Application of Genetic Stock Identification and Parentage‐Based Tagging in a Mixed‐Stock Recreational Chinook Salmon Fishery

2020 ◽  
Author(s):  
Alexander J. Jensen ◽  
Carl B. Schreck ◽  
Jon E. Hess ◽  
Sandra Bohn ◽  
Kathleen G. O’Malley ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Stock Identification ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Mixed Stock ◽  
Salmon Fishery

scholarly journals An improved method for predicting the accuracy of genetic stock identification

2008 ◽  
Vol 65 (7) ◽  
pp. 1475-1486 ◽  
Author(s):  
Eric C. Anderson ◽  
Robin S. Waples ◽  
Steven T. Kalinowski
Keyword(s):  
Conventional Method ◽  
Chinook Salmon ◽  
Cross Validation ◽  
Oncorhynchus Tshawytscha ◽  
Stock Identification ◽  
Improved Method ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Unbiased Estimates ◽  
Leave One Out

Estimating the accuracy of genetic stock identification (GSI) that can be expected given a previously collected baseline requires simulation. The conventional method involves repeatedly simulating mixtures by resampling from the baseline, simulating new baselines by resampling from the baseline, and analyzing the simulated mixtures with the simulated baselines. We show that this overestimates the predicted accuracy of GSI. The bias is profound for closely related populations and increases as more genetic data (loci and (or) alleles) are added to the analysis. We develop a new method based on leave-one-out cross validation and show that it yields essentially unbiased estimates of GSI accuracy. Applying both our method and the conventional method to a coastwide baseline of 166 Chinook salmon ( Oncorhynchus tshawytscha ) populations shows that the conventional method provides severely biased predictions of accuracy for some individual populations. The bias for reporting units (aggregations of closely related populations) is moderate, but still present.

Large-scale parentage-based tagging and genetic stock identification applied in assessing mixed-stock fisheries and hatchery brood stocks for coho salmon in British Columbia, Canada

2020 ◽  
Vol 77 (9) ◽  
pp. 1505-1517
Author(s):  
Terry D. Beacham ◽  
Kim Jonsen ◽  
Brenda McIntosh ◽  
Ben J.G. Sutherland ◽  
David Willis ◽  
...  
Keyword(s):  
British Columbia ◽  
Large Scale ◽  
Coho Salmon ◽  
Stock Identification ◽  
Stock Management ◽  
Brood Stock ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Salmon Fisheries ◽  
Mixed Stock

Direct DNA sequencing is powering a revolution in the application of genetics to resource management, with parentage-based tagging (PBT) increasingly applied to salmon fisheries and hatchery brood stock management and assessment. Genetic stock identification (GSI) and PBT were applied to assessment of 2018 coho salmon (Oncorhynchus kisutch) ocean fisheries and hatchery brood stocks in British Columbia (BC), Canada, with 6391 individuals successfully genotyped in fishery samples and 7805 individuals genotyped in 40 hatchery brood stocks. Population-specific contributions to mixed-stock fisheries and exploitation rates were estimated with coded-wire tags (CWTs) and GSI–PBT technologies for six populations. PBT assignments, verified by CWTs, were 100% accurate for 308 individuals with respect to population of origin and age. There was generally reasonably close agreement of estimated population-specific exploitation rates between CWT and genetic methods. We conclude that a genetic approach can improve upon the results available from the current CWT program for assessment and management of coho salmon fisheries and hatchery brood stocks in BC and provide information critical to aid in implementation of Canada’s Policy for Conservation of Wild Pacific Salmon.

scholarly journals Stock composition and ocean spatial distribution inference from California recreational Chinook salmon fisheries using genetic stock identification

2015 ◽  
Vol 170 ◽  
pp. 166-178 ◽  
Author(s):  
William H. Satterthwaite ◽  
Javier Ciancio ◽  
Eric Crandall ◽  
Melodie L. Palmer-Zwahlen ◽  
Allen M. Grover ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Chinook Salmon ◽  
Stock Identification ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Salmon Fisheries

scholarly journals Population and individual identification of Chinook salmon in British Columbia through parentage-based tagging and genetic stock identification with single nucleotide polymorphisms

2018 ◽  
Vol 75 (7) ◽  
pp. 1096-1105 ◽  
Author(s):  
Terry D. Beacham ◽  
Colin Wallace ◽  
Cathy MacConnachie ◽  
Kim Jonsen ◽  
Brenda McIntosh ◽  
...  
Keyword(s):  
British Columbia ◽  
Single Nucleotide Polymorphisms ◽  
Chinook Salmon ◽  
Individual Identification ◽  
Parental Genotype ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Genetic Stock ◽  
Single Nucleotide ◽  
Genetic Stock Identification

A study was undertaken to evaluate whether a parentage-based tagging (PBT) and genetic stock identification (GSI) program has the potential to emulate the results from an existing coded-wire tag (CWT) assessment program in British Columbia. A PBT–GSI approach was used to identify Chinook salmon (Oncorhynchus tshawytscha) to specific populations and brood years where 36 241 individuals from 45 populations were genotyped at 321 single nucleotide polymorphisms (SNPs). Known-origin and known-age age 1 juveniles from seven test populations were assigned via PBT (two parental genotypes required, 538 of 656 juveniles assigned; one parental genotype required, 636 of 656 juveniles assigned) with a minimum accuracy of 99.9%. Assignment accuracy via PBT of 1026 ages 1, 2, or 3 Chinook salmon returning to nine populations in 2015 or 2016 (two parental genotypes required, 556 of 1026 individuals assigned; one parental genotype required, 898 of 1026 individuals assigned) was a minimum of 99.8%. A PBT–GSI or PBT system of identification may provide an alternate cost-effective method of identification in the assessment and conservation of Canadian-origin Chinook salmon relative to the existing CWT program, thereby providing very high resolution of mixed-stock fishery samples containing both hatchery-origin (adipose fin clipped) and wild-origin (unclipped) populations.

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