DOI: 10.5061/dryad.fttdz091g
title: Genetic parentage reveals the (un)natural history of Central Valley Hatchery steelhead

description: 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 programs. In addition, adaptive genomic variation associated with
 life history development in this species varied among hatchery programs
 and was associated with the age of steelhead spawners only in the coastal
 lineage population. Environmental variation likely contributed to
 variation in phenotypic patterns observed over time, as our study period
 spanned both a marine heatwave and a serious drought in California. Our
 results highlight evidence of a strong genetic component underlying known
 phenotypic differences in life history traits between two steelhead
 lineages.
description: <em>SNP loci, genotyping, and basic population genetics
 analysis</em> Samples were genotyped with a panel
 of 96 biallelic SNP markers (Abadía-Cardoso <em>et al.
 </em>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 incompatibilities observed at each
 marker across the trios. Of the 23,670 genotyped samples, 83 yielded
 low-quality genotypes after the initial round of genotyping (indicated
 primarily by large fractions of missing genotypes). These samples were
 re-genotyped. Any individuals missing more than 10% of loci (fewer than 82
 successful genotype calls) were identified and removed.
description: # 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 iteroparity amongst programs. In
 addition, adaptive genomic variation associated with life history
 development in this species varied among hatchery programs and was
 associated with the age of steelhead spawners only in the coastal lineage
 population. ## Description of the data and file structure Steelhead were
 collected at the four Central Valley hatchery programs and fin clipped.
 Length was recorded (LENGTH), and samples were assigned a sample ID
 (SAMPLE_ID). ### Primary data files: These data are the base of all
 analyses for this manuscript. * Unprocessed metadata and genotypes
 (cvsh.csv and cvsh.rds) are the metadata and genotypes for steelhead from
 the four California Central Valley steelhead programs from 2011-2019. SNPs
 are in a two-column format (one column per allele). Metadata columns and
 descriptions (missing data reported as NA): NMFS_DNA_ID -- Unique ID given
 to each sample GENOTYPE_NUMBER -- Genotype replicas are recorded here
 BOX_ID -- Box number where the DNA sample is stored. BOX_POSITION --
 Position in the plate where there tissue sample is stored SAMPLE_ID -- ID
 associated with a sample before reaching our lab BATCH_ID -- Batch number
 given to a related group of samples PROJECT_NAME -- Project name tied to
 the DNA samples GENUS -- Genus of the sample SPECIES -- Species of the
 sample LENGTH -- Fork length measurements, millimeters (mm) WEIGHT -- Body
 weight, grams (g) SEX -- Phenotypic sex, recorded at the time of sample
 collection AGE -- Age of the specimen, if provided with sample
 REPORTED_LIFE_STAGE -- Life stage information provided with sample
 PHENOTYPE -- Miscellaneous physical characteristics provide with sample
 HATCHERY_MARK -- Information on the presence/absence of fin clips provided
 with sample TAG_NUMBER -- Information on fish tags provided with sample
 COLLECTION_DATE -- Date the sample was collected, which is also the
 fish's spawn date CollectionYear -- Brood year the sample was
 collected (samples collected in November or December are in the same brood
 year as those in the new calendar year) ESTIMATED_DATE -- If
 "yes" in this column, the collected date was estimated PICKER --
 Initials of the person preparing the samples for DNA extraction PICK_DATE
 -- Date the sample was prepared for DNA extraction LEFTOVER_SAMPLE -- If
 "no" or "none" in this column, there is no remaining
 tissue sample SAMPLE_COMMENTS -- Comments related to the sample
 NMFS_DNA_ID_1 -- repeat of the unique identifier STATE_F -- State where
 the sample was collected COUNTY_F -- County where the sample was collected
 WATERSHED -- Watershed where the samples were collected TRIB_1 --
 Additional tributary information about the collection TRIB_2 -- Additional
 tributary information about the collection WATER_NAME -- Name of river or
 creek where the sample was collected REACH_SITE -- Additional reach
 information about the collection HATCHERY -- Hatchery where the sample was
 collected SNPPIT.Descriptor -- Hatchery acronym STRAIN -- Additional
 information on the strain of the sample collected LATITUDE_F --
 Geolocation information LONGITUDE_F -- Geolocation information
 LOCATION_COMMENTS_F -- Location comments Sample_ID -- Additional sample
 information Columns AN through HQ are genotype columns (missing data
 reported as 0) for SNP loci. SNPs are in two-column format (one column per
 allele), with alleles listed as numbers (A=1, C=2, 3=G, 4=T) ###
 Additional data files: * Omy05 genotypes are in a separate file because
 Omy_R04944 was added to the panel in 2015. Metadata columns included are:
 NMFS_DNA_ID -- Unique ID given to each sample (conserved from
 cvsh.rds/cvsh.csv) SEX -- Phenotypic sex, recorded at the time of sample
 collection Genetic_Sex -- Genetic sex calculated from Sex_ID genotypes Sex
 -- Consensus sex from genetic and phenotypic sex. COLLECTION_DATE -- Date
 the sample was collected, which is also the fish's spawn date
 CollectionYear -- Brood year the sample was collected (samples collected
 in November or December are in the same brood year as those in the new
 calendar year) Omy_R04944 and Omy_R04044_1 -- Omy05 genotype from SNP
 locus Omy_R04944. SNPs are in two-column format (one column per allele),
 with alleles listed as numbers (A=1, C=2, 3=G, 4=T) SNPPIT.Descriptor --
 Hatchery acronym Reproducible R scripts to process these data for the
 analyses featured in the manuscript are included in the scripts/
 directory. These scripts are numbered in chronological order for these
 analyses and include downloads for necessary packages. Tables cited in the
 manuscript are in the tables/ directory, and figures cited in the
 manuscript are in the final_figures/ directory. The additional/ directory
 includes some shapefiles used to generate Figure 1. Download information
 for these shapefiles is provided in the map figure script (7_map.Rmd). The
 final version of Figure 1 was compiled using Adobe Illustrator. ##
 Sharing/Access information NA