Data from: Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon

Pleistocene glaciations drove repeated range contractions and expansions
shaping contemporary intraspecific diversity. Atlantic salmon (Salmo
salar) in the western and eastern Atlantic diverged >600,000 YBP,
with the two lineages isolated in different southern refugia during
glacial maxima, driving trans-Atlantic genomic and karyotypic divergence.
Here, we investigate genomic consequences of glacial isolation and
trans-Atlantic secondary contact using 108,870 single nucleotide
polymorphisms (SNPs) genotyped in 80 North American and European
populations. Throughout North America, we identified extensive
inter-individual variation and discrete linkage blocks within and between
chromosomes with known trans-Atlantic differences in rearrangements:
Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses
suggest independence of rearrangements, with Ssa01/Ssa23 showing high
European introgression (>50%) in northern populations indicative of
post-glacial trans-Atlantic secondary contact, contrasting low European
ancestry genome-wide (3%). Ssa08/Ssa29 showed greater intra-population
diversity suggesting a derived chromosome fusion polymorphism within North
America. Evidence of potential selection on both genomic regions suggests
that the adaptive role of rearrangements warrants further investigation in
Atlantic salmon. Our study highlights how Pleistocene glaciations can
influence large-scale intraspecific variation in genomic architecture of
northern species.