A method to bin alleles of genetic loci that maintains population heterogeneity

Canadian Journal of Fisheries and Aquatic Sciences

Volumn 62, Issue 7, 2005, Pages 1570-1579

  Bromaghin, Jeffrey F ^a   Crane, Penelope A ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; FISHERY; HETEROGENEITY; SALMONID;

ONCORHYNCHUS KETA; SALVELINUS MALMA;

EID: 26944454025     PISSN: 0706652X     EISSN: None     Source Type: Journal    
DOI: 10.1139/f05-093     Document Type: Article

References (40)

1. Agresti, A. 2002. Categorical data analysis. 2nd ed. John Wiley & Sons, New York.
2. Banks, M.A., Eichert, W., and Olsen, J.B. 2003. Which genetic loci have greater population assignment power? Bioinformatics, 19: 1436-1438.
3. Beacham, T.D., Candy, J.R., Supernault, K.J., Ming, T., Deagle, B., Schulze, A., Tuck, D., Kaukinen, K.H., Irvine, J.R., Miller, K.M., and Withler, R.E. 2001. Evaluation and application of microsatellite and major histocompatibility complex variation for stock identification of coho salmon in British Columbia. Trans. Am. Fish. Soc. 130: 116-1149.
4. Bernatchez, L., and Duchesne, P. 2000. Individual-based genotype analysis in studies of parentage and population assignment: how many loci, how many alleles? Can. J. Fish. Aquat. Sci. 57: 1-12.
5. Brown, B.L., Smouse, P.E., Epifanio, J.M., and Kobak, C.J. 1999. Mitochondrial DNA mixed-stock analysis of American shad: coastal harvests are dynamic and variable. Trans. Am. Fish. Soc. 128: 977-994.
6. Buonaccorsi, V.P., McDowell, J.R., and Graves, J.E. 2001. Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans). Mol. Ecol. 10: 1179-1196.
7. Cavalli-Sforza, L.L., and Edwards, A.W.F. 1967. Phylogenetic analysis: models and estimation procedures. Evolution, 21: 550-570.
8. Cornuet, J.M., Piry, S., Luikart, G., Estoup, A., and Solignac, M. 1999. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics, 153: 1989-2000.
9. Debevec, E.M., Gates, R.B., Masuda, M., Pella, J., Reynolds, J., and Seeb, L.W. 2000. SPAM (version 3.2): statistics program for analyzing mixtures. J. Hered. 91: 509-511.
10. Edgington, E.S. 1995. Randomization tests. 3rd ed. Marcel Dekker, New York.
11. Flannery, B.G. 2004. Application of molecular markers to mixed-stock analysis of Yukon River fall chum salmon. M.Sc. thesis, University of Alaska, Fairbanks.
12. Goudet, J., Raymond, M., de Meeus, T., and Rousset, F. 1996. Testing differentiation in diploid populations. Genetics, 144: 1933-1940.
13. Grant, W.S., Milner, G.B., Krasnowski, P., and Utter, F.M. 1980. Use of biochemical genetic variants for identification of sockeye salmon (Oncorhynchus nerka) stocks in Cook Inlet, Alaska. Can. J. Fish. Aquat. Sci. 37: 1236-1247.
14. Hallerman, E.M. (Editor). 2003. Population genetics: principles and applications for fisheries scientists. American Fisheries Society, Bethesda, Maryland.
15. Hedrick, P.W. 1999. Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution, 53: 313-318.
16. Johnson, N.L., Kotz, S., and Balakrishnan, N. 1997. Discrete multivariate distributions. John Wiley & Sons, New York.
17. Kalinowski, S.T. 2002. Evolutionary and statistical properties of three genetic distances. Mol. Ecol. 11: 1263-1273.
18. Kalinowski, S.T. 2004. Genetic polymorphism and mixed-stock fisheries analysis. Can. J. Fish. Aquat. Sci. 61: 1075-1082.
19. Manly, B. 1991. Randomization and Monte Carlo methods in biology. Chapman and Hall, New York.
20. Millar, R.B. 1990. Comparison of methods for estimating mixed stock fishery composition. Can. J. Fish. Aquat. Sci. 47: 2235-2241.
21. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
22. O'Connell, M., and Wright, J.M. 1997. Microsatellite DNA in fishes. Rev. Fish Biol. Fish. 7: 331-363.
23. Olsen, J.B., Habicht, C., and Seeb, J.E. 2004. Moderate and highly polymorphic microsatellites provide discordant estimates of population differentiation in sockeye salmon (Oncorhynchus nerka). Environ. Biol. Fishes, 69: 261-274.
24. Pella, J., and Masuda, M. 2001. Bayesian methods for analysis of stock mixtures from genetic characters. Fish. Bull. 99: 151-167.
25. Pella, J.J., and Milner, G.B. 1987. Use of genetic marks in stock composition analysis. In Population genetics and fishery management. Edited by N. Ryman and F. Utter. University of Washington Press, Seattle. pp. 247-276.
26. Rannala, B., and Mountain, J.L. 1997. Detecting immigration by using multilocus genotypes. Proc. Nat. Acad. Sci. U.S.A. 94: 9197-9201.
27. Rao, C.R. 1973. Linear statistical inference and its applications. 2nd ed. John Wiley & Sons, New York.
28. Raymond, M., and Rousset, F. 1995. An exact test for population differentiation. Evolution, 49: 1280-1283.
29. 2 and the problem of small samples. Mol. Biol. Evol. 6: 539-545.
30. Scribner, K.T., Crane, P.A., Spearman, W.J., and Seeb, L.W. 1998. DNA and allozyme markers provide concordant estimates of population differentiation: analyses of U.S. and Canadian populations of Yukon River fall-run chum salmon (Oncorhynchus keta). Can. J. Fish. Aquat. Sci. 55: 1748-1758.
31. Seeb, L.W., Crane, P.A., Kondzela, C.M., Wilmot, R.L., Urawa, S., Varnavskaya, N.V., and Seeb, J.E. 2004. Migration of Pacific Rim chum salmon on the high seas: insights from genetic data. Environ. Biol. Fishes, 69: 21-36.
32. Small, M.P., Withler, R.E., and Beacham, T.D. 1998. Population structure and stock identification of British Columbia coho salmon (Oncorhynchus kistuch) based on microsatellite DNA variation. Fish. Bull. 96: 843-858.
33. Smouse, P.E., and Chevillon, C. 1998. Analytical aspects of population-specific DNA fingerprinting for individuals. J. Hered. 89: 143-150.
34. Smouse, P.E., Kobak, C.J., and Xu, S. 1994. Some thoughts on information content in allozyme and DNA markers in genetic stock identification. In Application of DNA Technology to the Management of Pacific Salmon: Proceedings of the Workshop. Edited by L.K. Park, P. Moran, and R.S. Waples. US Department of Commerce, NOAA Tech. Memo. NMFS-NWFSC-17. pp. 121-126.
35. Stuart, A., Ord, J.K., and Arnold, S. 1999. Kendall's advanced theory of statistics. Vol. 2A. 6th ed. Arnold, London.
36. Ward, R.D., and Grewe, P.M. 1994. Appraisal of molecular genetic techniques in fisheries. Rev. Fish Biol. Fish. 4: 300-325.
37. Weir, B.S. 1990. Genetic data analysis. Sinauer Associates, Sunderland, Massachusetts.
38. Weir, B.S., and Cockerham, C.C. 1984. Estimating F-Statistics for the analysis of population structure. Evolution, 38: 1358-1370.
39. Winans, G.A., Paquin, M.M., Van Doornik, D.M., Baker, B.M., Thornton, P., Rawdig, D., Marshall, A., Moran, P., and Kalinowski, S. 2004. Genetic stock identification of steelhead in the Columbia River Basin: an evaluation of different molecular markers. N. Am. J. Fish. Manag. 24: 672-685.
40. Wood, C.C., McKinnell, S., Mulligan, T.J., and Fournier, D.A. 1987. Stock identification with the maximum-likelihood mixture model: sensitivity analysis and application to complex problems. Can. J. Fish. Aquat. Sci. 44: 866-881.