Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius)

In rapid radiation, the earliest components of evolutionary divergence are often difficult to resolve, which were always driven by the characteristics of taxa and the limitations of alternative analytical methods. The origin and radiation of the alpine butterfly Parnassius, a high-altitude mountainous insect group, can be attributed to the uplift of the Qinghai-Tibet Plateau (QTP). Despite detailed phylogenetic analyses of the genus, deep phylogenetic relationships among the major subgenera remain recalcitrant. In this study, 102 individuals from 10 representative Parnassius species were sampled to resolve the phylogenetic relationships among subgenera based on nuclear and mitochondrial genome data sets. Gene-tree/species-tree conflicts were detected by concatenation and multispecies coalescent (MSC) approaches. We recovered a well-supported species tree, despite these conflicts, and detected considerable phylogenetic discordance among genomic regions. The main explanation for the topol..., ,