Data from: Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar)

Delaying sexual maturation can lead to larger body size and higher reproductive success, but carries an increased risk of death before reproducing. Classical life history theory predicts that trade-offs between reproductive success and survival should lead to the evolution of an optimal strategy in a given population. However, variation in mating strategies generally persists, and in general, there remains a poor understanding of genetic and physiological mechanisms underlying this variation. One extreme case of this is in the Atlantic salmon (Salmo salar), which can show variation in the age at which they return from their marine migration to spawn (i.e. their “sea age”). This results in large size differences between strategies, with direct implications for individual fitness. Here, we used an Illumina Infinium SNP-array to identify regions of the genome associated with variation in sea age in a large population of Atlantic salmon in Northern Europe, implementing individual-based genome-wide association studies (GWAS) and population-based FST outlier analyses. We identified several regions of the genome which vary in association with phenotype and/or selection between sea ages, with nearby genes having functions related to muscle development, metabolism, immune response and mate choice. In addition, we found that individuals of different sea ages belong to different, yet sympatric populations in this system, indicating that reproductive isolation may be driven by divergence between stable strategies. Overall, this study demonstrates how genome-wide methodologies can be integrated with samples collected from wild, structured populations to understand their ecology and evolution in a natural context.

延迟性成熟可带来更大的体型与更高的繁殖成功率，但同时会提升繁殖前死亡的风险。经典生活史理论预测，繁殖成功率与存活之间的权衡应会促使特定种群演化出最优策略。然而，交配策略的变异通常持续存在，且目前学界对这类变异背后的遗传与生理机制仍缺乏深入理解。这类现象的一个极端案例见于大西洋鲑（Salmo salar）：该物种在从海洋洄游至淡水产卵的年龄上存在显著变异，即所谓的"海龄"差异。此类差异会导致不同策略个体间出现巨大体型差异，直接影响个体适合度。本研究针对北欧的一个大型大西洋鲑种群，采用Illumina Infinium SNP阵列开展实验，通过基于个体的全基因组关联分析（Genome-Wide Association Study，简称GWAS）与基于种群的FST离群值分析，鉴定与海龄变异相关的基因组区域。我们鉴定出多个基因组区域，其与不同海龄个体间的表型差异和/或选择压力存在关联异质性，这些区域邻近的基因功能涉及肌肉发育、代谢调控、免疫应答以及配偶选择。此外，我们发现不同海龄的个体隶属于该系统中不同但同域分布的种群，这表明生殖隔离可能由稳定策略间的适应性分化所驱动。总体而言，本研究展示了如何将全基因组研究方法与野生结构化种群的采集样本相结合，从而在自然生态背景下解析种群的生态与演化机制。