Whole genome data reveal discordance in the evolutionary history of Coenonympha butterflies

Understanding the distribution and drivers of gene conflict in organismal genomes is a vital aspect of phylogenetic analysis. As part of this study, whole genome resequencing data are used to produce different phylogenomic datasets for nearly all butterflies of the Coenonympha genus and their close relatives. Analysing these datasets, we find that discordance is elevated at multiple historically recalcitrant phylogenetic positions, and that both incomplete lineage sorting and gene flow have contributed to genealogical heterogeneity. These findings have implications for the taxonomy of this butterfly group and the study of its diversification history. In addition, this work lends support to a growing body of evidence that gene conflict driven by biological processes stands to confound phylogeny, even when extensive data are used.