Status report for genetic stock identification studies of Pacific Rim sockeye salmon (original) (raw)
2011
The Fishery Manuscript series was established in 1987 by the Division of Sport Fish for the publication of technically-oriented results of several years' work undertaken on a project to address common objectives, provide an overview of work undertaken through multiple projects to address specific research or management goal(s), or new and/or highly technical methods, and became a joint divisional series in 2004 with the Division of Commercial Fisheries. Fishery Manuscripts are intended for fishery and other technical professionals. Fishery Manuscripts are available through the Alaska State Library and on the Internet http://www.adfg.alaska.gov/sf/publications/ This publication has undergone editorial and peer review.
Significant genetic variation exists among populations of Chinook salmon from the Yukon River drainage, and use of this variation for providing estimates of stock composition of fishery harvests has been possible since 1992. Recent analyses using DNA markers confirmed the results of the earlier studies and provided the possibility for greater accuracy and precision of stock composition estimates, but one of the analyses used an unstandardized set of microsatellite markers. This report presents the results of a survey of 13 microsatellite loci (from a standardized set used by the Pacific Salmon Commission Chinook Technical Committee) in 2646 individual fish representing 11 U.S. Chinook salmon populations. Average genotyping success rate was approximately 83%, with the majority of failures in the Anvik collection (success rate ~30% in the Anvik). The number of alleles observed per locus ranged from five (Ots9) to forty-four (Omm1080), and the total across loci was 241. Estimates of per-locus F ST ranged from 0.013 to 0.054, suggesting a level of divergence among collections that should be useful for management applications. Our quality control process identified no genotyping errors. A parallel project was recently completed by the Canadian Department of Fisheries and Oceans (CDFO) to survey these loci in at least the 10 Canadian populations. U.S. and Canadian data are presently being combined, and joint analyses of the resolving power of the loci will be conducted and presented to the Joint Technical Committee.
Transactions of the American Fisheries Society, 2006
The variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was surveyed for over 48,000 sockeye salmon Oncorhynchus nerka sampled from 299 localities ranging from the Columbia River to Japan. For the microsatellite loci, the number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of stock composition of single-population mixtures. In an analysis of single-population mixtures where the Pacific Rim baseline was used for estimation of stock identification, 80% accuracy for the average population was achieved by employing approximately 80 alleles in the analysis. Increasing the accuracy of estimated stock compositions to 90% for the average population required approximately 400 microsatellite alleles. When all loci were used to estimate stock compositions, estimates were above 80% for all sampling sites or populations, above 90% for the lake of origin, and generally above 95% for the region of origin. Analysis of known-origin samples indicated that accurate lake or regional estimates of stock composition were obtained. The accuracy of identification of individual fish to the correct lake of origin was above 90%, regardless of whether the lakes were geographically widespread or within a single watershed. The estimated stock compositions of mixed-fishery samples from the western Bering Sea, from the continental shelf near Kodiak Island in the Gulf of Alaska, from Southeast Alaska, and from Johnstone Strait in southern British Columbia were markedly different among samples. These stock compositions reflected geographical variation in fishery locations and variation in the migration pathways of either juvenile or maturing sockeye salmon. Variation of DNA enabled us to estimate accurately the origin of individual fish and the composition of mixed-stock samples from any location in the Pacific Rim distribution of sockeye salmon.
Transactions of The American Fisheries Society, 2005
The variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was surveyed for over 48,000 sockeye salmon Oncorhynchus nerka sampled from 299 localities ranging from the Columbia River to Japan. For the microsatellite loci, the number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of stock composition of single-population mixtures. In an analysis of single-population mixtures where the Pacific Rim baseline was used for estimation of stock identification, 80% accuracy for the average population was achieved by employing approximately 80 alleles in the analysis. Increasing the accuracy of estimated stock compositions to 90% for the average population required approximately 400 microsatellite alleles. When all loci were used to estimate stock compositions, estimates were above 80% for all sampling sites or populations, above 90% for the lake of origin, and generally above 95% for the region of origin. Analysis of known-origin samples indicated that accurate lake or regional estimates of stock composition were obtained. The accuracy of identification of individual fish to the correct lake of origin was above 90%, regardless of whether the lakes were geographically widespread or within a single watershed. The estimated stock compositions of mixed-fishery samples from the western Bering Sea, from the continental shelf near Kodiak Island in the Gulf of Alaska, from Southeast Alaska, and from Johnstone Strait in southern British Columbia were markedly different among samples. These stock compositions reflected geographical variation in fishery locations and variation in the migration pathways of either juvenile or maturing sockeye salmon. Variation of DNA enabled us to estimate accurately the origin of individual fish and the composition of mixed-stock samples from any location in the Pacific Rim distribution of sockeye salmon.
Genetic Stock Identification of Chinook Salmon Harvest on the Yukon River 2008
2010
This investigation was financed by the United States Yukon River Research and Management Fund under project USRM 08-08, the Yukon River Restoration and Enhancement Fund under project 19N-08, and the State of Alaska. ADF&G Fishery Data Series was established in 1987 for the publication of Division of Sport Fish technically oriented results for a single project or group of closely related projects, and in 2004 became a joint divisional series with the Division of Commercial Fisheries. Fishery Data Series reports are intended for fishery and other technical professionals and are available through the Alaska State Library and on the Internet: http://www.sf.adfg.state.ak.us/statewide/divreports/html/intersearch.cfm This publication has undergone editorial and peer review.
Genetic Analysis of Snake River Sockeye Salmon (Oncorhynchus Nerka), 2003 Technical Report
2003
Primer sequences used to PCR amplify specific mitochondrial gene regions in Oncorhynchus nerka……………………...…... 46 Appendix B. Restriction endonucleases used to digest PCR amplified mitochondrial gene regions in this study. Number of polymorphic patterns observed indicated by (#)…………..…... 47 Appendix C. Summary of simple haplotypes by gene region and restriction endonuclease for each population……………………………... 48 Appendix D. Appendix D. Composite haplotypes and their simple haplotype digest scores sorted by occurrence (number of samples)……………………………………………………….. 50 Appendix E. Composite mtDNA haplotypes H1-H35 (Table 2) and their frequencies observed among 1720 O. nerka from 40 populations in the Pacific Northwest. Form types are resident kokanee (K), anadromous sockeye (S) and unknown (U)…………………………………………………………...… 51 Appendix F. Composite mtDNA haplotypes (H#, refer to Table 2) and their frequencies observed among 684 O. nerka from six Redfish Lake sample populations, separated by collection date. Form types are resident kokanee (K), anadromous sockeye (S) and unknown (U)…………………………………………………... 55 Appendix F. Composite mtDNA haplotypes (H#, refer to Table 2) and their frequencies observed among O. nerka from Idaho and Washington sample populations, separated by collection date. Form types are resident kokanee (K), anadromous sockeye (S) and unknown (U)……………………………………………....
2016
A genetic analysis of samples from the Chinook salmon (Oncorhynchus tshawytscha) bycatch of the 2014 Gulf of Alaska (GOA) trawl fisheries for walleye pollock (Gadus chalcogrammus), rockfish (Sebastes spp.), and arrowtooth flounder (Atheresthes stomias) was undertaken to determine the stock composition of the sample sets. Samples were genotyped for 43 single nucleotide polymorphism (SNP) DNA markers and results were estimated using the Alaska Department of Fish and Game (ADF&G) SNP baseline. In 2014, genetic samples were collected from Chinook salmon taken in the bycatch of the Gulf of Alaska (GOA) pollock trawl fisheries using a simple random sample protocol with trip being the primary unit. This is the first year for this sampling protocol and resulted in the largest available genetic sample set to date with 10.7% of the salmon bycatch successfully genotyped. Based on the analysis of 1,163 Chinook salmon bycatch samples, British Columbia (43%), West Coast U.S. (35%), Coastal Southe...
Transactions of the American Fisheries Society, 2010
We report stock composition estimates for immature (ocean-age .1 and .2) sockeye salmon Oncorhynchus nerka distributed across the Bering Sea in late summer and fall. We establish a baseline data set composed of single-nucleotide polymorphism markers that can achieve very high accuracies in identifying sockeye salmon stocks from throughout their range in Asia and North America. We demonstrate the capabilities of this data set to address high-seas salmon issues by analyzing samples collected by researchers from Russia, Japan, and the United States during late summer and fall 2002-2004 as part of the Bering-Aleutian Salmon International Survey. According to our findings, (1) Gulf of Alaska (GOA) stocks formed a significant portion of the immature sockeye salmon migrating in the eastern and central Bering Sea in summer and fall, and western GOA stocks had a broader distribution in the Bering Sea than eastern GOA stocks; (2) Asian stocks migrated as far east as the western Aleutian Islands and the Donut Hole area (international waters in the center of the Bering Sea); and (3) Bristol Bay stocks were the most widely distributed, accounting for more than one-half of the mixtures in all areas except the central and southern areas of the Russian Exclusive Economic Zone (REEZ) in the western Bering Sea and north of the western Aleutian Islands. These results provide a significant increase in our knowledge of the distribution of sockeye salmon, firmly establishing that the REEZ is a summer-fall feeding area for immature North American sockeye salmon, particularly stocks of southeastern Bristol Bay origin. Bristol Bay sockeye salmon appear to enter and exit the REEZ primarily along a migration route that extends across the Aleutian Basin.
Coastwide Salmonid Genetics Meeting 2010 : Genetic Adaptation of Salmonids Contents Walking Maps
2010
Genetic markers are rapidly replacing traditional physical tags as the markers of choice for ascertaining the population of origin of individuals or mixtures of individuals of Pacific salmon. With increased use of genetic stock identification technologies has come a rapid evolution in the choice of genetic marker types involved. Allele frequencies of earlier marker types (i.e. microsatellites) were assumed to be determined primarily by stochastic processes (migration and drift). Conversely, SNP markers are increasingly being discovered in coding regions of the genome, and therefore, diversifying selection may influence their allele frequencies. Incorporating SNPs influenced by diversifying selection may provide a greater ability to differentiate Pacific salmon populations than by using neutral markers alone. While this makes non-neutral SNPs highly informative for studies of mixed stock analysis, the stability of allele frequencies must be evaluated, requiring more frequent sampling of reference populations. Here, we identify four SNP markers from a panel of 45 as candidates for diversifying selection in sockeye salmon populations from the Copper River and adjacent coastal drainages in Southcentral Alaska. We assess the ability of these four markers to improve the accuracy and precision of stock composition estimates using 41 reference populations (n = 6,224). The average F ST was 0.089 for neutral loci and 0.262 for loci under diversifying selection. We also conducted leave-one-out tests to assess our ability to assign individuals to population of origin. Using the neutral marker panel, 42.9% and 69.7% of individuals assigned back to the correct population and reporting region, respectively. Adding the four markers under diversifying selection increased the correct assignment of individuals back to populations (47.7%) and reporting groups (79.6%). Our results indicate that markers under diversifying selection will increase our ability to track the homing and straying of individual fish and identify the composition of mixed populations.
2021
The National Marine Fisheries Service's Alaska Fisheries Science Center uses the NOAA Technical Memorandum series to issue informal scientific and technical publications when complete formal review and editorial processing are not appropriate or feasible. Documents within this series reflect sound professional work and may be referenced in the formal scientific and technical literature. The NMFS-AFSC Technical Memorandum series of the Alaska Fisheries Science Center continues the NMFS-F/NWC series established in 1970 by the Northwest Fisheries Center. The NMFS-NWFSC series is currently used by the Northwest Fisheries Science Center.
Minisatellite DNA variation and stock identification of coho salmon
Journal of Fish Biology, 1996
Geographic variation in minisatellite DNA variation was examined in 18 stocks of coho salmon Oncorhynchus kisutch from British Columbia and three stocks from Kamchatka or Western Alaska. Genomic DNA was restricted with MboI or HaeIII and hybridized with two minisatellite probes (pSsa-A34, OtsPBS-1). Allele frequencies and DNA band counts derived from the two probes were combined with band counts from the probe Ssa1 to show a regional stock structure. In British Columbia, stocks from the Fraser River were distinct from those on Vancouver Island, and all were differentiated from those on the mainland of British Columbia. Average heterozygosity at the Ssa-A34 locus was 71%. Compared with a previous study of British Columbia coho salmon population structure in which variation at 26 allozyme loci was examined, greater population differentiation and higher heterozygosity were observed at minisatellite loci. Estimated stock compositions of simulated mixtures of fishery samples from British Columbia stocks were accurate and precise, with the potential of identifying stocks within the drainage basin of a major river, the Fraser River. Minisatellite DNA variation may provide accurate and precise estimates of stock composition in actual fishery applications, and has the potential of identifying individual fish to region or stock of origin. 1996 The Fisheries Society of the British Isles
2014
Managing weak stocks in mixed-stock fisheries often relies on proxies derived from data-rich indicator stocks. For example, full cohort reconstruction of tagged Klamath River fall run Chinook salmon (Oncorhynchus tshawytscha) of northern California, USA, enables the use of detailed models to inform management. Information gained from this stock is also used in the management of the untagged, threatened California Coastal Chinook (CCC) salmon stock, by capping Klamath harvest rates. To evaluate use of this proxy, we used genetic stock identification (GSI) data to compare the two stocks' size-at-age and ocean distribution, two key factors influencing fishery exposure. We developed methods to account for both sampling and genetic assignment uncertainty in catch estimates. We found that, in 2010, the stocks were similar in size-at-age early in the year (age-3 and age-4), but CCC fish were larger later in the year. The stocks appeared similarly distributed early in the year (2010), but more concentrated near their respective source rivers later in the year (2010 and 2011). If these results are representative, relative fishery impacts on the two stocks might scale similarly early in the year but management changes later in the year might have differing impacts on the two stocks.
Transactions of the American Fisheries Society, 2000
Genetic data from sockeye salmon Oncorhynchus nerka were collected from all major systems in upper Cook Inlet, Alaska, that produce sockeye salmon, including the Kenai River drainage, a major system that was affected by the Exxon Valdez oil spill. The products of 29 enzymes encoded by 67 protein-encoding loci resolved by allozyme analysis revealed a substantial amount of genetic diversity among populations distributed both within and among major drainages. The data support a model of population structure based on the nursery lake. A gene diversity analysis estimated that 0.4% of the total variability was attributable to the effect of sampling at different sites within nursery lakes, compared with 7.5% among nursery lakes within regions and 2.9% among regions. This diversity probably arises from isolation and genetic drift within nursery lakes and the tendency of sockeye salmon to home with great fidelity. Sockeye salmon from these drainages are commercially harvested in mixed-stock aggregations in upper Cook Inlet. Mixedstock analyses using maximum likelihood methods with data from 27 loci were performed to estimate the proportion of source populations in upper Cook Inlet fisheries. Simulations indicated that six regional groups (Kenai River, Susitna and Yentna rivers, West Cook Inlet, Kasilof River, Northeast Cook Inlet, and Knik Arm) could be identified in mixtures at a level of precision and accuracy useful for fishery management. Samples from fisheries were analyzed both in-season (within 48 h) and postseason. Samples taken from within the rivers were also analyzed to evaluate the baseline and to estimate the contributions of individual spawning populations to the larger river systems.