Development of a standardized DNA database for chinook salmon

Fisheries

Volumn 32, Issue 11, 2007, Pages 540-552

  Seeb, L W ^a   Antonovich, A ^b   Banks, M A ^c   Beacham, T D ^d   Bellinger, M R ^c   Blankenship, S M ^e,f   Campbell, M R ^g   Decovich, N A ^b   Garza, J C ^e   Guthrie III, C M ^h   Lundrigan, T A ^a,i   Moran, P ^j   Narum, S R ^k   Stephenson, J J ^k   Supernault, K J ^d   Teel, D J ^j   Templin, W D ^b   Wenburg, J K ^l   Young, S F ^f   Smith, C T ^b,m  

^a UNIVERSITY OF WASHINGTON   (United States)

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

^c OREGON STATE UNIVERSITY   (United States)

^d PACIFIC BIOLOGICAL STATION   (Canada)

^e SOUTHWEST FISHERIES SCIENCE CENTER   (United States)

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

^g Idaho Department of Fish and Game   (United States)

^h NATIONAL MARINE FISHERIES SERVICE   (United States)

ⁱ UNIVERSITY OF VICTORIA   (Canada)

^j ALASKA FISHERIES SCIENCE CENTER   (United States)

^k Northwest Fisheries Science Center ^*  (United States)

^l U S FISH AND WILDLIFE SERVICE   (United States)

^m ABERNATHY FISH TECHNOLOGY CENTER   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ONCORHYNCHUS; ONCORHYNCHUS TSHAWYTSCHA;

EID: 38049125551     PISSN: 03632415     EISSN: None     Source Type: Journal    
DOI: 10.1577/1548-8446(2007)32[540:DOASDD]2.0.CO;2     Document Type: Article

References (33)

1. 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 micro-satellites in Chinook salmon (Oncorhynchus tshawytscha). Journal of Heredity 90:281-288; errata Journal of Heredity 90(3):U1-U1.
2. 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.
3. Beacham, T. D., K. J. Supernault, M. Wetklo, B. Deagle, K. Labaree, J. R. Irvine, J. R. Candy, K. M. Miller, R. J. Nelson, and R. E. Withler. 2003. The geographic basis for population structure in Fraser River Chinook salmon (Oncorhynchus tshawytscha). Fishery Bulletin 101:229-242.
4. Cairney, M., J. B. Taggart, and B. Hoyheim. 2000. Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids. Molecular Ecology 9:2175-2178.
5. Cavalli-Sforza, L. L., and A. W. Edwards. 1967. Phylogenetic analysis. Models and estimation procedures. American Journal of Human Genetics 19:233-257.
6. 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.
7. CTC (Joint Chinook Technical Committee). 2005. Annual exploitation rate analysis and model calibration, TCCHINOOK (05)-3, Dec. 28, 2005. Report to the Pacific Salmon Commission Vancouver, British Columbia, Canada. Available at: www.psc. org/publications_tech_techcommitteere.
8. Debevec, E. M., R. B. Gates, M. Masuda, J. Pella, J. Reynolds, and L. W. Seeb. 2000. SPAM (Version 3.2): Statistics program for analyzing mixtures. Journal of Heredity 91:509-511.
9. Felsenstein, J. 2004. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author, Department of Genome Sciences, University of Washington, Seattle. Available at: http://evolution.genetics.washingron.edu/ phylip/getme.html.
10. Greig, C. A., and M. A. Banks. 1999. Five multiplexed microsatellite loci for rapid response run identification of California's endangered winter Chinook salmon. Animal Genetics 30(4):318-320.
11. Greig, C., D. P. Jacobson, and M. A. Banks. 2003. New tctranucleotide microsatellitcs for fine-scale discrimination among endangered Chinook salmon (Oncorhynchus tshawytscha). Molecular Ecology Notes .3:376-379.
12. 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.
13. Hankin, D. G., J. H. Clark, R. B. Deriso, J. C. Garza, G. S. Morishima, B. E. Riddell, C. Schwarz, and J. B. Scott. 2005. Report of the expert panel on the future of the coded wire tag recovery program for Pacific salmon. Pacific Salmon Commission Technical Report 18, Vancouver, British Columbia. Available at: www.psc.org/pubs/CWT/EPfinalrcport. pdf.
14. LaHood, E. S., P. Moran, J. Olsen, W. S. Grant, and L. K. Park. 2002. Microsatellite allele ladders in two species of Pacific salmon: preparation and field-test results. Molecular Ecology Notes 2:187-190.
15. Mariani, S., W. F. Hutchinson, E. M. C. Hatfield, D. E. Ruzzante, E. J. Simmonds, T. G. Dahlgren, C. Andre, J. Brigham, E. Torstensen, and G. R. Carvalho. 2005. North Sea herring population structure revealed by microsatellite analysis. Marine Ecology Progress Series 303:245-257.
16. Marshall, A. R., M. Miller, C. Busack, and S. R. Phelps. 1991. Genetic stock identification analysis of three 1990 Washington ocean and Strait of Juan de Fuca Chinook salmon fisheries, GSI Summary Report 91-1, Washington Department of Fisheries, Salmon Research and Development, Olympia, Washington.
17. Mobrand, L. E., J. Barr, L. Blankenship, D. E. Campton, T. T. P. Evelyn, T. A. Flagg, C. V. Mahnken, L. W. Seeb, P. R. Seidel, and W. W. Smoker. 2005. Hatchery reform in Washington State: principles and emerging issues. Fisheries 30(6): 11-23.
18. Moran, P., D. J. Teel, E. S. LaHood, J. Drake, and S. Kalinowski. 2006. Standardising multi-laboratory microsatellite data in Pacific salmon: an historical view of the future. Ecology of Freshwater Fish 15:597-60.5.
19. 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.
20. Olsen, J. B., P. Bentzen, and J. E. Seeb. 1998. Characterization of seven microsatellite loci derived from pink salmon. Molecular Ecology 7:1083-1090.
21. Rexroad, C. E., III, 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.
22. Saitou, N., and M. Nei. 1987. The neighbor-joining method: n new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
23. Seeb, L. W., C. Habicht, W. D. Templin, K. E. Tarbox, R. Z. Davis, L. K. Brannian, and J. E. Seeb. 2000. Genetic diversity of sockeye salmon of Cook Inlet, Alaska, and its application to management of populations affected by the Exxon Vakkz oil spill. Transactions of the American Fisheries Society 129:1223-1249
24. 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.
25. Shaklee, J. B., and S. R. Phelps. 1990. Operation of a large-scale, multiagency program for genetic stock identification. American Fisheries Society Symposium 7:817-830.
26. Smith C. T., A. Antonovich, W. D. Templin, C. M. Elfstrom, S. R. Narum, and L. W. Seeb. In press. Impacts of marker class bias relative to locus-specific variability on population inferences in Chinook, salmon; a comparison of SNPs to STRs and allozymes. Transactions of the American Fisheries Society.
27. Smith, C. T., J. E. Seeb, P. Schwenke, and L. W. Seeb. 2005. Use of the 5'-nuclease reaction for SNP genotyping in Chinook salmon. Transactions of the American Fisheries Society 134:207-217.
28. Teel, D. J., P. A. Crane, C. M. Guthrie III, A. R. Marshall, D. M. VanDoornik, W. D. Templin, N. V. Varnavskaya, and L. W. Seeb. 1999. Comprehensive allozyme database discriminates Chinook salmon around the Pacific Rim. (NPAFC document 440). Alaska Department of Fish and Game, Division of Commercial Fisheries, Anchorage.
29. Weitkamp, L., and K. Neely. 2002. Coho salmon (Oncorhynchus kisutch) ocean migration patterns: insight from marine coded-wire tag recoveries. Canadian Journal of Fisheries and Aquatic Sciences 59:1100-1115.
30. White, B. A., and J. B. Shaklee. 1991. Need for replicated electrophoretic analyses in multiagency genetic stock identification (GSI) programs: examples from a pink salmon (Oncorhynchus gorbuscha) GSI fisheries study. Canadian Journal of Fisheries and Aquatic Sciences 48:1396-1407.
31. Williamson, K. S., J. F. Cordes, and B. May. 2002. Characterization of microsatellite loci in Chinook salmon (Oncorhynchus tshawyts cha) and cross-species amplification in other salmonids. Molecular Ecology Notes 2:17-19.
32. Wirgin, I.I., and J. R. Waldman. 1994. What DNA can do for you. Fisheries 19(7):16-27.
33. Wright, J. M., and P. Bentzen. 1994. Microsatellites: genetic markers for the future. Reviews in Fish Biology and Fisheries 4:384-388.