Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan

Wild populations of Atlantic salmon have declined worldwide. While the causes for this decline may be complex and numerous, increased mortality at sea is predicted to be one of the major contributing factors. Examining the potential changes occurring in the genome-wide composition of populations during this migration has the potential to tease apart some of the factors influencing marine mortality. Here, we genotyped 5568 SNPs in Atlantic salmon populations representing two distinct regional genetic groups and across two cohorts to test for differential allelic and genotypic frequencies between juveniles (smolts) migrating to sea and adults (grilses) returning to freshwater after one year at sea. Given the complexity of the traits potentially associated with sea mortality, we contrasted the outcomes of a single-locus FST based genome scan method with a new multi-locus framework to test for genetically-based differential mortality at sea. While numerous outliers were identified by the single-locus analysis, no evidence for parallel, temporally repeated selection was found. In contrast, the multi-locus approach detected repeated patterns of selection for a multi-locus group of 34 co-varying SNPs in one of the two populations. No significant pattern of selective mortality was detected in the other population, suggesting different causes of mortality among populations. These results first support the hypothesis that selection mainly causes small changes in allele frequencies among many co-varying loci rather than a small number of changes in loci with large effects. They also point out that moving away from the a strict “selective sweep paradigm” towards a multi-locus genetics framework may be a more useful approach for studying the genomic signatures of natural selection on complex traits in wild populations.

全球范围内的大西洋鲑野生种群数量均已出现下降。尽管种群衰退的成因复杂且多样，但海洋阶段死亡率上升被认为是主要驱动因素之一。解析种群洄游过程中全基因组组成的潜在变化，有助于厘清影响海洋阶段死亡率的部分因素。本研究对代表两个独立区域遗传类群、跨越两个同生群的大西洋鲑种群的5568个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）进行基因分型，以检测向海洋洄游的幼体（降海幼鲑smolts）与在海洋栖息一年后返回淡水的成体（一龄海归成鲑grilses）之间的等位基因频率与基因型频率差异。鉴于与海洋死亡率潜在相关的性状具有复杂性，我们对比了基于单基因座FST（固定指数，Fixation Index, FST）的全基因组扫描方法与全新的多基因座分析框架的结果，以检测海洋阶段基于遗传差异的死亡率差异。尽管单基因座分析鉴定出了多个异常位点，但未发现存在平行且在时间上重复的选择信号的证据。与之相反，多基因座分析方法在两个种群中的一个种群内，检测到了由34个共变异SNPs组成的基因座群的重复选择模式。另一个种群则未检测到显著的选择性死亡率模式，这表明不同种群的海洋死亡率成因存在差异。本研究结果首先支持这一假说：自然选择主要在众多共变异基因座中引发等位基因频率的微小变化，而非仅在少数效应显著的基因座中产生变异。同时，研究结果也表明，跳出严格的“选择性清除范式（selective sweep paradigm）”，采用多基因座遗传学框架，或许能更有效地研究野生种群复杂性状自然选择的基因组特征。