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 single nucleotide polymorphisms (SNPs) and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and the processes shaping them. We found evidence of high (mean F _ST = 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 (1–3 Mbp ) on four chromosomes (Ssa06, Ssa13, Ssa16 and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium, despite no significant 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.

中文翻译：

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欧洲和北美大西洋鲑（Salmo salar）之间的基因组分化的不同和链接的选择形状模式。

随着种群的分化，许多过程可以塑造分化的基因组模式。高分化区域可能是由于对选定基因座的差异选择，附近基因座的遗传搭接或针对有害等位基因的反复选择（链接的背景选择）而产生的；然后可以在重组减少的区域进一步提高这种差异。大西洋鲑（Salmo salar）在欧洲和北美洲> 600,000年前就存在分歧，尽管有一些二级接触的证据，但大多数遗传数据表明血统之间存在实质性分歧。这种与潜在基因流的深度分歧为研究早期物种形成过程中影响基因组格局的不同机制的作用提供了机会。在这里，我们使用184,295个单核苷酸多态性（SNP）和80个种群，研究了横跨大西洋的分化的基因组格局，重点关注高度分化的区域及其形成过程。我们发现了高（平均F _ST = 0.26）和各大洲之间的异质基因组分化。与高跨大西洋分化相关的基因组区域的大小从重要基因内的单个基因座（SNP）到大区域（1-3 Mbp）不等 ）在四个染色体上（Ssa06，Ssa13，Ssa16和Ssa19）。这些区域显示出与选择一致的特征，包括高连锁不平衡，尽管重组没有显着减少。与分化区域相关的过程的基因和功能富集可能突出了海洋航行和寄生虫抵抗力的大陆差异。我们的结果提供了对各大洲之间潜在差异的潜在机制的洞察力，以及接近固定的和潜在的适应性跨大西洋差异以及高全基因组分化背景的证据支持了大西洋鲑亚种的命名。