Data from: Population genomic analyses of early phase Atlantic salmon (Salmo salar) domestication/captive breeding.

Domestication can have adverse genetic consequences, which may reduce the fitness of individuals once released back into the wild. Many wild Atlantic salmon (Salmo salar L.) populations are threatened by anthropogenic influences and they are supplemented with captively bred fish. The Atlantic salmon is also widely used in selective breeding programs to increase the mean trait values for desired phenotypic traits. We analyzed a genome-wide set of SNPs in three domesticated Atlantic salmon strains and their wild conspecifics to identify loci underlying domestication. The genetic differentiation between domesticated strains and wild populations was low (FST < 0.03), and domesticated strains harbored similar levels of genetic diversity compared to their wild conspecifics. Only a few loci showed footprints of selection, and these loci were located in different linkage groups among the different wild population/hatchery strain comparisons. Simulated scenarios indicated that differentiation in quantitative trait loci exceeded that in neutral markers during the early phases of divergence only when the difference in the phenotypic optimum between populations was large. This study indicates that detecting selection using standard approaches in the early phases of domestication might be challenging unless selection is strong and the traits under selection show simple inheritance patterns.

驯化过程可产生不利的遗传后果，驯化个体一旦被放归野外，其适合度可能会下降。许多野生大西洋鲑（Atlantic salmon, *Salmo salar* L.）种群正受到人为活动的威胁，且通过人工繁育鱼类进行种群补充。大西洋鲑同时也被广泛应用于选择性育种项目，以提升目标表型性状的平均表型值。本研究对3个驯化大西洋鲑品系及其野生同种个体的全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点集进行分析，以鉴定与驯化过程相关的遗传位点。结果显示，驯化品系与野生种群间的遗传分化程度较低（固定指数Fixation Index, F_ST < 0.03），且驯化品系的遗传多样性水平与野生同种个体相当。仅有少量位点呈现选择印迹，且在不同野生种群/孵化场品系的对比中，这些位点分布于不同的连锁群。模拟实验结果表明，仅当种群间的表型最优值差异较大时，分化早期数量性状位点（Quantitative Trait Locus, QTL）的遗传分化程度才会超过中性标记的分化水平。本研究显示，若选择强度不高且目标性状的遗传模式较为复杂，采用常规方法在驯化早期检测选择信号可能极具挑战性。