Retracted: Monitoring Hatchery Broodstock Composition and Genetic Variation of Spring/Summer Chinook Salmon in the Columbia River Basin with Multigeneration Pedigrees

Abstract

Hatchery production of Chinook Salmon Oncorhynchus tshawytscha in the Columbia River basin comprises most of the anadromous salmonid production in this region. Hatchery facilities and programs serve to mitigate for impacts to salmonids due to the construction and operation of hydropower dams and habitat impacts from development in addition to the conservation and restoration of natural populations. A genetic method referred to as parentage‐based tagging (PBT) enables highly reliable detection of hatchery‐origin fish and inference of multigeneration pedigrees. This study compiles 11 years of PBT data from nearly 125,000 interior stream‐type Chinook Salmon from 24 spawning hatcheries located in tributaries of the mid‐ and upper Columbia River as well as the Salmon, Clearwater, and Grande Ronde River subbasins. Multigenerational pedigrees allowed investigation of the proportion of natural‐ and hatchery‐origin broodstock (pNOB and pHOB, respectively) for each hatchery and enumeration of the scale of production between segregated and integrated programs. We then compared how pHOB and the scale of production influenced the number of stray fish observed, genetic diversity, relatedness, and age‐class compositions within broodstocks. Over 91.0% of hatchery broodstock could be assigned back to their parents, and there was an overall rate of less than 1.0% of broodstock that were unintentionally incorporated into nonnatal hatchery programs. We evaluated 14 segregated programs with 0.0–10.0% pNOB, 7 intermediate programs (10.1–50.0% pNOB), and 3 integrated programs (>50.0% pNOB). There was no correlation between the scale of production or pNOB with the level of genetic diversity, but as production size increased, so did the effective number of breeders. This study demonstrates the utility of PBT as a monitoring tool for hatchery broodstocks, and results suggest that segregated and integrated programs have tradeoffs that generally align with their intended broodstock management purpose of providing fish for harvest and/or fish for supplementation or reintroduction.

Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

“…However, four of the populations from the iST lineage (Klickitat River, Tucannon River, Warms Springs River and Yakima River) did not cluster directly with the other iST populations. This was consistent with previous studies that have shown these four populations have experienced admixture from one of the other lineages (Hess et al, 2011; Horn et al, 2022; Narum et al, 2010; Smith et al, 2014). However, the increase in admixture in these populations did not appear to have a major effect on the frequency of early alleles in each population.…”

Utility of parentage‐based tagging for monitoring Coho salmon (Oncorhynchus kisutch) in the interior Columbia River basin

“…A trio assignment was accepted if the false discovery rate was less than 0.1 and the LOD score was greater than 14. These parameters were chosen based on the previous testing and work in Chinook salmon ( O. tshawytscha ) and steelhead trout ( O. mykiss ) to minimize false positive assignments (Hargrove et al., 2021; Hess et al., 2016; Horn et al., 2023). Parentage assignment was not performed for Willard NFH and Little White Salmon NFH as data from the potential parent years, 2012 and 2013 were not included in the PBT baseline.…”

“…A PBT based management system generates very similar information and can be less expensive than deploying CWTs (Beacham, Wallace, Jonsen, McIntosh, Candy, Willis, Lynch, Moore, et al., 2019). In addition, PBT typically has higher tagging rates compared to CWTs and can accurately identify stray fish among hatcheries and the composition of mixed stocks in fishery captures (Beacham et al., 2020; Beacham, Wallace, Jonsen, McIntosh, Candy, Willis, Lynch, Moore, et al., 2019; Beacham, Wallace, Jonsen, McIntosh, Candy, Willis, Lynch, & Withler, 2019; Horn et al., 2023; Steele et al., 2019).…”

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

“…We nonlethally collected fin clips from every spawning steelhead from 2011 to 2019, including during the record‐setting drought and marine heatwave events. These fin clips enabled both population genetic analysis and parentage‐based tagging (PBT; Anderson & Garza, 2006 ), which has been successfully employed to understand and manage anadromous fish populations (Abadía‐Cardoso et al., 2013 ; Evans et al., 2018 ; Horn et al., 2022 ). We reconstructed pedigrees with 13,576 parent‐offspring trios and 19,043 unique adult steelhead, representing nearly all steelhead spawned at four CCV hatcheries over 9 years, spanning two to three generations.…”