Data from: Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata

Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species throughout their respective ranges. Strong spatial genetic structure of both cp and mtDNA were detected in P. densata populations. Mitotypes specific to P. densata were likely generated by complex recombination events. A putative ancestral hybrid zone in the northeastern periphery of P. densata was identified, and we propose that the species then colonized the plateau by migrating westwards. Along the colonization route, consecutive bottlenecks and surfing of rare alleles caused a significant reduction of genetic diversity and strong population differentiation. The direction and intensity of introgression from parental species varied among geographic regions. In western parts of its range the species seems to have been isolated from seed and pollen flow from its parent species for a long time. The observed spatial distribution of genetic diversity in P. densata also appears to reflect the persistence of this species on the plateau during the last glaciation. Our results indicate that both ancient and contemporary population dynamics have contributed to the spatial distribution of genetic diversity in P. densata, which accordingly reflects its evolutionary history.西康松（Pinus densata）是一种令人瞩目的成功同倍体杂交物种，其占据了青藏高原东南部的广袤区域，而该区域内并无其两个亲本物种的分布，但学界对其涉及的定殖过程仍知之甚少。为阐明该物种如何在青藏高原定殖并建立种群，我们对西康松及其推定亲本物种各自分布范围内的54个种群，开展了父系遗传的叶绿体（cp）DNA与母系遗传的线粒体（mt）DNA变异情况的调查分析。研究发现，西康松种群的叶绿体DNA与线粒体DNA均呈现显著的空间遗传结构。西康松特有的线粒体单倍型（mitotypes）可能由复杂的重组事件产生。我们在西康松分布区的东北边缘识别出一处推定的祖先杂交带，并据此推测该物种通过向西迁徙完成了青藏高原的定殖过程。在该定殖路径上，连续的种群瓶颈事件与稀有等位基因的冲浪效应导致了遗传多样性的显著降低，以及种群间强烈的遗传分化。亲本物种向西康松的基因渐渗方向与强度，在不同地理区域存在显著差异。在其分布区西部，西康松长期与其亲本物种之间不存在种子与花粉的基因交流，处于生殖隔离状态。观测到的西康松遗传多样性空间分布格局，也反映了该物种在末次冰期期间于青藏高原的存续情况。本研究结果表明，古代与现代的种群动态共同塑造了西康松的遗传多样性空间分布格局，这一格局也相应地反映了该物种的演化历史。