scholarly journals Population structure of chum salmon and selection on the markers collected for stock identification

2021 ◽  
Author(s):  
Shuichi Kitada ◽  
Hirohisa Kishino
Keyword(s):  
Population Structure ◽  
Chum Salmon ◽  
Stock Identification

Population structure and stock identification of chum salmon (Oncorhynchus keta) from British Columbia determined with microsatellite DNA variation

2008 ◽  
Vol 86 (9) ◽  
pp. 1002-1014 ◽  
Author(s):  
Terry D. Beacham ◽  
Brian Spilsted ◽  
Khai D. Le ◽  
Michael Wetklo
Keyword(s):  
British Columbia ◽  
Population Structure ◽  
Chum Salmon ◽  
Oncorhynchus Keta ◽  
Stock Identification ◽  
Dna Variation ◽  
Coastal Fisheries ◽  
Chum Salmon Oncorhynchus Keta ◽  
Regional Estimates ◽  
Mixed Stock

Variation at 14 microsatellite loci was surveyed in 205 populations of chum salmon ( Oncorhynchus keta (Walbaum in Artedi, 1792)) from British Columbia to determine population structure and the possible application of microsatellites to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index (FST) over all populations and loci was 0.016, with individual locus values ranging from 0.006 to 0.059. Sixteen regional stocks were defined in British Columbia for stock identification applications. Analysis of simulated fishery samples suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. The main stocks that constitute the October 2007 samples of migrating chum salmon through Johnstone Strait in southern British Columbia were Fraser River (45%–64%), southern British Columbia mainland (22%), and east coast Vancouver Island (13%–28%), within the range of those to be expected in samples from Johnstone Strait. Microsatellites have the ability to provide fine-scale resolution of stock composition in British Columbia coastal fisheries.

scholarly journals Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon

2020 ◽  
Vol 10 (5) ◽  
pp. 1553-1561 ◽  
Author(s):  
Garrett McKinney ◽  
Megan V. McPhee ◽  
Carita Pascal ◽  
James E. Seeb ◽  
Lisa W. Seeb
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Network Analysis ◽  
Chum Salmon ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Population Substructure ◽  
Chromosome Inversion ◽  
Genomic Features ◽  
Chromosome Inversions

Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.

Biochemical Genetic Survey and Stock Identification of Chum Salmon (Oncorhynchus keta) in British Columbia

1987 ◽  
Vol 44 (10) ◽  
pp. 1702-1713 ◽  
Author(s):  
T. D. Beacham ◽  
A. P. Gould ◽  
R. E. Withler ◽  
C. B. Murray ◽  
L. W. Barner
Keyword(s):  
British Columbia ◽  
Chum Salmon ◽  
Electrophoretic Analysis ◽  
South Coast ◽  
Oncorhynchus Keta ◽  
Stock Identification ◽  
Fraser River ◽  
Genetic Method ◽  
Chum Salmon Oncorhynchus Keta ◽  
Queen Charlotte Islands

We examined genetic variability using electrophoretic analysis of 83 chum salmon (Oncorhynchus keta) stocks in British Columbia and used regional differences in genotypic frequencies of seven polymorphic loci to estimate stock compositions in a number of commercial and experimental test fisheries. Chum salmon from five regions could be discriminated: Queen Charlotte islands, north and central coast, west coast of Vancouver Island, the Fraser River and its tributaries, and the south coast (rivers draining into Johnstone Strait and the Strait of Georgia). Allelic frequencies from 33 stocks were generally stable over a period of 2 yr or more. South coast chum salmon was the dominant run migrating through upper Johnstone Strait in October 1982–85. The genetic method of stock identification provided managers with the relative proportions of Fraser River and other groups of chum salmon in a number of fisheries and allowed managers to regulate more effectively the exploitation rate of Fraser River chum salmon.

scholarly journals Development of molecular markers for genetic stock identification of chum salmon

2002 ◽  
Vol 68 (sup1) ◽  
pp. 353-356 ◽  
Author(s):  
SYUITI ABE ◽  
SHUNPEI SATO ◽  
HIROYUKI KOJIMA ◽  
JUNKO ANDO ◽  
HIRONORI ANDO ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Chum Salmon ◽  
Stock Identification ◽  
Genetic Stock ◽  
Genetic Stock Identification

Population Structure and Identification of North Pacific Ocean Chum Salmon (Oncorhynchus keta) Revealed by an Analysis of Minisateliite DNA Variation

1994 ◽  
Vol 51 (6) ◽  
pp. 1430-1442 ◽  
Author(s):  
Eric B. Taylor ◽  
Terry D. Beacham ◽  
Masahide Kaeriyama
Keyword(s):  
Population Structure ◽  
Pacific Ocean ◽  
North Pacific ◽  
Chum Salmon ◽  
North Pacific Ocean ◽  
Oncorhynchus Keta ◽  
The North ◽  
Yukon River ◽  
Regional Population ◽  
The North Pacific

We examined geographic variability in minisatellite DNA in chum salmon (Oncorhynchus keta) from 42 populations from the North Pacific Ocean to (1) determine the extent of regional population structure at minisatellite loci and (2) assess the ability of minisatellite variability to determine the geographic origin in individual chum salmon. Restriction fragments from 1.6 to 13.6 kilobase pairs in molecular weight were resolved with a minisatellite probe. The fragments were inherited from parent to offspring and appeared to represent segregation at two linked loci. Minisateliite DNA variability was negligible between annual samples from the same rivers, and chum salmon fell into three regional population groupings: (i) Japanese, (ii) Russian/Yukon River, and (iii) southeastern Alaska/British Columbia salmon. These regional groupings probably reflect historical patterns of postglacial dispersal of chum salmon from three distinct refugia in the North Pacific. We used restriction fragment counts as input to linear discriminant and neural network classification of independent test samples of salmon. Accuracies of 90–95, 81–86, and 72–80% were achieved when classifying fish as of either Japan/Russia/Yukon River versus southeastern Alaska/British Columbia origin, Japan versus Russia/Yukon River origin, or Russia versus Yukon River origin, respectively.

scholarly journals Stock identification of chum salmon Oncorhynchus keta from their maturity and scale chraracters.

1989 ◽  
Vol 55 (4) ◽  
pp. 651-656 ◽  
Author(s):  
Yukimasa Ishida ◽  
Soto Ito ◽  
Kenji Takagi
Keyword(s):  
Chum Salmon ◽  
Oncorhynchus Keta ◽  
Stock Identification ◽  
Chum Salmon Oncorhynchus Keta

Genetic stock identification of chum salmon in the Bering Sea and North Pacific Ocean using mitochondrial DNA microarray

Aquaculture ◽  
2007 ◽  
Vol 272 ◽  
pp. S238-S239
Author(s):  
S. Abe ◽  
S. Moriya ◽  
S. Sato ◽  
T. Azumaya ◽  
O. Suzuki ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Microarray ◽  
Bering Sea ◽  
North Pacific ◽  
Chum Salmon ◽  
North Pacific Ocean ◽  
Stock Identification ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
The Bering Sea

Population structure and stock identification of chum salmonOncorhynchus ketafrom Japan determined by microsatellite DNA variation

2008 ◽  
Vol 74 (5) ◽  
pp. 983-994 ◽  
Author(s):  
TerryD BEACHAM ◽  
Shunpei SATO ◽  
Shigehiko URAWA ◽  
KhaiD LE ◽  
Michael WETKLO
Keyword(s):  
Population Structure ◽  
Microsatellite Dna ◽  
Stock Identification ◽  
Dna Variation

Microsatellite Stock Identification of Chum Salmon on a Pacific Rim Basis

2009 ◽  
Vol 29 (6) ◽  
pp. 1757-1776 ◽  
Author(s):  
Terry D. Beacham ◽  
John R. Candy ◽  
C. Wallace ◽  
Shigehiko Urawa ◽  
Shunpei Sato ◽  
...  
Keyword(s):  
Chum Salmon ◽  
Pacific Rim ◽  
Stock Identification
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