Environmental Biology of Fishes

, Volume 94, Issue 1, pp 325–342 | Cite as

Understanding the adaptive consequences of hatchery-wild interactions in Alaska salmon



About 31% of salmon harvested in Alaska comes from the hatchery production of hundreds of millions of pink and chum salmon and smaller numbers of sockeye, Chinook, and coho salmon. The numbers of hatchery-reared juveniles released in some areas are greater than the numbers of juveniles from wild populations. However, virtually nothing is known about the effects of hatchery fish on wild populations in Alaska. Possible effects of these interactions can be inferred from studies of salmonids in other areas, from studies of other animals, and from theory. Numerous studies show a complex relationship between the genetic architecture of a population and its environment. Adaptive responses to nature and anthropogenic selection can be influenced by variation at a single gene, or more often, by the additive effects of several genes. Studies of salmonids in other areas show that hatchery practices can lead to the loss of genetic diversity, to shifts in adult run timing and earlier maturity, to increases in parasite load, to increases in straying, to altered levels of boldness and dominance, to shifts in juvenile out-migration timing, and to changes in growth. Controlled experiments across generations show, and theory predicts, that the loss of adaptive fitness in hatchery salmon, relative to fitness in wild salmon, can occur on a remarkably short time scale. All of these changes can influence survival and impose selective regimes that influence genetically based adaptive traits. The preservation of adaptive potential in wild populations is an important buffer against diseases and climate variability and, hence, should be considered in planning hatchery production levels and release locations. The protection of wild populations is the foundation for achieving sustained harvests of salmon in Alaska.


Adaptive potential Alaska Climate variability Domestication Genetic diversity Hatchery-wild interactions Mating behavior Pacific salmon Straying 


  1. Allendorf FW, Phelps SR (1980) Loss of genetic variation in a hatchery stock of cutthroat trout. Trans Am Fish Soc 109:537–543Google Scholar
  2. Araki H, Blouin MS (2005) Unbiased estimation of relative reproductive success of different groups: evaluation and correction of bias caused by parentage assignment. Mol Ecol 14:4097–4109PubMedGoogle Scholar
  3. Araki H, Cooper B, Blouin MS (2007a) Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild. Science 318:100–103PubMedGoogle Scholar
  4. Araki H, Ardren WR, Olsen E, Cooper B, Blouin MS (2007b) Reproductive success of captive-bred steelhead trout in the wild: evaluation of three hatchery programs in the Hood River. Conserv Biol 21:181–190PubMedGoogle Scholar
  5. Araki H, Waples RS, Arden WR, Cooper B, Blouin MS (2007c) Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms. Mol Ecol 16:953–966PubMedGoogle Scholar
  6. Araki H, Berejikian BA, Ford MJ, Blouin MS (2008) Fitness of hatchery-reared salmonids in the wild. Evol Appl 1:342–355Google Scholar
  7. Arkush KD, Giese AR, Mendonca HL, McBride AM, Marty GD, Hedrick PW (2002) Resistance to three pathogens in the endangered winter-run Chinook salmon (Oncorhynchus tshawytscha): effects of inbreeding and major histocompatibility complex genotypes. Can J Fish Aquat Sci 59:966–975Google Scholar
  8. Bachman RA (1984) Foraging behavior of free-ranging wild and hatchery brown trout in a stream. Trans Am Fish Soc 113:1–32Google Scholar
  9. Beacham TD (1988) A genetic analysis of early development in pink (Oncorhynchus gorbuscha) and chum salmon (Oncorhynchus keta) at three different temperatures. Genome 30:89–96PubMedGoogle Scholar
  10. Beamish RJ, Mahnken C, Neville CM (1997) Hatchery and wild production of Pacific salmon in relation to large-scale, natural shifts in the productivity of the marine environment. ICES J Mar Sci 54:1200–1215Google Scholar
  11. Bentzen P, Olsen JB, McLean JE, Seamons TR, Quinn TP (2001) Kinship analysis of Pacific salmon: insights into mating, homing, and timing of reproduction. J Hered 92:127–136PubMedGoogle Scholar
  12. Berejikian BA, Mathews SB, Quinn TP (1996) Effects of hatchery and wild ancestry and rearing environments on the development of agonistic behavior in steelhead trout (Oncorhynchus mykiss) fry. Can J Fish Aquat Sci 53:2004–2014Google Scholar
  13. Berejikian BA, Tezak EP, Schroder SL, Knudsen CM, Hard JJ (1997) Reproductive behavioral interactions between wild and captively reared coho salmon (Oncorhynchus kisutch). ICES J Mar Sci 54:1040–1050Google Scholar
  14. Berejikian BA, Tezak EP, LaRae AL (2000) Female mate choice and spawning behavior of Chinook salmon under experimental condition. J Fish Biol 57:647–661Google Scholar
  15. Bernatchez L, Landry C (2003) MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? J Evol Biol 16:363–377PubMedGoogle Scholar
  16. Blanchet S, Páez DJ, Bernatchez L, Dodson JJ (2008) An integrated comparison of captive-bred and wild Atlantic salmon (Salmo salar): implications for supportive breeding programs. Biol Conserv 141:1989–1999Google Scholar
  17. Blouin MS, Thuillier V, Cooper B, Amarasinghe V, Cluzel L, Araki H, Grunau C (2010) No evidence for large differences in genomic methylation between wild and hatchery steelhead (Oncorhynchus mykiss). Can J Fish Aquat Sci 67:217–224Google Scholar
  18. Bonasio R, Tu S, Reinberg D (2010) Molecular signals of epigenetic states. Science 330:612–613PubMedGoogle Scholar
  19. Borrell YJ, Pineda H, McCarthy I, Vázquez SJA, Lizana GB (2004) Correlations between fitness and heterozygosity at allozyme and microsatellite loci in the Atlantic salmon, Salmo salar L. Heredity 92:585–593PubMedGoogle Scholar
  20. Brännäs E (1995) First access to territorial space and exposure to strong predation pressure: a conflict in early emergin Atlantic salmon (Salmo salar) fry. Evol Biol 9:411–420Google Scholar
  21. Brenner RE, Moffitt SD, Grant WS (2011) Hatchery salmon straying studies in Prince William Sound, Alaska. Environ Biol Fish (this issue)Google Scholar
  22. Buhle ER, Holsman KK, Scheuerell MD, Albaugh A (2009) Using an unplanned experiment to evaluate the effects of hatchery and environmental variation on threatened populations of wild salmon. Biol Conserv 142:2449–2455Google Scholar
  23. Campbell WB, Emlen JM, Hershberger (1998) Thermally induced chronic developmental stress in coho salmon: integrating measures of mortality, early growth, and developmental instability. Oikos 81:398–410Google Scholar
  24. Campton DE (1995) Genetic effects of hatchery fish on wild populations of Pacific salmon and steelhead: what do we really know? Am Fish Soc Symp 15:337–353Google Scholar
  25. Campton DE (2004) Sperm competition in salmon hatcheries: the need to institutionalize genetically benign spawning protocols. Trans Am Fish Soc 133:1277–1289Google Scholar
  26. Campton DE, Allendor FW, Behnke RJ, Utter FM (1991) Reproductive success of hatchery and wild steelhead. Trans Am Fish Soc 120:816–822Google Scholar
  27. Candolin U (2003) The use of multiple cues in mate choice. Biol Revs 78:575–595Google Scholar
  28. Chilcote MW (2003) Relationship between natural productivity and the frequency of wild fish in mixed spawning populations of wild and hatchery steelhead (Oncorhychus mykiss). Can J Fish Aquat Sci 60:1057–1067Google Scholar
  29. Chilcote MW, Leider SA, Loch JJ (1986) Differential reproductive success of hatchery and wild summer-run steelhead under natural condition. Trans Am Fish Soc 115:726–735Google Scholar
  30. Consuegra S, Garcia de Leaniz C (2008) MHC-mediated mate choice increases parasite resistance in salmon. Proc R Soc Lond B 272:1397–1403Google Scholar
  31. Cooney RT, Brodeur RD (1998) Carrying capacity and North Pacific salmon production: stock-enhancement implications. Bull Mar Sci 62:443–464Google Scholar
  32. Cooper JC, Scholz AT, Hasler AD (1976) Experimental confirmation of the olfactory hypothesis with artificially imprinted coho salmon (Oncorhynchus kisutch). J Fish Res Board Can 33:703–710Google Scholar
  33. Crozier LG, Hendry AP, Lawson PW, Quinn TP, Mantua NJ, Battin J, Shaw RG, Huey RB (2008) Potential responses to climate change in organisms with complex life histories: evolution and plasticity in Pacific salmon. Ecol Appl 1:252–270Google Scholar
  34. Dickerson BR, Quinn TP, Willson MF (2002) Body size, arrival date, and reproductive success of pink salmon, Oncorhynchus gorbuscha. Ethol Ecol Evol 14:29–44Google Scholar
  35. Dickerson BR, Brinck KW, Willson MF, Bentzen P, Quinn TP (2005) Relative importance of salmon body size and arrival time at breeding grounds to reproductive success. Ecology 86:327–352Google Scholar
  36. Dittman AH, Quinn TP (1996) Homing in Pacific salmon: mechanisms and ecological basis. J Exp Biol 199:83–91PubMedGoogle Scholar
  37. Dwyer WP, Piper RG (1984) Three-year hatchery and field evaluation of four strains of rainbow trout. N Am J Fish Manag 4:216–221Google Scholar
  38. Einum S, Fleming IA (1999) Maternal effects of egg size in brown trout (Salmo trutta): norms of reaction to environmental quality. Proc R Soc Lond B 266:2095–2100Google Scholar
  39. Einum S, Fleming IA (2000) Highly fecund mothers sacrifice offspring survival to maximize fitness. Nature 405:565–567PubMedGoogle Scholar
  40. Eliason EJ, Clark TD, Hague MJ, Hanson LM, Gallagher ZS, Jefferies KM, Gale MK, Patterson DA, Hinch SG, Farrell AP (2011) Differences in thermal tolerances among sockeye salmon populations. Science 332:109–112PubMedGoogle Scholar
  41. Feng S, Jacobsen SE, Reik W (2010) Epigenetic reprogramming in plant and animal development. Science 330:622–627PubMedGoogle Scholar
  42. Finstad B, Heggberget TG (1993) Migration, growth and survival of wild and hatchery-reared anadromous Arctic charr (Salvelinus alpinus) in Finnmark, Northern Norway. J Fish Biol 43:303–312Google Scholar
  43. Fleming IA, Einum S (1997) Experimental tests of genetic divergence of farmed from wild Atlantic salmon due to domestication. ICES J Mar Sci 54:1051–1063Google Scholar
  44. Fleming IA, Gross MR (1992) Reproductive behavior of hatchery and wild coho salmon (Oncorhynchus kisutch): does it matter? Aquaculture 103:101–121Google Scholar
  45. Fleming IA, Gross MR (1993) Breeding success of hatchery and wild coho salmon (Oncorynchus kisutch) in competition. Ecol Appl 3:230–245Google Scholar
  46. Fleming IA, Hindar K, Mjolnerod IB, Johnsson B, Balstad T, Lamberg A (2000) Lifetime success and interactions of farm salmon invading a native population. Proc R Soc Lond B 267:1517–1523Google Scholar
  47. Fleming IA, Agustsson T, Finstad B, Johnson JI, Björnsson BT (2002) Effects of domestication on growth physiology and endocrinology of Atlantic salmon (Salmo salar). Can J Fish Aquat Sci 59:1323–1330Google Scholar
  48. Foote CJ, Brown GS, Wood CC (1997) Spawning success of males using alternative mating tactics in sockeye salmon, Oncorhynchus nerka. Can J Fish Aquat Sci 54:1785–1795Google Scholar
  49. Ford MJ (2002) Selection in captivity during supportive breeding may reduce fitness in the wild. Conserv Biol 16:815–825Google Scholar
  50. Ford MJ, Fuss H, Boelts B, LaHood E, Hard J, Miller J (2006) Changes in run timing and natural smolt production in a naturally spawning coho salmon (Oncorhynchus kisutch) population after 60 years of intensive hatchery supplementation. Can J Fish Aquat Sci 63:2343–2355Google Scholar
  51. Fraser DJ, Wei LK, Bernatchez L, Hansen MM, Taylor EB (2011) Extent and scale of local adaptation in salmonid fishes: review and meta-analysis. Heredity 106:404–420PubMedGoogle Scholar
  52. Fritts AL, Scott JL, Pearsons TN (2007) The effects of domestication on the relative vulnerability of hatchery and wild origin spring Chinook salmon (Oncorhynchus tshawytscha) to predation. Can J Fish Aquat Sci 64:813–818Google Scholar
  53. Funk WC, Tyburczy JA, Knudsen KL, Lindner KR, Allendorf FW (2005) Genetic basis of variation in morphololgical and life-history traits of a wild population of pink salmon. J Hered 96:24–31PubMedGoogle Scholar
  54. Garcia-Marin JL, Jorde PE, Ryman N, Utter F, Pla C (1991) Management implications of genetic differentiation between native and hatchery populations of brown trout (Salmo trutta) in Spain. Aquaculture 95:235–249Google Scholar
  55. Garrigan D, Hedrick PW (2001) Class I MHC polymorphism and evolution in endangered California Chinook and other Pacific salmon. Immunogenetics 53:483–489PubMedGoogle Scholar
  56. Gharrett AJ, Smoker WW (1991) Two generations of hybrids between even- and odd-year pink salmon (Oncorhynchus gorbuscha): a test for outbreeding depression? Can J Fish Aquat Sci 48:1744–1749Google Scholar
  57. Gharrett AJ, Smoker WW (1993) A perspective on the adaptive importance of genetic infrastructure in salmon populations to ocean ranching in Alaska. Fish Res 18:45–58Google Scholar
  58. Gharrett AJ, Smoker WW, Reisenbichler RR, Taylor SG (1999) Outbreeding depression in hybrids between odd- and even-broodyear pink salmon. Aquaculture 173:117–129Google Scholar
  59. Gilk SE, Wang IA, Hoover CL, Smoker WW, Taylor SG, Gray AK, Gharrett AJ (2004) Outbreeding depression in hybrids between spatially separated pink salmon, Oncorhynchus gorbuscha, populations: marine survival, homing ability, and variability in family size. Environ Biol Fish 69:287–297Google Scholar
  60. Gjedrem T (1983) Genetic variation in quantitative traits and selective breeding in fish and shellfish. Aquaculture 33:51–72Google Scholar
  61. Gomez-Uchida D, Seeb JE, Smith MJ, Habicht H, Quinn TP, Seeb LW (2011) Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations. BMC Evol Biol 11:48PubMedGoogle Scholar
  62. Goodier JL, Davidson WS (1994) Tc1 transposon-like sequences are widely distributed in salmonids. J Mol Biol 241:26–34PubMedGoogle Scholar
  63. GPRT (Genetic Policy Review Team) (1985) State of Alaska finfish genetics policy. Alaska Dep Fish Game, Juneau, AK, Available: http://www.cf.adfg.state.ak.us/geninfo/research/genetics/policy/finfish.php
  64. Grimholt U, Larsen S, Nordmo R, Midtlyng P, Kjoeglum S, Storset A, Saebø S, Stet RJM (2003) MHC polymorphism and disease resistance in Atlantic salmon (Salmo salar); facing pathogens with single expressed major histocompatibility class I and class II loci. Immunogenetics 55:210–219PubMedGoogle Scholar
  65. Hamada M, Kido Y, Himberg M, Reist JD, Ying C, Hasegawa M, Okada N (1997) A newly isolated family of short interspersed repetitive elements (SINEs) in coregonid fishes (whitefish) with sequences that are almost identical to those of the SmaI family of repeats: possible evidence for the horizontal transfer of SINEs. Genetics 146:355–367PubMedGoogle Scholar
  66. Hankin DG, Fitzgibbons J, Chen Y (2009) Unnatural random mating policies select for younger age at maturity in hatchery Chinook salmon (Oncorhynchus tshawytscha) populations. Can J Fish Aquat Sci 66:1505–1521Google Scholar
  67. Hansen LP, Jonsson B (1991) The effect of timing of Atlantic salmon smolt and post-smolt release on the distribution of adult return. Aquaculture 98:61–71Google Scholar
  68. Hauser L, Seamons TR, Dauer M, Naish KA, Quinn TP (2006) An empirical verification of population assignment methods by marking and parentage data: hatchery and wild steelhead (Oncorhynchus mykiss) in Forks Creek, Washington, USA. Mol Ecol 15:3157–3173PubMedGoogle Scholar
  69. Hawkins DK, Foote CJ (1998) Early survival and development of coastal cutthroat trout (Oncorhynchus clarki clarki), steelhead (Oncorhynchus mykiss), and reciprocal hybrids. Can J Fish Aquat Sci 55:2097–2104Google Scholar
  70. Hayes SA, Bond MH, Hanson CV, McFarlane RB (2004) Interactions between endangered wild and hatchery salmonids: can the pitfalls of artificial propagation be avoided in small coastal streams? J Fish Biol 65(Suppl A):101–121Google Scholar
  71. Heard WR (1991) Life history of pink salmon (Oncorhynchus gorbuscha). In: Groot C, Margolis L (eds) Pacific salmon life histories. UBC, Vancouver, pp 119–230Google Scholar
  72. Heard WR (2003) Alaska salmon enhancement: a successful program for hatchery and wild stocks. In: Nakamura Y, McVey JP, Leber K, Neidig C, Fox S, Churchill K (eds) Ecology of aquaculture species and enhancement of stocks. Proc 13th U.S.–Japan Meeting on Aquaculture. Sarasota, Florida, 3–4 December. UJNR Technical Report No. 30. Sarasota, FL: Mote Marine Laboratory, pp 149–169Google Scholar
  73. Hesthagen T, Flòystad L, Hegge O, Staurnes M, Skurdal J (1999) Comparative life-history characteristics of native and hatchery-reared brown trout, Salmo trutta L., in a sub-Alpine reservoir. Fish Manag Ecol 6:47–61Google Scholar
  74. Hey J, Brannon EL, Campton DE, Doyle RW, Fleming IA, Kinnison MT, Lande R, Olsen J, Philipp DP, Travis J, Wood CC, Doremus H (2005) Considering life history, behavioral and ecological complexity in defining conservation units for Pacific salmon: an independent panel report, requested by NOAA Fisheries. NW Fisheries Science Center, SeattleGoogle Scholar
  75. Hilborn R, Eggers D (2000) A review of the hatchery programs for pink salmon in Prince William Sound and Kodiak Island, Alaska. Trans Am Fish Soc 129:333–350Google Scholar
  76. Hilborn R, Eggers D (2001) A review of the hatchery programs for pink salmon in Prince William Sound and Kodiak Island, Alaska: response to comment. Trans Am Fish Soc 130:720–724Google Scholar
  77. Hilborn R, Quinn TP, Schindler DE, Rogers DE (2003) Biocomplexity and fisheries sustainability. Proc Natl Acad Sci USA 100:6564–6568PubMedGoogle Scholar
  78. Hindar K, Ryman N, Utter F (1991) Genetic effects of cultured fish on natural fish populations. Can J Fish Aquat Sci 48:945–957Google Scholar
  79. Hodgson S, Quinn TP (2002) The timing of adult sockeye salmon migration into fresh water: adaptations by populations to prevailing thermal regimes. Can J Zool 80:542–555Google Scholar
  80. Hoysak DJ, Liley NR, Taylor EB (2004) Raffles, roles, and the outcome of sperm competition in sockeye salmon. Can J Zool 82:1017–1026Google Scholar
  81. Hutchings JA (1991) The threat of extinction to native populations experiencing spawning intrusions by cultured Atlantic salmon. Aquaculture 98:119–132Google Scholar
  82. Huusko A, Vehanen T (2011) Do hatchery-reared brown trout affect the growth and habitat use of wild congeners? Fish Manag Ecol 18:258–261Google Scholar
  83. Jacob A, Nusslé BA, Evanno G, Müller WC (2007) Make dominance linked to size and age, but not to ‘good genes’ in brown trout (Salmo trutta). BMC Evol Biol 7:207. doi:10.1186/1471-2148-7-207 PubMedGoogle Scholar
  84. Jeffrey KJ, Bangham CR (2000) Do infectious diseases drive MHC diversity? Microbes Infect 2:1335–1341Google Scholar
  85. Jonsson B (1997) A review of ecological and behavioural interactions between cultured and wild Atlantic salmon. ICES J Mar Sci 54:1031–1039Google Scholar
  86. Jonsson B, Jonsson N (2006) Cultured Atlantic salmon in nature: a review of their ecology and interaction with wild fish. ICES J Mar Sci 63:1162–1181Google Scholar
  87. Jonsson B, Jonsson N, Hansen LP (1991) Differences in life history and migratory behavior between wild and hatchery-reared Atlantic salmon in nature. Aquaculture 98:69–78Google Scholar
  88. Karasov T, Messer PW, Petrov DA (2010) Evidence that adaptation in Drosophila is not limited by mutation at single sites. PLoS Genet 6(6):e1000924PubMedGoogle Scholar
  89. Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation. Ecol Lett 7:1225–1241Google Scholar
  90. Kido Y, Aono M, Yamaki T, Matsumoto K, Murata S, Saneyoshi M, Okada N (1991) Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. Proc Natl Acad Sci USA 88:2326–2330PubMedGoogle Scholar
  91. Knudsen CM, Schroder SL, Busack CA, Johnston MV, Pearson TN, Bosch WJ, Fast DE (2006) Comparison of life history traits between first-generation hatchery and wild upper Yakima River spring Chinook salmon. Trans Am Fish Soc 135:1130–1144Google Scholar
  92. Knudsen CM, Schroder SL, Busack C, Johnston MV, Pearsons TN, Strom CR (2008) Comparison of female reproductive traits and progeny of first-generation hatchery and wild upper Yakima River spring Chinook salmon. Trans Am Fish Soc 137:1433–1445Google Scholar
  93. Kostow KE (2004) Differences in juvenile phenotypes and survival between hatchery stocks and a natural population provide evidence for modified selection due to captive breeding. Can J Fish Aquat Sci 61:577–589Google Scholar
  94. Kostow K (2009) Factors that contribute to the ecological risks of salmon and hatchery programs and some mitigating strategies. Rev Fish Biol Fish 19:9–31Google Scholar
  95. Kostow KE, Zhou S (2006) The effect of an introduced summer steelhead hatchery stock on the productivity of a wild winter steelhead population. Trans Am Fish Soc 135:825–841Google Scholar
  96. Kramerov DA, Vassetzky NS (2005) Short retroposons in eukaryotic genomes. Int Rev Cytol 247:165–221PubMedGoogle Scholar
  97. Labelle M (1992) Straying patterns of coho salmon (Oncorhynchus kisutch) stocks from southeast Vancouver Island, British Columbia. Can J Fish Aquat Sci 49:1843–1855Google Scholar
  98. Lachance S, Magnan P (1990) Performance of domestic hybrid, and wild strains of brook trout, Salvelinus fontinalis, after stocking: the impact of intra- and interspecific competition. Can J Fish Aquat Sci 47:2278–2284Google Scholar
  99. Laikre L, Schwartz MK, Waples RS, Ryman N, GeM Working Group (2010) Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals. Trends Ecol Evol 25:520–529PubMedGoogle Scholar
  100. Landry C, Bernatchez L (2001) Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar). Mol Ecol 10:2525–2539PubMedGoogle Scholar
  101. Landry C, Garant D, Duchesne BL (2001) ‘Good genes as heterozygosity’: the major histocompatibility complex and mate choice in Atlantic salmon (Salmo salar). Proc R Soc Lond B 268:1279–1285Google Scholar
  102. Langefors Å, Lohm J, Grahn M, Andersen Ø, von Schantz T (2000) Association between major histocompatibility complex class IIB alleles and resistance to Aeromonas salmonicida in Atlantic salmon. Proc R Soc Lond B 268:479–485Google Scholar
  103. Leary RF, Allendorf FW, Knudsen KL (1985) Developmental Instability as an Indicator of Reduced Genetic Variation in Hatchery. Trans Am Fish Soc 114:230–235Google Scholar
  104. Leider SA, Chilcote LJJ, Loch JJ (1986) Comparative life history characteristics of hatchery and wild steelhead trout (Salmo gairdneri) of summer and winter races in the Kalama River, Washington. Can J Fish Aquat Sci 43:1398–1409Google Scholar
  105. Lynch M, O’Hely M (2001) Captive breeding and the genetic fitness of natural populations. Conserv Genet 2:363–378Google Scholar
  106. Lynch M, Blanchard J, Houle D, Kibota T, Schultz S, Vassilieva L, Willis J (1999) Perspective: spontaneous deleterious mutation. Evolution 53:645–663Google Scholar
  107. Mackey G, McLean JE, Quinn TP (2001) Comparisons of run timing, spatial distribution and length of wild and newly established hatchery populations of steelhead in Forks Creek, Washington. N Am J Fish Manag 21:717–724Google Scholar
  108. Malaga-Trillo E, Zaleska-Rutczynska Z, McAndrew B, Vincek V, Figueroa F, Sultmann H, Klein J (1998) Linkage relationships and haplotype polymorphism among cichlid Mhc Class B loci. Genetics 149:1527–1537PubMedGoogle Scholar
  109. Mantua NJ, Hare SR (2002) The Pacific decadal oscillation. J Oceanogr 58:35–44Google Scholar
  110. Mantua NJ, Hare SR, Zhang Y, Wallace JM, Francis RC (1997) A Pacific interdecadal climate oscillation with impacts on salmon production. Bull Am Meterol Soc 78:1069–1079Google Scholar
  111. Matveev V, Okada N (2009) Retroposons of salmonid fishes (Actinopterygii: Salmonoidei) and their evolution. Gene 434:16–28PubMedGoogle Scholar
  112. McDermid JL, Sloan WN, Wilson CC, Shuter BJ (2010) Early life history variation among hatchery- and wild-origin lake trout reared in a hatchery environment. Trans Am Fish Soc 139:21–28Google Scholar
  113. McGinnity P, Stone C, Taggart JB, Cooke D, Cotter D, Hynes R, McCamley C, Cross T, Ferguson A (1997) Genetic impact of escaped farmed Atlantic salmon (Salmo salar L.) on native populations: use of DNA profiling to assess freshwater performance of wild, farmed, and hybrid progeny in a natural river environment. ICES J Mar Sci 54:998–1008Google Scholar
  114. McGinnity P, Prodöhl P, Ferguson A, Hynes R, ó Maoiléidigh N, Baker N, Cotter D, O’Hea B, Cooke D, Rogan G, Taggart J, Cross T (2003) Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with Fitness reduction and potential extinction of wild populations escaped farm salmon. Proc Roy Soc Lond B 270:2443–2450Google Scholar
  115. McGinnity P, Jennings E, deEyto E, Allott N, Samuelsson P, Rogan G, Whelan K, Cross T (2009) Impact of naturally spawning captive-bred Atlantic salmon on wild populations: depressed recruitment and increased risk of climate-mediated extinction. Proc Roy Soc Lond B 276:3601–3610Google Scholar
  116. McGregor AJ, Lane S, Thomason MA, Zhivotovsky LA, Smoker WW, Gharrett AJ (1998) Migration timing, a life history trait important in the genetic structure of pink salmon. N Pac Anadr Fish Comm Bull 1:262–273Google Scholar
  117. McIsaac DO, Quinn TP (1988) Evidence for a hereditary component in homing behavior of chinook [sic] salmon (Oncorhynchus tshawytscha). Can J Fish Aquat Sci 45:2201–2205Google Scholar
  118. McLean JE, Bentzen P, Quinn TP (2003) Differential reproductive success of sympatric naturally spawning hatchery and wild steelhead trout (Oncorhynchus mykiss) through the adult stage. Can J Fish Aquat Sci 60:433–440Google Scholar
  119. Mesa MG (1991) Variation in feeding, aggression, and position choice between hatchery and wild cutthroat trout in an artificial stream. Trans Am Fish Soc 120:723–727Google Scholar
  120. Metcalfe NB, Valdimarsson SK, Morgan IJ (2003) The relative roles of domestication, rearing environment, prior residence and body size in deciding territorial contests between hatchery and wild juvenile salmon. J Appl Ecol 40:535–544Google Scholar
  121. Miller KM, Withler RE (1996) Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon. Immunogenetics 43:337–351PubMedGoogle Scholar
  122. Miller KM, Withler RE (1998) The salmonids class I MHC: limited diversity in a primitive teleost. Immunol Rev 166:279–293PubMedGoogle Scholar
  123. Miller KM, Kaukinen KH, Beacham TD, Withler RE (2001) Geographic heterogeneity in natural selection on an MHC locus in sockeye salmon. Genetica 111:237–257PubMedGoogle Scholar
  124. Mobrand LE, Barr J, Blankenship L, Campton DE, Evelyn TTP, Flagg TA, Mahnken CVW, Seeb LW, Seidel PR, Smoker WW (2005) Hatchery reform in Washington State: principles and emerging issues. Fisheries 30:11–23Google Scholar
  125. Murata S, Takasaki N, Saitoh M, Okada N (1993) Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc Natl Acad Sci USA 90:6995–6999PubMedGoogle Scholar
  126. Murata S, Takasaki N, Okazaki T, Kobayashi T, Numachi K, Chang K-H, Okada N (1998) Molecular evidence from short interspersed elements (SINEs) that Oncorhynchus masou (cherry salmon) is monophyletic. Can J Fish Aquat Sci 55:1864–1870Google Scholar
  127. Naish KA, Hard JJ (2008) Bridging the gap between genotype and phenotype: linking genetic variation, selection and adaptation in fishes. Fish Fish 9:396–422Google Scholar
  128. Naish KA, Taylor JE III, Levin PS, Quinn TP, Winton JR, Huppert D, Hilborn R (2008) An evaluation of the effects of conservation and fishery enhancement hatcheries on wild populations of salmon. Adv Mar Biol 53:61–194Google Scholar
  129. Neff BD, Pitcher TE (2005) Genetic quality and sexual selection: an integrated framework for good genes and compatible genes. Mol Ecol 14:19–38PubMedGoogle Scholar
  130. Neff BD, Garner SR, Heath JW, Heath (2008) The MHC and non-random mating in a captive population of Chinook salmon. Heredity 101:175–185PubMedGoogle Scholar
  131. Neville HM, Isaak DJ, Dunham JB, Thurow RF, Reiman BE (2006) Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: insights from spatial autocorrelation analysis of individual genotypes. Mol Ecol 15:4589–4602PubMedGoogle Scholar
  132. Nicholas J, McIntosh B, Bowles E (2005) Oregon coastal coho assessment. Part 1: synthesis of the coastal ESU assessment. Final report. Oregon Watershed Enhancement Board and Oregon Dept Fish Wildlife, Salem Oregon, USA [cited in Buhle et al. 2009]Google Scholar
  133. Nielsen JL, Pavey SA (2010) Perspectives: gene expression in fisheries management. Curr Zool 56:157–174Google Scholar
  134. Norris AT, Bradley DG, Cunningham EP (1999) Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations. Aquaculture 180:247–264Google Scholar
  135. Pearsons TN, Fritts AL, Scott JL (2007) The effects of hatchery domestication on competitive dominance of juvenile spring Chinook salmon (Oncorhynchus tshawytscha). Can J Fish Aquat Sci 64:803–812Google Scholar
  136. Pitcher TE, Neff BD (2006) MHC class IIB alleles contribute to both additive and non-additive genetic effects on survival in Chinook salmon. Mol Ecol 15:2357–2365PubMedGoogle Scholar
  137. Powers DA, Lauerman T, Crawford D, De Michele L (1991) Genetic mechanisms for adapting to a changing environment. Annu Rev Genet 25:629–659PubMedGoogle Scholar
  138. Puurtinen M, Ketola T, Kotiaho JS (2009) The good–genes and compatible–genes benefits of mate choice. Am Nat 174:741–752PubMedGoogle Scholar
  139. Quinn TP (1993) A review of homing and straying of wild and hatchery produced salmon. Fish Res 18:29–44Google Scholar
  140. Quinn TP, Nemeth RS, McIsaac DO (1991) Homing and straying patterns of fall chinook [sic] salmon in the lower Columbia River. Trans Am Fish Soc 120:150–156Google Scholar
  141. Quinn TP, Peterson JA, Gallucci VF, Hershberger WK, Brannon EL (2002) Artificial selection and environmental change: countervailing factors affecting the timing of spawning in coho and Chinook salmon. Trans Am Fish Soc 131:591–598Google Scholar
  142. Raleigh RF (1971) Innate control of migrations of salmon and trout fry from natal gravels to rearing areas. Ecology 52:291–297Google Scholar
  143. Reed DH, Frankham R (2001) How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis. Evolution 55:1095–1103PubMedGoogle Scholar
  144. Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conserv Biol 17:230–237Google Scholar
  145. Reisenbichler RR, McIntyre JD (1977) Genetic differences in growth and survival of juvenile hatchery and wild steelhead trout, Salmo gairdneri. J Fish Res Board Can 34:123–128Google Scholar
  146. Reisenbichler RR, Rubin SP (1999) Genetic changes from artificial propagation of Pacific salmon affect the productivity and viability of supplemented populations. ICES J Mar Sci 56:459–466Google Scholar
  147. Rhymer JM, Simberloff D (1996) Extinction by hybridization and introgression. Ann Rev Ecol Syst 27:83–109Google Scholar
  148. Riddell BE, Leggett WC (1981) Evidence of an adaptive basis for geographic variation in body morphology and time of downstream migration of juvenile Atlantic salmon (Salmo salar). Can J Fish Aquat Sci 38:308–320Google Scholar
  149. Ridley M (2004) Evolution, 3rd edn. Blackwell, Malden, 751 pGoogle Scholar
  150. Rosenau ML, McPhail JD (1987) Inherited differences in agonistic behavior between two populations of coho salmon. Trans Am Fish Soc 116:646–654Google Scholar
  151. Royer TC, Grosch CE, Mysak LA (2001) Interdecadal variability of Northeast Pacific coastal freshwater and its implications on biological productivity. Prog Oceanogr 49:95–111Google Scholar
  152. Ruggerone GT, Zimmermann M, Myers KW, Nielsen JL, Rogers DE (2003) Competition between Asian pink salmon (Oncorhynchus gorbuscha) and Alaskan sockeye salmon (O. nerka) in the North Pacific Ocean. Fish Oceanogr 12:209–219Google Scholar
  153. Ryman N, Laikre L (1991) Effects of supportive breeding on the genetically effective population size. Conserv Biol 5:325–329Google Scholar
  154. Ryman N, Ståhl G (1980) Genetic changes in hatchery stocks of brown trout (Salmo trutta). Can J Fish Aquat Sci 37:82–87Google Scholar
  155. Schindler DE, Hilborn R, Chasco B, Boatright CP, Quinn TP, Rogers LA, Webster MS (2010) Population diversity and the portfolio effect in an exploited species. Nature 465:609–612PubMedGoogle Scholar
  156. Seeb JE, Habicht C, Templin WD, Seeb LW, Shaklee JB, Utter FM (1999) Allozyme and mitochondrial DNA variation describe ecologically important genetic structure of even-year pink salmon inhabiting Prince William Sound, Alaska. Ecol Freshw Fish 8:122–140Google Scholar
  157. Smoker WW, Heard WR (2007) Productivity of Alaska’s salmon hatchery ocean ranching program and management of biological risk to wild Pacific salmon. In: Bert TM (ed) Ecological and genetic implications of aquaculture activities. Springer, Dordrecht, pp 361–381Google Scholar
  158. Smoker WW, Gharrett AJ, Stekoll MS (1998) Genetic variation of return date in a population of pink salmon: a consequence of fluctuating environment and dispersive selection? Alaska Fish Res Bull 5:46–54Google Scholar
  159. Steele JH (1998) Regime shifts in marine ecosystems. Ecol Appl 8(Supplement):S33–S36Google Scholar
  160. Sunderström LF, Petersson E, Höjesjö J, Johnsson JI, Järvi (2004) Hatchery selection promotes boldness in newly hatched brown trout (Salmo trutta): implications for dominance. Behav Ecol 15:192–198Google Scholar
  161. Swain DP, Riddell BE (1990) Variation in agonistic behavior between newly emerged juveniles from hatchery and wild populations of coho salmon, Oncorhynchus kisutch. Can J Fish Aquat Sci 47:566–571Google Scholar
  162. Tafalla C, Estepa A, Coll JM (2006) Fish transposons and their potential use in aquaculture. J Biotechnol 123:397–412PubMedGoogle Scholar
  163. Takasaki N, Yamaki T, Hamada M, Park L, Okada N (1997) The salmon SmaI family of short interspersed repetitive elements (SINEs): interspecific and intraspecific variation in the insertion of SINEs in the genomes of chum and pink salmon. Genetics 146:369–380PubMedGoogle Scholar
  164. Tave D (1993) Genetics for fish hatchery managers. Van Nostrand Reinhold, New YorkGoogle Scholar
  165. Taylor SG (1980) Marine survival of pink salmon fry from early and late spawners. Trans Am Fish Soc 109:79–82Google Scholar
  166. Taylor EB (1991) A review of local adaptation in Salmonidae, with particular reference to Pacific and Atlantic salmon. Aquaculture 98:185–207Google Scholar
  167. Thériault V, Moyer GR, Jackson LS, Blouin MS, Banks MA (2011) Reduced reproductive success of hatchery coho salmon in the wild: insights into most likely mechanisms. Mol Ecol 20:1860–1869PubMedGoogle Scholar
  168. Thomas GL, Mathisen OA (1993) Biological interactions of natural and enhanced stocks of salmon. Fish Res 18:1–17Google Scholar
  169. Turner SM, Chaves-Campos J, DeWoody JA (2009) Parental relatedness and major histocompatibility effects on early embryo survivorship in Atlantic salmon. Genetica 137:99–109PubMedGoogle Scholar
  170. Unwin MJ, Glova GJ (1997) Changes in life history parameters in a naturally spawning population of chinook salmon (Oncorhynchus tshawytscha) associated with releases of hatchery-reared fish. Can J Fish Aquat Sci 54:1235–1245Google Scholar
  171. Utter F (1998) Genetic problems of hatchery-reared progeny released into the wild, and how to deal with them. Bull Mar Sci 62:623–640Google Scholar
  172. Verspoor E (1988) Widespread hybridization between native Atlantic salmon, Salmo salar, and introduced brown trout, S. trutta, in eastern Newfoundland. J Fish Biol 32:327–334Google Scholar
  173. Verspoor E (1997) Genetic diversity among Atlantic salmon (Salmo salar L.) populations. ICES J Mar Sci 54:965–973Google Scholar
  174. Vincent RE (1960) Some influences of domestication upon three stocks of brook trout (Salvelinus fontinalis Mitchill). Trans Am Fish Soc 89:35–52Google Scholar
  175. Wang S, Hard JJ, Utter F (2002) Genetic variation and fitness in salmonids. Conserv Genet 3:321–333Google Scholar
  176. Waples RS (1991) Genetic interactions between hatchery and wild salmonids: lessons from the Pacific Northwest. Can J Fish Aquat Sci 48(Supplement 1):124–133Google Scholar
  177. Waples RS, Do C (1994) Genetic risk associated with supplementation of Pacific Salmonids: captive broodstock programs. Can J Fish Aquat Sci 51(S1):310–329Google Scholar
  178. Waples RS, Gustafson RG, Weitkamp LA, Myers JM, Johnson OW, Busby PJ, Hard JJ, Bryant GJ, Waknitz FW, Neely K, Teel D, Grant WS, Winans GA, Phelps S, Marshall A, Baker BM (2001) Characterizing diversity in salmon in the Pacific Northwest. J Fish Biol 59(suppl A):1–41Google Scholar
  179. Waples RS, Zabel RW, Scheuerell MD, Sanderson BL (2008) Evolutionary responses by native species to major anthropogenic changes to their ecosystems: Pacific salmon in the Columbia River hydropower system. Mol Ecol 17:84–96PubMedGoogle Scholar
  180. Weber ED, Fausch DK (2003) Interactions between hatchery and wild salmonids in streams: differences in biology and evidence for competition. Can J Fish Aquat Sci 69:1018–1036Google Scholar
  181. Wedekind C, Rudolfsen G, Jacob A, Urbach D, Müller R (2007) The genetic consequences of hatchery-induced sperm competition in salmonids. Biol Conserv 137:180–188Google Scholar
  182. Wertheimer AC, Smoker WW, Joyce TL, Heard WR (2001) Hatchery pink salmon in Prince William Sound: enchancement or replacement? Trans Am Fish Soc 130:712–720Google Scholar
  183. Wessel ML, Smoker WW, Fagen RM, Joyce J (2006) Variation of agonistic behavior among juvenile Chinook salmon (Oncorhynchus tshawytscha) of hatchery, hybrid, and wild origin. Can J Fish Aquat Sci 63:438–477Google Scholar
  184. White B (2010) Alaska salmon enhancement program 2007 annual report. Fish Manag Rep 10–05, 53 pGoogle Scholar
  185. Withler RE (1988) Genetic consequences of fertilizing chinook [sic] salmon (Oncorhynchus tswawytscha) eggs with pooled milt. Aquaculture 68:15–25Google Scholar
  186. Wong BBM (2004) Superior fighters make mediocre fathers in the Pacific blue-eye fish. Anim Behav 67:583–590Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Commercial Fisheries Division, Alaska Department of Fish and GameAnchorageUSA

Personalised recommendations