Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Evolution

Volumn 54, Issue 2, 2000, Pages 640-651

  Allendorf, F W ^a   Seeb, L W ^b  

^a UNIVERSITY OF MONTANA   (United States)

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

Author keywords

Allozymes; Gene flow; Microsatellites; Mitochondrial DNA; Natural selection

Indexed keywords

DIVERGENCE; GENETIC MARKER; GENETIC VARIATION; SALMONID;

ONCORHYNCHUS NERKA;

EID: 0034065845     PISSN: 00143820     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.0014-3820.2000.tb00065.x     Document Type: Article

References (70)

1. Aagaard, J. E., K. V. Krutovskii, and S. H. Strauss. 1998. RAPDs and allozymes exhibit similar levels of diversity and differentiation among populations and races of Douglas-fir. Heredity 81: 69-78.
2. Allendorf, F. W., and R. G. Danzmann. 1997. Secondary tetrasomic segregation of MDH-B and preferential pairing of homeologues in rainbow trout. Genetics 145:1083-1092.
3. Allendorf, F. W., and G. H. Thorgaard. 1984. Tetraploidy and the evolution of salmonid fishes. Pp. 1-53 in B. J. Turner, ed. Evolutionary genetics of fishes. Plenum Press, New York.
4. Allendorf, F. W., and R. S. Waples. 1996. Conservation and genetics of salmonid fishes. Pp. 238-280 in J. C. Avise and J. L. Hamrick, eds. Conservation genetics: case histories from nature. Chapman and Hall, New York.
5. 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). J. Hered. 90:281-288.
6. Barker, J. S. F., S. S. Moore, D. J. S. Hetzel, D. Evans, S. G. Tan, and K. Byrne. 1997. Genetic diversity of Asian water buffalo (Bubalus bubalis): Microsatellite variation and a comparison with protein-coding loci. Anim. Genet. 28:103-115.
7. Beaumont, M. A., and R. A. Nichols. 1996. Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Lond. B Biol. Sci. 263:1619-1626.
8. Birky, C. W., Jr., T. Maruyama, and P. Fuerst. 1983. An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics 103: 513-527.
9. Bowcock, A. M., J. R. Kidd, J. L. Mountain, J. M. Hebert, L. Carotenuto, K. K. Kidd, and L. L. Cavalli-Sforza. 1991. Drift, admixture, and selection in human evolution: A study with DNA polymorphisms. Proc. Nat. Acad. Sci. U.S.A. 88:839-843.
10. Buonaccorsi, V. P., K. S. Reece, L. W. Morgan, and J. E. Graves. 1999. Geographic distribution of molecular variance within the blue marlin (Makaira nigricans): a hierarchical analysis of allozyme, single-copy nuclear DNA, and mitochondrial DNA markers. Evolution 53:568-579.
11. Burger, C. V., W. J. Spearman, and M. A. Cronin. 1997. Genetic differentiation of sockeye salmon subpopulations from a geologically young Alaskan lake system. Trans. Am. Fish. Soc. 126: 926-938.
12. Cagigas, M. E., E. Vazquez, G. Blanco, and J. A. Sánchez. 1999. Combined assessment of genetic variability in populations of brown trout (Salmo trutta L.) based upon allozymes, microsatellites, and RAPD markers. Mar. Biotechnol. 1:286-296.
13. 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. Can. J. Fish. Aquatic Sci. 50:708-715.
14. Crow, J. F., and K. Aoki. 1984. Group selection for a polygenic behavioral trait: Estimating the degree of population subdivision. Proc. Nat. Acad. Sci., USA 81:6073-6077.
15. Dubreuil, P., and A. Charcosset. 1998. Genetic diversity within and among maize populations: a comparison between isozyme and nuclear RFLP loci. Theor. Appl. Genet. 96:577-587.
16. Engel, L. J. 1972. Studies on the Russian River red salmon sport fishery, Alaska Department of Fish and Game. Federal Aid in Fish Restoration, Annual Report of Progress, 1971-1972. Project F-9-4, Vol. 13.
17. Estoup, A., P. Presa, F. Krieg, D. Vaiman, and R. Guyomard. 1993. (CT)(n) and (GT)(n) microsatellites: a new class of genetic markers for Salmo trutta (brown trout). Heredity 71:488-496.
18. Estoup, A., F. Rousset, Y. Michalakis, J. M. Cornuet, M. Adriamanga, and R. Guyomard. 1998. Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta). Mol. Ecol. 7:339-353.
19. Goudet, J. 1995. FSTAT (vers. 1.2): a computer program to calculate F-statistics. J. Hered. 86:485-486.
20. Grant, W. S., G. B. Milner, P. Krasnowski, and F. M. Utter. 1980. Use of biochemical genetic variants for identification of sockeye salmon (Oncorhynchus nerka) stocks in Cook Inlet, Alaska. Can. J. Fish. Aquatic Sci. 37:1236-1247.
21. Hedrick, P. W. 1999. Perspective: Highly variable loci and their interpretation in evolution and conservation. Evolution 53: 313-318.
22. Jin, L., and R. Chakraborty. 1995. Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics. Heredity 74:274-285.
23. Johnson, S. L., M. A. Gates, M. Johnson, W. S. Talbot, S. Horne, K. Baik, S. Rude, J. R. Wong, and J. H. Postlethwait. 1996. Centromere-linkage analysis and consolidation of the zebrafish genetic map. Genetics 142:1277-1288.
24. Karl, S. A., and J. C. Avise. 1992. Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs. Science 256: 100-102.
25. Latta, R. G., and J. B. Mitton. 1997. A comparison of population differentiation across four classes of gene marker in limber pine (Pinus flexilis James). Genetics 146:1153-1163.
26. Leary, R. F., F. W. Allendorf, S. R. Phelps, and K. L. Knudsen. 1987. Genetic divergence and identification of seven cutthroat trout subspecies and rainbow trout. Trans. Am. Fish. Soc. 116: 580-587.
27. Leary, R. F., F. W. Allendorf, and K. L. Knudsen. 1993. Null allele heterozygotes at two lactate dehydrogenase loci in rainbow trout have decreased developmental stability. Genetica 89:3-13.
28. Leberg, P. L. 1992. Effects of population bottlenecks on genetic diversity as measured by allozyme electrophoresis. Evolution 46:477-494.
29. Le Corre, V., S. Dumolinlapegue, and A. Kremer. 1997. Genetic variation at allozyme and RAPD loci in sessile oak, Quercus petraea (Matt) Liebl: the role of history and geography. Mol. Ecol. 6:519-529.
30. Lewontin, R. C. 1991. Twenty-five years ago in genetics, electrophoresis in the development of evolutionary genetics-milestone or millstone? Genetics 128:657-662.
31. Lewontin, R. C., and J. Krakauer. 1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74:175-195.
32. Luikart, G., W. B. Sherwin, B. M. Steele, and F. W. Allendorf. 1998. Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Mol. Ecol. 7: 963-974.
33. Lynch, M., and B. G. Milligan. 1994. Analysis of population genetic structure with RAPD markers. Mol. Ecol. 3:91-100.
34. May, B., J. E. Wright, and M. Stoneking. 1979. Joint segregation of biochemical loci in Salmonidae: results from experiments with Salvelinus and review of the literature on other species. J. Fish. Res. Bd. Can. 36:1114-1128.
35. McDonald, J. H. 1994. Detecting natural selection by comparing geographic variation in protein and DNA polymorphisms. Pp. 88-100 in B. Golding, ed. Non-neutral evolution: theories and molecular data. Chapman and Hall, New York.
36. McDonald, J. H., B. C. Verrelli, and L. B. Geyer. 1996. Lack of geographic variation in anonymous nuclear polymorphisms in the American oyster, Crassostrea virginica. Mol. Biol. Evol. 13: 1114-1118.
37. McElroy, D., P. Moran, E. Bermingham, and I. Kornfield. 1992. REAP: an integrated environment for the manipulation and phylogenetic analysis of restriction data. J. Hered. 83:157-158.
38. Michalakis, Y., and L. Excoffier. 1996. A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142:1061-1064.
39. 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. Can. J. Fish. Aquatic Sci. 53:120-126.
40. Nauta, M. J., and F. J. Weissing. 1996. Constraints on allele size at microsatellite loci: implications for genetic differentiation. Genetics 143:1021-1032.
41. Neigel, J. E., and J. C. Avise. 1993. Application of a random walk model to geographic distributions of animal mitochondrial DNA variation. Genetics 135:1209-1220.
42. Park, L. K., M. A. Brainard, D. A. Dightman, and G. A. Winans. 1993. Low levels of intraspecific variation in the mitochondrial DNA of chum salmon (Oncorhynchus keta). Mol. Mar. Biol. Biotech. 2:362-370.
43. Pogson, G. H., K. A. Mesa, and R. G. Boutilier. 1995. Genetic population structure and gene flow in the Atlantic cod, Gadus morhua: a comparison of allozyme and nuclear RFLP loci. Genetics 139:375-385.
44. Quinn, T. P. 1985. Homing and the evolution of sockeye salmon (Oncorhynchus nerka). Contrib. Mar. Sci. 27:356-366.
45. Raybould, A. F., J. Goudet, R. J. Mogg, C. J. Gliddon, and A. J. Gray. 1996. Genetic structure of a linear population of Beta vulgaris ssp. maritima (sea beet) revealed by isozyme and RFLP analysis. Heredity 76:111-117.
46. Raymond, M., and F. Rousset. 1995a. GENEPOP (version 1. 2): population genetics software for exact tests and ecumenicism. J. Hered. 86:248-249.
47. _. 1995b. An exact test for population differentiation. Evolution 49:1280-1283.
48. Reger, R. D., and D. S. Pinney. 1996. Late Wisconsin glaciation of the Cook Inlet region with emphasis on Kenai lowland and implications for early peopling. Pp. 13-35 in N. Y. Davis and W. E. Davis, eds. Adventures through time: readings in the anthropology of Cook Inlet, Alaska; proceedings of a symposium. Cook Inlet Historical Society, Anchorage, AK.
49. 2 and the problem of small samples. Mol. Biol. Evol. 6:539-545.
50. Ross, K. G., D. D. Shoemaker, M. J. Krieger, C. J. DeHeer, and L. Keller. 1999. Assessing genetic structure with multiple classes of molecular markers: a case study involving the introduced fire ant Solenopsis invicta. Mol. Biol. Evol. 16:525-543.
51. Sakamoto, T., N. Okamoto, Y. Ikeda, Y. Nakamura, and T. Sato. 1994. Dinucleotide-repeat polymorphism in DNA of rainbow trout and its application in fisheries science. J. Fish Biol. 44: 1093-1096.
52. Sánchez, J. A., C. Clabby, D. Ramos, G. Blanco, F. Flavin, E. Vázquez, and R. Powell. 1996. Protein and microsatellite single locus variability in Salmo salar L (Atlantic salmon). Heredity 77:423-432.
53. Schneider, S., J.-M. Kueffer, D. Roessli, and L. Excoffier. 1996. Arlequin ver. 1.1.: A software for population genetic data analysis. Genetics and Biometry Laboratory, Univ. of Geneva, Switzerland.
54. Scribner, K. T., J. W. Arntzen, and T. Burke. 1994. Comparative analysis of intra- and interpopulation genetic diversity in Bufo bufo, using allozyme, single-locus microsatellite, minisatellite, and multilocus minisatellite data. Mol. Biol. Evol. 11:737-748.
55. Scribner, K. T., P. A. Crane, W. J. Spearman, and L. W. Seeb. 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. Aquatic Sci. 1748-1758.
56. Seeb, J. E., C. Habicht, J. B. Olsen, P. Bentzen, J. B. Shaklee, and L. W. Seeb. 1998. Allozyme, mtDNA, and microsatellite variants describe structure of populations of pink and sockeye salmon in Alaska. N. Pac. Anadr. Fish. Comm. Bull. 1:300-318.
57. Seeb, L. W., C. Habicht, W. D. Templin, K. E. Tarbox, R. Z. Davis, L. K. Brannian, and J. E. Seeb. In press. Genetic diversity of sockeye salmon (Oncorhynchus nerka) of Cook Inlet, Alaska, and its application to restoration of populations affected by the Exxon Valdez oil spill. Trans. Am. Fish. Soc.
58. Shaklee, J. B., F. W. Allendorf, D. C. Morizot, and G. S. Whitt. 1990. Gene nomenclature for protein-coding loci in fish. Trans. Am. Fish. Soc. 119:2-15.
59. Slatkin, M. 1987. Gene flow and the geographic structure of natural populations. Science 236:787-792.
60. _. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457-462.
61. Spruell, P., K. L. Pilgrim, B. A. Greene, C. Habicht, K. L. Knudsen, K. R. Lindner, J. B. Olsen, G. K. Sage, J. E. Seeb, and F. W. Allendorf. 1999. Inheritance of nuclear DNA markers in gynogenetic haploid pink salmon. J. Hered. 90:289-296.
62. Waples, R. S. 1988. Estimation of allele frequencies at isoloci. Genetics 118:371-384.
63. _. 1995. Evolutionarily significant units and the conservation of biological diversity under the Endangered Species Act. Pp. 8-27 in J. L Nielsen and D. A. Powers, eds. Evolution and the aquatic ecosystem: defining unique units in population conservation. American Fisheries Society Symposium no. 17, Bethesda, MD.
64. Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
65. Wilmot, R. L., and C. V. Burger. 1985. Genetic differences among populations of Alaskan sockeye salmon. Trans. Am. Fish. Soc. 114:236-243.
66. Wood, C. C. 1995. Life history variation and population structure in sockeye salmon. Pp. 195-216 in J. L. Nielsen, ed. Evolution and the aquatic ecosystem: defining unique units in population conservation. American Fisheries Society Symposium no. 17, Bethesda, MD.
67. Wood, C. C., B. E. Riddell, D. T. Rutherford, and R. E. Withler. 1994. Biochemical genetic survey of sockeye salmon (Oncorhynchus nerka) in Canada. Can. J. Fish. Aquatic Sci. 51:114-131.
68. Wright, S. 1951. The genetical structure of populations. Ann. Eugen. 15:323-354.
69. Zaykin, D. V., and A. I. Pudovkin. 1992. Two programs to estimate significance of chi-square values using pseudo-probability tests. J. Hered. 84:152.
70. Zhivotovsky, L. A., A. J. Gharrett, A. J. McGregor, M. K. Glubokovsky, and M. W. Feldman. 1994. Gene differentiation in Pacific salmon (Oncorhynchus sp.): facts and models with reference to pink salmon (O. gorbuscha). Can. J. Fish. Aquatic Sci. 51:223-232.