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Fig S1. Assignment of samples to populations using STRUCTURE with K = 9. Sample colors indicate assignment to nine population clusters; individuals that did not assign to any population with > 50% probability are shown in grey. Fig. S2. NMDS ordination of all 540 puma genotypes. Symbols indicate samples from northern region, southern region, and a transitional zone (AZ north of I-40 and the Manzano Mountains in NM), where samples did not consistently assign to northern or southern clusters using STRUCTURE or ordinations. Table. S1. Pairwise FST (upper diagonal) and DLR values between 34 sample groups. Underlined FST values were significant before Bonferroni correction (P < 0.05), and bold values remained significant after correction.

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