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) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16, and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium despite no local reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.

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 Scientific, USA), and raw data was processed using Axiom Analysis Suite (AAS) software (version 2.0.0.35) following the manufacturers best-practices workflow. AAS assigns all SNP assays to one of six categories based on data clustering, and for each dataset, only genotypes from those SNPs classified as PolyHighResolution (PHR), NoMinorHomo (NMH), and MonoHighResolution (MHR) were used in the subsequent analysis (n=185,074 SNPs across all datasets). SNPs were further filtered for a minor allele frequency (MAF) cutoff of 0.01 across all sites resulting in a genomic dataset with 184,295 SNPs. 

File format is genepop. Missing data are coded as 000000, and alleles are coded as 001 and 002.