scholarly journals Stock Identification of Chum Salmon Overwintering in the Gulf of Alaska by Using a New SNP Baseline

2021 ◽  
Author(s):  
Shigehiko Urawa ◽  
Terry Beacham ◽  
Ben Sutherland ◽  
Shunpei Sato
Keyword(s):  
Chum Salmon ◽  
Gulf Of Alaska ◽  
Stock Identification

scholarly journals Stock-Specific Abundance of Chum Salmon in the Central Gulf of Alaska during Winter

2016 ◽  
Vol 6 (1) ◽  
pp. 153-160
Author(s):  
Shigehiko Urawa ◽  
Terry Beacham ◽  
Shunpei Sato ◽  
Toshiki Kaga ◽  
Beverly Agler ◽  
...  
Keyword(s):  
Chum Salmon ◽  
Gulf Of Alaska

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 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 Stock-Specific Abundance of Chum Salmon in the Central Gulf of Alaska during Winter

2016 ◽  
Vol 6 (1) ◽  
pp. 153-160
Author(s):  
Shigehiko Urawa ◽  
Terry Beacham ◽  
Shunpei Sato ◽  
Toshiki Kaga ◽  
Beverly Agler ◽  
...  
Keyword(s):  
Chum Salmon ◽  
Gulf Of Alaska

scholarly journals In-field genetic stock identification of overwintering coho salmon in the Gulf of Alaska: Evaluation of Nanopore sequencing for remote real-time deployment

2021 ◽  
Author(s):  
Christoph M. Deeg ◽  
Ben J. G. Sutherland ◽  
Tobi J. Ming ◽  
Colin Wallace ◽  
Kim Jonsen ◽  
...  
Keyword(s):  
Real Time ◽  
Coho Salmon ◽  
Gulf Of Alaska ◽  
Amplicon Sequencing ◽  
Stock Identification ◽  
Nanopore Sequencing ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Batch Sizes ◽  
Sequencing Platforms

Genetic stock identification (GSI) by single nucleotide polymorphism (SNP) sequencing has become the gold standard for stock identification in Pacific salmon, which are found in mixed-stocks during the oceanic phase of their lifecycle. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third-generation single-molecule sequencing platforms, like the Oxford Nanopore minION, provide base calling on portable, pocket-sized sequencers and hold promise for the application of real-time, in-field stock identification on variable batch sizes. Here we report and evaluate utility and comparability of at-sea stock identification of coho salmon Oncorhynchus kisutch based on targeted SNP amplicon sequencing on the minION platform during the International Year of the Salmon Signature Expedition to the Gulf of Alaska in the winter of 2019. Long read sequencers are not optimized for short amplicons, therefore we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at-sea yielded stock assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls agreed with Ion Torrent based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed coho salmon in the queried baseline dataset contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time, accuracy, throughput, and cost, as well as augmentation of the existing baselines, specifically in stocks from coastal northern BC and Alaska. If successfully implemented, Nanopore sequencing will provide an alternative method to the large-scale laboratory approach. Genotyping by amplicon sequencing in the hands of diverse stakeholders could inform management decisions over a broad expanse of the coast by allowing the analysis of small batches in remote areas in near real-time.

Times of Annulus Formation on Scales of Sockeye, Pink, and Chum Salmon in the Gulf of Alaska

1966 ◽  
Vol 23 (9) ◽  
pp. 1403-1410 ◽  
Author(s):  
H. T. Bilton ◽  
S. A. M. Ludwig
Keyword(s):  
Chum Salmon ◽  
Annual Ring ◽  
Pink Salmon ◽  
Gulf Of Alaska ◽  
Oncorhynchus Gorbuscha ◽  
Annulus Formation ◽  
Canadian Research

On scales of pink (Oncorhynchus gorbuscha), chum (O. keta), and possibly sockeye (O. nerka) salmon caught by Canadian research vessels throughout the Gulf of Alaska at various times of the year, the annual ring began to form sometime between early November and January. Many of the sockeye and pink salmon had completed the annulus sometime in December or January, whereas the chum salmon completed their's later, in February or March. For both sockeye and chum salmon, scales of younger fish tended to commence new growth at an earlier date than did those of older fish.

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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