Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees

Many wild Atlantic salmon (Salmo salar) populations are threatened by
introgressive hybridization from domesticated fish that have escaped from
aquaculture facilities. A detailed understanding of the hybridization
dynamics between wild salmon and aquaculture escapees requires
discrimination of different hybrid classes, however markers currently
available to discriminate the two types of parental genome have limited
power to do this. Using a high-density Atlantic salmon SNP array in
combination with pooled-sample allelotyping and an Fst outlier approach,
we identified 200 SNPs that differentiated an important Atlantic salmon
stock from the escapees potentially hybridizing with it. By simulating
multiple generations of wild-escapee hybridization involving wild
populations in two major phylogeographic lineages, and a genetically
diverse set of escapees, we showed that both the complete set of SNPs and
smaller sub-sets could reliably assign individuals to different hybrid
classes up to the third hybrid (F3) generation. This set of markers will
be a useful tool for investigating the genetic interactions between native
wild fish and aquaculture escapes in many Atlantic salmon populations.