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...