Table S1 Information of red panda samples used in this study

Table S2 Information of nine microsatellite loci used in this study, including label type, allele size and number of alleles (A) found in each locus

Table S3 Variable nucleotide sites of mtDNA control region haplotypes in this study. Dots (.) indicate identical nucleotides

Table S4 Distribution of mtDNA control region haplotypes among five red panda populations

Table S5 Medians of current (N0) and ancestral effective population sizes (N1) and time since population decline (T) for the QL, XXL and GLG populations based on a generation time of 2 or 6 years, using Bayesian MSVAR simulations

Fig. S1 Comparison of allelic richness (the number of alleles) among four populations of red pandas. Allelic richness was estimated from nine-locus combined genotypes and extrapolated beyond the sample sizes using ARES.

Fig. S2 Unrooted maximum-likelihood (ML) tree based on HKY distances among mtDNA CR haplotypes of red pandas. Bootstrap values are given next to nodes based on 1000 bootstrap simulations.

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