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.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过程的认知仍相对匮乏。针对东南亚地区——该区域被认为蕴藏着丰富的隐蔽多样性——开展的遗传支系地理分布研究寥寥无几。本研究基于线粒体DNA（mtDNA）的ND1及细胞色素b（cytochrome b）基因共1800 bp的序列片段，对斑腿泛树蛙（Polypedates leucomystax）复合群（样本量n=172）的演化历史展开探究，并检验了与气候、地质及扩散模式相关的假说。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，同时存在广泛的同域支系，且整体呈现出南北聚类的格局。宽松分子钟分析与种群扩张检验表明，初始分支发生（cladogenesis）发生于中新世，后续的上新世-更新世物种分化则分别对应干旱加剧时期与季风气候系统的形成。物种分化速率在更新世早期之前始终相对稳定，此后呈指数级增长。本研究未得到距离隔离（isolation-by-distance）的明确证据，同时仅发现部分景观特征可能对扩散起到部分阻碍作用。最后，本研究分析显示，岛屿种群与大陆种群的分化发生在智人（Homo sapiens）殖民东南亚之前，表明人类介导的历史扩散并未推动该复合群的岛屿物种分化。研究结果表明，晚更新世的种群扩张使得斑腿泛树蛙复合群在华南及中南半岛形成了广泛的同域支系，并进一步阐明了该复合群内支系的演化历史。