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.巽他陆块（Sundaland）作为印度-马来群岛的次大陆，拥有活跃多变的气候、地质与地理演化历史，相应孕育了高度多样的生物区系。该生物区系的分布呈现复杂的生物地理格局，存在高水平的地方性特有现象与大量隐存多样性——即遗传分化水平远超基于表型预期的类群。尽管巽他地区昆虫类群拥有极高的物种丰富度与复杂的分布模式，针对其开展的生物地理学研究仍较为匮乏。 本研究针对裳凤蝶属（Troides）鸟翼凤蝶类群，运用分子“博物馆基因组学（museomics）”技术，对1890年代至1990年代采集的馆藏标本进行测序，构建了涵盖39485至59905个单核苷酸多态性（SNP）位点以及完整线粒体基因组（mitogenomes）的种间与种内数据集。依托该数据集，本研究对巽他陆块特有amphrysus物种群（amphrysus-group）的物种界定、生物地理格局与分化时间展开了系统探究。 该物种群的起源时间被估算为中新世晚期至上新世早期，后续的物种分化发生于更新世的不同物种复合群内部。分化较早的类群分布于婆罗洲，而后期分化的类群则以巽他陆块西部为分布中心。后期分化物种复合群的亚种间分化发生于距今100万年以上，与巽他陆架的海侵事件时间高度重合。爪哇种群相较于其他巽他陆块种群，展现出显著更高的遗传分化水平。 鉴于T. amphrysis euthydemus (Fruhstorfer, 1913) 新异名（syn. nov.）与T. amphrysus ruficollis (Butler, 1879) 之间的遗传分化程度极低，本研究将前者归为后者的同物异名。本研究在楔纹裳凤蝶（Troides cuneifera Oberthür 1879）与美丽裳凤蝶（Troides miranda Butler 1869）的物种复合群中发现了存在隐存物种级多样性的遗传证据，建议针对这两个类群开展后续分类学研究。 综上，本研究结果为裳凤蝶属（Troides）的演化动态以及更新世冰期如何塑造巽他陆块昆虫多样性格局提供了全新视角。