Detecting Genotypic Changes Associated with Selective Mortality at Sea in Atlantic Salmon: Polygenic Multilocus Analysis Surpasses Genome Scan

Here, we genotyped 5568 SNPs in Atlantic salmon populations across two cohorts to test for differential allelic and genotypic frequencies between juveniles (smolts) migrating to sea and adults (grilses) returning to freshwater after one year at sea. Given the complexity of the traits potentially associated with sea mortality, we contrasted the outcomes of a single-locus F_ST based genome scan method with a new multi-locus framework to test for genetically-based differential mortality at sea. While numerous outliers were identified by the single-locus analysis, no evidence for parallel, temporally repeated selection was found. In contrast, the multi-locus approach detected repeated patterns of selection for a multi-locus group of 34 SNPs in one of the two populations. No significant pattern of selective mortality was detected in the other population, suggesting different causes of mortality among populations. Overall, these results support the hypothesis that selection mainly causes small changes in allele frequencies among many co-varying loci rather than a small number of changes in loci with large effects. Consequently, moving away from the “selective sweep paradigm” and towards a multi-locus genetics framework may be a more useful approach for studying the genomic signatures of natural selection on complex traits in wild populations.