Amplicon capture phylogenomics provides new insights into the phylogeny and evolution of alpine Parnassius butterflies (Lepidoptera: Papilionidae)

Abstract The alpine butterfly genus Parnassius is a popular model group for studying biogeography, evolution, conservation biology, and ecology. Despite its scientific importance, a comprehensive and robust phylogeny of this group is still lacking. In this study, we used an amplicon capture strategy to sequence 144 nuclear protein‐coding genes and complete mitochondrial genomes for 60 Parnassius specimens covering 42 species and all eight subgenera of Parnassius . Our results strongly support the monophyly of the genus and eight subgenera. The relationships among subgenera are robustly resolved as ( Sachaia , ( Kreizbergia , ( Driopa , ( Parnassius , ( Tadumia , Lingamius ), ( Kailasius , Koramius ))))), which is different from all previous results. Biogeographic and divergence time analyses indicate that the ancestor of Parnassius originated in an area including the Himalayas and Tibetan Plateau (HTP) and Mongolian steppes in the middle Miocene approximately 13.19 Mya. The middle Miocene global cooling event (starting from ~13.9 Mya) probably provided climatic opportunities for the diversification of cold‐adapted Parnassius . The ancestral state reconstruction analyses suggest that the ancestor of Parnassius butterflies most likely lived in a medium elevational area (2000–4000 m) and fed on Papaveraceae plants. The host shift from Papaveraceae to Crassulaceae in the subgenus Parnassius increases the species diversity of this subgenus, concurring with the “escape and radiate” hypothesis. Overall, our work provides valuable nuclear gene and mitochondrial genome data and a robust phylogenetic framework of Parnassius for future studies of the taxonomy, evolution, and ecology of this group.