Stock identification for conservation of threatened or endangered species

Stock Identification Methods

Volumn , Issue , 2005, Pages 609-629

  Banks, Michael A ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882488351     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012154351-8/50030-7     Document Type: Chapter

References (58)

1. Banks M., Eichert W., Olsen J. Which genetic loci have greater population assignment power?. Bioinformatics 2003, 19:1436-1438.
2. Banks M.A., Baldwin B.A., Hedgecock D. Research on chinook salmon (Oncorhynchus tshawytscha) stock structure using microsatellite DNA. Bulletin of National Research Institute of Aquaculture 1996, 2(Suppl):5-9.
3. Banks M.A., Blouin M.S., Baldwin B.A., Rashbrook V.K., Fitzgerald H.A., et al. Isolation and inheritance of novel microsatellites in chinook salmon (Onchorhynchus tschawytscha). Journal of Heredity 1999, 90:281-288.
4. Banks M.A., Eichert W. WHICHRUN (Version 3.2): a computer program for population assignment of individuals based on multilocus genotype data. Journal of Heredity 2000, 91:87-89.
5. Banks M.A., Jacobson D. Which genetic markers and GSI methods are more appropriatefor defining marine distribution and migration of salmon?. North Pacific Anadromous Fish Commission Technical Note 2004, 5. in press.
6. Banks M.A., Rashbrook V.K., Calavetta M.J., Dean C.A., Hedgecock D. Analysis of microsatellite DNA resolves genetic structure and diversity of chinook salmon (Oncorhychus, tshawytscha) in California's Central Valley. Canadian Journal of Fisheries and Aquatic Sciences 2000, 57:915-927.
7. Bartley D., Gall G.A.E., Bentley B., Brodziak Gomulkiewicz J.R., et al. Geographic variation in population genetic structure of chinook salmon from California and Oregon. Fishery Bulletin, U.S. 1992, 90:77-100.
8. Belkhir K., Borsa P., Chikhi L., Raufaste N., Bonhomme F. GENETIX 4.04, logiciel sous Windows TM pour la génétique des populations 2002, Laboratoire Génome, Populations, Interactions: CNRS UMR 5000, Université de Montpellier II, Montpellier. http://www.univmontp2.fr/7Egenetix/genetix/genetix.htm.
9. Berkson J. Coded wire tag analysis on Snake River spring, summer, and fall chinook. Letter dated February 19, 1992, to NMFS, ETSD from Portland, Oregon 1991, Columbia River Inter-Tribal Fish Commission, Portland.
10. Bingham N., Harthorne A. Spring-run Chinook Salmon Work Group: A cooperative approach to watershed management in California. Sustainable Fisheries Management 2000, Lewis, New York. E.E. Knudsen, C.R. Steward, D.D. Mac-Donald, J.E. Williams, D.W. Reiser (Eds.).
11. Black W., Baer C., Antolin M., DuTeau N. Population genomics: genome-wide sampling of insect populations. Annual Review of Entomology 2001, 46:441-469.
12. Blanchong J.A., Scribner K.T., Winterstein S.R. Assignment of individuals to populations: Bayesian methods and multi-locus genotypes. Journal of Wildlife Management 2002, 66:321-329.
13. Bolker B., Okuyama T., Bjorndal K., Bolten A. Sea Turtle stock estimation using genetic markers: accounting for sampling error of rare genotypes. Ecological Applications 2003, 13:763-775.
14. Brun M., Sabbagh D., Kim S., Dougherty E.R. Corrected small-sample estimation of the Bayes error. Bioinformatics 2003, 19:944-951.
15. California Department of Fish and Game Sacramento Winter-Run Chinook Salmon. 2000-2001 Biennial Report prepared for the Fish and Game Commission by the Habitat Conservation Division 2002.
16. Clark F. California salmon catch records. California Fish and Game 1940, 26:49-66.
17. Cornuet J.-M., Piry S., Luikart G., Estoup A., Solignan M. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 1999, 153:1989-2000.
18. Cummings S., Brannon E., Adams K., Thorgard G. Genetic analysis to establish captive breeding priorities for endangered Snake River sockeye salmon. Conservation Biology 1997, 11:662-669.
19. Debevec E.M., Gates R.B., Masuda M., Pella J., Reynolds J., et al. SPAM (Version 3.2): statistics program for analyzing mixtures. Journal of Heredity 2000, 91:509-510.
20. Fournier D., Beacham T., Riddell B., Busack C. Estimating stock composition in mixed fisheries using morphometric, meristic, and electrophoretic characteristics. Canadian Journal of Fisheries and Aquatic Sciences 1984, 41:400-408.
21. Greig C., Jaconson D., Banks M.A. New tetranucleotide microsatellites for fine-scale discrimination among endangered Chinook salmon (Oncorhynchus tshawytscha). Molecular Ecology Notes 2003, 3:376-379.
22. Hedgecock D., Banks M., Rashbrook V., Dean C., Blankenship S. Applications of population genetics to conservation of chinook salmon diversity in the Central Valley. Fish Bulletin 2001, 179:45-70.
23. Huppert D. Understanding the U.S.-Canada Salmon Wars: Why the Pacific Salmon Treaty Has Not Brought Peace? 1995, http://www.wsg.washington.edu/salmon/huppertreport.html.
24. Kalinowski S. Genetic Mixture Analysis 1.0 2003, Department of Ecology, Montana State University, Bozeman MT.
25. Kondzela C., Hawkins S., Guthrie C., Wilmot R. Origins of sockeye and chum salmon seized from the the F/V Petropavlovsk (NPAFC doc. 598) 2002, Auke Bay Fisheries Laboratory, Alaska Fisheries Science Center, NOAA Fisheries, Juneau, AK.
26. Luikart G., England P., Tallmon D., Jordan S., Taberlet P. The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics 2003, 4:981-994.
27. Marshall A.R., Blankenship H.L., Commor W.P. Genetic characterization of naturally spawned Snake River fall-run chinook salmon. Transactions of the American Fisheries Society 2000, 129:680-689.
28. Matthews G., Waokes R. Status review for Snake River spring and summer chinook slamon. NOAA Technical Memorandum NMFS-F/NWC-200 1991.
29. Meacham C., Clark J. Pacific salmon management-the view from Alaska. Alaska Fishery Research Bulletin 1994, 1:76-80.
30. Millar R.B. Maximum likelihood estimation of mixed stock fishery composition. Canadian Journal of Fisheries and Aquatic Science 1987, 44:583-590.
31. NOAA Fisheries Status review for Snake River spring and summer Chinook salmon. NOAA Technical Memorandum NMFS-F/NWC-200, June 1991 1991.
32. NOAA FISHERIES Endangered and threatened species; status of Sacramento River winter-run chinook salmon. Federal Register 1994, vol. 59(no. 2):440-450. January 4, 1994.
33. NOAA FISHERIES Endangered and threatened species; West Coast chinook salmon; listing status change; proposed rule. Federal Register 1998, 63 # 45:11482.
34. Olsen J.B., Bentzen P., Banks M.A., Shaklee J.B., Young S. Microsatellites reveal population identity of individual pink salmon to allow supportive breeding of a population at risk of extinction. Transactions of the American Fisheries Society 2000, 129:232-242.
35. Pacific Fishery Management Council Preseason report III: Analysis of Council-adopted management measures for 995 ocean salmon fisheries (with appendices) 1995.
36. Pacific Salmon Commission Annual Report for 1999/2000 2000, Appendix D, Annex IV, Chapter 3.
37. Paetkau D., Calvert W., Stirling I., Strobeck C. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 1995, 4:347-354.
38. Pella J., Masuda M. Bayesian methods for analysis of stock mixtures from genetic characters. Fisheries Bulletin 2001, 99:151-167.
39. Pella J., Milner G.B. Use of genetic marks in stock composition analysis. Population Genetics and Fisheries Management 1987, University of Washington Press, Seattle, WA. N. Rayman, F.M. Utter (Eds.).
40. Rosel P., France S., Wang J., Kocher T. Genetic structure of harbor porpoise (Phocoena phocoena) populations in the Northwestern, Atlantic based on mitochondrial and nucelar markers. Molecular Ecology 1999, 8:S41-S54.
41. Rosenberg N., Li L., Ward R., Pritchard J. Informativeness of genetic markers for inference of ancestry. American Journal of Human Genetics 2003, 73:402-1422.
42. Sahu S.K., Cheng R. A fast distance-based approach for determining the number of components in mixtures. Canadian Journal of Statistics 2003, 31:3-22.
43. 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 (Oncorhynchus keta). Canadian Journal of Fisheries and Aquatic Sciences 1998, 55:1748-1758.
44. Shaklee J.B., Beacham T., Seeb L.W., White B. Managing fisheries using genetic data: case studies from four species of Pacific salmon. Fisheries Research 1999, 43:45-78.
45. Shoemaker J.S., Painter I.S., Weir B.S. Bayesian statistics in genetics: a guide for the unitiated. Trends in Genetics 1999, 15:354-358.
46. Shriver M.D., Smith M.W., Jin L., Marcini A., Akey J.M., et al. Ethnic-affiliation estimation by use of population-specific DNA markers. American Journal of Human Genetics 1997, 60:957-964.
47. Smouse P., Waples R., Tworek J. A genetic mixture analysis for use with incomplete source population data. Canadian Journal of Fisheries and Aquatic Sciences 1990, 47:620-634.
48. Snyder N., Snyder H. The California Condor: A Saga of Natural History and Conservation 2000, Academic Press, San Diego, CA.
49. Van den Boom D., Jurinke C., McGinniss M., Berkenkamp S. Microsatellites: perspectives and potentials of mass spectrometric analysis. Expert Reviews of Molecular Diagnostics 2001, 1:383-393.
50. Wall J., Pritchard J. Haplotype blocks and linkage disequilibrium in the human genome. Nature Reviews Genetics 2003, 4:587-597.
51. Waples R.S., Johnson O., Jones R. Status review for Snake River sockeye salmon. NOAA Technical Memorandum 1991, Northwest Center, Seattle.
52. Waples R.S., Jones R., Beckham B., Swan G. Status review for Snake River fall chinook salmon: NOAA Technical Memorandum. NMFS-F/NWC-201 1991.
53. Waples R.S., Teel D.J., Myers J.M., Marshall A.R. Life history divergence in Chinook salmon: historic contingency and parallel evolution. Evolution 2004, in press.
54. Weir B.S., Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution 1984, 38:1358-1370.
55. Wilmot R., Kindzela C., Guthrie C., Moles A., Pella J., et al. Origins of sockeye and chum salmon seized from the F/V Arctic Wind (NPAFC doc) 2000, Auke Bay Fisheries Laboratory, Alaska Fisheries Science Center, NOAA Fisheries, 11305 Glacier Highway, Juneau, Alaska.
56. Winans G.A., Viele D., Grover A., Palmer-Zwahlen M., Teel D., et al. An update of genetic stock identification of chinook salmon in the Pacific Northwest: test fisheries in California. Reviews in Fisheries Science 2001, 9:213-237.
57. Xu S., Kobak C., Smouse P. Constrained least squares estimation of mixed population stock composition from mtDNA haplotype frequency data. Canadian Journal of Fisheries and Aquatic Sciences 1994, 51:417-425.
58. Yoshimaya R.M. A history of salmon and people in the Central Valley region of California. Reviews in Fisheries Science 1999, 7:197-239.