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.

Reply to the comment by Crook and Koster (2006) 'Temporal change in fish assemblages in the lower Goulburn River, south-eastern Australia'

2006 ◽  
Vol 57 (3) ◽  
pp. 309
Author(s):  
Carmel A. Pollino ◽  
Pat Feehan ◽  
Michael R. Grace ◽  
Barry T. Hart
Keyword(s):  
Multivariate Statistics ◽  
Fish Assemblages ◽  
Temporal Change ◽  
Spatial Scales ◽  
Fish Communities ◽  
Data Sets ◽  
Catchment Scale ◽  
Eastern Australia ◽  
Spatial Differences ◽  
The Stability

In an earlier paper, multivariate statistics were used on historic fisheries data sets to show spatial differences between fish communities in the Goulburn Catchment (Victoria, Australia). In this reply paper, some further statistical analyses are presented to provide evidence for the assertion that fish communities at each site were stable over the temporal scale of the data was valid. Indeed, evidence for the stabilisation and persistence of fish communities after a major disturbance has also been recognised in other studies. Furthermore, in making judgements about the stability and persistence of fish communities, the scale of a study is an important factor, with patterns at the catchment scale often not being the same as those at smaller spatial scales.

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.

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%).

scholarly journals Genomic changes associated with reproductive and migratory ecotypes in sockeye salmon (Oncorhynchus nerka)

2017 ◽  
Author(s):  
Andrew J Veale ◽  
Michael A Russello
Keyword(s):  
Life History ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Multiple Comparisons ◽  
Nucleotide Polymorphisms ◽  
Life History Variation ◽  
Genomic Changes ◽  
Outlier Loci ◽  
Patterns And Processes ◽  
Genomic Regions

AbstractMechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms (SNPs), 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Eighty-six of these outliers were present in multiple comparisons, with thirty-three detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser and Snake). We also detected several islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The SNPs and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.

scholarly journals Enhanced genetic differentiation of Japanese chum salmon identified from a meta-analysis of allele frequencies

2019 ◽  
Author(s):  
Shuichi Kitada ◽  
Hirohisa Kishino
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Chum Salmon ◽  
Meta Analysis ◽  
Distribution Range ◽  
Allele Frequencies ◽  
Geographical Information ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Athletic Ability

AbstractThe number of individuals returning to Japan, the location of the world’s largest chum salmon hatchery program, has declined substantially over two decades. To find the genetic cause of this severe decline never previously experienced, we analyzed published genetic data sets for adult chum salmon, namely, 10 microsatellites, 53 single nucleotide polymorphisms (SNPs) and a combined mitochondrial DNA locus (mtDNA3), and three isozymes, from 576 locations in the distribution range (n = 76,363). The SNPs were selected for stock identification to achieve high accuracy, were highly differentiated in the distribution range and included important genes related to reproduction, growth and immune responses. By contrasting the genetic differentiation of these genes with the population structure estimated from the neutral microsatellite markers, we identified genes that distort the neutral population structure. We matched the sampling locations of SNPs and isozymes with those of microsatellites based on geographical information, and performed regression analyses of SNP and isozyme allele frequencies of matched locations on the population structure. TreeMix analysis indicated two admixture events, from Japan/Korea to Russia and the Alaskan Peninsula. Meta-analysis of allele frequencies identified three outliers, mtDNA3 (control region and NADH-3), GnRH373 (gonadotropin-releasing hormone) and U502241 (unknown), which showed enhanced differentiation in Japanese/Korean populations compared with the others. GnRH improves stream odor discrimination and has increased expression in adult chum salmon brains during homing migration, suggesting that the current admixture was caused by GnRH373 differentiation. mtDNA plays a key role in endurance exercise training, energy metabolism and oxygen consumption, suggesting that the significant reduction in mtDNA3 allele frequencies reduced aerobic athletic ability, as observed in YouTube videos. Our analyses relied on limited data sets, though they were the best available. Clearly, genome-wide data will be needed to fully address this issue.

Genetic Models for Cyclic Dominance in Sockeye Salmon (Oncorhynchus nerka)

1992 ◽  
Vol 49 (2) ◽  
pp. 281-292 ◽  
Author(s):  
Carl Walters ◽  
J. C. Woodey
Keyword(s):  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Large Fraction ◽  
Fishing Mortality ◽  
Age At Maturity ◽  
Dominant Trait ◽  
High Productivity ◽  
Cyclic Patterns ◽  
The Face ◽  
The Stability

A simple genetic mechanism may be partly responsible for maintaining violent cycles in abundance of some Fraser River sockeye salmon (Oncorhynchus nerka) stocks. If age at maturity is highly heritable, spawning runs in low cycle lines may have high percentages of age 5 spawners that tend to produce offspring that will return at age 5, due to production of low percentages of such spawners by preceding high cycle lines. Then even if each low cycle line has a high productivity per spawner, a large fraction of this productivity may be "lost" to the cycle line, in the form of age 5 recruits to other cycle lines. In the face of high fishing mortality, even a small relative loss from any cycle line may cause it to remain small relative to other lines. This model explains several observations, such as high productivity per spawner in low cycle lines, that cannot be explained by previous hypotheses involving depensatory predation or food supply. However, it is unlikely that genetic effects alone are responsible for the stability of cyclic patterns, unless low offcycle runs consist entirely of "temporal colonizer" genotypes that produce a high proportion of age 5 offspring as a dominant trait.

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.

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