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Fig. S1 Three example patterns produced by Geneland with K = 3 (classes 1–3), illustrating the instability of the result.

Appendix S1 Genetic structure estimated by the Bayesian clustering software, TESS and Geneland

Appendix S2 Frequencies of non-private haplotypes for the 11 colonies of Rhinoluphus cornutus pumilus on Okinawa-jima and Kume-jima

Appendix S3 The results of pairwise exact tests for haplotype frequencies of Rhinolophus cornutus pumilus among colonies on Okinawa-jima and Kume-jima. To control for multiple comparisons, significant P-values were adjusted for using the false discovery rate procedure

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