Loss of Genetic Integrity in Hatchery Steelhead Produced by Juvenile-Based Broodstock and Wild Integration: Conflicts in Production and Conservation Goals

REFERENCES

• Allendorf, F.W. 1993. Delay of adaptation to captive breeding by equalizing family size. Conservation Biology 7:416–419.
   Web of Science ®Google Scholar
• Allendorf, F.W., and G.K. Luikart. 2007. Conservation and the genetics of populations. Blackwell Scientific Publications, Oxford, UK.
   Google Scholar
• Allendorf, F.W., and S.R. Phelps. 1981. Use of allelic frequencies to describe population structure. Canadian Journal of Fisheries and Aquatic Sciences 38:1507–1514.
   Web of Science ®Google Scholar
• Allendorf, F.W., and N. Ryman. 1987. Genetic management of hatchery stocks. Pages 141–159 in N. Ryman and F. Utter, editors. Population genetics and fishery management. Blackburn Press, Caldwell, New Jersey.
   Google Scholar
• Araki, H., W.R. Ardren, E. Olsen, B. Cooper, and M.S. Blouin. 2007. Reproductive success of captive-bred steelhead trout in the wild: evaluation of three hatchery programs in the Hood River. Conservation Biology 21:181–190.
   PubMed Web of Science ®Google Scholar
• Araki, H., and C. Schmid. 2010. Is hatchery stocking a help or harm?: evidence, limitations and future directions in ecological and genetic surveys. Aquaculture 308(Supplement 1):S2–S11.
   Web of Science ®Google Scholar
• Cairney, M., J.B. Taggart, and B. Høyheim. 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
• Christie, M.R., M.L. Marine, R.A. French, R.S. Waples, and M.S. Blouin. 2012. Effective size of a wild salmonid population is greatly reduced by hatchery supplementation. Heredity 109:254–260.
   PubMed Web of Science ®Google Scholar
• Eldridge, W., and K. Killebrew. 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
• Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices , version 2.9.3. Available: http://www2.unil.ch/popgen/softwares/fstat.htm. (May 2014).
   Google Scholar
• Gow, J.L., P. Tamkee, J. Heggenes, G.A. Wilson, and E.B. Taylor. 2011. Little impact of hatchery supplementation that uses native broodstock on the genetic structure and diversity of steelhead trout revealed by a large-scale spatio-temporal microsatellite survey. Evolutionary Applications 4:763–782.
   PubMed Web of Science ®Google Scholar
• Hayes, M.C., R.R. Reisenbichler, S.P. Rubin, D.C. Drake, K.D. Stenberg, and S.F. Young. 2012. Effectiveness of an integrated hatchery program: can genetic-based performance differences between hatchery and wild Chinook Salmon be avoided? Canadian Journal of Fisheries and Aquatic Sciences 70:147–158.
   Web of Science ®Google Scholar
• Hedrick, P., D. Hedgecock, S. Hamelberg, and S. Croci. 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
• Hess, M.A., C.D. Rabe, J.L. Vogel, J.J. Stephenson, D.D. Nelson, and S.R. Narum. 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
• Hindar, K., N. Ryman, and F. Utter. 1991. Genetic effects of cultured fish on natural fish populations. Canadian Journal of Fisheries and Aquatic Sciences 48:945–957.
   Web of Science ®Google Scholar
• Hulett, P.L., C.S. Sharpe, C.W. Wagemann, M. Nickum, and P. Mazik. 2004. Critical need for rigorous evaluation of salmonid propagation programs using local wild broodstock. Pages 253–262. in M. J. Nickum, P. M. Mazik, J. G. Nickum, and D. D. MacKinlay, editors. Propagated fish in resource management. American Fisheries Society, Symposium 44, Bethesda, Maryland.
   Google Scholar
• Kennedy, B.M., W.L. Gale, and K.G. Ostrand. 2007. Relationship between smolt gill Na+, K+ ATPase activity and migration timing to avian predation risk of steelhead trout (Oncorhynchus mykiss) in a large estuary. Canadian Journal of Fisheries and Aquatic Sciences 64:1506–1516.
   Web of Science ®Google Scholar
• Krueger, C.C., and B. May. 1991. Ecological and genetic effects of salmonid introductions in North America. Canadian Journal of Fisheries and Aquatic Sciences 48(Supplement 1):66–77.
   Web of Science ®Google Scholar
• Le Vay, L., G.R. Carvalho, E.T. Quinitio, J.H. Lebata, V.N. Ut, and H. Fushimi. 2007. Quality of hatchery-reared juveniles for marine fisheries stock enhancement. Aquaculture 268(1–4):169–180.
   Web of Science ®Google Scholar
• Mobrand, L.E., J. Barr, L. Blankenship, D.E. Campton, T.T. P. Evelyn, T.A. Flagg, C.V. W. Mahnken, LW. Seeb, P.R. Seidel, and W.W. Smoker. 2005. Hatchery reform in Washington State: principles and emerging issues. Fisheries 30(6):11–23.
   Web of Science ®Google Scholar
• Moyer, G.R., M.S. Blouin, and M.A. Banks. 2007. The influence of family-correlated survival on Nb/N for progeny from integrated multi- and single-generation hatchery stocks of Coho Salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic Sciences 64:1258–1265.
   Web of Science ®Google Scholar
• Naish, K.A., J.E. Taylor III, P.S. Levin, T.P. Quinn, J.R. Winton, D. Huppert, and R. Hilborn. 2007. An evaluation of the effects of conservation and fishery enhancement hatcheries on wild populations of salmon. Advances in Marine Biology 53:61–194.
   PubMed Web of Science ®Google Scholar
• Paquet, P.J., T. Flagg, A. Appleby, J. Barr, L. Blankenship, D. Campton, M. Delarm, T. Evelyn, D. Fast, J. Gislason, P. Kline, D. Maynard, L. Mobrand, G. Nandor, P. Seidel, and S. Smith. 2011. Hatcheries, conservation, and sustainable fisheries—achieving multiple goals: results of the Hatchery Scientific Review Group's Columbia River basin review. Fisheries 36:547–561.
   Web of Science ®Google Scholar
• Peakall, R.O. D., and P.E. Smouse. 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
• Queller, D. C., and K. F. Goodnight. 1989. Estimating relatedness using genetic markers. Evolution 43:258–275.
   PubMed Web of Science ®Google Scholar
• Raymond, M., and F. Rousset. 1995. GENEPOP (version-1.2)–population-genetics software for exact tests and ecumenicism. Journal of Heredity 86:248–249.
   Web of Science ®Google Scholar
• Rexroad, C.E., R.L. Coleman, A.M. Martin, W.K. Hershberger, and J. Killefer. 2001. Thirty-five polymorphic microsatellite markers for Rainbow Trout (Oncorhynchus mykiss). Animal Genetics 32:317–319.
   PubMed Web of Science ®Google Scholar
• Rice, W.R. 1989. Analyzing tables of statistical tests. Evolution 43:223–225.
   PubMed Web of Science ®Google Scholar
• Ryman, N. 1994. Supportive breeding and effective population size: differences between inbreeding and variance effective numbers. Conservation Biology 8:888–890.
   Web of Science ®Google Scholar
• Ryman, N., P.E. Jorde, and L. Laikre. 1995. Supportive breeding and variance effective population size. Conservation Biology 9:1619–1628.
   Web of Science ®Google Scholar
• Ryman, N., and L. Laikre. 1991. Effects of supportive breeding on the genetically effective population size. Conservation Biology 5:325–329.
   Web of Science ®Google Scholar
• Scribner, K.T., J.R. Gust, and R.L. Fields. 1996. Isolation and characterization of novel salmon microsatellite loci: cross-species amplification and population genetic applications. Canadian Journal of Fisheries and Aquatic Sciences 53:833–841.
   Web of Science ®Google Scholar
• Spies, I.B., D.J. Brasier, P.T. L. O’Reilly, T.R. Seamons, and P. Bentzen. 2005. Development and characterization of novel tetra-, tri-, and dinucleotide microsatellite markers in Rainbow Trout (Oncorhynchus mykiss). Molecular Ecology Notes 5:278–281.
   Web of Science ®Google Scholar
• Tessier, N., L. Bernatchez, and J.M. Wright. 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
• Van Doornik, D.M., B.A. Berejikian, L.A. Campbell, and E.C. Volk. 2010. The effect of a supplementation program on the genetic and life history characteristics of an Oncorhynchus mykiss population. Canadian Journal of Fisheries and Aquatic Sciences 67:1449–1458.
   Web of Science ®Google Scholar
• Verspoor, E. 1988. Reduced genetic variability in first-generation hatchery populations of Atlantic Salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 45:1686–1690.
   Web of Science ®Google Scholar
• Wang, J., and N. Ryman. 2001. Genetic effects of multiple generations of supportive breeding. Conservation Biology 15:1619–1631.
   Web of Science ®Google Scholar
• Waples, R. 1998. Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity 89:438–450.
   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. 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 C. Do. 1994. Genetic risk associated with supplementation of Pacific salmonids: captive broodstock programs. Canadian Journal of Fisheries and Aquatic Sciences 51(Supplement 1):310–329.
   Web of Science ®Google Scholar
• Waples, R.S., and C. Do. 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
• Weir, B.S., and C.C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370.
   PubMed Web of Science ®Google Scholar
• Williamson, K.S., J.F. Cordes, and B. May. 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