Data for "Phylogenomics reveals the evolution, biogeography, and diversification of voles in the Hengduan Mountains"

The Hengduan Mountains (HDM) of Southwest China are a biodiversity hotspot whose temperate flora and fauna are among the world's richest. However, the origin and evolution of biodiversity in the HDM region remain poorly understood, especially in mammals. Given that the HDM region shows the highest richness of vole species in the world, we used whole-exome capture sequencing data from the most comprehensive sampling of HDM voles performed to date to investigate their evolutionary history and diversification patterns. We reconstructed a robust species phylogeny and re-estimated the divergence times of the HDM voles. We found that all HDM vole species could be divided into a western lineage (Volemys, Proedromys, and Neodon) and an eastern lineage (Caryomys and Eothenomys), and the two lineages originated from two migration events from North Eurasia to the HDM approximately 9 million years ago (Mya). Both vole lineages underwent a significant acceleration of net diversification from 8-5 Mya, which was temporally congruent with the orogeny of the HDM region. We also identified strong intertribal gene flow among the HDM voles and hypothesized that frequent gene flow might have facilitated the speciation burst of the HDM voles. Our study highlights the importance of both environmental and biotic factors in shaping the biodiversity of mammals in mountain ecosystems.

中国西南横断山脉（Hengduan Mountains, HDM）是全球生物多样性热点区域，其温带动植物区系堪称全球最为丰富的类群之一。然而，横断山脉地区生物多样性的起源与演化机制仍未得到充分解析，尤以哺乳动物类群为甚。鉴于横断山脉拥有全球最为丰富的田鼠物种多样性，本研究借助迄今最为全面的横断山脉田鼠采样所获得的全外显子组捕获测序（whole-exome capture sequencing）数据，探究其演化历史与多样化模式。我们重建了稳健的田鼠物种系统发育树，并重新估算了横断山脉田鼠的分化时间。研究结果显示，所有横断山脉田鼠物种均可划分为两个演化支：西部支系（涵盖Volemys、Proedromys及Neodon属）与东部支系（涵盖Caryomys及Eothenomys属），且这两个支系均起源于约900万年前（Mya）从北欧亚大陆向横断山脉的两次迁徙事件。两支田鼠演化支的净多样化速率均在800万至500万年前出现显著提升，该时间节点与横断山脉地区的造山运动时期高度吻合。此外，我们还在横断山脉田鼠中检测到强烈的族间基因流，并推测频繁的基因流可能推动了横断山脉田鼠的物种形成爆发。本研究凸显了环境与生物因子在塑造山地生态系统哺乳动物生物多样性过程中的双重重要意义。