Museomics reveals patterns of within-species divergence and diversification in Troides birdwings (Lepidoptera: Papilionidae)

Sundaland, a subcontinent situated in the Indo-Malay Archipelago, is characterized by a dynamic climatic, geological, and geographical history and a correspondingly diverse biota. The distribution of this biota follows complex biogeographical patterns, with high levels of local endemism and frequent instances of hidden diversity—greater genetic differentiation than expected based on phenotype. Biogeographical studies on Sundaic insects are scarce, despite high species richness and complex distributions. By applying molecular “museomics” techniques to a species group of Troides birdwing butterflies, we generated inter- and intraspecific datasets comprising 39,485 to 59,905 SNP positions and complete mitogenomes from museum specimens collected between the 1890s and 1990s. These datasets allowed the investigation of taxonomic status, biogeography, and divergence timing within the Sundaland endemic amphrysus group. The origin of the group was estimated between the late Miocene and early Pliocene, and subsequent intraspecific divergence took place during the Pleistocene. Earlier-diverging taxa were found on Borneo, while later-diverging taxa had distributions centered in western Sundaland. Divergence between subspecies of later-diverging species complexes occurred <1 million years ago, overlapping with marine incursions on the Sunda Shelf. Javan populations showed comparatively high genetic differentiation from those on other Sundaic landmasses. We found genetic evidence of possible hidden species-level diversity within two species complexes. Contrastingly, T. amphrysus euthydemus (Fruhstorfer 1913) syn. nov. is synonymized with T. amphrysus ruficollis (Butler 1879), given the low divergence between these two species. Together, these results provide a perspective on Triodes evolutionary dynamics and the role of Pleistocene glaciations in shaping patterns of Sundaland’s insect diversity.