Data from: Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence-related genes.

Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study we used a dense SNP array to identify candidate loci potentially underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene–environment association, and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at sub-drainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis, and immune defence. These included the large-effect age-at-maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations, and that is also a candidate for local selection over the global range of Atlantic salmon. This region co-localized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and co-varies with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.

阐明局域环境适应的遗传基础，可深化我们对生命多样性演化规律的理解。本研究采用高密度单核苷酸多态性阵列（SNP array），对一个大型大西洋鲑（Salmo salar）种群内的精细尺度局域适应相关候选基因座进行筛选。通过整合异常值分析、基因-环境关联分析与单倍型纯合性分析，我们鉴定出多个带有强烈歧化选择信号的基因组区域。其中部分候选区域已在既往研究中被报道，这表明相同的基因座在子流域、区域乃至大陆尺度的大西洋鲑种群中均具有适应重要性。尤为值得关注的是，我们在与性成熟调控、能量稳态及免疫防御相关的基因侧翼区域，检测到了与局域选择相符的选择信号，其中包括效应显著的成熟年龄调控基因vgll3、已被证实的肥胖基因mc4r，以及主要组织相容性复合体II（MHC II）。最引人注目的是，我们证实大西洋鲑染色体Ssa09上存在一个在亚种群间分化程度极高的基因组区域，该区域在大西洋鲑的全球分布范围内也被列为局域选择的候选靶点。该区域与红大马哈鱼（Oncorhynchus nerka）中与产卵生态型强相关的单倍型存在共定位现象，且有间接证据表明，二者的选择靶点可能均为six6基因。尽管该区域的等位变异与上游集水区面积相关，且与产卵洄游返场时序存在共变关系，但其在大西洋鲑中的表型效应仍不明确。本研究结果可为大西洋鲑的种群管理提供新的参考依据，并为后续研究开辟了多个方向。