Grandparent inference from genetic data: The potential for parentage-based tagging programs to identify offspring of hatchery strays

Self Cite

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.

Section: Discussionmentioning

confidence: 99%

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

Horn

Hess

Harmon

et al. 2022

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“…Analysis of our microsatellite marker panel revealed that as few as seven microsatellite markers could confidently identify full-sibling individuals (Figure 2), implying that a smaller marker panel may have been sufficient to infer parentage. A reduction in marker panel size could decrease costs associated with genotyping; however, smaller marker panels may suffer from elevated false positive and false negative rates when used for parentage analysis (Delomas and Campbell 2022). In our study, false positive and false negative rates were 0% and 2.7%, respectively, and were in line with estimates from other studies.…”

Section: Discussionmentioning

confidence: 99%

Largemouth Bass Hatchery Contributions Quantified via Parentage‐Based Tagging

Hargrove

Dockendorf

Potoka

et al. 2022

Largemouth Bass Micropterus salmoides are the focus of a billion-dollar (US$1 × 10 9 ) recreational fishery in North America and are subject to widespread hatchery supplementation efforts. Parentage-based tagging (PBT) uses genetic samples taken from hatchery broodstock to genetically "tag" offspring and represents a valuable approach to inform fisheries management and assess hatchery contributions in the wild. This study used a robust microsatellite panel for PBT with Largemouth Bass that reliably discriminated among individuals and siblings and that had low parentage error rates (i.e., false assignments). Genetic data from three cohorts of hatchery broodstock (184 individuals sampled across 3 years) were used to quantify the impacts of planting 150,346 fingerling Largemouth Bass into Lake Mattamuskeet, North Carolina. Parentage-based tagging detected low overall levels of hatchery contributions in the wild (4.1%), which varied as a function of collection year (range = 1.5-7.7%). Furthermore, hatchery contributions varied by broodstock cohort, with PBT detections being attributed to broodstock from only two of the three stocking years. The application of PBT for Largemouth Bass represents a cost-effective and practical approach to tag large numbers of hatchery offspring, monitor supplementation efforts, and evaluate the efficacy of different hatchery practices.

“…Once libraries were sequenced, data were run through in‐house quality control pipelines to ensure that there was no contamination, sample failure, or duplication and a random number of samples were rerun to ensure genotype calls match (Delomas et al. 2019). Genotypes of the 9,830 broodstock baseline and adult returns used in this analysis can be found at http://fishgen.net, data set ID #20210320.…”

Section: Methodsmentioning

confidence: 99%

Improving Abundance Estimates of Spring–Summer Snake River Chinook Salmon for Fisheries Management

Coykendall

Delomas

Belnap

et al. 2022

The Columbia River basin is home to a run of spring–summer Chinook Salmon Oncorhynchus tshawytscha that returns to the Snake River drainage of Idaho, Oregon, and Washington in the Pacific Northwest. Historically, the run was one of the more productive throughout the Columbia River basin. However, Snake River spring–summer Chinook Salmon have experienced declines in abundance due to overfishing, habitat degradation, and dams. Several stocks are listed as threatened under the U.S. Endangered Species Act and are supported by mitigation hatcheries funded by Idaho Power Company, the Lower Snake River Compensation Plan, and the Bonneville Power Administration. To maximize tribal and state harvest of returning hatchery adults, minimize impacts on wild fish, and ensure that enough hatchery fish return to meet broodstock needs, careful fisheries management is required. Since 2008, managers have used hatchery adults, PIT‐tagged as juveniles and detected at Lower Granite Dam, to generate adult abundance estimates. In season, these estimates inform state and tribal harvest shares and ensure that broodstock needs are met. Postseason, they provide smolt‐to‐adult survival and return rates. Since 2012, parentage‐based tagging (PBT) has provided an alternative method to estimate stock‐ and age‐specific returns at Lower Granite Dam, since returning hatchery adults sampled at Lower Granite Dam can be assigned to their parents. We compared stock‐specific abundance estimates between PIT‐ and PBT‐derived methodologies for return years 2016–2019. Across all years, PIT tag estimates accounted for 65% of the PBT‐based estimates at Lower Granite Dam across all age‐groups and release sites combined. This underrepresentation across all groups equated to 49,833 fish that were not accounted for in PIT tag abundance estimates. It is clear that PBT‐based estimates should aide in‐season harvest management and postseason run reconstruction to avoid the known bias of estimates from PIT tags, especially during years of low returns when increased accuracy is critical.