Data from: Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon

Studies of the oceanic and near-shore distributions of Pacific salmon, whose migrations typically span thousands of kilometers, have become increasingly valuable in the presence of climate change, increasing hatchery production, and potentially high rates of bycatch in offshore fisheries. Genetics data offer considerable insights into both the migratory routes as well as the evolutionary histories of the species. However, these types of studies require extensive datasets from spawning populations originating from across the species? range. Single nucleotide polymorphisms (SNPs) have been particularly amenable for multi-national applications because they are easily shared, require little inter-laboratory standardization, and can be assayed through increasingly efficient technologies. Here we discuss the development of a dataset for 114 populations of chum salmon through a collaboration among North American and Asian researchers, termed PacSNP. PacSNP is focused on developing the database and applying it to problems of international interest. A dataset spanning the entire range of species provides a unique opportunity to examine patterns of variability, and we review issues associated with SNP development. We found evidence of ascertainment bias within the dataset, variable linkage relationships between SNPs associated with ancestral groupings, and outlier loci with alleles associated with latitude.针对迁徙跨度通常可达数千公里的太平洋鲑（Pacific salmon）的海洋及近岸分布研究，在气候变化、孵化场养殖规模持续扩大以及近海渔业副渔获率潜在偏高的背景下，其研究价值日益凸显。遗传学数据能够为该物种的洄游路径与演化历史提供重要见解。然而此类研究需要获取覆盖该物种整个分布范围内产卵种群的大规模数据集。单核苷酸多态性（Single Nucleotide Polymorphism, SNP）尤其适用于跨国研究场景，因其易于共享、实验室间标准化需求极低，且可通过日益高效的技术完成分型检测。本文基于北美与亚洲研究者的合作，构建了覆盖114个狗鲑（chum salmon）种群的数据集，命名为PacSNP。该项目致力于完善该数据库，并将其应用于具有国际关注度的科研问题。覆盖该物种全分布范围的数据集为解析遗传变异模式提供了独特契机，本文同时综述了SNP开发过程中的相关技术问题。本研究在该数据集中发现了检出偏倚（ascertainment bias）：与祖先类群相关的SNPs间存在可变连锁关系，同时存在携带与纬度相关等位基因的离群位点。