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.

scholarly journals Estimation of Conservation Unit and population contribution to Chinook salmon mixed-stock fisheries in British Columbia, Canada using direct DNA sequencing for single nucleotide polymorphisms

2021 ◽  
Author(s):  
Terry D. Beacham ◽  
Colin G. Wallace ◽  
Kim Jonsen ◽  
Ben J. G. Sutherland ◽  
Carrie Gummer ◽  
...  
Keyword(s):  
British Columbia ◽  
Single Nucleotide Polymorphisms ◽  
Chinook Salmon ◽  
Fishery Management ◽  
The United States ◽  
Assessment System ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Genetic Stock ◽  
Single Nucleotide

Determination of population structure and stock identification is a general problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For Chinook salmon (Oncorhynchus tshawytscha), a stock identification baseline comprised of some 125,198 individuals from 369 populations ranging from Russia to California was employed for genetic stock identification (GSI). GSI analysis based upon variation at up to 547 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 68 Conservation Units (CUs) in British Columbia, 23 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian Chinook salmon.

Single-nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska

2014 ◽  
Vol 71 (5) ◽  
pp. 698-708 ◽  
Author(s):  
Wesley A. Larson ◽  
James E. Seeb ◽  
Carita E. Pascal ◽  
William D. Templin ◽  
Lisa W. Seeb
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Genetic Stock ◽  
Single Nucleotide ◽  
Genetic Stock Identification

Genetic stock identification (GSI), an important tool for fisheries management that relies upon the ability to differentiate stocks of interest, can be difficult when populations are closely related. Here we genotyped 11 850 single-nucleotide polymorphisms (SNPs) from existing DNA sequence data available in five closely related populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. We then converted a subset of 96 of these SNPs displaying high differentiation into high-throughput genotyping assays. These 96 SNPs (RAD96) and 191 SNPs developed previously (CTC191) were screened in 28 populations from western Alaska. Regional assignment power was evaluated for five different SNP panels, including a panel containing the 96 SNPs with the highest FST across the CTC191 and RAD96 panels (FST96). Assignment tests indicated that SNPs in the RAD96 were more useful for GSI than those in the CTC191 and that increasing the number of reporting groups in western Alaska from one to three was feasible with the FST96. Our approach represents an efficient way to discover SNPs for GSI and should be applicable to other populations and species.

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.

Accurate estimation of conservation unit contribution to coho salmon mixed-stock fisheries in British Columbia, Canada, using direct DNA sequencing for single nucleotide polymorphisms

2020 ◽  
Vol 77 (8) ◽  
pp. 1302-1315 ◽  
Author(s):  
Terry D. Beacham ◽  
Colin Wallace ◽  
Kim Jonsen ◽  
Brenda McIntosh ◽  
John R. Candy ◽  
...  
Keyword(s):  
British Columbia ◽  
Single Nucleotide Polymorphisms ◽  
Fishery Management ◽  
Coho Salmon ◽  
The United States ◽  
Assessment System ◽  
Accurate Estimation ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Determination of population structure and stock identification is a ubiquitous problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For coho salmon (Oncorhynchus kisutch), a stock identification baseline composed of some 57 982 individuals from 332 populations ranging from southeast Russia to California was employed for genetic stock identification (GSI). GSI analysis based upon variation at up to 480 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 37 conservation units (CU) in British Columbia, 13 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian coho salmon.

A comparison of stock and individual identification for sockeye salmon (Oncorhynchus nerka) in British Columbia provided by microsatellites and single nucleotide polymorphisms

2010 ◽  
Vol 67 (8) ◽  
pp. 1274-1290 ◽  
Author(s):  
Terry D. Beacham ◽  
B. McIntosh ◽  
C. Wallace
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Individual Identification ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Individual Assignment ◽  
Assignment Accuracy ◽  
Accuracy And Precision

Variation at 14 microsatellite loci, one major histocompatibility complex (MHC) locus, and 49 single nucleotide polymorphism (SNPs) loci was surveyed in 44 populations of sockeye salmon ( Oncorhynchus nerka ) over 16 regions from southern and central British Columbia, Canada. Sequential addition of the five highest rated SNPs to the suite of 14 microsatellites provided the equivalent average accuracy when compared with the current suite of microsatellites and MHC. Six microsatellites provided the equivalent average stock identification resolution and individual assignment accuracy compared with 46 SNPs. For regional stock compositions, 53–104 SNPs were projected to be required to provide accuracy and precision equivalent to the microsatellites. For population-specific stock compositions, 75–79 SNPs were projected to be required to provide accuracy and precision equivalent to the microsatellites. Equivalency in individual assignment accuracy to region was estimated to require 100 SNPs of the quality evaluated in the study, whereas equivalent accuracy in assignment to specific populations was estimated to require 124 SNPs. Applications that incorporate the existing power of a combined microsatellite–SNP approach are the best current technique available for sockeye salmon stock identification applications in southern British Columbia.

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