Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of the evolutionary mechanisms impending or favouring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (Mallotus villosus ). We first assembled a 490‐Mbp draft genome of M. villosus to map our RAD sequence reads. Then, we used a large data set of genome‐wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they probably diverged from 3.8 to 1.8 million years ago and experienced secondary contacts. Within each lineage, our analyses provided evidence for large N_e and high gene flow among spawning sites. Within the Northwest Atlantic lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype–environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that both shared polymorphisms among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.

中文翻译：

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共同的祖先多态性和染色体重排是海洋鱼类局部适应的潜在驱动力。

基因流通过影响从头突变的命运，维持遗传遗传变异并推动适应性渗入，对于局部适应具有极其重要的意义。此外，尽管基因流量很高，但作为染色体重排的结构变异仍可促进适应。但是，我们对在存在基因流的情况下促进或促进局部适应的进化机制的理解仍然仅限于有限数量的研究系统。在这项研究中，我们检查了人口历史，共同的祖先多态性以及冰川世系之间的基因流如何促进海鱼毛鳞鱼（Mallotus villosus）对海况的局部适应。我们首先组装的490-MBP基因组草图M. villosus来映射我们的RAD序列读数。然后，我们使用了从西北大西洋31个产卵场收集的1,310个个体中进行基因分型的大型基因组范围内的单核苷酸多态性（25,904个过滤SNP）。我们重建了三个冰川世系之间的分歧历史，表明它们可能从3.8年前分裂到了180万年前，并且经历了二次接触。在每个血统中，我们的分析都为较大的N _e提供了证据 和产卵位点之间的高基因流。在西北大西洋沿袭中，我们检测到多态性染色体重排，导致三个单倍群的出现。基因型与环境的联系揭示了产卵区普遍适应环境条件的分子特征。我们的研究还表明，由于存在的遗传变异或基因渗入，谱系之间共有多态性，并且染色体重排可能在存在高基因流的情况下有助于局部适应。