Genetic Monitoring of Threatened Chinook Salmon Populations: Estimating Introgression of Nonnative Hatchery Stocks and Temporal Genetic Changes

REFERENCES

• Araki , H. , Berejikian , B. A. , Ford , M. J. and Blouin , M. S. 2008 . Fitness of hatchery-reared salmonids in the wild . Evolutionary Applications , 1 : 342 – 355 .
   PubMed Web of Science ®Google Scholar
• Araki , H. , Cooper , B. and Blouin , M. S. 2007 . Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild . Science , 318 : 100 – 103 .
   PubMed Web of Science ®Google Scholar
• Belkhir , K. , Borsa , P. , Chikhi , L. , Raufaste , N. and Bonhomme , F. 2003 . GENETIX: programs for Windows for the genetic analysis of populations , Montpellier , , France : Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II . Available: kimura.univ-montp2.fr/genetix. (February 2013)
   Google Scholar
• Benjamini , Y. and Yekutieli , D. 2001 . The control of the false discovery rate in multiple testing under dependency . Annals of Statistics , 29 : 1165 – 1188 .
   Web of Science ®Google Scholar
• Berejikian , B. A. , Tezak , E. P. , Park , L. , LaHood , E. , Schroder , S. L. and Beall , E. 2001 . Male competition and breeding success in captively reared and wild Coho Salmon (Oncorhynchus kisutch) . Canadian Journal of Fisheries and Aquatic Sciences , 58 : 804 – 810 .
   Web of Science ®Google Scholar
• Berejikian , B. A. , Tezak , E. P. , Schroder , S. L. , Knudsen , C. M. and Hard , J. J. 1997 . Reproductive behavioral interactions between wild and captively reared Coho Salmon (Oncorhynchus kisutch) . ICES Journal of Marine Science , 54 : 1040 – 1050 .
   Web of Science ®Google Scholar
• Berntson , E. A. , Carmichael , R. W. , Flesher , M. W. , Ward , E. J. and Moran , P. 2011 . Diminished reproductive success of steelhead from a hatchery supplementation program (Little Sheep Creek, Imnaha Basin, Oregon) . Transactions of the American Fisheries Society , 140 : 685 – 698 .
   Web of Science ®Google Scholar
• Boe , S. J. , Crump , C. A. , Weldert , R. L. and Wolf , J. 2011 . Lower Snake River compensation plan, confederated tribes of the Umatilla Indian Reservation: evaluation studies for 1 January 2008 to 31 December 2008 , La Grande , , Oregon : U.S. Fish and Wildlife Service, Confederated Tribes of the Umatilla Indian Reservation, Project 421 . Available: www.fws.gov/lsnakecomplan/Reports/CTUIRreports.html. (October 2012)
   Google Scholar
• Carmichael , R. W. and Messmer , R. T. 1995 . “ Status of supplementing Chinook Salmon natural production in the Imnaha River basin ” . In Uses and effects of cultured fishes in aquatic ecosystems , Edited by: Schramm , H. L. Jr. and Piper , R. G. 284 – 291 . Bethesda , Maryland : American Fisheries Society, Symposium 15 .
   Google Scholar
• Cavalli-Sforza , L. L. and Edwards , A. W. F. 1967 . Phylogenetic analysis: models and estimation procedures . American Journal of Human Genetics , 19 : 233 – 257 .
   PubMed Web of Science ®Google Scholar
• CBFWA (Columbia Basin Fish and Wildlife Authority) . 2008 . 2008 status of fish and wildlife resources in the Columbia River basin , Portland , Oregon : CBFWA .
   Google Scholar
• Chapman , D. W. 1986 . Salmon and steelhead abundance in the Columbia River in the nineteenth century . Transactions of the American Fisheries Society , 115 : 662 – 670 .
   Web of Science ®Google Scholar
• Choi , J. H. , Jung , H. Y. , Kim , H. S. and Cho , H. G. 2000 . PhyloDraw: a phylogenetic tree drawing system . Bioinformatics , 16 : 1056 – 1058 .
   PubMed Web of Science ®Google Scholar
• Christie , M. R. , Marine , M. L. , French , R. A. , Waples , R. S. and Blouin , M. S. 2012 . Effective size of a wild salmonid population is greatly reduced by hatchery supplementation . Heredity , 109 : 254 – 260 .
   PubMed Web of Science ®Google Scholar
• Crateau , E. 1997 . Straying of hatchery origin spring/summer-run Chinook Salmon in the Grande Ronde basin . NOAA Technical Memorandum NMFS-NWFSC-30
   Google Scholar
• Eldridge , W. H. and Killebrew , K. 2008 . Genetic diversity over multiple generations of supplementation: an example from Chinook Salmon using microsatellite and demographic data . Conservation Genetics , 9 : 13 – 28 .
   Web of Science ®Google Scholar
• Excoffier , L. , Laval , G. and Schneider , S. 2005 . Arlequin (version 3.0): an integrated software package for population genetics data analysis . Evolutionary Bioinformatics Online , 1 : 47 – 50 .
   PubMed Web of Science ®Google Scholar
• Faubet , P. and Gaggiotti , O. E. 2008 . A new Bayesian method to identify the environmental factors that influence recent migration . Genetics , 178 : 1491 – 1504 .
   PubMed Web of Science ®Google Scholar
• Faubet , P. , Waples , R. S. and Gaggiotti , O. E. 2007 . Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates . Molecular Ecology , 16 : 1149 – 1166 .
   PubMed Web of Science ®Google Scholar
• Felsenstein , J. 2005 . PHYLIP (phylogeny inference package) version 3.65 , Seattle : University of Washington . Available: http://evolution.genetics.washington.edu/phylip.html. (January 2010)
   Google Scholar
• Fleming , I. A. and Gross , M. R. 1993 . Breeding success of hatchery and wild Coho Salmon (Oncorhynchus kisutch) in competition . Ecological Applications , 3 : 230 – 245 .
   PubMed Web of Science ®Google Scholar
• Ford , M. , Budy , P. , Busack , C. , Chapman , D. , Cooney , T. , Fisher , T. , Geiselman , J. , Hillman , T. , Lukas , J. , Peven , C. , Toole , C. , Weber , E. and Wilson , P. 2001 . Upper Columbia River steelhead and spring Chinook Salmon population structure and biological requirements: final report, March 2001 , Seattle : National Marine Fisheries Service, Northwest Fisheries Science Center .
   Google Scholar
• Fraser , D. J. , Weir , L. K. , Bernatchez , L. , Hansen , M. M. and Taylor , E. B. 2011 . Extent and scale of local adaptation in salmonid fishes: review and meta-analysis . Heredity , 106 : 404 – 420 .
   PubMed Web of Science ®Google Scholar
• Goodman , D. 2004 . “ Salmon supplementation: demography, evolution, and risk assessment ” . In Propagated fish in resource management , Edited by: Nickum , M. J. , Mazik , P. M. , Nickum , J. G. and MacKinlay , D. D. 217 – 232 . Bethesda , Maryland : American Fisheries Society, Symposium 44 .
   Google Scholar
• Guo , S. W. and Thompson , E. A. 1992 . Performing the exact test of Hardy–Weinberg proportion for multiple alleles . Biometrics , 48 : 361 – 372 .
   PubMed Web of Science ®Google Scholar
• Hansen , M. M. , Fraser , D. J. , Meier , K. and Mensberg , K. L. D. 2009 . Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of Brown Trout populations subject to stocking and population declines . Molecular Ecology , 18 : 2549 – 2562 .
   PubMed Web of Science ®Google Scholar
• Hansen , M. M. , Meier , K. and Mensberg , K. L. D. 2010 . Identifying footprints of selection in stocked Brown Trout populations: a spatio-temporal approach . Molecular Ecology , 19 : 1787 – 1800 .
   PubMed Web of Science ®Google Scholar
• Hedrick , P. W. , Hedgecock , D. , Hamelberg , S. and Croci , S. J. 2000 . The impact of supplementation in winter-run Chinook Salmon on effective population size . Journal of Heredity , 91 : 112 – 116 .
   PubMed Web of Science ®Google Scholar
• Heggenes , J. , Beere , M. , Tamkee , P. and Taylor , E. B. 2006 . Genetic diversity in steelhead before and after conservation hatchery operation in a coastal, boreal river . Transactions of the American Fisheries Society , 135 : 251 – 267 .
   Web of Science ®Google Scholar
• Hess , M. A. , Rabe , C. D. , Vogel , J. L. , Stephenson , J. J. , Nelson , D. D. and Narum , S. R. 2012 . Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook Salmon . Molecular Ecology , 21 : 5236 – 5250 .
   PubMed Web of Science ®Google Scholar
• Hesse , J. A. , Harbeck , J. R. and Carmichael , R. W. 2006 . Monitoring and evaluation plan for northeast Oregon hatchery Imnaha and Grande Ronde subbasin spring Chinook Salmon , Portland , Oregon : 2006 Technical Report to Bonneville Power Administration, Project 198805301 .
   Google Scholar
• HSRG (Hatchery Scientific Review Group) . 2009 . Columbia River hatchery reform system-wide report , Seattle : Pacific Northwest Hatchery Reform Project . Available: www.hatcheryreform.us. (May 2011)
   Google Scholar
• Hulett , P. L. , Sharpe , C. S. and Wagemann , C. W. 2004 . “ Critical need for rigorous evaluation of salmonid propagation programs using local wild broodstock ” . In Propagated fish in resource management , Edited by: Nickum , M. J. , Mazik , P. M. , Nickum , J. G. and MacKinlay , D. D. 253 – 262 . Bethesda , Maryland : American Fisheries Society, Symposium 44 .
   Google Scholar
• Kalinowski , S. T. 2005 . HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness . Molecular Ecology Notes , 5 : 187 – 189 .
   Web of Science ®Google Scholar
• Kalinowski , S. T. , Wagner , A. P. and Taper , M. L. 2006 . ml-relate: a computer program for maximum likelihood estimation of relatedness and relationship . Molecular Ecology Notes , 6 : 576 – 579 .
   Web of Science ®Google Scholar
• Kostow , K. E. , Marshall , A. R. and Phelps , S. R. 2003 . Naturally spawning hatchery steelhead contribute to smolt production but experience low reproductive success . Transactions of the American Fisheries Society , 132 : 780 – 790 .
   Web of Science ®Google Scholar
• Laythe , L. L. 1950 . The fishery development program in the lower Columbia River . Transactions of the American Fisheries Society , 78 : 42 – 55 .
   Google Scholar
• Leider , S. A. , Hulett , P. L. , Loch , J. J. and Chilcote , M. W. 1990 . Electrophoretic comparison of the reproductive success of naturally spawning transplanted and wild steelhead trout through the returning adult stage . Aquaculture , 88 : 239 – 252 .
   Web of Science ®Google Scholar
• Lichatowich , J. A. 1999 . Salmon without rivers: a history of the Pacific salmon crisis , Washington , D.C. : Island Press .
   Google Scholar
• Lowry , R. 2012 . VassarStats: website for statistical computation Vassar College , Poughkeepsie, New York Available: VassarStats.net. (May 2012)
   Google Scholar
• Marshall , S. L. 2010 . A brief history of the lower Snake River compensation plan hatchery program for spring and summer Chinook Salmon , Boise , Idaho : U.S. Fish and Wildlife Service, Lower Snake River Compensation Plan . Available: www.fws.gov/lsnakecomplan. (January 2013)
   Google Scholar
• Matala , A. P. , Hess , J. E. and Narum , S. R. 2011 . Resolving adaptive and demographic divergence among Chinook Salmon populations in the Columbia River basin . Transactions of the American Fisheries Society , 140 : 783 – 807 .
   Web of Science ®Google Scholar
• Matthews , G. M. and Waples , R. S. 1991 . Status review for Snake River spring and summer Chinook Salmon . NOAA Technical Memorandum NMFS F/NWC-200
   Google Scholar
• McClure , M. M. , Utter , F. M. , Baldwin , C. , Carmichael , R. W. , Hassemer , P. F. , Howell , P. J. , Spruell , P. , Cooney , T. D. , Schaller , H. A. and Petrosky , C. E. 2008 . Evolutionary effects of alternative artificial propagation programs: implications for viability of endangered anadromous salmonids . Evolutionary Applications , 1 : 356 – 375 .
   PubMed Web of Science ®Google Scholar
• Monzyk , F. R. , Hoffnagle , T. L. , Carmichael , R. W. , Eddy , D. L. and Keniry , P. J. 2007 . Lower Snake River compensation plan: Oregon spring Chinook Salmon evaluation studies, 2004 annual progress report , Salem : Oregon Department of Fish and Wildlife .
   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 . 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
• NMFS (National Marine Fisheries Service) . 1992 . Endangered and threatened species; threatened status for Snake River spring/summer Chinook Salmon, threatened status for Snake River fall Chinook Salmon . Federal Register , 57 : 14653 – 14662 . 78(22 April 1992)
   Google Scholar
• NMFS (National Marine Fisheries Service) . 2012 . Northwest fisheries science center salmonid database: abundance , Seattle : National Oceanic and Atmospheric Administration, NMFS, Northwest Fisheries Science Center . Available: webapps.nwfsc.noaa.gov. (January 2012)
   Google Scholar
• Olsen , E. , Pierce , P. , McLean , M. and Hatch , K. 1992 . Stock summary reports for Columbia River anadromous salmonids , Portland , Oregon : Annual Report to the Bonneville Power Administration, Document 94402-2, Project 88-108 . Available: efw.bpa.gov/searchpublications./(January 2012)
   Google Scholar
• Pastor , S. M. 2004 . “ An evaluation of fresh water recoveries of fish released from national fish hatcheries in the Columbia River basin, and observations of straying ” . In Propagated fish in resource management , Edited by: Nickum , M. J. , Mazik , P. M. , Nickum , J. G. and MacKinlay , D. D. 87 – 98 . Bethesda , Maryland : American Fisheries Society, Symposium 44 .
   Google Scholar
• Peakall , R. and Smouse , P. E. 2006 . genalex 6: genetic analysis in Excel—population genetic software for teaching and research . Molecular Ecology Notes , 6 : 288 – 295 .
   Web of Science ®Google Scholar
• Piggott , M. P. , Bellemain , E. , Taberlet , P. and Taylor , A. C. 2004 . A multiplex pre-amplification method that significantly improves microsatellite amplification and error rates for faecal DNA in limiting conditions . Conservation Genetics , 5 : 417 – 420 .
   Web of Science ®Google Scholar
• RASP (Regional Assessment of Supplementation Project) . 1992 . Supplementation in the Columbia basin summary report series , Portland , Oregon : Report to the Bonneville Power Administration, Project 85-62 . Available: efw.bpa.gov/searchpublications./(January 2012)
   Google Scholar
• Reisenbichler , R. R. 2004 . “ Uncertainty and research needs for supplementing wild populations of anadromous Pacific salmon ” . In Propagated fish in resource management , Edited by: Nickum , M. J. , Mazik , P. M. , Nickum , J. G. and MacKinlay , D. D. 263 – 275 . Bethesda , Maryland : American Fisheries Society, Symposium 44 .
   Google Scholar
• Reisenbichler , R. R. and Rubin , S. P. 1999 . Genetic changes from artificial propagation of Pacific salmon affect the productivity and viability of supplemented populations . ICES Journal of Marine Science , 56 : 459 – 466 .
   Web of Science ®Google Scholar
• Rousset , F. 2008 . genepop’007: a complete re-implementation of the genepop software for Windows and Linux . Molecular Ecology Resources , 8 : 103 – 106 .
   PubMed Web of Science ®Google Scholar
• Ryman , N. and Laikre , L. 1991 . Effects of supportive breeding on the genetically effective population size . Conservation Biology , 5 : 325 – 329 .
   Web of Science ®Google Scholar
• Schroder , S. L. , Knudsen , C. M. , Pearsons , T. N. , Kassler , T. W. , Young , S. F. , Busack , C. A. and Fast , D. E. 2008 . Breeding success of wild and first-generation hatchery female spring Chinook Salmon spawning in an artificial stream . Transactions of the American Fisheries Society , 137 : 1475 – 1489 .
   Web of Science ®Google Scholar
• Schwartz , M. K. , Luikart , G. and Waples , R. S. 2007 . Genetic monitoring as a promising tool for conservation and management . Trends in Ecology and Evolution , 22 : 25 – 33 .
   PubMed Web of Science ®Google Scholar
• Small , M. P. , Currens , K. , Johnson , T. H. , Frye , A. E. and Von Bargen , J. F. 2009 . Impacts of supplementation: genetic diversity in supplemented and unsupplemented populations of summer Chum Salmon (Oncorhynchus keta) in Puget Sound (Washington, USA) . Canadian Journal of Fisheries and Aquatic Sciences , 66 : 1216 – 1229 .
   Web of Science ®Google Scholar
• Tessier , N. , Bernatchez , L. and Wright , J. M. 1997 . Population structure and impact of supportive breeding inferred from mitochondrial and microsatellite DNA analyses in land-locked Atlantic Salmon Salmo salar L . Molecular Ecology , 6 : 735 – 750 .
   Web of Science ®Google Scholar
• Thériault , V. , Moyer , G. R. , Jackson , L. S. , Blouin , M. S. and Banks , M. A. 2011 . Reduced reproductive success of hatchery Coho Salmon in the wild: insights into most likely mechanisms . Molecular Ecology , 20 : 1860 – 1869 .
   PubMed Web of Science ®Google Scholar
• Van Doornik , D. M. , Waples , R. S. , Baird , M. C. , Moran , P. and Berntson , E. A. 2011 . Genetic monitoring reveals genetic stability within and among threatened Chinook Salmon populations in the Salmon River, Idaho . North American Journal of Fisheries Management , 31 : 96 – 105 .
   Web of Science ®Google Scholar
• Waples , R. S. 1991 . Genetic interactions between hatchery and wild salmonids: lessons from the Pacific Northwest . Canadian Journal of Fisheries and Aquatic Sciences , 48 ( Supplement 1 ) : 124 – 133 .
   Web of Science ®Google Scholar
• Waples , R. S. 2005 . Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? . Molecular Ecology , 14 : 3335 – 3352 .
   PubMed 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. and Do , C. 2010 . Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution . Evolutionary Applications , 3 : 244 – 262 .
   PubMed Web of Science ®Google Scholar
• Waples , R. S. , Masuda , M. and Pella , J. 2007 . salmonnb: a program for computing cohort-specific effective population sizes (Nb ) in Pacific salmon and other semelparous species using the temporal method . Molecular Ecology Notes , 7 : 21 – 24 .
   Web of Science ®Google Scholar
• Waples , R. S. and Teel , D. J. 1990 . Conservation genetics of Pacific salmon: I. temporal changes in allele frequency . Conservation Biology , 4 : 144 – 156 .
   Web of Science ®Google Scholar
• Waples , R. S. , Teel , D. J. and Aebersold , P. B. 1991 . A genetic monitoring and evaluation program for supplemented populations of salmon and steelhead in the Snake River basin Portland , Oregon Annual Report of Research to the Bonneville Power Administration, Project 89-096, Available: efw.bpa.gov/searchpublications./ (October 2012)
   Google Scholar
• Zar , J. H. 1984 . Biostatistical analysis , Englewood Cliffs , , New Jersey : Prentice-Hall .
   Google Scholar