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Fig. S1 Wild dog DLA-DRB1 alleles aligned to allele DLA-DRB1*90101.

Fig. S2 (a) Genetic structure of wild dog populations based on Bayesian clustering analyses (STRUCTURE) of samples at 10 microsatellite loci. Shown is the uppermost level of structuring (K=4) and finer scale population structuring (K=7) as indicated by the ΔK statistic (panel c). Columns are individuals, with the proportion of an individual’s genotype assigned to each cluster (K) denoted by different colours. Colours correspond with location map in Figure 5 and population three letter codes with Table 5. (b) Likelihood probability profile estimated from STRUCTURE 2.2 at K1-10 showing the mean and variance at each K. (c) ΔK at each value of K, averaged across 10 replicates.

Table S1 Details of the origin of the wild dog samples used in this study including the name, country and region of the monitoring area, the sampling years, the number of animals in the monitoring area, number of animals and packs sampled, and monitoring area three letter abbreviations.

Table S2 Details about the source of samples.

Table S3 Information on microsatellite primers used in this study isolated from the domestic dog (see Breen et al. 2001; Guyon et al. 2003; Neff et al. 1999).

Table S4 Sample sizes (n) and distribution of mtDNA haplotypes across wild dog populations.

Table S5 Original (as submitted by Girman et al. 2001), corrected and new mtDNA haplotype sequences detected in African wild dogs.

Table S6 Official DLA-DRB1 names alleles given in the paper.

Table S7 Results from hierarchical analysis of molecular variance (AMOVA) computed in Arlequin v 3.11 (Excoffier 2006).

Table S8 Pairwise bootstrapped Dest (Jost 2008) estimates of genetic differentiation between wild dog populations.

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