Fig. S1. Individual Admixture Proportions and 90% Confidence Intervalsbased on 17 Microsatellite

Fig. S1. Individual admixture proportions and 90% confidence intervalsbased on 17 microsatellite loci for each of four wild populationsintrogressedby(a)Nevaand (b)Narvahatchery stocks. The y-axis depicts the proportion of the genomefrom hatchery stock.

Fig. S2. The effect of the level of genetic divergence on the accuracy of identification of hybrid categories: pure (green squares), F1 (red triangles), F2 (gray diamonds), F1×hatchery (orange circles) and F1×wild (blue crosses) backcross.The trends for each hybrid categoryare presentedas logarithmic trend lines of the same colors.

Fig. S3. Estimated size of genomic regions (in cM) showing (a) elevated and (b) reduced introgression in four studied salmon populations.

Fig. S4. Genomic regions showing elevated and reduced introgression from two hatchery stocks (Neva and Narva) to wildVasalemma, Keila and Loobu populations. P-values for each SNP (−log10transformed)were plotted against their respective positions on the autosomal chromosomes.

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