Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar) ...

• Main Authors: Lehnert, Sarah, Kess, Tony, Bentzen, Paul, Clément, Marie, Bradbury, Ian
• Format: Dataset
• Language: English
• Published: Dryad 2020
• Subjects: Salmo salar; SNP array; Canada; Norway; Atlantic salmon; North Atlantic
• Online Access: https://dx.doi.org/10.5061/dryad.hdr7sqvfc; https://datadryad.org/stash/dataset/doi:10.5061/dryad.hdr7sqvfc

As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 SNPs and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and processes shaping them. We found evidence of high (mean FST=0.26) ... : Genotypes for Canadian populations are uploaded here. Genotypes for European populations were uploaded previously by Barson et al., (2015) (https://datadryad.org/stash/dataset/doi:10.5061/dryad.23h4q) Overall methods for genotyping: Genotypes from Atlantic salmon were compiled from previous studies (Barson et al., 2015; Lehnert et al., 2019; Sylvester, Beiko, et al., 2018; Sylvester, Bentzen, et al., 2018) and cover a total of 80 populations spanning the North Atlantic Ocean. Samples cover a total of 26 populations in Canada (n=546 individuals) and 54 populations in Norway (n=913 individuals). Genotypes were generated using a species specific 220,000 targeted, bi-allelic SNP Affymetrix Axiom array designed by the Centre for Integrative Genetics (CIGENE, Ås, Norway). These SNPs were a subset of those in the 930K XHD Ssal array (dbSNP accession numbers ss1867919552–ss1868858426) designed using Norwegian aquaculture salmon. Genotyping was performed according to the Affymetrix axiom array protocol (Thermofisher ...