Population genomics reveals repeated signals of adaptive divergence in the Atlantic salmon of northeastern Europe

Our ability to examine genetic variation across entire genomes have
enabled many studies searching for the genetic basis of local adaptation.
These studies have identified numerous loci as candidates for differential
local selection, however relatively few have examined the overlap among
candidate loci identified from independent studies of the same species in
different geographic areas or evolutionary lineages. We used an
allelotyping approach with a 220K SNP array to characterize the population
genetic structure of Atlantic salmon in northeastern Europe and ask
whether the same genomic segments emerged as outliers among populations in
different geographic regions. Genome-wide data recapitulated the
phylogeographic structure previously inferred from mtDNA and
microsatellite markers. Independent analyses of three genetically and
geographically distinct groups of populations repeatedly inferred the same
17 haploblocks to contain loci under differential local selection. The
most strongly supported of these replicated haploblocks had known strong
associations with life history variation or immune response in Atlantic
salmon. Our results are consistent with these genomic segments harbouring
large-effect loci which have a major role in Atlantic salmon
diversification and are ideal targets for validation studies.