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

Transactions of the American Fisheries Society

Volumn 135, Issue 1, 2006, Pages 174-187

  Beacham, Terry D ^a   McIntosh, Brenda ^a   MacConnachie, Cathy ^a   Miller, Kristina M ^a   Withler, Ruth E ^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; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GENETIC VARIATION; LAST GLACIATION; POPULATION STRUCTURE; SALMONID;

ALASKA; ALSEK VALLEY; ASIA; BRISTOL BAY; BRITISH COLUMBIA; CANADA; COLUMBIA RIVER; EURASIA; FAR EAST; JAPAN; KODIAK ISLAND; NORTH AMERICA; PACIFIC OCEAN; PACIFIC RIM; QUEEN CHARLOTTE ISLANDS; UNITED STATES; WASHINGTON [UNITED STATES];

ONCORHYNCHUS; ONCORHYNCHUS NERKA;

EID: 33746271381     PISSN: 00028487     EISSN: 15488659     Source Type: Journal    
DOI: 10.1577/T05-149.1     Document Type: Article

References (39)

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. Applied Biosystems. 2000. Gene Scan Analysis software, version 3.1. Applied Biosystems, Foster City, California.
3. Applied Biosystems. 2001. ABI Prism Genotype 2.5 software. Applied Biosystems, Foster City, California.
4. 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.
5. Beacham, T. D., J. R. Candy, B. McIntosh, C. MacConnachie, A. Tabata, K. Kaukinen, L. Deng, K. M. Miller, R. E. Withler, and N. V. Varnavskaya. 2005a. Estimation of stock composition and individual identification of sockeye salmon on a Pacific Rim basis using microsatellite and major histocompatibility complex variation. Transactions of the American Fisheries Society 134:1124-1146.
6. Beacham, T. D., M. Lapointe, J. R. Candy, B. McIntosh, C. MacConnachie, A. Tabata, K. Kaukinen, L. Deng, K. M. Miller, and R. E. Withler. 2004b. Stock identification of Fraser River sockeye salmon using microsatellites and major histocompatibility complex variation. Transactions of the American Fisheries Society 133:1106-1126.
7. Beacham, T. D., L. Margolis, and R. J. Nelson. 1998. A comparison of methods of stock identification for sockeye salmon (Oncorhynchus nerka) in Barkley Sound, British Columbia. North Pacific Anadromous Fish Commission Bulletin 1:227-239.
8. Beacham, T. D., B. McIntosh, and C. MacConnachie. 2004a. Population structure of lake-type and river-type sockeye salmon in transboundary rivers of northern British Columbia, Canada. Journal of Fish Biology 65:389-402.
9. Beacham, T. D., B. McIntosh, and C. MacConnachie. 2005b. Population structure and stock identification of sockeye salmon in coastal lakes in British Columbia, Canada. Canadian Journal of Zoology. 83:834-844.
10. 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 56:1-14.
11. Beacham, T. D., C. C. Wood, R. E. Withler, and K. M. Miller. 2000. Application of microsatellite DNA variation to estimation of stock composition and escapement of Skeena River sockeye salmon (Oncorhynchus nerka). North Pacific Anadromous Fish Commission Bulletin 2:263-276.
12. Bernatchez, L., and P. Duchesne. 2000. Individual-based genotype analysis in studies of parentage and population assignment: how many loci, how many alleles? Canadian Journal of Fisheries and Aquatic Sciences 57:1-12.
13. Bickham, J. W., C. C. Wood, and J. C. Patton. 1995. Biogeographic implications of cytochrome b sequences and allozymes in sockeye (Oncorhynchus nerka). Journal of Heredity 86:140-144.
14. 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.
15. Burgner, R. L. 1991. Life history of sockeye salmon Oncorhynchus nerka. Pages 3-117 in C. Groot and L. Margolis, editors. Pacific salmon life histories. University of British Columbia Press, Vancouver.
16. Cavalli-Sforza, L. L., and A. W. F. Edwards. 1967. Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics 19:233-257.
17. Felsenstein, J. 1993. PHYLIP: phylogeny inference package. University of Washington, Seattle.
18. 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.
19. Gustafson, R. G., and G. A. Winans. 1999. Distribution and population genetic structure of river- and sea-type sockeye salmon in western North America. Ecology of Freshwater Fish 8:181-193.
20. Kalinowski, S. T. 2002. How many alleles per locus should be used to estimate genetic distances? Heredity 88:62-65.
21. Karlstrom, T. N. V., and G. E. Ball, editors. 1969. The Kodiak Island refugium: its geology, flora, and history. Ryerson Press, Toronto.
22. 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. (September 2002).
23. Morris, D. B., K. R. Richard, and J. M. Wright. 1996. Microsatellites from rainbow trout (Oncorhynchus mykiss) and their use for genetic study of salmonids. Canadian Journal of Fisheries and Aquatic Sciences 53:120-126.
24. 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.
25. Nelson, R. J., C. C. Wood, G. Cooper, C. Smith, and B. Koop. 2003. Population structure of sockeye salmon of the central coast of British Columbia: implications for recovery planning. North American Journal of Fisheries Management 23:703-720.
26. Perriere, G., and M. Gouy. 1996. WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78:364-369.
27. Scribner, K. T., J. R. Gust, and R. L. Fields. 1996. Isolation and characterization of novel salmon microsateuite loci: cross-species amplification and population genetic applications. Canadian Journal of Fisheries and Aquatic Sciences 53:833-841.
28. Smith, C. T., B. F. Koop, and R. J. Nelson. 1998. Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids. Molecular Ecology 7:1613-1621.
29. Varnavskaya, N. V., C. C. Wood, and R. J. Everett. 1994a. 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.
30. Varnavskaya, N. V., C. C. Wood, R. J. Everett, R. L. Wilmot, V. S. Varnavsky, V. V. Midanaya, and T. P. Quinn. 1994b. Genetic differentiation of subpopulations of sockeye salmon (Oncorhynchus nerka) within lakes of Alaska, British Columbia, and Kamchatka, Russia. Canadian Journal of Fisheries and Aquatic Sciences 51(Supplement 1): 147-157.
31. 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.
32. 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.
33. Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
34. Winans, G. A., P. B. Aebersold, and R. S. Waples. 1996. Allozyme variability of Oncorhynchus nerka in the Pacific Northwest, with special consideration to populations of Redfish Lake, Idaho. Transactions of the American Fisheries Society 125:645-663.
35. Winans, G. A., and S. Urawa. 2000. Allozyme variability of Oncorhynchus nerka in Japan. Ichthyological Research 47:343-352.
36. 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.
37. Wood, C. C. 1995. Life history variation and population structure in sockeye salmon. Pages 195-216 in J. L. Neilsen and D. A. Powers, editors. Evolution and the aquatic ecosystem: defining unique units in population conservation. American Fisheries Society, Symposium 17, Bethesda, Maryland.
38. Wood, C. C., B. E. Riddell, and D. T. Rutherford. 1987. Alternative juvenile life histories of sockeye salmon (Oncorhynchus nerka) and their contribution to production in the Stikine River, northern British Columbia. Canadian Special Publication of Fisheries and Aquatic Sciences 96:12-24.
39. 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.