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Data from: Species diversification in the sky islands of southwestern China revealed by genomic, introgression and demographic analyses of Asian shrew moles

Li, Yi-Xian1; Chen, Zhong-Zheng2; Li, Quan1; Zhang, Tao1; Cheng, Feng3; Song, Wen-Yu4; Li, Xue-You1; He, Shui-Wang1; Wang, Hong-Jiao1; Onditi, Kenneth Otieno1; Jiang, Xue-Long1

Published Aug 20, 2025 on Dryad. https://doi.org/10.5061/dryad.t1g1jwtc9

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Aug 20, 2025 version files 74.90 GB

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Abstract

The mountains of Southwest China, a global biodiversity hotspot, have a unique “sky island” landscape with high diversity of both ancient and recently formed species. While their distribution patterns offer significant insights into diversification processes, the complex geological and climatic history, combined with dynamic histories of gene flow in endemic taxa, makes unravelling this history challenging. This study focuses on Asian shrew moles (genus Uropsilus), an ancient group endemic to this region with an unresolved taxonomic system. By combining phylogenomic, introgression, and demographic history analyses, we investigated the historical patterns of species diversification in this genus. We detected phylogenetic discordances among rapidly diverged lineages, driven by incomplete lineage sorting, both recent and ancient gene flow, and ghost introgression. The gene flow patterns revealed strong genetic isolation in the Hengduan Mountains region, contrasted by more extensive dispersal or connectivity in areas to its east, while suggesting potential ring-like diversification around the Sichuan Basin. Demographic history indicated that rapidly diverged lineages south of the Yangtze River exhibited significantly different responses to climatic fluctuations compared to other lineages, with the East Asian monsoon likely driving their radiative differentiation and dispersal. Our study demonstrates the impacts of mountain uplift, climatic changes, and the connectivity of sky island refugia in shaping the diverse patterns of species differentiation and their distribution.