A Comparison of Stock and Individual Identification for Chinook Salmon in British Columbia Provided by Microsatellites and Single-Nucleotide Polymorphisms

REFERENCES

• Anderson , E. C. 2010 . Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased . Molecular Ecology Resources , 10 : 701 – 710 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• 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. 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 .
   Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• Beacham , T. D. , Lapointe , M. , Candy , J. R. , McIntosh , B. , MacConnachie , C. , Tabata , A. , Kaukinen , K. , Deng , L. , Miller , K. M. and Withler , R. E. 2004 . Stock identification of Fraser River sockeye salmon (Oncorhynchus nerka) using microsatellites and major histocompatibility complex variation . Transactions of the American Fisheries Society , 133 : 1117 – 1137 .
   Web of Science ®Google Scholar
• Beacham , T. D. , McIntosh , B. and Wallace , C. 2010 . A comparison of stock and individual identification for sockeye salmon (Oncorhynchus nerka) in British Columbia provided by microsatellites (STRs) and single-nucleotide polymorphisms (SNPs) . Canadian Journal of Fisheries and Aquatic Sciences , 67 : 1274 – 1290 .
   Web of Science ®Google Scholar
• Beacham , T. D. , McIntosh , B. and Wallace , C. 2011 . A comparison of polymorphism of genetic markers and population sample sizes required for mixed-stock analysis of sockeye salmon (Oncorhynchus nerka) in British Columbia . Canadian Journal of Fisheries and Aquatic Sciences , 68 : 550 – 562 .
   Web of Science ®Google Scholar
• Beacham , T. D. , Urawa , S. , Le , K. D. and Wetklo , M. 2008a . Population structure and stock identification of chum salmon from Japan determined with microsatellite DNA variation . Fisheries Science , 74 : 983 – 994 .
   Web of Science ®Google Scholar
• Beacham , T. D. , Wetklo , M. , Wallace , C. , Olsen , J. B. , Flannery , B. G. , Wenburg , J. K. , Templin , W. D. , Antonovich , A. and Seeb , L. W. 2008b . The application of microsatellites for stock identification of Yukon River Chinook salmon . North American Journal of Fisheries Management , 28 : 283 – 295 .
   Web of Science ®Google Scholar
• Beacham , T. D. , Winther , I. , Jonsen , K. L. , Wetklo , M. , Deng , L. and Candy , J. R. 2008c . The application of rapid microsatellite-based stock identification to management of a Chinook salmon troll fishery off the Queen Charlotte Islands, British Columbia . North American Journal of Fisheries Management , 28 : 849 – 855 .
   Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Campbell , N. R. and Narum , S. R. 2008 . Identification of novel single-nucleotide polymorphisms in Chinook salmon and variation among life history types . Transactions of the American Fisheries Society , 137 : 96 – 106 .
   Web of Science ®Google Scholar
• Danzmann , R. G. , Cairney , M. , Davidson , W. S. , Ferguson , M. M. , Gharbi , K. , Guyomard , R. , Holm , L. E. , Leder , E. , Okamoto , N. , Ozaki , A. , Rexroad , C. E. III , Sakamoto , T. , Taggart , J. B. and Woram , R. A. 2005 . A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae) . Genome , 48 : 1037 – 1051 .
   PubMed Web of Science ®Google Scholar
• 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 – 511 .
   PubMed Web of Science ®Google Scholar
• Glover , K. A. , Hansen , M. M. , Lien , S. , Als , T. D. , Høyheim , B. and Skaala , Ø. 2010 . A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment . BMC (BioMed Central) Genetics , 11 : 2
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• Grieg , C. A. and Banks , M. A. 1999 . Five multiplexed microsatellite loci for rapid response run identification of California's endangered winter Chinook salmon . Animal Genetics , 30 : 318 – 320 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• Haasl , R. J. and Payseur , B. A. 2010 . Multilocus inference of population structure: a comparison between single-nucleotide polymorphisms and microsatellites . Heredity , 106 : 158 – 171 .
   PubMed Web of Science ®Google Scholar
• Hedrick , P. W. 2005 . A standardized genetic differentiation measure . Evolution , 59 : 1633 – 1638 .
   PubMed Web of Science ®Google Scholar
• Hess , J. E. , Matala , A. P. and Narum , S. R. 2011 . Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of Chinook salmon in the Columbia River basin . Molecular Ecology Resources , 11 ( Supplement 1 ) : 137 – 149 .
   PubMed Web of Science ®Google Scholar
• Kalinowski , S. T. 2002 . How many alleles per locus should be used to estimate genetic distances? . Heredity , 88 : 62 – 65 .
   PubMed Web of Science ®Google Scholar
• Kalinowski , S. T. 2004 . Genetic polymorphism and mixed-stock fisheries analysis . Canadian Journal of Fisheries and Aquatic Sciences , 61 : 1075 – 1082 .
   Web of Science ®Google Scholar
• Kalinowski , S. T. , Manlove , K. R. and Taper , M. L. 2007 . ONCOR: software for genetic stock identification , Bozeman : Montana State University . Available: www.montana.edu/kalinowski/Software/ONCOR.htm. (September 2008)
   Google Scholar
• Miller , K. M. , Beacham , T. D. and Ming , T. J. 2008 . Report to the Northern Endowment Fund on project NF-2007-I4: Chinook salmon SNP development , Vancouver : Pacific Salmon Commission .
   Google Scholar
• Narum , S. R. , Banks , M. , Beacham , T. , Bellinger , R. , Campbell , M. , DeKoning , J. , Elz , A. , Guthrie , C. , Kozfkay , C. , Miller , K. , Moran , P. , Phillips , R. , Seeb , L. , Smith , C. , Warheit , K. , Young , S. and Garza , J. C. 2008 . Differentiating populations at broad and fine geographic scales with microsatellites and single-nucleotide polymorphisms . Molecular Ecology , 17 : 3464 – 3477 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• Olsen , J. B. , Bentzen , P. and Seeb , J. E. 1998 . Characterization of seven microsatellite loci derived from pink salmon . Molecular Ecology , 7 : 1087 – 1090 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• Parken , C. K. , Candy , J. R. , Irvine , J. R. and Beacham , T. D. 2008 . Genetic and coded wire tag results combine to allow more precise management of a complex Chinook salmon aggregate . North American Journal of Fisheries Management , 28 : 328 – 340 .
   Web of Science ®Google Scholar
• Pereira da Silva , W. P. and Pereira da Silva , C. D. 2007 . Lab Fit curve fitting software (nonlinear regression and treatment of data program), version 7.2.46 (1999–2009) . Available: www.labfit.net. (August 2009)
   Google Scholar
• PSC (Pacific Salmon Commission) . 2008 . Recommendations for application of genetic stock identification (GSI) methods to management of ocean salmon fisheries: special report of the GSI Steering Committee and the Pacific Salmon Commission's Committee on Scientific Cooperation . PSC Technical Report 23, Vancouver
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Rexroad , C. E. , Coleman , R. L. , Gustafson , A. L. , Hershberger , W. K. and Killefer , J. 2002 . Development of rainbow trout microsatellite markers from repeat enriched libraries . Marine Biotechnology , 4 : 12 – 16 .
   PubMed Web of Science ®Google Scholar
• 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 : 283 – 319 .
   Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Sakamoto , T. , Danzmann , R. G. , Gharbi , K. , Howard , P. , Ozaki , A. , Khoo , S. K. , Woram , R. A. , Okamoto , N. , Ferguson , M. M. , Holm , L. E. , Guyomard , R. and Hoyheim , B. 2000 . A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates . Genetics , 155 : 1331 – 1345 .
   PubMed Web of Science ®Google Scholar
• Seeb , L. W. , Antonovich , A. , Banks , M. A. , Beacham , T. D. , Bellinger , M. R. , Campbell , M. , Decovich , N. A. , Garza , J. C. , Guthrie , C. M. III , 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 .
   Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• Smith , C. T. , Antonovich , A. , Templin , W. D. , Elfstrom , C. M. , Narum , S. R. and Seeb , L. W. 2007 . Impacts of marker class bias relative to locus-specific variability on population inferences in Chinook salmon: a comparison of single-nucleotide polymorphisms with short tandem repeats and allozymes . Transactions of the American Fisheries Society , 136 : 1674 – 1687 .
   Web of Science ®Google Scholar
• Smith , C. T. , Baker , J. , Park , L. , Seeb , L. W. , Elfstrom , C. , Abe , S. and Seeb , J. E. 2005a . Characterization of 13 single-nucleotide-polymorphism markers for chum salmon . Molecular Ecology , 14 : 259 – 262 .
   Web of Science ®Google Scholar
• Smith , C. T. , Elfstrom , C. , Seeb , L. W. and Seeb , J. E. 2005b . Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon . Molecular Ecology Notes , 5 : 4193 – 4203 .
   Web of Science ®Google Scholar
• 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 : 1613 – 1621 .
   PubMed Web of Science ®Google Scholar
• Smith , C. T. , Seeb , J. E. , Schwenke , P. and Seeb , L. W. 2005c . Use of the 5′-nuclease reaction for single-nucleotide-polymorphism genotyping in Chinook salmon . Transactions of the American Fisheries Society , 134 : 207 – 217 .
   Web of Science ®Google Scholar
• Smith , C. T. , Templin , W. D. , Seeb , J. E. and Seeb , L. W. 2005d . Single-nucleotide polymorphisms (SNPs) 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 .
   Web of Science ®Google Scholar
• Waples , R. S. , Teel , D. J. , Myers , J. M. and Marshall , A. R. 2004 . Life history divergence in Chinook salmon: historic contingency and parallel evolution . Evolution , 58 : 386 – 403 .
   PubMed Web of Science ®Google Scholar
• Williamson , K. , Cordes , S. , Jan , 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 .
   Web of Science ®Google Scholar