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.

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.

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.

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.

Biochemical Genetic Survey of Sockeye Salmon (Oncorhynchus nerka) in Canada

1994 ◽  
Vol 51 (S1) ◽  
pp. 114-131 ◽  
Author(s):  
Chris C. Wood ◽  
Brian E. Riddell ◽  
Dennis T. Rutherford ◽  
Ruth E. Withler
Keyword(s):  
Sockeye Salmon ◽  
Gene Diversity ◽  
Oncorhynchus Nerka ◽  
River System ◽  
Allozyme Variation ◽  
Stock Identification ◽  
River Systems ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Spawning Sites

Allozyme variation was examined in sockeye salmon (Oncorhynchus nerka) from 83 distinct spawning sites representing all major sockeye-producing river systems in Canada. Of 33 nonselected loci examined, only 14 were highly polymorphic (q > 0.05) and 10 were less polymorphic (0 < q ≤ 0.05). No two populations were fixed for different alleles at any locus, but allele frequencies ranged from 0.01 to 0.86 at PGM-1* and from 0.07 to 0.89 at ALAT*, the two most variable loci. Mean heterozygosity ranged from 2.3 to 5.6% (mean 4.1%) across all sites. Hierarchical analysis was used to partition relative gene diversity among river systems (6.3%), major drainages within a river system (2.9%), nursery lakes within drainages (7.0%), spawning sites within lakes (1.0%), and individuals within spawning sites (82.8%). Extensive differentiation among nursery lakes affords excellent opportunities for genetic stock identification within river systems, but the relatively weak regional structuring limits opportunities for coast-wide stock identification. Genetic variation at highly structured loci corroborates the view that modern populations in Canada originated from sockeye that survived the late Wisconsin Glaciation in the Bering and Columbia refuges, and also suggests the existence of coastal refuges in British Columbia.

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.

Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka ) samples from British Columbia, Canada (1985-94)

2019 ◽  
Vol 42 (4) ◽  
pp. 533-547 ◽  
Author(s):  
Krishna K. Thakur ◽  
Raphaël Vanderstichel ◽  
Karia Kaukinen ◽  
Omid Nekouei ◽  
Emilie Laurin ◽  
...  
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Infectious Agent

Recent Colonization of a Major Salmon-Producing Lake in British Columbia by Pacific Lamprey (Lampetra tridentata)

1984 ◽  
Vol 41 (2) ◽  
pp. 278-285 ◽  
Author(s):  
Susan P. Farlinger ◽  
Richard J. Beamish
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Nursery Area ◽  
Commercial Fishery ◽  
Rock Slide ◽  
Pacific Lamprey ◽  
Natural Lake ◽  
Lampetra Tridentata

Pacific lamprey (Lampetra tridentata) were first observed in Babine Lake, the largest natural lake wholly contained in British Columbia, in 1963 and are currently found along approximately 15% of the length of the lake near the outlet. The number of spawning adults in 1982 was estimated to be 7281. Since Babine Lake is a major nursery area for sockeye salmon (Oncorhynchus nerka), the colonization of this lake by a parasitic lamprey is of concern, particularly if the species can become nonanadromous. The colonization may be beneficial if a commercial fishery can be sustained and if the species does not begin to feed in freshwater. The reason for the recent colonization is unknown but it coincides with increased human manipulation of fishes and habitat, including the removal of a major rock slide, 65 km downstream of the lake.

An Investigation of the Relative Efficiencies of Natural and Artificial Propagation of Sockeye Salmon (Oncorhynchus nerka) at Cultus Lake, British Columbia

1938 ◽  
Vol 4a (3) ◽  
pp. 151-161 ◽  
Author(s):  
R. E. Foerster
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Free Swimming ◽  
Artificial Propagation ◽  
Natural Spawning ◽  
Significant Difference ◽  
Percentage Efficiency

From three tests each of natural propagation and of artificial propagation involving liberation of free-swimming fry and two tests of artificial propagation involving planting of eyed eggs, it was found that no statistically significant difference occurred between the three methods. Computing the percentage efficiency as the number of seaward migrants produced from the total eggs handled, natural propagation varied from 1.05% to 3.23%—an average of 1.80%; fry liberation from 2.42% to 4.54%—an average of 3.24%; and egg planting from 1.45% to 4.71%—an average of 3.08%. Losses occurring during the five years' stripping and hatchery operations were recorded and, based on total eggs, the hatchery product available for distribution represented from 61.0% to 86.0% for egg planting and from 63.4% to 78.5% for fry liberation. There occurred a lake mortality of approximately 96% of the number of fry liberated. The conclusion was reached that in an area such as Cultus lake, where a natural run of sockeye occurred with a reasonable expectancy of successful spawning, artificial propagation, as commonly practised, provided no advantage over natural spawning, as a means of maintaining the run.

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