Data from: 'Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies'
Description
Phylogenetic inference is challenged by genealogical heterogeneity amongst genetic markers. Such discordance is driven predominantly by incomplete lineage sorting (ILS) and interspecific gene flow, and bears attendant consequences for the accurate resolution of species relationships. Understanding the distribution of gene conflict in organismal genomes is, therefore, a key aspect of phylogenetic analysis. In the study associated with this repository, three large phylogenomic datasets (i.e., whole mitogenomes, conserved nuclear protein-coding loci, and genomic windows) were used to probe the extent to which discordance pervaded the unresolved phylogeny of Coenonympha (Nymphalidae) butterflies. Discordance was found to be elevated at multiple historically recalcitrant phylogenetic positions. In particular, species relationships near the crown of Coenonympha and within a rapidly diversifying subclade (the hero group) remained difficult to resolve, suggesting that ILS and gene flow have obscured the evolution of this genus. These findings have implications for the taxonomy of this butterfly group and the study of its diversification history. In addition, this work lended support to a growing body of evidence that gene conflict driven by biological processes stands to confound phylogeny, even when extensive data are used.
Files
Steps to reproduce
For the methods of data collection and generation, see the associated manuscript. The file "README.md" at the head of the zipped directory contains information about the sources and types of data presented in this repository.