Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this paper, we describe the development of a medium density Atlantic salmon SNP-array based on Expressed Sequence Tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP-array for conservation, management and aquaculture.

Genotypes_Dryad6176 SNP genotypes for 1295 samples used in submitted analysis (all but Foyle River population). For access to genotypes from Foyle River samples, please contact Dr. Dennis Ensing at Agri-Food & Biosciences Institute, Fisheries & Aquatic Ecosystems Branch . See paper for information on genotyping and SNP discovery.Baltic_Cfit_InputInput file for Cfit software. Includes populations geographic distances along the Baltic-Atlantic continuum (see paper) and allele counts for each populations.Barents_Cfit_InputInput file for Cfit software. Includes geographic distances for populations along the Barents-Atlantic continuum (see paper) as well as allele counts for each populations.