Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan

Wild populations of Atlantic salmon have declined worldwide. While the
causes for this decline may be complex and numerous, increased mortality
at sea is predicted to be one of the major contributing factors. Examining
the potential changes occurring in the genome-wide composition of
populations during this migration has the potential to tease apart some of
the factors influencing marine mortality. Here, we genotyped 5568 SNPs in
Atlantic salmon populations representing two distinct regional genetic
groups and 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 FST 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 co-varying
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. These results first 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. They also point out that moving away
from the a strict “selective sweep paradigm” 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.