Successful re-introduction of captively-bred Atlantic salmon (Salmo salar) populations to their historical natal river systems may be difficult until patterns of local genetic adaptation by the parr stage are better understood. Divergence in parr size, shape, pigmentation, and SNP allele frequencies was compared for five endangered salmon populations from the Bay of Fundy. Differences among populations in body weight at age, morphometrics, and parr mark pigmentation persisted in a common hatchery environment. Twelve out of 207 mapped SNPs were identified as outliers under diversifying selection by Arlequin 3.5’s hierarchical island neutrality test and one of these was also identified by Bayescan 2. FST, the molecular divergence for the 12 outlier SNPs was comparable to PST, the phenotypic divergence, but FST for the remaining195 “neutral” SNPs was significantly smaller. One SNP in a trypsin inhibitor showed a strong phylogenetic signal between inner and outer Bay of Fundy that was correlated with the slower growth rates, deeper bodies, and longer pectoral fins of parr from inner Bay rivers. Mantel tests for seven populations showed a significant correlation between the matrix of pairwise FST values for the non-outlier “neutral” SNPs only for the matrix of body weights at age. Thus with the exception of body weight, pairwise distances among these complex traits were not correlated with molecular genetic distance estimated from neutral SNP markers. However, the matrix of parr mark numbers was inversely correlated with the matrix of parr mark contrast values and may therefore represent convergent local genetic adaptation.
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