scholarly journals Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada

2018 ◽  
Vol 12 (2) ◽  
pp. 230-254 ◽  
Author(s):  
Terry D. Beacham ◽  
Colin Wallace ◽  
Kim Jonsen ◽  
Brenda McIntosh ◽  
John R. Candy ◽  
...  
Keyword(s):  
British Columbia ◽  
Large Scale ◽  
Coho Salmon ◽  
Stock Identification ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Salmon Fisheries

scholarly journals Comparison of Coded-wire Tagging with Parentage-based Tagging and Genetic Stock Identification in Large-scale Coho Salmon Fisheries Applications in British Columbia, Canada

2019 ◽  
pp. 173-175
Author(s):  
Terry Beacham ◽  
Colin Wallace ◽  
Kim Jonsen ◽  
Brenda McIntosh ◽  
John Candy ◽  
...  
Keyword(s):  
British Columbia ◽  
Large Scale ◽  
Coho Salmon ◽  
Stock Identification ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Salmon Fisheries

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 Assessment of mixed-stock fisheries and hatchery broodstocks for coho salmon in British Columbia, Canada via parentage-based tagging and genetic stock identification

2022 ◽  
Vol 245 ◽  
pp. 106136
Author(s):  
Terry D. Beacham ◽  
Kim Jonsen ◽  
Ben J.G. Sutherland ◽  
Cheryl Lynch ◽  
Eric B. Rondeau
Keyword(s):  
British Columbia ◽  
Coho Salmon ◽  
Stock Identification ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Mixed Stock

scholarly journals In-field genetic stock identification of overwintering coho salmon in the Gulf of Alaska: Evaluation of Nanopore sequencing for remote real-time deployment

2021 ◽  
Author(s):  
Christoph M. Deeg ◽  
Ben J. G. Sutherland ◽  
Tobi J. Ming ◽  
Colin Wallace ◽  
Kim Jonsen ◽  
...  
Keyword(s):  
Real Time ◽  
Coho Salmon ◽  
Gulf Of Alaska ◽  
Amplicon Sequencing ◽  
Stock Identification ◽  
Nanopore Sequencing ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Batch Sizes ◽  
Sequencing Platforms

Genetic stock identification (GSI) by single nucleotide polymorphism (SNP) sequencing has become the gold standard for stock identification in Pacific salmon, which are found in mixed-stocks during the oceanic phase of their lifecycle. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third-generation single-molecule sequencing platforms, like the Oxford Nanopore minION, provide base calling on portable, pocket-sized sequencers and hold promise for the application of real-time, in-field stock identification on variable batch sizes. Here we report and evaluate utility and comparability of at-sea stock identification of coho salmon Oncorhynchus kisutch based on targeted SNP amplicon sequencing on the minION platform during the International Year of the Salmon Signature Expedition to the Gulf of Alaska in the winter of 2019. Long read sequencers are not optimized for short amplicons, therefore we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at-sea yielded stock assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls agreed with Ion Torrent based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed coho salmon in the queried baseline dataset contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time, accuracy, throughput, and cost, as well as augmentation of the existing baselines, specifically in stocks from coastal northern BC and Alaska. If successfully implemented, Nanopore sequencing will provide an alternative method to the large-scale laboratory approach. Genotyping by amplicon sequencing in the hands of diverse stakeholders could inform management decisions over a broad expanse of the coast by allowing the analysis of small batches in remote areas in near real-time.

scholarly journals Population and individual identification of coho salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags

2017 ◽  
Vol 74 (9) ◽  
pp. 1391-1410 ◽  
Author(s):  
Terry D. Beacham ◽  
Colin Wallace ◽  
Cathy MacConnachie ◽  
Kim Jonsen ◽  
Brenda McIntosh ◽  
...  
Keyword(s):  
Coho Salmon ◽  
Direct Sequencing ◽  
Parentage Analysis ◽  
Individual Identification ◽  
Parental Genotype ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Assignment Probability

Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual coho salmon (Oncorhynchus kisutch) to specific populations and brood years. In total, 20 242 individuals from 117 populations were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Coho salmon from 15 populations were assigned via parentage analysis that required the genotypes of both parents. The overall accuracy of assignment for 1939 coho salmon to the correct population was 100%, and to correct brood year within population was also 100%. Inclusion of individuals requiring only a single parental genotype for identification resulted in assignments of 2101 individuals, with an accuracy of 99.95% (2000–2001) to population and 100.0% to age. With 23 regions defined by the coded-wire tag (CWT) program, and individuals displaying an assignment probability <0.85 excluded from the analysis, mean regional assignment accuracy of individuals via GSI was 98.4% over all 23 regions. A PBT–GSI or PBT system of identification will provide an alternate method of identification in the assessment and management of Canadian-origin coho salmon relative to the existing CWT program.

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.

Comprehensive microsatellite baseline for genetic stock identification of Atlantic salmon (Salmo salar L.) in northernmost Europe

2017 ◽  
Vol 74 (8) ◽  
pp. 2159-2169 ◽  
Author(s):  
Mikhail Ozerov ◽  
Juha-Pekka Vähä ◽  
Vidar Wennevik ◽  
Eero Niemelä ◽  
Martin-A. Svenning ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Stock Identification ◽  
Genetic Stock ◽  
Atlantic Salmon Salmo Salar ◽  
Genetic Stock Identification
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