Stock Identification of Sockeye Salmon (Oncorhynchus nerka) with Scale Pattern Recognition

1982 ◽  
Vol 39 (4) ◽  
pp. 611-617 ◽  
Author(s):  
Rodney C. Cook
Keyword(s):  
Sockeye Salmon ◽  
Classification Scheme ◽  
Oncorhynchus Nerka ◽  
Measurement Data ◽  
Gulf Of Alaska ◽  
Error Rates ◽  
Classification Error ◽  
Density Functions ◽  
Stock Identification ◽  
Gaussian Density

The non-Gaussian density functions underlying polynomial discrimant functions are employed in a classification scheme designed for sockeye salmon (Oncorhynchus nerka). A leaving-one-out approach is used to estimate the smoothing parameters in the density functions and to obtain nearly unbiased estimates of expected actual error rates in the classification scheme. The result is that all available observations of known origin may be used to determine the discriminant rule and estimate classification error rates. These are needed to obtain point estimates of the proportions of subpopulations present in areas of intermingling. Several additional improvements over the polynomial discriminant method are noted. The scheme is applied to scale measurement data of sockeye salmon from Bristol Bay, the Gulf of Alaska, and the Kamchatka Peninsula.Key words: stock identification, discriminant analysis, sockeye salmon

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.

Cross Correlations Between Reconstructed Ocean Abundances of Bristol Bay and British Columbia Sockeye Salmon (Oncorhynchus nerka)

1984 ◽  
Vol 41 (12) ◽  
pp. 1814-1824 ◽  
Author(s):  
Randall M. Peterman ◽  
Fred Y. C Wong
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Population Analysis ◽  
Oncorhynchus Nerka ◽  
Survival Rates ◽  
Gulf Of Alaska ◽  
Time Lags ◽  
Bristol Bay ◽  
Reconstruction Methods ◽  
Cross Correlations

Anecdotal reports of a tendency for British Columbia sockeye salmon (Oncorhynchus nerka) to be low when Bristol Bay, Alaska, returns are high prompted a reconstruction of minimum abundances of sockeye resident in the Gulf of Alaska each year from the early 1950s to mid-1970s. This backwards reconstruction using Fry's virtual population analysis was done by using catch, escapement, and age structure data for each area in British Columbia and Bristol Bay. Use of more sophisticated backwards reconstruction methods was precluded by lack of age-specific annual survival rates by stock. Ocean abundances of British Columbia and Bristol Bay sockeye show significant autocorrelations at periods consistent with the cyclic dominant patterns of their largest stocks. Cross correlations at lag 0 between ocean abundances of various ages of fish from these two regions show one case of a significant inverse relation in abundances. In addition, there are significant cross correlations between British Columbia and Bristol Bay ocean abundances at various time lags, showing that cycles in their abundances are out of synchrony. This lack of synchrony persisted longer than would be expected from cyclic dominance patterns and age at maturity of British Columbia and Bristol Bay sockeye, and several alternative explanations of this asynchrony are discussed.

Identification of Sockeye Salmon (Oncorhynchus nerka) Stocks in the Stikine River Based on Egg Size Measurements

1985 ◽  
Vol 42 (11) ◽  
pp. 1696-1701 ◽  
Author(s):  
P. C. Craig
Keyword(s):  
Body Weight ◽  
Egg Size ◽  
Sockeye Salmon ◽  
Pattern Analysis ◽  
Oncorhynchus Nerka ◽  
Egg Mass ◽  
Stock Identification ◽  
Mass Measurements ◽  
Lake System ◽  
Identification Method

The Stikine River in southeastern Alaska supports two principal stocks of sockeye salmon (Oncorhynchus nerka). An expedient means of separating these stocks when they enter freshwater is by egg size and egg mass measurements. Eggs of sockeye that spawn in the Tahltan Lake system are smaller than sockeye spawning elsewhere in the Stikine drainage, a difference supported by an independent stock identification method (scale pattern analysis). Tahltan females have only slightly developed ovaries (1–3% of body weight) and small eggs (2.0–3.5 mm) when they enter freshwater; they enter the river earlier (2–3 wk) and travel farther upstream to spawn than non-Tahltan sockeye. The latter group has more developed ovaries (5–16% of body weight) and larger eggs (3.5–6.2 mm) when they enter the river. Thus, an assessment of egg sizes of sockeye caught in the river can provide on-site information about stock composition and run timing. These data and escapement counts at Tahltan Lake indicate that the total escapement to the Stikine in 1983 was 61 000 to 71 000 sockeye of which 45–53% were Tahltan stock and 47–55% spawned eleswhere in the drainage.

Variants of Lactate Dehydrogenase Isozymes in Sera of Sockeye Salmon (Oncorhynchus nerka)

1969 ◽  
Vol 26 (1) ◽  
pp. 15-19 ◽  
Author(s):  
H. O. Hodgins ◽  
W. E. Ames ◽  
F. M. Utter
Keyword(s):  
British Columbia ◽  
Lactate Dehydrogenase ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Gulf Of Alaska ◽  
Bristol Bay ◽  
Lactate Dehydrogenase Isozymes ◽  
Skeena River ◽  
Total Body ◽  
Ldh Isozymes

Three phenotypes of lactate dehydrogenase (LDH) isozymes were found in sera of sockeye salmon (Oncorhynchus nerka), presumably representing B′B′, B′B, and BB genotypes. No association was obvious between LDH phenotype of sera and sex or total body length.Of 1006 sera from Asian, Bristol Bay, and Gulf of Alaska stocks, 826 were B′B′ and 180 were B′B or BB. Of 591 sera from Washington and British Columbia stocks, 589 were B′B′ and 2 were B′B; both of the B-allele phenotypes were found in fish captured at the Skeena River in northern British Columbia. These findings suggested that LDH isozymes should be useful in studies on ocean distribution of sockeye salmon and in characterizing certain Asian and Alaskan sockeye salmon populations.

Simulation of Dispersal of Sockeye Salmon (Oncorhynchus nerka) Underyearlings in Babine Lake

1977 ◽  
Vol 34 (9) ◽  
pp. 1379-1388 ◽  
Author(s):  
S. E. Simms ◽  
P. A. Larkin
Keyword(s):  
Computer Program ◽  
Density Function ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Lake Basin ◽  
Density Functions ◽  
Directional Bias ◽  
Natural Movement ◽  
Reflection Principles ◽  
Bivariate Density

The movement of underyearling sockeye salmon (Oncorhynchus nerka) in Babine Lake was computer simulated using a grid array with reflection principles applied for the complex shoreline boundaries. Dispersal was in accord with bivariate density functions summed appropriately to give 25 discrete components, with the standard deviations related to observed swimming speeds. Directionally biased dispersal was simulated using the lognormal density function. Natural movement of sockeye underyearlings in Babine Lake suggests three seasonal periods: (1) May 25–June 12; (2) July 13–August 28; (3) August 29–October 12. For (1), natural movement is best simulated by assuming that 90% of the fish move with a 10:90 bias toward southward movement, while 10% of the fish move at random; for (2), the best assumptions are that 50% of the fish move with a 90:10 bias for northward movement and 50% move at random; for (3), the best simulation assumed that 100% of the fry move at random. Considering the simplicity of the model assumptions, the fit to the data for natural movements is good. To construct a better predictive model the directional bias mimicked by the lognormal density function should be divided into components related to physical circulation in the lake basin and components related to fry behavior. The architecture of the computer program is briefly described and could be applied to other salmon dispersal studies. Key words: sockeye salmon, simulation, natural movements, fry distribution

Relationship among adult body length, abundance, and ocean temperature for British Columbia and Alaska sockeye salmon (Oncorhynchus nerka), 1967–1997

1999 ◽  
Vol 56 (10) ◽  
pp. 1716-1720 ◽  
Author(s):  
Brian J Pyper ◽  
Randall M Peterman
Keyword(s):  
British Columbia ◽  
Time Series ◽  
Body Length ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Gulf Of Alaska ◽  
Reduced Body ◽  
Adult Body ◽  
Northeastern Pacific ◽  
Length Data

Body length of adult Pacific sockeye salmon (Oncorhynchus nerka) has decreased significantly in recent years. We used 69 time series of age-specific body-length data (1967-1997) for 30 sockeye salmon stocks from southern British Columbia to western Alaska to test hypotheses about the effects of oceanographic conditions and competition on growth rate of sockeye salmon. Using principal components analysis (PCA), we constructed a single time series (PC1) that represented the dominant pattern of variability in length-at-age shared among these stocks. Taking into account time trends and autocorrelation in residuals, we found that increases in total Gulf of Alaska sockeye abundance and increases in sea-surface temperature (SST) across the Gulf of Alaska were significantly associated with reduced adult body length. Abundance and SST together accounted for 71% of the variability in PC1. Although researchers have documented increases in both abundance of sockeye salmon and their food in the northeastern Pacific Ocean over the last few decades, it is possible that increased food was more than offset by increased sockeye abundance, leading to greater competition and reduced body size.

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.

Infectious Hematopoietic Necrosis Virus: Prevalence in Certain Alaskan Sockeye Salmon, Oncorhynchus nerka

1976 ◽  
Vol 33 (1) ◽  
pp. 186-188 ◽  
Author(s):  
Roger S. Grischkowsky ◽  
Donald F. Amend
Keyword(s):  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Gulf Of Alaska ◽  
Necrosis Virus ◽  
Cook Inlet ◽  
Bristol Bay ◽  
Virus Prevalence ◽  
Kodiak Island ◽  
Infectious Hematopoietic Necrosis ◽  
First Time

Infectious hematopoietic necrosis (IHN) virus is reported for the first time in Alaskan sockeye salmon (Oncorhynchus nerka). The virus was isolated from moribund juveniles at Kitoi Bay and from adults of 16 spawning stocks throughout the Bristol Bay, Kodiak Island, Cook Inlet, and the Gulf of Alaska areas.

Density-Dependent Growth in Early Ocean Life of Sockeye Salmon (Oncorhynchus nerka)

1984 ◽  
Vol 41 (12) ◽  
pp. 1825-1829 ◽  
Author(s):  
Randall M. Peterman
Keyword(s):  
British Columbia ◽  
Body Size ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Management Strategies ◽  
Gulf Of Alaska ◽  
Density Dependent ◽  
Adult Body Size ◽  
Adult Body ◽  
Dependent Growth

Significant decreases in adult body size and marine growth rate occur in seven British Columbia and Bristol Bay, Alaska, sockeye salmon (Oncorhynchus nerka) stocks when large numbers of sockeye are present in the Gulf of Alaska. These density-dependent effects arise mainly during early ocean life and are probably due to competition for food. The total sockeye abundance in the Gulf of Alaska is at least as important as within-stock abundance in determining final adult body size. British Columbia sockeye show a 10–22% decrease in adult body weight at high abundance of conspecifics. Thus, future evaluations of management strategies cannot simply focus on individual stocks, but must take a broader perspective which includes other sockeye 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.

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