Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland, Canada.
Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada.
Mol Ecol. 2019 Apr;28(8):2074-2087. doi: 10.1111/mec.15065. Epub 2019 Apr 29.
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 years before present, with the two lineages isolated in different southern refugia during glacial maxima, driving trans-Atlantic genomic and karyotypic divergence. Here, we investigate the genomic consequences of glacial isolation and trans-Atlantic secondary contact using 108,870 single nucleotide polymorphisms genotyped in 80 North American and European populations. Throughout North America, we identified extensive interindividual 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 with low European ancestry genome-wide (3%). Ssa08/Ssa29 showed greater intrapopulation diversity, suggesting a derived chromosome fusion polymorphism that evolved 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.
更新世冰期驱动了大西洋鲑（Salmo salar）的多次范围收缩和扩张，塑造了其当代种内多样性。大西洋鲑在大西洋西部和东部的两个谱系在距今 60 多万年前就已经分化，在冰期最大值期间，这两个谱系在不同的南部避难所中隔离，导致了跨大西洋的基因组和染色体组的分化。在这里，我们利用在 80 个北美和欧洲群体中测定的 108870 个单核苷酸多态性，研究了冰川隔离和跨大西洋二次接触的基因组后果。在整个北美，我们发现了广泛的个体间变异和离散的连锁块，这些连锁块在染色体之间和内部都存在已知的跨大西洋差异：Ssa01/Ssa23 易位和 Ssa08/Ssa29 融合。空间遗传分析表明，这些重排是相互独立的，Ssa01/Ssa23 在北部群体中具有较高的欧洲渗入率（>50%），表明存在冰期后的跨大西洋二次接触，而在全基因组范围内欧洲血统较低（3%）。Ssa08/Ssa29 表现出更高的种群内多样性，这表明在北美的一个衍生的染色体融合多态性。对这两个基因组区域的潜在选择证据表明，重排的适应性作用值得进一步研究。我们的研究强调了更新世冰期如何影响北方物种基因组结构的大规模种内变异。
