Figure S1. Schematic representation of the relative position of the primers used to amplify the complete cytochrome b. The primer sequences are listed in Table 2.

Figure S2. Maximum likelihood (ML) tree of 57 haplotypes generated in PhyML, with corresponding support from 1000 bootstrap replicates in ML and posterior probabilities in MrBayes (ML/Bayesian) of each major clade and lineage. Colours correspond to lineages (see Figs 1–3), with newly identified haplotypes in this study indicated by coloured text. Certain inner groups with strong support are highlighted with coloured text corresponding to their lineage assignment.

Table S1. Genetic variation overall and within the identified clades and lineages. Number of individuals (n) and number of haplotypes (H). Nucleotide (π) and haplotype (h) diversities and associated standard deviations. Sum of square deviations (SSDs), Fu's (1997) FS and Tajima's (1989) D, with significance determined from 10 000 coalescent simulations (*P < 0.05; **P < 0.01; ***P < 0.001, respectively). Estimates of τ with 95% confidence intervals (95% CIs) with corresponding estimates of time since expansion (TSE) for lineages corresponding to all neutrality tests (see Material and methods), using the mutation rate derived from Mustela erminea.

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