Data from: Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current Large Marine Ecosystem

Chinook Salmon is an economically and ecologically important species, and populations from the west coast of North America are a major component of fisheries in the North Pacific Ocean. The anadromous life history strategy of this species generates populations (or stocks) that typically are differentiated from neighboring populations. In many cases, it is desirable to discern the stock of origin of an individual fish or the stock composition of a mixed sample to monitor the stock-specific effects of anthropogenic impacts and alter management strategies accordingly. Genetic stock identification (GSI) provides such discrimination, and we describe here a novel GSI baseline composed of genotypes from more than 8000 individual fish from 69 distinct populations at 96 single nucleotide polymorphism (SNP) loci. The populations included in this baseline represent the likely sources for more than 99% of the salmon encountered in ocean fisheries of California and Oregon. This new genetic baseline permits GSI with the use of rapid and cost-effective SNP genotyping, and power analyses indicate that it provides very accurate identification of important stocks of Chinook Salmon. In an ocean fishery sample, GSI assignments of more than 1000 fish, with our baseline, were highly concordant (98.95%) at the reporting unit level with information from the physical tags recovered from the same fish. This SNP baseline represents an important advance in the technologies available to managers and researchers of this species.奇努克鲑鱼（Chinook Salmon）是兼具经济与生态价值的重要物种，北美西海岸种群是北太平洋渔业的核心组成部分。该物种的溯河洄游生活史策略会形成与邻近种群存在显著遗传分化的种群（或称群体）。在多数研究与管理场景中，甄别单尾鱼类的起源群体或混合样本的群体组成，有助于追踪人为活动对特定群体的影响，并据此针对性调整渔业管理策略。遗传群体识别（Genetic Stock Identification, GSI）可实现此类精准区分。本文构建了一套全新的GSI基准数据集，其基因型数据来源于69个独立种群的8000余尾个体，覆盖96个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点。该基准数据集涵盖的种群，覆盖了加州与俄勒冈州海洋渔业中99%以上所捕获奇努克鲑鱼的潜在来源种群。这套新型遗传基准数据集可依托快速且经济高效的SNP基因分型技术开展GSI分析，效能评估结果显示，其可对重要的奇努克鲑鱼群体实现极高精度的识别。在某次海洋渔业样本中，依托该基准数据集对千余尾鱼类开展GSI分型后，其结果与从同批样本回收的物理标记信息在报告单元层面的吻合度高达98.95%。这套SNP基准数据集为该物种的管理者与研究者提供了一项重要的技术进步。