Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

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.