Data from: Population genomic analyses of early phase Atlantic salmon (Salmo salar) domestication/captive breeding.

• Main Authors: Mäkinen, Hannu, Vasemägi, Anti, McGinnity, Philip, Cross, Tom F., Primmer, Craig, Primmer, Craig R.
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2014
• Subjects: Captive Populations; Salmo salar; Aquaculture; Atlantic salmon
• Online Access: https://doi.org/10.5061/dryad.5p7s0

Domestication can have adverse genetic consequences, which may reduce the fitness of individuals once released back into the wild. Many wild Atlantic salmon (Salmo salar L.) populations are threatened by anthropogenic influences and they are supplemented with captively bred fish. The Atlantic salmon is also widely used in selective breeding programs to increase the mean trait values for desired phenotypic traits. We analyzed a genome-wide set of SNPs in three domesticated Atlantic salmon strains and their wild conspecifics to identify loci underlying domestication. The genetic differentiation between domesticated strains and wild populations was low (FST < 0.03), and domesticated strains harbored similar levels of genetic diversity compared to their wild conspecifics. Only a few loci showed footprints of selection, and these loci were located in different linkage groups among the different wild population/hatchery strain comparisons. Simulated scenarios indicated that differentiation in quantitative trait loci exceeded that in neutral markers during the early phases of divergence only when the difference in the phenotypic optimum between populations was large. This study indicates that detecting selection using standard approaches in the early phases of domestication might be challenging unless selection is strong and the traits under selection show simple inheritance patterns. Saint_John_Genotype_data File contains SNP genotypes for the River Saint John Atlantic salmon strain and their wild conspecifics. River Burrishoole Genotype_data File contains SNP genotype data for River Burrishoole Atlantic salmon strain and their wild conspecifics. Vindel Genotype_data File contains SNP genotype data for River Vindel/Ume Atlantic salmon strain and and their wild conspecifics.