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Figure S1 Boxplots depicting the distribution of major allele frequencies for each population (MID). The number of SNPs per population with 5× coverage are given above each boxplot. Major allele frequencies were estimated by maximum likelihood while accounting for sequence errors.

Figure S2 Posterior probability distributions for locus-specific ϕST for 125 loci with more ≥ 25 haplotypes (A) and six loci with ≥ 90 haplotypes. Posterior probability distributions were estimated from 24,000 MCMC iterations and were smoothed using a Gaussian kernel density function. These loci posses levels of variation that are similar to levels of variation for loci generally used in population genetic analyses.

Figure S3 Scree plot (A) and Shepard plot (B) from NMDS analysis. The former shows the relationship between the number of dimensions used for NMDS and the sum of squared differences between the ordination-based distances and the distances predicted by regression (stress). The latter depicts the relationship between genome-level pair-wise ϕST and ordination-based distances (points) as well as the predicted values from regressing the latter on the former (solid line). These plots suggest that the three dimensions used for NMDS captured the structure of the pair-wise ϕST well.

Figure S4 Boxplots depicting the distribution of major allele frequencies for simulated data. Dashed blue lines denote the major allele frequency used for each set of simulations.

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