DOI: 10.5061/dryad.wstqjq2sx
title: Genotype data for: Demographic and genetic consequences of a steelhead supplementation program

description: Supplementation of naturally-spawning populations by the addition of
 hatchery-spawned individuals is commonly conducted for recovery of
 threatened and endangered populations and to support harvest
 opportunities. We present an analysis of steelhead, the anadromous form of
 Rainbow Trout (Oncorhynchus mykiss), returning to an integrated
 supplemented population in Southwest Washington over the course of 15
 years. The goal of the supplementation program was to evaluate whether use
 of a juvenile captive broodstock and an integrated paradigm could be used
 to increase adult returns while avoiding negative genetic impacts to the
 population. Estimates of relative reproductive success (RRS) for fish
 spawned in the hatchery ranged from 2.4 for hatchery-origin females to 6.4
 for natural-origin males, indicating that fish spawned in the hatchery
 produced more returning adult progeny than did fish allowed to spawn in
 the natural environment. We observed a slight reduction in reproductive
 success (RS) for hatchery-origin (relative to natural-origin) fish when
 spawning in the natural environment, but the difference was
 non-significant for males and marginally significant for females. In
 contrast to the relatively weak relationship between RS and origin (male P
 = 0.347, η2 = 0.008; female P = 0.066, η2 = 0.037), we observed a
 strong relationship between RS and return year (male P &lt;
 0.001, η2 = 0.896; female P &lt; 0.001, η2 = 0.867)
 (i.e., hatchery- and natural-origin fish did well or poorly together each
 year). Hatchery-origin fish exhibited reduced genetic diversity, as well
 as evidence of increased temporal population structure among hatchery
 fish. We suspect the latter is an artifact of cultural practices that
 reduce diversity in age at smoltification. We conclude that the program
 was successful in achieving an increase in adult return, but not in
 avoiding negative genetic effects on the population, and that any lasting
 impacts of supplementation remain to be determined.
description: Samples were genotyped using the Genotyping-in-Thousands by
 Sequencing (GT-Seq) method developed by Campbell et al. (2015). The GT-Seq
 protocol included pre-amplification of a primer pool of 379 SNP loci,
 (“Omy_379”; Shawn Narum, Columbia River Inter-Tribal Fish Commission,
 personal communication), and barcode amplification resulting in a unique
 barcode for each sample. This was followed by a normalization step using a
 SequalPrep<sup>TM</sup> Normalization Plate Kit (Thermo Fisher
 Scientific, Waltham, MA) and pooling the normalized product for amplicon
 size selection using AMPure XP beads (Beckman Coulter Brea, CA) and a
 magnetic rack. Quantification of libraries was done by qPCR using KAPA
 Library Quantification Kit for Illumina® platforms (Roche Basel,
 Switzerland).  Libraries were then normalized to 4nM and verified using a
 Quibit Fluorometer (Invitrogen Life Technologies Waltham, MA) according to
 the manufacturer’s protocol, and were processed on a NextSeq 5500
 (Illumina, Inc.). To determine laboratory error rate, a
 quality assessment/quality control (QA/QC) was performed by selecting one
 column (eight samples) from each 96-well plate of extracted DNA, and
 building a new library based on those samples. The GT-Seq protocol was as
 described above, except that the QA/QC library was processed on a MiSeq
 (Illumina, Inc.). Genotype data were extracted from the resulting sequence
 data using the bioinformatic scripts developed by Campbell et al.
 (2015).
description: # Genotype data for Demographic and genetic consequences of a Steelhead
 supplementation program
 [https://doi.org/10.5061/dryad.wstqjq2sx](https://doi.org/10.5061/dryad.wstqjq2sx) Genotypes for 291 single nucleotide polymorphism loci in steelhead captured in Abernathy Creek, WA. The data were used to conduct parentage analysis and infer reproductive success of hatchery- and natural-origin fish spawning in the hatchery and natural environments. ## Description of the data and file structure Genotype data are presented in two-column format (i.e., each allele in its own column), with the locus names indicated in the header row for each column. The Category column indicates how each individual was classified at the time of collection. The Year column indicates spawn year for captive brood individuals, and return year for returning adults. Numeric allele calls are coded as follows: A = 1, C = 2, G = 3, T = 4, deletion = 5, and missing data = 0. ## <br>