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.

针对迁徙距离通常可达数千公里的太平洋鲑鱼海洋及近岸分布的研究，在气候变化、孵化场繁育规模扩大以及近海渔业副渔获率可能居高不下的背景下，其科研价值日益凸显。遗传学数据可为该物种的洄游路径与演化历史提供重要见解。然而，此类研究需要覆盖该物种整个分布范围内所有产卵种群的大规模数据集。单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs）尤其适用于跨国研究应用，因其易于共享、仅需极低程度的实验室间标准化流程，且可通过日益高效的技术手段完成分型检测。本文通过北美与亚洲研究者的合作，阐述了针对114个狗鲑种群构建数据集的过程，该数据集被命名为PacSNP。PacSNP项目致力于搭建该数据库，并将其应用于具有全球关注度的科学问题。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，同时本文还梳理了单核苷酸多态性开发过程中涉及的相关问题。本研究在该数据集中发现了ascertainment偏倚（ascertainment bias），与祖先类群相关的单核苷酸多态性之间存在可变的连锁关系，同时还发现了携带与纬度相关等位基因的异常位点。