Genetic Variation in Sockeye Salmon (Oncorhynchus nerka) Populations of Asia and North America

1994 ◽  
Vol 51 (S1) ◽  
pp. 132-146 ◽  
Author(s):  
Nataly V. Varnavskaya ◽  
Chris C. Wood ◽  
Rebecca J. Everett
Keyword(s):  
Population Structure ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
High Variability ◽  
Allele Frequencies ◽  
Habitat Characteristics ◽  
Ice Age ◽  
Variant Allele ◽  
Composition Analysis ◽  
Protein Coding

We investigated population structure in sockeye salmon, Oncorhynchus nerka, in relation to ecological characteristics and geographical distribution using allozyme allelic frequencies compiled from new and previously published analyses for 71 populations (300 collections) throughout the species' range. Up to 87 protein-coding loci were screened in some samples, but of these, 55% were monomorphic, and another 31% were only slightly polymorphic with variant allele frequencies <0.01. Only 8 loci were moderately or highly polymorphic with variant allele frequencies exceeding 0.10 in at least some collections. The highest variation ever reported in salmon was discovered at LDH-B2* where the *100 allele was fixed in some populations but rare in others. Genetic differentiation was typically greater among populations within regions than among regions. However, stock composition analysis based on patterns of variation at the nine most useful loci appears to be feasible for most major stocks examined in this study. The low level of polymorphism in sockeye despite high variability at a few polymorphic loci is attributed to precise homing to natal rivers and interactions among several colonizing races that survived the Pleistocene ice age in isolated refugia with different habitat characteristics.

The genetic population structure of lacustrine sockeye salmon, Oncorhynchus nerka, in Japan as the endangered species

2011 ◽  
Vol 92 (4) ◽  
pp. 539-550 ◽  
Author(s):  
Yuichiro Kogura ◽  
James E. Seeb ◽  
Noriko Azuma ◽  
Hideaki Kudo ◽  
Syuiti Abe ◽  
...  
Keyword(s):  
Population Structure ◽  
Endangered Species ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Genetic Population Structure ◽  
Genetic Population

Relationships between habitat characteristics and breeding population densities in sockeye salmon (Oncorhynchus nerka)

2011 ◽  
Vol 68 (5) ◽  
pp. 758-767 ◽  
Author(s):  
Douglas C. Braun ◽  
John D. Reynolds
Keyword(s):  
Sockeye Salmon ◽  
Woody Debris ◽  
Oncorhynchus Nerka ◽  
Information Criterion ◽  
Breeding Population ◽  
Habitat Characteristics ◽  
Population Densities ◽  
Ecological Processes ◽  
Risk Of Predation ◽  
Stream Characteristics

We examine the importance of stream habitat characteristics in governing variation in spawning densities of sockeye salmon ( Oncorhynchus nerka ) across 32 streams in the Fraser River Basin, British Columbia, Canada. We used mixed-effects models to examine four competing hypotheses for the influence of abiotic stream characteristics acting on either adult salmon or embryo mortality. All models that received support using Akaike’s information criterion included stream characteristics that are associated with cover. These included the percent area of pools, percentage of the banks that were undercut, and large woody debris (in that order). These results suggest the importance of stream characteristics, which reduce risk of predation on adults, in determining spawning sockeye salmon densities. Thus, identification of a small number of physical characteristics of streams provides insight into ecological processes that determine population densities. This information can be used to quantify habitat quality, which can guide habitat prioritization for conservation.

Homing in Wild Sockeye Salmon (Oncorhynchus nerka) Populations as Inferred from Differences in Parasite Prevalance and Allozyme Allele Frequencies

1987 ◽  
Vol 44 (11) ◽  
pp. 1963-1971 ◽  
Author(s):  
T. P. Quinn ◽  
C. C. Wood ◽  
L. Margolis ◽  
B. E. Riddell ◽  
K. D. Hyatt
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Pacific Salmon ◽  
Oncorhynchus Nerka ◽  
Genetic Differences ◽  
Allele Frequencies ◽  
Wild Populations ◽  
Central Coast ◽  
Barkley Sound ◽  
Quantitative Estimates

Although it is widely accepted that adult Pacific salmon (Oncorhynchus spp.) spawn in their natal stream, there are few quantitative estimates of homing precision in wild populations. The prevalence of two myxosporean parasites, Myxobolus neurobius and Henneguya salminicola, indicated very precise homing in certain sockeye salmon (O. nerka) populations in British Columbia (Long and Owikeno lakes on the central coast and Sproat, Great Central, and Henderson lakes on Barkley Sound, Vancouver Island). These populations were also sampled for electrophoretic differences at 23 loci. Genetic differences were found among all five populations, and estimates of straying from these data corroborated the parasitological evidence that straying is rare (< 1%).

Application of microsatellite DNA variation to estimation of stock composition and escapement of Nass River sockeye salmon (Oncorhynchus nerka)

1999 ◽  
Vol 56 (2) ◽  
pp. 297-310 ◽  
Author(s):  
Terry D Beacham ◽  
Chris C Wood
Keyword(s):  
Microsatellite Dna ◽  
Sockeye Salmon ◽  
Fishery Management ◽  
Pacific Salmon ◽  
Oncorhynchus Nerka ◽  
River Mouth ◽  
Large River ◽  
Allele Frequencies ◽  
Dna Variation ◽  
Mixed Stock

Spawning escapements of individual Pacific salmon stocks returning to remote spawning locations throughout large river systems can in theory be estimated by mixed-stock analysis of appropriately weighted samples from test fisheries near the river mouth. However, the feasibility of this approach has usually been limited by practical difficulties in identifying closely related populations within the same watershed. Microsatellite DNA techniques offer new promise for overcoming these limitations as illustrated for sockeye salmon (Oncorhynchus nerka) in the Nass River of northern British Columbia. Variation at six microsatellite DNA loci (Omy77, Ots3, Ots100, Ots103, Ots107, and Ots108) was surveyed from about 1400 fish from nine stocks in the Nass River drainage as well as from 249 fish in a test fishery conducted in the lower river during 1996. Five stocks were surveyed in more than one year, and variation in allele frequencies among stocks was, on average, about 10 times greater than annual variation within stocks. Allele frequencies of stocks where the juveniles do not rear in lakes ("riverine" or "sea type") were more similar to each other compared with frequencies from lake-rearing stocks. Significant differences in allele frequencies were observed among most stocks at all loci. About 4.5% of observed variation over all loci was attributable to stock differentiation. Simulated mixed-stock samples suggested that the six microsatellite DNA loci surveyed should provide the ability to provide relatively accurate and precise estimates of stock composition when utilized for fishery management applications. The estimated proportion of Meziadin Lake sockeye salmon in the 1996 test fishery was about 73%, in close agreement with an estimate derived from direct tagging of fish in the test fishery.

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.

Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka)

2012 ◽  
Vol 69 (5) ◽  
pp. 916-929 ◽  
Author(s):  
Daniel Gomez-Uchida ◽  
James E. Seeb ◽  
Christopher Habicht ◽  
Lisa W. Seeb
Keyword(s):  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Temporal Changes ◽  
Allele Frequencies ◽  
Annual Number ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Snp Data ◽  
Spatial Differences ◽  
The Stability

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon ( Oncorhynchus nerka ) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-fold) smaller than spatial differences in allele frequencies when based on nuclear SNPs. Second, the magnitude of temporal change was consistent with a model of genetic drift: (i) SNPs with high levels of differentiation (large θ) and candidates for diversifying selection were not more likely to show significant temporal changes than small-θ SNPs; and (ii) the fraction of single-locus significant tests was consistent with theoretical predictions relating sample size and the annual number of breeders (Nb). Third, estimates of Nb were bound by infinitely large upper 95% confidence intervals, except for one paired collection with unique life-history attributes of both a smoltification phase and generation time shorter than the other paired collections. Use of multigenerational SNP data sets seems a safe practice in management of Alaska sockeye salmon that could be extended to other large, wild aquatic populations.

Population dynamics and asynchrony at fine spatial scales: a case history of sockeye salmon (Oncorhynchus nerka) population structure in Alaska, USA

2012 ◽  
Vol 69 (2) ◽  
pp. 297-306 ◽  
Author(s):  
Thomas P. Quinn ◽  
Harry B. Rich ◽  
Dido Gosse ◽  
Nicolas Schtickzelle
Keyword(s):  
Population Structure ◽  
Sockeye Salmon ◽  
Pacific Salmon ◽  
Spatial Scales ◽  
Oncorhynchus Nerka ◽  
Abiotic Factors ◽  
Small Scale ◽  
Isolated Populations ◽  
Factors Affecting ◽  
Panmictic Population

Pacific salmon (Oncorhynchus spp.) exemplify the ways in which populations are structured by homing and the abiotic factors affecting their dynamics in discrete breeding and rearing habitats. What is the finest spatial scale of their population structure, and where do clusters of spatially proximate breeding groups lie along the continuum from isolated populations – metapopulation – patchy panmictic population? To investigate these questions, we monitored sockeye salmon, Oncorhynchus nerka, spawning in a complex of habitats ~1 km apart, joining to form a single stream flowing into Iliamna Lake, Alaska, USA. Annual surveys revealed levels of asynchrony in productivity that were comparable with values reported for sockeye salmon spawning in separate streams flowing into lakes elsewhere in Bristol Bay. A mark–recapture study revealed very little movement of spawning adults among habitats. The ponds occupied at highest density varied among years, and salmon consistently arrived and spawned later in one pond than the others. These results are consistent with the hypothesis that the salmon structured as a small-scale metapopulation rather than a single panmictic population.

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