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Table S1 Voucher specimen numbers for each population. Acronyms are YU for College of Life Sciences, Yunnan University; SKLGRE for State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; SCUM for Sichuan University Museum.

Table S2 Pairwise FST values among the 71 populations of the Nanorana yunnanensis. Populations are numbered as in Table  1. Significant level set to P < 0.05 after 10 000 permutations. FST values are below diagonal, and P values are above diagonal, where ‘+’ indicates significance and ‘−’ P > 0.05.

Fig. S1 Reconstruction of drainage basin history due to river capture/reversals of major rivers in eastern Tibet (from Clark et  al. 2004). Colors represent individual drainage basins drawn on top of grayscale topography. (a) Interpreted pattern prior to the major captures, where the upper Yangtze, middle Yangtze, upper Mekong, upper Salween and the Tsangpo rivers drained together to the South China Sea through the paleo-Red River (blue). (b) Capture/reversal of the middle Yangtze River redirects drainage away from Red River and into the East China Sea through the lower Yangtze River (green). (c) Capture of the upper Yangtze River to the east into the lower Yangtze River, and the upper Mekong and upper Salween rivers obtain their modern drainage positions (green, yellow and orange, respectively). Capture of the Tsangpo River to the south through the Irrawaddy River (red). (d) Capture of the Tsangpo River through the Brahmaputra River into its modern course (pink). This final configuration is the modern drainage basin pattern.

Fig. S2 Mismatch distributions for each major haplotype lineage and some sublineages of Nanorana yunnanensis. The abscissa shows the number of pairwise differences between compared haplotypes. The ordinate shows the frequency for each value. The histograms represent the observed frequencies of pairwise divergences among haplotypes and the line refers to the expectation under the model of population expansion. (a–i): Mismatch distributions for the lineages and sublineages W, W1,W2, C, C1, C2, E, E1 and E2, respectively.

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