Pacific Rim Chinook salmon genetic stock identification baseline of SNP genotypes

Genetic stock identification (GSI) can be an effective tool for fisheries management, but development of reference baselines can be challenging for species with broad geographic distributions. Mixed stock fisheries of Chinook salmon (Oncorhynchus tshawytscha) have utilized GSI analyses for decades with various genetic baselines, but these have largely become outdated with advances in technology that enable more efficient genotyping. In this study, we compiled a large genetic baseline of single nucleotide polymorphism (SNP) markers for 391 populations that encompass the entire geographic range of Chinook salmon. Using cross validation simulations, we demonstrated that a multi-tiered assignment approach can provide high accuracy at both tier 1 (broad scale with three coastwide reporting groups; 97.8% mean accuracy) and tier 2 (fine scale regional reporting groups; up to 97.7% mean accuracy) levels. Realistic mixture simulations showed that this multi-tiered approach can provide highly eff..., We assembled SNP data that was provided by the genetics laboratories of several different agencies. The data has been tested for its ability to perform genetic stock identification estimates., , # Coastwide Chinook SNP GSI Baseline [https://doi.org/10.5061/dryad.dz08kps5b](https://doi.org/10.5061/dryad.dz08kps5b) This dataset contains genotypes that can be used to make genetic stock identification estimates of Chinook salmon. ## Description of the data and file structure The files are formatted for the program Ms.GSI. There is a single Tier1 baseline file, and three Tier2 baseline files containing genotypes (file names = (`*_Genotypes.csv`). These files contain the columns: sampletype - should be \"reference\" for all individuals indiv - Unique identifier for each individual collection - the population or sample each individual belongs to repunit - the reporting group each individual belongs to Subsequent columns contain the genotypes for each locus (2 columns per locus) Each baseline file also has an accompanying `pop_info` file (file names = \"*pop_info.csv\"). These files have the columns: collection - Population or sample corresponding to those in the baseline file...,遗传种群识别（Genetic stock identification, GSI）可作为渔业管理的有效工具，但对于地理分布广泛的物种而言，构建参考基线往往颇具挑战。奇努克鲑鱼（Oncorhynchus tshawytscha）的混合种群渔业已依托各类遗传基线开展GSI分析数十年，但随着能够实现更高效基因分型的技术进步，这些基线大多已过时。本研究整合构建了覆盖奇努克鲑鱼全部地理分布范围的391个种群的单核苷酸多态性（single nucleotide polymorphism, SNP）标记大型遗传基线。通过交叉验证模拟，我们证实多层级归属分析方法可在层级1（广域尺度，包含3个海岸报告组；平均准确率达97.8%）与层级2（精细尺度区域报告组；平均准确率最高达97.7%）两个层面均实现较高准确率。现实混合模拟表明，该多层级方法可实现高效……我们整合了多家不同机构遗传学实验室提供的SNP数据。该数据已针对其开展遗传种群识别估算的能力进行了验证。 # 海岸范围奇努克鲑鱼SNP GSI基线 https://doi.org/10.5061/dryad.dz08kps5b 本数据集包含可用于奇努克鲑鱼遗传种群识别估算的基因型数据。 ## 数据与文件结构说明 所有文件均适配Ms.GSI程序格式。包含1个层级1基线文件，以及3个包含基因型数据的层级2基线文件（文件命名格式为`*_Genotypes.csv`）。 这些文件包含以下列： sampletype — 所有个体的该字段值均应为"reference" indiv — 每个个体的唯一标识符 collection — 每个个体所属的种群或样本组 repunit — 每个个体所属的报告组 后续列则为每个基因座的基因型数据（每个基因座对应2列） 每个基线文件均附带对应的`pop_info`文件（文件命名格式为`*pop_info.csv`）。此类文件包含以下列： collection — 对应基线文件中的种群或样本组……