DOI: 10.5061/dryad.hdr7sqvfc
title: Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)

description: 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 &gt;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.
description: 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 <i>Ssa</i>l 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. 
description: File format is genepop. Missing data are coded as 000000, and
 alleles are coded as 001 and 002.