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dc.date.available
2024-11-13T12:43:46Z
dc.identifier.citation
Ramirez, Martin Javier; Burgo, Agustina; (2024): Systematics of the color-polymorphic spider genus Cybaeolus, with comments on the phylogeny of the family Hahniidae (Araneae): Phylogenetic dataset, trees and images at full resolution. Consejo Nacional de Investigaciones Científicas y Técnicas. (dataset). http://hdl.handle.net/11336/248075
dc.identifier.uri
http://hdl.handle.net/11336/248075
dc.description.abstract
Original images and phylogenetic analysis of the spiders of the genus Cybaeulus, with outgroups in the marronoid clade. Data from six DNA markers, analyzed with maximum likelihood and parsimony.
dc.rights
info:eu-repo/semantics/embargoedAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.title
Systematics of the color-polymorphic spider genus Cybaeolus, with comments on the phylogeny of the family Hahniidae (Araneae): Phylogenetic dataset, trees and images at full resolution
dc.type
dataset
dc.date.updated
2024-11-13T12:29:38Z
dc.description.fil
Fil: Ramirez, Martin Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
dc.description.fil
Fil: Burgo, Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
dc.rights.embargoDate
2025-07-01
dc.datacite.PublicationYear
2024
dc.datacite.Creator
Ramirez, Martin Javier
dc.datacite.Creator
Burgo, Agustina
dc.datacite.affiliation
Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"
dc.datacite.affiliation
Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"
dc.datacite.affiliation
Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"
dc.datacite.affiliation
Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"
dc.datacite.publisher
Consejo Nacional de Investigaciones Científicas y Técnicas
dc.datacite.subject
Zoología, Ornitología, Entomología, Etología
dc.datacite.subject
Ciencias Biológicas
dc.datacite.subject
CIENCIAS NATURALES Y EXACTAS
dc.datacite.ContributorType
DataCurator
dc.datacite.ContributorType
DataCurator
dc.datacite.ContributorName
Grismado, Cristian José
dc.datacite.ContributorName
Martínez García, Leonel Antonio
dc.datacite.date
11/11/2024
dc.datacite.DateType
Creado
dc.datacite.language
eng
dc.datacite.version
1.0
dc.datacite.description
Imaging: Incident light images were taken with a Leica DFC 290 digital camera mounted on a Leica M165 C stereo microscope, or with a Leica DFC 295 digital camera on a Leica M205 A stereo microscope. Transmitted light images were taken with a Nikon DXM1200 digital camera mounted on an Olympus BH2 compound microscope. Extended focal range images were assembled with Helicon Focus 5.3. Male and female genitalia were cleared with clove oil in an excavated slide and illustrated using the same Olympus BH2 compound microscope with camera lucida. For the scanning electron micrographs (SEM) the samples were gradually dehydrated to 100% ethanol, critical point dried and coated with gold-palladium, and examined with a Hitachi SEM s-4700 at the American Museum of Natural History (AMNH). Female genitalia was digested with pancreatine for SEM examination. To illustrate color polymorphism, we mainly imaged individuals collected in the field and directly preserved in ethanol 95% and stored at -18° C, since they better maintain their natural coloration. Phylogenetic analysis: We obtained sequences from 26 samples of the three known species of Cybaeolus, and of five additional species of Hahniidae. To these, we added legacy sequences of Cybaeolus and of other genera of Hahniidae, as well as representatives of the remaining families in the marronoid clade. For the new sequences, the extraction and amplification of DNA was made in the Laboratory of Molecular Tools at Museo Argentino de Ciencias Naturales (MACN), from tissues preserved in absolute alcohol at -18ºC. We targeted the markers histone H3 (H3), cytochrome oxidase subunit I (CO1), 28S ribosomal RNA (28S) and 16S ribosomal RNA (16S), previously used to estimate relationships of marronoid spiders (Wheeler et al., 2017). Details of extraction, primers and PCR protocols are the same as in Magalhaes & Ramírez (2022). Sequencing was outsourced to Macrogen Inc., South Korea. The resulting chromatograms were analyzed individually to detect contaminated sequences or ambiguous portions. In addition to these sequences obtained in the laboratory, we combined our data with additional sequences from previous work (Wheeler et al., 2017; Rivera-Quiroz et al., 2020), using the markers mentioned above plus 12S ribosomal RNA (12S) and 18S ribosomal RNA (18S). For the CO1 marker, additional sequences obtained by the Arachnology Division at MACN and deposited in the BOLDSYSTEMS platform (https://www.boldsystems.org/) were also used. Sequences were aligned with MAFFT Online v.7.463 (Katoh & Standley, 2013), using the L-INS-I algorithm. See Table 1 for list of vouchers and sequence identifiers. Maximum likelihood: For the maximum likelihood analyses we used the program IQ-TREE 2.2.0 (Minh et al., 2020), partitioning the data by marker, and selecting the best combination of partitions and evolution models by Bayesian information criterion (best fitting models were TPM2+I+G4 for H3, GTR+F+I+G4 for 18S, GTR+F+I+G4 for 16S and 12S together, GTR+F+I+G4 for CO1, and GTR+F+I+G4 for 28S). Since the relationships of outgroup taxa in the resulting trees were slightly different to that found in recent phylogenomic studies, we used the study of Gorneau et al. (2023) based on ultraconserved elements as a backbone topology to constrain our tree search, considering only the taxa in common with our analysis (see supplementary Fig. S1); this means that all the rest of the taxa are free to move anywhere during tree search. Support for groups (branches) was estimated by 1000 cycles of ultrafast bootstrapping. Ten independent runs were performed; of those, six converged into nearly identical log likelihood values (-57417.7725 to -57417.9604) and identical topologies; the tree with top-ranking log likelihood is presented in Results, after collapsing branches with bootstrap below 0.5. To estimate the support of an alternative topology with Cybaeolus as sister to the rest of the hahniids, we used TNT 1.6 (Goloboff & Morales, 2023) to modify the optimal tree placing Cybaeolus in such position, and asked for the frequency of the branch of interest (all hahniids except Cybaeolus) in the 1000 bootstrapped trees previously saved by IQTREE. Ancestral character states for the arrangement of spinnerets (grouped; separated in a transversal line) were estimated by maximum likelihood on the optimal tree, using the R packages phytools and ape, under the models ER and ARD, and the best fitting model selected by the Akaike information criterion. Parsimony: For the parsimony analyses we used TNT 1.6. For the equal weights analysis, a heuristic search was made using a driven search with the default parameters of the “new technologies”, aiming for 10 independent hits to minimum length. The resulting trees were then submitted to an additional round of tree-bisection reconnection (TBR) branch swapping. These results were compared to a simpler search strategy of 300 random addition sequences, each followed by TBR, which produced 20 hits to minimal length. As both strategies reached the same trees with multiple independent hits, it is likely that the optimal trees were found. Finally, the strict consensus of all the optimal trees was obtained, and on this consensus the support values were calculated by means of 1000 bootstrap pseudoreplicates.
dc.datacite.DescriptionType
Métodos
dc.datacite.FundingReference
PICT-2019-2745
dc.datacite.FundingReference
PICTO-2021-MALVINAS-00018
dc.datacite.FunderName
Ministerio de Ciencia, Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica. Fondo para la Investigación Científica y Tecnológica
dc.datacite.FunderName
Ministerio de Ciencia, Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica. Fondo para la Investigación Científica y Tecnológica
dc.subject.keyword
Phylogeny
dc.subject.keyword
Spinning organs
dc.subject.keyword
Marronoid spiders
dc.subject.keyword
South America
dc.datacite.resourceTypeGeneral
dataset
dc.conicet.datoinvestigacionid
21122
dc.datacite.awardTitle
Biogeografía integrativa de arácnidos neotropicales
dc.datacite.awardTitle
Orígenes y evolución de la biota terrestre de las Islas Malvinas
dc.datacite.geolocation
Argentina
dc.datacite.geolocation
Chile
dc.datacite.formatedDate
2024
Archivos del conjunto de datos
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CO1.fas
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93.33Kb
16S.fas
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20.82Kb
Fig_29_ParticionesConstrained9_treefile_cutoff_50_treefile
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11.39Kb
Cybaeolus_pusillus_images.zip
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317.5Mb
Fig_s03_parsimony_constrained.tre
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68.86Kb
Fig_s02_ConcatUnconstrained_contree
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4.624Kb
Cybaeolus_rastellus_images.zip
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175.5Mb
CybaeolusDNA.tnt
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328.3Kb
Cybaeolus_delfini_images.zip
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712.1Mb
H3.fas
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20.12Kb
Fig_s01_ConstrainTree.nwk
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645bytes
18S.fas
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77.77Kb
12S.fas
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9.067Kb
28S.fas
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115.9Kb