Table S1. Confusion matrix showing genotype call accuracy for quality cutoffs used to generate the two datasets.

Table S2. Demographic parameters inferred from each of the five beach mouse subspecies, using a second mainland population (FL-2) as the ancestral population.

Figure S1. ROC curves of the four genotype quality metrics (quality-by-depth, QD; site quality, QUAL; mapped read depth, DP; and genotype quality, GQ).

Figure S2. Results of Structure analysis performed using genome-wide SNP data (N = 2236 SNPs).

Figure S3. Genetic variation in a 5-kb region including Mc1r and surrounding regions in SRIBM (fixed for the derived mutation in Mc1r) and a mainland population.

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