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Genetic Baseline For Cook Inlet Coho Salmon And Evaluations For Mixed Stock Analysis
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Book Synopsis Genetic Baseline for Cook Inlet Coho Salmon and Evaluations for Mixed Stock Analysis by : Andrew W. Barclay
Download or read book Genetic Baseline for Cook Inlet Coho Salmon and Evaluations for Mixed Stock Analysis written by Andrew W. Barclay and published by . This book was released on 2019 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report describes the updated genetic baseline for Cook Inlet coho salmon and includes new evaluations for mixed stock analysis (MSA) in Cook Inlet. Coho salmon are harvested in commercial fisheries in Upper Cook Inlet, Alaska, with an average annual harvest of 180,005 fish (2008?2017). Harvests often occur in areas where stocks intermingle, so the exploitation and productivity of individual stocks are not well known. This lack of knowledge hinders fishery management based on the sustained yield principle. Genetic analysis, using single nucleotide polymorphism (SNP) technology, can discriminate among discrete fish stocks in fishery samples when adequate stock structure exists. Here, we update a previously reported baseline of 84 populations using 86 SNP markers with an additional 10 populations and a set of 82 SNP markers included in the previous baseline to determine population structure and test potential reporting groups for MSA. Testing of potential reporting groups revealed 11 groups with adequate genetic divergence to meet the criteria for reporting groups. The data presented in this report will allow for additional baseline evaluation tests tailored for specific MSA study objectives pertinent to Cook Inlet mixed stock fisheries in the future.
Book Synopsis Current Status of Genetic Studies of Coho Salmon from Southcentral Alaska and Evaluations for Mixed Stock Analysis in Cook Inlet by : Andrew W. Barclay
Download or read book Current Status of Genetic Studies of Coho Salmon from Southcentral Alaska and Evaluations for Mixed Stock Analysis in Cook Inlet written by Andrew W. Barclay and published by . This book was released on 2017 with total page 47 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report describes the current status of genetic studies for coho salmon in Southcentral Alaska and initial evaluations for mixed-stock analysis (MSA) in Cook Inlet. Coho salmon are harvested in commercial fisheries in Upper Cook Inlet, Alaska, with an average annual harvest of 171,273 fish (2005-2014). Harvests often occur in areas where stocks intermingle, so the exploitation and productivity of individual stocks are not well known. This lack of knowledge hinders fishery management based on the sustained yield principle. Mixed-stock analysis has been used to estimate stock compositions of fishery mixtures in coho salmon elsewhere in the Pacific Northwest; however, only limited baseline existed for Cook Inlet. Within Cook Inlet, we examined a baseline of 84 populations for 86 single nucleotide polymorphism markers to examine population structure and test for potential reporting groups (stocks). From the southern edge of the Kenai Peninsula, we analyzed 3 populations to investigate the genetic legacy of stocking programs in the area. Population structure indicated that populations generally cluster by drainage, with the most genetically distinct populations in the more southerly drainages and in the upper reaches of the larger drainages. Testing of potential reporting groups revealed 7 groups with adequate genetic divergence to meet the criteria for reporting groups. Due to the sparse representation of collections in the baseline for the Yentna River drainage, additional representation within this drainage would be prudent before using it as its own reporting group in MSA. The data presented in this report will allow for additional baseline evaluation tests tailored for specific MSA study objectives pertinent to Cook Inlet mixed-stock fisheries in the future. The 3 populations from the southern edge of the Kenai Peninsula were most similar to each other, but divergent from Cook Inlet populations, suggesting little genetic introgression from stocking programs.
Book Synopsis Genetic Stock Identification of Upper Cook Inlet Coho Salmon Harvest, 2013-2015 by : Andrew W. Barclay
Download or read book Genetic Stock Identification of Upper Cook Inlet Coho Salmon Harvest, 2013-2015 written by Andrew W. Barclay and published by . This book was released on 2017 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt: Coho salmon support important fisheries in Upper Cook Inlet. The commercial fishery harvests an average of 170,410 fish annually (2006-2015) during their homeward migration, but little is known about stock contributions. Without stock-specific harvest information, the exploitation and productivity of stocks cannot be estimated, limiting management based on sustained yield. Here we report the genetic mixed stock analysis of coho salmon harvested in the 2013-2015 test and commercial drift and set gillnet fisheries of Upper Cook Inlet. Analyses were performed using a previously reported baseline of 84 populations and 86 SNP markers. No consistent spatial or temporal patterns were observed in the stock compositions of either the southern or northern offshore test fisheries across years. However, within years, the stock compositions of the 2 test fisheries were similar. Samples from the commercial coho salmon fisheries in Upper Cook Inlet represented 77-86% of the harvest. Northern Cook Inlet coho salmon stocks (Northwest CI/Yentna, Susitna, and Knik) made up the majority of the harvest and we found several consistent temporal and spatial patterns of stock compositions within the commercial fishery across all 3 years. In the Central District drift gillnet fishery, stock proportions were fairly consistent within years until August, when proportions of Northwest CI/Yentna increased in tandem with fishery restrictions. In the Northern District set gillnet harvest, Northern stock proportions decreased and proportions of Turnagain/Northeast CI coho salmon increased after about August 12; General Subdistrict (south) harvests were dominated by Susitna and Northwest CI/Yentna coho salmon, General Subdistrict (north) harvests were dominated by Knik, and Eastern Subdistrict harvests were dominated by Turnagain/Northeast CI coho salmon. These and future Cook Inlet coho salmon commercial stock composition estimates will aid in the development of brood tables, provide for development of coho salmon escapement goals using spawner-recruit analysis, and provide data for annual run forecasts.
Book Synopsis Genetic Baseline for Upper Cook Inlet Chinook Salmon by : Andrew W. Barclay
Download or read book Genetic Baseline for Upper Cook Inlet Chinook Salmon written by Andrew W. Barclay and published by . This book was released on 2015 with total page 33 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chinook salmon support important commercial, sport, personal use, subsistence, and educational fisheries in Cook Inlet, Alaska with annual harvests that can exceed 90,000 fish. Many populations contribute to these harvests, which often occur in areas where stocks intermingle, so the exploitation and productivity of individual stocks are not well known. This lack of knowledge compromises both protection of stocks from overharvest and utilization of stocks with fish in excess of spawning needs. Genetic analysis, using single nucleotide polymorphism (SNP) technology, can discriminate among discrete fish stocks in fishery samples if adequate stock structure exists. Here, we update a peviously reported baseline of 30 populations using 46 SNP markers with an additional 25 populations and a subset of 42 SNP markers to determine population structure and test potential reporting groups for mixed stock analysis (MSA). After nearly doubling the number of populations in the baseline, southern region stocks continue to have greater genetic diversity than northern region stocks.
Book Synopsis Genetic Mixed Stock Analysis of Upper Cook Inlet Coho Salmon Harvest, 2016 by : Andrew W. Barclay
Download or read book Genetic Mixed Stock Analysis of Upper Cook Inlet Coho Salmon Harvest, 2016 written by Andrew W. Barclay and published by . This book was released on 2018 with total page 71 pages. Available in PDF, EPUB and Kindle. Book excerpt: Coho salmon support important commercial and sport fisheries in Upper Cook Inlet. The Upper Cook Inlet commercial fishery harvests an average of 167,372 fish annually (2007?2016). Genetic mixed stock analysis of coho salmon harvested in test and commercial drift and set gillnet fisheries of Upper Cook Inlet was first reported for 2013?2015 harvests. Here we report genetic mixed stock analysis results for the 2016 Upper Cook coho salmon harvest. Both spatial and temporal patterns in stock composition were observed in the offshore test fishery transect: higher proportions of Turnagain/Northeast CI on the Western end and Susitna and Knik on the Eastern end, and higher proportions of Turnagain/Northeast CI and Susitna in early July and Knik in late July. Samples represented 84% of the commercial coho salmon harvest in Upper Cook Inlet. Northern Cook Inlet coho salmon stocks Northwest CI/Yentna, Susitna, and Knik made up the majority of the harvest. In August in the Central District drift gillnet fishery, proportions of Northwest CI/Yentna increased and Susitna and Knik coho salmon decreased. In the Northern District set gillnet harvest, after about August 8, Northwest CI/Yentna, Susitna, and Knik stock proportions decreased and proportions of Turnagain/Northeast CI coho salmon increased. General Subdistrict (south) harvests were dominated by Susitna and Northwest CI/Yentna, General Subdistrict (north) harvests were dominated by Knik, and Eastern Subdistrict harvests were dominated by Turnagain/Northeast CI coho salmon. These and future Cook Inlet coho salmon commercial stock composition estimates will aid in the development of brood tables to establish escapement goals using spawner-recruit analysis, and provide data for annual run forecasts.
Book Synopsis Report to the Alaska State Legislature on Status of Cook Inlet Coho and Sockeye Salmon Genetic Projects, 2015 by : Andrew W. Barclay
Download or read book Report to the Alaska State Legislature on Status of Cook Inlet Coho and Sockeye Salmon Genetic Projects, 2015 written by Andrew W. Barclay and published by . This book was released on 2016 with total page 20 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report summarizes the status of activities associated with legislative increments directed at Cook Inlet coho Oncorhynchus kisutch and sockeye O. nerka salmon genetic studies conducted by the Division of Commercial Fisheries Gene Conservation Laboratory and Central Region staff. The coho salmon study involved 3 investigative phases. In Phase I, analysis of existing samples indicated that sufficient population genetic structure exists among populations of Cook Inlet coho salmon to warrant construction of a full genetic baseline for genetic stock identification. In Phase II, development of the genetic baseline indicated 8 potential genetic reporting groups for genetic stock identification of Cook Inlet coho salmon fishery samples. The final report for Phase II will be published in the spring of 2016. In Phase III genetic stock identification was used to estimate the stock composition of harvests in test and commercial fisheries of Cook Inlet for the 2013-2015 seasons. Results from these analyses will be used to determine spatial and temporal distribution of coho salmon in the offshore test fishery and commercial harvest and to estimate the total harvest of selected stocks in the commercial salmon fisheries. During this period over 23,000 samples were collected for analysis from the Central District drift gill net fishery, Upper subdistrict set gillnet fishery, General and Eastern subdistrict set gillnet fisheries, and the northern and southern offshore test fisheries. The final report for Phase III is expected to be completed by the end of summer 2016. A fourth study, for sockeye salmon, will analyze the DNA from archived scales to retrospectively estimate historic stock compositions of Cook Inlet harvests. This is the third year of that 5 year project in which the laboratory will reconstruct escapement and total runs of sockeye salmon for Susitna River and the major systems in Upper Cook Inlet.
Book Synopsis Genetic Mixed Stock Analysis of Upper Cook Inlet Sockeye Salmon Harvest, 2014 by : Andrew W. Barclay
Download or read book Genetic Mixed Stock Analysis of Upper Cook Inlet Sockeye Salmon Harvest, 2014 written by Andrew W. Barclay and published by . This book was released on 2018 with total page 34 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic mixed stock analysis has been used to estimate the stock compositions of sockeye salmon Oncorhynchus nerka harvested in commercial fisheries in Upper Cook Inlet (UCI), Alaska, since 2005. Here we report the genetic mixed stock analysis of samples representing 90.5% of the 2014 UCI commercial fishery harvests. Postseason analyses were performed using a previously reported baseline of 69 populations and 96 single nucleotide polymorphic markers, with the addition of 2 populations in the West reporting group (Harriet Creek and Packers Lake late run). Some stock composition patterns in the commercial fishery were similar to previous years. Drift gillnet and eastern fisheries captured greater proportions of Kenai and Kasilof rivers fish than western and northern fisheries; western set gillnet fisheries harvested a greater proportion of fish from the west side of Cook Inlet, but the drift gillnet fishery harvested greater numbers of west side fish; set gillnet fisheries closer to the Kenai or Kasilof river mouths harvested larger proportions of fish from those rivers; and set gillnet fishing areas in the Northern District generally harvested fish from nearby rivers. Unexpectedly, Susitna River fish made up a higher fraction of the drift gillnet harvest when the fleet was restricted to eastern Cook Inlet waters than when they were not restricted to eastern waters. Estimates of stock-specific harvests for UCI commercial fisheries in 2014 build upon previous years in refining understanding of productivity and the effect of management actions on the stock composition of commercial sockeye salmon harvests.
Book Synopsis Genetic Baseline for Mixed Stock Analyses of Sockeye Salmon Harvested in Southeast Alaska for Pacific Salmon Treaty Applications, 2018 by : Serena D. Rogers Olive
Download or read book Genetic Baseline for Mixed Stock Analyses of Sockeye Salmon Harvested in Southeast Alaska for Pacific Salmon Treaty Applications, 2018 written by Serena D. Rogers Olive and published by . This book was released on 2018 with total page 60 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sockeye salmon (Oncorhynchus nerka) are an important resource in Southeast Alaska (SEAK) and are harvested in subsistence, personal use, sport, and commercial fisheries. Commercial fisheries for sockeye salmon in SEAK have been prosecuted for over 100 years, with many fisheries harvesting mixed stocks composed of sockeye salmon originating from as far north as Prince William Sound and as far south as Washington. The Alaska Department of Fish and Game uses genetic mixed stock analysis to estimate stock compositions for harvest management and to meet Pacific Salmon Treaty obligations. This report describes the methods used to develop a genetic baseline of single nucleotide polymorphism allele frequencies to be used for genetic mixed stock analysis of sockeye salmon in SEAK fisheries. This baseline includes 28,609 individuals from 345 collections representing 238 populations in up to 9 reporting groups spanning from Prince William Sound to Washington. We used repeated 100% proof tests to measure the baseline's ability to accurately allocate mixed stock samples to reporting groups. Correct allocations in these tests ranged from 92.6% to 99.5%. The ability of this baseline to perform accurately in proof tests was due to the large amount of genetic variation found among populations both within and among the reporting groups. This baseline has been used successfully to estimate the stock composition of Pacific Salmon Treaty and domestic sockeye salmon stocks harvested in SEAK commercial fisheries.
Book Synopsis Genetic Stock Identification of Upper Cook Inlet Sockeye Salmon Harvest, 2005-2008 by : Andrew W. Barclay
Download or read book Genetic Stock Identification of Upper Cook Inlet Sockeye Salmon Harvest, 2005-2008 written by Andrew W. Barclay and published by . This book was released on 2010 with total page 109 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report updates previously reported analyses of genetic population structure and mixed-stock analysis of sockeye salmon, Oncorhynchus nerka, originating from all major spawning systems and harvested in commercial fisheries in Upper Cook Inlet, Alaska.
Book Synopsis Genetic Stock Identification of Upper Cook Inlet Sockeye Salmon Harvest, 2009 by : Andrew W. Barclay
Download or read book Genetic Stock Identification of Upper Cook Inlet Sockeye Salmon Harvest, 2009 written by Andrew W. Barclay and published by . This book was released on 2010 with total page 54 pages. Available in PDF, EPUB and Kindle. Book excerpt: This reports on mixed-stock analysis based on genetic data which was used to estimate the stock compositions of sockeye salmon (Oncorhynchus nerka) harvested in commercial fisheries in upper Cook Inlet, Alaska.
Book Synopsis Pink Salmon Genetic Baseline for Lower Cook Inlet, 2021–2022 by : Andrew W. Barclay
Download or read book Pink Salmon Genetic Baseline for Lower Cook Inlet, 2021–2022 written by Andrew W. Barclay and published by . This book was released on 2022 with total page 14 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genetic Stock Identification of Upper Cook Inlet Sockeye Salmon Harvest, 2011 by : Andrew W. Barclay
Download or read book Genetic Stock Identification of Upper Cook Inlet Sockeye Salmon Harvest, 2011 written by Andrew W. Barclay and published by . This book was released on 2014 with total page 60 pages. Available in PDF, EPUB and Kindle. Book excerpt: This reports on mixed-stock analysis based on genetic data which was used to estimate the stock compositions of sockeye salmon (Oncorhynchus nerka) harvested in commercial fisheries in upper Cook Inlet, Alaska.
Book Synopsis Genetic Baseline of North American Sockeye Salmon for Mixed Stock Analyses of Kodiak Management Area Commercial Fisheries, 2014-2016 by : Kyle Shedd
Download or read book Genetic Baseline of North American Sockeye Salmon for Mixed Stock Analyses of Kodiak Management Area Commercial Fisheries, 2014-2016 written by Kyle Shedd and published by . This book was released on 2016 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Precise, accurate estimates of stock-specific harvests of sockeye salmon (Oncorhynchus nerka) are lacking for commercial fisheries in the Kodiak Management Area (KMA. Such information would be useful for reconstructing runs, building accurate brood tables to define escapement goals, and refining management by identifying spatial and temporal harvest patterns of local and non-local stocks. Hence, the department developed a genetic baseline for mixed-stock analysis (MSA) to estimate the stock compositions of sockeye salmon harvests in select KMA commercial salmon fisheries from 2014-2016. This report describes the methodology used to build a baseline, examines costs and benefits of a reduced marker set, describes the performance of the baseline for MSA, and provides guidance on how to interpret biases documented in the MSA tests when evaluating future stock composition estimates of KMA fishery mixtures. This genetic baseline uses single nucleotide polymorphism (SNP) markers and builds on the Western Alaska Salmon Stock Identification Project (WASSIP) sockeye salmon baseline to include additional populations in KMA and extends coverage south from Cape Suckling, Alaska to the Columbia River, Washington. The final baseline contains 65,332 individuals from 762 collections representing 473 populations in 15 reporting groups. Mean population sample size was 138 individuals. We used 2 types of tests to measure the baseline’s ability to correctly allocate to reporting groups: 100% proof tests and fishery scenario tests. Correct allocations for 100% proof tests averaged 98.2%, ranged from 80.4% to 99.6%, and 73 of the 75 proof tests met our goal of 90% correct allocation. Fishery scenario tests did not indicate any consistent directional biases among reporting groups, but misallocation was observed between Frazer and Ayakulik. Reducing the baseline from 96 to 48 SNPs had negligible effects on MSA estimates. This baseline will provide accurate and precise estimates of stock composition in KMA sockeye salmon fisheries.
Book Synopsis Population Genetics and Mixed Stock Analysis of Chum Salmon (Oncorhynchus Keta) with Molecular Genetics by : Michael R. Garvin
Download or read book Population Genetics and Mixed Stock Analysis of Chum Salmon (Oncorhynchus Keta) with Molecular Genetics written by Michael R. Garvin and published by . This book was released on 2012 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chum salmon (Oncorhynchus keta) are important for subsistence and commercial harvest in Alaska. Variability of returns to western Alaskan drainages that caused economic hardship for stakeholders has led to speculation about reasons, which may include both anthropogenic and environmental causes in the marine environment. Mixed stock analysis (MSA) compares genetic information from an individual caught at sea to a reference baseline of genotypes to assign it to its population of origin. Application of genetic baselines requires several complex steps that can introduce bias. The bias may reduce the accuracy of MSA and result in overly-optimistic evaluations of baselines. Moreover, some applications that minimize bias cannot use informative haploid mitochondria) variation. Costs of baseline development are species-specific and difficult to predict. Finally, because populations of western Alaskan chum salmon demonstrate weak genetic divergence, samples from mixtures cannot be accurately assigned to a population of origin. The chapters of this thesis address three challenges. The first chapter describes technical aspects of genetic marker development. The second chapter describes a method to evaluate the precision and accuracy of a genetic baseline that accepts any type of data and reduces bias that may have been introduced during baseline development. This chapter also includes a method that places a cost on baseline development by predicting the number of markers needed to achieve a given accuracy. The final chapter explores the reasons for the weak genetic structure of western Alaskan chum salmon populations. The results of those analyses and both geological and archaeological data suggest that recent environmental and geological processes may be involved. The methods and analyses in this thesis can be applied to any species and may be particularly useful for other western Alaskan species.
Download or read book Technical Report written by and published by . This book was released on 2003 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Recommendations for Application of Genetic Stock Identification (GSI) Methods to Management of Ocean Salmon Fisheries by : Pacific Salmon Commission. GSI Steering Committee
Download or read book Recommendations for Application of Genetic Stock Identification (GSI) Methods to Management of Ocean Salmon Fisheries written by Pacific Salmon Commission. GSI Steering Committee and published by . This book was released on 2008 with total page 48 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Operational Plan by : Justin T. Priest
Download or read book Operational Plan written by Justin T. Priest and published by . This book was released on 2020 with total page 9 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This project is a two-year effort to collect tissue samples from coho salmon Oncorhynchus kisutch populations across Southeast Alaska to create a more comprehensive genetic baseline. Previous genetic tissue sampling of coho salmon in Southeast Alaska has been conducted opportunistically in conjunction with other field work; this project will add to existing sample collections and target undersampled populations, with a focus on populations in transboundary rivers and the Northern Boundary Area that are managed under the Pacific Salmon Treaty. The creation of a genetic baseline for coho salmon will assist in future stock management by allowing population differentiation to inform regulatory decisions and allow for genetic stock identification (GSI) of commercial harvests."--Page 1
