Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees

Many wild Atlantic salmon (Salmo salar) populations are threatened by introgressive hybridization from domesticated fish that have escaped from aquaculture facilities. A detailed understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes, however markers currently available to discriminate the two types of parental genome have limited power to do this. Using a high-density Atlantic salmon SNP array in combination with pooled-sample allelotyping and an Fst outlier approach, we identified 200 SNPs that differentiated an important Atlantic salmon stock from the escapees potentially hybridizing with it. By simulating multiple generations of wild-escapee hybridization involving wild populations in two major phylogeographic lineages, and a genetically diverse set of escapees, we showed that both the complete set of SNPs and smaller sub-sets could reliably assign individuals to different hybrid classes up to the third hybrid (F3) generation. This set of markers will be a useful tool for investigating the genetic interactions between native wild fish and aquaculture escapes in many Atlantic salmon populations.许多野生大西洋鲑（Salmo salar）种群正受到水产养殖设施逃逸的驯化鱼类引发的渐渗杂交的威胁。要深入解析野生鲑与水产逃逸个体间的杂交动态，需对不同杂交类群进行精准区分，但当前可用于区分两类亲本基因组的遗传标记，其分辨能力较为有限。本研究结合高密度大西洋鲑单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片、混合样本等位基因分型技术与F_ST异常值检测方法，鉴定出200个可有效区分某一重要大西洋鲑野生种群与其潜在杂交对象——水产逃逸个体的SNP位点。通过模拟涉及两大主要系统地理谱系野生种群以及遗传多样性丰富的逃逸群体的多代野生-逃逸个体杂交过程，本研究证实，无论是全套SNP位点还是较小的位点子集，均可可靠地将个体归类至不同杂交类群，直至第三代杂交（F3）世代。这套标记将成为研究众多大西洋鲑种群中原生野生鱼类与水产逃逸个体间遗传互作的实用工具。