Data from: Evolution of sex determination loci in Atlantic salmon

Teleost fish exhibit a remarkable diversity in the control of sex determination, offering the opportunity to identify novel differentiation mechanisms and their ecological consequences. Here, we perform GWAS using 4715 fish and 46,501 SNP to map sex determination to three separate genomic locations in Atlantic salmon (Salmo salar). To characterize each, whole genome sequencing was performed to 30-fold depth of coverage using 20 fish representing each of three identified sex lineages. SNP polymorphism reveals male fish carry a single copy of the male specific region, consistent with an XX/XY or male heterogametric sex system. Haplotype analysis revealed deep divergence between the putatively ancestral locus on chromosome 2, compared with loci on chromosomes 3 and 6. Haplotypes in fish carrying either the chromosome 3 or 6 loci were nearly indistinguishable, indicating a founding event that occurred following the speciation event that defines defined Salmo salar from other salmonids. These findings highlight the evolutionarily fluid state of sex determination systems in salmonids, and resolve to the sequence level differences in animals with divergent sex lineages.

硬骨鱼类（Teleost fish）在性别决定调控机制上展现出极高的多样性，为探究全新的性别分化机制及其生态效应提供了绝佳契机。本研究针对大西洋鲑（*Salmo salar*）开展全基因组关联分析（Genome-Wide Association Study, GWAS），共纳入4715尾个体与46501个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，将性别决定位点定位至三个独立的基因组区域。为解析每个性别决定区域的特征，研究针对三个已鉴定的性别谱系各选取20尾个体进行全基因组测序，测序深度达30倍覆盖度。单核苷酸多态性分析显示，雄性个体仅携带一份雄性特异性区域，这与XX/XY型或雄性异配性别决定系统的特征相符。单倍型分析结果表明，2号染色体上的推定祖先位点与3号、6号染色体上的位点之间存在显著分化。携带3号或6号染色体性别位点的个体，其单倍型几乎无法区分，这说明该性别位点的起源事件发生在大西洋鲑从其他鲑科鱼类物种分化形成之后。本研究结果凸显了鲑科鱼类性别决定系统在演化层面的高度动态性，并明确了不同性别谱系个体间的序列水平差异。