Pacific Rim population structure of Chinook salmon as determined from microsatellite analysis

Transactions of the American Fisheries Society

Volumn 135, Issue 6, 2006, Pages 1604-1621

  Beacham, Terry D ^a   Jonsen, Kimberly L ^a   Supernault, Janine ^a   Wetklo, Michael ^a   Deng, Langtuo ^a   Varnavskaya, Natalia ^b  

^a PACIFIC BIOLOGICAL STATION   (Canada)

^b Kamchatka Fisheries and Oceanography Research Institute   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANNUAL VARIATION; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GENETIC VARIATION; GEOGRAPHICAL REGION; LAST GLACIATION; POPULATION STRUCTURE; SALMONID; SPAWNING;

ALSEK RIVER; BRITISH COLUMBIA; CANADA; COLUMBIA RIVER; KLAMATH RIVER; NORTH AMERICA; PACIFIC OCEAN; PACIFIC RIM; PUGET SOUND; UNITED STATES; WASHINGTON [UNITED STATES];

ONCORHYNCHUS TSHAWYTSCHA;

EID: 34247597511     PISSN: 00028487     EISSN: 15488659     Source Type: Journal    
DOI: 10.1577/T06-071.1     Document Type: Article

References (52)

1. Allendorf, F. W., and L. W. Seeb. 2000. Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers. Evolution 54:640-651.
2. Banks, M. A., M. S. Blouin, B. A. Baldwin, V. K. Rashbrook, H. A. Fitzgerald, S. M. Blankenship, and D. Hedgecock. 1999. Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha). Journal of Heredity 90:281-288.
3. Banks, M. A., V. K. Rashbrook, M. J. Calavetta, C. A. Dean, and D. Hedgecock. 2000. Analysis of microsatellite DNA resolves genetic structure and diversity of Chinook salmon (Oncorhynchus tshawytscha) in California's Central Valley. Canadian Journal of Fisheries and Aquatic Sciences 57:915-927.
4. Beacham, T. D., J. R. Candy, K. L. Jonsen, J. Supernault, M. Wetklo, L. Deng, K. M. Miller, R. E. Withler, and N. Varnavskaya. 2006a. Estimation of stock composition and individual identification of Chinook salmon across the Pacific Rim using microsatellite variation. Transactions of the American Fisheries Society 135:861-888.
5. Beacham, T. D., B. McIntosh, C. MacConnachie, K. M. Miller, R. E. Withler, and N. Varnavskaya. 2006b. Pacific Rim population structure of sockeye salmon as determined from microsatellite analysis. Transactions of the American Fisheries Society 135:174-187.
6. Beacham, T. D., C. B. Murray, and R. E. Withler. 1989. Age, morphology, and biochemical genetic variation of Yukon River Chinook salmon. Transactions of the American Fisheries Society 118:46-63.
7. Beacham, T. D., K. J. Supernault, M. Wetklo, B. Deagle, K. Labaree, J. Irvine, J. R. Candy, K. M. Miller, R. J. Nelson, and R. E. Withler. 2003. The geographic basis of population structure of Fraser River Chinook salmon, Oncorhynchus tshawytscha. Fishery Bulletin 101:229-242.
8. Beacham, T. D., R. E. Withler, and T. A. Stevens. 1996. Stock identification of Chinook salmon (Oncorhynchus tshawytscha) using minisatellite DNA variation. Canadian Journal of Fisheries and Aquatic Sciences 53:380-394.
9. Beacham, T. D., and C. C. Wood. 1999. Application of microsatellite DNA variation to estimation of stock composition and escapement of Nass River sockeye salmon (Oncorhynchus nerka). Canadian Journal of Fisheries and Aquatic Sciences 56:297-310.
10. Bostock, H. S. 1969. Kluane Lake, Yukon Territory, its drainage and allied problems (115G and 115F). Geological Survey of Canada. Department of Energy, Mines and Resources, Paper 69-28, Ottawa.
11. Brannon, E. L., M. S. Powell, T. P. Quinn, and A. Talbot. 2004. Population structure of Columbia River basin Chinook salmon and steelhead trout. Reviews in Fisheries Science 12:99-232.
12. Buchholz, W. G., S. J. Miller, and W. J. Spearman. 2001. Isolation and characterization of chum salmon microsatellite loci and use across species. Animal Genetics 32:160-167.
13. Candy, J. R., J. R. Irvine, C. K. Parken, S. L. Lemke, R. E. Bailey, M. Wetklo, and K. Jonsen. 2002. A discussion paper on possible new stock groupings (conservation units) for Fraser River Chinook salmon. Canadian Science Advisory Secretariat Research Document 2002/ 085.
14. Cavalli-Sforza, L. L., and A. W. F. Edwards. 1967. Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics 19:233-257.
15. Cronin, M. A., W. J. Spearman, R. L. Wilmot, J. C. Patton, and J. W. Bickham. 1993. Mitochondrial DNA variation in Chinook (Oncorhynchus tshawytscha) and chum salmon (O. keta) detected by restriction enzyme analysis of polymerase chain reaction (PCR) products. Canadian Journal of Fisheries and Aquatic Sciences 50:708-715.
16. Estoup, A., P. Jarne, and J.-M. Cornuet. 2002. Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Molecular Ecology 11:1591-1604.
17. Felsenstein, J. 1993. PHYLIP: Phylogeny inference package. University of Washington, Seattle.
18. Ford, M. J. 1998. Testing models of migration and isolation among populations of Chinook salmon (Oncorhynchus tshawytscha). Evolution 52:539-557.
19. Gharrett, A. J., S. M. Shirley, and G. R. Tromble. 1987. Genetic relationships among populations of Alaskan Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences 44:765-774.
20. Goudet, J. 1995. FSTAT: A program for IBM PC compatibles to calculate Weir and Cockerham's (1984) estimators of F-statistics (version 1.2). Journal of Heredity 86:485-486.
21. Guthrie, C. M., III, and R. L. Wilmot. 2004. Genetic structure of wild chinook salmon populations of southeast Alaska and northern British Columbia. Environmental Biology of Fishes 69:81-93.
22. Healey, M. C. 1983. Coastwide distribution and ocean migration patterns of stream- and ocean-type Chinook salmon, Oncorhynchus tshawytscha. Canadian Field-Naturalist 97:427-433.
23. Healey, M. C. 1991. The life history of Chinook salmon (Oncorhynchus tshawytscha). Pages 311-393 in C. Groot and L. Margolis, editors. Life history of Pacific salmon. University of British Columbia Press, Vancouver.
24. Kalinowski, S. T. 2005. Do polymorphic loci require large sample sizes to estimate genetic distances? Heredity 94:33-36.
25. Lewis, P. O., and D. Zaykin. 2001. Genetic Data Analysis: computer program for the analysis of allelic data, version 1.0 (d16c). Available: http://lewis.eeb.uconn.edu/lewishome/software.html.2. (September 2002).
26. McPhail, J. D., and C. C. Lindsey. 1970. Freshwater fishes of northwestern Canada and Alaska. Fisheries Research Board of Canada Bulletin 173.
27. Miller, K. M., R. E. Withler, and T. D. Beacham. 1996. Stock identification of coho salmon (Oncorhynchus kisutch) using minisatellite DNA variation. Canadian Journal of Fisheries and Aquatic Sciences 53:181-195.
28. Nelson, R. J., and T. D. Beacham. 1999. Isolation and cross species amplification of microsatellite loci useful for study of Pacific salmon. Animal Genetics 30:228-229.
29. Nelson, R. J., M. P. Small, T. D. Beacham, and K. J. Supernault. 2001. Population structure of Fraser River Chinook salmon (Oncorhynchus tshawytscha): an analysis using microsatellite DNA markers. Fishery Bulletin 99:94-107.
30. Nelson, R. J., T. D. Beacham, and M. P. Small. 1998. Microsatellite analysis of the population structure of a Vancouver Island sockeye salmon (Oncorhynchus nerka) stock complex using non-denaturing gel electrophoresis. Molecular Marine Biology and Biotechnology 7:312-319.
31. O'Connell, M., R. G. Danzmann, J. M. Comuet, J.M. Wright, and M. M. Ferguson. 1997. Differentiation of rainbow trout populations in Lake Ontario and the evaluation of the stepwise mutation and infinite allele mutation models using microsatellite variability. Canadian Journal of Fisheries and Aquatic Sciences 54:1391-1399.
32. Olsen, J. B., P. Bentzen, and J. E. Seeb. 1998. Characterization of seven microsatellite loci derived from pink salmon. Molecular Ecology 7:1083-1090.
33. O'Reilly, P. T., L. C. Hamilton, S. K. McConnell, and J. M. Wright. 1996. Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Canadian Journal of Fisheries and Aquatic Sciences 53:2292-2298.
34. Perriere, G., and M. Gouy. 1996. WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78:364-369.
35. Rasmussen, C., C. O. Ostberg, D. R. Clifton, J. L. Holloway, and R. J. Rodriguez. 2003. Identification of a genetic marker that discriminates ocean-type and stream-type Chinook salmon in the Columbia River basin. Transactions of the American Fisheries Society 132:131-142.
36. Reisenbichler, R. R., F. M. Utter, and C. C. Kruger. 2003. Genetic concepts and uncertainties in restoring fish populations and species. Pages 149-183 in R. C. Wissmar and P. A. Bisson, editors. Strategies for restoring river ecosystems: sources of variability and uncertainty in natural and managed systems. American Fisheries Society, Bethesda, Maryland.
37. Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
38. Shaklee, J. B., T. D. Beacham, L. Seeb, and B. A. White. 1999. Managing fisheries using genetic data: case studies from four species of Pacific salmon. Fisheries Research 43:45-78.
39. Teel, D. J., G. B. Milner, G. A. Winans, and W. S. Grant. 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.
40. Tessier, N., and L. Bernatchez. 1999. Stability of population structure and genetic diversity across generations assessed by microsatellites among sympatric populations of landlocked Atlantic salmon (Salmo salar L.). Molecular Ecology 8:169-179.
41. Utter, F. M., D. W. Chapman, and A. R. Marshall. 1995. Genetic population structure and history of Chinook salmon of the upper Columbia River. Pages 149-165 in J. L. Nielsen and D. A. Powers, editors. Evolution and the aquatic ecosystem: defining unique units in population conservation. American Fisheries Society, Symposium 17, Bethesda, Maryland.
42. Utter, F., G. Miler, G. Stahl, and D. Teel. 1989. Genetic population structure of Chinook salmon, Oncorhynchus tshawytscha, in the Pacific Northwest. U.S. Fishery Bulletin 87:239-264.
43. Varnavskaya, N. V., C. C. Wood, and R. J. Everett. 1994. Genetic variation in sockeye salmon (Oncorhynchus nerka) populations of Asia and North America. Canadian Journal of Fisheries and Aquatic Sciences 51(Supplement 1): 132-146.
44. Waples, R. S. 1990. Temporal changes of allele frequency in Pacific salmon populations: implications for mixed-stock fishery analysis. Canadian Journal of Fisheries and Aquatic Sciences 47:968-976.
45. Waples, R. S., D. J. Teel, J. M. Myers, and A. R. Marshall. 2004. Life-history divergence in Chinook salmon: Historic contingency and parallel evolution. Evolution 58:386-403.
46. Warner, B. C., R. W. Mathews, and J. J. Clague. 1982. Ice-free conditions on the Queen Charlotte Islands, British Columbia, at the height of the late Wisconsin glaciation. Science 218:675-677.
47. Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
48. Wilson, G. M., W. K. Thomas, and A. T. Beckenbach. 1987. Mitochondrial DNA analysis of Pacific Northwest populations of Oncorhynchus tshawytscha. Canadian Journal of Fisheries and Aquatic Sciences 44:1301-1305.
49. Winans, G. A. 1989. Genetic variability in Chinook salmon stocks from the Columbia River basin. North American Journal of Fisheries Management 9:47-52.
50. Withler, R. E., K. D. Le, R. J. Nelson, K. M. Miller, and T. D. Beacham. 2000. Intact genetic structure and high levels of genetic diversity in bottlenecked sockeye salmon, Oncorhynchus nerka, populations of the Fraser River, British Columbia, Canada. Canadian Journal of Fisheries and Aquatic Sciences 57:1985-1998.
51. Wood, C. C., B. E. Riddell, D. T. Rutherford, and R. E. Withler. 1994. Biochemical genetic survey of sockeye salmon (Oncorhynchus nerka) in Canada. Canadian Journal of Fisheries and Aquatic Sciences 51(Supplement 1):114-131.
52. Wood, C. C. 1995. Life history variation and population structure in sockeye salmon. Pages 195-216 in J. L. Nielsen and D. A. Powers, editors. Evolution and the aquatic ecosystem: defining unique units in population conservation. American Fisheries Society, Symposium 17, Bethesda, Maryland.