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

Sundaland, a subcontinent situated in the Indo-Malay Archipelago, is characterised 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. Despite their high species richness and complex distributions, there is a paucity of biogeographical studies on Sundaic insects. By applying molecular “museomics” techniques to a species group of Troides birdwing butterflies, we generated inter- and intraspecific datasets comprising 39,485 - 59,905 SNP positions and complete mitogenomes from museum specimens collected between the 1890’s and 1990’s. Using these datasets, we were able to investigate the species 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 divergence took place during the Pleistocene within the different species complexes. Earlier-diverging taxa were found on Borneo whilst later-diverging taxa had distributions centred 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. T. amphrysis euthydemus (Fruhstorfer, 1913) syn. nov. is synonymized with T. amphrysus ruficollis (Butler, 1879) given the low divergence between these two species. We found genetic evidence of possible hidden species-level diversity within the species complexes Troides cuneifera Oberthür 1879 and Troides miranda Butler 1869, for which we recommend further taxonomic work. Together, these results provide a perspective on Triodes evolutionary dynamics and the role of Pleistocene glaciations in shaping patterns of insect diversity in Sundaland.