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.

A comparison of polymorphism of genetic markers and population sample sizes required for mixed-stock analysis of sockeye salmon (Oncorhynchus nerka) in British Columbia

2011 ◽  
Vol 68 (3) ◽  
pp. 550-562 ◽  
Author(s):  
Terry D. Beacham ◽  
B. McIntosh ◽  
C. G. Wallace
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Population Sample ◽  
Identification Accuracy ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Sample Sizes ◽  
Genetic Stock ◽  
Baseline Sample

We evaluated two questions: (i) do microsatellites require larger population baseline sample sizes than single nucleotide polymorphisms (SNPs) to allow the accuracy provided by the microsatellites in genetic stock identification (GSI) applications to be expressed, and (ii) do less genetically distinct populations require larger population baseline sample sizes than more distinct populations to improve population-specific accuracy in GSI applications? Forty-six SNP loci were surveyed in 40 populations of sockeye salmon ( Oncorhynchus nerka ) over 16 regions from southern and central British Columbia and were split into two groups: the top 23 SNPs evaluated for stock identification for British Columbia sockeye salmon and the poorest 23 nuclear SNPs. Fourteen microsatellites were surveyed and split into two groups, with loci from the top 7 loci for stock identification accuracy assembled in one group, and the remaining 7 microsatellites assigned to a second group. SNPs and microsatellites with lower stock identification power required larger population sample sizes to allow expression of stock identification potential. To achieve the same level of population-specific accuracy, SNPs required fewer individuals to be sampled in a population than did microsatellites. Less genetically distinct populations required larger population sample sizes to achieve a given level of accuracy in estimated stock compositions.

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.

Identification of Sockeye Salmon (Oncorhynehus nerka) Stocks in Mixed-stock Fisheries in British Columbia and Southeast Alaska using Biological Markers

1989 ◽  
Vol 46 (12) ◽  
pp. 2108-2120 ◽  
Author(s):  
Chris C. Wood ◽  
Dennis T. Rutherford ◽  
Skip McKinnell
Keyword(s):  
British Columbia ◽  
Biological Markers ◽  
Sockeye Salmon ◽  
Annual Variation ◽  
Stock Identification ◽  
Southeast Alaska ◽  
Accuracy And Precision ◽  
Biochemical Genetic ◽  
Mixed Stock ◽  
Reference Samples

We demonstrate the present analytical capability and the potential for coast-wide stock identification of sockeye salmon (Oncorhynchus nerka) using reference sampling data from 51 principal stocks in British Columbia and Southeast Alaska situated between the Fraser and Taku Rivers. We evaluate the relative accuracy and precision of stock composition estimates from maximum likelihood mixture analysis with four types of biological markers, either alone or in combination; these include freshwater age, six scale pattern variables, the prevalence of the brain parasite Myxobolus neurobius, and five biochemical genetic (electrophoretic) traits. Using all markers in combination, estimates of mixing proportions for all test mixtures are acceptable for most purposes (roughly ± 10% with 95% confidence) providing all samples are representative and mixture samples are large ([Formula: see text] fish). The reliability of these estimates is greatly reduced when reference samples are corrupted to simulate observed annual variation in scale pattern markers. Annual variation may preclude the use of scale pattern markers for complicated stock identification problems where representative reference samples cannot be obtained annually, or until after the fishing period. In contrast, no significant annual variation is detectable for biochemical genetic and brain parasite markers in stocks that have been sampled repeatedly. Using only these stable markers, contributions from about 15 different groups of the 51 stocks can be estimated with acceptable precision, but in general, estimates for individual stocks are unreliable.

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.

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.

Population structure and stock identification of sockeye salmon (Oncorhynchus nerka) in coastal lakes in British Columbia, Canada

2005 ◽  
Vol 83 (6) ◽  
pp. 834-844 ◽  
Author(s):  
T D Beacham ◽  
B McIntosh ◽  
C MacConnachie
Keyword(s):  
British Columbia ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Coastal Lakes ◽  
Queen Charlotte Islands ◽  
Accuracy And Precision ◽  
The Mean ◽  
Mixed Stock

Population structure of sockeye salmon, Oncorhynchus nerka (Walbaum, 1792), from coastal lakes in British Columbia was determined from a survey of variation of 14 microsatellite loci, with approximately 6400 sockeye salmon analyzed from 40 populations. Populations from the Queen Charlotte Islands displayed fewer alleles per locus than did populations in other regions. Genetic differentiation among the populations surveyed was observed, with the mean FST for all loci being 0.077 (SD = 0.006). Differentiation among populations was approximately 13 times greater than annual variation within populations. Regional structuring of the populations surveyed was observed. The accuracy and precision of the estimated stock compositions generally increased as the number of observed alleles at the loci increased. Simulated mixed-stock samples generated from observed population frequencies in different regions suggested that variation at microsatellite loci provided reasonably accurate and precise estimates of stock composition for potential samples from marine or freshwater fisheries.

Fecundity and Egg Retention of Some Sockeye Salmon (Oncorhynchus nerka) Stocks in British Columbia

1986 ◽  
Vol 43 (8) ◽  
pp. 1643-1655 ◽  
Author(s):  
J. I. Manzer ◽  
I. Miki
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Absolute Fecundity ◽  
Egg Retention ◽  
Inadequate Sample Size ◽  
Egg Number ◽  
The Mean ◽  
The Relationship ◽  
Individual Fecundity

The fecundity and egg retention of anadromous female sockeye salmon (Oncorhynchus nerka) collected during 1971–82 from several stocks in British Columbia undergoing controlled fertilization to enhance adult sockeye production were examined. The relationship between egg number and postorbital–hypural length based on 863 females representing 14 stocks was not consistent between all age-types, stocks, and years, probably because of inadequate sample size in some instances. Combined samples, however, revealed a significant positive relationship between postorbital–hypural length and egg number for age 1.2, 1.3, and 2.2 females. Mean absolute fecundity for the respective age-types was 3218, 4125, and 3544 eggs. For samples of 10 or more females, significant stock and annual differences were detected when individual mean absolute fecundity was adjusted to a postorbital–hypural length of 447 mm, but not for females of different age. A comparison of mean fecundities for coastal stocks with historical data for interior British Columbia stocks suggests that coastal stocks are 18% more fecund than interior stocks. Possible causal mechanisms for this regional difference are hypothesized. Examination of 796 carcasses (representing five stocks) for egg retention revealed a range from totally spawned to totally unspawned females, with 56% of the carcasses containing 20 eggs or less and 68% containing 50 eggs or less. The mean egg retention based on all samples combined was estimated to be 6.5% of the mean individual fecundity. This value was reduced to 3.9% when stock means were averaged.

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