Data from: Genealogy and palaeodrainage basins in Yunnan Province: phylogeography of the Yunnan spiny frog, Nanorana yunnanensis (Dicroglossidae)

Historical drainage patterns adjacent to the Qinghai-Tibetan Plateau differed markedly from those of today. We examined the relationship between drainage history and geographic patterns of genetic variation in the Yunnan spiny frog, Nanorana yunnanensis, using approximately 981 base pairs of mitochondrial DNA (mtDNA) partial sequences from encoding genes ND1 and ND2, and intervening areas including complete tRNA Ile, tRNA Gln, and tRNA Met. Two null hypotheses were tested, including (1) that genetic patterns do not correspond to the development of drainage systems and (2) that populations had been stable and not experienced population expansion, bottlenecking and selection. Genealogical analyses identified three, major, well-supported maternal lineages, each of which had two sublineages. These divergent lineages were completely concordant with six geographical regions. Genetic structure and divergence were strongly congruent with historical rather than contemporary drainage patterns. Most lineages and sublineages were formed through population fragmentation events during the rearrangement of paleodrainage basins in the early Pliocene and early Pleistocene. Sympatric lineages occurred only in localities at the boundaries of major drainages, likely reflecting secondary contact of previously allopatric populations. Extensive population expansion probably occurred early in the Middle Pleistocene accompanying dramatic climatic oscillations.青藏高原周边的历史水系格局与现代水系格局存在显著差异。本研究以云南棘蛙（*Nanorana yunnanensis*）为研究对象，基于其线粒体DNA（mtDNA）中编码基因ND1、ND2及完整的转运RNA异亮氨酸（tRNA Ile）、转运RNA谷氨酰胺（tRNA Gln）、转运RNA甲硫氨酸（tRNA Met）的间隔区域共约981个碱基对的部分序列，探究了水系演化历史与该物种种质遗传变异地理格局之间的关联。本研究检验了两项零假设：其一，遗传格局与水系系统的发育无关联；其二，种群保持稳定，未经历种群扩张、种群瓶颈与选择作用。谱系分析共识别出3个支持度较高的主要母系支系，每个支系又包含2个亚支系。这些分化支系与6个地理区域完全吻合。种群的遗传结构与分化程度与历史水系格局而非现代水系格局高度一致。多数支系与亚支系形成于上新世早期与更新世早期古流域盆地重组过程中的种群片段化事件。同域分布的支系仅出现于主要水系的交界区域，这大概率反映了先前异域分布种群的二次接触。伴随剧烈的气候波动，大规模的种群扩张极有可能发生在中更新世早期。