Managing fisheries using genetic data: Case studies from four species of Pacific salmon

Fisheries Research

Volumn 43, Issue 1-3, 1999, Pages 45-78

  Shaklee, James B ^a   Beacham, Terry D ^b   Seeb, Lisa ^c   White, Bruce A ^d  

^a WASHINGTON DEPARTMENT OF FISH AND WILDLIFE   (United States)

^b PACIFIC BIOLOGICAL STATION   (Canada)

^c ALASKA DEPARTMENT OF FISH AND GAME   (United States)

^d Pacific Salmon Commission   (Canada)

Author keywords

Chinook; Chum; Coho; Fisheries management; Genetics; GSI; Pink salmon

Indexed keywords

FISHERY MANAGEMENT; GENETIC ANALYSIS; SALMONID FISHERY; STOCK IDENTIFICATION;

ONCORHYNCHUS; ONCORHYNCHUS GORBUSCHA; ONCORHYNCHUS KETA; ONCORHYNCHUS KISUTCH; ONCORHYNCHUS TSHAWYTSCHA; SALMONIDAE;

EID: 0032718203     PISSN: 01657836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0165-7836(99)00066-1     Document Type: Conference Paper

References (100)

1. ADFG (Alaska Department of Fish and Game), 1997. SPAM 95, ver 2.0: Statistics program for analyzing mixtures. Special Publication 13, Alaska Department of Fish and Game, Commercial Fisheries Management and Development Division, Anchorage.
2. Aebersold, P.B., Winans, G.A., Teel, D.J., Milner, G.B., Utter, F.M., 1987. Manual for starch gel electrophoresis: A method for the detection of genetic variation. NOAA Technical Report NMFS 61, US Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, 19 pp.
3. Anonymous, 1994. Interim estimates of coho stock composition for 1984-1991 southern area fisheries and for 1987-1991 northern panel area fisheries, Pac. Sal. Comm. Coho Tech. Comm. Rep. TCCOHO 94-1, 25 pp.
4. Banks M.A., Baldwin B.A., Hedgecock D. Research on chinook salmon (Oncorhynchus tshawytscha) stock structure using microsatellite DNA. Bull. Natl. Res. Inst. Aquacult. Suppl. 2:1996;5-9.
5. Banks M.A., Blouin M.S., Baldwin B.A., Rashbrook V.K., Fitzgerald H.A., Blankenship S.M., Hedgecock D. Isolation and inheritance of novel microsatellites in chinook salmon (Oncorhynchus tshawytscha). J. Heredity. 90:1999;281-288.
6. Bartley D.M., Bentley B., Olin P.G., Gall G.A.E. Population genetic structure of coho salmon (Oncorhynchus kisutch) in California. Cal. Fish. Game. 78:1992;88-104.
7. Beacham T.D. The use of minisatellite DNA variation for stock identification of chum salmon, Oncorhynchus keta. Fish. Bull. (US). 94:1996;611-626.
8. Beacham T.D., Gould A.P., Withler R.E., Murray C.B., Barner L.W. Biochemical genetic survey and stock identification of chum salmon (Oncorhynchus keta) in British Columbia. Can. J. Fish. Aquat. Sci. 44:1987;1702-1713.
9. Beacham T.D., Miller K.M., Withler R.E. Minisatellite DNA variation and stock identification of coho salmon. J. Fish Biol. 49:1996;411-429.
10. Beacham T.D., Withler R.E., Gould A.P. Biochemical genetic stock identification of chum salmon (Oncorhynchus keta) in southern British Columbia. Can. J. Fish. Aquat. Sci. 42:1985;437-448.
11. Beacham T.D., Withler R.E., Gould A.P. Biochemical genetic stock identification of pink salmon (Oncorhynchus gorbuscha) in southern British Columbia and Puget Sound. Can. J. Fish. Aquat. Sci. 42:1985;1474-1483.
12. Beacham T.D., Withler R.E., Wood C.C. Stock identification of sockeye salmon by means of minisatellite DNA variation. North Am. J. Fish. Mgmt. 15:1995;249-265.
13. Beacham T.D., Wood C.C. Application of microsatellite DNA variation to estimation of stock composition and escapement of Nass River sockeye salmon (Oncorhynchus nerka). Can. J. Fish. Aquat. Sci. 56:1999;1-14.
14. Berst, A.H., Simon, R.C., (Eds.), 1981. Proceedings of the Stock Concept International Symposium (STOCS). Can. J. Fish. Aquat. Sci. 38, 1457-1923.
15. Brodziak J., Bentley B., Bartley D., Gall G.A.E., Gomulkiewicz R., Mangel M. Tests of genetic stock identification using coded wire tagged fish. Can. J. Fish. Aquat. Sci. 49:1992;1507-1517.
16. Brunner P.C., Douglas M.R., Bernatchez L. Microsatellite and mitochondrial DNA assessment of population structure and stocking effects in Arctic charr Salvelinus alpinus (Teleostei: Salmonidae) from central alpine lakes. Mol. Ecol. 7:1998;209-223.
17. Cavalli-Sforza L.L., Edwards A.W.F. Phylogenetic analysis, models and estimation procedures. Evolution. 21:1967;550-570.
18. Cook R.C. Stock identification of sockeye salmon (Oncorhynchus nerka) with scale pattern recognition. Can. J. Fish. Aquat. Sci. 39:1982;611-617.
19. Cronin M.A., Spearman W.J., Wilmot R.L., Patton J.C., Bickham J.W. Mitochondrial DNA variation in chinook (Oncorhynchus tshawytscha) and chum salmon (O. keta) detected by restriction enzyme analysis of polymerase chain reaction (PCR) products. Can. J. Fish. Aquat. Sci. 50:1993;708-715.
20. Efron B., Tibshirani R. Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Stat. Sci. 1986:1986;54-77.
21. Eggers, D.M., Rowell, K., Barrett, B., 1991. Stock composition of sockeye and chum salmon catches in southern Alaska Peninsula fisheries in June. Fishery Research Bulletin no. 91-01, Alaska Department of Fish and Game, Division of Commercial Fisheries, Juneau, AK, 49 pp.
22. Estoup A., Rousset F., Michalakis Y., Cornuet J.-M., Adriamanga M., Guyomard R. Comparative analysis of microsatellites and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta). Mol. Ecol. 7:1998;339-355.
23. Fontaine P.-M., Dodson J.J., Bernatchez L., Slettan A. A genetic test of metapopulation structure in Atlantic salmon (Salmo salar) using microsatellites. Can. J. Fish. Aquat. Sci. 54:1997;2434-2442.
24. Fournier D.A., Beacham T.D., Riddell B.E., Busack C.A. Estimating stock composition in mixed stock fisheries using morphometric, meristic, and electrophoretic characteristics. Can. J. Fish. Aquat. Sci. 41:1984;400-408.
25. Grant W.S., Milner G.B., Krasnowski P., Utter F.M. Use of biochemical genetic variants for identification of sockeye salmon (Oncorhynchus nerka) stocks in Cook Inlet, Alaska. Can. J. Fish. Aquat. Sci. 37:1980;1236-1247.
26. Grimholt U., Olsaker I., Lingaas F., Lie O. A study of variability in the MHC class II 1 and class I 2 domain exons of Atlantic salmon (Salmo salar). Anim. Genet. 25:1994;147-153.
27. Groot, C., Margolis, L. (Eds.), 1991. Pacific Salmon Life Histories. UBC Press, Vancouver, 564 pp.
28. Harris, H., Hopkinson, D.A., 1976. Handbook of Enzyme Electrophoresis in Human Genetics. American Elsevier Publ. Co., New York, NY.
29. Hourston, A.S., Vernon, E.H., Holland, G.A., 1965. The migration, composition, exploitation and abundance of odd-year pink salmon runs in and adjacent to the Fraser River Convention Area. Int. Pac. Salmon Fish. Comm. Bull. XVII, 151 pp.
30. Jefferts K.B., Bergman P.K., Fiscus H.F. A coded-wire identification system for macro-organisms. Nature (London). 198:1963;460-462.
31. Johnson J.K. Regional overview of coded wire tagging of anadromous salmon and steelhead in northwest America. Am. Fish. Soc. Symp. 7:1990;782-816.
32. Koljonen M.L. Distinguishing between resident and migrating Atlantic salmon (Salmo salar) stocks by genetic stock composition analysis. Can. J. Fish. Aquat. Sci. 52:1995;665-674.
33. Koljonen M.L., McKinnell S. Assessing seasonal changes in stock composition of Atlantic salmon catches in the Baltic Sea with genetic stock identification. J. Fish Biol. 49:1996;998-1018.
34. Koljonen M.L., Pella J.J. The advantage of using smolt age with allozymes for assessing wild stock contributions to Atlantic salmon catches in the Baltic Sea. ICES J. Mar. Sci. 54:1997;1015-1030.
35. Kondzela C.M., Guthrie C.M., Hawkins S.L., Russell C.D., Helle J.H., Gharrett A.J. Genetic relationships among chum salmon populations in southeast Alaska and northern British Columbia. Can. J. Fish. Aquat. Sci. 51(Suppl. 1):1994;50-64.
36. Masuda, M., Nelson, S., Pella, J., 1991. The computer programs for computing conditional maximum likelihood estimates of stock composition from discrete characters. USA-DOC-NOAA-NMFS, Auke Bay Laboratory, Auke Bay, Alaska, 71 pp.
37. May B., Wright J.E., Stoneking M. Joint segregation of biochemical loci in Salmonidae: results from experiments with Salvelinus and review of the literature on other species. J. Fish. Res. Bd. Can. 36:1979;1114-1128.
38. McConnell S.K., O'Reilly P., Hamilton L., Wright J.N., Bentzen P. Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations. Can. J. Fish. Aquat. Sci. 52:1995;1863-1872.
39. Millar R.B. Maximum likelihood estimation of mixed stock fishery composition. Can. J. Fish. Aquat. Sci. 44:1987;583-590.
40. Miller K.M., Withler R.E. Mhc diversity in Pacific salmon: population structure and trans-species allelism. Hereditas. 127:1997;83-95.
41. Miller, M., LeFleur, C., Marshall, A., Hirose, P., 1993. Genetic stock identification estimates of spring chinook stock composition in the Columbia River winter gill net fishery 1987-1992. WDF Technical Report 121, WDF, Olympia, WA, 13 pp. + 3 appendices.
42. Miller K.M., Withler R.E., Beacham T.D. Stock identification of coho salmon (Oncorhynchus kisutch) using minisatellite DNA variation. Can. J. Fish. Aquat. Sci. 53:1996;181-195.
43. Milner, G.B., 1993. Isozyme variation of coho salmon (Oncorhynchus kisutch) and its potential to estimate stock composition in mixed-stock fisheries. In: Berg, L., Delaney, P.W. (Eds.), Proceedings of the Coho Salmon Workshop. Nanaimo, BC, 26-28 May 1993, pp 182-192. Vancouver, BC, Department of Fisheries and Oceans.
44. Milner, G.B., Teel, D.J., Utter, F.M., Burley, C.L., 1981. Columbia River stock identification study, validation of genetic method. NOAA, NWAFC, Seattle, WA 98112, 35 pp. + 2 appendices.
45. Moran P., Dightman D.A., Waples R.S., Park L.K. PCR-RFLP analysis reveals substantial population-level variation in the introns of Pacific salmon (Oncorhynchus spp.). Mol. Mar. Biol. Biotech. 6:1997;315-327.
46. Neave, F., Yonemori, T., Bakkala, R.G., 1976. Distribution and origin of chum salmon in offshore waters of the North Pacific Ocean. Int. North Pac. Fish. Comm. Bull. 35, 79 pp.
47. Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 89:1978;583-590.
48. ODFW, WDFW, 1995. Status Report Columbia River fish runs and fisheries, 1938-1994. Oregon Department of Fish and Wildlife, Portland, OR, 291 pp.
49. Olsen J.B., Seeb L.W., Bentzen P., Seeb J.E. Genetic interpretation of broad-scale microsatellite polymorphism in odd-year pink salmon. Trans. Am. Fish. Soc. 127:1998;535-550.
50. Pacific Salmon Commission, 1996. Report of the Fraser River Panel to the Pacific Salmon Commission on the 1993 Fraser River sockeye and pink salmon fishing season. Vancouver, BC, 58 pp.
51. Park L.K., Brainard M.A., Dightman D.A., Winans G.A. Low levels of intraspecific variation in the mitochondrial DNA of chum salmon (Oncorhynchus keta). Mol. Mar. Biol. Biotech. 2:1993;362-370.
52. Park L.K., Moran P., Dightman D.A. A polymorphism in intron D of the chinook salmon growth hormone 2 gene. Anim. Genet. 26:1995;277-285.
53. Pella, J.J., Milner, G.B., 1987. Use of genetic marks in stock composition analysis. In: Ryman, N., Utter, F. (Eds.), Population Genetics and Fishery Management. Washington Sea Grant, University of Washington Press, Seattle, pp. 247-276.
54. Phelps S.R., LeClair L.L., Young S., Blankenship H.L. Genetic diversity patterns of chum salmon in the Pacific Northwest. Can. J. Fish. Aquat. Sci. 51(Suppl. 1):1994;65-83.
55. Redner R.A., Walker H.F. Mixture densities, maximum likelihood and the EM algorithm. SIAM Rev. 26:1984;195-239.
56. Ricker, W.E., 1972. Hereditary and environmental factors affecting certain salmonid populations. In: Simon, R.C., Larkin, P. (Eds.), The Stock Concept in Pacific Salmon. H.R. MacMillan Lectures in Fisheries, University of British Columbia. Vancouver, BC. pp. 19-160.
57. Rohlf, F.J., 1994. NTSYS-pc. Numerical Taxonomy and Multivariate Analysis System, Version 1.80. Exeter Software, Setauket, NY.
58. Saiki R.K., Gelfand D.H., Stoffel S., Scharf S.J., Higuchi R., Horn G.T., Mullis K.B., Erlich H.A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 239:1988;487-491.
59. Salo, E.O., 1991. Life history of chum salmon (Oncorhynchus keta). In: Groot, C., Margolis, L. (Eds.), Pacific Salmon Life Histories. UBC Press, University of British Columbia.Vancouver, pp. 231-309.
60. Scribner K.T., Crane P.A., Spearman W.J., Seeb L.W. DNA and allozyme markers provide concordant estimates of population differentiation: analyses of US and Canadian populations of Yukon River fall-run chum salmon. Can. J. Fish. Aquat. Sci. 55:1998;1748-1758.
61. Scribner K.T., Gust J.R., Fields R.L. Isolation and characterization of novel salmon microsatellite loci - cross-species amplification and population genetic applications. Can. J. Fish. Aquat. Sci. 53:1996;833-841.
62. Seeb L.W., Crane P.A. High genetic heterogeneity in chum salmon in Western Alaska, the contact zone between northern and southern lineages. Trans. Am. Fish. Soc. 128:1999;58-87.
63. Seeb L.W., Crane P.A. Allozymes and mitochondrial DNA discriminate Asian and North American populations of chum salmon in mixed-stock fisheries along the south coast of the Alaska Peninsula. Trans. Am. Fish. Soc. 128:1999;88-103.
64. Seeb J.E., Habicht C., Olsen J.B., Bentzen P., Shaklee J.B., Seeb L.W. Allozyme, mtDNA, and microsatellite variants describe structure of populations of pink and sockeye salmon in Alaska. North Pacific Anad. Fish Comm. Bull. 1:1998;300-318.
65. Shaklee, J.B., 1991. Simulation and other analysis of the 1991 Columbia River spring chinook GSI baseline. WDF Technical Report 115, WDF, Olympia, WA, 40 pp.
66. Shaklee J.B., Busack C., Marshall A., Miller M., Phelps S.R. The electrophoretic analysis of salmonid mixed-stock fisheries. Prog. Clinical Biol. Res. 344:1990;235-265.
67. Shaklee J.B., Klaybor S., Young S., White B.A. Genetic structure of odd-year pink salmon (Oncorhynchus gorbuscha) from Washington and British Columbia and potential mixed-stock fishery application. J. Fish Biol. 39(Suppl. A):1991;21-34.
68. Shaklee J.B., Phelps S.R. Operation of a large-scale, multiagency genetic stock identification program. Am. Fish. Soc. Symp. 7:1990;817-830.
69. Shaul L.D., Clark J.E. Use of coded wire tag data to estimate aggregate stock composition of salmon catches in multiple mixed-stock fisheries. Am. Fish. Soc. Symp. 7:1990;613-622.
70. Small M.P., Beacham T.D., Withler R.E., Nelson R.J. Discriminating coho salmon (Oncorhynchus kisutch) populations within the Fraser River, British Columbia using microsatellite DNA markers. Mol. Ecol. 7:1998;141-155.
71. Small M.P., Withler R.E., Beacham T.D. Population structure and stock identification of British Columbia coho salmon (Oncorhynchus kisutch) based on microsatellite DNA variation. Fish. Bull. (US). 96:1998;843-858.
72. Smouse, P.E., Kobak, C.J., Xu, S., 1994. Some thoughts on information content in allozyme and DNA markers in genetic stock identification. In: Park, L.K., Moran, P., Waples, R.S. (Eds.), Application of DNA Technology to the Management of Pacific Salmon: Proceedings of the Workshop. US Department of Commerce, NOAA Tech. Memo. NMFS-NWFSC-17, pp. 121-126.
73. Smouse P.E., Waples R.S., Tworek J.A. A genetic mixture analysis for use with incomplete source population data. Can. J. Fish. Aquat. Sci. 47:1990;620-634.
74. Sokal, R.R., Rohlf, F.J., 1981. Biometry, 2nd ed. Freeman, San Francisco.
75. Swofford D.L., Selander R.B. BIOSYS-1, A FORTRAN program for the comprehensive analysis of electrophoretic data in population genetics and systematics. J. Hered. 72:1981;281-283.
76. Taylor E.B., Beacham T.D., Kaeriyama M. Population structure and identification of north Pacific Ocean chum salmon (Oncorhynchus keta) revealed by an analysis of minisatellite DNA variation. Can. J. Fish. Aquat. Sci. 51:1994;1430-1442.
77. US v. Oregon Technical Advisory Committee. 1997. Updated tables and appendices for the biological assessment of the impacts of anticipated 1996-1998 winter, spring, and summer season Columbia River mainstem and tributary fisheries on listed Snake River salmon species under the Endangered Species Act. National Marine Fisheries Service, Northwest Region. Seattle, WA.
78. Utter F., Milner G., Stahl G., Teel D. Genetic population structure of chinook salmon, Oncorhynchus tshawytscha in the Pacific Northwest. Fish. Bull. (US). 87:1989;239-264.
79. Utter F., Ryman N. Genetic markers and mixed stock fisheries. Fisheries. 18(8):1993;11-21.
80. Utter F.M., Teel D.J., Milner G.B., McIssac D. Genetic estimates of stock compositions of 1983 chinook salmon harvests of the Washington coast and the Columbia River. Fish. Bull. (US). 85:1987;13-23.
81. Vernon, E.H., Hourston, A.S., Holland, G.A., 1964. The migration and exploitation of pink salmon runs in and adjacent to the Fraser River Convention Area in 1959. Int. Pac. Salmon Fish. Comm. Bull. XV, 296 pp.
82. Waldman J.R., Hart J.T., Wirgin I.I. Stock composition of the New York Bight Atlantic sturgeon fishery based on analysis of mitochondrial DNA. Trans. Am. Fish. Soc. 125:1996;364-371.
83. Waples, R.S., Johnson, O.W., Aebersold, P.B., Shiflett, C.K., VanDoornik, D.M., Teel, D.J., Cook, A.E., 1993. A genetic monitoring and evaluation program for supplemented populations of salmon and steelhead in the Snake River Basin, BPA Annual Report 1992 (project 89-096), Portland, 156 pp.
84. Wehrhahn C.F., Powell R. Electrophoretic variation, regional differences, and gene flow in the coho salmon (Oncorhynchus kisutch) of southern British Columbia. Can. J. Fish. Aquat. Sci. 44:1987;822-831.
85. Weir, B.S, 1990. Genetic Data Analysis. Sinauer Associates, Inc. Sunderland, MA.
86. White, B.A., 1996. Genetic stock identification of Fraser River pink salmon: methodology and management application. Pacific Salmon Comm. Tech. Rep. 7, 44 pp.
87. White, B.A., 1998. Fraser River pink salmon catch and exploitation patterns: 1989-1995. Pacific Salmon Comm. Tech. Rep. 10, 52 pp.
88. White B.A., Shaklee J.B. Need for replicated electrophoretic analyses in multiagency genetic stock identification (GSI) programs: examples from a pink salmon (Oncorhynchus gorbuscha) GSI fisheries study. Can. J. Fish. Aquat. Sci. 48:1991;1396-1407.
89. Wilmot R.L., Everett R.J., Spearman W.J., Baccus R., Varnavskaya N.V., Putivkin S.V. Genetic stock structure of Western Alaska chum salmon and a comparison with Russian Far East stocks. Can. J. Fish. Aquat. Sci. 51(Suppl. 1):1994;84-94.
90. Wilmot R.L., Kondzela C.M., Guthrie C.M., Masuda M. Genetic stock identification of chum salmon harvested incidentally in the 1994 and 1995 Bering Sea trawl fishery. North Pacific Anad. Fish Comm. Bull. 1:1998;285-299.
91. Winans G.A., Aebersold P.B., Ishida Y., Urawa S. Genetic stock identification of chum salmon in highseas test fisheries in the Western North Pacific Ocean and Bering Sea. North Pacific Anad. Fish Comm. Bull. 1:1998;220-226.
92. Winans G.A., Aebersold P.B., Urawa S., Varnavskaya N.V. Determining continent of origin of chum salmon (Oncorhynchus keta) using genetic stock identification techniques: status of allozyme baseline in Asia. Can. J. Fish. Aquat. Sci. 51(Suppl. 1):1994;95-113.
93. Winans, G.A., Aebersold, P.B., Waples, R.S., 1989. Genetic stock identification of chum salmon in high seas fisheries using allozyme data from stocks in the Pacific Basin. Proceedings of the Pacific Salmon International Symposium. Yuzhno-Sakhalinsk, USSR, 9-18 September 1989.
94. Wirgin I., Jessop B., Courtenay S., Pedersen M., Maceda S., Waldman J.R. Mixed-stock analysis of striped bass in two rivers of the Bay of Fundy as revealed by mitochondrial DNA. Can. J. Fish. Aquat. Soc. 52:1995;961-970.
95. Wirgin I.I., Maceda L., Waldman J.R., Crittenden R.N. Use of mitochondrial DNA polymorphisms to estimate the relative contributions of Hudson River and Chesapeake Bay striped bass stocks to the mixed fishery on the Atlantic coast. Trans. Am. Fish. Soc. 122:1993;669-684.
96. Wirgin I.I., Waldman J.R., Maceda L., Stabile J., Vecchio V.J. Mixed-stock analysis of Atlantic coast striped bass (Morone saxatilis) using nuclear DNA and mitochondrial DNA. Can. J. Fish. Aquat. Sci. 54:1997;2814-2826.
97. Withler R.E., Beacham T.D., Ming T.J., Miller K.M. Species identification of Pacific salmon by means of a major histocompatibility complex gene. N. Am. J. Fish. Manage. 17:1997;929-938.
98. Wood C.C., McKinnell S., Mulligan T.J., Fournier D.A. Stock identification with the maximum-likelihood mixture model, sensitivity analysis and application to complex problems. Can. J. Fish. Aquat. Sci. 44:1987;866-881.
99. Wood C.C., Rutherford D.T., McKinnell S. Identification of sockeye salmon (Oncorhynchus nerka) stocks in mixed-stock fisheries in British Columbia and Southeast Alaska using biological markers. Can. J. Fish. Aquat. Sci. 46:1989;2108-2120.
100. Wright, S., 1978. Evolution and the Genetics of Populations, vol. 4. Variability Within and Among Natural Populations, University of Chicago Press, Chicago.