Genetic parentage reveals the (un)natural history of Central Valley Hatchery steelhead

Populations composed of individuals descended from multiple distinct genetic lineages often feature significant differences in phenotypic frequencies. We considered hatchery production of steelhead, the migratory anadromous form of the salmonid species Oncorhynchus mykiss, and investigated how differences among genetic lineages and environmental variation impacted life history traits. We genotyped 23,670 steelhead returning to the four California Central Valley hatcheries over nine years from 2011–2019, confidently assigning parentage to 13,576 individuals to determine the age and date of spawning, and rates of iteroparity and repeat spawning within each year. We found steelhead from different genetic lineages showed significant differences in adult life-history traits despite inhabiting similar environments. Differences between coastal and Central Valley steelhead lineages contributed to significant differences in age at return, timing of spawning, and rates of iteroparity amongst prog..., SNP loci, genotyping, and basic population genetics analysis Samples were genotyped with a panel of 96 biallelic SNP markers (Abadía-Cardoso et al. 2013), including a Y chromosome-linked marker to determine genetic sex (Brunelli et al. 2008). However, the marker composition of the panel varied slightly over time, with 92 loci genotyped across all years of the study; markers not typed across all years were removed from downstream analyses (Table S1). All individuals were genotyped using TaqMan assays (Applied Biosystems) on 96.96 Dynamic Genotyping Arrays with the EP1 Genotyping System (Fluidigm Corporation) following the manufacturer’s protocols. Two negative controls were included in each array, and genotypes were called using SNP GENOTYPING ANALYSIS SOFTWARE V 3.1.1 (Fluidigm). To evaluate genotyping error rates for each SNP marker we inferred parent-offspring trios using parentage analysis (see below) and estimated the minimum genotyping error rate expected to produce the Mendelian i..., , # California Central Valley Hatchery steelhead broodstock SNP parentage, 2011-2019 [Access this dataset on Dryad](10.5702/qlm.1266rr) This dataset contains the metadata and SNP genotypes for the steelhead sampled at the four California Central Valley (CCV) from 2011-2019. We reconstructed pedigrees, conducted population genetic analyses, analyzed life history characteristics (age at spawning, iteroparity, timing of spawning), and considered Omy05 genotype and phenotype. Metadata records, SNP genotype data, pedigree analysis results, and R notebooks were used to complete the analyses. The use of these data and R code will enable the reproduction of all presented results. We found steelhead from different genetic lineages showed significant differences in adult life-history traits despite inhabiting similar environments. Differences between coastal and Central Valley steelhead lineages contributed to significant differences in age at return, timing of spawning, and rates of iteropari...由多个独立遗传谱系的个体构成的种群，其表型频率往往存在显著差异。本研究以硬头鳟（steelhead）——大麻哈鱼科物种虹鳟（*Oncorhynchus mykiss*）的溯河洄游型——的孵化场繁育为研究对象，探讨了遗传谱系间差异与环境变异如何影响其生活史性状。我们对2011至2019年这9年间，回游至加利福尼亚中央山谷4个孵化场的23670尾硬头鳟进行了基因分型，成功为13576个个体完成可靠的亲本归属鉴定，以此推算产卵年龄、产卵日期，以及各年度内的多次产卵率与重复产卵频次。研究发现，尽管栖息环境相似，不同遗传谱系的硬头鳟成体生活史性状仍存在显著差异。海岸与中央山谷硬头鳟谱系间的差异，导致洄游年龄、产卵时间以及多次产卵率等性状存在显著分歧……本研究涉及单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点分析、基因分型与基础种群遗传学研究。 本研究采用包含96个双等位基因SNP标记的分型面板（Abadía-Cardoso等，2013）对样本进行基因分型，其中包含一个用于鉴定遗传性别的Y染色体连锁标记（Brunelli等，2008）。不过该分型面板的标记组成随时间略有变动，本研究所有年度均完成分型的位点共92个；未能在所有研究年度完成分型的标记已被移除出后续分析之外（附表S1）。所有个体均采用TaqMan探针法（应用生物系统公司，Applied Biosystems），在搭载EP1分型系统的96.96动态基因分型阵列（Fluidigm Corporation）上，严格按照制造商操作规程完成基因分型。每块阵列均设置两个阴性对照，基因型分型结果通过SNP GENOTYPING ANALYSIS SOFTWARE V 3.1.1（Fluidigm公司）完成判定。为评估每个SNP标记的基因分型错误率，我们通过亲本归属分析（详见下文）推断亲本-子代三联体，并估算了符合孟德尔遗传规律所需的最低基因分型错误率……# 加利福尼亚中央山谷孵化场硬头鳟亲本品系SNP亲本归属数据，2011-2019 [可在Dryad平台获取本数据集](10.5702/qlm.1266rr) 本数据集包含2011至2019年间采自加利福尼亚中央山谷（CCV）4个孵化场的硬头鳟样本的元数据与SNP基因型数据。 我们重建了系谱信息，开展了种群遗传学分析，对生活史特征（产卵年龄、多次产卵特性、产卵时间）进行了研究，并分析了Omy05基因型与表型的关联。本研究的完成依托于元数据记录、SNP基因型数据、系谱分析结果以及R分析脚本笔记。 使用本数据集与配套R代码即可复现本文所有研究结果。 我们发现，尽管栖息环境相似，不同遗传谱系的硬头鳟成体生活史性状仍存在显著差异。海岸与中央山谷硬头鳟谱系间的差异，导致洄游年龄、产卵时间以及多次产卵率等性状存在显著分歧……