Parentage‐based tagging using mothers balances accuracy and cost for discriminating between natural and stocked recruitment for inland fisheries

Abstract

Hatchery programmes are frequently used to supplement inland fisheries, yet achieving successful management outcomes often requires information on stocked versus naturally reproduced fish abundance. Parentage‐based tagging – genetically assigning offspring to their parents – has potential to be an effective approach for distinguishing stocked and naturally reproduced fish. However, several challenges may limit its application to inland fisheries, including genetic relatedness among populations that can affect identification accuracy and high costs of genotyping large broodstocks. Here, we demonstrate the efficacy of parentage‐based tagging based on broodmothers in the Lake Ontario Chinook Salmon fishery, which uses thousands of broodparents and has potential for substantial relatedness between stocked and naturally reproduced fish. Restricting parent sampling to broodmothers reduced costs by two‐thirds, was logistically pragmatic, and achieved >95% accuracy in distinguishing stocked from naturally reproduced salmon. Combined, these results highlight the potential wide applicability of parentage‐based tagging for assessing stocking programmes in inland waters.

Inferring precocial Chinook Salmon production through single‐parentage assignments

“…Finally, a common approach in parentage analysis is to assign offspring to two parents, but study systems exist in which it is impractical to sample all parents contributing to a pool of offspring. In these cases, single-parentage analysis has the potential to be a useful analytical tool, and various studies have demonstrated its utility for fisheries managers (Seamons et al 2004;Ford et al 2015;Sard et al 2021;Fitzpatrick et al 2023). However, few studies have employed a single-parentage methodology that explicitly reports false-positive and false-negative assignment rates in the face of family structure within the parental samples.…”

“…2021; Fitzpatrick et al. 2023). However, few studies have employed a single‐parentage methodology that explicitly reports false‐positive and false‐negative assignment rates in the face of family structure within the parental samples.…”

Optimization of an amplicon sequencing‐based microsatellite panel and protocol for stock identification and kinship inference of lake trout (Salvelinus namaycush)

“…Both SNPs and sequencing-based microsatellites have been used in previous studies that implemented CKMR (e.g., Hillary et al, 2018;Prystupa et al, 2021) and PBT (e.g., Fitzpatrick et al, 2023;Steele et al, 2019). However, while PBT is essentially focused on parentoffspring pairs (although see Delomas & Campbell, 2022), CKMR can make use of half-sibling pairs and studies seeking do so using GTseq typically employ panels with several thousand loci.…”

“…More recently, sequencing‐based microsatellite panels have emerged as an economical alternative as their inherently higher polymorphism allows for reduced reagent and sequencing costs while still providing high inferential power capable of resolving complex relationships and facilitating standardization among multiple labs (Layton et al, 2020 ). Both SNPs and sequencing‐based microsatellites have been used in previous studies that implemented CKMR (e.g., Hillary et al, 2018 ; Prystupa et al, 2021 ) and PBT (e.g., Fitzpatrick et al, 2023 ; Steele et al, 2019 ). However, while PBT is essentially focused on parent‐offspring pairs (although see Delomas & Campbell, 2022 ), CKMR can make use of half‐sibling pairs and studies seeking do so using GTseq typically employ panels with several thousand loci.…”