Selective and non-selective evolutionary signatures found in the simplest replicative biological entities

Abstract

This repository contains the datasets and analytical scripts supporting the study “Selective and non-selective evolutionary signatures found in the simplest replicative biological entities”, which investigates the evolutionary forces shaping mitovirus (Mitoviridae) genomes. The study combines quantitative analyses of nucleotide composition, dinucleotide relative frequencies, synonymous codon usage bias, codon-position–specific GC content, and RNA secondary structure stability (minimum free energy), together with protein-based phylogenetic reconstruction of RNA-dependent RNA polymerase (RdRp) sequences. Open reading frames were systematically predicted from publicly available sequences, and multiple sequence structure alignments and maximum-likelihood phylogenies were generated to provide an evolutionary framework. Comprehensive genomic datasets were evaluated using multivariate approaches, including quadratic discriminant analysis, to assess their potential as complementary classification criteria at the genus level. Although no single quantitative genomic signature proved sufficient for taxonomic discrimination beyond protein phylogeny, the analyses revealed pronounced structural divergence within the genus Kvaramitovirus, supporting the hypothesis of an ancestral circularization event that altered evolutionary constraints. Overall, the data indicate that mitovirus genome composition reflects the combined action of neutral processes and natural selection, with selective pressures likely playing a dominant role in maintaining genome stability and replicative fitness.