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

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.

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.

Bacterioplankton, Phytoplankton, and Zooplankton Communities in a British Columbia Coastal Lake Before and After Nutrient Reduction

1986 ◽  
Vol 43 (8) ◽  
pp. 1504-1514 ◽  
Author(s):  
F. Joan Hardy ◽  
Ken S. Shortreed ◽  
John G. Stockner
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Inorganic Nitrogen ◽  
Size Fraction ◽  
Growing Season ◽  
Nutrient Reduction ◽  
Nitrogen And Phosphorus ◽  
Coastal Lake ◽  
Before And After ◽  
High Concentrations

Inorganic nitrogen and phosphorus were applied weekly during the growing season from 1980 to 1982 and twice weekly in 1983 to Hobiton Lake, a warm monomictic coastal lake in British Columbia. The lake was not fertilized in 1984. Average numbers of bacteria during the growing season decreased from a high of 1.53 × 106∙mL−1 in the fertilized condition to 0.84 × 106∙mL−1 in the unfertilized condition. Chlorophyll a concentrations decreased from a maximum seasonal average of 2.69 μg∙L−1 (1981) to 1.30 μg∙L−1 (1984), and algal numbers decreased from 5.83 × 104∙mL−1 (1983) to 2.29 × 104∙mL−1 (1984). Although the numbers of phytoplankton in each size fraction (picoplankton, nanoplankton, or microplankton) decreased in the unfertilized condition, the greatest change was an almost fourfold decrease in picoplankton, which consisted of 90% cyanobacteria (primarily Synechococcus spp.). Abundance of the large diatoms Rhizosolenia spp. and Melosira spp. increased in 1984, resulting in an increase in average seasonal algal volume. Average densities of medium (0.15–0.84 mm) and large (0.85–1.5 mm) zooplankton were greatest in 1982, while rotifers and small zooplankton (0.10–0.14 mm) were most dense in 1984 following nutrient reduction. The lake had relatively high concentrations of planktivorous juvenile sockeye salmon (Oncorhynchus nerka) that appeared to minimize any direct effect of nutrient additions on zooplankton densities.

A widespread decrease in productivity of sockeye salmon (Oncorhynchus nerka) populations in western North America

2012 ◽  
Vol 69 (8) ◽  
pp. 1255-1260 ◽  
Author(s):  
Randall M. Peterman ◽  
Brigitte Dorner
Keyword(s):  
Sockeye Salmon ◽  
Spatial Scales ◽  
Oncorhynchus Nerka ◽  
Geographic Area ◽  
Fraser River ◽  
Western North America ◽  
Southeast Alaska ◽  
The Past ◽  
Large Geographic Area ◽  
Marine Areas

We used data on 64 stocks of sockeye salmon ( Oncorhynchus nerka ) from British Columbia (B.C.), Washington, and Alaska to determine whether recent decreases in abundance and productivity observed for Fraser River, B.C., sockeye have occurred more widely. We found that decreasing time trends in productivity have occurred across a large geographic area ranging from Washington, B.C., southeast Alaska, and up through the Yakutat peninsula, Alaska, but not in central and western Alaska. Furthermore, a pattern of predominantly shared trends across southern stocks and opposite trends between them and stocks from western Alaska was present in the past (1950–1985), but correlations have intensified since then. The spatial extent of declining productivity of sockeye salmon has important implications for management as well as research into potential causes of the declines. Further research should focus on mechanisms that operate at large, multiregional spatial scales, and (or) in marine areas where numerous correlated sockeye stocks overlap.

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.

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.

The Influence of Climate on the Stock and Recruitment of Pink and Sockeye Salmon from the Fraser River, British Columbia, Canada

2004 ◽  
Vol 133 (6) ◽  
pp. 1396-1412 ◽  
Author(s):  
R. J. Beamish ◽  
J. T. Schnute ◽  
A. J. Cass ◽  
C. M. Neville ◽  
R. M. Sweeting
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Fraser River ◽  
Stock And Recruitment
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