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Fig. S1 Plot of genetic vs. geographical distance for pairwise population comparisons using Slatkin’s linearized ΦST to calculate genetic distance on population sizes > 2.

Fig. S2 Mismatch distribution of Rhinolophus ferrumequinum for different geographical groupings (a) east China (b) Japan (c) west Asia and (d) Europe. Solid black lines indicate the observed frequency of pairwise distributions, dashed black lines indicate the expected Poisson distribution under a model of population expansion and the solid grey lines indicate the upper and lower confidence intervals for the expected. Russia is not shown as it has too few pairwise differences.

Fig. S3 Estimated population structure. Each individual is represented by a vertical line which is partitioned into K coloured segments, the length of each colour being proportional to the estimated membership coefficient (Q). Black lines separate individuals of different populations as indicated by the labels at the bottom of the figure. Labels above the figure indicate the regional affiliation of each population.

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