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Table S1 Number and proportion of outlier SNPs detected potentially under divergent selection using hierarchical or pairwise genome scans and number of times outliers have been found potentially under divergent selection.

Fig. S1 LD (D') over all SNPs.

Fig. S2 Frequencies in freshwater and anadromous populations of the most frequent allele in freshwater for SNPs found under divergent selection between anadromous and freshwater populations.

Fig. S3 Frequencies in freshwater and anadromous populations of the most frequent allele in freshwater for SNPs repeatedly found under divergent selection between anadromous and freshwater populations.

Fig. S4 Sliding window analysis on LG8.

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