Data from: Genealogy and demographic history of a widespread amphibian throughout Indochina

Relatively little is known about spatial patterns of cryptic diversity in tropical species and the processes that generate them. Few studies examine the geographic distribution of genetic lineages in Southeast Asia, an area hypothesized to harbor substantial cryptic diversity. We investigated the evolutionary history of Asian tree frogs of the Polypedates leucomystax complex (n = 172) based on 1800 bp of the mtDNA genes ND 1 and cytochrome b and tested hypotheses pertaining to climate, geology and dispersal patterns. Analyses revealed substantial genetic diversity and lineage divergence throughout the region with evidence for widespread sympatric lineages and a general north versus south clustering. Relaxed molecular clock analysis and tests for demographic expansion identified an initial cladogenesis during the Miocene with subsequent Plio–Pleistocene diversification, which corresponded to periods of increased aridity and the onset of monsoonal weather systems, respectively. Rates of diversification were relatively constant until the Early Pleistocene when rates increased exponentially. We found equivocal evidence for both isolation-by-distance and a potential role of some landscape features as partial barriers to dispersal. Finally, our analyses showed that divergence between insular and mainland populations occurred before Homo sapiens colonized Southeast Asia suggesting that historical human-mediated dispersal did not drive insular diversification. Our results suggested that demographic expansion in the Late Pleistocene resulted in widespread sympatric lineages in the P. leucomystax complex throughout southern China and Indochina, and further clarified the evolutionary history of lineages within P. leucomystax.

目前学界对热带物种隐蔽多样性（cryptic diversity）的空间分布格局及其形成机制的认知仍相对有限。东南亚被推测蕴藏着极为丰富的隐蔽多样性，但针对该区域遗传支系地理分布的针对性研究却为数不多。本研究以亚洲斑腿泛树蛙复合体（Polypedates leucomystax complex，样本量n=172）为研究对象，基于线粒体DNA（mtDNA）的ND1与细胞色素b（cytochrome b）基因共1800 bp的序列片段，解析其演化历史，并检验与气候、地质及扩散模式相关的多项假说。分析结果显示，整个研究区域内存在显著的遗传多样性与支系分化，证据表明存在广泛的同域支系，且整体呈现南北聚类的分布特征。松弛分子钟分析（relaxed molecular clock analysis）与种群扩张检验结果表明，支系分化最初发生于中新世，后续的物种多样化过程则发生于上新世-更新世时期，二者分别对应区域干旱加剧时段与季风气候系统的形成阶段。种群多样化速率在早更新世之前整体保持相对稳定，直至早更新世时期才出现指数级增长。本研究得到的距离隔离效应与部分景观特征作为扩散半屏障的潜在作用的相关证据均不明确。此外，分析结果显示，岛屿种群与大陆种群的分化早于智人（Homo sapiens）殖民东南亚的时间，这表明历史上人类介导的扩散并未推动该复合体的岛屿支系多样化进程。本研究结果显示，晚更新世的种群扩张使得斑腿泛树蛙复合体的同域支系广泛分布于中国南部与中南半岛，并进一步阐明了该复合体内部支系的演化历史。