147
Views
28
CrossRef citations to date
0
Altmetric
Article

The Application of Microsatellites for Stock Identification of Yukon River Chinook Salmon

, , , , , , , & show all
Pages 283-295 | Received 31 Oct 2006, Accepted 02 May 2007, Published online: 09 Jan 2011

References

  • ADFG (Alaska Department of Fish and Game). 2007 . Gene Conservation Laboratory data Division of Commercial Fisheries, Alaska Department of Fish and Game . Available: www.cf.adfg.state.ak.us/geninfo/research/genetics/genetics.php. (January 2008)
  • Banks , M. A. , Blouin , M. S. , Baldwin , B. A. , Rashbrook , V. K. , Fitzgerald , H. A. , Blankenship , S. M. and Hedgecock , D. 1999 . Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha) . Journal of Heredity , 90 : 281 – 288 .
  • Banks , M. A. , Rashbrook , V. R. , Calavetta , M. J. , Dean , C. A. and Hedgecock , D. 2000 . Analysis of microsatellite DNA resolves genetic structure and diversity of Chinook salmon (Oncorhynchus tshawytscha) . Canadian Journal of Fisheries and Aquatic Sciences , 57 : 915 – 927 .
  • Beacham , T. D. , Candy , J. R. , Jonsen , K. L. , Supernault , J. , Wetklo , M. , Deng , L. , Miller , K. M. and Withler , R. E. 2006a . Estimation of stock composition and individual identification of Chinook salmon across the Pacific Rim using microsatellite variation . Transactions of the American Fisheries Society , 135 : 861 – 888 .
  • Beacham , T. D. , Candy , J. R. , McIntosh , B. , MacConnachie , C. , Tabata , A. , Kaukinen , K. , Deng , L. , Miller , K. M. , Withler , R. E. and Varnavskaya , N. V. 2005 . Estimation of stock composition and individual identification of sockeye salmon on a Pacific Rim basis using microsatellite and major histocompatibility complex variation . Transactions of the American Fisheries Society , 134 : 1124 – 1146 .
  • Beacham , T. D. , Candy , J. R. , Supernault , K. J. , Wetklo , M. , Deagle , B. , Labaree , K. , Irvine , J. R. , Miller , K. M. , Nelson , R. J. and Withler , R. E. 2003 . Evaluation and application of microsatellites for population identification of Fraser River Chinook salmon (Oncorhynchus tshawytscha) . U.S. National Marine Fisheries Service Fishery Bulletin , 101 : 243 – 259 .
  • Beacham , T. D. , Jonsen , K. L. , Supernault , J. , Wetklo , M. , Deng , L. and Varnavskaya , N. 2006b . Pacific Rim population structure of Chinook salmon as determined from microsatellite variation . Transactions of the American Fisheries Society , 135 : 1604 – 1621 .
  • Beacham , T. D. , Murray , C. B. and Withler , R. E. 1989 . Age, morphology, and biochemical genetic variation of Yukon River Chinook salmon . Transactions of the American Fisheries Society , 118 : 46 – 63 .
  • Bernatchez , L. and Duchesne , P. 2000 . Individual-based genotype analysis in studies of parentage and population assignment: how many loci, how many alleles . Canadian Journal of Fisheries and Aquatic Sciences , 57 : 1 – 12 .
  • Brabets , T. P. , Wang , B. and Meade , R. H. 2000 . Environmental and hydrologic overview of the Yukon River basin, Alaska and Canada Anchorage, Alaska : U.S. Geological Survey . Water-Resources Investigations Report 99-4204
  • Buchholz , W. G. , Miller , S. J. and Spearman , W. J. 2001 . Isolation and characterization of chum salmon microsatellite loci and use across species . Animal Genetics , 32 : 162 – 165 .
  • Cairney , M. , Taggart , J. B. and Hoyheim , B. 2000 . Characterization of microsatellite and minisatellite loci in Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids . Molecular Ecology , 9 : 2175 – 2178 .
  • Debevec , E. M. , Gates , R. B. , Masuda , M. , Pella , J. , Reynolds , J. M. and Seeb , L. W. 2000 . SPAM, version 3.2: statistics program for analyzing mixtures . Journal of Heredity , 91 : 509 – 510 .
  • DFO (Department of Fisheries and Oceans (Canada)). 2007 . Molecular genetics laboratory program Available: www.pac.dfo-mpo.gc.ca/sci/mgl/data_e.htm. (January 2008)
  • Estoup , A. , Presa , P. , Krieg , F. , Vaiman , D. and Guyomard , R. 1993 . (CT)n and (GT)n microsatellites: a new class of genetic markers for Salmo trutta L. (brown trout) . Heredity , 71 : 488 – 496 .
  • Flannery , B. , Beacham , T. , Wetklo , M. , Smith , C. , Templin , W. , Antonovich , A. , Seeb , L. , Miller , S. , Schlei , O. and Wenburg , J. 2006 . “ Run timing, migratory patterns, and harvest information of Chinook salmon stocks within the Yukon River ” . In U.S. Fish and Wildlife Service, Alaska Fisheries Technical Report 92 Anchorage, Alaska
  • Gilbert , C. H. 1922 . The salmon of the Yukon River . U.S. Bureau of Fisheries Bulletin , 38 : 317 – 332 .
  • Goudet , J. 1995 . FSTAT: a program for IBM PC compatibles to calculate Weir and Cockerham's (1984) estimators of F-statistics, version 1.2 . Journal of Heredity , 86 : 485 – 486 .
  • Grieg , C. , Jacobson , D. P. and Banks , M. A. 2003 . New tetranucleotide microsatellites for fine-scale discrimination among endangered Chinook salmon (Oncorhynchus tshawytscha) . Molecular Ecology Notes , 3 : 376 – 379 .
  • IUBMB (International Union of Biochemistry and Molecular Biology). 1992 . Enzyme nomenclature 1992 San Diego, California : Academic Press .
  • Kalinowski , S. T. 2002 . How many alleles per locus should be used to estimate genetic distances . Heredity , 88 : 62 – 65 .
  • Kalinowski , S. T. 2004 . Genetic polymorphism and mixed-stock fisheries analysis . Canadian Journal of Fisheries and Aquatic Sciences , 61 : 1075 – 1082 .
  • McBride , D. N. and Marshall , S. L. 1983 . Feasibility of scale pattern analysis to identify the origins of Chinook salmon (Oncorhynchus tshawytscha Walbaum) in the lower Yukon River commercial gillnet fishery, 1980–1981 Anchorage, Alaska : Alaska Department of Fish and Game, Division of Commercial Fisheries . Informational Leaflet 208
  • Nelson , R. J. and Beacham , T. D. 1999 . Isolation and cross species amplification of microsatellite loci useful for study of Pacific salmon . Animal Genetics , 30 : 228 – 229 .
  • O'Connell , M. , Danzmann , R. G. , Cornuet , J. M. , Wright , J. M. and Ferguson , M. M. 1997 . Differentiation of rainbow trout stocks in Lake Ontario and the evaluation of the stepwise mutation and infinite allele mutation models using microsatellite variability . Canadian Journal of Fisheries and Aquatic Sciences , 54 : 1391 – 1399 .
  • Olsen , J. B. , Bentzen , P. and Seeb , J. E. 1998 . Characterization of seven microsatellite loci derived from pink salmon . Molecular Ecology , 7 : 1083 – 1090 .
  • Olsen , J. B. , Wilson , S. L. , Kretschmer , E. J. , Jones , K. C. and Seeb , J. E. 2000 . Characterization of 14 tetranucleotide microsatellite loci derived from sockeye salmon . Molecular Ecology , 9 : 2185 – 2187 .
  • O'Reilly , P. T. , Canino , M. F. , Bailey , K. M. and Bentzen , P. 2004 . Inverse relationship between F ST and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure . Molecular Ecology , 13 : 1799 – 1814 .
  • O'Reilly , P. T. , Hamilton , L. C. , McConnell , S. K. and Wright , J. M. 1996 . Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites . Canadian Journal of Fisheries and Aquatic Sciences , 53 : 2292 – 2298 .
  • Pella , J. and Masuda , M. 2001 . Bayesian methods for analysis of stock mixtures from genetic characters. U.S . National Marine Fisheries Service Fishery Bulletin , 99 : 151 – 167 .
  • Rannala , B. and Mountain , J. L. 1997 . Detecting immigration by using multilocus genotypes . Proceedings of the National Academy of Sciences of the USA , 94 : 9197 – 9201 .
  • Rexroad , C. E. , Coleman , R. L. , Martin , A. M. , Hershberger , W. K. and Killefer , J. 2001 . Thirty-five polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss) . Animal Genetics , 32 : 317 – 319 .
  • Rosenberg , N. A. , Li , L. M. , Ward , R. and Pritchard , J. K. 2003 . Informativeness of genetic markers for inference of ancestry . American Journal of Human Genetics , 73 : 1402 – 1422 .
  • Ryman , N. , Palm , S. , Andre , C. , Carvalho , G. R. , Dahlgren , T. G. , Jorde , P. E. , Laikre , L. , Larsson , L. C. , Palme , A. and Ruzzante , D. E. 2006 . Power for detecting genetic divergence: differences between statistical methods and marker loci . Molecular Ecology , 15 : 2031 – 2045 .
  • Scribner , K. T. , Gust , J. R. and Fields , R. L. 1996 . Isolation and characterization of novel salmon microsatellite loci: cross-species amplification and population genetic application . Canadian Journal of Fisheries and Aquatic Sciences , 53 : 833 – 841 .
  • Seeb , L. W. , Antonovich , A. , Banks , M. A. , Beacham , T. D. , Bellinger , M. R. , Blankenship , S. M. , Campbell , M. R. , Decovich , N. A. , Garza , J. C. , Guthrie , C. M. III , Lundrigan , T. A. , Moran , P. , Narum , S. R. , Stephenson , J. J. , Supernault , K. J. , Teel , D. J. , Templin , W. D. , Wenburg , J. K. , Young , S. F. and Smith , C. T. 2007 . Development of a standardized DNA database for Chinook salmon . Fisheries , 32 : 540 – 552 .
  • Shaklee , J. B. , Beacham , T. D. , Seeb , L. and White , B. A. 1999 . Managing fisheries using genetic data: case studies from four species of Pacific salmon . Fisheries Research , 43 : 45 – 78 .
  • Small , M. P. , Beacham , T. D. , Withler , R. E. and Nelson , R. J. 1998 . Discriminating coho salmon within the Fraser River, British Columbia, using microsatellite DNA markers . Molecular Ecology , 7 : 141 – 155 .
  • Smith , C. T. , Antonovich , A. , Templin , W. D. , Elfstrom , C. M. , Narum , S. R. and Seeb , L. W. “ Effects of natural selection and ascertainment bias on population genetic inferences in Chinook salmon ” . In Transactions of the American Fisheries Society
  • Smith , C. T. , Koop , B. F. and Nelson , R. J. 1998 . Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids . Molecular Ecology , 7 : 1614 – 1616 .
  • Smith , C. T. , Templin , W. D. , Seeb , J. E. and Seeb , L. W. 2005 . Single nucleotide polymorphisms provide rapid and accurate estimates of the proportions of U.S. and Canadian Chinook salmon caught in Yukon River fisheries . North American Journal of Fisheries Management , 25 : 944 – 953 .
  • Templin , W. D. , Decovich , N. A. and Seeb , L. W. 2006 . Yukon River Chinook salmon genetic baseline: survey of Pacific Salmon Commission loci for U.S. populations Anchorage : Alaska Department of Fish and Game . Fishery Data Series 06-46
  • Templin , W. D. , Wilmot , R. L. , Guthrie , C. M. III and Seeb , L. W. 2005 . United States and Canadian Chinook salmon stocks in the Yukon River can be segregated based on genetic characteristics . Alaska Fishery Research Bulletin , 11 : 44 – 60 .
  • Weir , B. S. and Cockerham , C. C. 1984 . Estimating F-statistics for the analysis of stock structure . Evolution , 38 : 1358 – 1370 .
  • Williamson , K. S. , Cordes , J. F. and May , B. 2002 . Characterization of microsatellite loci in Chinook salmon (Oncorhynchus tshawytscha) and cross-species amplification in other salmonids . Molecular Ecology Notes , 2 : 17 – 19 .
  • Wilmot , R. L. , Everett , R. E. , Spearman , W. J. and Baccus , R. 1992 . Genetic stock identification of Yukon River chum and Chinook salmon 1987 to 1990 Anchorage, Alaska : U.S. Fish and Wildlife Service . Progress Report

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.