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

Abstract Under 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. 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 datasets. 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 topological discordance among subgenera was extensive incomplete lineage sorting (ILS), whereas introgression events were not prominent. The origin and explosive radiation of Parnassius (i.e., rapid succession of speciation events) in the late Miocene associated with environmental events on the plateau led to short internal branches, thereby increasing ILS and topological conflicts, especially among closely related subgenera. Our results also suggested that MSC approaches (SNP and AFLP Package for Phylogenetic analysis [SNAPP] and SVDquartets) are accurate and superior to the concatenation approach; in particular, SVDquartets can explicitly accommodate gene‐tree/species‐tree conflicts caused by high ILS and demonstrate strong robustness. Finally, we explored the phylogenomic data by testing multiple sources of phylogenomic conflict to clarify the strengths and limitations of different approaches, while considering phylogenetic signal variation in mitochondrial loci. We anticipate that the phylogeny described here will be the backbone of future evolutionary studies of the genus and will provide insight into phylogenetic discordance due to rapid radiation.