Status report for genetic stock identification studies of Pacific Rim sockeye salmon (original) (raw)
Related papers
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.
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...