Data from: Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod (Gadus macrocephalus)

The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation-by-distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction-site associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the Eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation-by-distance signal along coastlines that mirrored previous microsatellite results, and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥ 84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coast samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation-by-distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low FST marine species.将种群作为管理单元进行辨识，是物种实现可持续开发利用的基本前提。若缺乏清晰的种群边界，不仅会阻碍空间管理单元的划定，还会给基于种群归属分析与混合种群分析的混捕渔业评估工作带来极大困扰。诸多海洋物种（如太平洋鳕鱼）均呈现距离隔离模式，即存在显著的遗传分化，却无清晰的种群边界。本研究采用限制性酶切位点关联DNA（restriction-site associated DNA, RAD）测序技术，对太平洋鳕鱼的种群结构展开探究，并评估其将个体遗传归属到推定起源种群的效能。研究样本采集于东太平洋的物种全域分布范围，覆盖从萨利什海至阿留申群岛的区域。研究共对276个个体进行测序，最终鉴定得到6425个推定的双等位基因单核苷酸多态性位点。研究发现，沿海岸线存在显著的距离隔离信号，这与此前基于微卫星标记的研究结果一致；同时，沿海样本与萨利什海内陆水域样本间存在显著遗传分化，且未发现这两个种群间存在杂交的证据。基于两种方法的个体遗传归属成功率整体较高（≥84%），但该成功率从南到北呈逐渐下降趋势。对个体起源地理区域的归属同样取得良好效果，捕获位点与归属位点间的平均距离为220千米。异常位点分析显示，沿海岸线群体中潜在受选择的位点数量多于萨利什海群体与沿海群体间的位点数量，这表明相较于近岸与远岸环境差异，纬度梯度环境因子带来的适应性选择更为多样。本研究结果不仅验证了此前关于萨利什海种群存在显著遗传分化以及沿海岸线存在距离隔离的观测结论，同时也证明，即便在低遗传分化系数（FST）的海洋物种中，借助现代基因组技术也可为种群边界划定与渔业管理提供科学支撑。