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Fig. S1 Probability of contemporary population samples of Oncorhynchus nerka representing 1–17 clusters determined from 12 replicate analyses using STRUCTURE 2.2 (Pritchard et  al. 2000; Falush et  al. 2003) and the associated ΔK statistic, which measures the steepness of increase of P(D) and indicates the most likely number of clusters (Evanno et  al. 2005).

Fig. S2 STRUCTURE results for the individual genotype analysis of the 17 contemporary Oncorhynchus nerka samples assuming six different clusters of individuals (= 6) using an admixture model and no prior population information.

Fig. S3 Probability of mixed historical sample of 603 sockeye salmon from 1924 representing 1–12 clusters determined from 20 replicate analyses using STRUCTURE 2.2 (Pritchard et  al. 2000; Falush et  al. 2003) and the associated ΔK statistic, which measures the steepness of increase of P(D) and indicates the most likely number of clusters (Evanno et  al. 2005).

Fig. S4 Probability of Group A (as identified in initial STRUCTURE run) representing 1–12 clusters determined from 20 replicate analyses using STRUCTURE 2.2 (Pritchard et  al. 2000; Falush et  al. 2003) and the associated ΔK statistic, which measures the steepness of increase of P(D) and indicates the most likely number of clusters (Evanno et  al. 2005).

Fig. S5 Probability of Group B (as identified in initial STRUCTURE run) representing 1–12 clusters determined from 20 replicate analyses using STRUCTURE 2.2 (Pritchard et  al. 2000; Falush et  al. 2003) and the associated ΔK statistic, which measures the steepness of increase of P(D) and indicates the most likely number of clusters (Evanno et  al. 2005).

Fig. S6 Probability of Group C (as identified in initial STRUCTURE run) representing 1–12 clusters determined from 20 replicate analyses using STRUCTURE 2.2 (Pritchard et  al. 2000; Falush et  al. 2003) and the associated ΔK statistic, which measures the steepness of increase of P(D) and indicates the most likely number of clusters (Evanno et  al. 2005).

Fig. S7 STRUCTURE results for the individual genotype analysis of contemporary Oncorhynchus nerka samples (N = 1103) combined with scale samples from 1924 (Groups A, B1, B2, and C; N = 603) assuming seven different clusters of individuals (= 7) using an admixture model and no prior population information.

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