Examining Genetic Lineages of Chinook Salmon in the Columbia River Basin

References

• Beacham , T. D. , Jonsen , K. L. , Supernault , J. , Wetklo , M. , Deng , L. and Varnavskaya , N. 2006 . Pacific Rim population structure of Chinook salmon as determined from microsatellite analysis . Transactions of the American Fisheries Society , 135 : 1604 – 1621 .
   Web of Science ®Google Scholar
• Benjamini , Y. and Yekutieli , D. 2001 . The control of false discovery rate under dependency . Annals of Statistics , 29 : 1165 – 1188 .
   Web of Science ®Google Scholar
• Brannon , E. L. , Powell , M. S. , Quinn , T. P. and Talbot , A. J. 2004 . Population structure of Columbia River basin Chinook salmon and steelhead trout . Reviews in Fisheries Science , 12 : 99 – 232 .
   Web of Science ®Google Scholar
• Cavalli-Sforza , L. L. and Edwards , W. W. F. 1967 . Phylogenetic analysis; models and estimation procedures . Evolution , 32 : 550 – 570 .
   Web of Science ®Google Scholar
• Ford , M. J. 1998 . Testing models of migration and isolation among populations of Chinook salmon (Oncorhynchus tshawytscha) . Evolution , 52 : 539 – 557 .
   PubMed Web of Science ®Google Scholar
• Frankel , O. H. and Soule , M. E. 1981 . Conservation and evolution Cambridge, , UK : Cambridge University Press .
   Google Scholar
• Garza , J. C. and Williamson , E. G. 2001 . Detection of reduction in population size using data from microsatellite loci . Molecular Ecology , 10 : 305 – 318 .
   PubMed Web of Science ®Google Scholar
• Gradstein , F. M. , Ogg , J. G. and Smith , A. G. 2004 . A geologic time scale 2004 Cambridge, , UK : Cambridge University Press .
   Google Scholar
• Gustafson , R. G. , Waples , R. S. , Myers , J. M. , Weitkamp , L. A. , Bryant , G. J. , Johnson , O. W. and Hard , J. J. 2007 . Pacific salmon extinctions: Quantifying lost and remaining diversity . Conservation Biology , 21 : 1009 – 1020 .
   PubMed Web of Science ®Google Scholar
• Healey , M. C. 1991 . “ Life history of Chinook salmon (Oncorhynchus tshawytscha). ” . In Pacific salmon life histories Edited by: Groot , C. and Margolis , L. 311 – 395 . Vancouver : UBC Press .
   Google Scholar
• Hedrick , P. W. 2005 . A standardized genetic differentiation measure . Evolution , 59 : 1633 – 1638 .
   PubMed Web of Science ®Google Scholar
• Kalinowski , S. T. 2005 . HP-Rare: A computer program for performing rarefaction on measures of allelic diversity . Molecular Ecology Notes , 5 : 187 – 189 .
   Web of Science ®Google Scholar
• Langella , O. 2001 . Populations: Population genetic structure (individuals or populations distances, phylogenetic trees) Available: pgecnrsgiffr/bioinfo/populations/. (August 2009).
   Google Scholar
• Myers , J. , Busack , C. , Rawding , D. , Marshall , A. , Teel , D. , Van Doornik , D. M. and Maher , M. T. 2006 . “ Historical population structure of Pacific salmonids in the Willamette River and lower Columbia River basins. ” . In NOAA Technical Memorandum NMFS-NWFSC-73
   Google Scholar
• Myers , J. M. , Kope , R. G. , Bryant , G. J. , Teel , D. , Lierheimer , L. J. , Wainwright , T. C. , Grant , W. S. , Waknitz , F. W. , Neely , K. , Lindley , S. T. and Waples , R. S. 1998 . “ Status review of Chinook salmon from Washington, Idaho, Oregon, and California. ” . In NOAA Technical Memorandum NMFS-NWFSC-35
   Google Scholar
• Narum , S. R. 2006 . Beyond Bonferroni: Less conservative analyses for conservation genetics . Conservation Genetics , 7 : 783 – 787 .
   Web of Science ®Google Scholar
• Narum , S. R. , Arnsberg , W. D. , Talbot , A. J. and Powell , M. S. 2007a . Reproductive isolation following reintroduction of Chinook salmon with alternative life histories . Conservation Genetics , 8 : 1123 – 1132 .
   Web of Science ®Google Scholar
• Narum , S. R. , Banks , M. , Beacham , T. D. , Bellinger , M. R. , Campbell , M. R. , DeKoning , J. , Elz , A. , Guthrie , C. M. III , Kozfkay , C. , Miller , K. M. , Moran , P. , Phillips , R. , Seeb , L. W. , Smith , C. T. , Warheit , K. , Young , S. F. and Garza , J. C. 2008 . Differentiating salmon populations at broad and fine geographic scales with microsatellites and SNPs . Molecular Ecology , 17 : 3464 – 3477 .
   PubMed Web of Science ®Google Scholar
• Narum , S. R. , Stephenson , J. J. and Campbell , M. R. 2007b . Genetic variation and structure of Chinook salmon life history types in the Snake River . Transactions of the American Fisheries Society , 136 : 1252 – 1262 .
   Web of Science ®Google Scholar
• Nehlsen , W. , Williams , J. E. and Lichatowich , J. A. 1991 . Pacific salmon at the crossroads: Stocks at risk from California, Oregon, Idaho, and Washington . Fisheries , 16 (2) : 4 – 20 .
   Web of Science ®Google Scholar
• Page , R. D. M. 1996 . TREEVIEW: An application to display phylogenetic trees on personal computers . Computer Applications in the Biosciences , 12 : 357 – 358 .
   PubMedGoogle Scholar
• Park , S. D. E. 2001 . Trypanotolerance in West African cattle and the population genetic effects of selection Dublin : University of Dublin . Doctoral dissertation.
   Google Scholar
• Pritchard , J. , Stephens , M. and Donnelly , P. 2000 . Inference of population structure using multilocus genotype data . Genetics , 155 : 945 – 959 .
   PubMed Web of Science ®Google Scholar
• Quinn , T. P. 1993 . A review of homing and straying of wild and hatchery-produced salmon . Fisheries Research , 18 : 29 – 44 .
   Web of Science ®Google Scholar
• Rasmussen , C. , Ostberg , C. O. , Clifton , D. R. , Holloway , J. L. and Rodriguez , R. J. 2003 . Identification of a genetic marker that discriminates ocean and stream-type Chinook salmon in the Columbia River basin . Transactions of the American Fisheries Society , 132 : 131 – 142 .
   Web of Science ®Google Scholar
• Raymond , M. and Rousset , F. 1995 . GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism . Journal of Heredity , 86 : 248 – 249 .
   Web of Science ®Google Scholar
• Rice , W. R. 1989 . Analyzing tables of statistical tests . Evolution , 43 : 223 – 225 .
   PubMed Web of Science ®Google Scholar
• Seeb , L. W. , Antonovich , A. , Banks , M. A. , Beacham , T. D. , Bellinger , M. R. , Blankenship , S. M. , Campbell , M. , 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 .
   Web of Science ®Google Scholar
• Shrimpton , J. M. and Heath , D. D. 2003 . Census vs. effective population size in Chinook salmon: Large- and small-scale environmental perturbation effects . Molecular Ecology , 12 : 2571 – 2583 .
   PubMed Web of Science ®Google Scholar
• Smith , C. T. , Antonovich , A. , Elfstrom , C. M. , Narum , S. R. and Seeb , L. W. 2007 . Impacts of marker class bias relative to locus-specific variability on population inferences: 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
• Teel , D. J. , Milner , G. B. , Winans , G. A. and Grant , W. S. 2000 . Genetic population structure and origin of life history types in Chinook salmon in British Columbia, Canada . Transactions of the American Fisheries Society , 129 : 194 – 209 .
   Web of Science ®Google Scholar
• Utter , F. M. , Allendorf , F. W. and May , B. P. The use of protein variation in the management of salmonid populations. Transactions of the North American Wildlife and Natural Resources Conference. Edited by: Sabol , K. pp. 373 – 384 . Washington, D.C. : Wildlife Management Institute .
   Google Scholar
• Utter , F. and Epifanio , J. 2002 . Marine aquaculture: Genetics potentialities and pit falls . Reviews in Fish Biology and Fisheries , 12 : 59 – 77 .
   Web of Science ®Google Scholar
• Utter , F. , Milner , G. , Stahl , G. and Teel , D. 1989 . Genetic population structure of Chinook salmon, Oncorhynchus tshawytscha, in the Pacific northwest. U.S . National Marine Fisheries Service Fishery Bulletin , 87 : 239 – 264 .
   Web of Science ®Google Scholar
• Waples , R. S. 1991 . Pacific salmon, Oncorhynchus spp., and the definition of ‘species” under the Endangered Species Act . Marine Fisheries Review , 53 : 11 – 22 .
   Google Scholar
• Waples , R. S. 2006 . A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci . Conservation Genetics , 7 : 167 – 184 .
   Web of Science ®Google Scholar
• Waples , R. S. and Do , C. 2008 . LDNE: A program for estimating effective population size from data on linkage disequilibrium . Molecular Ecology Resources , 8 : 753 – 756 .
   PubMed Web of Science ®Google Scholar
• Waples , R. S. , Pess , G. R. and Beechie , T. 2008 . Evolutionary history of Pacific salmon in dynamic environments . Evolutionary Applications , 1 : 189 – 206 .
   PubMed 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: Historical contingency and parallel evolution . Evolution , 58 : 386 – 403 .
   PubMed Web of Science ®Google Scholar
• Winans , G. A. 1989 . Genetic variability in Chinook salmon stocks from the Columbia River basin . North American Journal of Fisheries Management , 9 : 47 – 52 .
   Google Scholar