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.

DNA-Level Variation of Sockeye Salmon in Southeast Alaska and the Nass and Skeena Rivers, British Columbia, with Applications to Stock Identification

2005 ◽  
Vol 25 (3) ◽  
pp. 763-776 ◽  
Author(s):  
Terry D. Beacham ◽  
John R. Candy ◽  
Brenda McIntosh ◽  
Cathy MacConnachie ◽  
Amy Tabata ◽  
...  
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Stock Identification ◽  
Level Variation ◽  
Southeast Alaska

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.

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.

scholarly journals Importance of sample size for estimating prevalence: A case example of infectious hematopoietic necrosis viral RNA detection in mixed-stock Fraser River Sockeye salmon (Oncorhynchus nerka), British Columbia, Canada.

2020 ◽  
Author(s):  
Emilie Laurin ◽  
Julia Bradshaw ◽  
Laura Hawley ◽  
Ian A. Gardner ◽  
Kyle A Garver ◽  
...  
Keyword(s):  
British Columbia ◽  
Sample Size ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Small Sample ◽  
Viral Rna ◽  
Sample Sizes ◽  
Apparent Prevalence ◽  
Infectious Hematopoietic Necrosis ◽  
Mixed Stock

Proper sample size must be considered when designing infectious-agent prevalence studies for mixed-stock fisheries, because bias and uncertainty complicate interpretation of apparent (test)-prevalence estimates. Sample size varies between stocks, often smaller than expected during wild-salmonid surveys. Our case example of 2010-2016 survey data of Sockeye salmon (Oncorhynchus nerka) from different stocks of origin in British Columbia, Canada, illustrated the effect of sample size on apparent-prevalence interpretation. Molecular testing (viral RNA RT-qPCR) for infectious hematopoietic necrosis virus (IHNv) revealed large differences in apparent-prevalence across wild salmon stocks (much higher from Chilko Lake) and sampling location (freshwater or marine), indicating differences in both stock and host life-stage effects. Ten of the 13 marine non-Chilko stock-years with IHNv-positive results had small sample sizes (< 30 samples per stock-year) which, with imperfect diagnostic tests (particularly lower diagnostic sensitivity), could lead to inaccurate apparent-prevalence estimation. When calculating sample size for expected apparent prevalence using different approaches, smaller sample sizes often led to decreased confidence in apparent-prevalence results and decreased power to detect a true difference from a reference value.

Population structure and stock identification of chum salmon (Oncorhynchus keta) from British Columbia determined with microsatellite DNA variation

2008 ◽  
Vol 86 (9) ◽  
pp. 1002-1014 ◽  
Author(s):  
Terry D. Beacham ◽  
Brian Spilsted ◽  
Khai D. Le ◽  
Michael Wetklo
Keyword(s):  
British Columbia ◽  
Population Structure ◽  
Chum Salmon ◽  
Oncorhynchus Keta ◽  
Stock Identification ◽  
Dna Variation ◽  
Coastal Fisheries ◽  
Chum Salmon Oncorhynchus Keta ◽  
Regional Estimates ◽  
Mixed Stock

Variation at 14 microsatellite loci was surveyed in 205 populations of chum salmon ( Oncorhynchus keta (Walbaum in Artedi, 1792)) from British Columbia to determine population structure and the possible application of microsatellites to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index (FST) over all populations and loci was 0.016, with individual locus values ranging from 0.006 to 0.059. Sixteen regional stocks were defined in British Columbia for stock identification applications. Analysis of simulated fishery samples suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. The main stocks that constitute the October 2007 samples of migrating chum salmon through Johnstone Strait in southern British Columbia were Fraser River (45%–64%), southern British Columbia mainland (22%), and east coast Vancouver Island (13%–28%), within the range of those to be expected in samples from Johnstone Strait. Microsatellites have the ability to provide fine-scale resolution of stock composition in British Columbia coastal fisheries.

Genetic Relationships Among Chum Salmon Populations in Southeast Alaska and Northern British Columbia

1994 ◽  
Vol 51 (S1) ◽  
pp. 50-64 ◽  
Author(s):  
C. M. Kondzela ◽  
C. M. Guthrie ◽  
S. L. Hawkins ◽  
C. d. Russell ◽  
J. H. Helle ◽  
...  
Keyword(s):  
British Columbia ◽  
Chum Salmon ◽  
Genetic Relationships ◽  
The United States ◽  
Oncorhynchus Keta ◽  
Significant Heterogeneity ◽  
Southeast Alaska ◽  
Queen Charlotte Islands ◽  
Spawning Time ◽  
Mixed Stock

Allozymes from 46 loci were analyzed from chum salmon (Oncorhynchus keta) collected at 61 locations in southeast Alaska and northern British Columbia. Of the 42 variable loci, 21 had a common allele frequency <0.95. We observed significant heterogeneity within and among six regional groups: central southeast Alaska, Prince of Wales Island area, southern southeast Alaska – northern British Columbia, north-central British Columbia, and two groups in the Queen Charlotte Islands. Genetic variation among regions was significantly greater than within regions. The three island groups were distinct from each other and from the mainland populations. Allele frequencies were stable over time in 14 of 15 locations sampled for more than 1 yr. The geographic basis for heterogeneity among regions is confounded in part by spawning-time differences. The Prince of Wales and Queen Charlotte populations spawn in the fall; the mainland populations spawn mainly in the summer, although some overlap exists. Overall, most genetic diversity (97%) occurred within sampling locations; the remaining diversity was distributed almost equally within and among regions. Our genetic data may provide fishery managers a means to estimate stock composition in the mixed-stock fisheries near this boundary between the United States and Canada.

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.

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 Microsatellite Mixed-Stock Identification of Coho Salmon in British Columbia

2012 ◽  
Vol 4 (1) ◽  
pp. 85-100 ◽  
Author(s):  
Terry D. Beacham ◽  
John R. Candy ◽  
Colin Wallace ◽  
Michael Wetklo ◽  
Langtuo Deng ◽  
...  
Keyword(s):  
British Columbia ◽  
Coho Salmon ◽  
Stock Identification ◽  
Mixed Stock
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