Data from: Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau

Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the southeastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow, and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of southeastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographic changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographic regions especially in the western range. Gene flow in P. densata was restricted to geographically neighboring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.密枝松（Pinus densata）是一种生态适应性卓越的同倍体杂交种（homoploid hybrid），经多轮殖民扩散事件，现已广泛栖息于青藏高原东南部地貌多样的广袤区域。此前学界已明确其起源区域、向高原的殖民路径，以及与亲本物种的基因渐渗（introgression）方向，但对其种群的隔离与分化历史却知之甚少。本研究针对19个具有代表性的密枝松及其亲本物种种群，对其8个核基因座的核苷酸多态性进行了检测，并结合该数据与溯祖模拟（coalescence simulations）分析，评估了该物种种群规模、基因流的历史变化，以及时空维度上的分化动态。研究结果显示，密枝松的起源时间可追溯至中新世晚期，这与青藏高原东南部的近期隆升事件相契合。该物种随后的地理区域分化始于上新世晚期，由区域地形变化与更新世冰期（Pleistocene glaciations）共同驱动。密枝松的祖先种群有效种群大小（effective population size）较大，但其中部与西部种群均由少量奠基个体建立，这表明其从祖先杂交带向西迁移的过程中经历了严重的瓶颈效应（bottlenecks）。在脱离祖先种群后，密枝松的所有地理区域种群均发生了种群扩张，其中西部分布区的扩张尤为显著。密枝松的基因流仅局限于地理相邻的种群之间，进而导致不同区域类群间出现显著的遗传分化。本研究揭示的密枝松分化与种群历史动态新认知，有助于深化我们对其在青藏高原上物种形成过程（speciation process）的理解。