation & purification MH - Europe/epidemiology MH - Funeral Rites/history MH - History, Medieval MH - Humans MH - Plague/history/*microbiology MH - Polymerase Chain Reaction/methods MH - Tooth/*microbiology MH - Yersinia pestis/genetics/*isolation & purification EDAT- 2004/02/10 05:00 MHDA- 2004/04/10 05:00 CRDT- 2004/02/10 05:00 PHST- 2004/02/10 05:00 [pubmed] PHST- 2004/04/10 05:00 [medline] PHST- 2004/02/10 05:00 [entrez] AID - 10.1099/mic.0.26594-0 [doi] PST - ppublish SO - Microbiology (Reading). 2004 Feb;150(Pt 2):341-354. doi: 10.1099/mic.0.26594-0. PMID- 14608462 OWN - NLM STAT- MEDLINE DCOM- 20040429 LR - 20211203 IS - 0937-9827 (Print) IS - 0937-9827 (Linking) VI - 118 IP - 1 DP - 2004 Feb TI - Genetic analysis of human remains found in two eighteenth century Yakut graves at At-Dabaan. PG - 24-31 AB - We extracted DNA from three skeletons belonging to the Yakut population, which were excavated from the At-Dabaan site (dating back 300 years) in the Sakha Republic (Russia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these three skeletons were not close relatives but probably linked to the same clan structure. Comparison of their haplotypes with the haplotypes of 8,774 Eurasian individuals suggested a relative specificity and continuity of part of the Yakut mitochondrial gene pool during the last 3 centuries. FAU - Ricaut, François-Xavier AU - Ricaut FX AD - Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, 11 rue Humann, 67085 Strasbourg, France. fx.ricaut@infonie.fr FAU - Kolodesnikov, Sergei AU - Kolodesnikov S FAU - Keyser-Tracqui, Christine AU - Keyser-Tracqui C FAU - Alekseev, Anatoly Nikoyevich AU - Alekseev AN FAU - Crubézy, Eric AU - Crubézy E FAU - Ludes, Bertrand AU - Ludes B LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20031108 PL - Germany TA - Int J Legal Med JT - International journal of legal medicine JID - 9101456 RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - Base Sequence MH - DNA, Mitochondrial/*genetics MH - Ethnicity/*genetics MH - Genetics, Population MH - History, 18th Century MH - Humans MH - Molecular Sequence Data MH - Siberia MH - Tandem Repeat Sequences/*genetics EDAT- 2003/11/11 05:00 MHDA- 2004/04/30 05:00 CRDT- 2003/11/11 05:00 PHST- 2003/07/04 00:00 [received] PHST- 2003/10/14 00:00 [accepted] PHST- 2003/11/11 05:00 [pubmed] PHST- 2004/04/30 05:00 [medline] PHST- 2003/11/11 05:00 [entrez] AID - 10.1007/s00414-003-0411-6 [doi] PST - ppublish SO - Int J Legal Med. 2004 Feb;118(1):24-31. doi: 10.1007/s00414-003-0411-6. Epub 2003 Nov 8. PMID- 15040907 OWN - NLM STAT- MEDLINE DCOM- 20040527 LR - 20101118 IS - 0379-0738 (Print) IS - 0379-0738 (Linking) VI - 139 IP - 2-3 DP - 2004 Jan 28 TI - Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. PG - 141-9 AB - We explore different designs to estimate both nuclear and mitochondrial human DNA (mtDNA) content based on the detection of the 5' nuclease activity of the Taq DNA polymerase using fluorogenic probes and a real-time quantitative PCR detection system. Human mtDNA quantification was accomplished by monitoring the real-time progress of the PCR-amplification of two different fragment sizes (113 and 287 bp) within the hypervariable region I (HV1) of the mtDNA control region, using two fluorogenic probes to specifically determine the mtDNA copy of each fragment size category. This mtDNA real-time PCR design has been used to assess the mtDNA preservation (copy number and degradation state) of DNA samples retrieved from 500 to 1500 years old human remains that showed low copy number and highly degraded mtDNA. The quantification of nuclear DNA was achieved by real-time PCR of a segment of the X-Y homologous amelogenin (AMG) gene that allowed the simultaneous estimation of a Y-specific fragment (AMGY: 112 bp) and a X-specific fragment (AMGX: 106 bp) making possible not only haploid or diploid DNA quantitation but also sex determination. The AMG real-time PCR design has been used to quantify a set of 57 DNA samples from 4-5 years old forensic bone remains with improved sensitivity compared with the slot-blot hybridization method. The potential utility of this technology to improve the quality of some PCR-based forensic and ancient DNA studies (microsatellite typing and mtDNA sequencing) is discussed. FAU - Alonso, Antonio AU - Alonso A AD - Instituto Nacional de Toxicología, Servicio de Biología, Luis Cabrera 9, 28002 Madrid, Spain. a.alonso@mju.es FAU - Martín, Pablo AU - Martín P FAU - Albarrán, Cristina AU - Albarrán C FAU - García, Pilar AU - García P FAU - García, Oscar AU - García O FAU - de Simón, Lourdes Fernández AU - de Simón LF FAU - García-Hirschfeld, Julia AU - García-Hirschfeld J FAU - Sancho, Manuel AU - Sancho M FAU - de La Rúa, Concepción AU - de La Rúa C FAU - Fernández-Piqueras, Jose AU - Fernández-Piqueras J LA - eng PT - Journal Article PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 0 (AMELX protein, human) RN - 0 (Amelogenin) RN - 0 (Dental Enamel Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Amelogenin MH - Animals MH - Cell Nucleus/genetics MH - DNA/*analysis MH - DNA Fingerprinting/*methods MH - Dental Enamel Proteins/genetics MH - Female MH - Forensic Anthropology/methods MH - *Gene Dosage MH - Hominidae/genetics MH - Humans MH - Male MH - Polymerase Chain Reaction/*methods MH - Sex Determination Analysis MH - Tandem Repeat Sequences MH - Tooth Germ EDAT- 2004/03/26 05:00 MHDA- 2004/05/28 05:00 CRDT- 2004/03/26 05:00 PHST- 2003/09/15 00:00 [received] PHST- 2003/10/03 00:00 [accepted] PHST- 2004/03/26 05:00 [pubmed] PHST- 2004/05/28 05:00 [medline] PHST- 2004/03/26 05:00 [entrez] AID - S0379073803004237 [pii] AID - 10.1016/j.forsciint.2003.10.008 [doi] PST - ppublish SO - Forensic Sci Int. 2004 Jan 28;139(2-3):141-9. doi: 10.1016/j.forsciint.2003.10.008. PMID- 15568989 OWN - NLM STAT- MEDLINE DCOM- 20050322 LR - 20220408 IS - 0066-4197 (Print) IS - 0066-4197 (Linking) VI - 38 DP - 2004 TI - Genetic analyses from ancient DNA. PG - 645-79 AB - About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research. FAU - Pääbo, Svante AU - Pääbo S AD - Max Planck Institute for Evolutionary Anthropology, D-04013 Leipzig, Germany. paabo@eva.mpg.de FAU - Poinar, Hendrik AU - Poinar H FAU - Serre, David AU - Serre D FAU - Jaenicke-Despres, Viviane AU - Jaenicke-Despres V FAU - Hebler, Juliane AU - Hebler J FAU - Rohland, Nadin AU - Rohland N FAU - Kuch, Melanie AU - Kuch M FAU - Krause, Johannes AU - Krause J FAU - Vigilant, Linda AU - Vigilant L FAU - Hofreiter, Michael AU - Hofreiter M LA - eng PT - Journal Article PT - Review PL - United States TA - Annu Rev Genet JT - Annual review of genetics JID - 0117605 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Animals, Domestic MH - *Archaeology MH - Behavior MH - Cloning, Molecular MH - DNA/*genetics/metabolism MH - DNA Damage MH - DNA, Mitochondrial/genetics MH - Deamination MH - Diet MH - *Fossils MH - Geologic Sediments MH - Hominidae/genetics MH - Humans MH - Mummies MH - Phylogeny MH - Sequence Analysis, DNA RF - 176 EDAT- 2004/12/01 09:00 MHDA- 2005/03/23 09:00 CRDT- 2004/12/01 09:00 PHST- 2004/12/01 09:00 [pubmed] PHST- 2005/03/23 09:00 [medline] PHST- 2004/12/01 09:00 [entrez] AID - 10.1146/annurev.genet.37.110801.143214 [doi] PST - ppublish SO - Annu Rev Genet. 2004;38:645-79. doi: 10.1146/annurev.genet.37.110801.143214. PMID- 14708953 OWN - NLM STAT- MEDLINE DCOM- 20040203 LR - 20131213 IS - 0025-6196 (Print) IS - 0025-6196 (Linking) VI - 79 IP - 1 DP - 2004 Jan TI - Cardiovascular disease resulting from a diet and lifestyle at odds with our Paleolithic genome: how to become a 21st-century hunter-gatherer. PG - 101-8 AB - Our genetic make-up, shaped through millions of years of evolution, determines our nutritional and activity needs. Although the human genome has remained primarily unchanged since the agricultural revolution 10,000 years ago, our diet and lifestyle have become progressively more divergent from those of our ancient ancestors. Accumulating evidence suggests that this mismatch between our modern diet and lifestyle and our Paleolithic genome is playing a substantial role in the ongoing epidemics of obesity, hypertension, diabetes, and atherosclerotic cardiovascular disease. Until 500 generations ago, all humans consumed only wild and unprocessed food foraged and hunted from their environment. These circumstances provided a diet high in lean protein, polyunsaturated fats (especially omega-3 [omega-3] fatty acids), monounsaturated fats, fiber, vitamins, minerals, antioxidants, and other beneficial phytochemicals. Historical and anthropological studies show hunter-gatherers generally to be healthy, fit, and largely free of the degenerative cardiovascular diseases common in modern societies. This review outlines the essence of our hunter-gatherer genetic legacy and suggests practical steps to re-align our modern milieu with our ancient genome in an effort to improve cardiovascular health. FAU - O'Keefe, James H Jr AU - O'Keefe JH Jr AD - Mid America Heart Institute, Cardiovascular Consultants, Kansas City, MO 64111, USA. jhokeefe@cc-pc.com FAU - Cordain, Loren AU - Cordain L LA - eng PT - Historical Article PT - Journal Article PT - Review PL - England TA - Mayo Clin Proc JT - Mayo Clinic proceedings JID - 0405543 RN - 0 (Fatty Acids, Monounsaturated) RN - 0 (Fatty Acids, Omega-3) RN - 0 (Trans Fatty Acids) SB - IM CIN - Mayo Clin Proc. 2004 May;79(5):703; author reply 703-4, 707. doi: 10.1016/S0025-6196(11)62310-0. PMID: 15132422 MH - Beverages MH - Cardiovascular Diseases/history/*prevention & control MH - Diet/*history MH - Energy Intake MH - Exercise MH - Fatty Acids, Monounsaturated/administration & dosage MH - Fatty Acids, Omega-3/administration & dosage MH - Genome, Human MH - History, Ancient MH - Humans MH - *Life Style MH - Meat MH - Trans Fatty Acids/adverse effects RF - 75 EDAT- 2004/01/08 05:00 MHDA- 2004/02/05 05:00 CRDT- 2004/01/08 05:00 PHST- 2004/01/08 05:00 [pubmed] PHST- 2004/02/05 05:00 [medline] PHST- 2004/01/08 05:00 [entrez] AID - S0025-6196(11)63262-X [pii] AID - 10.4065/79.1.101 [doi] PST - ppublish SO - Mayo Clin Proc. 2004 Jan;79(1):101-8. doi: 10.4065/79.1.101. PMID- 14660491 OWN - NLM STAT- MEDLINE DCOM- 20040809 LR - 20220316 IS - 8750-7587 (Print) IS - 0161-7567 (Linking) VI - 96 IP - 1 DP - 2004 Jan TI - Eating, exercise, and "thrifty" genotypes: connecting the dots toward an evolutionary understanding of modern chronic diseases. PG - 3-10 AB - Survival of Homo sapiens during evolution was dependent on the procurement of food, which in turn was dependent on physical activity. However, food supply was never consistent. Thus it is contended that the ancient hunter-gatherer had cycles of feast and famine, punctuated with obligate periods of physical activity and rest. Hence, gene selection in the Late-Paleolithic era was probably influenced by physical activity and rest. To ensure survival during periods of famine, certain genes evolved to regulate efficient intake and utilization of fuel stores. Such genes were termed "thrifty genes" in 1962. Furthermore, convincing evidence shows that this ancient genome has remained essentially unchanged over the past 10,000 years and certainly not changed in the past 40-100 years. Although the absolute caloric intake of modern-day humans is likely lower compared with our hunter-gatherer ancestors, it is nevertheless in positive caloric balance in the majority of the US adult population mainly due to the increased sedentary lifestyle in present society. We contend that the combination of continuous food abundance and physical inactivity eliminates the evolutionarily programmed biochemical cycles emanating from feast-famine and physical activity-rest cycles, which in turn abrogates the cycling of certain metabolic processes, ultimately resulting in metabolic derangements such as obesity and Type 2 diabetes. In this context, we postulate that perhaps a crucial mechanism to break the stall of the metabolic processes would be via exercise through the regulation of "physical activity genes," some of which may also be potential candidates for the "thrifty genes" of our hunter-gatherer ancestors. Therefore, the identification of such "thrifty gene" candidates would help provide insight into the pathogenetic processes of the numerous physical inactivity-mediated disorders. FAU - Chakravarthy, Manu V AU - Chakravarthy MV AD - Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St Louis 63110, USA. FAU - Booth, Frank W AU - Booth FW LA - eng GR - AR-19393/AR/NIAMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PT - Review PL - United States TA - J Appl Physiol (1985) JT - Journal of applied physiology (Bethesda, Md. : 1985) JID - 8502536 SB - IM MH - *Biological Evolution MH - *Chronic Disease MH - Energy Metabolism/genetics MH - Feeding Behavior/*physiology MH - Genotype MH - Humans MH - Physical Exertion/*physiology MH - Starvation/*genetics/metabolism RF - 53 EDAT- 2003/12/09 05:00 MHDA- 2004/08/10 05:00 CRDT- 2003/12/09 05:00 PHST- 2003/12/09 05:00 [pubmed] PHST- 2004/08/10 05:00 [medline] PHST- 2003/12/09 05:00 [entrez] AID - 96/1/3 [pii] AID - 10.1152/japplphysiol.00757.2003 [doi] PST - ppublish SO - J Appl Physiol (1985). 2004 Jan;96(1):3-10. doi: 10.1152/japplphysiol.00757.2003. PMID- 14580590 OWN - NLM STAT- MEDLINE DCOM- 20040716 LR - 20191108 IS - 0047-2484 (Print) IS - 0047-2484 (Linking) VI - 45 IP - 3 DP - 2003 Sep TI - The thermal history of human fossils and the likelihood of successful DNA amplification. PG - 203-17 AB - Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site. FAU - Smith, Colin I AU - Smith CI AD - Fossil Fuels and Environmental Geochemistry, NRG, Drummond Building, University of Newcastle, NE1 7RU Newcastle upon Tyne, UK. FAU - Chamberlain, Andrew T AU - Chamberlain AT FAU - Riley, Michael S AU - Riley MS FAU - Stringer, Chris AU - Stringer C FAU - Collins, Matthew J AU - Collins MJ LA - eng PT - Comparative Study PT - Journal Article PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 SB - IM MH - Animals MH - Australia MH - *Climate MH - Europe MH - *Fossils MH - Hominidae/*genetics MH - Humans MH - *Nucleic Acid Amplification Techniques MH - Survival MH - Time Factors EDAT- 2003/10/29 05:00 MHDA- 2004/07/17 05:00 CRDT- 2003/10/29 05:00 PHST- 2003/10/29 05:00 [pubmed] PHST- 2004/07/17 05:00 [medline] PHST- 2003/10/29 05:00 [entrez] AID - S0047248403001064 [pii] AID - 10.1016/s0047-2484(03)00106-4 [doi] PST - ppublish SO - J Hum Evol. 2003 Sep;45(3):203-17. doi: 10.1016/s0047-2484(03)00106-4. PMID- 12782040 OWN - NLM STAT- MEDLINE DCOM- 20041021 LR - 20190628 IS - 0003-2697 (Print) IS - 0003-2697 (Linking) VI - 318 IP - 1 DP - 2003 Jul 1 TI - Poly(A) tailing of ancient DNA: a method for reproducible microsatellite genotyping. PG - 124-31 AB - Microsatellites could be of great potential use in the analysis of ancient remains, but so far such analyses have failed to be reproducible mainly because of the high degree of ancient DNA (aDNA) degradation. During PCR, annealing of the primers to the complementary sequences of microsatellites occurs together with cross-annealing of partially degraded repeated sequences. This could create chimeric alleles that do not correspond to the authentic ones. Here we report a simple method for processing aDNA fragments prior to PCR that greatly reduces the production of chimeric alleles. This approach eliminates aDNA molecules broken within the repeats as targets for Taq polymerase by adding poly(A) tails at the 3(') ends of the DNA fragments, which disrupts the homology in the region and thus prevents annealing out of register. We have analyzed one dinucleotide- (D6S337) and two trinucleotide-containing loci (IT15 and SCA1) using poly(A)-tailed and the same untreated aDNA as template. aDNAs were isolated from 28 human remains, 600 and 7000 years of age. In repeated experiments with untreated aDNAs we obtained three to five times more alleles compared to poly(A)-tailed aDNAs. According to our results, modification of aDNA by poly(A) tailing is an efficient pretreatment for accurate genotyping. FAU - Culjković, Biljana AU - Culjković B AD - Faculty of Biology, University of Belgrade, Studentski trg 16, P.O. Box 52, Belgrade 11000, Yugoslavia. FAU - Savić, Dusanka AU - Savić D FAU - Stojković, Oliver AU - Stojković O FAU - Romac, Stanka AU - Romac S LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Anal Biochem JT - Analytical biochemistry JID - 0370535 RN - 24937-83-5 (Poly A) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Archaeology/history MH - DNA/analysis/*chemistry/genetics/history MH - DNA Fragmentation MH - Dinucleotide Repeats/genetics MH - Genotype MH - History, Ancient MH - Humans MH - Microsatellite Repeats/*genetics MH - Poly A/analysis/*chemistry/genetics MH - Polymerase Chain Reaction/methods MH - Trinucleotide Repeats/genetics MH - Yugoslavia EDAT- 2003/06/05 05:00 MHDA- 2004/10/22 09:00 CRDT- 2003/06/05 05:00 PHST- 2003/06/05 05:00 [pubmed] PHST- 2004/10/22 09:00 [medline] PHST- 2003/06/05 05:00 [entrez] AID - S000326970300160X [pii] AID - 10.1016/s0003-2697(03)00160-x [doi] PST - ppublish SO - Anal Biochem. 2003 Jul 1;318(1):124-31. doi: 10.1016/s0003-2697(03)00160-x. PMID- 14527199 OWN - NLM STAT- MEDLINE DCOM- 20031125 LR - 20191108 IS - 0018-7143 (Print) IS - 0018-7143 (Linking) VI - 75 IP - 3 DP - 2003 Jun TI - Hypersensitive PCR, ancient human mtDNA, and contamination. PG - 355-64 AB - When highly efficient polymerase was used with high cycle numbers (50-60), strong amplifications were observed, but negative controls were also unexpectedly amplified in a study of ancient human mtDNA from 2000-year-old skeletons. The results of a series of tests revealed that the hypersensitive polymerase chain reaction (PCR) generated by higher cycles and the presence of contaminant DNA (though at extremely low levels) should be responsible for the amplification of negative controls. We suggest that PCR sensitivity be optimized to take advantage of highly efficient polymerase and at the same time prevent "background DNA" from becoming "contaminant DNA" and obscuring the analysis of authentic ancient DNA. We propose the use of multiple positive controls when amplifying ancient human mtDNA samples to indicate the sensitivity of individual PCR amplifications and to monitor the contamination levels of modern human DNA. This study provides some suggestions as to how to amplify and analyze ancient human mtDNA when unavoidable and extremely tiny amounts of modern human DNA exist. FAU - Yang, Dongya Y AU - Yang DY AD - Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada. FAU - Eng, Barry AU - Eng B FAU - Saunders, Shelley R AU - Saunders SR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology/*methods MH - Bone and Bones/chemistry MH - DNA, Mitochondrial/*analysis MH - Humans MH - Polymerase Chain Reaction/*methods MH - Sensitivity and Specificity EDAT- 2003/10/07 05:00 MHDA- 2003/12/03 05:00 CRDT- 2003/10/07 05:00 PHST- 2003/10/07 05:00 [pubmed] PHST- 2003/12/03 05:00 [medline] PHST- 2003/10/07 05:00 [entrez] AID - 10.1353/hub.2003.0050 [doi] PST - ppublish SO - Hum Biol. 2003 Jun;75(3):355-64. doi: 10.1353/hub.2003.0050. PMID- 12808718 OWN - NLM STAT- MEDLINE DCOM- 20030815 LR - 20101118 IS - 0353-9504 (Print) IS - 0353-9504 (Linking) VI - 44 IP - 3 DP - 2003 Jun TI - Specific quantification of human genomes from low copy number DNA samples in forensic and ancient DNA studies. PG - 273-80 AB - We reviewed the current methodologies used for human DNA quantitation in forensic and ancient DNA studies, including sensitive hybridization methods based on the detection of nuclear alpha-satellite repetitive DNA regions or more recently developed fluorogenic real-time polymerase chain reaction (PCR) designs for the detection of both nuclear and mitochondrial DNA regions. Special emphasis has been put on the applicability of recently described different real-time PCR designs targeting different fragments of the HV1 mtDNA control region, and a segment of the X-Y homologous amelogenin gene. The importance of these quantitative assays is to ensure the consistency of low copy number DNA typing (STR profiling and mtDNA sequencing). FAU - Alonso, Antonio AU - Alonso A AD - Instituto Nacional de Toxicología, Servicio de Biología, Luis Cabrera 9, 28002 Madrid, Spain. a.alonso@mju.es FAU - Martin, Pablo AU - Martin P FAU - Albarrán, Cristina AU - Albarrán C FAU - García, Pilar AU - García P FAU - Primorac, Dragan AU - Primorac D FAU - García, Oscar AU - García O FAU - Fernández de Simón, Lourdes AU - Fernández de Simón L FAU - García-Hirschfeld, Julia AU - García-Hirschfeld J FAU - Sancho, Manuel AU - Sancho M FAU - Fernández-Piqueras, Jose AU - Fernández-Piqueras J LA - eng PT - Journal Article PL - Croatia TA - Croat Med J JT - Croatian medical journal JID - 9424324 RN - 0 (Amelogenin) RN - 0 (Complementarity Determining Regions) RN - 0 (DNA, Mitochondrial) RN - 0 (Dental Enamel Proteins) SB - IM MH - Amelogenin MH - Complementarity Determining Regions MH - DNA Fingerprinting/*methods MH - DNA, Mitochondrial/genetics MH - Dental Enamel Proteins/genetics MH - Forensic Anthropology/*methods MH - Humans MH - Polymerase Chain Reaction/methods MH - Sequence Analysis, DNA MH - Sex Determination Analysis/methods MH - Tandem Repeat Sequences EDAT- 2003/06/17 05:00 MHDA- 2003/08/16 05:00 CRDT- 2003/06/17 05:00 PHST- 2003/06/17 05:00 [pubmed] PHST- 2003/08/16 05:00 [medline] PHST- 2003/06/17 05:00 [entrez] PST - ppublish SO - Croat Med J. 2003 Jun;44(3):273-80. PMID- 12740954 OWN - NLM STAT- MEDLINE DCOM- 20030916 LR - 20161025 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 121 IP - 2 DP - 2003 Jun TI - Brief communication: ancient DNA prospects from Sri Lankan highland dry caves support an emerging global pattern. PG - 112-6 AB - Recovery of ancient DNA has become an increasingly important tool in elucidating the origins of past populations and their relationships. Unfortunately, many human skeletal remains do not contain original DNA amplifiable by polymerase chain reaction (PCR). Amino-acid racemization has proven to be a useful predictor of ancient DNA results. We analyzed the relative levels of amino-acid preservation and racemization of human samples from two highland dry-cave sites in Sri Lanka, and found that amino-acid enantiomer ratios were inconsistent with successful authentic DNA recovery. A review of the literature reveals that these results are consistent with a global pattern of poor DNA preservation in the tropics. CI - Copyright 2003 Wiley-Liss, Inc. FAU - Reed, Floyd A AU - Reed FA AD - Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA. far4@cornell.edu FAU - Kontanis, Elias J AU - Kontanis EJ FAU - Kennedy, Kenneth A R AU - Kennedy KA FAU - Aquadro, Charles F AU - Aquadro CF LA - eng GR - R01 GM036431/GM/NIGMS NIH HHS/United States PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Amino Acids) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acids/analysis MH - Archaeology/*methods MH - DNA/*analysis/*history MH - History, Ancient MH - Humans MH - *Microclimate MH - *Preservation, Biological MH - Sri Lanka MH - Tropical Climate EDAT- 2003/05/13 05:00 MHDA- 2003/09/17 05:00 CRDT- 2003/05/13 05:00 PHST- 2003/05/13 05:00 [pubmed] PHST- 2003/09/17 05:00 [medline] PHST- 2003/05/13 05:00 [entrez] AID - 10.1002/ajpa.10211 [doi] PST - ppublish SO - Am J Phys Anthropol. 2003 Jun;121(2):112-6. doi: 10.1002/ajpa.10211. PMID- 12740952 OWN - NLM STAT- MEDLINE DCOM- 20030916 LR - 20081121 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 121 IP - 2 DP - 2003 Jun TI - Mitochondrial DNA from pre-Columbian Ciboneys from Cuba and the prehistoric colonization of the Caribbean. PG - 97-108 AB - To assess the genetic affinities of extinct Ciboneys (also called Guanajuatabeys) from Cuba, 47 pre-Columbian skeletal samples belonging to this group were analyzed using ancient DNA techniques. At the time of European contact, the center and east of Cuba were occupied by agriculturalist Taino groups, while the west was mainly inhabited by Ciboneys, hunter-gatherers who have traditionally been considered a relic population descending from the initial colonization of the Caribbean. The mtDNA hypervariable region I (HVR-I) and haplogroup-specific markers were amplified and sequenced in 15 specimens using overlapping fragments; amplification from second extractions from the same sample, independent replication in different laboratories, and cloning of some PCR products support the authenticity of the sequences. Three of the five major mtDNA Amerindian lineages (A, C, and D) are present in the sample analyzed, in frequencies of 0.07, 0.60, and 0.33, respectively. Different phylogenetic analyses seem to suggest that the Caribbean most likely was populated from South America, although the data are still inconclusive, and Central American influences cannot be discarded. Our hypothesis is that the colonization of the Caribbean mainly took place in successive migration movements that emanated from the same area in South America, around the Lower Orinoco Valley: the first wave consisted of hunter-gatherer groups (ancestors of the Ciboneys), a subsequent wave of agriculturalists (ancestors of the Tainos), and a latter one of nomadic Carib warriors. However, further genetic studies are needed to confirm this scenario. CI - Copyright 2003 Wiley-Liss, Inc. FAU - Lalueza-Fox, C AU - Lalueza-Fox C AD - Secció d' Antropologia, Departament of Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Spain. FAU - Gilbert, M T P AU - Gilbert MT FAU - Martínez-Fuentes, A J AU - Martínez-Fuentes AJ FAU - Calafell, F AU - Calafell F FAU - Bertranpetit, J AU - Bertranpetit J LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Bone and Bones/chemistry MH - Caribbean Region MH - Cuba MH - DNA, Mitochondrial/*genetics/isolation & purification MH - Emigration and Immigration/*history MH - Genetic Variation/genetics MH - Genetic Vectors MH - Haplotypes/genetics MH - History, Ancient MH - Humans MH - Indians, North American/*genetics/history MH - Sequence Analysis, DNA MH - Tooth/chemistry EDAT- 2003/05/13 05:00 MHDA- 2003/09/17 05:00 CRDT- 2003/05/13 05:00 PHST- 2003/05/13 05:00 [pubmed] PHST- 2003/09/17 05:00 [medline] PHST- 2003/05/13 05:00 [entrez] AID - 10.1002/ajpa.10236 [doi] PST - ppublish SO - Am J Phys Anthropol. 2003 Jun;121(2):97-108. doi: 10.1002/ajpa.10236. PMID- 12743370 OWN - NLM STAT- MEDLINE DCOM- 20030716 LR - 20181113 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 100 IP - 11 DP - 2003 May 27 TI - Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. PG - 6593-7 AB - During the late Pleistocene, early anatomically modern humans coexisted in Europe with the anatomically archaic Neandertals for some thousand years. Under the recent variants of the multiregional model of human evolution, modern and archaic forms were different but related populations within a single evolving species, and both have contributed to the gene pool of current humans. Conversely, the Out-of-Africa model considers the transition between Neandertals and anatomically modern humans as the result of a demographic replacement, and hence it predicts a genetic discontinuity between them. Following the most stringent current standards for validation of ancient DNA sequences, we typed the mtDNA hypervariable region I of two anatomically modern Homo sapiens sapiens individuals of the Cro-Magnon type dated at about 23 and 25 thousand years ago. Here we show that the mtDNAs of these individuals fall well within the range of variation of today's humans, but differ sharply from the available sequences of the chronologically closer Neandertals. This discontinuity is difficult to reconcile with the hypothesis that both Neandertals and early anatomically modern humans contributed to the current European gene pool. FAU - Caramelli, David AU - Caramelli D AD - Dipartimento di Biologia Animale e Genetica, Università di Firenze, Via del Proconsolo 12, 50122 Florence, Italy. FAU - Lalueza-Fox, Carles AU - Lalueza-Fox C FAU - Vernesi, Cristiano AU - Vernesi C FAU - Lari, Martina AU - Lari M FAU - Casoli, Antonella AU - Casoli A FAU - Mallegni, Francesco AU - Mallegni F FAU - Chiarelli, Brunetto AU - Chiarelli B FAU - Dupanloup, Isabelle AU - Dupanloup I FAU - Bertranpetit, Jaume AU - Bertranpetit J FAU - Barbujani, Guido AU - Barbujani G FAU - Bertorelle, Giorgio AU - Bertorelle G LA - eng SI - GENBANK/AY283027 SI - GENBANK/AY283028 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030512 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Base Sequence MH - *Biological Evolution MH - DNA Primers MH - DNA, Mitochondrial/genetics MH - Europe MH - Hominidae/*genetics MH - Humans MH - Molecular Sequence Data PMC - PMC164492 EDAT- 2003/05/14 05:00 MHDA- 2003/07/17 05:00 PMCR- 2003/11/27 CRDT- 2003/05/14 05:00 PHST- 2003/05/14 05:00 [pubmed] PHST- 2003/07/17 05:00 [medline] PHST- 2003/05/14 05:00 [entrez] PHST- 2003/11/27 00:00 [pmc-release] AID - 1130343100 [pii] AID - 1006593 [pii] AID - 10.1073/pnas.1130343100 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2003 May 27;100(11):6593-7. doi: 10.1073/pnas.1130343100. Epub 2003 May 12. PMID- 12674098 OWN - NLM STAT- MEDLINE DCOM- 20030618 LR - 20191107 IS - 0047-2484 (Print) IS - 0047-2484 (Linking) VI - 44 IP - 3 DP - 2003 Mar TI - Ancient human DNA from Sungir? PG - 389-92 FAU - Ovchinnikov, Igor V AU - Ovchinnikov IV AD - Department of Dermatology, Prebyterian Medical Center, Vanderbilt Clinic 15-202, Columbia University, New York, NY 10032, USA. io44@columbia.edu FAU - Goodwin, William AU - Goodwin W LA - eng PT - Journal Article PL - England TA - J Hum Evol JT - Journal of human evolution JID - 0337330 RN - 0 (Complementarity Determining Regions) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical/*methods MH - Complementarity Determining Regions MH - DNA, Mitochondrial/*isolation & purification MH - Female MH - *Fossils MH - Humans MH - Male MH - Polymerase Chain Reaction MH - Reproducibility of Results MH - Russia MH - Sequence Analysis, DNA MH - Specimen Handling EDAT- 2003/04/04 05:00 MHDA- 2003/06/19 05:00 CRDT- 2003/04/04 05:00 PHST- 2003/04/04 05:00 [pubmed] PHST- 2003/06/19 05:00 [medline] PHST- 2003/04/04 05:00 [entrez] AID - 10.1016/s0047-2484(03)00003-4 [doi] PST - ppublish SO - J Hum Evol. 2003 Mar;44(3):389-92. doi: 10.1016/s0047-2484(03)00003-4. PMID- 12713151 OWN - NLM STAT- MEDLINE DCOM- 20030520 LR - 20191107 IS - 0018-7143 (Print) IS - 0018-7143 (Linking) VI - 75 IP - 1 DP - 2003 Feb TI - Ancient DNA analysis of the delta F508 mutation. PG - 105-15 AB - When working with highly degraded DNA, validating the results of a slightly polymorphic system always complicates the analysis because of the difficulties in recognizing contamination and artifacts. Recognition can be greatly simplified by employing a multiplex reaction that coamplifies the fragments together with several highly polymorphic markers, for instance, short tandem repeats. In this work, we successfully included newly designed oligonucleotide primers for the detection of delta F508, the most frequent mutation causing cystic fibrosis, in the commercial AmpFlSTR Profiler Plus PCR Amplification Kit (PE Applied Biosystems). This coamplification enabled us to test the hypothesis of a heterozygote advantage associated with cystic fibrosis-specifically, higher resistance to toxin-mediated diarrheas--in a Sicilian skeletal sample of individuals who died in a cholera epidemic in 1837. The proposed method should also be suitable for the genetic characterization of other slightly polymorphic loci tested on human and animal ancient DNA; it should permit simple authentication of results by comparing the fingerprints obtained from independent amplifications repeated several times. FAU - Bramanti, Barbara AU - Bramanti B AD - Historical Anthropology and Human Ecology, University of Göttingen, Germany. FAU - Hummel, Susanne AU - Hummel S FAU - Chiarelli, Brunetto AU - Chiarelli B FAU - Herrmann, Bernd AU - Herrmann B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA Primers) RN - 9007-49-2 (DNA) SB - IM MH - Cystic Fibrosis/*genetics MH - DNA/genetics/isolation & purification MH - *DNA Mutational Analysis MH - DNA Primers MH - Humans MH - Sicily EDAT- 2003/04/26 05:00 MHDA- 2003/05/21 05:00 CRDT- 2003/04/26 05:00 PHST- 2003/04/26 05:00 [pubmed] PHST- 2003/05/21 05:00 [medline] PHST- 2003/04/26 05:00 [entrez] AID - 10.1353/hub.2003.0017 [doi] PST - ppublish SO - Hum Biol. 2003 Feb;75(1):105-15. doi: 10.1353/hub.2003.0017. PMID- 12598688 OWN - NLM STAT- MEDLINE DCOM- 20031009 LR - 20221207 IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 20 IP - 2 DP - 2003 Feb TI - Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA. PG - 214-9 AB - The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modern data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (approximately 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modern populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed. FAU - Yao, Yong-Gang AU - Yao YG AD - Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. FAU - Kong, Qing-Peng AU - Kong QP FAU - Man, Xiao-Yong AU - Man XY FAU - Bandelt, Hans-Jürgen AU - Bandelt HJ FAU - Zhang, Ya-Ping AU - Zhang YP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asian People MH - China MH - DNA, Mitochondrial/*analysis MH - Evolution, Molecular MH - Gene Frequency MH - Genetic Variation MH - Genetics, Population MH - Haplotypes MH - Humans MH - Paleontology MH - Polymorphism, Genetic MH - Principal Component Analysis MH - Sequence Analysis, DNA/*methods EDAT- 2003/02/25 04:00 MHDA- 2003/10/10 05:00 CRDT- 2003/02/25 04:00 PHST- 2003/02/25 04:00 [pubmed] PHST- 2003/10/10 05:00 [medline] PHST- 2003/02/25 04:00 [entrez] AID - 10.1093/molbev/msg026 [doi] PST - ppublish SO - Mol Biol Evol. 2003 Feb;20(2):214-9. doi: 10.1093/molbev/msg026. PMID- 12505472 OWN - NLM STAT- MEDLINE DCOM- 20030401 LR - 20190901 IS - 0379-0738 (Print) IS - 0379-0738 (Linking) VI - 131 IP - 1 DP - 2003 Jan 9 TI - "Ancient" protocols for the crime scene? Similarities and differences between forensic genetics and ancient DNA analysis. PG - 59-64 AB - We provide a short overview on some current issues in the fields of forensic genetics and ancient DNA (aDNA) analysis. We discuss about the existence of the possible points of contact between the two disciplines, in terms of open problems and the inherent approach to their solution. We mainly focus on the problem of results authentication, its theoretical and technical aspects. FAU - Capelli, C AU - Capelli C AD - Immunohematology Laboratory, Department of Forensic Medicine, Catholic University, Largo F. Vito, 1 00168 Rome, Italy. capelli.c@iol.it FAU - Tschentscher, F AU - Tschentscher F FAU - Pascali, V L AU - Pascali VL LA - eng PT - Journal Article PL - Ireland TA - Forensic Sci Int JT - Forensic science international JID - 7902034 RN - 9007-49-2 (DNA) SB - IM MH - DNA/*analysis MH - Forensic Medicine/*methods/*trends MH - Humans MH - Reproducibility of Results EDAT- 2002/12/31 04:00 MHDA- 2003/04/02 05:00 CRDT- 2002/12/31 04:00 PHST- 2002/12/31 04:00 [pubmed] PHST- 2003/04/02 05:00 [medline] PHST- 2002/12/31 04:00 [entrez] AID - S0379073802003961 [pii] AID - 10.1016/s0379-0738(02)00396-1 [doi] PST - ppublish SO - Forensic Sci Int. 2003 Jan 9;131(1):59-64. doi: 10.1016/s0379-0738(02)00396-1. PMID- 12923304 OWN - NLM STAT- MEDLINE DCOM- 20031016 LR - 20041117 IS - 1234-1983 (Print) IS - 1234-1983 (Linking) VI - 44 IP - 3 DP - 2003 TI - Molecular phylogenetics employing modern and ancient DNA. PG - 269-90 AB - Comparative studies of DNA in recent populations and characterisation of ancient hereditary material have contributed very interesting facts to our understanding of evolution of modern mankind. Analysis of DNA homology in related species, assessment of mutations and polymorphisms in various populations and new DNA sequence data from prehistoric finds allowed - via sophisticated DNA extraction techniques, PCR, sequencing and digitalised processing of genetic information - insights into possible roots of Homo sapiens and related species, migration patterns and ancient cultural habits, thus enrhing the palaeoanthropological discipline. However, a presentation of this development would not be complete without pointing towards the methodological limitations and manifold presentations burdened with artifacts, data misinterpretation and unjustified conclusions. Presently, this modern field of research is in its consolidation phase and new parameters for quality control and authentication are being implemented to avoid spectacular but unfounded reports. It is expected that most of the problems connected to old biomolecules may be closely related to fossilisation parameters. The future challenge will be the full understanding of the complex and multi-faceted processes underlying diagenesis, including the elucidation of nucleic acid postmortem damage". FAU - Pusch, Carsten M AU - Pusch CM AD - Institute of Anthropology and Human Genetics, Division of Molecular Genetics, Wilhelmstr. 27, D-72074 Tübingen, Germany. carsten.pusch@uni-tuebingen.de FAU - Broghammer, Martina AU - Broghammer M FAU - Blin, Nikolaus AU - Blin N LA - eng PT - Journal Article PL - England TA - J Appl Genet JT - Journal of applied genetics JID - 9514582 RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Motifs MH - Animals MH - DNA/analysis MH - *Evolution, Molecular MH - *Fossils MH - Humans MH - Microscopy, Electron MH - *Phylogeny MH - Sequence Analysis, DNA MH - Sequence Analysis, Protein EDAT- 2003/08/19 05:00 MHDA- 2003/10/17 05:00 CRDT- 2003/08/19 05:00 PHST- 2003/08/19 05:00 [pubmed] PHST- 2003/10/17 05:00 [medline] PHST- 2003/08/19 05:00 [entrez] AID - 145 [pii] PST - ppublish SO - J Appl Genet. 2003;44(3):269-90. PMID- 12687766 OWN - NLM STAT- MEDLINE DCOM- 20030827 LR - 20190605 IS - 0074-0276 (Print) IS - 0074-0276 (Linking) VI - 98 Suppl 1 DP - 2003 TI - Enterobius vermicularis: ancient DNA from North and South American human coprolites. PG - 67-9 AB - A molecular paleoparasitological diagnostic approach was developed for Enterobius vermicularis. Ancient DNA was extracted from 27 coprolites from archaeological sites in Chile and USA. Enzymatic amplification of human mtDNA sequences confirmed the human origin. We designed primers specific to the E. vermicularis 5S ribosomal RNA spacer region and they allowed reproducible polymerase chain reaction identification of ancient material. We suggested that the paleoparasitological microscopic identification could accompany molecular diagnosis, which also opens the possibility of sequence analysis to understand parasite-host evolution. FAU - Iñiguez, Alena M AU - Iñiguez AM AD - Laboratório de Genética Molecular de Microorganismos, Departamento de Genética, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brasil. alena@ioc.fiocruz.br FAU - Reinhard, Karl J AU - Reinhard KJ FAU - Araújo, Adauto AU - Araújo A FAU - Ferreira, Luiz Fernando AU - Ferreira LF FAU - Vicente, Ana Carolina P AU - Vicente AC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - Brazil TA - Mem Inst Oswaldo Cruz JT - Memorias do Instituto Oswaldo Cruz JID - 7502619 RN - 0 (DNA, Helminth) RN - 0 (DNA, Mitochondrial) RN - 0 (RNA, Helminth) RN - 0 (RNA, Ribosomal, 5S) SB - IM MH - Animals MH - Chile MH - DNA, Helminth/*genetics MH - DNA, Mitochondrial/*genetics MH - Enterobius/*genetics MH - Feces/*parasitology MH - *Fossils MH - Humans MH - RNA, Helminth/genetics MH - RNA, Ribosomal, 5S/*genetics MH - United States EDAT- 2003/04/12 05:00 MHDA- 2003/08/28 05:00 CRDT- 2003/04/12 05:00 PHST- 2003/04/12 05:00 [pubmed] PHST- 2003/08/28 05:00 [medline] PHST- 2003/04/12 05:00 [entrez] AID - 10.1590/s0074-02762003000900013 [doi] PST - ppublish SO - Mem Inst Oswaldo Cruz. 2003;98 Suppl 1:67-9. doi: 10.1590/s0074-02762003000900013. PMID- 12687765 OWN - NLM STAT- MEDLINE DCOM- 20030827 LR - 20190605 IS - 0074-0276 (Print) IS - 0074-0276 (Linking) VI - 98 Suppl 1 DP - 2003 TI - Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach. PG - 63-5 AB - The aim of this work was to determine approaches that would improve the quality of ancient DNA (aDNA) present in coprolites to enhance the possibility of success in retrieving specific sequence targets. We worked with coprolites from South American archaeological sites in Brazil and Chile dating up to 7,000 years ago. Using established protocols for aDNA extraction we obtained samples showing high degradation as usually happens with this kind of material. The reconstructive polymerization pretreatment was essential to overcome the DNA degradation and the serial dilutions helped with to prevent polymerase chain reaction (PCR) inhibitors. Moreover, the random amplified polymorphic DNA-PCR has been shown to be a reliable technique for further experiments to recover specific aDNA sequences. FAU - Iñiguez, Alena M AU - Iñiguez AM AD - Laboratório de Genética Molecular de Microorganismos, Departamento de Genética, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brasil. alena@ioc.fiocruz.br FAU - Araújo, Adauto AU - Araújo A FAU - Ferreira, Luiz Fernando AU - Ferreira LF FAU - Vicente, Ana Carolina P AU - Vicente AC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Brazil TA - Mem Inst Oswaldo Cruz JT - Memorias do Instituto Oswaldo Cruz JID - 7502619 RN - 0 (DNA, Helminth) SB - IM MH - Animals MH - DNA, Helminth/genetics/*isolation & purification MH - Electrophoresis, Agar Gel MH - Feces/*parasitology MH - *Fossils MH - Humans MH - Paleopathology/methods MH - *Random Amplified Polymorphic DNA Technique EDAT- 2003/04/12 05:00 MHDA- 2003/08/28 05:00 CRDT- 2003/04/12 05:00 PHST- 2003/04/12 05:00 [pubmed] PHST- 2003/08/28 05:00 [medline] PHST- 2003/04/12 05:00 [entrez] AID - 10.1590/s0074-02762003000900012 [doi] PST - ppublish SO - Mem Inst Oswaldo Cruz. 2003;98 Suppl 1:63-5. doi: 10.1590/s0074-02762003000900012. PMID- 12489041 OWN - NLM STAT- MEDLINE DCOM- 20030221 LR - 20240527 IS - 0002-9297 (Print) IS - 1537-6605 (Electronic) IS - 0002-9297 (Linking) VI - 72 IP - 1 DP - 2003 Jan TI - Distribution patterns of postmortem damage in human mitochondrial DNA. PG - 32-47 AB - The distribution of postmortem damage in mitochondrial DNA retrieved from 37 ancient human DNA samples was analyzed by cloning and was compared with a selection of published animal data. A relative rate of damage (rho(v)) was calculated for nucleotide positions within the human hypervariable region 1 (HVR1) and cytochrome oxidase subunit III genes. A comparison of damaged sites within and between the regions reveals that damage hotspots exist and that, in the HVR1, these correlate with sites known to have high in vivo mutation rates. Conversely, HVR1 subregions with known structural function, such as MT5, have lower in vivo mutation rates and lower postmortem-damage rates. The postmortem data also identify a possible functional subregion of the HVR1, termed "low-diversity 1," through the lack of sequence damage. The amount of postmortem damage observed in mitochondrial coding regions was significantly lower than in the HVR1, and, although hotspots were noted, these did not correlate with codon position. Finally, a simple method for the identification of incorrect archaeological haplogroup designations is introduced, on the basis of the observed spectrum of postmortem damage. FAU - Gilbert, M Thomas P AU - Gilbert MT AD - Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, Oxford, United Kingdom. FAU - Willerslev, Eske AU - Willerslev E FAU - Hansen, Anders J AU - Hansen AJ FAU - Barnes, Ian AU - Barnes I FAU - Rudbeck, Lars AU - Rudbeck L FAU - Lynnerup, Niels AU - Lynnerup N FAU - Cooper, Alan AU - Cooper A LA - eng GR - WT_/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20021212 PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Mitochondrial) RN - 0 (Mitochondrial Proteins) RN - EC 1.9.3.1 (Electron Transport Complex IV) RN - EC 3.2.2.- (DNA Glycosylases) RN - EC 3.2.2.- (N-Glycosyl Hydrolases) RN - EC 3.2.2.- (Uracil-DNA Glycosidase) SB - IM EIN - Am J Hum Genet. 2003 Mar;72(3):779 MH - Animals MH - DNA Damage/*genetics MH - *DNA Glycosylases MH - DNA, Mitochondrial/*genetics MH - Electron Transport Complex IV/genetics MH - Haplotypes/genetics MH - Humans MH - Mitochondria/*genetics/*pathology MH - Mitochondrial Proteins/genetics MH - Mutagenesis/genetics MH - N-Glycosyl Hydrolases/metabolism MH - Polymerase Chain Reaction MH - *Postmortem Changes MH - Species Specificity MH - Tooth/pathology MH - Uracil-DNA Glycosidase MH - Ursidae/genetics PMC - PMC420011 EDAT- 2002/12/19 04:00 MHDA- 2003/02/22 04:00 PMCR- 2003/07/01 CRDT- 2002/12/19 04:00 PHST- 2002/06/03 00:00 [received] PHST- 2002/09/26 00:00 [accepted] PHST- 2002/12/19 04:00 [pubmed] PHST- 2003/02/22 04:00 [medline] PHST- 2002/12/19 04:00 [entrez] PHST- 2003/07/01 00:00 [pmc-release] AID - S0002-9297(07)60502-3 [pii] AID - 024144 [pii] AID - 10.1086/345378 [doi] PST - ppublish SO - Am J Hum Genet. 2003 Jan;72(1):32-47. doi: 10.1086/345378. Epub 2002 Dec 12. PMID- 12461639 OWN - NLM STAT- MEDLINE DCOM- 20030611 LR - 20061115 IS - 0937-9827 (Print) IS - 0937-9827 (Linking) VI - 116 IP - 6 DP - 2002 Dec TI - AB0 blood group genotyping of ancient DNA by PCR-RFLP. PG - 327-33 AB - The paper presents an PCR-RFLP-based method to determine AB0 blood groups at the genotype level. In order to ensure the applicability of the method to severely degraded DNA, new sets of primers were designed that amplify 103/104 bp and 64 bp sequences on exon 6 and exon 7 of chromosome 9, respectively. The amplification of the two PCR products and the subsequent RFLP analysis with four endonucleases was revealed to be an effective and reliable way to determine AB0 bloodgroups at the genotype level, distinguishing the alleles A, B, 0(1), 0(1v), and 0(2). PCR analysis of severely degraded sample material may possibly require higher cycle numbers. Therefore, the experiments presented here including those on positive control samples, were carried out employing 45 amplification cycles in order to ensure the validity of the amplification and RFLP analysis. As positive controls, small amounts of modern intact DNA extracted from saliva samples of 12 individuals with known AB0 phenotypes were used. The protocols for the AB0 typing were then applied to ancient degraded DNA extracted from 15 archaeological bones and teeth about 250 and 3,000 years old, respectively. The results presented for the archaeological sample material are based on repeated analysis derived from two independently processed DNA extracts of each sample. Moreover, the authentification process for the results derived from the archaeological samples included repeated multiplex STR genotyping of the extracts, showing the genetic uniqueness of the extracts which is the strongest possible indicator for the authenticity of an unknown DNA sample. Additionally, it was possible to compare the STR typing results to those from previous studies using the same material. Both the AB0 typing and the STR typing revealed fully reproducible results in all cases. FAU - Hummel, Susanne AU - Hummel S AD - Historische Anthropologie, Bürgerstrasse 50, 37073 Göttingen, Germany. shummel1@gwdg.de FAU - Schmidt, Diane AU - Schmidt D FAU - Kahle, Melanie AU - Kahle M FAU - Herrmann, Bernd AU - Herrmann B LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20021023 PL - Germany TA - Int J Legal Med JT - International journal of legal medicine JID - 9101456 RN - 0 (ABO Blood-Group System) RN - 9007-49-2 (DNA) SB - IM MH - *ABO Blood-Group System MH - Alleles MH - Archaeology MH - Bone and Bones/chemistry MH - DNA/analysis/*blood/*genetics MH - Forensic Anthropology MH - Forensic Dentistry MH - Gene Amplification MH - Genotype MH - Humans MH - Polymerase Chain Reaction MH - Polymorphism, Restriction Fragment Length MH - Reproducibility of Results MH - Sequence Analysis EDAT- 2002/12/04 04:00 MHDA- 2003/06/12 05:00 CRDT- 2002/12/04 04:00 PHST- 2001/09/12 00:00 [received] PHST- 2002/05/07 00:00 [accepted] PHST- 2002/12/04 04:00 [pubmed] PHST- 2003/06/12 05:00 [medline] PHST- 2002/12/04 04:00 [entrez] AID - 10.1007/s00414-002-0315-x [doi] PST - ppublish SO - Int J Legal Med. 2002 Dec;116(6):327-33. doi: 10.1007/s00414-002-0315-x. Epub 2002 Oct 23. PMID- 12489338 OWN - NLM STAT- MEDLINE DCOM- 20030128 LR - 20191106 IS - 0940-9602 (Print) IS - 0940-9602 (Linking) VI - 184 IP - 6 DP - 2002 Nov TI - [Molecular-cytogenetic analysis of ancient DNA (aDNA) from preparations from the Meckel collection in Halle (Saale)]. PG - 541-5 FAU - Tönnies, Holger AU - Tönnies H AD - Institut für Humangenetik, Humboldt-Universität Berlin, Charité Campus Virchow-Klinikum, Augustenburger Platz 1, D-13353 Berlin. FAU - Klunker, Rudyard AU - Klunker R FAU - Saar, Kathrin AU - Saar K FAU - Göbbel, Luminita AU - Göbbel L FAU - Musil, Anette AU - Musil A FAU - Schultka, Rüdiger AU - Schultka R LA - ger PT - Journal Article TT - Molekular-zytogenetische Analysen an alter DNA (aDNA) anhand von Präparaten der Meckelschen Sammlungen zu Halle Saale. PL - Germany TA - Ann Anat JT - Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft JID - 100963897 RN - 9007-49-2 (DNA) SB - IM MH - Chromosomes, Human/genetics MH - DNA/*genetics MH - Germany MH - Humans MH - Karyotyping MH - Nucleic Acid Hybridization/methods MH - Umbilical Cord/chemistry EDAT- 2002/12/20 04:00 MHDA- 2003/01/29 04:00 CRDT- 2002/12/20 04:00 PHST- 2002/12/20 04:00 [pubmed] PHST- 2003/01/29 04:00 [medline] PHST- 2002/12/20 04:00 [entrez] AID - 10.1016/s0940-9602(02)80094-2 [doi] PST - ppublish SO - Ann Anat. 2002 Nov;184(6):541-5. doi: 10.1016/s0940-9602(02)80094-2. PMID- 12209571 OWN - NLM STAT- MEDLINE DCOM- 20021011 LR - 20041117 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 119 IP - 1 DP - 2002 Sep TI - Investigation of the link between visceral surface rib lesions and tuberculosis in a Medieval skeletal series from England using ancient DNA. PG - 27-36 AB - Seven human skeletons from a large assemblage from a rural English Medieval burial site show lesions, predominantly proliferative in nature, on the visceral surfaces of the ribs. In order to investigate whether these rib lesions were regularly associated with tuberculous infection, these individuals, together with a group of age- and sex-matched control skeletons without bony signs of infection, were subjected to polymerase chain reaction (PCR) assays aimed at detecting traces of DNA from infecting microorganisms of the Mycobacterium tuberculosis complex. The results provided no evidence for any regular association between visceral surface rib lesions and the presence of M. tuberculosis complex DNA in the study group. The significance of these findings for the paleopathological interpretation of visceral surface rib lesions is discussed. CI - Copyright 2002 Wiley-Liss, Inc. FAU - Mays, S AU - Mays S AD - Ancient Monuments Laboratory, English Heritage Centre for Archaeology, Fort Cumberland, Eastney, Portsmouth PO4 9LD, UK. simon.mays@english-heritage.org.uk FAU - Fysh, E AU - Fysh E FAU - Taylor, G M AU - Taylor GM LA - eng PT - Historical Article PT - Journal Article PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Bacterial) SB - IM MH - Adolescent MH - Adult MH - Child MH - DNA, Bacterial/*genetics MH - England MH - Female MH - History, Medieval MH - Humans MH - Male MH - Middle Aged MH - Mycobacterium tuberculosis/*genetics MH - Paleopathology MH - Polymerase Chain Reaction MH - Ribs/*pathology MH - Tuberculosis, Pulmonary/*history/microbiology EDAT- 2002/09/05 10:00 MHDA- 2002/10/12 04:00 CRDT- 2002/09/05 10:00 PHST- 2002/09/05 10:00 [pubmed] PHST- 2002/10/12 04:00 [medline] PHST- 2002/09/05 10:00 [entrez] AID - 10.1002/ajpa.10099 [doi] PST - ppublish SO - Am J Phys Anthropol. 2002 Sep;119(1):27-36. doi: 10.1002/ajpa.10099. PMID- 12167530 OWN - NLM STAT- MEDLINE DCOM- 20030114 LR - 20181130 IS - 0378-1097 (Print) IS - 0378-1097 (Linking) VI - 213 IP - 2 DP - 2002 Aug 6 TI - Molecular analysis of ancient microbial infections. PG - 141-7 AB - The detection of ancient microbial DNA offers a new approach for the study of infectious diseases, their occurrence, frequency and host-pathogen interaction in historic times and populations. Moreover, data obtained from skeletal and mummified tissue may represent an important completion of contemporary phylogenetic analyses of pathogens. In the last few years, a variety of bacterial, protozoal and viral infections have been detected in ancient tissue samples by amplification and characterization of specific DNA fragments. This holds particularly true for the identification of the Mycobacterium tuberculosis complex, which seems to be more robust than other microbes due to its waxy, hydrophobic and lipid-rich cell wall. These observations provided useful information about the occurrence, but also the frequency of tuberculosis in former populations. Moreover, these studies suggest new evolutionary models and indicate the route of transmission between human and animals. Until now, other pathogens, such as Mycobacterium leprae, Yersinia pestis, Plasmodium falciparum and others, have occasionally been identified - mostly in single case studies or small sample sizes - as well, although much less information is available on these pathogens in ancient settings. The main reason therefore seems to be the degradation and modification of ancient DNA by progressive oxidative damage. Furthermore, the constant risk of contamination by recent DNA forces to take time and cost effective measures and renders the analysis of ancient microbes difficult. Nevertheless, the study of microbial ancient DNA significantly contributes to the understanding of transmission and spread of infectious diseases, and potentially to the evolution and phylogenetic pathways of pathogens. FAU - Zink, Albert R AU - Zink AR AD - Division of Paleopathology, Institute of Pathology, Academic Teaching Hospital München-Bogenhausen, Engelschalkingerstrasse 77, Germany. FAU - Reischl, Udo AU - Reischl U FAU - Wolf, Hans AU - Wolf H FAU - Nerlich, Andreas G AU - Nerlich AG LA - eng PT - Historical Article PT - Journal Article PT - Review PL - England TA - FEMS Microbiol Lett JT - FEMS microbiology letters JID - 7705721 RN - 0 (DNA, Bacterial) SB - IM MH - Animals MH - Biological Evolution MH - Communicable Diseases/*history MH - DNA, Bacterial/analysis/genetics MH - History, Ancient MH - Humans MH - Mummies MH - Paleopathology MH - Tuberculosis/epidemiology/*history/microbiology RF - 27 EDAT- 2002/08/09 10:00 MHDA- 2003/01/15 04:00 CRDT- 2002/08/09 10:00 PHST- 2002/08/09 10:00 [pubmed] PHST- 2003/01/15 04:00 [medline] PHST- 2002/08/09 10:00 [entrez] AID - S0378109702008145 [pii] AID - 10.1111/j.1574-6968.2002.tb11298.x [doi] PST - ppublish SO - FEMS Microbiol Lett. 2002 Aug 6;213(2):141-7. doi: 10.1111/j.1574-6968.2002.tb11298.x. PMID- 12140248 OWN - NLM STAT- MEDLINE DCOM- 20030210 LR - 20180109 IS - 0737-4038 (Print) IS - 0737-4038 (Linking) VI - 19 IP - 8 DP - 2002 Aug TI - A reanalysis of the ancient mitochondrial DNA sequences recovered from Neandertal bones. PG - 1359-66 AB - Recent reports analyzing mitochondrial DNA sequences from Neandertal bones have claimed that Neandertals and modern humans are different species. The phylogenetic analyses carried out in these articles did not take into account the high substitution rate variation among sites observed in the human mitochondrial D-loop region and also lack an estimation of the parameters of the nucleotide substitution model. The separate phylogenetic position of Neandertals is not supported when these factors are considered. Our analysis shows that Neandertal-Human and Human-Human pairwise distance distributions overlap more than what previous studies suggested. We also show that the most ancient Neandertal HVI region is the most divergent when compared with modern human sequences. However, the opposite would be expected if the sequence had not been modified since the death of the specimen. Such incongruence is discussed in the light of diagenetic modifications in ancient Neandertal DNA sequences. FAU - Gutiérrez, Gabriel AU - Gutiérrez G AD - Departamento de Genética, Universidad de Sevilla, Spain. ggpozo@us.es FAU - Sánchez, Diego AU - Sánchez D FAU - Marín, Antonio AU - Marín A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Evol JT - Molecular biology and evolution JID - 8501455 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Bone and Bones MH - DNA, Mitochondrial/chemistry/*genetics MH - Databases, Nucleic Acid MH - *Fossils MH - Hominidae/*genetics MH - Humans MH - Likelihood Functions MH - Mice MH - Nucleic Acid Conformation MH - Phylogeny MH - Sequence Analysis, DNA EDAT- 2002/07/26 10:00 MHDA- 2003/02/11 04:00 CRDT- 2002/07/26 10:00 PHST- 2002/07/26 10:00 [pubmed] PHST- 2003/02/11 04:00 [medline] PHST- 2002/07/26 10:00 [entrez] AID - 10.1093/oxfordjournals.molbev.a004197 [doi] PST - ppublish SO - Mol Biol Evol. 2002 Aug;19(8):1359-66. doi: 10.1093/oxfordjournals.molbev.a004197. PMID- 12098752 OWN - NLM STAT- MEDLINE DCOM- 20021021 LR - 20220330 IS - 0001-3765 (Print) IS - 0001-3765 (Linking) VI - 74 IP - 2 DP - 2002 Jun TI - Molecular variability in Amerindians: widespread but uneven information. PG - 223-63 AB - A review was made in relation to the molecular variability present in North, Central, and South American Indian populations. It involved results from ancient DNA, mitochondrial DNA in extant populations, HLA and other autosomal markers, X and Y chromosome variation, as well as data from parasitic viruses which could show coevolutionary changes. The questions considered were their origin, ways in which the early colonization of the continent took place, types and levels of the variability which developed, peculiarities of the Amerindian evolutionary processes, and eventual genetic heterogeneity which evolved in different geographical areas. Although much information is already available, it is highly heterogeneous in relation to populations and types of genetic systems investigated. Unfortunately, the present trend of favoring essentially applied research suggest that the situation will not basically improve in the future. FAU - Salzano, Francisco M AU - Salzano FM AD - Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS. francisco.salzano@ufrgs.br LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Brazil TA - An Acad Bras Cienc JT - Anais da Academia Brasileira de Ciencias JID - 7503280 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - DNA, Mitochondrial/genetics MH - Genetic Markers MH - *Genetic Variation MH - Humans MH - Indians, Central American/*genetics MH - Indians, North American/*genetics MH - Indians, South American/*genetics MH - Polymorphism, Genetic RF - 296 EDAT- 2002/07/06 10:00 MHDA- 2002/10/22 04:00 CRDT- 2002/07/06 10:00 PHST- 2002/07/06 10:00 [pubmed] PHST- 2002/10/22 04:00 [medline] PHST- 2002/07/06 10:00 [entrez] AID - S0001-37652002000200005 [pii] AID - 10.1590/s0001-37652002000200005 [doi] PST - ppublish SO - An Acad Bras Cienc. 2002 Jun;74(2):223-63. doi: 10.1590/s0001-37652002000200005. PMID- 11842404 OWN - NLM STAT- MEDLINE DCOM- 20020409 LR - 20081121 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 117 IP - 3 DP - 2002 Mar TI - Nuclear and mitochondrial genetic variation in the Yanomamö: a test case for ancient DNA studies of prehistoric populations. PG - 246-59 AB - Ancient DNA provides a potentially revolutionary way to study biological relationships in prehistoric populations, but genetic patterns are complex and require careful interpretation based on robust, well-tested models. In this study, nuclear and mitochondrial markers were compared in the Yanomamö, to assess how well each data set could differentiate among closely related groups. The villages selected for the study share a recent fission history and are closely related to each other, as would likely be the case among prehistoric peoples living in the same valley or region. The Yanomamö generally practice village-level endogamy, but some migration and gene flow are known to occur between villages. Nuclear and mitochondrial DNA data were compared using F-statistics and genetic distance analyses. The nuclear data performed as expected, males and females from the same village were similar, and the villages were genetically distinct, with the magnitude of genetic differences correlated with historical relationship. However, mtDNA analyses did not yield the expected results. The genetic distances between villages did not correlate with historical relationship, and the sexes were significantly different from each other in two villages. Both the Lane and Sublett and the Spence methods, used to test for archaeological residence patterns, were consistent with endogamy. Hence, ancient DNA can, in principle, provide us with a unique opportunity to study genetic structure and gene flow in archaeological populations. However, interpretations, particularly those based on single loci such as mitochondrial DNA, should be cautious because sex-specific migration and sampling issues may have dramatic effects. CI - Copyright 2002 Wiley-Liss, Inc. FAU - Williams, Sloan R AU - Williams SR AD - Department of Anthropology, University of Illinois at Chicago, Chicago, Illinois, 60607, USA. sloanw@uic.edu FAU - Chagnon, Napoleon A AU - Chagnon NA FAU - Spielman, Richard S AU - Spielman RS LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) RN - 9007-49-2 (DNA) SB - IM MH - Adult MH - Cultural Characteristics MH - *DNA MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration MH - Female MH - Genetic Markers MH - *Genetic Variation MH - Humans MH - Indians, North American/*genetics MH - Male MH - Polymerase Chain Reaction MH - Population Dynamics EDAT- 2002/02/14 10:00 MHDA- 2002/04/18 10:01 CRDT- 2002/02/14 10:00 PHST- 2002/02/14 10:00 [pubmed] PHST- 2002/04/18 10:01 [medline] PHST- 2002/02/14 10:00 [entrez] AID - 10.1002/ajpa.10035 [pii] AID - 10.1002/ajpa.10035 [doi] PST - ppublish SO - Am J Phys Anthropol. 2002 Mar;117(3):246-59. doi: 10.1002/ajpa.10035. PMID- 12653310 OWN - NLM STAT- MEDLINE DCOM- 20030416 LR - 20191025 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - Suppl 35 DP - 2002 TI - Ancient DNA in anthropology: methods, applications, and ethics. PG - 92-130 AB - Anthropologists were quick to recognize the potential of new techniques in molecular biology to provide additional lines of evidence on questions long investigated in anthropology, as well as those questions that, while always of interest, could not have been addressed by more traditional techniques. The earliest ancient DNA studies, both within anthropology and in other fields, lacked rigorous hypothesis testing. However, more recently the true value of ancient DNA studies is being realized, and methods are being applied to a wide variety of anthropological questions. We review the most common methods and applications to date, and describe promising avenues of future research. We find that ancient DNA analyses have a valuable place in the array of anthropological techniques, but argue that such studies must not be undertaken merely to demonstrate that surviving DNA is present in organic remains, and that no such work should be performed before a careful consideration of the possible ethical ramifications of the research is undertaken. FAU - Kaestle, Frederika A AU - Kaestle FA AD - Department of Anthropology, Indiana University, Bloomington, Indiana 47405-7100, USA. kaestle@indiana.edu FAU - Horsburgh, K Ann AU - Horsburgh KA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Anthropology, Cultural/methods MH - Anthropology, Physical/ethics/*methods MH - DNA/*analysis MH - *Evolution, Molecular MH - Female MH - Genetics, Population/ethics/*methods MH - Genotype MH - Humans MH - Male MH - Pedigree MH - Phylogeny MH - Species Specificity RF - 510 EDAT- 2003/03/26 05:00 MHDA- 2003/04/17 05:00 CRDT- 2003/03/26 05:00 PHST- 2003/03/26 05:00 [pubmed] PHST- 2003/04/17 05:00 [medline] PHST- 2003/03/26 05:00 [entrez] AID - 10.1002/ajpa.10179 [doi] PST - ppublish SO - Am J Phys Anthropol. 2002;Suppl 35:92-130. doi: 10.1002/ajpa.10179. PMID- 12177525 OWN - NLM STAT- MEDLINE DCOM- 20021001 LR - 20081121 IS - 1234-1983 (Print) IS - 1234-1983 (Linking) VI - 43 IP - 3 DP - 2002 TI - Documenting ancient DNA quality via alpha satellite amplification and assessment of clone sequence diversity. PG - 351-64 AB - C/G-->T/A nucleotide alterations have been shown to hamper the straightforward interpretation of mitochondrial DNA sequence data derived from ancient tissues. Attempting to characterise this finding with respect to nuclear DNA, we contrasted two established protocols: (i) an enzymatic repair of damaged DNA, thereby translating and closing nicks in the DNA, and (ii) the application of N-phenacylthiazolium bromide, which cleaves glucose-derived protein crosslinks, presumably derived from Maillard reactions. We used medieval human bones that were refractory to standard PCR procedures. Due to negligible presence of short tandem repeat loci and also mitochondrial sequences, the extracted ancient DNA needed a higher copy PCR system to yield amplification products. The chosen PCR target was specific alphoid repetitive DNA with an experimentally determined minimum of 1000 copies per haploid genome. Alphoid repeat segments were generated from both contemporary DNA and DNA extracts of two human skeletons dating from 450-600 AD (omitting uracil N-glycosylase pre-treatment of the extracted samples), and were subsequently cloned and sequenced. The sequences were evaluated for the number and type of nucleotide alterations noted after the different pre-treatments, and were compared to our alphoid consensus sequence generated from modern DNA. Both methods failed to reflect the expected 32% variability among single alphoid repeats (accounting for locus-specific differences and polymerase errors) as well as to display the actual 2.88 ratio of transitions to transversions. Our data obtained from high-copy-number nuclear DNA mirror the phenomenon of sequence deviations observed in mitochondrial DNA extracted from old specimens. FAU - Pusch, Carsten M AU - Pusch CM AD - Institute of Anthropology and Human Genetics, Department of Molecular Genetics, Tübingen, Germany. carsten.pusch@uni-tuebingen.de FAU - Kayademir, Tuncay AU - Kayademir T FAU - Prangenberg, Kurt AU - Prangenberg K FAU - Conard, Nicholas J AU - Conard NJ FAU - Czarnetzki, Alfred AU - Czarnetzki A FAU - Blin, Nikolaus AU - Blin N LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Appl Genet JT - Journal of applied genetics JID - 9514582 RN - 0 (DNA, Satellite) SB - IM MH - Base Sequence MH - Bone and Bones/*chemistry MH - DNA, Satellite/*analysis MH - Gene Amplification MH - Genetic Variation MH - Genotype MH - Humans MH - Molecular Sequence Data MH - Paleopathology MH - Polymerase Chain Reaction/*methods MH - Repetitive Sequences, Nucleic Acid MH - Reproducibility of Results MH - Sensitivity and Specificity MH - Sequence Homology, Nucleic Acid EDAT- 2002/08/15 10:00 MHDA- 2002/10/03 04:00 CRDT- 2002/08/15 10:00 PHST- 2002/08/15 10:00 [pubmed] PHST- 2002/10/03 04:00 [medline] PHST- 2002/08/15 10:00 [entrez] AID - 109 [pii] PST - ppublish SO - J Appl Genet. 2002;43(3):351-64. PMID- 11846037 OWN - NLM STAT- MEDLINE DCOM- 20020305 LR - 20240823 IS - 1420-682X (Print) IS - 1420-9071 (Electronic) IS - 1420-682X (Linking) VI - 59 IP - 1 DP - 2002 Jan TI - Molecular paleontology. PG - 97-111 AB - Molecular paleontology, i.e., the recovery of DNA from ancient human, animal, and plant remains is an innovative research field that has received progressively more attention from the scientific community since the 1980s. In the last decade, the field was punctuated by claims which aroused great interest but eventually turned out to be fakes--the most famous being the sequence of dinosaur DNA later shown to be of human origin. At present, the discipline is characterized by some certainties and many doubts. We know, for example, that we have reasonable chances to recover authentic DNA from a mammoth carcass, while our chances are negligible (or nonexistent) in the case of a dynastic mummy from Egypt. On the other hand, though we are developing convincing models of DNA decay in bone, we are not yet able to predict whether a certain paleontological or archeological site will yield material amenable to DNA analysis. This article reviews some of the most important and promising investigations using molecular paleontology approaches, such as studies on the conservation of DNA in human bone, the quest for ancient DNA in permafrost-frozen fauna, the Tyrolean iceman, and the Neandertals. FAU - Marota, I AU - Marota I AD - Laboratory of Molecular Archaeo-Anthropology/Ancient DNA, UNICAM, Camerino, Italy. isolina@cambio.unicam.it FAU - Rollo, F AU - Rollo F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Switzerland TA - Cell Mol Life Sci JT - Cellular and molecular life sciences : CMLS JID - 9705402 RN - 0 (Ice) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*analysis/chemistry/*isolation & purification/metabolism MH - *Evolution, Molecular MH - Freezing MH - Hominidae/*genetics MH - Humans MH - Ice MH - Mammals/*genetics MH - Mummies MH - Paleontology/*methods MH - Reproducibility of Results PMC - PMC11337491 EDAT- 2002/02/16 10:00 MHDA- 2002/03/07 10:01 PMCR- 2002/01/01 CRDT- 2002/02/16 10:00 PHST- 2002/02/16 10:00 [pubmed] PHST- 2002/03/07 10:01 [medline] PHST- 2002/02/16 10:00 [entrez] PHST- 2002/01/01 00:00 [pmc-release] AID - CMLS 10171 [pii] AID - 10.1007/s00018-002-8408-8 [doi] PST - ppublish SO - Cell Mol Life Sci. 2002 Jan;59(1):97-111. doi: 10.1007/s00018-002-8408-8. PMID- 11596002 OWN - NLM STAT- MEDLINE DCOM- 20011204 LR - 20061115 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 116 IP - 3 DP - 2001 Nov TI - Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo. PG - 230-5 AB - Ancient DNA from the bone remains of 25 out of 28 pre-Columbian individuals from the Late Classic-Postclassic Maya site of Xcaret, Quintana Roo, was recovered, and mitochondrial DNA (mtDNA) was amplified by using the polymerase chain reaction. The presence of the four founding Amerindian mtDNA lineages was investigated by restriction analysis and by direct sequencing in selected individuals. The mtDNA lineages A, B, and C were found in this population. Eighty-four percent of the individuals were lineage A, whereas lineages B and C were present at low frequencies, 4% and 8%, respectively. Lineage D was absent from our sample. One individual did not possess any of the four lineages. Six skeletons out of 7 dated from the Late Classic period were haplotype A, whereas 11 skeletons out of 16 dated from the Postclassic period were also haplotype A. The distribution of mtDNA lineages in the Xcaret population contrasts sharply with that found in ancient Maya from Copán, which lack lineages A and B. On the other hand, our results resemble more closely the frequencies of mtDNA lineages found in contemporary Maya from the Yucatán Peninsula and in other Native American contemporary populations of Mesoamerican origin. CI - Copyright 2001 Wiley-Liss, Inc. FAU - González-Oliver, A AU - González-Oliver A AD - Departamento de Biología, Facultad de Ciencias, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico. FAU - Márquez-Morfín, L AU - Márquez-Morfín L FAU - Jiménez, J C AU - Jiménez JC FAU - Torre-Blanco, A AU - Torre-Blanco A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - Bone and Bones MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - Fossils MH - *Genetics, Population MH - Humans MH - Indians, North American/*genetics MH - Mexico MH - Pedigree MH - Polymerase Chain Reaction EDAT- 2001/10/12 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/10/12 10:00 PHST- 2001/10/12 10:00 [pubmed] PHST- 2002/01/05 10:01 [medline] PHST- 2001/10/12 10:00 [entrez] AID - 10.1002/ajpa.1118 [pii] AID - 10.1002/ajpa.1118 [doi] PST - ppublish SO - Am J Phys Anthropol. 2001 Nov;116(3):230-5. doi: 10.1002/ajpa.1118. PMID- 11758690 OWN - NLM STAT- MEDLINE DCOM- 20020116 LR - 20191105 IS - 0018-7143 (Print) IS - 0018-7143 (Linking) VI - 73 IP - 5 DP - 2001 Oct TI - Authenticating ancient human mitochondrial DNA. PG - 689-713 AB - The use of ancient DNA techniques in human studies has been hampered by problems of contamination with modern human DNA. The main problem has been that the object of study belongs to the same species as the observer, and the complete elimination of the contamination risk is seemingly unlikely. Contamination has even been detected in the most specialized laboratories in this field. In these kinds of studies it is therefore very important to detect contamination and to distinguish contaminants from authentic results. Here, we report the use of a strategy to authenticate the identity of ancient mitochondrial DNA (mtDNA), based on the previously established relationship between D-loop sequence substitutions and haplogroup-specific restriction site changes. Forty-four individuals from a 16th-century necropolis were analyzed, from which 28 control region sequences were obtained. These sequences were preclassified into haplogroups, according to the observed motifs. Subsequently, the DNA extracts from which the sequences were obtained, along with independent extracts of subsets of the same individuals, were subjected to restriction fragment length polymorphism (RFLP) analysis to compare and corroborate the results. Using this approach, 24 sequences were authenticated, while two were discarded because of result mismatches. The final distribution of the haplogroups in the sample, and the differences in the sequences, are two additional criteria of authentication. FAU - Montiel, R AU - Montiel R AD - Unitat d'Antropologia, Facultat de Ciències, Universitat Autònoma de Barcelona, Bellaterra, Spain. FAU - Malgosa, A AU - Malgosa A FAU - Francalacci, P AU - Francalacci P LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 0 (DNA, Mitochondrial) RN - 0 (Peptides, Cyclic) RN - 130304-73-3 (D-loop peptide, synthetic) SB - IM MH - Adult MH - Amino Acid Substitution/genetics MH - DNA Fingerprinting/*methods MH - DNA, Mitochondrial/genetics/*history MH - Female MH - Forensic Anthropology/*methods/standards MH - Haplotypes MH - History, 15th Century MH - History, 16th Century MH - Humans MH - Male MH - Peptides, Cyclic/*genetics/*history MH - Polymerase Chain Reaction MH - Polymorphism, Restriction Fragment Length MH - Restriction Mapping MH - Sequence Analysis, DNA/*methods/standards MH - Spain MH - Specimen Handling/standards MH - Tooth EDAT- 2002/01/05 10:00 MHDA- 2002/01/17 10:01 CRDT- 2002/01/05 10:00 PHST- 2002/01/05 10:00 [pubmed] PHST- 2002/01/17 10:01 [medline] PHST- 2002/01/05 10:00 [entrez] AID - 10.1353/hub.2001.0069 [doi] PST - ppublish SO - Hum Biol. 2001 Oct;73(5):689-713. doi: 10.1353/hub.2001.0069. PMID- 11808678 OWN - NLM STAT- MEDLINE DCOM- 20020306 LR - 20191105 IS - 1386-7415 (Print) IS - 1386-7415 (Linking) VI - 22 IP - 5 DP - 2001 Sep TI - The privacy of Tutankhamen--utilising the genetic information in stored tissue samples. PG - 437-49 AB - Recent technical developments in genetic testing has led to a situation where the DNA in previously stored tissue samples can be extracted and used for genetic analysis. This raises the question of how to decide whether a specific use of such samples should be allowed. Using the genetic testing of ancient DNA in general, and the DNA of the pharaoh Tutankhamen in particular as examples this paper analyses the question. It investigates whether ethical frameworks based on proxy consent, cultural affiliation, ownership, or the privacy rights of the dead are appropriate and justifiable in this context. The conclusion is that frameworks based on proxy consent, cultural affiliation, and ownership are not very useful. FAU - Holm, S AU - Holm S AD - Institute of Medicine, Law and Bioethics, University of Manchester, UK. soren.holm@man.ac.uk LA - eng PT - Journal Article PL - Netherlands TA - Theor Med Bioeth JT - Theoretical medicine and bioethics JID - 9805378 SB - IM MH - Austria MH - Cadaver MH - *Cultural Characteristics MH - Decision Making MH - Egypt MH - Famous Persons MH - Genetic Privacy/*standards MH - *Genetic Research MH - Humans MH - Indians, North American MH - *Mummies MH - Ownership MH - *Third-Party Consent MH - Tissue Banks/standards MH - Tissue Preservation MH - Tissue and Organ Harvesting MH - United States OID - KIE: 101283 OTO - KIE OT - Analytical Approach OT - Biomedical and Behavioral Research OT - Genetics and Reproduction GN - KIE: Holm, Soren GN - KIE: 29 refs. GN - KIE: KIE Bib: genetic research; genetic screening; human experimentation/informed consent EDAT- 2002/01/26 10:00 MHDA- 2002/03/07 10:01 CRDT- 2002/01/26 10:00 PHST- 2002/01/26 10:00 [pubmed] PHST- 2002/03/07 10:01 [medline] PHST- 2002/01/26 10:00 [entrez] AID - 10.1023/a:1013010918460 [doi] PST - ppublish SO - Theor Med Bioeth. 2001 Sep;22(5):437-49. doi: 10.1023/a:1013010918460. PMID- 11388352 OWN - NLM STAT- MEDLINE DCOM- 20010628 LR - 20190619 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 292 IP - 5522 DP - 2001 Jun 1 TI - Human origins and ancient human DNA. PG - 1655-6 FAU - Cooper, A AU - Cooper A FAU - Rambaut, A AU - Rambaut A FAU - Macaulay, V AU - Macaulay V FAU - Willerslev, E AU - Willerslev E FAU - Hansen, A J AU - Hansen AJ FAU - Stringer, C AU - Stringer C LA - eng PT - Comment PT - Letter PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) SB - IM EIN - Science 2001 Jun 22;292(5525):2252 CON - Science. 2001 Jan 12;291(5502):230-1. doi: 10.1126/science.291.5502.230. PMID: 11253828 MH - Africa MH - Animals MH - Australia MH - Base Sequence MH - Biological Evolution MH - DNA Damage MH - DNA, Mitochondrial/*genetics MH - Hominidae/*genetics MH - Humans MH - *Paleontology MH - *Phylogeny MH - Specimen Handling EDAT- 2001/06/05 10:00 MHDA- 2001/06/29 10:01 CRDT- 2001/06/05 10:00 PHST- 2001/06/05 10:00 [pubmed] PHST- 2001/06/29 10:01 [medline] PHST- 2001/06/05 10:00 [entrez] AID - 10.1126/science.292.5522.1655 [doi] PST - ppublish SO - Science. 2001 Jun 1;292(5522):1655-6. doi: 10.1126/science.292.5522.1655. PMID- 11331901 OWN - NLM STAT- MEDLINE DCOM- 20010531 LR - 20220408 IS - 1471-0056 (Print) IS - 1471-0056 (Linking) VI - 2 IP - 5 DP - 2001 May TI - Ancient DNA. PG - 353-9 AB - DNA that has been recovered from archaeological and palaeontological remains makes it possible to go back in time and study the genetic relationships of extinct organisms to their contemporary relatives. This provides a new perspective on the evolution of organisms and DNA sequences. However, the field is fraught with technical pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human remains are studied. FAU - Hofreiter, M AU - Hofreiter M AD - Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany. FAU - Serre, D AU - Serre D FAU - Poinar, H N AU - Poinar HN FAU - Kuch, M AU - Kuch M FAU - Pääbo, S AU - Pääbo S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Nat Rev Genet JT - Nature reviews. Genetics JID - 100962779 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Biological Evolution MH - DNA/*genetics MH - Humans MH - *Paleontology MH - *Phylogeny RF - 71 EDAT- 2001/05/02 10:00 MHDA- 2001/06/02 10:01 CRDT- 2001/05/02 10:00 PHST- 2001/05/02 10:00 [pubmed] PHST- 2001/06/02 10:01 [medline] PHST- 2001/05/02 10:00 [entrez] AID - 35072071 [pii] AID - 10.1038/35072071 [doi] PST - ppublish SO - Nat Rev Genet. 2001 May;2(5):353-9. doi: 10.1038/35072071. PMID- 11309754 OWN - NLM STAT- MEDLINE DCOM- 20010621 LR - 20101118 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 115 IP - 1 DP - 2001 May TI - Absence of regional affinities of Neandertal DNA with living humans does not reject multiregional evolution. PG - 95-8 AB - The recent extraction of mitochondrial DNA sequences from three European Neandertal fossils has led many to the conclusion that ancient DNA analysis supports the African replacement model of modern human origins and rejects models of multiregional evolution that propose some Neandertal ancestry in living humans. This conclusion is based, in part, on the lack of regional affinity of Neandertal DNA to that from living Europeans. Consideration of migration matrix models shows that this conclusion is premature, since under a model of interregional gene flow we expect to see similar levels of Neandertal ancestry in all contemporary regions, and living Europeans should not necessarily show closer affinity. The absence of regional affinity in Neandertal DNA does not distinguish between replacement and multiregional models. FAU - Relethford, J H AU - Relethford JH AD - Department of Anthropology, State University of New York College at Oneonta, Oneonta, New York 13820, USA. relethjh@oneonta.edu LA - eng PT - Journal Article PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM EIN - Am J Phys Anthropol. 2003 Feb;120(2):209. MH - Africa MH - Animals MH - Anthropology, Physical MH - *Biological Evolution MH - DNA Fingerprinting MH - DNA, Mitochondrial/*genetics MH - *Emigration and Immigration MH - Europe MH - *Gene Frequency MH - Hominidae/*genetics MH - Humans MH - Models, Theoretical EDAT- 2001/04/20 10:00 MHDA- 2001/06/22 10:01 CRDT- 2001/04/20 10:00 PHST- 2001/04/20 10:00 [pubmed] PHST- 2001/06/22 10:01 [medline] PHST- 2001/04/20 10:00 [entrez] AID - 10.1002/ajpa.1060 [doi] PST - ppublish SO - Am J Phys Anthropol. 2001 May;115(1):95-8. doi: 10.1002/ajpa.1060. PMID- 11309745 OWN - NLM STAT- MEDLINE DCOM- 20010621 LR - 20071114 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 115 IP - 1 DP - 2001 May TI - Ancient mitochondrial DNA evidence for prehistoric population movement: the Numic expansion. PG - 1-12 AB - The mitochondrial DNA of modern Native Americans has been shown to fall into one of at least five haplogroups (A, B, C, D, or X) whose frequencies differ among tribal groups. The frequencies of these five haplogroups in a collection of ancient individuals from Western Nevada dating to between approximately 350-9,200 years BP were determined. These data were used to test the hypothesis, supported by archaeological and linguistic data, that the current inhabitants of the Great Basin, the Numic speakers, are recent immigrants into the area who replaced the previous non-Numic inhabitants. The frequency distributions of haplogroups in the ancient and modern Native Americans differed significantly, suggesting that there is a genetic discontinuity between the ancient inhabitants and the modern Numic speakers, providing further support for the Recent Numic Expansion hypothesis. The distribution of mitochondrial haplogroups of the ancient inhabitants of the Great Basin is most similar to those of some of the modern Native American inhabitants of California. FAU - Kaestle, F A AU - Kaestle FA AD - Department of Anthropology, Yale University, New Haven, Connecticut 06520, USA. frederika.kaestle@yale.edu FAU - Smith, D G AU - Smith DG LA - eng GR - RR00169/RR/NCRR NIH HHS/United States GR - RR05090/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - Anthropology, Physical MH - DNA, Mitochondrial/*genetics MH - *Genetics, Population MH - Haplotypes MH - Humans MH - Indians, North American/*genetics MH - Language MH - Movement MH - *Phylogeny EDAT- 2001/04/20 10:00 MHDA- 2001/06/22 10:01 CRDT- 2001/04/20 10:00 PHST- 2001/04/20 10:00 [pubmed] PHST- 2001/06/22 10:01 [medline] PHST- 2001/04/20 10:00 [entrez] AID - 10.1002/ajpa.1051 [doi] PST - ppublish SO - Am J Phys Anthropol. 2001 May;115(1):1-12. doi: 10.1002/ajpa.1051. PMID- 11296282 OWN - NLM STAT- MEDLINE DCOM- 20010510 LR - 20181113 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 98 IP - 8 DP - 2001 Apr 10 TI - A molecular analysis of dietary diversity for three archaic Native Americans. PG - 4317-22 AB - DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2-4 different animal species and 4-8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue. FAU - Poinar, H N AU - Poinar HN AD - Max-Planck-Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany. Poinar@eva.mpg.de FAU - Kuch, M AU - Kuch M FAU - Sobolik, K D AU - Sobolik KD FAU - Barnes, I AU - Barnes I FAU - Stankiewicz, A B AU - Stankiewicz AB FAU - Kuder, T AU - Kuder T FAU - Spaulding, W G AU - Spaulding WG FAU - Bryant, V M AU - Bryant VM FAU - Cooper, A AU - Cooper A FAU - Pääbo, S AU - Pääbo S LA - eng SI - GENBANK/AF354048 SI - GENBANK/AF354049 SI - GENBANK/AF354050 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Base Sequence MH - DNA, Mitochondrial MH - *Diet MH - Feces MH - *Fossils MH - Gas Chromatography-Mass Spectrometry MH - Humans MH - *Indians, North American MH - Molecular Sequence Data MH - Sequence Homology, Nucleic Acid MH - Texas PMC - PMC31832 EDAT- 2001/04/11 10:00 MHDA- 2001/05/22 10:01 PMCR- 2001/10/10 CRDT- 2001/04/11 10:00 PHST- 2001/04/11 10:00 [pubmed] PHST- 2001/05/22 10:01 [medline] PHST- 2001/04/11 10:00 [entrez] PHST- 2001/10/10 00:00 [pmc-release] AID - 98/8/4317 [pii] AID - 061014798 [pii] AID - 0147 [pii] AID - 10.1073/pnas.061014798 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4317-22. doi: 10.1073/pnas.061014798. PMID- 11289521 OWN - NLM STAT- MEDLINE DCOM- 20010419 LR - 20200306 IS - 0022-2615 (Print) IS - 0022-2615 (Linking) VI - 50 IP - 4 DP - 2001 Apr TI - Molecular analysis of skeletal tuberculosis in an ancient Egyptian population. PG - 355-366 LID - 10.1099/0022-1317-50-4-355 [doi] AB - A paleomicrobiological study was performed on 37 skeletal tissue specimens from cadavers in the necropolis of Thebes-West, Upper Egypt, (2120-500 BC) and four from the necropolis of Abydos (3000 BC). The subjects had typical macromorphological evidence of osseous tuberculosis (n = 3), morphological alterations that were not specific, but probably resulted from tuberculosis (n = 17), or were without morphological osseous changes (n = 21). DNA was extracted from these bone samples and amplified by PCR with a primer pair that recognised the Mycobacterium tuberculosis complex insertion sequence IS6110. To confirm specificity of the analysis, the amplification products of several samples were subjected to restriction enzyme digestion, or direct sequencing, or both. In 30 of the 41 cases analysed, ancient DNA was demonstrated by amplification by the presence of the human beta-actin or the amelogenin gene and nine of these cases were positive for M. tuberculosis DNA. The results were confirmed by restriction endonuclease digestion and sequencing. A positive result for M. tuberculosis DNA was seen in two of the three cases with typical morphological signs of tuberculosis and amplifiable DNA, in five of 13 non-specific, but probable cases (including two cases from c. 3000 BC), but also in two of 14 cases without pathological bone changes. These observations confirm that tuberculosis may be diagnosed unequivocally in skeletal material from ancient Egypt, even dating back to c. 3000 BC. As a positive molecular reaction was observed in most of the typical cases of skeletal tuberculosis, in about one-third of non-specific, but probable tuberculous osseous changes and, surprisingly, in about one-seventh of unremarkable samples, this suggests that infection with M. tuberculosis was relatively frequent in ancient Egypt. FAU - Zink, Albert AU - Zink A AD - *Department of Pathology, Ludwig-Maximillians-Universität, D-80337 München, †Department of Pathology, Friedrich-Alexander Universität Erlangen-Nürnberg, D-91054, ‡Institute of Medical Microbiology and Hygiene, University, D-93053 Regensburg and §Department of Diagnostic Radiology, Ludwig-Maximilians-Universität, D-80336 München, Germany. FAU - Haas, Christian J AU - Haas CJ AD - *Department of Pathology, Ludwig-Maximillians-Universität, D-80337 München, †Department of Pathology, Friedrich-Alexander Universität Erlangen-Nürnberg, D-91054, ‡Institute of Medical Microbiology and Hygiene, University, D-93053 Regensburg and §Department of Diagnostic Radiology, Ludwig-Maximilians-Universität, D-80336 München, Germany. FAU - Reischl, Udo AU - Reischl U AD - *Department of Pathology, Ludwig-Maximillians-Universität, D-80337 München, †Department of Pathology, Friedrich-Alexander Universität Erlangen-Nürnberg, D-91054, ‡Institute of Medical Microbiology and Hygiene, University, D-93053 Regensburg and §Department of Diagnostic Radiology, Ludwig-Maximilians-Universität, D-80336 München, Germany. FAU - Szeimies, Ulrike AU - Szeimies U AD - *Department of Pathology, Ludwig-Maximillians-Universität, D-80337 München, †Department of Pathology, Friedrich-Alexander Universität Erlangen-Nürnberg, D-91054, ‡Institute of Medical Microbiology and Hygiene, University, D-93053 Regensburg and §Department of Diagnostic Radiology, Ludwig-Maximilians-Universität, D-80336 München, Germany. FAU - Nerlich, Andreas G AU - Nerlich AG AD - *Department of Pathology, Ludwig-Maximillians-Universität, D-80337 München, †Department of Pathology, Friedrich-Alexander Universität Erlangen-Nürnberg, D-91054, ‡Institute of Medical Microbiology and Hygiene, University, D-93053 Regensburg and §Department of Diagnostic Radiology, Ludwig-Maximilians-Universität, D-80336 München, Germany. LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Med Microbiol JT - Journal of medical microbiology JID - 0224131 RN - 0 (Amelogenin) RN - 0 (DNA Transposable Elements) RN - 0 (DNA, Bacterial) RN - 0 (DNA-Binding Proteins) RN - 0 (Dental Enamel Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Sex-Determining Region Y Protein) RN - 0 (Transcription Factors) SB - IM MH - Amelogenin MH - Bone and Bones/*microbiology MH - DNA Transposable Elements MH - DNA, Bacterial/*analysis/isolation & purification MH - DNA-Binding Proteins/genetics MH - Dental Enamel Proteins/genetics MH - Egypt, Ancient/epidemiology MH - Female MH - History, Ancient MH - Humans MH - Male MH - Mycobacterium tuberculosis/classification/genetics/*isolation & purification MH - *Nuclear Proteins MH - *Paleopathology MH - Polymerase Chain Reaction MH - Sex Determination Analysis/methods MH - Sex-Determining Region Y Protein MH - *Transcription Factors MH - Tuberculosis, Osteoarticular/epidemiology/*history/microbiology/pathology EDAT- 2001/04/06 10:00 MHDA- 2001/04/21 10:01 CRDT- 2001/04/06 10:00 PHST- 2001/04/06 10:00 [pubmed] PHST- 2001/04/21 10:01 [medline] PHST- 2001/04/06 10:00 [entrez] AID - 10.1099/0022-1317-50-4-355 [doi] PST - ppublish SO - J Med Microbiol. 2001 Apr;50(4):355-366. doi: 10.1099/0022-1317-50-4-355. PMID- 11305426 OWN - NLM STAT- MEDLINE DCOM- 20010503 LR - 20061115 IS - 0022-1198 (Print) IS - 0022-1198 (Linking) VI - 46 IP - 2 DP - 2001 Mar TI - Improved MtDNA sequence analysis of forensic remains using a "mini-primer set" amplification strategy. PG - 247-53 AB - Mitochondrial DNA (mtDNA) analysis of highly degraded skeletal remains is often used for forensic identification due largely to the high genome copy number per cell. Literature from the "ancient DNA" field has shown that highly degraded samples contain populations of intact DNA molecules that are severely restricted in size (1-4). Hand et al. have demonstrated the targeting and preferential amplification of authentic human DNA sequences with small amplicon products of 150 bp or less (1,2). Given this understanding of ancient DNA preservation and amplification, we report an improved approach to forensic mtDNA analysis of hypervariable regions 1 and 2 (HV1/HV2) in highly degraded specimens. This "mini-primer set" (MPS) amplification strategy consists of four overlapping products that span each of the HV regions and range from 126 to 170 bp, with an average size of 141 bp. For this study, 11 extracts representing a range of sample quality were prepared from nonprobative forensic specimens. We demonstrate a significant increase in MPS amplification success when compared to testing methods using approximately 250 bp amplicons. Further, 16 of 17 independent amplifications previously "unreported" due to mixed sequences provided potentially reportable sequence data from a single, authentic template with MPS testing. FAU - Gabriel, M N AU - Gabriel MN AD - MtDNA Section, The Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, USA. FAU - Huffine, E F AU - Huffine EF FAU - Ryan, J H AU - Ryan JH FAU - Holland, M M AU - Holland MM FAU - Parsons, T J AU - Parsons TJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Forensic Sci JT - Journal of forensic sciences JID - 0375370 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Bone and Bones MH - DNA Primers MH - DNA, Mitochondrial/*genetics MH - Forensic Anthropology/*methods MH - Humans MH - *Nucleic Acid Amplification Techniques MH - Polymerase Chain Reaction MH - Reference Values MH - Specimen Handling MH - Time Factors EDAT- 2001/04/18 10:00 MHDA- 2001/05/05 10:01 CRDT- 2001/04/18 10:00 PHST- 2001/04/18 10:00 [pubmed] PHST- 2001/05/05 10:01 [medline] PHST- 2001/04/18 10:00 [entrez] PST - ppublish SO - J Forensic Sci. 2001 Mar;46(2):247-53. PMID- 11209041 OWN - NLM STAT- MEDLINE DCOM- 20010426 LR - 20181113 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 98 IP - 2 DP - 2001 Jan 16 TI - Ancient DNA and the origin of modern humans. PG - 390-1 FAU - Relethford, J H AU - Relethford JH AD - Department of Anthropology, State University of New York College at Oneonta, Oneonta, NY 13820, USA. relethjh@oneonta.edu LA - eng PT - Comment PT - Comparative Study PT - Journal Article PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Mitochondrial) SB - IM CON - Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):537-42. doi: 10.1073/pnas.98.2.537. PMID: 11209053 MH - Africa, Eastern MH - Animals MH - Archaeology MH - Australia MH - *Biological Evolution MH - Chromosomes, Human, Pair 11/genetics MH - DNA, Mitochondrial/*genetics MH - Emigration and Immigration MH - Evolution, Molecular MH - Fossils MH - Hominidae/classification/*genetics MH - Humans MH - Species Specificity PMC - PMC33358 EDAT- 2001/02/24 11:00 MHDA- 2001/05/01 10:01 PMCR- 2001/07/16 CRDT- 2001/02/24 11:00 PHST- 2001/02/24 11:00 [pubmed] PHST- 2001/05/01 10:01 [medline] PHST- 2001/02/24 11:00 [entrez] PHST- 2001/07/16 00:00 [pmc-release] AID - 98/2/390 [pii] AID - 5789 [pii] AID - 10.1073/pnas.98.2.390 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):390-1. doi: 10.1073/pnas.98.2.390. PMID- 11584593 OWN - NLM STAT- MEDLINE DCOM- 20011101 LR - 20151119 IS - 1472-9792 (Print) IS - 1472-9792 (Linking) VI - 81 IP - 4 DP - 2001 TI - Mycolic acids and ancient DNA confirm an osteological diagnosis of tuberculosis. PG - 259-65 AB - SETTING: The underlying trends in the past epidemiology of tuberculosis (TB) are obscure, requiring recourse to the archaeological record. It would therefore be of value to develop methods for reliable TB diagnosis in ancient populations. OBJECTIVE: To test the capability of two biomarkers, Mycobacterium tuberculosis complex mycolic acids and a DNA target (IS6110), for confirming an osteological diagnosis of TB in medieval individuals, based on the presence of Pott's disease and/or rib lesions. DESIGN: Osteological examination of three archaeological individuals (Medieval: approximately 1000 years old) revealed a Pott's disease case, one with no changes consistent with TB and one with rib lesions. Rib samples from these individuals were examined for the presence of Mycobacterium tuberculosis complex mycolic acids and mycobacterial DNA. RESULTS: Mycobacterium tuberculosis complex mycolic acids and the DNA target were detected in the Pott's disease case, whilst mycolic acids (insufficient for confirmation) alone were detected in the rib lesion case. CONCLUSIONS: Biomarkers provide a sensitive tool to detect ancient TB. Mycobacterium tuberculosis DNA is not distributed homogeneously, making multiple sampling essential. Mycolic acids seem more reliable for ancient TB diagnosis than IS6110. The demonstrated stability of mycolic acids show that they may be of value in tracing the palaeoepidemiology of tuberculosis back into antiquity. FAU - Gernaey, A M AU - Gernaey AM AD - Fossil Fuels and Environmental Geochemistry, Department of Chemistry, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK. namg1@talkZ1.com FAU - Minnikin, D E AU - Minnikin DE FAU - Copley, M S AU - Copley MS FAU - Dixon, R A AU - Dixon RA FAU - Middleton, J C AU - Middleton JC FAU - Roberts, C A AU - Roberts CA LA - eng PT - Historical Article PT - Journal Article PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 0 (Biomarkers) RN - 0 (DNA, Bacterial) RN - 0 (Mycolic Acids) SB - IM MH - Adult MH - Biomarkers/analysis MH - Chromatography, High Pressure Liquid MH - DNA, Bacterial/*analysis MH - History, Medieval MH - Humans MH - Male MH - Mycobacterium tuberculosis/*chemistry MH - Mycolic Acids/*analysis MH - Paleopathology MH - Polymerase Chain Reaction/methods MH - Ribs/microbiology MH - Tuberculosis, Osteoarticular/*diagnosis/history MH - Tuberculosis, Spinal/diagnosis/history EDAT- 2001/10/05 10:00 MHDA- 2001/11/03 10:01 CRDT- 2001/10/05 10:00 PHST- 2001/10/05 10:00 [pubmed] PHST- 2001/11/03 10:01 [medline] PHST- 2001/10/05 10:00 [entrez] AID - S1472-9792(01)90295-1 [pii] AID - 10.1054/tube.2001.0295 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2001;81(4):259-65. doi: 10.1054/tube.2001.0295. PMID- 11196299 OWN - NLM STAT- MEDLINE DCOM- 20010329 LR - 20180928 IS - 0736-6205 (Print) IS - 0736-6205 (Linking) VI - 30 IP - 1 DP - 2001 Jan TI - Hybridization screening of very short PCR products for paleoepidemiological studies of Chagas' disease. PG - 102-4, 106, 108-9 AB - Single strands of very short PCR products can be covalently immobilized to a slide and then easily detected by probe hybridization. In this work, the PCR product was a 70-nucleotide segment of ancient DNA, representing a portion of repeat mini-circle DNA from the kinetoplast of Trypanosoma cruzi, the infectious agent of Chagas' disease (American Trypanosomiasis). The target segment was initially established to be present in soft tissue samples taken from four "naturally" mummified Andean bodies using PCR followed by cloning and sequencing. Hybridization screening of the covalently immobilized PCR products positively identified products from 25 of 27 specimens of different tissues from these four mummies. The method appears to be ideal for the purpose of screening a large number of specimens when the target PCR product is very short. FAU - Madden, M AU - Madden M AD - Whiteside Institute for Clinical Research, Duluth, MN, USA. mmadden@d.umn.edu FAU - Salo, W L AU - Salo WL FAU - Streitz, J AU - Streitz J FAU - Aufderheide, A C AU - Aufderheide AC FAU - Fornaciari, G AU - Fornaciari G FAU - Jaramillo, C AU - Jaramillo C FAU - Vallejo, G A AU - Vallejo GA FAU - Yockteng, R AU - Yockteng R FAU - Arriaza, B AU - Arriaza B FAU - Cárdenas-Arroyo, F AU - Cárdenas-Arroyo F FAU - Guhl, F AU - Guhl F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Technical Report PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA, Kinetoplast) RN - 0 (RNA Probes) SB - IM MH - Animals MH - Base Sequence MH - Chagas Disease/*genetics/parasitology MH - DNA, Kinetoplast/*genetics MH - Humans MH - Molecular Sequence Data MH - Mummies/parasitology MH - Nucleic Acid Hybridization MH - Paleopathology MH - Polymerase Chain Reaction MH - RNA Probes MH - Sequence Homology, Nucleic Acid MH - Trypanosoma cruzi/*genetics EDAT- 2001/02/24 12:00 MHDA- 2001/04/03 10:01 CRDT- 2001/02/24 12:00 PHST- 2001/02/24 12:00 [pubmed] PHST- 2001/04/03 10:01 [medline] PHST- 2001/02/24 12:00 [entrez] AID - 10.2144/01301st07 [doi] PST - ppublish SO - Biotechniques. 2001 Jan;30(1):102-4, 106, 108-9. doi: 10.2144/01301st07. PMID- 11204924 OWN - NLM STAT- MEDLINE DCOM- 20010301 LR - 20061115 IS - 0369-8114 (Print) IS - 0369-8114 (Linking) VI - 48 IP - 10 DP - 2000 Dec TI - [Recent developments of spoligotyping as applied to the study of epidemiology, biodiversity and molecular phylogeny of the Mycobacterium tuberculosis complex]. PG - 921-32 AB - Spoligotyping (for 'spacer-oligonucleotide-typing'), a rapid method for genotyping of Mycobacterium tuberculosis complex using the principle of reverse hybridization, is based on the structure of the direct repeat (DR) locus. The DR locus is made up of a variable number of 36 bp DR repeats that are separated by unique inter-DR sequences of 35 to 41 bp. Fast and highly discriminatory, spoligotyping is an useful alternative to the IS6110-RFLP reference method for molecular typing of M. tuberculosis, in particular for isolates possessing five or few copies of IS6110. In this paper, we review the state of the art of spoligotyping through its main current applications. After a brief introduction to the principle of the technique and its description, we successively review recently published results concerning the molecular epidemiology of tuberculosis in humans and cattle, and discuss the main genotyping strategies currently in use to fingerprint the M. tuberculosis complex organisms. We also describe the recent applications of spoligotyping to study ancient DNA and report on recent developments of this technique to study the biodiversity of the M. tuberculosis complex, its contribution towards improved taxonomy and phylogenetics of the M. tuberculosis complex. Last but not least, potential applications of spoligotyping to study DNA recombination mechanisms are also discussed. FAU - Sola, C AU - Sola C AD - Unité de la tuberculose et des mycobactéries, Institut Pasteur de Guadeloupe, Morne Jolivière, BP 484, 97165 Pointe-à-Pitre, Guadeloupe. csola@pasteur.gp FAU - Filliol, I AU - Filliol I FAU - Legrand, E AU - Legrand E FAU - Rastogi, N AU - Rastogi N LA - fre PT - English Abstract PT - Journal Article PT - Review TT - Développements récents du spoligotypage appliqués à l'étude de l'épidémiologie, de la biodiversité, et de la phylogénie moléculaire du complexe Mycobacterium tuberculosis. PL - France TA - Pathol Biol (Paris) JT - Pathologie-biologie JID - 0265365 RN - 0 (DNA, Intergenic) RN - 0 (Oligonucleotides) SB - IM MH - Animals MH - Cattle MH - DNA, Intergenic MH - *Ecosystem MH - *Evolution, Molecular MH - Genotype MH - Humans MH - Mycobacterium tuberculosis/classification/*genetics MH - Nucleic Acid Hybridization MH - Oligonucleotides MH - *Phylogeny MH - Repetitive Sequences, Nucleic Acid MH - Tuberculosis/*epidemiology/microbiology RF - 57 EDAT- 2001/02/24 12:00 MHDA- 2001/03/07 10:01 CRDT- 2001/02/24 12:00 PHST- 2001/02/24 12:00 [pubmed] PHST- 2001/03/07 10:01 [medline] PHST- 2001/02/24 12:00 [entrez] PST - ppublish SO - Pathol Biol (Paris). 2000 Dec;48(10):921-32. PMID- 11185910 OWN - NLM STAT- MEDLINE DCOM- 20010301 LR - 20081121 IS - 0039-9450 (Print) IS - 0039-9450 (Linking) VI - 45 IP - 16 DP - 2000 Dec TI - [Human dispersal across the earth disclosed by ancient DNA analysis]. PG - 2572-8 FAU - Ueda, S AU - Ueda S AD - Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. LA - jpn PT - Journal Article PT - Review PL - Japan TA - Tanpakushitsu Kakusan Koso JT - Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme JID - 0413762 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Asia MH - DNA/*genetics MH - Europe MH - *Fossils MH - Genetic Variation MH - Hominidae/*genetics MH - Humans MH - *Phylogeny MH - *Sequence Analysis, DNA RF - 28 EDAT- 2001/02/24 12:00 MHDA- 2001/03/07 10:01 CRDT- 2001/02/24 12:00 PHST- 2001/02/24 12:00 [pubmed] PHST- 2001/03/07 10:01 [medline] PHST- 2001/02/24 12:00 [entrez] PST - ppublish SO - Tanpakushitsu Kakusan Koso. 2000 Dec;45(16):2572-8. PMID- 11082781 OWN - NLM STAT- MEDLINE DCOM- 20010102 LR - 20061115 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 3 DP - 2000 Sep TI - Cremation practices and the survival of ancient DNA: burnt bone analyses via RAPD-mediated PCR. PG - 237-51 AB - Numerous burial rites have been developed in different time periods of human cultural evolution. One of the most interesting burial practices was the ritual cremation of human bodies. Due to the respective cultural and religious background, brand graves are known where human remains had been buried together with burnt bones of animal origin. To date, burnt bone samples have been refractory to PCR-mediated amplification. D/L values of aspartic acid far greater than 80 x 10(-3) were measured in the samples thus indicating the presence of severely nicked and fragmented nucleic acids. In order to differentiate between burial gift of animal origin and burnt human specimens we established a highly sensitive protocol that addresses all the shortcomings connected to degraded ancient DNA. With the novel procedure it was possible to classify 4 specimens ranging from 2,000-5,000 BP on the basis of mitochondrial DNA sequences. FAU - Pusch, C M AU - Pusch CM AD - Molecular Genetics Laboratory, University Eye Hospital, University of Tübingen. cpusch@hgmp.mrc.ac.uk FAU - Broghammer, M AU - Broghammer M FAU - Scholz, M AU - Scholz M LA - eng PT - Clinical Trial PT - Comparative Study PT - Journal Article PT - Randomized Controlled Trial PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (DNA, Mitochondrial) SB - IM MH - Age Determination by Skeleton MH - Animals MH - Bone and Bones/*chemistry MH - DNA Damage/*genetics MH - DNA, Mitochondrial/*genetics MH - Humans MH - *Mortuary Practice MH - *Paleontology MH - Polymerase Chain Reaction/*methods MH - Sensitivity and Specificity MH - Sequence Analysis, DNA EDAT- 2000/11/18 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/11/18 11:00 PHST- 2000/11/18 11:00 [pubmed] PHST- 2001/02/28 10:01 [medline] PHST- 2000/11/18 11:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Sep;58(3):237-51. PMID- 10989644 OWN - NLM STAT- MEDLINE DCOM- 20000928 LR - 20190513 IS - 0002-9173 (Print) IS - 0002-9173 (Linking) VI - 114 IP - 3 DP - 2000 Sep TI - Detection of leprosy in ancient human skeletal remains by molecular identification of Mycobacterium leprae. PG - 428-36 AB - We isolated ancient DNA from skeletal remains obtained from a South German ossuary (approximately 1400-1800 AD) and from a 10th century Hungarian cemetery partially indicating macromorphologic evidence of leprosy. In samples taken of 2 skulls from Germany and of 1 hard palate from Hungary, Mycobacterium leprae-specific fragments of RLEP1 and RLEP3 were amplified using polymerase chain reaction (PCR), thereby confirming their specificity by sequencing. In another case, PCR with primers targeting IS6110 of Mycobacterium tuberculosis gave positive results only for a mandibular specimen. No signal for any mycobacterial DNA was observed in samples from 2 Hungarian foot bones. In ancient material, osseous involvement of M leprae may be detected and distinguished from other mycobacterial infections by specific PCR. In the small bones of leprous hands and feet, not enough M leprae DNA seems to be present for detection. This supports the view that rhinomaxillary leprous alterations result from direct bacterial involvement, while osseous mutilations of hands and feet result from a nervous involvement and/or secondary infections due to small lacerations of the overlying soft tissues. FAU - Haas, C J AU - Haas CJ AD - Department of Pathology, Zentralklinikum Augsburg, Ludwig-Maximilians-Universität München, Munich, Germany. FAU - Zink, A AU - Zink A FAU - Pálfi, G AU - Pálfi G FAU - Szeimies, U AU - Szeimies U FAU - Nerlich, A G AU - Nerlich AG LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Am J Clin Pathol JT - American journal of clinical pathology JID - 0370470 RN - 0 (DNA, Bacterial) RN - 0 (Peptides, Cyclic) RN - 0 (leech excitatory peptide, Hirudo nipponia) SB - IM EIN - Am J Clin Pathol 2000 Dec;114(6):985 MH - Base Sequence MH - Bone and Bones/*microbiology MH - DNA, Bacterial/*analysis MH - Female MH - History, Medieval MH - History, Modern 1601- MH - Humans MH - Leprosy/*diagnosis/history/microbiology MH - Male MH - Middle Aged MH - Molecular Sequence Data MH - Mycobacterium leprae/genetics/*isolation & purification MH - Paleopathology/*methods MH - Peptides, Cyclic MH - Polymerase Chain Reaction MH - Sequence Analysis, DNA EDAT- 2000/09/16 11:00 MHDA- 2000/09/30 11:01 CRDT- 2000/09/16 11:00 PHST- 2000/09/16 11:00 [pubmed] PHST- 2000/09/30 11:01 [medline] PHST- 2000/09/16 11:00 [entrez] AID - 10.1093/ajcp/114.3.428 [doi] PST - ppublish SO - Am J Clin Pathol. 2000 Sep;114(3):428-36. doi: 10.1093/ajcp/114.3.428. PMID- 10954626 OWN - NLM STAT- MEDLINE DCOM- 20001010 LR - 20061115 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 113 IP - 1 DP - 2000 Sep TI - Brief communication: discouraging prospects for ancient DNA from India. PG - 129-33 FAU - Kumar, S S AU - Kumar SS AD - Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. FAU - Nasidze, I AU - Nasidze I FAU - Walimbe, S R AU - Walimbe SR FAU - Stoneking, M AU - Stoneking M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (Amino Acids) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acids/analysis MH - Bone and Bones/chemistry MH - Chromatography, High Pressure Liquid MH - DNA/*chemistry MH - Humans MH - India MH - Isomerism MH - *Paleopathology MH - Polymerase Chain Reaction EDAT- 2000/08/23 11:00 MHDA- 2000/10/14 11:01 CRDT- 2000/08/23 11:00 PHST- 2000/08/23 11:00 [pubmed] PHST- 2000/10/14 11:01 [medline] PHST- 2000/08/23 11:00 [entrez] AID - 10.1002/1096-8644(200009)113:1<129::AID-AJPA12>3.0.CO;2-2 [pii] AID - 10.1002/1096-8644(200009)113:1<129::AID-AJPA12>3.0.CO;2-2 [doi] PST - ppublish SO - Am J Phys Anthropol. 2000 Sep;113(1):129-33. doi: 10.1002/1096-8644(200009)113:1<129::AID-AJPA12>3.0.CO;2-2. PMID- 10954622 OWN - NLM STAT- MEDLINE DCOM- 20001010 LR - 20081121 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 113 IP - 1 DP - 2000 Sep TI - Context of maternal lineages in the Greater Southwest. PG - 85-101 AB - We present mitochondrial haplogroup characterizations of the prehistoric Anasazi of the United States (US) Southwest. These data are part of a long-term project to characterize ancient Great Basin and US Southwest samples for mitochondrial DNA (mtDNA) diversity. Three restriction site polymorphisms (RSPs) and one length polymorphism identify four common Native American matrilines (A, B, C, and D). The Anasazi (n = 27) are shown to have a moderate frequency of haplogroup A (22%), a high frequency of haplogroup B (56%), and a low frequency of C (15%). Haplogroup D has not yet been detected among the Anasazi. In comparison to modern Native American groups from the US Southwest, the Anasazi are shown to have a distribution of haplogroups similar to the frequency pattern exhibited by modern Pueblo groups. A principal component analysis also clusters the Anasazi with some modern (Pueblo) Southwestern populations, and away from other modern (Athapaskan speaking) Southwestern populations. The Anasazi are also shown to have a significantly different distribution of the four haplogroups as compared to the eastern Great Basin Great Salt Lake Fremont (n = 32), although both groups cluster together in a principal component analysis. The context of our data suggests substantial stability within the US Southwest, even in the face of the serious cultural and biological disruption caused by colonization of the region by European settlers. We conclude that although sample numbers are fairly low, ancient DNA (aDNA) data are useful for assessing long-term populational affinities and for discerning regional population structure. CI - Copyright 2000 Wiley-Liss, Inc. FAU - Carlyle, S W AU - Carlyle SW AD - Department of Anthropology, University of Utah, Salt Lake City, Utah 84112-0060, USA. carlyle@anthro.utah.edu FAU - Parr, R L AU - Parr RL FAU - Hayes, M G AU - Hayes MG FAU - O'Rourke, D H AU - O'Rourke DH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*chemistry MH - Female MH - Genetic Variation MH - Haplotypes MH - Humans MH - Indians, North American/*genetics MH - Southwestern United States EDAT- 2000/08/23 11:00 MHDA- 2000/10/14 11:01 CRDT- 2000/08/23 11:00 PHST- 2000/08/23 11:00 [pubmed] PHST- 2000/10/14 11:01 [medline] PHST- 2000/08/23 11:00 [entrez] AID - 10.1002/1096-8644(200009)113:1<85::AID-AJPA8>3.0.CO;2-1 [pii] AID - 10.1002/1096-8644(200009)113:1<85::AID-AJPA8>3.0.CO;2-1 [doi] PST - ppublish SO - Am J Phys Anthropol. 2000 Sep;113(1):85-101. doi: 10.1002/1096-8644(200009)113:1<85::AID-AJPA8>3.0.CO;2-1. PMID- 10970224 OWN - NLM STAT- MEDLINE DCOM- 20000831 LR - 20220408 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 289 IP - 5482 DP - 2000 Aug 18 TI - Ancient DNA: do it right or not at all. PG - 1139 FAU - Cooper, A AU - Cooper A FAU - Poinar, H N AU - Poinar HN LA - eng PT - Comment PT - Letter PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA Primers) RN - 9007-49-2 (DNA) SB - IM CON - Science. 2000 Jul 28;289(5479):530-1. doi: 10.1126/science.289.5479.530. PMID: 10939960 MH - Cloning, Molecular MH - *DNA MH - DNA Primers MH - *Fossils MH - Humans MH - Polymerase Chain Reaction/*standards MH - Publishing MH - Reproducibility of Results MH - Research/*standards EDAT- 2000/09/02 11:00 MHDA- 2000/09/02 11:01 CRDT- 2000/09/02 11:00 PHST- 2000/09/02 11:00 [pubmed] PHST- 2000/09/02 11:01 [medline] PHST- 2000/09/02 11:00 [entrez] AID - 10.1126/science.289.5482.1139b [doi] PST - ppublish SO - Science. 2000 Aug 18;289(5482):1139. doi: 10.1126/science.289.5482.1139b. PMID- 10939960 OWN - NLM STAT- MEDLINE DCOM- 20000808 LR - 20190619 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 289 IP - 5479 DP - 2000 Jul 28 TI - 5TH International Ancient DNA Conference. Divining diet and disease from DNA. PG - 530-1 AB - Some 110 scientists from a range of disciplines gathered in the overcast British midlands for the 5th International Ancient DNA Conference, held here from 12 to 14 July. Among the attractions were new insights into the diets of early Americans gleaned from ancient human coprolites and intriguing reports of nuclear DNA and ancient viral sequences extracted from mammoth bones. FAU - Stokstad, E AU - Stokstad E LA - eng PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Viral) RN - 9007-49-2 (DNA) SB - IM CIN - Science. 2000 Aug 18;289(5482):1139. doi: 10.1126/science.289.5482.1139b. PMID: 10970224 MH - Animals MH - Bone and Bones/virology MH - DNA/*analysis/history MH - DNA, Viral/analysis/*history MH - Diet/*history MH - Elephants/*genetics/virology MH - Feces/*chemistry MH - Female MH - Fossils MH - History, Ancient MH - Humans MH - Male MH - Texas EDAT- 2000/08/12 00:00 MHDA- 2000/08/12 00:01 CRDT- 2000/08/12 00:00 PHST- 2000/08/12 00:00 [pubmed] PHST- 2000/08/12 00:01 [medline] PHST- 2000/08/12 00:00 [entrez] AID - 10.1126/science.289.5479.530 [doi] PST - ppublish SO - Science. 2000 Jul 28;289(5479):530-1. doi: 10.1126/science.289.5479.530. PMID- 10871390 OWN - NLM STAT- MEDLINE DCOM- 20000718 LR - 20241120 IS - 1362-4962 (Electronic) IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 28 IP - 12 DP - 2000 Jun 15 TI - A simple and efficient method for PCR amplifiable DNA extraction from ancient bones. PG - E67 AB - A simple and effective modified ethanol precipitation-based protocol is described for the preparation of DNA from ancient human bones. This method is fast and requires neither hazardous chemicals nor special devices. After the powdering and incubating of the bone samples Dextran Blue was added as a carrier for removing the PCR inhibitors with selective ethanol precipitation. This method could eliminate the time-consuming separate decalcification step, dialysis, application of centrifugation-driven microconcentrators and the second consecutive PCR amplification. The efficiency of this procedure was demonstrated on ten 500-1200-year-old human bones from four different Hungarian burial sites. A mitochondrial specific primer pair was used to obtain sequence information from the purified ancient DNA. The PCR amplification, after our DNA extraction protocol, was successful from each of the 10 bone samples investigated. The results demonstrate that extraction of DNA from ancient bone samples with this new approach increases the success rate of PCR amplification. FAU - Kalmár, T AU - Kalmár T AD - Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, POB 521, H-6701, Szeged, Hungary and Department of Anthropology, University of Szeged, Egyetem u. 2, H-6725, Szeged, Hungary. klampar@nucleus.szbk.u-szeged.hu FAU - Bachrati, C Z AU - Bachrati CZ FAU - Marcsik, A AU - Marcsik A FAU - Raskó, I AU - Raskó I LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 9007-49-2 (DNA) SB - IM MH - Adolescent MH - Adult MH - Aged MH - Bone and Bones/*chemistry MH - DNA/history/*isolation & purification MH - Female MH - History, 15th Century MH - History, Medieval MH - Humans MH - Hungary MH - Male MH - Middle Aged MH - Molecular Sequence Data MH - Polymerase Chain Reaction/*methods PMC - PMC102752 EDAT- 2000/06/28 00:00 MHDA- 2000/07/25 00:00 PMCR- 2000/06/15 CRDT- 2000/06/28 00:00 PHST- 2000/06/28 00:00 [pubmed] PHST- 2000/07/25 00:00 [medline] PHST- 2000/06/28 00:00 [entrez] PHST- 2000/06/15 00:00 [pmc-release] AID - gnd068 [pii] AID - 10.1093/nar/28.12.e67 [doi] PST - ppublish SO - Nucleic Acids Res. 2000 Jun 15;28(12):E67. doi: 10.1093/nar/28.12.e67. PMID- 10962710 OWN - NLM STAT- MEDLINE DCOM- 20001107 LR - 20151119 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 2 DP - 2000 Jun TI - [Molecular genetic analysis for taxonomic determination of fossil skull fragments of Warendorf-Neuwarendorf]. PG - 129-35 AB - The isolation and examination DNA segments from prehistoric and fossil bone samples has become one of the biggest challenges in anthropology within the past years. By using specially developed and/or adapted genetic methods, it is possible under laboratory conditions to amplify portions of DNA from bone remains in states of good preservation by the polymerase chain reaction (PCR). DNA sequence data can provide far more specific answers to palaeanthropological questions than one would expect solely by morphologic comparison. Here we introduce an alternative approach for the classification of total ancient DNA by means of Southern hybridisation techniques. FAU - Scholz, M AU - Scholz M AD - Osteologische Sammlung der Universität Tübingen. FAU - Pusch, C M AU - Pusch CM LA - ger PT - English Abstract PT - Journal Article TT - Molekulargenetische Analysen zur taxonomischen Bestimmung des fossilen Schädelfragments aus Warendorf-Neuwarendorf. PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (DNA Probes) RN - 9007-49-2 (DNA) SB - IM MH - Anthropology, Physical MH - DNA/*genetics MH - DNA Probes MH - *Fossils MH - Germany MH - Humans MH - In Situ Hybridization MH - *Paleopathology MH - Polymerase Chain Reaction MH - Skull/*anatomy & histology EDAT- 2000/08/30 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/08/30 11:00 PHST- 2000/08/30 11:00 [pubmed] PHST- 2001/02/28 10:01 [medline] PHST- 2000/08/30 11:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Jun;58(2):129-35. PMID- 10832878 OWN - NLM STAT- MEDLINE DCOM- 20000925 LR - 20061115 IS - 0173-0835 (Print) IS - 0173-0835 (Linking) VI - 21 IP - 8 DP - 2000 May TI - Voltage-induced release of nucleic acids from palaeontological samples. PG - 1488-92 AB - Most of the protocols for the recovery of ancient DNA from palaeontological specimens are time-consuming and tend to yield inconsistent polymerase chain reaction (PCR) results. "Voltage-induced release" is a novel and rapid approach for the extraction of ancient DNA. Nucleic acids are directly electrophoresed out of powder derived from hard and soft tissues. This technique is much faster than other methods in which pulverized tissue conventionally undergoes time-consuming crude lysis steps. The total preparation time is 5-6 h. The reliability of the voltage-induced release method was validated by (i) measuring the ratio of D-to L-enantiomers of the amino acids aspartic acid, alanine, and leucine, and (ii) by specific PCR amplification of four single-copy markers of human chromosome 17 and 18. We compare voltage-induced release to a frequently used silica-based protocol. DNA extracted employing voltage-induced release was more effective in PCR amplifications, which may be attributed to the effective removal of PCR inhibitors. FAU - Bachmann, L AU - Bachmann L AD - Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL 60605-2496, USA. bachmann@fmppr.fmnh.org FAU - Scholz, M AU - Scholz M FAU - Broghammer, M AU - Broghammer M FAU - Giddings, I AU - Giddings I FAU - Pusch, C M AU - Pusch CM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Electrophoresis JT - Electrophoresis JID - 8204476 RN - 9007-49-2 (DNA) SB - IM MH - DNA/*isolation & purification MH - Electric Conductivity MH - *Fossils MH - Humans MH - Polymerase Chain Reaction/methods EDAT- 2000/06/01 09:00 MHDA- 2000/09/30 11:01 CRDT- 2000/06/01 09:00 PHST- 2000/06/01 09:00 [pubmed] PHST- 2000/09/30 11:01 [medline] PHST- 2000/06/01 09:00 [entrez] AID - 10.1002/(SICI)1522-2683(20000501)21:8<1488::AID-ELPS1488>3.0.CO;2-N [pii] AID - 10.1002/(SICI)1522-2683(20000501)21:8<1488::AID-ELPS1488>3.0.CO;2-N [doi] PST - ppublish SO - Electrophoresis. 2000 May;21(8):1488-92. doi: 10.1002/(SICI)1522-2683(20000501)21:8<1488::AID-ELPS1488>3.0.CO;2-N. PMID- 10816792 OWN - NLM STAT- MEDLINE DCOM- 20000712 LR - 20041117 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 1 DP - 2000 Mar TI - Molecular genetic analysis of the polymorphic apolipoprotein E in modern and ancient human DNA samples. PG - 93-8 AB - In this report, methodical bases for the molecular genetic analysis of the three common apolipoprotein E alleles APOE*2, APOE*3 and APOE*4 in DNA isolated from ancient human skeletal remains are described. Considering that ancient DNA target regions for amplification are generally quite small, the detection method is based on short amplification products in the range from 71 bp to 75 bp. The applicability of the modified method for APOE genotyping was examined in modern human DNA samples. FAU - Wiechmann, I AU - Wiechmann I AD - Institute of Anthropology and Human Genetics, University of München. I.Wiechmann@lrz.uni-muenchen.de LA - eng PT - Historical Article PT - Journal Article PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (Apolipoproteins E) RN - 9007-49-2 (DNA) SB - IM MH - Apolipoproteins E/*history MH - DNA/history MH - *Genetics, Population MH - History, Ancient MH - Humans MH - Paleodontology MH - Peru MH - *Polymerase Chain Reaction MH - Polymorphism, Genetic/*genetics EDAT- 2000/05/19 09:00 MHDA- 2000/07/15 11:00 CRDT- 2000/05/19 09:00 PHST- 2000/05/19 09:00 [pubmed] PHST- 2000/07/15 11:00 [medline] PHST- 2000/05/19 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Mar;58(1):93-8. PMID- 10816789 OWN - NLM STAT- MEDLINE DCOM- 20000712 LR - 20061115 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 1 DP - 2000 Mar TI - Palaeogenetic analysis of (pre)historic artifacts and its significance for anthropology. PG - 69-76 AB - The possibility of isolating ancient DNA (aDNA) from all kinds of (pre)historic anthropogenetic artifacts opens new perspectives. This study applies palaeogenetic techniques to three anthropological issues: 1. Palaeodiet. DNA sequences from organic residues in vessels identify Precolumbian Aztec diet. 2. (Pre)historic husbandry and economic structures. aDNA data can reveal the species and the genetic evolutionary stage of animals and plants and show the manner and the extent of their growth, cultivation, or domestication. 3. Production techniques, use, and functionality. Identification of the plant or animal source of an archaeological find can reveal the use or the function of the find. Examples from a Celtic "sausage-end" and an Aztec "eye salve" are given. FAU - Burger, J AU - Burger J AD - Institute of Zoology and Anthropology, University of Göttingen. jburger@gwdg.de FAU - Hummel, S AU - Hummel S FAU - Pfeiffer, I AU - Pfeiffer I FAU - Herrmann, B AU - Herrmann B LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 SB - IM MH - *Archaeology MH - Female MH - *Forensic Anthropology MH - Genetics, Population MH - Germany MH - History, Ancient MH - Humans MH - Life Style MH - Male MH - *Paleopathology MH - Polymerase Chain Reaction EDAT- 2000/05/19 09:00 MHDA- 2000/07/15 11:00 CRDT- 2000/05/19 09:00 PHST- 2000/05/19 09:00 [pubmed] PHST- 2000/07/15 11:00 [medline] PHST- 2000/05/19 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Mar;58(1):69-76. PMID- 10816787 OWN - NLM STAT- MEDLINE DCOM- 20000712 LR - 20101118 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 1 DP - 2000 Mar TI - Paleopathological and molecular evidence of human bone tuberculosis in Iron Age Lithuania. PG - 57-62 AB - Skeletal remains of two individuals, showing lesions suggestive of bone tuberculosis, from the archaeological sites of Marvele and Sukioniai in Lithuania were analyzed at the DNA level. The diagnosis of bone tuberculosis was confirmed in the remains from Marvele by amplifiying a 245-bp fragment of a repetitive insertion element-like sequence (IS 6110) of Mycobacterium tuberculosis DNA. This is direct evidence for the presence of tuberculosis in Lithuania at the beginning of the first millennium AD. The individual from Sukioniai was found to be tuberculosis-negative. No PCR product was obtained for the 245-bp target sequence or for a smaller 123-bp DNA fragment specific for Mycobacterium tuberculosis. However, amplifiable ancient DNA appeared to be present in the examined specimen as was shown by the results of the DNA-based sex identification, which indicated, consistent with the bone morphology, a male individual. FAU - Faerman, M AU - Faerman M AD - Laboratory of Biological Anthropology and Ancient DNA, Hadassah School of Dental Medicine, Hebrew University, Jerusalem, Israel. FAU - Jankauskas, R AU - Jankauskas R LA - eng PT - Historical Article PT - Journal Article PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 SB - IM MH - Adult MH - Female MH - *Forensic Anthropology MH - History, Ancient MH - Humans MH - Lithuania MH - Male MH - Mycobacterium tuberculosis/*genetics MH - *Paleopathology MH - *Polymerase Chain Reaction MH - Sex Determination Processes MH - Tuberculosis, Osteoarticular/*history EDAT- 2000/05/19 09:00 MHDA- 2000/07/15 11:00 CRDT- 2000/05/19 09:00 PHST- 2000/05/19 09:00 [pubmed] PHST- 2000/07/15 11:00 [medline] PHST- 2000/05/19 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Mar;58(1):57-62. PMID- 10816786 OWN - NLM STAT- MEDLINE DCOM- 20000712 LR - 20061115 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 1 DP - 2000 Mar TI - Ancient DNA fragments longer than 300 bp. PG - 51-6 AB - It is widely assumed that ancient DNA (aDNA) extracts contain no authentic templates longer than 300 bp. Here we present results which show that fragments of up to 800 bp in length can be reproducibly amplified from aDNA extracts. The amplification involves the short tandem repeat (STR) locus HUMVWA31A. Authentication of the amplified fragments is carried out by measures of expectancy. FAU - Haack, K AU - Haack K AD - Institute of Zoology and Anthropology, University of Göttingen. FAU - Hummel, S AU - Hummel S FAU - Hummel, B AU - Hummel B LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (Peptide Fragments) RN - 9007-49-2 (DNA) SB - IM MH - DNA/*genetics MH - *Forensic Anthropology MH - History, 18th Century MH - History, Ancient MH - Humans MH - Paleopathology MH - Peptide Fragments/*genetics MH - *Polymerase Chain Reaction MH - Reproducibility of Results MH - Tandem Repeat Sequences/genetics EDAT- 2000/05/19 09:00 MHDA- 2000/07/15 11:00 CRDT- 2000/05/19 09:00 PHST- 2000/05/19 09:00 [pubmed] PHST- 2000/07/15 11:00 [medline] PHST- 2000/05/19 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Mar;58(1):51-6. PMID- 10816784 OWN - NLM STAT- MEDLINE DCOM- 20000712 LR - 20061115 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 1 DP - 2000 Mar TI - Ancient DNA-typing approaches for the determination of kinship in a disturbed collective burial site. PG - 37-44 AB - Several DNA-typing approaches are applied for identification and kinship analysis. Autosomal Short Tandem Repeat (STR) typing produces the genetic fingerprint that is unique to an individual. Y-chromosomal STR typing identifies individuals of the same paternal lineage, and sequence analysis of the hypervariable region of the mitochondrion can identify maternally related individuals. The combined approach of these DNA-typing methods allows the determination of kinship even in complex collective burial situations. In a bronze age collective site, the typing methods were tested for applicability to ancient DNA. For each approach, results were obtained, leading to the conclusion that the determination of kinship is achievable. FAU - Schultes, T AU - Schultes T AD - Institute of Zoology and Anthropology, University of Göttingen. tschult@gwdg.de FAU - Hummel, S AU - Hummel S FAU - Herrmann, B AU - Herrmann B LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 0 (DNA, Mitochondrial) SB - IM MH - Bone and Bones/pathology MH - *DNA Fingerprinting MH - DNA, Mitochondrial/genetics MH - Female MH - *Forensic Anthropology MH - *Genetics, Population MH - Germany MH - History, Ancient MH - Humans MH - Male MH - Mortuary Practice MH - Paleopathology MH - *Paternity MH - Reproducibility of Results MH - Y Chromosome EDAT- 2000/05/19 09:00 MHDA- 2000/07/15 11:00 CRDT- 2000/05/19 09:00 PHST- 2000/05/19 09:00 [pubmed] PHST- 2000/07/15 11:00 [medline] PHST- 2000/05/19 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Mar;58(1):37-44. PMID- 10816783 OWN - NLM STAT- MEDLINE DCOM- 20000712 LR - 20061115 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 1 DP - 2000 Mar TI - STR-genotyping of archaeological human bone: experimental design to improve reproducibility by optimisation of DNA extraction. PG - 29-35 AB - The analysis of degraded DNA with the help of short tandem repeat loci (STRs) is an important source of information both in forensic casework and in the anthropological context. The reproducibility of STR-genotyping of highly degraded or "ancient" DNA can be reduced by the generation of artifacts during PCR amplification. The frequency and amount of these artifacts--allelic dropout and the generation of shadow bands--are related to the quality and quantity of the extracted DNA amplified in a PCR reaction. Therefore, one important strategy to increase the reproducibility of STR-genotyping of samples containing degraded DNA is the optimisation of the DNA extraction. FAU - Schmerer, W M AU - Schmerer WM AD - Institute for Zoology and Anthropology, Georg-August-University Göttingen, Germany. wschmer@gwdg.de FAU - Hummel, S AU - Hummel S FAU - Herrmann, B AU - Herrmann B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 9007-49-2 (DNA) SB - IM MH - *Archaeology MH - Artifacts MH - Bone and Bones/*pathology MH - DNA/*genetics MH - *Forensic Anthropology MH - *Genotype MH - Humans MH - Polymerase Chain Reaction MH - Reproducibility of Results EDAT- 2000/05/19 09:00 MHDA- 2000/07/15 11:00 CRDT- 2000/05/19 09:00 PHST- 2000/05/19 09:00 [pubmed] PHST- 2000/07/15 11:00 [medline] PHST- 2000/05/19 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Mar;58(1):29-35. PMID- 10816781 OWN - NLM STAT- MEDLINE DCOM- 20000712 LR - 20100629 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 1 DP - 2000 Mar TI - Megaplex DNA typing can provide a strong indication of the authenticity of ancient DNA amplifications by clearly recognizing any possible type of modern contamination. PG - 15-21 AB - Recent experiments revealed the perfect applicability of megaplex typing by autosomal short tandem repeats (STRs) to degraded DNA. The advantages of megaplex approaches lie in reduced amounts of sample material that are necessary and in remarkable time saving. Furthermore, megaplex typing clearly recognizes possible contaminations and thus has a large potential for indicating authenticity in ancient DNA analysis. This is demonstrated by three examples in which various types of contaminations could clearly be identified as such and even traced back to their origin. This would have been impossible using control samples, due to the sporadic nature of these types of contaminations. FAU - Hummel, S AU - Hummel S AD - Institute of Zoology and Anthropology, University of Göttingen. shummel1@gwdg.de FAU - Bramanti, B AU - Bramanti B FAU - Schultes, T AU - Schultes T FAU - Kahle, M AU - Kahle M FAU - Haffner, S AU - Haffner S FAU - Herrmann, B AU - Herrmann B LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 SB - IM MH - Artifacts MH - *DNA Fingerprinting MH - Gene Amplification/*genetics MH - History, Ancient MH - Humans MH - *Paleopathology MH - *Polymerase Chain Reaction MH - Sensitivity and Specificity MH - Specimen Handling MH - Tandem Repeat Sequences/*genetics EDAT- 2000/05/19 09:00 MHDA- 2000/07/15 11:00 CRDT- 2000/05/19 09:00 PHST- 2000/05/19 09:00 [pubmed] PHST- 2000/07/15 11:00 [medline] PHST- 2000/05/19 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Mar;58(1):15-21. PMID- 10816779 OWN - NLM STAT- MEDLINE DCOM- 20000712 LR - 20101118 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 58 IP - 1 DP - 2000 Mar TI - Molecular sex identification of stillborn and neonate individuals ("Traufkinder") from the burial site Aegerten. PG - 1-8 AB - The study reconstructs the sex ratio of 121 stillborn and neonate individuals from the early modern burial site Aegerten, Switzerland. The immature individuals, who were not baptised before death, were buried along the walls of the church. To perform a molecular sex identification, bone samples from the infants were collected from different skeletal elements. Ancient DNA (aDNA) was isolated by a combination of automated phenol/chloroform extraction and precipitation with silica powder. A combination of manuell Chelex extraction and purification kit was also used to perform an extraction. Finally, the aDNA extracts were amplified with a primer system that amplifies a part of the amelogenin gene located on the human sex chromosomes. The morphometrical sex determination of the children suggests a large disproportion of female individuals (about 60%). This finding was compared to PCR-based amplification results. In contrast, the results of the molecular sex identification were a high proportion of male individuals. Looking at these results, it should be noted that the high mortality of male individuals during the last months of pregnancy and during the first month after birth is in accordance with the natural sequence of death also found in recent populations. FAU - Lassen, C AU - Lassen C AD - State Criminal Investigation Agency of Lower Saxony, Section of Forensic Molecular Genetics, Hannover. FAU - Hummel, S AU - Hummel S FAU - Herrmann, B AU - Herrmann B LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 SB - IM MH - Female MH - Fetal Death/*history MH - History, 15th Century MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - History, 19th Century MH - History, Medieval MH - Humans MH - Infant MH - Infant, Newborn MH - Male MH - Paleopathology MH - Pregnancy MH - *Sex Determination Processes MH - *Sex Ratio MH - Switzerland EDAT- 2000/05/19 09:00 MHDA- 2000/07/15 11:00 CRDT- 2000/05/19 09:00 PHST- 2000/05/19 09:00 [pubmed] PHST- 2000/07/15 11:00 [medline] PHST- 2000/05/19 09:00 [entrez] PST - ppublish SO - Anthropol Anz. 2000 Mar;58(1):1-8. PMID- 10683241 OWN - NLM STAT- MEDLINE DCOM- 20000508 LR - 20071115 IS - 0003-2697 (Print) IS - 0003-2697 (Linking) VI - 279 IP - 1 DP - 2000 Mar 1 TI - Degenerate oligonucleotide-primed preamplification of ancient DNA allows the retrieval of authentic DNA sequences. PG - 118-22 FAU - Pusch, C M AU - Pusch CM AD - Molecular Genetics Laboratory, University Eye Hospital, University of Tübingen, Auf der Morgenstelle 15, Tübingen, 72076, Germany. FAU - Nicholson, G J AU - Nicholson GJ FAU - Bachmann, L AU - Bachmann L FAU - Scholz, M AU - Scholz M LA - eng PT - Journal Article PL - United States TA - Anal Biochem JT - Analytical biochemistry JID - 0370535 RN - 0 (DNA Primers) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Sequence MH - Cattle MH - DNA/*genetics/isolation & purification MH - DNA Primers/genetics MH - Evaluation Studies as Topic MH - *Fossils MH - Humans MH - Paleontology/*methods MH - Polymerase Chain Reaction/*methods MH - Swine EDAT- 2000/02/23 09:00 MHDA- 2000/05/16 09:00 CRDT- 2000/02/23 09:00 PHST- 2000/02/23 09:00 [pubmed] PHST- 2000/05/16 09:00 [medline] PHST- 2000/02/23 09:00 [entrez] AID - S0003-2697(99)94463-9 [pii] AID - 10.1006/abio.1999.4463 [doi] PST - ppublish SO - Anal Biochem. 2000 Mar 1;279(1):118-22. doi: 10.1006/abio.1999.4463. PMID- 10618586 OWN - NLM STAT- MEDLINE DCOM- 20000222 LR - 20101118 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 111 IP - 1 DP - 2000 Jan TI - Ancient DNA analysis of human populations. PG - 5-23 AB - The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. The resultant increase in number of samples and polymorphic sites assayed and the number of studies published may give the impression that all technological hurdles associated with aDNA technology have been overcome. However, analysis of aDNA is still plagued by two issues that emerged at the advent of aDNA technology, namely the inability to amplify a significant number of samples and the contamination of samples with modern DNA. Herein, we analyze five well-preserved skeletal specimens from the western United States dating from 800-1600 A.D. These specimens yielded DNA samples with levels of contamination ranging from 0-100%, as determined by the presence or absence of New World-specific mitochondrial markers. All samples were analyzed by a variety of protocols intended to assay genetic variability and detect contamination, including amplification of variously sized DNA targets, direct DNA sequence analysis of amplification products and sequence analysis of cloned amplification products, analysis of restriction fragment length polymorphisms, quantitation of target DNA, amino acid racemization, and amino acid quantitation. Only the determination of DNA sequence from a cloned amplification product clearly revealed the presence of both ancient DNA and contaminating DNA in the same extract. Our results demonstrate that the analysis of aDNA is still an excruciatingly slow and meticulous process. All experiments, including stringent quality and contamination controls, must be performed in an environment as free as possible of potential sources of contaminating DNA, including modern DNA extracts. Careful selection of polymorphic markers capable of discriminating between ancient DNA and probable DNA contaminants is critical. Research strategies must be designed with a goal of identifying all DNA contaminants in order to differentiate convincingly between contamination and endogenous DNA. CI - Copyright 2000 Wiley-Liss, Inc. FAU - Kolman, C J AU - Kolman CJ AD - Smithsonian Center for Materials Research and Education, Suitland, Maryland 20746-0534, USA. ckolman@mail.nih.gov FAU - Tuross, N AU - Tuross N LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Biological Evolution MH - DNA/*analysis MH - DNA, Mitochondrial/genetics MH - Hominidae/*genetics MH - Humans MH - Nucleic Acid Amplification Techniques MH - Reproducibility of Results MH - Sequence Analysis, DNA/*methods MH - Specimen Handling EDAT- 2000/01/05 09:00 MHDA- 2000/02/26 09:00 CRDT- 2000/01/05 09:00 PHST- 2000/01/05 09:00 [pubmed] PHST- 2000/02/26 09:00 [medline] PHST- 2000/01/05 09:00 [entrez] AID - 10.1002/(SICI)1096-8644(200001)111:1<5::AID-AJPA2>3.0.CO;2-3 [pii] AID - 10.1002/(SICI)1096-8644(200001)111:1<5::AID-AJPA2>3.0.CO;2-3 [doi] PST - ppublish SO - Am J Phys Anthropol. 2000 Jan;111(1):5-23. doi: 10.1002/(SICI)1096-8644(200001)111:1<5::AID-AJPA2>3.0.CO;2-3. PMID- 10626565 OWN - NLM STAT- MEDLINE DCOM- 20000127 LR - 20191103 IS - 0803-5326 (Print) IS - 0803-5326 (Linking) VI - 88 IP - 433 DP - 1999 Dec TI - DNA from fossils: the past and the future. PG - 133-40 AB - The recovery of DNA from archaeological and palaeontological remains has intrigued scientists for many years. The DNA molecule is a relatively weak molecule compared with other biomacromolecules in tissues, but the sequence of its bases holds insights into questions that cannot be resolved by standard palaeontological methods. Recent advances in the field, such as the recovery of DNA sequences from coprolites found in the southwestern USA, as well as from the Neanderthal-type specimen, have shed new light on populations that are now extinct. A better understanding of how DNA is preserved in fossils, as well as the use of novel agents that can release the DNA from archaeological and palaeontological materials, will likely lead to new successes in the field. The analysis of ancient DNA may provide new clues about human evolution and answer questions, for example, relating to the diversity of the Neanderthals and the mammoths. FAU - Poinar, H N AU - Poinar HN AD - Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany. poinar@eva.mpg.de LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Norway TA - Acta Paediatr Suppl JT - Acta paediatrica (Oslo, Norway : 1992). Supplement JID - 9315043 RN - 9007-49-2 (DNA) SB - IM MH - DNA/*analysis MH - *Fossils MH - History, 20th Century MH - History, Medieval MH - Humans MH - Influenza, Human/history MH - Tuberculosis/history EDAT- 2000/01/08 00:00 MHDA- 2000/01/08 00:01 CRDT- 2000/01/08 00:00 PHST- 2000/01/08 00:00 [pubmed] PHST- 2000/01/08 00:01 [medline] PHST- 2000/01/08 00:00 [entrez] AID - 10.1111/j.1651-2227.1999.tb14423.x [doi] PST - ppublish SO - Acta Paediatr Suppl. 1999 Dec;88(433):133-40. doi: 10.1111/j.1651-2227.1999.tb14423.x. PMID- 10541662 OWN - NLM STAT- MEDLINE DCOM- 19991123 LR - 20190826 IS - 0028-1042 (Print) IS - 0028-1042 (Linking) VI - 86 IP - 10 DP - 1999 Oct TI - Proving the authenticity of ancient DNA by comparative genomic hybridization. PG - 500-3 AB - In PCR-supported amplification of ancient, degraded DNA, contamination with contemporary DNA can lead to false-positive results, which frequently give rise to discussions in which the mere existence of ancient DNA is doubted. Our confirmation of ancient DNA using comparative genome hybridization (CGH) eliminates these doubts. Unlike PCR methods, CGH requires no amplification of the DNA to be analyzed if adequate amounts of specimen DNA is used. Thus, false results traceable to contaminations are practically ruled out. The examples provided here prove the authenticity of ancient DNA for a 250-year-old and a 3,000-year-old sample. At the same time, the CGH of ancient DNA offers the chance to gain insight into the pattern of DNA degradation and to monitor the preservation of certain chromosomal segments. FAU - Hummel, S AU - Hummel S AD - Historische Anthropologie und Humanökologie, Institut für Zoologie und Anthropologie, Universität Göttingen, Bürgerstrasse 50, D-37073 Göttingen, Germany. shummel1@gwdg.de FAU - Herrmann, B AU - Herrmann B FAU - Rameckers, J AU - Rameckers J FAU - Müller, D AU - Müller D FAU - Sperling, K AU - Sperling K FAU - Neitzel, H AU - Neitzel H FAU - Tönnies, H AU - Tönnies H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Naturwissenschaften JT - Die Naturwissenschaften JID - 0400767 RN - 9007-49-2 (DNA) SB - IM MH - *Chromosomes, Human MH - Congenital Abnormalities/embryology/genetics MH - DNA/*genetics MH - Fetus MH - Humans MH - Karyotyping MH - Nucleic Acid Hybridization/*methods MH - Paleontology/methods MH - Polymerase Chain Reaction/*methods MH - Telomere/genetics EDAT- 1999/10/29 00:00 MHDA- 1999/10/29 00:01 CRDT- 1999/10/29 00:00 PHST- 1999/10/29 00:00 [pubmed] PHST- 1999/10/29 00:01 [medline] PHST- 1999/10/29 00:00 [entrez] AID - 90860500.114 [pii] AID - 10.1007/s001140050663 [doi] PST - ppublish SO - Naturwissenschaften. 1999 Oct;86(10):500-3. doi: 10.1007/s001140050663. PMID- 10411967 OWN - NLM STAT- MEDLINE DCOM- 19991014 LR - 20111117 IS - 0353-9504 (Print) IS - 0353-9504 (Linking) VI - 40 IP - 3 DP - 1999 Sep TI - Histological analysis and ancient DNA amplification of human bone remains found in caius iulius polybius house in pompeii. PG - 392-7 AB - Thirteen skeletons found in the Caius Iulius Polybius house, which has been the object of intensive study since its discovery in Pompeii 250 years ago, have provided an opportunity to study either bone diagenesis by histological investigation or ancient DNA by polymerase chain reaction analysis. DNA analysis was done by amplifying both X- and Y-chromosomes amelogenin loci and Y-specific alphoid repeat locus. The von Willebrand factor (vWF) microsatellite locus on chromosome 12 was also analyzed for personal identification in two individuals showing alleles with 10/11 and 12/12 TCTA repeats, respectively. Technical problems were the scarcity of DNA content from osteocytes, DNA molecule fragmentation, microbial contamination which change bone structure, contaminating human DNA which results from mishandling, and frequent presence of Taq DNA polymerase inhibiting molecules like polyphenols and heavy metals. The results suggest that the remains contain endogenous human DNA that can be amplified and analyzed. The amplifiability of DNA corresponds to the bone preservation and dynamics of the burial conditions subsequent to the 79 A.D. eruption. FAU - Cipollaro, M AU - Cipollaro M AD - Istituto di Farmacologia e Tossicologia and C.R.I.S.C.E.B., 2.a Universita degli Studi di Napoli, Via Costantinopoli 16, 80138 Naples, Italy. cipollar@unina.it FAU - Di Bernado, G AU - Di Bernado G FAU - Forte, A AU - Forte A FAU - Galano, G AU - Galano G FAU - De Masi, L AU - De Masi L FAU - Galderisi, U AU - Galderisi U FAU - Guarino, F M AU - Guarino FM FAU - Angelini, F AU - Angelini F FAU - Cascino, A AU - Cascino A LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Croatia TA - Croat Med J JT - Croatian medical journal JID - 9424324 RN - 0 (Amelogenin) RN - 0 (Dental Enamel Proteins) RN - 0 (Enzyme Inhibitors) RN - 0 (Flavonoids) RN - 0 (Metals) RN - 0 (Phenols) RN - 0 (Polymers) RN - 0 (Polyphenols) RN - 0 (von Willebrand Factor) RN - 9007-49-2 (DNA) RN - EC 2.7.7.- (Taq Polymerase) SB - IM MH - Alleles MH - Amelogenin MH - Bone and Bones/*anatomy & histology MH - Chromosome Mapping MH - Chromosomes, Human, Pair 12/genetics MH - DNA/*analysis/genetics MH - DNA Fragmentation MH - Dental Enamel Proteins/genetics MH - Enzyme Inhibitors/adverse effects MH - Female MH - *Flavonoids MH - Gene Amplification MH - History, Ancient MH - Humans MH - Italy MH - Male MH - Metals/adverse effects MH - Microsatellite Repeats/genetics MH - Osteocytes/metabolism MH - *Paleontology MH - Phenols/adverse effects MH - Polymerase Chain Reaction MH - Polymers/adverse effects MH - Polyphenols MH - Repetitive Sequences, Nucleic Acid/genetics MH - Taq Polymerase/antagonists & inhibitors MH - X Chromosome/genetics MH - Y Chromosome/genetics MH - von Willebrand Factor/genetics EDAT- 1999/07/21 00:00 MHDA- 1999/07/21 00:01 CRDT- 1999/07/21 00:00 PHST- 1999/07/21 00:00 [pubmed] PHST- 1999/07/21 00:01 [medline] PHST- 1999/07/21 00:00 [entrez] PST - ppublish SO - Croat Med J. 1999 Sep;40(3):392-7. PMID- 10411891 OWN - NLM STAT- MEDLINE DCOM- 19990823 LR - 20240914 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 96 IP - 15 DP - 1999 Jul 20 TI - Protein preservation and DNA retrieval from ancient tissues. PG - 8426-31 AB - The retrieval of DNA from fossils remains controversial. To substantiate claims of DNA recovery, one needs additional information on the preservation of other molecules within the same sample. Flash pyrolysis with GC and MS was used to assess the quality of protein preservation in 11 archaeological and paleontological remains, some of which have yielded ancient DNA sequences authenticated via a number of criteria and some of which have consistently failed to yield any meaningful DNA. Several samples, including the Neanderthal-type specimen from which DNA sequences were recently reported, yielded abundant pyrolysis products assigned to 2,5-diketopiperazines of proline-containing dipeptides. The relative amounts of these products provide a good index of the amount of peptide hydrolysis and DNA preservation. Of these samples, four stem from arctic or subarctic regions, emphasizing the importance of cooler temperatures for the preservation of macromolecules. Flash pyrolysis with GC and MS offers a rapid and effective method for assessing fossils for the possibility of DNA preservation. FAU - Poinar, H N AU - Poinar HN AD - Max-Planck-Institute for Evolutionary Anthropology, Inselstrasse 22, Leipzig D-04103, Germany. poinar@eva.mpg.de FAU - Stankiewicz, B A AU - Stankiewicz BA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Amino Acids) RN - 0 (Hydantoins) RN - 0 (Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acids/analysis MH - Animals MH - Archaeology MH - DNA/*chemistry MH - *Fossils MH - Humans MH - Hydantoins/analysis MH - Mass Spectrometry MH - Paleontology MH - Proteins/*chemistry MH - Sequence Analysis, DNA MH - *Tissue Preservation PMC - PMC17532 EDAT- 1999/07/21 00:00 MHDA- 1999/07/21 00:01 PMCR- 2000/01/20 CRDT- 1999/07/21 00:00 PHST- 1999/07/21 00:00 [pubmed] PHST- 1999/07/21 00:01 [medline] PHST- 1999/07/21 00:00 [entrez] PHST- 2000/01/20 00:00 [pmc-release] AID - 2162 [pii] AID - 10.1073/pnas.96.15.8426 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8426-31. doi: 10.1073/pnas.96.15.8426. PMID- 10435439 OWN - NLM STAT- MEDLINE DCOM- 19990922 LR - 20211203 IS - 0173-0835 (Print) IS - 0173-0835 (Linking) VI - 20 IP - 8 DP - 1999 Jun TI - Ethnic affinities of the ancient human Jety-Asar population by mitochondrial DNA analysis. PG - 1729-32 AB - An anthropological study of the remains has indicated uniformity of the ancient human Jety-Asar population (Central Asia) and suggests a mixed Euro-Mongoloid genesis. DNA was extracted from teeth from three Caucasoid skulls recovered from a burial site dated at approximately 2000 years ago. Ancient mitochondrial DNA (mtDNA) was analysed by restriction fragment length polymorphism (RFLP) analysis for the A, B, C and D haplogroups and the sequencing of hypervariable region I of the mtDNA control region. The full set of mtDNA control region variants determined for Jety-Asar specimens was only found among a modern Mongolian population (Mongoloid people), indicating some discordance of molecular and morphological data. FAU - Ovchinnikov, I AU - Ovchinnikov I AD - Institute of Gerontology, Moscow, Russia. oigor@hotmail.com FAU - Buzhilova, A AU - Buzhilova A FAU - Mednikova, M AU - Mednikova M FAU - Goodwin, W AU - Goodwin W FAU - Curry, G AU - Curry G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Electrophoresis JT - Electrophoresis JID - 8204476 RN - 0 (DNA, Mitochondrial) SB - IM MH - DNA, Mitochondrial/*genetics MH - *Ethnicity MH - Humans MH - *Paleontology MH - Polymorphism, Restriction Fragment Length EDAT- 1999/08/06 10:00 MHDA- 2000/08/12 11:00 CRDT- 1999/08/06 10:00 PHST- 1999/08/06 10:00 [pubmed] PHST- 2000/08/12 11:00 [medline] PHST- 1999/08/06 10:00 [entrez] AID - 10.1002/(SICI)1522-2683(19990101)20:8<1729::AID-ELPS1729>3.0.CO;2-# [pii] AID - 10.1002/(SICI)1522-2683(19990101)20:8<1729::AID-ELPS1729>3.0.CO;2-# [doi] PST - ppublish SO - Electrophoresis. 1999 Jun;20(8):1729-32. doi: 10.1002/(SICI)1522-2683(19990101)20:8<1729::AID-ELPS1729>3.0.CO;2-#. PMID- 10435437 OWN - NLM STAT- MEDLINE DCOM- 19990922 LR - 20061115 IS - 0173-0835 (Print) IS - 0173-0835 (Linking) VI - 20 IP - 8 DP - 1999 Jun TI - Ancient DNA profiling by megaplex amplications. PG - 1717-21 AB - Simultaneous amplification of nine human short tandem repeat (STR) DNA sequences and the amelogenin locus allows reducing to an absolute minimum the amount of sample material that is necessary for genetic identification or kinship analysis. Valuable remains can be studied this way without any visible damage, as is demonstrated by typing the DNA of a tooth root from the Saxon warrior Widukind, who died about 1200 years ago. The broad applicability of the megaplex approach is shown by typing bone and teeth specimens ranging from a few months to 3000 years of age employing AmpFISTR Profiler Plus. Additionally, megaplex STR typing is the method of choice for proving the authenticity of molecular results derived from ancient degraded DNA. FAU - Hummel, S AU - Hummel S AD - Historic Anthropology and Human Ecology, University of Goettingen, Germany. shummel1@gwdg.de FAU - Schultes, T AU - Schultes T FAU - Bramanti, B AU - Bramanti B FAU - Herrmann, B AU - Herrmann B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Electrophoresis JT - Electrophoresis JID - 8204476 RN - 0 (Amelogenin) RN - 0 (Dental Enamel Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Amelogenin MH - *Anthropology, Physical MH - DNA/*genetics MH - Dental Enamel Proteins/genetics MH - Female MH - Humans MH - Male MH - Tandem Repeat Sequences EDAT- 1999/08/06 10:00 MHDA- 2000/08/12 11:00 CRDT- 1999/08/06 10:00 PHST- 1999/08/06 10:00 [pubmed] PHST- 2000/08/12 11:00 [medline] PHST- 1999/08/06 10:00 [entrez] AID - 10.1002/(SICI)1522-2683(19990101)20:8<1717::AID-ELPS1717>3.0.CO;2-D [pii] AID - 10.1002/(SICI)1522-2683(19990101)20:8<1717::AID-ELPS1717>3.0.CO;2-D [doi] PST - ppublish SO - Electrophoresis. 1999 Jun;20(8):1717-21. doi: 10.1002/(SICI)1522-2683(19990101)20:8<1717::AID-ELPS1717>3.0.CO;2-D. PMID- 10435436 OWN - NLM STAT- MEDLINE DCOM- 19990922 LR - 20041117 IS - 0173-0835 (Print) IS - 0173-0835 (Linking) VI - 20 IP - 8 DP - 1999 Jun TI - Optimized DNA extraction to improve reproducibility of short tandem repeat genotyping with highly degraded DNA as target. PG - 1712-6 AB - The reproducibility of short tandem repeat (STR) genotyping of highly degraded DNA is often reduced due to artifacts generated during polymerase chain reaction (PCR) amplification. The frequency and amount of these artifacts are related to the quality and quantity of the DNA amplified. Consequently, the aim of this investigation was the optimization of DNA extraction to increase the reproducibility of STR genotyping of samples containing highly degraded DNA. Starting from a standard extraction protocol, systematic variation of individual parameters resulted in optimized protocols for three categories of ancient human bone material (different degrees of DNA degradation) and a consensus protocol for the extraction of a broad range of ancient DNA preservation states. FAU - Schmerer, W M AU - Schmerer WM AD - Historical Anthropology and Human Ecology, Institute for Zoology and Anthropology, Göttingen, Germany. wschmer@gwdg.de FAU - Hummel, S AU - Hummel S FAU - Herrmann, B AU - Herrmann B LA - eng PT - Journal Article PL - Germany TA - Electrophoresis JT - Electrophoresis JID - 8204476 RN - 9007-49-2 (DNA) SB - IM MH - DNA/*genetics MH - Genotype MH - Humans MH - Reproducibility of Results MH - *Tandem Repeat Sequences EDAT- 1999/08/06 10:00 MHDA- 2000/08/12 11:00 CRDT- 1999/08/06 10:00 PHST- 1999/08/06 10:00 [pubmed] PHST- 2000/08/12 11:00 [medline] PHST- 1999/08/06 10:00 [entrez] AID - 10.1002/(SICI)1522-2683(19990101)20:8<1712::AID-ELPS1712>3.0.CO;2-6 [pii] AID - 10.1002/(SICI)1522-2683(19990101)20:8<1712::AID-ELPS1712>3.0.CO;2-6 [doi] PST - ppublish SO - Electrophoresis. 1999 Jun;20(8):1712-6. doi: 10.1002/(SICI)1522-2683(19990101)20:8<1712::AID-ELPS1712>3.0.CO;2-6. PMID- 11148985 OWN - NLM STAT- MEDLINE DCOM- 20010125 LR - 20041117 IS - 0037-8771 (Print) IS - 0037-8771 (Linking) VI - 75 IP - 5-6 DP - 1999 May-Jun TI - Use of the amplification refractory mutation system (ARMS) in the study of HbS in predynastic Egyptian remains. PG - 27-30 AB - We conducted a molecular investigation of the presence of sicklemia in six predynastic Egyptian mummies (about 3200 BC) from the Anthropological and Ethnographic Museum of Turin. Previous studies of these remains showed the presence of severe anemia, while histological preparations of mummified tissues revealed hemolytic disorders. DNA was extracted from dental samples with a silica-gel method specific for ancient DNA. A modification of the polymerase chain reaction (PCR), called amplification refractory mutation system (ARMS) was then applied. ARMS is based on specific priming of the PCR and it permits diagnosis of single nucleotide mutations. In this method, amplification can occur only in the presence of the specific mutation being studied. The amplified DNA was analyzed by electrophoresis. In samples of three individuals, there was a band at the level of the HbS mutated fragment, indicating that they were affected by sicklemia. On the basis of our results, we discuss the possible uses of new molecular investigation systems in paleopathological diagnoses of genetic diseases and viral, bacterial and fungal infections. FAU - Marin, A AU - Marin A AD - Dipartimento di Biologia Animale e dell'Uomo, Università degli Studi di Torino. FAU - Cerutti, N AU - Cerutti N FAU - Massa, E R AU - Massa ER LA - eng PT - Journal Article PL - Italy TA - Boll Soc Ital Biol Sper JT - Bollettino della Societa italiana di biologia sperimentale JID - 7506962 RN - 0 (Hemoglobin, Sickle) RN - 9007-49-2 (DNA) SB - IM MH - Anemia, Sickle Cell/ethnology/*genetics/pathology MH - DNA/*analysis/isolation & purification MH - Egypt/ethnology MH - Hemoglobin, Sickle/*genetics MH - Humans MH - *Mummies/pathology MH - Mutation MH - Polymerase Chain Reaction/*methods MH - Tooth/chemistry EDAT- 2001/01/10 11:00 MHDA- 2001/02/28 10:01 CRDT- 2001/01/10 11:00 PHST- 2001/01/10 11:00 [pubmed] PHST- 2001/02/28 10:01 [medline] PHST- 2001/01/10 11:00 [entrez] PST - ppublish SO - Boll Soc Ital Biol Sper. 1999 May-Jun;75(5-6):27-30. PMID- 10352937 OWN - NLM STAT- MEDLINE DCOM- 19990812 LR - 20101118 IS - 1018-4813 (Print) IS - 1018-4813 (Linking) VI - 7 IP - 4 DP - 1999 May-Jun TI - Reconstruction of a historical genealogy by means of STR analysis and Y-haplotyping of ancient DNA. PG - 469-77 AB - Archaeological excavations in St Margaretha's church at Reichersdorf, Germany, in 1993 led to the discovery of eight skeletons, so far assumed to be of the Earls of Königsfeld, who used the church as a family sepulchre over a period of seven generations from 1546 to 1749. DNA-based sex testing and analysis of autosomal short tandem repeat systems (STR) was carried out to confirm the assumption of kinship. Since five of the individuals were determined as males, analysis of Y-specific STRs seemed feasible. A comparison of Y-haplotypes revealed that one individual could not be linked to the Königsfeld patrilineage, an observation supported by autosomal STR evidence. Two individuals typed as females posed an identification problem, since supposedly only male members of the family were buried in St Margaretha's. Nevertheless, these individuals could tentatively be identified as members of the House of Königsfeld through genetic fingerprinting. FAU - Gerstenberger, J AU - Gerstenberger J AD - Institut für Zoologie und Anthropologie, Universität Göttingen, Germany. FAU - Hummel, S AU - Hummel S FAU - Schultes, T AU - Schultes T FAU - Häck, B AU - Häck B FAU - Herrmann, B AU - Herrmann B LA - eng PT - Historical Article PT - Journal Article PL - England TA - Eur J Hum Genet JT - European journal of human genetics : EJHG JID - 9302235 RN - 9007-49-2 (DNA) SB - IM MH - Burial MH - DNA/*genetics MH - DNA Fingerprinting MH - Female MH - Germany MH - *Haplotypes MH - History, 16th Century MH - History, 17th Century MH - History, 18th Century MH - Humans MH - Male MH - Paternity MH - *Pedigree MH - Polymerase Chain Reaction MH - Sex Determination Analysis MH - Tandem Repeat Sequences/*genetics MH - Y Chromosome/*genetics EDAT- 1999/06/03 00:00 MHDA- 1999/06/03 00:01 CRDT- 1999/06/03 00:00 PHST- 1999/06/03 00:00 [pubmed] PHST- 1999/06/03 00:01 [medline] PHST- 1999/06/03 00:00 [entrez] AID - 10.1038/sj.ejhg.5200322 [doi] PST - ppublish SO - Eur J Hum Genet. 1999 May-Jun;7(4):469-77. doi: 10.1038/sj.ejhg.5200322. PMID- 10190328 OWN - NLM STAT- MEDLINE DCOM- 19990420 LR - 20190722 IS - 0340-6717 (Print) IS - 0340-6717 (Linking) VI - 104 IP - 2 DP - 1999 Feb TI - Amplification of Y-chromosomal STRs from ancient skeletal material. PG - 164-6 AB - The adaptation to ancient DNA analysis of a Y-chromosomal STR (short tandem repeat) multiplex comprising the four STR systems DYS19, DYS390, and DYS389I/II shows the suitability of Y-chromosomal STR typing on ancient human remains. A new primer site for the system, DYS389I/II, resulting in products shortened by 94 bp, was chosen to serve the special needs of amplification of ancient DNA. For the first time, it was possible to amplify STR loci of the Y chromosome from historical and prehistorical bones of up to 3000 years old. FAU - Schultes, T AU - Schultes T AD - Historische Anthropologie und Humanökologie, Institut für Zoologie und Anthropologie, Universität Göttingen, Germany. tschult@gwdg.de FAU - Hummel, S AU - Hummel S FAU - Herrmann, B AU - Herrmann B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Hum Genet JT - Human genetics JID - 7613873 SB - IM MH - Bone and Bones/pathology MH - Child MH - *Gene Amplification MH - Humans MH - Infant MH - *Tandem Repeat Sequences MH - *Y Chromosome EDAT- 1999/04/06 00:00 MHDA- 1999/04/06 00:01 CRDT- 1999/04/06 00:00 PHST- 1999/04/06 00:00 [pubmed] PHST- 1999/04/06 00:01 [medline] PHST- 1999/04/06 00:00 [entrez] AID - 10.1007/s004390050930 [doi] PST - ppublish SO - Hum Genet. 1999 Feb;104(2):164-6. doi: 10.1007/s004390050930. PMID- 10091255 OWN - NLM STAT- MEDLINE DCOM- 19990428 LR - 20181113 IS - 0962-8436 (Print) IS - 1471-2970 (Electronic) IS - 0962-8436 (Linking) VI - 354 IP - 1379 DP - 1999 Jan 29 TI - Analysis of ancient DNA from a prehistoric Amerindian cemetery. PG - 153-9 AB - The Norris Farms No. 36 cemetery in central Illinois has been the subject of considerable archaeological and genetic research. Both mitochondrial DNA (mtDNA) and nuclear DNA have been examined in this 700-year-old population. DNA preservation at the site was good, with about 70% of the samples producing mtDNA results and approximately 15% yielding nuclear DNA data. All four of the major Amerindian mtDNA haplogroups were found, in addition to a fifth haplogroup. Sequences of the first hypervariable region of the mtDNA control region revealed a high level of diversity in the Norris Farms population and confirmed that the fifth haplogroup associates with Mongolian sequences and hence is probably authentic. Other than a possible reduction in the number of rare mtDNA lineages in many populations, it does not appear as if European contact significantly altered patterns of Amerindian mtDNA variation, despite the large decrease in population size that occurred. For nuclear DNA analysis, a novel method for DNA-based sex identification that uses nucleotide differences between the X and Y copies of the amelogenin gene was developed and applied successfully in approximately 20 individuals. Despite the well-known problems of poor DNA preservation and the ever-present possibility of contamination with modern DNA, genetic analysis of the Norris Farms No. 36 population demonstrates that ancient DNA can be a fruitful source of new insights into prehistoric populations. FAU - Stone, A C AU - Stone AC AD - Department of Anthropology, Pennsylvania State University, University Park 16802, USA. acstone@u.arizona.edu FAU - Stoneking, M AU - Stoneking M LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (Amelogenin) RN - 0 (DNA, Mitochondrial) RN - 0 (Dental Enamel Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Amelogenin MH - DNA/genetics/*history/isolation & purification MH - DNA, Mitochondrial/genetics/*history/isolation & purification MH - Dental Enamel Proteins/genetics MH - Evolution, Molecular MH - Female MH - Genetic Variation MH - Genetics, Population MH - Haplotypes MH - History, Medieval MH - Humans MH - Illinois MH - Indians, North American/genetics/*history MH - Male MH - Paleontology MH - Polymerase Chain Reaction MH - Sex Determination Analysis PMC - PMC1692451 EDAT- 1999/03/26 00:00 MHDA- 1999/03/26 00:01 PMCR- 2001/01/29 CRDT- 1999/03/26 00:00 PHST- 1999/03/26 00:00 [pubmed] PHST- 1999/03/26 00:01 [medline] PHST- 1999/03/26 00:00 [entrez] PHST- 2001/01/29 00:00 [pmc-release] AID - 10.1098/rstb.1999.0368 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 1999 Jan 29;354(1379):153-9. doi: 10.1098/rstb.1999.0368. PMID- 10091251 OWN - NLM STAT- MEDLINE DCOM- 19990428 LR - 20181113 IS - 0962-8436 (Print) IS - 1471-2970 (Electronic) IS - 0962-8436 (Linking) VI - 354 IP - 1379 DP - 1999 Jan 29 TI - How microbial ancient DNA, found in association with human remains, can be interpreted. PG - 111-9 AB - The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies. FAU - Rollo, F AU - Rollo F AD - Dipartimento di Biologia Molecolare, Cellulare e Animale, Università di Camerino, Italy. rollo@cambio.unicam.it FAU - Marota, I AU - Marota I LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Philos Trans R Soc Lond B Biol Sci JT - Philosophical transactions of the Royal Society of London. Series B, Biological sciences JID - 7503623 RN - 0 (DNA Primers) RN - 0 (DNA, Bacterial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Sequence MH - Colon/microbiology MH - DNA/genetics/*history/isolation & purification MH - DNA Primers/genetics MH - DNA, Bacterial/genetics/history/isolation & purification MH - Evolution, Molecular MH - History, Ancient MH - History, Medieval MH - Humans MH - Microbiology MH - *Mummies MH - Paleontology MH - Polymerase Chain Reaction PMC - PMC1692447 EDAT- 1999/03/26 00:00 MHDA- 1999/03/26 00:01 PMCR- 2001/01/29 CRDT- 1999/03/26 00:00 PHST- 1999/03/26 00:00 [pubmed] PHST- 1999/03/26 00:01 [medline] PHST- 1999/03/26 00:00 [entrez] PHST- 2001/01/29 00:00 [pmc-release] AID - 10.1098/rstb.1999.0364 [doi] PST - ppublish SO - Philos Trans R Soc Lond B Biol Sci. 1999 Jan 29;354(1379):111-9. doi: 10.1098/rstb.1999.0364. PMID- 10436657 OWN - NLM STAT- MEDLINE DCOM- 19991124 LR - 20190607 IS - 0036-4665 (Print) IS - 0036-4665 (Linking) VI - 40 IP - 6 DP - 1998 Nov-Dec TI - Paleoparasitology: perspectives with new techniques. PG - 371-6 AB - Paleoparasitology is the study of parasites found in archaeological material. The development of this field of research began with histological identification of helminth eggs in mummy tissues, analysis of coprolites, and recently through molecular biology. An approach to the history of paleoparasitology is reviewed in this paper, with special reference to the studies of ancient DNA identified in archaeological material. FAU - Araújo, A AU - Araújo A AD - Fundação Oswaldo Cruz, Escola Nacional de Saúde Pública, Rio de Janeiro, Brasil. FAU - Reinhard, K AU - Reinhard K FAU - Bastos, O M AU - Bastos OM FAU - Costa, L C AU - Costa LC FAU - Pirmez, C AU - Pirmez C FAU - Iñiguez, A AU - Iñiguez A FAU - Vicente, A C AU - Vicente AC FAU - Morel, C M AU - Morel CM FAU - Ferreira, L F AU - Ferreira LF LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Brazil TA - Rev Inst Med Trop Sao Paulo JT - Revista do Instituto de Medicina Tropical de Sao Paulo JID - 7507484 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Archaeology MH - DNA/*isolation & purification MH - Feces/*parasitology MH - Forecasting MH - History, 20th Century MH - Humans MH - Molecular Biology/*methods MH - Mummies/*parasitology MH - Paleontology/history/*trends MH - Parasite Egg Count MH - Parasitology/history/*trends MH - Polymerase Chain Reaction EDAT- 1999/08/07 00:00 MHDA- 1999/08/07 00:01 CRDT- 1999/08/07 00:00 PHST- 1999/08/07 00:00 [pubmed] PHST- 1999/08/07 00:01 [medline] PHST- 1999/08/07 00:00 [entrez] AID - 10.1590/s0036-46651998000600006 [doi] PST - ppublish SO - Rev Inst Med Trop Sao Paulo. 1998 Nov-Dec;40(6):371-6. doi: 10.1590/s0036-46651998000600006. PMID- 9830142 OWN - NLM STAT- MEDLINE DCOM- 19981218 LR - 20090929 IS - 0266-8254 (Print) IS - 0266-8254 (Linking) VI - 27 IP - 5 DP - 1998 Nov TI - Mycobacterium tuberculosis complex DNA in calcified pleura from remains 1400 years old. PG - 265-9 AB - Mycobacterium tuberculosis complex DNA was isolated and identified in calcified pleura from remains 1400 years old, with the polymerase chain reaction. This is the first demonstration of tuberculosis in non-mummified archaeological tissue other than bone; the presence of mycobacterial mycolic acids in the sample supports this conclusion. The study of ancient DNA from microbial pathogens is of interest as it enables verification of traditional diagnoses, may answer long-standing questions in the history of disease, and provides ancient DNA sequences that can be compared with those of modern isolates. FAU - Donoghue, H D AU - Donoghue HD AD - Department of Bacteriology, University College London, UK. h.donoghue@ucl.ac.uk FAU - Spigelman, M AU - Spigelman M FAU - Zias, J AU - Zias J FAU - Gernaey-Child, A M AU - Gernaey-Child AM FAU - Minnikin, D E AU - Minnikin DE LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Lett Appl Microbiol JT - Letters in applied microbiology JID - 8510094 RN - 0 (DNA, Bacterial) RN - 0 (Mycolic Acids) SB - IM MH - Chromatography, High Pressure Liquid MH - DNA, Bacterial/*isolation & purification MH - Electrophoresis, Agar Gel MH - Humans MH - Male MH - Mycobacterium tuberculosis/genetics/*isolation & purification MH - Mycolic Acids/analysis MH - Paleopathology MH - Pleura/*microbiology MH - Polymerase Chain Reaction EDAT- 1998/11/27 00:00 MHDA- 1998/11/27 00:01 CRDT- 1998/11/27 00:00 PHST- 1998/11/27 00:00 [pubmed] PHST- 1998/11/27 00:01 [medline] PHST- 1998/11/27 00:00 [entrez] PST - ppublish SO - Lett Appl Microbiol. 1998 Nov;27(5):265-9. PMID- 9770538 OWN - NLM STAT- MEDLINE DCOM- 19981112 LR - 20190501 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 95 IP - 21 DP - 1998 Oct 13 TI - Detection of 400-year-old Yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia. PG - 12637-40 AB - Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on which to base such research. We hypothesized that it would be a lasting refuge for Yersinia pestis, the plague agent. DNA extracts were made from the dental pulp of 12 unerupted teeth extracted from skeletons excavated from 16th and 18th century French graves of persons thought to have died of plague ("plague teeth") and from 7 ancient negative control teeth. PCRs incorporating ancient DNA extracts and primers specific for the human beta-globin gene demonstrated the absence of inhibitors in these preparations. The incorporation of primers specific for Y. pestis rpoB (the RNA polymerase beta-subunit-encoding gene) and the recognized virulence-associated pla (the plasminogen activator-encoding gene) repeatedly yielded products that had a nucleotide sequence indistinguishable from that of modern day isolates of the bacterium. The specific pla sequence was obtained from 6 of 12 plague skeleton teeth but 0 of 7 negative controls (P < 0.034, Fisher exact test). A nucleic acid-based confirmation of ancient plague was achieved for historically identified victims, and we have confirmed the presence of the disease at the end of 16th century in France. Dental pulp is an attractive target in the quest to determine the etiology of septicemic illnesses detected in ancient corpses. Molecular techniques could be applied to this material to resolve historical outbreaks. FAU - Drancourt, M AU - Drancourt M AD - Unité des Rickettsies, Centre National de la Recherche Scientifique UPRES-A 6020, Université de la Méditerranée, Marseille, France. FAU - Aboudharam, G AU - Aboudharam G FAU - Signoli, M AU - Signoli M FAU - Dutour, O AU - Dutour O FAU - Raoult, D AU - Raoult D LA - eng SI - GENBANK/AF008578 PT - Journal Article PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA Primers) RN - 0 (DNA, Bacterial) SB - IM MH - Base Sequence MH - DNA Primers MH - DNA, Bacterial/*isolation & purification MH - Dental Pulp/*microbiology MH - Forensic Medicine MH - Humans MH - Yersinia pestis/*genetics PMC - PMC22883 EDAT- 1998/10/15 00:00 MHDA- 1998/10/15 00:01 PMCR- 1999/04/13 CRDT- 1998/10/15 00:00 PHST- 1998/10/15 00:00 [pubmed] PHST- 1998/10/15 00:01 [medline] PHST- 1998/10/15 00:00 [entrez] PHST- 1999/04/13 00:00 [pmc-release] AID - 1735 [pii] AID - 10.1073/pnas.95.21.12637 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12637-40. doi: 10.1073/pnas.95.21.12637. PMID- 9705702 OWN - NLM STAT- MEDLINE DCOM- 19980813 LR - 20190619 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 281 IP - 5375 DP - 1998 Jul 17 TI - A fruitful scoop for ancient DNA. PG - 319-20 FAU - Stokstad, E AU - Stokstad E LA - eng PT - Comment PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) RN - 0 (DNA, Plant) RN - 0 (N-phenacylthiazolium bromide) RN - 0 (Thiazoles) SB - IM CON - Science. 1998 Jul 17;281(5375):402-6. doi: 10.1126/science.281.5375.402. PMID: 9665881 MH - Animals MH - DNA, Mitochondrial/analysis/*isolation & purification MH - DNA, Plant/analysis/*isolation & purification MH - Diet MH - Feces/*chemistry MH - *Fossils MH - Hominidae MH - Humans MH - *Sloths/genetics MH - Thiazoles EDAT- 1998/08/15 00:00 MHDA- 1998/08/15 00:01 CRDT- 1998/08/15 00:00 PHST- 1998/08/15 00:00 [pubmed] PHST- 1998/08/15 00:01 [medline] PHST- 1998/08/15 00:00 [entrez] AID - 10.1126/science.281.5375.319b [doi] PST - ppublish SO - Science. 1998 Jul 17;281(5375):319-20. doi: 10.1126/science.281.5375.319b. PMID- 9647790 OWN - NLM STAT- MEDLINE DCOM- 19980731 LR - 20101118 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 247 IP - 3 DP - 1998 Jun 29 TI - Ancient DNA in human bone remains from Pompeii archaeological site. PG - 901-4 AB - aDNA extraction and amplification procedures have been optimized for Pompeian human bone remains whose diagenesis has been determined by histological analysis. Single copy genes amplification (X and Y amelogenin loci and Y specific alphoid repeat sequences) have been performed and compared with anthropometric data on sexing. FAU - Cipollaro, M AU - Cipollaro M AD - CRISCEB, 2.a Università degli Studi di Napoli, Italy. FAU - Di Bernardo, G AU - Di Bernardo G FAU - Galano, G AU - Galano G FAU - Galderisi, U AU - Galderisi U FAU - Guarino, F AU - Guarino F FAU - Angelini, F AU - Angelini F FAU - Cascino, A AU - Cascino A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Amelogenin) RN - 0 (Dental Enamel Proteins) RN - 0 (Genetic Markers) RN - 9007-49-2 (DNA) SB - IM MH - Amelogenin MH - Ancient Lands MH - Anthropometry MH - Bone and Bones/*chemistry MH - DNA/*chemistry MH - Dental Enamel Proteins MH - Female MH - *Fossils MH - Genetic Markers/genetics MH - Humans MH - Italy MH - Male MH - Microscopy, Polarization MH - Polymerase Chain Reaction MH - Repetitive Sequences, Nucleic Acid MH - Sex Determination Analysis/methods MH - X Chromosome/genetics MH - Y Chromosome/genetics EDAT- 1998/07/02 00:00 MHDA- 1998/07/02 00:01 CRDT- 1998/07/02 00:00 PHST- 1998/07/02 00:00 [pubmed] PHST- 1998/07/02 00:01 [medline] PHST- 1998/07/02 00:00 [entrez] AID - S0006-291X(98)98881-7 [pii] AID - 10.1006/bbrc.1998.8881 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 1998 Jun 29;247(3):901-4. doi: 10.1006/bbrc.1998.8881. PMID- 9601629 OWN - NLM STAT- MEDLINE DCOM- 19980812 LR - 20190728 IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 8 IP - 10 DP - 1998 May 7 TI - Svante Pääbo: pushing ancient DNA to the limit. PG - R329-30 FAU - Dickman, S AU - Dickman S LA - eng PT - Biography PT - Historical Article PT - Journal Article PT - Portrait PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Archaeology/*history MH - DNA/*analysis MH - History, 20th Century MH - Hominidae/genetics MH - Humans MH - Mummies MH - Sweden PS - Pääbo S FPS - Pääbo, S EDAT- 1998/05/28 00:00 MHDA- 1998/05/28 00:01 CRDT- 1998/05/28 00:00 PHST- 1998/05/28 00:00 [pubmed] PHST- 1998/05/28 00:01 [medline] PHST- 1998/05/28 00:00 [entrez] AID - S0960-9822(98)70212-X [pii] AID - 10.1016/s0960-9822(98)70212-x [doi] PST - ppublish SO - Curr Biol. 1998 May 7;8(10):R329-30. doi: 10.1016/s0960-9822(98)70212-x. PMID- 9569974 OWN - NLM STAT- MEDLINE DCOM- 19980528 LR - 20101118 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 56 IP - 1 DP - 1998 Mar TI - Molecular genetic sex determination of Medieval human remains from north Russia: comparison with archaeological and anthropological criteria. PG - 7-15 AB - Sex determination presents a difficult problem in archaeology and anthropology in cases of fragmentary or juvenile remains, and where grave goods are absent. Here, a molecular genetic analysis of the sex of human remain from the Early Medieval cemetery at Nefedievo, North Russia, was carried out and the results were compared with archaeological and anthropological data. Teeth without cavities (15 samples) and bones (9 samples) were used as the ancient DNA source. The repetitive sequences in DYZ1, DYZ3, DXZ3 loci, and a unique sequence in the first intron of the X-Y homologous gene amelogenin, were amplified. Sex was determined in 87.5% of the samples by archaeological criteria, in 95.8% of the samples by anthropological methods, and in 79.2% of the samples by DNA analysis. PCR allowed the sex of infant's remains to be identified in individual where the sex could not be determined by anthropological methods and in three remains where sex could not be inferred from archaeological data. Uneven preservation of nuclear DNA loci was evident. FAU - Ovchinnikov, I V AU - Ovchinnikov IV AD - Genetic Identification Center, Moscow, Russia. FAU - Ovtchinnikova, O I AU - Ovtchinnikova OI FAU - Druzina, E B AU - Druzina EB FAU - Buzhilova, A P AU - Buzhilova AP FAU - Makarov, N A AU - Makarov NA LA - eng PT - Comparative Study PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 9007-49-2 (DNA) SB - IM MH - Adult MH - Age Determination by Teeth MH - Anthropology, Physical/methods MH - Archaeology MH - Bone and Bones/chemistry MH - Child MH - DNA/analysis MH - Female MH - History, Medieval MH - Humans MH - Male MH - Mortuary Practice/history MH - Polymerase Chain Reaction MH - Russia MH - *Sex Determination Processes MH - Tooth/chemistry EDAT- 1998/05/07 00:00 MHDA- 1998/05/07 00:01 CRDT- 1998/05/07 00:00 PHST- 1998/05/07 00:00 [pubmed] PHST- 1998/05/07 00:01 [medline] PHST- 1998/05/07 00:00 [entrez] PST - ppublish SO - Anthropol Anz. 1998 Mar;56(1):7-15. PMID- 9503587 OWN - NLM STAT- MEDLINE DCOM- 19980406 LR - 20190921 IS - 0958-1669 (Print) IS - 0958-1669 (Linking) VI - 9 IP - 1 DP - 1998 Feb TI - New uses for old DNA. PG - 49-53 AB - Several years have elapsed since the last report of million-year-old DNA, coinciding with increased standards for experimental procedures in ancient DNA research. Whereas many earlier studies are now regarded as erroneous, the recent successful characterisation of Neanderthal DNA has set new standards for the field. Researchers continue to find new ways to exploit preserved genetic information in studies of more recent remains, widening the utility of ancient DNA. FAU - Cooper, A AU - Cooper A AD - Department of Biological Anthropology, Oxford University, UK. alan.cooper@bioanth.ox.ac.uk FAU - Wayne, R AU - Wayne R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Curr Opin Biotechnol JT - Current opinion in biotechnology JID - 9100492 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/analysis/*genetics MH - *Fossils MH - *Genome, Human MH - Humans MH - Paleontology/*methods MH - Phylogeny MH - Time Factors RF - 52 EDAT- 1998/03/21 00:00 MHDA- 1998/03/21 00:01 CRDT- 1998/03/21 00:00 PHST- 1998/03/21 00:00 [pubmed] PHST- 1998/03/21 00:01 [medline] PHST- 1998/03/21 00:00 [entrez] AID - S0958-1669(98)80083-9 [pii] AID - 10.1016/s0958-1669(98)80083-9 [doi] PST - ppublish SO - Curr Opin Biotechnol. 1998 Feb;9(1):49-53. doi: 10.1016/s0958-1669(98)80083-9. PMID- 9443981 OWN - NLM STAT- MEDLINE DCOM- 19980312 LR - 20201209 IS - 0305-1048 (Print) IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 26 IP - 3 DP - 1998 Feb 1 TI - Repair of degraded duplex DNA from prehistoric samples using Escherichia coli DNA polymerase I and T4 DNA ligase. PG - 857-9 AB - The most notable feature of DNA extracted from prehistoric material is that it is of poor quality. Amplification of PCR products from such DNA is consequently an exception. Here we present a simple method for the repair of degraded duplex DNA using the enzymes Escherichia coli DNA polymerase I and T4 DNA ligase. Adjacent sequences separated by nicks do not split up into intact strands during the denaturation step of PCR. Thus the target DNA is refractory to amplification. The proposed repair of nicked, fragmented ancient DNA results in an increase of amplification efficiency, such that the correct base order of the respective nuclear DNA segment can be obtained. FAU - Pusch, C M AU - Pusch CM AD - Molecular Genetics Laboratory, University Eye Hospital, University of T-ubingen, D-72076 T-ubingen, Auf der Morgenstelle 15, Germany. carsten.pusch@uni-tuebingen.de FAU - Giddings, I AU - Giddings I FAU - Scholz, M AU - Scholz M LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Antigens, Neoplasm) RN - 0 (Blood Proteins) RN - 0 (HPR protein, human) RN - 0 (Haptoglobins) RN - 9007-49-2 (DNA) RN - EC 2.7.7.7 (DNA Polymerase I) RN - EC 6.5.1.- (DNA Ligases) SB - IM MH - *Antigens, Neoplasm MH - Base Sequence MH - Blood Proteins/genetics MH - DNA/*chemistry/history MH - *DNA Damage MH - *DNA Ligases MH - *DNA Polymerase I MH - DNA Repair MH - Escherichia coli/enzymology MH - Germany MH - *Haptoglobins MH - History, Ancient MH - Humans MH - Molecular Sequence Data MH - Polymerase Chain Reaction/*methods PMC - PMC147318 EDAT- 1998/03/14 00:00 MHDA- 1998/03/14 00:01 PMCR- 1998/02/01 CRDT- 1998/03/14 00:00 PHST- 1998/03/14 00:00 [pubmed] PHST- 1998/03/14 00:01 [medline] PHST- 1998/03/14 00:00 [entrez] PHST- 1998/02/01 00:00 [pmc-release] AID - gkb171 [pii] AID - 10.1093/nar/26.3.857 [doi] PST - ppublish SO - Nucleic Acids Res. 1998 Feb 1;26(3):857-9. doi: 10.1093/nar/26.3.857. PMID- 9445806 OWN - NLM STAT- MEDLINE DCOM- 19980129 LR - 20061115 IS - 0016-6758 (Print) IS - 0016-6758 (Linking) VI - 33 IP - 10 DP - 1997 Oct TI - [Molecular genetic characteristics of the neolithic population of the Baikal region: RFLP analysis of the ancient mitochondrial DNA from osseous remains found in the Ust-Ida I burial ground]. PG - 1418-25 AB - Nineteen mtDNA samples from osseous remains found in the Ust-Ida I burial ground (middle Angara River) were analyzed. An ancient population dated back to 4020-3210 B.C. by radiocarbon (14C) analysis and archeologically assigned to the Neolithic Isakovo culture of the Baikal region was described in terms of molecular genetics. Data on restriction-site polymorphisms in fragment 16,106-16,545 of the mtDNA D-loop were obtained for seven restriction endonucleases. On the basis of these data, the mitotypic structure and nucleotide diversity of the ancient population were determined. The molecular genetic characteristics of the Neolithic population were compared to the modern populations of Siberia, Mongolia, and Urals. The data obtained indicate that the studied Baikal Neolithic population was ancestral for the modern indigenous Siberian population. The time of divergence of the three regional populations (5572 years ago) was estimated from the genetic distances between the Neolithic and modern Siberian populations, assuming that the average rate of nucleotide substitution was constant. This estimation agrees with the results of the radiocarbon dating (5542-5652 years ago). The fact that the studied samples were 14C-dated allowed the rate of nucleotide substitution in the studied region of mtDNA D-loop to be directly determined. FAU - Naumova, O Iu AU - Naumova OIu FAU - Rychkov, S Iu AU - Rychkov SIu FAU - Bazaliĭskiĭ, V I AU - Bazaliĭskiĭ VI FAU - Mamonova, N N AU - Mamonova NN FAU - Sulerzhitskiĭ, L D AU - Sulerzhitskiĭ LD FAU - Rychkov, Iu G AU - Rychkov IuG LA - rus PT - English Abstract PT - Journal Article TT - Molekuliarno-geneticheskaia kharakteristika neoliticheskoĭ populiatsii Pribaĭkal'ia. Analiz PDRF drevneĭ mtDNK iz ostankov v Mogil'nike ust'-Ida I. PL - Russia (Federation) TA - Genetika JT - Genetika JID - 0047354 RN - 0 (DNA, Mitochondrial) SB - IM MH - Ancient Lands MH - Bone and Bones/*physiology MH - Burial MH - DNA, Mitochondrial/*genetics MH - Humans MH - *Polymorphism, Restriction Fragment Length MH - Russia EDAT- 1998/01/31 00:00 MHDA- 1998/01/31 00:01 CRDT- 1998/01/31 00:00 PHST- 1998/01/31 00:00 [pubmed] PHST- 1998/01/31 00:01 [medline] PHST- 1998/01/31 00:00 [entrez] PST - ppublish SO - Genetika. 1997 Oct;33(10):1418-25. PMID- 9306399 OWN - NLM STAT- MEDLINE DCOM- 19971106 LR - 20061115 IS - 1087-0156 (Print) IS - 1087-0156 (Linking) VI - 15 IP - 9 DP - 1997 Sep TI - Ancient DNA is thirteen years old. PG - 855-8 AB - The first successful recovery of ancient DNA, from quagga and human mummies inspired significant enough interest to open an entire field of research. Efforts from many research groups, often in a hunt for the oldest sequences, showed that ancient DNA was a poor substrate for the enzymes used in molecular biology; it is present in tiny amounts, hard to purify, and frequently damaged. These obstacles have been partially overcome by the use of drastic laboratory precautions and by the introduction of polymerase chain reaction and phylogenetic studies. Ancient DNA analysis now finds applications in many research domains. FAU - Audic, S AU - Audic S AD - E.P.91 Structural and Genetic Information IBSM-CNRS, Marseille, France. FAU - Béraud-Colomb, E AU - Béraud-Colomb E LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Nat Biotechnol JT - Nature biotechnology JID - 9604648 RN - 0 (DNA, Bacterial) RN - 0 (DNA, Plant) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Archaeology MH - Communicable Diseases/genetics MH - DNA/chemistry/*genetics MH - DNA, Bacterial/chemistry/genetics MH - DNA, Plant/chemistry/genetics MH - Genetic Diseases, Inborn/genetics MH - Humans MH - *Paleontology MH - Polymerase Chain Reaction MH - Templates, Genetic RF - 62 EDAT- 1997/11/05 00:00 MHDA- 1997/11/05 00:01 CRDT- 1997/11/05 00:00 PHST- 1997/11/05 00:00 [pubmed] PHST- 1997/11/05 00:01 [medline] PHST- 1997/11/05 00:00 [entrez] AID - 10.1038/nbt0997-855 [doi] PST - ppublish SO - Nat Biotechnol. 1997 Sep;15(9):855-8. doi: 10.1038/nbt0997-855. PMID- 9378116 OWN - NLM STAT- MEDLINE DCOM- 19971112 LR - 20090929 IS - 0173-0835 (Print) IS - 0173-0835 (Linking) VI - 18 IP - 9 DP - 1997 Aug TI - Ancient and modern mitochondrial DNA sequences and the colonization of the Pacific. PG - 1529-33 AB - Mitochondrial DNA (mtDNA) is a valuable tool for the study of recent human evolution because it is easy to analyse, is inherited uniparentally and has a relatively rapid rate of evolution. mtDNA analysis has been used extensively for the elucidation of the pattern of migrations of human populations. Several studies have focused on the Pacific because Polynesia was settled by humans for the first time relatively recently and there is a wealth of archaeological and linguistic data to complement genetic data on the region. Results of mtDNA analyses on modern-day Pacific populations indicate reduced genetic variability, and suggest that the Polynesians descend from people who migrated relatively recently from island Southeast Asia and that a population bottleneck occurred during the settlement of the central Pacific. Several informative polymorphisms have been identified in the hypervariable control region of mtDNA in modern-day Pacific populations that are helpful in tracing the ancestral affinities of these people. Studies of these mtDNA polymorphisms in ancient bones of prehistoric Pacific islanders indicate that the proto-Polynesian colonizers may have descended from the early settlers of island Melanesia. Although fraught with technical difficulties, studies of ancient DNA can provide valuable evidence on the genetic affinities of past peoples. FAU - Hagelberg, E AU - Hagelberg E AD - Department of Biological Anthropology, University of Cambridge, UK. eh13@cus.cam.ac.uk LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Germany TA - Electrophoresis JT - Electrophoresis JID - 8204476 RN - 0 (DNA, Mitochondrial) SB - IM MH - Asia/ethnology MH - DNA, Mitochondrial/*chemistry MH - Emigration and Immigration MH - Fossils MH - Gene Deletion MH - Genetic Variation MH - Humans MH - Pacific Islands MH - Polynesia RF - 50 EDAT- 1997/08/01 00:00 MHDA- 1997/10/23 00:01 CRDT- 1997/08/01 00:00 PHST- 1997/08/01 00:00 [pubmed] PHST- 1997/10/23 00:01 [medline] PHST- 1997/08/01 00:00 [entrez] AID - 10.1002/elps.1150180907 [doi] PST - ppublish SO - Electrophoresis. 1997 Aug;18(9):1529-33. doi: 10.1002/elps.1150180907. PMID- 9230295 OWN - NLM STAT- MEDLINE DCOM- 19970826 LR - 20190705 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 90 IP - 1 DP - 1997 Jul 11 TI - Facts and artifacts of ancient DNA. PG - 1-3 FAU - Lindahl, T AU - Lindahl T AD - Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, Hertfordshire, United Kingdom. LA - eng PT - Comment PT - Journal Article PT - Review PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM CON - Cell. 1997 Jul 11;90(1):19-30. doi: 10.1016/s0092-8674(00)80310-4. PMID: 9230299 MH - Animals MH - *Artifacts MH - Base Sequence MH - Bone and Bones/chemistry MH - DNA/*chemistry MH - DNA, Mitochondrial/chemistry MH - *Fossils MH - Germany MH - Hominidae/genetics MH - Humans RF - 7 EDAT- 1997/07/11 00:00 MHDA- 1997/07/11 00:01 CRDT- 1997/07/11 00:00 PHST- 1997/07/11 00:00 [pubmed] PHST- 1997/07/11 00:01 [medline] PHST- 1997/07/11 00:00 [entrez] AID - S0092-8674(00)80306-2 [pii] AID - 10.1016/s0092-8674(00)80306-2 [doi] PST - ppublish SO - Cell. 1997 Jul 11;90(1):1-3. doi: 10.1016/s0092-8674(00)80306-2. PMID- 9341088 OWN - NLM STAT- MEDLINE DCOM- 19971022 LR - 20061115 IS - 0003-5548 (Print) IS - 0003-5548 (Linking) VI - 55 IP - 2 DP - 1997 Jun TI - [Classification of isolated skeletal elements using aDNA typing]. PG - 207-16 AB - Analysis of ancient DNA of material found in the Lichtensteinhöhle, a burial site of the Younger Bronze Age has been used for the first time to assign isolated skeletal elements to corresponding individuals. The method involved DNA typing through amplification of five Short Tandem Repeat loci which are also used in forensic genetics for the determination of kinship and identification. From all of the examined bone samples DNA was successfully extracted and amplification by means of Polymerase Chain Reaction could be carried out. For the skeletal elements allelic profiles which are specific for an individual were set up. These profiles made it possible to recognize bones belonging to one individual. Elements which were not from this individual could be excluded with certainty by aDNA analysis. FAU - Schultes, T AU - Schultes T AD - Institut für Anthropologie, Universität Göttingen. FAU - Hummel, S AU - Hummel S FAU - Herrmann, B AU - Herrmann B LA - ger PT - English Abstract PT - Historical Article PT - Journal Article TT - Zuordnung isolierter Skelettelemente mittels aDNA-typing. PL - Germany TA - Anthropol Anz JT - Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur JID - 0372377 RN - 9007-49-2 (DNA) SB - IM MH - Bone and Bones/*metabolism MH - Burial/history MH - DNA/genetics/*history MH - Germany MH - History, Ancient MH - Humans MH - Paleopathology MH - *Polymerase Chain Reaction MH - Repetitive Sequences, Nucleic Acid/*genetics EDAT- 1997/06/01 00:00 MHDA- 1997/10/27 00:01 CRDT- 1997/06/01 00:00 PHST- 1997/06/01 00:00 [pubmed] PHST- 1997/10/27 00:01 [medline] PHST- 1997/06/01 00:00 [entrez] PST - ppublish SO - Anthropol Anz. 1997 Jun;55(2):207-16. PMID- 9106549 OWN - NLM STAT- MEDLINE DCOM- 19970508 LR - 20200824 IS - 0002-9297 (Print) IS - 1537-6605 (Electronic) IS - 0002-9297 (Linking) VI - 60 IP - 4 DP - 1997 Apr TI - Reply to Stoneking: ancient DNA--how do you really know when you have it? PG - 1001-3 FAU - Cooper, A AU - Cooper A LA - eng PT - Comment PT - Letter PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 9007-49-2 (DNA) SB - IM CON - Am J Hum Genet. 1995 Dec;57(6):1259-62. PMID: 8533753 MH - Archaeology/standards MH - Artifacts MH - *Bone and Bones MH - DNA/*isolation & purification MH - *Fossils MH - Gene Amplification MH - Genetics/standards MH - Humans PMC - PMC1712466 EDAT- 1997/04/01 00:00 MHDA- 1997/04/01 00:01 PMCR- 1997/10/01 CRDT- 1997/04/01 00:00 PHST- 1997/04/01 00:00 [pubmed] PHST- 1997/04/01 00:01 [medline] PHST- 1997/04/01 00:00 [entrez] PHST- 1997/10/01 00:00 [pmc-release] PST - ppublish SO - Am J Hum Genet. 1997 Apr;60(4):1001-3. PMID- 9404456 OWN - NLM STAT- MEDLINE DCOM- 19980127 LR - 20061115 IS - 0037-9026 (Print) IS - 0037-9026 (Linking) VI - 191 IP - 4 DP - 1997 TI - [History of the rabbit and ancient DNA]. PG - 537-44 AB - Present populations of Rabbits (Oryctolagus cuniculus) are organized into two well defined groups A and B according to their mitochondrial DNA sequences. Group A is restricted to the South Western part of the Iberian Peninsula while group B is found everywhere else. Domestic breeds belong to the latter. As evidenced from data on ancient bones (up to 12,000 years BP) the mitochondrial type B1, predominant in domestic animals, originated from Spain. B1 animals were introduced in France by man between late Roman times and Middle Ages. FAU - Loreille, O AU - Loreille O AD - Centre de Génétique Moléculaire, CNRS 91198, Gif-dur-Yvette. FAU - Mounolou, J C AU - Mounolou JC FAU - Monnerot, M AU - Monnerot M LA - fre PT - English Abstract PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't TT - Histoire des lapins et ADN ancien. PL - France TA - C R Seances Soc Biol Fil JT - Comptes rendus des seances de la Societe de biologie et de ses filiales JID - 7505439 RN - 0 (DNA, Mitochondrial) SB - IM MH - Animals MH - Cell Lineage MH - DNA, Mitochondrial/genetics/*history MH - Evolution, Molecular MH - Geography MH - History, Ancient MH - Humans MH - Rabbits EDAT- 1997/01/01 00:00 MHDA- 1997/12/24 00:01 CRDT- 1997/01/01 00:00 PHST- 1997/01/01 00:00 [pubmed] PHST- 1997/12/24 00:01 [medline] PHST- 1997/01/01 00:00 [entrez] PST - ppublish SO - C R Seances Soc Biol Fil. 1997;191(4):537-44. PMID- 8755923 OWN - NLM STAT- MEDLINE DCOM- 19960925 LR - 20221207 IS - 0002-9297 (Print) IS - 1537-6605 (Electronic) IS - 0002-9297 (Linking) VI - 59 IP - 2 DP - 1996 Aug TI - The retrieval of ancient human DNA sequences. PG - 368-76 AB - DNA was extracted from approximately 600-year-old human remains found at an archaeological site in the southwestern United States, and mtDNA fragments were amplified by PCR. When these fragments were sequenced directly, multiple sequences seemed to be present. From three representative individuals, DNA fragments of different lengths were quantified and short overlapping amplification products cloned. When amplifications started from <40 molecules, clones contained several different sequences. In contrast, when they were initiated by a few thousand molecules, unambiguous and reproducible results were achieved. These results show that more experimental work than is often applied is necessary to ensure that DNA sequences amplified from ancient human remains are authentic. In particular, quantitation of the numbers of amplifiable molecules is a useful tool to determine the role of contaminating contemporary molecules and PCR errors in amplifications from ancient DNA. FAU - Handt, O AU - Handt O AD - Zoological Institute, University of Munich, Germany. FAU - Krings, M AU - Krings M FAU - Ward, R H AU - Ward RH FAU - Pääbo, S AU - Pääbo S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (DNA, Mitochondrial) SB - IM MH - Archaeology/*methods MH - Arizona MH - Asian People/*genetics MH - Base Sequence MH - DNA, Mitochondrial/*isolation & purification MH - Humans MH - *Indians, North American MH - Molecular Sequence Data MH - *Mummies MH - Polymerase Chain Reaction/methods MH - Reproducibility of Results MH - Sequence Analysis, DNA PMC - PMC1914746 EDAT- 1996/08/01 00:00 MHDA- 1996/08/01 00:01 PMCR- 1997/02/01 CRDT- 1996/08/01 00:00 PHST- 1996/08/01 00:00 [pubmed] PHST- 1996/08/01 00:01 [medline] PHST- 1996/08/01 00:00 [entrez] PHST- 1997/02/01 00:00 [pmc-release] PST - ppublish SO - Am J Hum Genet. 1996 Aug;59(2):368-76. PMID- 8838911 OWN - NLM STAT- MEDLINE DCOM- 19961203 LR - 20110418 IS - 0018-7143 (Print) IS - 0018-7143 (Linking) VI - 68 IP - 2 DP - 1996 Apr TI - Amplification of human short tandem repeats from medieval teeth and bone samples. PG - 185-99 AB - The suitability of typing hypervariable DNA loci for the genetic analysis of prehistoric populations is demonstrated for the first time. Alleles of the human short tandem repeat locus VWA31/A have been amplified from ancient teeth and bone samples derived from an early medieval burial site at Weingarten, Germany, using the polymerase chain reaction. The DNA results for 76 individuals reveal remarkable similarity of the allelic frequencies between the past and modern populations. A surplus of apparent homozygotes in the ancient population is most likely due to a stochastic problem of amplification of degraded DNA. Therefore technical obstacles for the application to ancient DNA were evaluated. The substantial perspectives of using microsatellite typing for the analysis of heritable diseases, determination of relatedness, and establishment of genealogies in prehistoric populations are outlined. FAU - Zierdt, H AU - Zierdt H AD - Institut für Anthropologie, Universität Göttingen, Germany. FAU - Hummel, S AU - Hummel S FAU - Herrmann, B AU - Herrmann B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Hum Biol JT - Human biology JID - 0116717 RN - 9007-49-2 (DNA) SB - IM MH - Alleles MH - *Anthropology MH - Base Sequence MH - Bone and Bones MH - DNA/*analysis/genetics MH - Gene Amplification MH - Humans MH - Molecular Sequence Data MH - Polymerase Chain Reaction MH - Repetitive Sequences, Nucleic Acid/*genetics EDAT- 1996/04/01 00:00 MHDA- 1996/04/01 00:01 CRDT- 1996/04/01 00:00 PHST- 1996/04/01 00:00 [pubmed] PHST- 1996/04/01 00:01 [medline] PHST- 1996/04/01 00:00 [entrez] PST - ppublish SO - Hum Biol. 1996 Apr;68(2):185-99. PMID- 8779335 OWN - NLM STAT- MEDLINE DCOM- 19960919 LR - 20190116 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 99 IP - 4 DP - 1996 Apr TI - Ancient DNA analysis of Fremont Amerindians of the Great Salt Lake Wetlands. PG - 507-18 AB - Skeletal remains of 47 individuals from the Great Salt Lake Wetlands, affiliated principally with Bear River (A.D. 400-1000) and Levee Phase (A.D. 1000-1350) Fremont cultural elements, were assessed for four mitochondrial DNA (mtDNA) markers that, in particular association, define four haplogroups (A, B, C, and D) widely shared among contemporary Amerindian groups. The most striking result is the absence of haplogroup A in this Fremont series, despite its predominance in contemporary Amerindian groups. Additionally, haplogroup B, defined by the presence of a 9bp deletion in region V, is present at the moderately high frequency of 60%. Haplogroups C and D are present at low frequencies. An additional haplotype, "N," observed in some modern populations and two other prehistoric samples, is also present in this Fremont skeletal collection. FAU - Parr, R L AU - Parr RL AD - Laboratory of Biological Anthropology, University of Utah, Salt Lake City 84112, USA. FAU - Carlyle, S W AU - Carlyle SW FAU - O'Rourke, D H AU - O'Rourke DH LA - eng PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA Primers) RN - 0 (DNA, Mitochondrial) SB - IM MH - Base Sequence MH - Bone and Bones/*chemistry MH - DNA Primers/chemistry MH - DNA, Mitochondrial/*analysis/genetics MH - Gene Frequency MH - Haplotypes MH - History, Medieval MH - Humans MH - Indians, North American/genetics/*history MH - Molecular Sequence Data MH - Utah EDAT- 1996/04/01 00:00 MHDA- 2000/06/20 09:00 CRDT- 1996/04/01 00:00 PHST- 1996/04/01 00:00 [pubmed] PHST- 2000/06/20 09:00 [medline] PHST- 1996/04/01 00:00 [entrez] AID - 10.1002/(SICI)1096-8644(199604)99:4<507::AID-AJPA1>3.0.CO;2-R [pii] AID - 10.1002/(SICI)1096-8644(199604)99:4<507::AID-AJPA1>3.0.CO;2-R [doi] PST - ppublish SO - Am J Phys Anthropol. 1996 Apr;99(4):507-18. doi: 10.1002/(SICI)1096-8644(199604)99:4<507::AID-AJPA1>3.0.CO;2-R. PMID- 8650373 OWN - NLM STAT- MEDLINE DCOM- 19960722 LR - 20051116 IS - 0039-9450 (Print) IS - 0039-9450 (Linking) VI - 41 IP - 5 DP - 1996 Apr TI - [Ancient DNA]. PG - 733-7 FAU - Ueda, S AU - Ueda S AD - Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan. LA - jpn PT - Journal Article PT - Review PL - Japan TA - Tanpakushitsu Kakusan Koso JT - Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme JID - 0413762 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Archaeology MH - Base Sequence MH - DNA/*genetics MH - Family MH - Humans MH - Molecular Sequence Data MH - Repetitive Sequences, Nucleic Acid/genetics RF - 19 EDAT- 1996/04/01 00:00 MHDA- 1996/04/01 00:01 CRDT- 1996/04/01 00:00 PHST- 1996/04/01 00:00 [pubmed] PHST- 1996/04/01 00:01 [medline] PHST- 1996/04/01 00:00 [entrez] PST - ppublish SO - Tanpakushitsu Kakusan Koso. 1996 Apr;41(5):733-7. PMID- 8614634 OWN - NLM STAT- MEDLINE DCOM- 19960606 LR - 20190501 IS - 0305-1048 (Print) IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 24 IP - 7 DP - 1996 Apr 1 TI - DNA damage and DNA sequence retrieval from ancient tissues. PG - 1304-7 AB - Gas chromatography/mass spectrometry (GC/MS) was used to determine the amounts of eight oxidative base modifications in DNA extracted from 11 specimens of bones and soft tissues, ranging in age from 40 to >50 000 years. Among the compounds assayed hydantoin derivatives of pyrimidines were quantitatively dominant. From five of the specimens endogenous ancient DNA sequences could be amplified by PCR. The DNA from these specimens contained substantially lower amounts of hydantoins than the six specimens from which no DNA could be amplified. Other types of damage, e.g. oxidation products of purines, did not correlate with the inability to retrieve DNA sequences. Furthermore, all samples with low amounts of damage and from which DNA could be amplified stemmed from regions where low temperatures have prevailed throughout the burial period of the specimens. FAU - Höss, M AU - Höss M AD - Zoological Institute, University of Munich, Germany. FAU - Jaruga, P AU - Jaruga P FAU - Zastawny, T H AU - Zastawny TH FAU - Dizdaroglu, M AU - Dizdaroglu M FAU - Pääbo, S AU - Pääbo S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Archaeology/*methods MH - DNA/*isolation & purification/metabolism MH - Gas Chromatography-Mass Spectrometry MH - Humans MH - Oxidation-Reduction MH - Polymerase Chain Reaction/*methods PMC - PMC145783 EDAT- 1996/04/01 00:00 MHDA- 1996/04/01 00:01 PMCR- 1996/04/01 CRDT- 1996/04/01 00:00 PHST- 1996/04/01 00:00 [pubmed] PHST- 1996/04/01 00:01 [medline] PHST- 1996/04/01 00:00 [entrez] PHST- 1996/04/01 00:00 [pmc-release] AID - 5w0219 [pii] AID - 10.1093/nar/24.7.1304 [doi] PST - ppublish SO - Nucleic Acids Res. 1996 Apr 1;24(7):1304-7. doi: 10.1093/nar/24.7.1304. PMID- 8587143 OWN - NLM STAT- MEDLINE DCOM- 19960328 LR - 20190905 IS - 0022-2844 (Print) IS - 0022-2844 (Linking) VI - 41 IP - 6 DP - 1995 Dec TI - Repetitive DNA sequences located in the central region of the human mdr1 (multidrug resistance) gene may account for a gene fusion event during its evolution. PG - 974-8 AB - The mdr1 gene, first member of the human multidrug-resistance gene family, is a major gene involved in cellular resistance to several drugs used in anticancer chemotherapy. Its product, the drug-excreting P-glycoprotein, shows a bipartite structure formed by two similar adjacent halves. According to one hypothesis, the fusion of two related ancestral genes during evolution could have resulted in this structure. The DNA sequence analysis of the introns located in the region connecting the two halves of the human mdr1 gene revealed a highly conserved poly(CA).poly (TG) sequence in intron 15 and repeated sequences of the Alu family in introns 14 and 17. These repeated sequences most likely represent "molecular fossils" of ancient DNA elements which were involved in such a recombination event. FAU - Pauly, M AU - Pauly M AD - Laboratoire de Recherche sur le Cancer et les Maladies du Sang, Centre Universitaire de Luxembourg, Grand-Duchy of Luxembourg. FAU - Kayser, I AU - Kayser I FAU - Schmitz, M AU - Schmitz M FAU - Ries, F AU - Ries F FAU - Hentges, F AU - Hentges F FAU - Dicato, M AU - Dicato M LA - eng SI - GENBANK/X69317 SI - GENBANK/X69318 SI - GENBANK/X78081 SI - GENBANK/X83289 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - J Mol Evol JT - Journal of molecular evolution JID - 0360051 SB - IM MH - Base Sequence MH - Drug Resistance, Multiple/*genetics MH - *Evolution, Molecular MH - Humans MH - Molecular Sequence Data MH - Polymorphism, Restriction Fragment Length MH - *Repetitive Sequences, Nucleic Acid MH - Sequence Analysis EDAT- 1995/12/01 00:00 MHDA- 1995/12/01 00:01 CRDT- 1995/12/01 00:00 PHST- 1995/12/01 00:00 [pubmed] PHST- 1995/12/01 00:01 [medline] PHST- 1995/12/01 00:00 [entrez] AID - 10.1007/BF00173178 [doi] PST - ppublish SO - J Mol Evol. 1995 Dec;41(6):974-8. doi: 10.1007/BF00173178. PMID- 8533753 OWN - NLM STAT- MEDLINE DCOM- 19960201 LR - 20200824 IS - 0002-9297 (Print) IS - 1537-6605 (Electronic) IS - 0002-9297 (Linking) VI - 57 IP - 6 DP - 1995 Dec TI - Ancient DNA: how do you know when you have it and what can you do with it? PG - 1259-62 FAU - Stoneking, M AU - Stoneking M LA - eng PT - Editorial PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 9007-49-2 (DNA) SB - IM CIN - Am J Hum Genet. 1997 Apr;60(4):1001-3. PMID: 9106549 MH - Anthropology MH - DNA/*genetics MH - Genetic Techniques MH - Humans PMC - PMC1801427 EDAT- 1995/12/01 00:00 MHDA- 1995/12/01 00:01 PMCR- 1996/06/01 CRDT- 1995/12/01 00:00 PHST- 1995/12/01 00:00 [pubmed] PHST- 1995/12/01 00:01 [medline] PHST- 1995/12/01 00:00 [entrez] PHST- 1996/06/01 00:00 [pmc-release] PST - ppublish SO - Am J Hum Genet. 1995 Dec;57(6):1259-62. PMID- 7638613 OWN - NLM STAT- MEDLINE DCOM- 19950914 LR - 20190618 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 269 IP - 5226 DP - 1995 Aug 18 TI - Ancient DNA. The trials and tribulations of cracking the prehistoric code. PG - 923-4 FAU - Williams, N AU - Williams N LA - eng PT - Congress PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - DNA/*genetics/history MH - DNA, Mitochondrial/genetics MH - Emigration and Immigration MH - Europe MH - Genetics, Population/*history MH - History, Ancient MH - Humans MH - Indians, North American/genetics MH - *Paleontology EDAT- 1995/08/18 00:00 MHDA- 1995/08/18 00:01 CRDT- 1995/08/18 00:00 PHST- 1995/08/18 00:00 [pubmed] PHST- 1995/08/18 00:01 [medline] PHST- 1995/08/18 00:00 [entrez] AID - 10.1126/science.7638613 [doi] PST - ppublish SO - Science. 1995 Aug 18;269(5226):923-4. doi: 10.1126/science.7638613. PMID- 7750909 OWN - NLM STAT- MEDLINE DCOM- 19950621 LR - 20180215 IS - 0301-0163 (Print) IS - 0301-0163 (Linking) VI - 43 IP - 4 DP - 1995 TI - Ancient DNA. PG - 118-20 AB - The investigation of molecular traits for evolutionary studies is a valuable alternative to the classic morphological approach. Since the mid-1980s molecular evolution has extended its field of investigation into the past. This has become possible with development of the polymerase chain reaction, which allows amplification of, and hence the study of, DNA from individuals long since dead. Many ancient, mostly extinct, animals and plants have been studied in order to determine their phylogenetic relationships with extant species. The biochemical properties of ancient DNA are also under investigation. The modifications that this molecule undergoes over long periods of time are of great interest as attempts are made to retrieve DNA from increasingly older remains. FAU - Höss, M AU - Höss M AD - Zoological Institute, University of Munich, Germany. LA - eng PT - Journal Article PT - Review PL - Switzerland TA - Horm Res JT - Hormone research JID - 0366126 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - *Biological Evolution MH - DNA/*genetics MH - Humans MH - *Paleontology MH - Phylogeny RF - 8 EDAT- 1995/01/01 00:00 MHDA- 1995/01/01 00:01 CRDT- 1995/01/01 00:00 PHST- 1995/01/01 00:00 [pubmed] PHST- 1995/01/01 00:01 [medline] PHST- 1995/01/01 00:00 [entrez] AID - 10.1159/000184253 [doi] PST - ppublish SO - Horm Res. 1995;43(4):118-20. doi: 10.1159/000184253. PMID- 7980476 OWN - NLM STAT- MEDLINE DCOM- 19941220 LR - 20171116 IS - 0265-9247 (Print) IS - 0265-9247 (Linking) VI - 16 IP - 10 DP - 1994 Oct TI - Ancient DNA: using molecular biology to explore the past. PG - 719-26 AB - Ancient DNA has been discovered in many types of preserved biological material, including bones, mummies, museum skins, insects in amber and plant fossils, and has become an important research tool in disciplines as diverse as archaeology, conservation biology and forensic science. In archaeology, ancient DNA can contribute both to the interpretation of individual sites and to the development of hypotheses about past populations. Site interpretation is aided by DNA-based sex typing of fragmentary human bones, and by the use of genetic techniques to assess the degree of kinship between the remains of different individuals. On a broader scale, population migrations can be traced by studying genetic markers in ancient DNA, as in recent studies of the colonisation of the Pacific islands, while ancient DNA in preserved plant remains can provide information on the development of agriculture. FAU - Brown, T A AU - Brown TA AD - Department of Biochemistry and Applied Molecular Biology, UMIST, Manchester, UK. FAU - Brown, K A AU - Brown KA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Bioessays JT - BioEssays : news and reviews in molecular, cellular and developmental biology JID - 8510851 RN - 0 (Genetic Markers) RN - 9007-49-2 (DNA) SB - IM MH - Agriculture MH - Alleles MH - Animals MH - *Archaeology MH - Base Sequence MH - DNA/chemistry/*genetics MH - Fossils MH - Genetic Markers MH - Genetic Techniques MH - Humans MH - Insecta/genetics MH - Molecular Biology/methods MH - Molecular Sequence Data MH - Mummies MH - Plants/genetics MH - Skin/chemistry RF - 59 EDAT- 1994/10/01 00:00 MHDA- 1994/10/01 00:01 CRDT- 1994/10/01 00:00 PHST- 1994/10/01 00:00 [pubmed] PHST- 1994/10/01 00:01 [medline] PHST- 1994/10/01 00:00 [entrez] AID - 10.1002/bies.950161006 [doi] PST - ppublish SO - Bioessays. 1994 Oct;16(10):719-26. doi: 10.1002/bies.950161006. PMID- 7807714 OWN - NLM STAT- MEDLINE DCOM- 19950201 LR - 20111117 IS - 0047-1887 (Print) IS - 0047-1887 (Linking) VI - 48 IP - 5 DP - 1994 Oct TI - Efficient amplification of the HLA-DQA1 gene in single genomes using a semi-nested polymerase chain reaction. PG - 329-35 AB - A semi-nested polymerase chain reaction (PCR) was introduced to amplification of the HLA-DQA1 gene, which is a single-copy gene, in a single genome. The limitation of template DNA for genotyping is 1 ng of genomic DNA, or more in the case of ordinary PCR. When reamplification with the same primers was performed, primer dimer was generated and the sensitivity was not improved. We designed a semi-nested primer for the second round of PCR, using the semi-nested PCR, more than 3 pg of template DNA could be amplified and typed. Furthermore, this method was applied to amplify DQA1 gene in single human sperm having haploid DNA, and followed by typing with sequence-specific oligonucleotide (SSO) probes. The semi-nested PCR technique was found to enhance the sensitivity of the amplification reaction and allowed the successful typing of the HLA-DQA1 gene. This is helpful for genotyping from samples with extremely small amounts of DNA, such as forensic or ancient DNA samples. FAU - Uchihi, R AU - Uchihi R AD - Department of Legal Medicine, Nagoya University School of Medicine, Japan. FAU - Yamamoto, T AU - Yamamoto T FAU - Kojima, T AU - Kojima T FAU - Tamaki, K AU - Tamaki K FAU - Katsumata, Y AU - Katsumata Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Japan TA - Nihon Hoigaku Zasshi JT - Nihon hoigaku zasshi = The Japanese journal of legal medicine JID - 0413715 RN - 0 (HLA-DQ Antigens) RN - 0 (HLA-DQ alpha-Chains) RN - 0 (HLA-DQA1 antigen) SB - IM MH - Base Sequence MH - *Gene Amplification MH - *Genes, MHC Class II MH - *Genome, Human MH - HLA-DQ Antigens/*genetics MH - HLA-DQ alpha-Chains MH - Humans MH - Molecular Sequence Data MH - Polymerase Chain Reaction/methods EDAT- 1994/10/01 00:00 MHDA- 1994/10/01 00:01 CRDT- 1994/10/01 00:00 PHST- 1994/10/01 00:00 [pubmed] PHST- 1994/10/01 00:01 [medline] PHST- 1994/10/01 00:00 [entrez] PST - ppublish SO - Nihon Hoigaku Zasshi. 1994 Oct;48(5):329-35. PMID- 7979081 OWN - NLM STAT- MEDLINE DCOM- 19941208 LR - 20181113 IS - 0035-8843 (Print) IS - 1478-7083 (Electronic) IS - 0035-8843 (Linking) VI - 76 IP - 5 DP - 1994 Sep TI - Ancient DNA. PG - 351 FAU - Spigelman, M AU - Spigelman M LA - eng PT - Letter PL - England TA - Ann R Coll Surg Engl JT - Annals of the Royal College of Surgeons of England JID - 7506860 RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Bacterial/*isolation & purification MH - Humans MH - *Mummies MH - Polymerase Chain Reaction PMC - PMC2502362 EDAT- 1994/09/01 00:00 MHDA- 1994/09/01 00:01 PMCR- 1995/09/01 CRDT- 1994/09/01 00:00 PHST- 1994/09/01 00:00 [pubmed] PHST- 1994/09/01 00:01 [medline] PHST- 1994/09/01 00:00 [entrez] PHST- 1995/09/01 00:00 [pmc-release] PST - ppublish SO - Ann R Coll Surg Engl. 1994 Sep;76(5):351. PMID- 8020619 OWN - NLM STAT- MEDLINE DCOM- 19940804 LR - 20190629 IS - 0014-4754 (Print) IS - 0014-4754 (Linking) VI - 50 IP - 6 DP - 1994 Jun 15 TI - Inter- and intrapopulation studies of ancient humans. PG - 585-91 AB - For a genetic analysis of ancient human populations to be useful, it must be demonstrated that the DNA samples under investigation represent a single human population. Toward that end, we have analyzed human DNA from the Windover site (7000-8000 BP). MHC-I analysis, using allele-specific oligonucleotide hybridization to PCR amplified Windover DNA, microsatellite analysis by PCR of the APO-A2 repeat and mtD-loop 3' region sequencing on multiple individuals spanning nearly the full range of estimated burial dates all confirm the hypothesis that there is a persistence of both nuclear and mitochondrial haplotypes at Windover throughout its entire period of use. Thus, Windover can be considered a single population. Neighbor-joining tree analysis of mtDNA sequences suggests that some mitochondrial types are clearly related to extant Amerind types, whereas others, more distantly related, may reflect genetically distinct origins. A more complete sequence analysis will be required to firmly resolve this issue. Calibrating genetic relationships deduced by tree analysis, radiocarbon dates and burial position, yields a human mtD-loop DNA rate of evolution of 3700 to 14,000 years per percent change. Both values are within the range of recent, independently calculated values using estimates of evolutionary divergence or theoretical population genetics. Thus we are beginning to realize the promise of ancient DNA analysis to experimentally answer heretofore unapproachable questions regarding human prehistory and genetic change. FAU - Hauswirth, W W AU - Hauswirth WW AD - Department of Immunology and Medical Microbiology, College of Medicine, University of Florida, Gainesville 32610-0266. FAU - Dickel, C D AU - Dickel CD FAU - Rowold, D J AU - Rowold DJ FAU - Hauswirth, M A AU - Hauswirth MA LA - eng PT - Journal Article PL - Switzerland TA - Experientia JT - Experientia JID - 0376547 RN - 0 (DNA, Mitochondrial) RN - 0 (Histocompatibility Antigens Class I) RN - 9007-49-2 (DNA) SB - IM MH - Alleles MH - Base Sequence MH - Brain Chemistry MH - DNA/*analysis MH - DNA, Mitochondrial/analysis MH - *Fossils MH - Histocompatibility Antigens Class I/genetics MH - Humans MH - Indians, North American/*genetics MH - Molecular Sequence Data MH - Nucleic Acid Hybridization MH - Polymerase Chain Reaction EDAT- 1994/06/15 00:00 MHDA- 1994/06/15 00:01 CRDT- 1994/06/15 00:00 PHST- 1994/06/15 00:00 [pubmed] PHST- 1994/06/15 00:01 [medline] PHST- 1994/06/15 00:00 [entrez] AID - 10.1007/BF01921729 [doi] PST - ppublish SO - Experientia. 1994 Jun 15;50(6):585-91. doi: 10.1007/BF01921729. PMID- 7517371 OWN - NLM STAT- MEDLINE DCOM- 19940804 LR - 20190629 IS - 0014-4754 (Print) IS - 0014-4754 (Linking) VI - 50 IP - 6 DP - 1994 Jun 15 TI - The biochemistry of ancient DNA in bone. PG - 530-5 AB - The amount of DNA in ancient bone was determined by ethidium bromide staining after the removal of the potent Taq inhibitor, fulvic acid. A complete decalcification and a perfusion protocol were used to recover DNA from bone. A variety of purification techniques including molecular sieve, hydroxyapatite binding and 'Magic' preparations yielded DNA that spanned from 3.4 micrograms/g of bone to below detectable limits. Fulvic acid was shown to interfere with the quantification of DNA derived from ancient human skeletal material one hundred to over seven thousand years old. Scanning UV in the 300 to 230 nm range is a simple and sensitive technique for documenting fulvic acid contamination in ancient bone extracts. FAU - Tuross, N AU - Tuross N AD - Conservation Analytical Laboratory, Smithsonian Institution, Washington District of Columbia 20560. LA - eng PT - Journal Article PL - Switzerland TA - Experientia JT - Experientia JID - 0376547 RN - 0 (Benzopyrans) RN - 0 (Nucleic Acid Synthesis Inhibitors) RN - 9007-49-2 (DNA) RN - EC 2.7.7.- (Taq Polymerase) RN - EN464416SI (Ethidium) RN - XII14C5FXV (fulvic acid) SB - IM MH - Benzopyrans/isolation & purification MH - Bone and Bones/*chemistry MH - DNA/*analysis MH - Decalcification Technique MH - Ethidium MH - *Fossils MH - Humans MH - Nucleic Acid Synthesis Inhibitors MH - Paleontology MH - Staining and Labeling MH - Taq Polymerase EDAT- 1994/06/15 00:00 MHDA- 1994/06/15 00:01 CRDT- 1994/06/15 00:00 PHST- 1994/06/15 00:00 [pubmed] PHST- 1994/06/15 00:01 [medline] PHST- 1994/06/15 00:00 [entrez] AID - 10.1007/BF01921721 [doi] PST - ppublish SO - Experientia. 1994 Jun 15;50(6):530-5. doi: 10.1007/BF01921721. PMID- 8019234 OWN - NLM STAT- MEDLINE DCOM- 19940729 LR - 20190501 IS - 0959-8138 (Print) IS - 1468-5833 (Electronic) IS - 0959-8138 (Linking) VI - 308 IP - 6940 DP - 1994 May 21 TI - Studying ancient DNA. PG - 1370 FAU - Spigelman, M AU - Spigelman M LA - eng PT - Historical Article PT - Letter PT - Research Support, Non-U.S. Gov't PL - England TA - BMJ JT - BMJ (Clinical research ed.) JID - 8900488 RN - 0 (DNA, Bacterial) SB - IM MH - DNA, Bacterial/*history/isolation & purification MH - History, Ancient MH - Humans MH - *Mummies MH - Mycobacterium tuberculosis/genetics/isolation & purification MH - Tuberculosis/history PMC - PMC2540251 EDAT- 1994/05/21 00:00 MHDA- 1994/05/21 00:01 PMCR- 1994/05/21 CRDT- 1994/05/21 00:00 PHST- 1994/05/21 00:00 [pubmed] PHST- 1994/05/21 00:01 [medline] PHST- 1994/05/21 00:00 [entrez] PHST- 1994/05/21 00:00 [pmc-release] AID - 10.1136/bmj.308.6940.1370 [doi] PST - ppublish SO - BMJ. 1994 May 21;308(6940):1370. doi: 10.1136/bmj.308.6940.1370. PMID- 8179883 OWN - NLM STAT- MEDLINE DCOM- 19940615 LR - 20061115 IS - 0736-6205 (Print) IS - 0736-6205 (Linking) VI - 16 IP - 2 DP - 1994 Feb TI - A reliable method for the removal of co-purifying PCR inhibitors from ancient DNA. PG - 232-5 FAU - Goodyear, P D AU - Goodyear PD AD - U.M.D.S. Guy's Hospital, London, UK. FAU - MacLaughlin-Black, S AU - MacLaughlin-Black S FAU - Mason, I J AU - Mason IJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 0 (DNA Primers) RN - 9007-49-2 (DNA) SB - IM MH - Base Sequence MH - Biotechnology MH - Chromatography, Ion Exchange MH - DNA/*genetics/*isolation & purification MH - DNA Primers/genetics MH - Fossils MH - Humans MH - Molecular Sequence Data MH - Polymerase Chain Reaction/*methods EDAT- 1994/02/01 00:00 MHDA- 1994/02/01 00:01 CRDT- 1994/02/01 00:00 PHST- 1994/02/01 00:00 [pubmed] PHST- 1994/02/01 00:01 [medline] PHST- 1994/02/01 00:00 [entrez] PST - ppublish SO - Biotechniques. 1994 Feb;16(2):232-5. PMID- 7702279 OWN - NLM STAT- MEDLINE DCOM- 19950503 LR - 20171116 IS - 0151-9638 (Print) IS - 0151-9638 (Linking) VI - 121 IP - 6-7 DP - 1994 TI - [Preservation of cutaneous structures of egyptian mummies. An ultrastructural study]. PG - 470-5 AB - INTRODUCTION: The recent development of studies applied to ancient materials may be explained by the application of molecular biology techniques on the extracted ancient DNA mainly the polymerase chain reaction (PCR), the ultrasensitive DNA-amplification technique that hit the headlines in the late 1980s. PCR was used to amplify human immunodeficiency virus (HIV), genetic material in stored tissue specimens and to document people who died in 1976. In addition, recent discoveries of mummified bodies in ice of the Tyrolean Alps or Greenland allowed a new approach in archeological studies. Mummies are a good material for investigations of ancient tissues. The studies concern the techniques of embalming, tissue preservation and palepathological aspects. In cutaneous paleopathology, mummies from Egypt, South or North America and Europe were considered. Various skin lesions were characterized: histiocytoma, Chagas' disease, smallpox, syphilis. Recently drugs (cocaine, hashish and nicotine) were extracted from skin and head hair of Egyptian mummies. Only a few studies were concerned with the ultrastructure of the skin of such mummies. MATERIAL AND METHODS: We had the opportunity to obtain skin samples of two Egyptian mummies. One of them was embalmed between 150 BC-90 AC. The skin was studied by transmission electron microscopy. As the mummified materials had dried out and shrunk, it was necessary to rehydrate them for ultrastructural observation. Skin samples were fragmented into small pieces before fixation with 2 p. 100 glutaraldehyde in sodium cacodylate buffer for 10 days (allowing for removal of the materials used for embalming). The samples were then washed in the same buffer for 10 days. After washing the pieces were post-fixed with 1 p. 100 osmium tetroxyde, dehydrated and embedded in Epoxy medium. RESULTS: With this process, it was possible to observe the excellent preservation of the cutaneous structures. The epidermis was well preserved. It was possible to observe the different cell layers and mainly the upper layers. The nuclei and the desmosomes of keratinocytes were recognized. Intercellular spaces were narrow. Desmosomes showed dense thickenings of the cell membrane on both sides and an intercellular band with narrow lucent spaces adjacent to the dense cell membrane. The nuclei showed dense spots of chromatin and in the cytoplasm recognizable tonofilament bundles were identified. Langerhans cells and melanocytes were not observed. In the dermis, the collagen fibrils formed thick bundles and showed the characteristic axial periodicity. Elastic fibers were also recognized showing two main components: the amorphous substance and the fibrils. Throughout the dermis, a number of round or oval structures were found. They had the typical appearance of spores of bacteria. In the centre, they had an electron dense and granular core surrounded by an inner membrane and a spore coat. DISCUSSION: Only a few investigations were performed on the ultrastructure of the skin of the Egyptian mummies. In the majority of cases, the epidermis was not preserved. The present work demonstrates the good preservation of epidermal structures and specially desmosomes and intercellular connections. The presence of spores of bacteria was previously reported. These spores enter a highly resistant resting phase in order to survive in a dormant state for a long period of starvation or other adverse environmental conditions. Similar investigations were performed on skin obtained from Eskimo mummies preserved by the extremely cold and dry polar weather. In these conditions, the authors reported the observation of melanocytes, vessels and nerves. Additionally, biochemical investigations demonstrated the very good preservation of collagen and glycosaminoglycans of the dermal extracellular matrix. FAU - Perrin, C AU - Perrin C AD - INSERM U346 Peau humaine et Immunité, Clinique Dermatologique, Hôpital Edouard-Herriot, Lyon. FAU - Noly, V AU - Noly V FAU - Mourer, R AU - Mourer R FAU - Schmitt, D AU - Schmitt D LA - fre PT - Historical Article PT - Journal Article TT - Préservation des structures cutanées des momies d'Egypte. Etude ultrastructurale. PL - France TA - Ann Dermatol Venereol JT - Annales de dermatologie et de venereologie JID - 7702013 RN - 9007-34-5 (Collagen) SB - IM MH - Collagen/ultrastructure MH - Desmosomes/ultrastructure MH - Egypt, Ancient MH - Epidermis/ultrastructure MH - Extracellular Matrix/ultrastructure MH - Fluid Therapy MH - History, Ancient MH - Humans MH - In Situ Hybridization MH - Microscopy, Electron, Scanning Transmission MH - Mummies/*pathology MH - Paleopathology MH - Skin/*ultrastructure EDAT- 1994/01/01 00:00 MHDA- 1994/01/01 00:01 CRDT- 1994/01/01 00:00 PHST- 1994/01/01 00:00 [pubmed] PHST- 1994/01/01 00:01 [medline] PHST- 1994/01/01 00:00 [entrez] PST - ppublish SO - Ann Dermatol Venereol. 1994;121(6-7):470-5. PMID- 8255287 OWN - NLM STAT- MEDLINE DCOM- 19940110 LR - 20041117 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 366 IP - 6455 DP - 1993 Dec 9 TI - Ancient DNA. Less cause for grave concern. PG - 513 FAU - Sykes, B AU - Sykes B LA - eng PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Mitochondrial) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Anthropometry MH - Bone and Bones/anatomy & histology/chemistry MH - DNA/*genetics/isolation & purification MH - DNA, Mitochondrial/genetics MH - Escherichia coli/genetics MH - Female MH - Humans MH - Male MH - *Paleontology EDAT- 1993/12/09 00:00 MHDA- 1993/12/09 00:01 CRDT- 1993/12/09 00:00 PHST- 1993/12/09 00:00 [pubmed] PHST- 1993/12/09 00:01 [medline] PHST- 1993/12/09 00:00 [entrez] AID - 10.1038/366513a0 [doi] PST - ppublish SO - Nature. 1993 Dec 9;366(6455):513. doi: 10.1038/366513a0. PMID- 8296875 OWN - NLM STAT- MEDLINE DCOM- 19940228 LR - 20081121 IS - 0002-9483 (Print) IS - 0002-9483 (Linking) VI - 92 IP - 4 DP - 1993 Dec TI - Ancient DNA from a pre-Columbian Amerindian population. PG - 463-71 AB - Ancient DNA was obtained from skeletal remains from the Norris Farms #36 cemetery, a pre-Columbian archeological site in central Illinois that dates to A.D. 1300. Four mitochondrial DNA (mtDNA) markers were analyzed that delineate the four primary mtDNA lineages found in contemporary Amerindian populations. mtDNA types were determined for 50 individuals; 49 belonged to one of these four lineages. One lineage occurred only in males, suggesting an immigration of maternally related males into this community. There was no significant spatial patterning of mtDNA lineages within the cemetery. This survey of ancient DNA variation in a pre-Columbian population supports the view that the initial colonization of the New World comprised just four primary mtDNA lineages. FAU - Stone, A C AU - Stone AC AD - Department of Anthropology, Pennsylvania State University, University Park 16802. FAU - Stoneking, M AU - Stoneking M LA - eng PT - Comparative Study PT - Historical Article PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Am J Phys Anthropol JT - American journal of physical anthropology JID - 0400654 RN - 0 (DNA, Mitochondrial) RN - 0 (Genetic Markers) SB - IM MH - Adult MH - Base Sequence MH - DNA, Mitochondrial/*history MH - Female MH - Genetic Markers MH - *Genetic Variation MH - History, Medieval MH - Humans MH - Illinois MH - Indians, North American/classification/genetics/*history MH - Male MH - Molecular Sequence Data MH - Phylogeny MH - Polymerase Chain Reaction MH - Sequence Deletion EDAT- 1993/12/01 00:00 MHDA- 1993/12/01 00:01 CRDT- 1993/12/01 00:00 PHST- 1993/12/01 00:00 [pubmed] PHST- 1993/12/01 00:01 [medline] PHST- 1993/12/01 00:00 [entrez] AID - 10.1002/ajpa.1330920405 [doi] PST - ppublish SO - Am J Phys Anthropol. 1993 Dec;92(4):463-71. doi: 10.1002/ajpa.1330920405. PMID- 8235556 OWN - NLM STAT- MEDLINE DCOM- 19931220 LR - 20190821 IS - 0036-8733 (Print) IS - 0036-8733 (Linking) VI - 269 IP - 5 DP - 1993 Nov TI - Ancient DNA. PG - 86-92 FAU - Pääbo, S AU - Pääbo S AD - University of Munich. LA - eng PT - Journal Article PL - United States TA - Sci Am JT - Scientific American JID - 0404400 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Sequence MH - *Biological Evolution MH - Bone and Bones/chemistry MH - Cloning, Molecular MH - DNA/*chemistry MH - *Fossils MH - Horses/genetics MH - Humans MH - Molecular Sequence Data MH - *Mummies MH - Muscles/chemistry MH - Polymerase Chain Reaction MH - Sequence Homology, Nucleic Acid MH - Skin/chemistry EDAT- 1993/11/01 00:00 MHDA- 1993/11/01 00:01 CRDT- 1993/11/01 00:00 PHST- 1993/11/01 00:00 [pubmed] PHST- 1993/11/01 00:01 [medline] PHST- 1993/11/01 00:00 [entrez] AID - 10.1038/scientificamerican1193-86 [doi] PST - ppublish SO - Sci Am. 1993 Nov;269(5):86-92. doi: 10.1038/scientificamerican1193-86. PMID- 7901907 OWN - NLM STAT- MEDLINE DCOM- 19931129 LR - 20190618 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 262 IP - 5134 DP - 1993 Oct 29 TI - Going for the old: ancient DNA draws a crowd. PG - 655-6 AB - Approximately 170 researchers interested in reconstructing the past convened for the 2nd International Conference on Ancient DNA, held in Washington, D.C., from 7 to 9 October. While rejuvenated celluloid dinosaurs have grabbed headlines this year, these scientists were more concerned with topics such as tracing ancient human populations and understanding how DNA can survive the millennia. FAU - Fischman, J AU - Fischman J LA - eng PT - Congress PT - Historical Article PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*history MH - History, Ancient MH - Humans MH - Paleontology EDAT- 1993/10/29 00:00 MHDA- 1993/10/29 00:01 CRDT- 1993/10/29 00:00 PHST- 1993/10/29 00:00 [pubmed] PHST- 1993/10/29 00:01 [medline] PHST- 1993/10/29 00:00 [entrez] AID - 10.1126/science.7901907 [doi] PST - ppublish SO - Science. 1993 Oct 29;262(5134):655-6. doi: 10.1126/science.7901907. PMID- 1415267 OWN - NLM STAT- MEDLINE DCOM- 19921112 LR - 20200824 IS - 0002-9297 (Print) IS - 1537-6605 (Electronic) IS - 0002-9297 (Linking) VI - 51 IP - 5 DP - 1992 Nov TI - A new source of polymorphic DNA markers for sperm typing: analysis of microsatellite repeats in single cells. PG - 985-91 AB - We show that dinucleotide and tetranucleotide repeat polymorphisms can be analyzed in single cells without using radioactivity or denaturing gels. This provides a rich new source of DNA polymorphisms for genetic mapping by sperm typing. The recombination fraction between two CA repeat polymorphisms was determined after whole genome amplification of single sperm, followed by typing of two different aliquots, one aliquot for each polymorphic locus. Single-cell analysis of microsatellites may also be valuable both for preimplantation genetic disease diagnosis based on single-blastomere or polar-body analysis and for the typing of forensic or ancient DNA samples containing very small amounts of nucleic acid. FAU - Hubert, R AU - Hubert R AD - Department of Molecular Biology, University of Southern California, Los Angeles 90089-1340. FAU - Weber, J L AU - Weber JL FAU - Schmitt, K AU - Schmitt K FAU - Zhang, L AU - Zhang L FAU - Arnheim, N AU - Arnheim N LA - eng GR - GM36745/GM/NIGMS NIH HHS/United States GR - HG00248/HG/NHGRI NIH HHS/United States GR - HG00328/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Am J Hum Genet JT - American journal of human genetics JID - 0370475 RN - 0 (Apolipoprotein C-II) RN - 0 (Apolipoproteins C) RN - 0 (Genetic Markers) RN - 0 (Oligodeoxyribonucleotides) SB - IM GS - APOC2 MH - Apolipoprotein C-II MH - Apolipoproteins C/genetics MH - Base Sequence MH - Genetic Markers/*genetics MH - Heterozygote MH - Humans MH - Male MH - Molecular Sequence Data MH - Oligodeoxyribonucleotides/genetics MH - Polymerase Chain Reaction MH - Polymorphism, Genetic/*genetics MH - Recombination, Genetic MH - Repetitive Sequences, Nucleic Acid/*genetics MH - *Spermatozoa PMC - PMC1682826 EDAT- 1992/11/01 00:00 MHDA- 1992/11/01 00:01 PMCR- 1993/05/01 CRDT- 1992/11/01 00:00 PHST- 1992/11/01 00:00 [pubmed] PHST- 1992/11/01 00:01 [medline] PHST- 1992/11/01 00:00 [entrez] PHST- 1993/05/01 00:00 [pmc-release] PST - ppublish SO - Am J Hum Genet. 1992 Nov;51(5):985-91. PMID- 1408822 OWN - NLM STAT- MEDLINE DCOM- 19921125 LR - 20190501 IS - 0305-1048 (Print) IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 20 IP - 19 DP - 1992 Oct 11 TI - A rapid chemiluminescent method for quantitation of human DNA. PG - 5061-5 AB - A sensitive and simple method for the quantitation of human DNA is described. This method is based on probe hybridization to a human alpha satellite locus, D17Z1. The biotinylated probe is hybridized to sample DNA immobilized on nylon membrane. The subsequent binding of streptavidin-horseradish peroxidase to the bound probe allows for chemiluminescent detection using a luminol-based reagent and X-ray film. Less than 150 pg of human DNA can easily be detected with a 15 minute exposure. The entire procedure can be performed in 1.5 hours. Microgram quantities of nonhuman DNA have been tested and the results indicate very high specificity for human DNA. The data on film can be scanned into a computer and a commercially available program can be used to create a standard curve where DNA quantity is plotted against the mean density of each slot blot signal. The methods described can also be applied to the very sensitive determination of quantity and quality (size) of DNA on Southern blots. The high sensitivity of this quantitation method requires the consumption of only a fraction of sample for analysis. Determination of DNA quantity is necessary for RFLP and many PCR-based tests where optimal results are obtained only with a relatively narrow range of DNA quantities. The specificity of this quantitation method for human DNA will be useful for the analysis of samples that may also contain bacterial or other non-human DNA, for example forensic evidence samples, ancient DNA samples, or clinical samples. FAU - Walsh, P S AU - Walsh PS AD - Roche Molecular Systems, Alameda, CA 94501. FAU - Varlaro, J AU - Varlaro J FAU - Reynolds, R AU - Reynolds R LA - eng PT - Journal Article PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA Probes) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Base Sequence MH - Blood Stains MH - Cattle MH - DNA/*analysis/blood MH - DNA Probes MH - Genome, Human MH - Hair/chemistry MH - Humans MH - Luminescent Measurements MH - Male MH - Microchemistry/methods MH - Molecular Sequence Data PMC - PMC334284 EDAT- 1992/10/11 00:00 MHDA- 1992/10/11 00:01 CRDT- 1992/10/11 00:00 PHST- 1992/10/11 00:00 [pubmed] PHST- 1992/10/11 00:01 [medline] PHST- 1992/10/11 00:00 [entrez] AID - 10.1093/nar/20.19.5061 [doi] PST - ppublish SO - Nucleic Acids Res. 1992 Oct 11;20(19):5061-5. doi: 10.1093/nar/20.19.5061. PMID- 1522919 OWN - NLM STAT- MEDLINE DCOM- 19921009 LR - 20190824 IS - 0028-1042 (Print) IS - 0028-1042 (Linking) VI - 79 IP - 8 DP - 1992 Aug TI - Improved efficiency in amplification of ancient DNA and its sequence analysis. PG - 359-60 FAU - Hummel, S AU - Hummel S AD - Institut für Anthropologie der Universität, Göttingen, FRG. FAU - Nordsiek, G AU - Nordsiek G FAU - Herrmann, B AU - Herrmann B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Naturwissenschaften JT - Die Naturwissenschaften JID - 0400767 RN - 9007-49-2 (DNA) SB - IM MH - Base Sequence MH - Bone and Bones/chemistry MH - DNA/analysis/*genetics MH - Escherichia coli/genetics MH - Female MH - Humans MH - Male MH - Molecular Sequence Data MH - *Paleontology MH - Polymerase Chain Reaction/*methods EDAT- 1992/08/01 00:00 MHDA- 1992/08/01 00:01 CRDT- 1992/08/01 00:00 PHST- 1992/08/01 00:00 [pubmed] PHST- 1992/08/01 00:01 [medline] PHST- 1992/08/01 00:00 [entrez] AID - 10.1007/BF01140179 [doi] PST - ppublish SO - Naturwissenschaften. 1992 Aug;79(8):359-60. doi: 10.1007/BF01140179. PMID- 1631067 OWN - NLM STAT- MEDLINE DCOM- 19920814 LR - 20190501 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 89 IP - 13 DP - 1992 Jul 1 TI - Whole genome amplification from a single cell: implications for genetic analysis. PG - 5847-51 AB - We have developed an in vitro method for amplifying a large fraction of the DNA sequences present in a single haploid cell by repeated primer extensions using a mixture of 15-base random oligonucleotides. We studied 12 genetic loci and estimate that the probability of amplifying any sequence in the genome to a minimum of 30 copies is not less than 0.78 (95% confidence). Whole genome amplification beginning with a single cell, or other samples with very small amounts of DNA, has significant implications for multipoint mapping by sperm or oocyte typing and possibly for genetic disease diagnosis, forensics, and the analysis of ancient DNA samples. FAU - Zhang, L AU - Zhang L AD - Department of Molecular Biology, University of Southern California, Los Angeles, 90089-1340. FAU - Cui, X AU - Cui X FAU - Schmitt, K AU - Schmitt K FAU - Hubert, R AU - Hubert R FAU - Navidi, W AU - Navidi W FAU - Arnheim, N AU - Arnheim N LA - eng GR - GM36745/GM/NIGMS NIH HHS/United States GR - HG00328/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Oligodeoxyribonucleotides) SB - IM GS - APOC2 GS - HBG2 GS - LDLR GS - PTH GS - STS MH - Base Sequence MH - Genes MH - Humans MH - Male MH - Molecular Sequence Data MH - Oligodeoxyribonucleotides/chemistry MH - Polymerase Chain Reaction/*methods MH - Polymorphism, Genetic MH - Prenatal Diagnosis/methods MH - Repetitive Sequences, Nucleic Acid MH - Spermatozoa PMC - PMC49394 EDAT- 1992/07/01 00:00 MHDA- 1992/07/01 00:01 PMCR- 1993/01/01 CRDT- 1992/07/01 00:00 PHST- 1992/07/01 00:00 [pubmed] PHST- 1992/07/01 00:01 [medline] PHST- 1992/07/01 00:00 [entrez] PHST- 1993/01/01 00:00 [pmc-release] AID - 10.1073/pnas.89.13.5847 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5847-51. doi: 10.1073/pnas.89.13.5847. PMID- 1642883 OWN - NLM STAT- MEDLINE DCOM- 19920910 LR - 20061115 IS - 0736-6205 (Print) IS - 0736-6205 (Linking) VI - 12 IP - 6 DP - 1992 Jun TI - PCR libraries of ancient DNA using a generalized PCR method. PG - 811-4, 817 AB - We describe a generalized PCR method that will amplify fragments of DNA without any knowledge of sequence using a single primer. Although we are presently using this method to amplify DNA fragments isolated from ancient preserved tissues, in effect, producing PCR libraries, it may prove to have other applications. FAU - Foo, I AU - Foo I AD - Department of Biochemistry, University of Minnesota, Duluth 55812. FAU - Salo, W L AU - Salo WL FAU - Aufderheide, A C AU - Aufderheide AC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biotechniques JT - BioTechniques JID - 8306785 RN - 9007-49-2 (DNA) SB - IM MH - Base Sequence MH - DNA/*analysis MH - *Genomic Library MH - Humans MH - Molecular Sequence Data MH - *Mummies MH - Polymerase Chain Reaction/*methods EDAT- 1992/06/01 00:00 MHDA- 1992/06/01 00:01 CRDT- 1992/06/01 00:00 PHST- 1992/06/01 00:00 [pubmed] PHST- 1992/06/01 00:01 [medline] PHST- 1992/06/01 00:00 [entrez] PST - ppublish SO - Biotechniques. 1992 Jun;12(6):811-4, 817. PMID- 1910205 OWN - NLM STAT- MEDLINE DCOM- 19911022 LR - 20190618 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 253 IP - 5026 DP - 1991 Sep 20 TI - Ancient DNA: still busy after death. PG - 1354-6 FAU - Cherfas, J AU - Cherfas J LA - eng PT - News PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Cloning, Molecular MH - DNA/*genetics MH - Egypt MH - Florida MH - *Fossils MH - Haplorhini/*genetics MH - Humans MH - *Mummies MH - Plants/genetics EDAT- 1991/09/20 00:00 MHDA- 1991/09/20 00:01 CRDT- 1991/09/20 00:00 PHST- 1991/09/20 00:00 [pubmed] PHST- 1991/09/20 00:01 [medline] PHST- 1991/09/20 00:00 [entrez] AID - 10.1126/science.1910205 [doi] PST - ppublish SO - Science. 1991 Sep 20;253(5026):1354-6. doi: 10.1126/science.1910205. PMID- 1861718 OWN - NLM STAT- MEDLINE DCOM- 19910905 LR - 20041117 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 352 IP - 6334 DP - 1991 Aug 1 TI - Ancient DNA. The past comes alive. PG - 381-2 FAU - Sykes, B AU - Sykes B LA - eng PT - Comment PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA, Mitochondrial) SB - IM CON - Nature. 1991 Aug 1;352(6334):427-9. doi: 10.1038/352427a0. PMID: 1861721 MH - Animals MH - Cloning, Molecular MH - DNA, Mitochondrial/*genetics MH - *Fossils MH - Gene Amplification MH - Humans EDAT- 1991/08/01 00:00 MHDA- 1991/08/01 00:01 CRDT- 1991/08/01 00:00 PHST- 1991/08/01 00:00 [pubmed] PHST- 1991/08/01 00:01 [medline] PHST- 1991/08/01 00:00 [entrez] AID - 10.1038/352381a0 [doi] PST - ppublish SO - Nature. 1991 Aug 1;352(6334):381-2. doi: 10.1038/352381a0. PMID- 2928314 OWN - NLM STAT- MEDLINE DCOM- 19890428 LR - 20190501 IS - 0027-8424 (Print) IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 86 IP - 6 DP - 1989 Mar TI - Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. PG - 1939-43 AB - Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, including two extinct animals (the marsupial wolf and giant ground sloth). The DNA obtained was invariably of a low average molecular size and damaged by oxidative processes, which primarily manifest themselves as modifications of pyrimidines and sugar residues as well as baseless sites and intermolecular cross-links. This renders molecular cloning difficult. However, the polymerase chain reaction can be used to amplify and study short mitochondrial DNA sequences that are of anthropological and evolutionary significance. This opens up the prospect of performing diachronical studies of molecular evolutionary genetics. FAU - Pääbo, S AU - Pääbo S AD - Department of Biochemistry, University of California, Berkeley 94720. LA - eng SI - GENBANK/M25424 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 9007-49-2 (DNA) RN - EC 2.7.7.7 (DNA-Directed DNA Polymerase) SB - IM MH - Animals MH - Base Sequence MH - Biological Evolution MH - Chromatography, High Pressure Liquid MH - *Cloning, Molecular MH - *DNA/genetics/isolation & purification/ultrastructure MH - DNA Damage MH - DNA-Directed DNA Polymerase MH - Electrophoresis, Agar Gel MH - *Fossils MH - *Gene Amplification MH - Humans MH - Microscopy, Electron MH - Molecular Sequence Data MH - *Mummies MH - Oxidation-Reduction MH - *Paleontology MH - Repetitive Sequences, Nucleic Acid PMC - PMC286820 EDAT- 1989/03/01 00:00 MHDA- 1989/03/01 00:01 PMCR- 1989/09/01 CRDT- 1989/03/01 00:00 PHST- 1989/03/01 00:00 [pubmed] PHST- 1989/03/01 00:01 [medline] PHST- 1989/03/01 00:00 [entrez] PHST- 1989/09/01 00:00 [pmc-release] AID - 10.1073/pnas.86.6.1939 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 1989 Mar;86(6):1939-43. doi: 10.1073/pnas.86.6.1939. PMID- 3186445 OWN - NLM STAT- MEDLINE DCOM- 19881214 LR - 20190501 IS - 0305-1048 (Print) IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 16 IP - 20 DP - 1988 Oct 25 TI - Mitochondrial DNA sequences from a 7000-year old brain. PG - 9775-87 AB - Pieces of mitochondrial DNA from a 7000-year-old human brain were amplified by the polymerase chain reaction and sequenced. Albumin and high concentrations of polymerase were required to overcome a factor in the brain extract that inhibits amplification. For this and other sources of ancient DNA, we find an extreme inverse dependence of the amplification efficiency on the length of the sequence to be amplified. This property of ancient DNA distinguishes it from modern DNA and thus provides a new criterion of authenticity for use in research on ancient DNA. The brain is from an individual recently excavated from Little Salt Spring in southwestern Florida and the anthropologically informative sequences it yielded are the first obtained from archaeologically retrieved remains. The sequences show that this ancient individual belonged to a mitochondrial lineage that is rare in the Old World and not previously known to exist among Native Americans. Our finding brings to three the number of maternal lineages known to have been involved in the prehistoric colonization of the New World. FAU - Pääbo, S AU - Pääbo S AD - Department of Biochemistry, University of California, Berkeley 94720. FAU - Gifford, J A AU - Gifford JA FAU - Wilson, A C AU - Wilson AC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA, Mitochondrial) RN - EC 2.7.7.7 (DNA-Directed DNA Polymerase) SB - IM MH - *Anthropology MH - Base Sequence MH - *Brain Chemistry MH - DNA, Mitochondrial/*genetics/isolation & purification MH - DNA-Directed DNA Polymerase MH - Electrophoresis, Agar Gel MH - Gene Amplification MH - Humans MH - Molecular Sequence Data PMC - PMC338778 EDAT- 1988/10/25 00:00 MHDA- 1988/10/25 00:01 CRDT- 1988/10/25 00:00 PHST- 1988/10/25 00:00 [pubmed] PHST- 1988/10/25 00:01 [medline] PHST- 1988/10/25 00:00 [entrez] AID - 10.1093/nar/16.20.9775 [doi] PST - ppublish SO - Nucleic Acids Res. 1988 Oct 25;16(20):9775-87. doi: 10.1093/nar/16.20.9775.