A comparison of several measures of genetic distance and population structure with microsatellite data: Bias and sampling variance

Canadian Journal of Fisheries and Aquatic Sciences

Volumn 55, Issue 1, 1998, Pages 1-14

  Ruzzante, Daniel E ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC DISTANCE; MICROSATELLITE DNA; POPULATION STRUCTURE; SAMPLE SIZE;

GADUS; GADUS MORHUA; GADUS MORHUS;

EID: 0031922381     PISSN: 0706652X     EISSN: None     Source Type: Journal    
DOI: 10.1139/f97-203     Document Type: Article

References (52)

1. Amos, B., Schlötterer, C., andTautz, D. 1993. Social structure of pilot whales revealed by analytical DNA profiling. Science (Washington, D.C.), 260: 670-672.
2. Bentzen, P., Cook, D., Denti, D., Harris, A., Hofman, J., and Wright, J.M. 1990. One tube DNA extraction procedure for molecular fingerprinting. Fingerprint News, 2(4): 17-21.
3. Bentzen, P., Taggart, C.T., Ruzzante, D.E, and Cook, D. 1996. Microsatellite polymorphism and the population structure of cod (Gadus morhua) in the northwest Atlantic. Can. J. Fish. Aquat. Sci. 53(12): 2706-2721.
4. Bowcock, A.M., Ruiz-Linares, A., Tomfohrde, J., Minch, E., Kidd, J.R., and Cavalli-Sforza, L.L. 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature (London), 368: 455-457.
5. Brooker, A.L., Cook, D., Bentzen, P., Wright, J.M., and Doyle, R.W. 1994. Organization of microsatellites differs between mammals and cold-water teleost fish. Can. J. Fish. Aquat. Sci. 51: 1959-1966.
6. Carvalho, G.R., and Hauser, L. 1994. Molecular genetics and the stock concept in fisheries. Rev. Fish Biol. Fish. 4: 326-350.
7. Cavalli-Sforza, L.L., and Edwards, A.W.F. 1967. Phylogenetic analysis: models and estimation procedures. Evolution, 21: 550-570.
8. Clark, A.G., Hamilton, J.F., and Chambers, G.F. 1995. Inference of population subdivision from VNTR distributions of New Zealanders. Genetica, 96: 37-49.
9. Deka, R., Chakraborty, R., and Ferrell, R.E. 1991. A population genetic study of six VNTR loci in three ethnically defined populations. Genomics, 11: 83-92.
10. n repeats in chimpanzees. Genomics, 22: 226-230.
11. Di Rienzo, A., Peterson, A.C., Garza, J.C., Valdes, A.M., Slatkin, M., and Freimer, N.B. 1994. Mutational processes of simple-sequence repeat loci in human populations. Proc. Natl. Acad. Sci. U.S.A. 91: 3166-3170.
12. Edwards, A., Hammond, H.A., Jin, L., Caskey, C.T., and Chakraborty, R. 1992. Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics, 12: 241-253.
13. Garza, J.C., Slatkin, M., and Freimer, N.B. 1995. Microsatellite allele frequency in humans and chimpanzees, with implications for constraints on allele size. Mol. Biol. Evol. 12: 594-603.
14. Goldstein, D.B., Ruiz-Linares, A., Cavalli-Sforza, L.L., and Feldman, M.W. 1995a. An evaluation of genetic distances for use with microsatellite loci. Genetics, 139: 463-471.
15. Goldstein, D.B., Ruiz-Linares, A., Cavalli-Sforza, L.L., and Feldman, M.W. 1995b. Genetic absolute dating based on microsatellites and the origin of modem humans. Proc. Natl. Acad. Sci. U.S.A. 92: 6723-6727.
16. Goodman, S.J. 1997. RST CALC: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance. Mol. Ecol. 6: 881-885.
17. Griffin, D.A., and Lochmann, S.E. 1993. Petrel V cruise 31 to Western Bank, 22 November - 16 December, 1992. OPEN Rep. No. 1993/1, Department of Oceanography, Dalhousie University, Halifax, N.S.
18. Hearne C.M., Ghosh, S., and Todd, J.A. 1992. Microsatellites for linkage analysis of genetic traits. Trends Genet. 8: 288-294.
19. Jarne, P., and Lagoda, P.J.L. 1996. Microsatellites, from molecules to populations and back. Trends Ecol. Evol. 11(10): 424-429.
20. Kellogg, K.A., Markert, J.A., Stauffer, J.R., Kocher, T.D. 1995. Microsatellite variation demonstrates multiple paternity in lekking cichlid fishes from Lake Malawi, Africa. Proc. R. Soc. London, Ser. B, 260: 79-84.
21. Kimmel, M., Chakraborty, R., Stivers, D.N., and Deka, R. 1996. Dynamics of repeat polymorphisms under a forward-backward mutation model: within- and between-population variability at microsatellite loci. Genetics, 143: 549-555.
22. Lochmann, S.E., Taggart, C.T., Griffin, D.A., Thompson, K.R., and Maillet, G.A. 1997. Abundance and condition of larval cod (Gadus morhua) at a convergent front on Western Bank, Scotian Shelf. Can. J. Fish. Aquat. Sci. 54(7): 1461-1479.
23. McConnell, S.K.J., Ruzzante, D.E., O'Reilly, P.T., Hamilton, L., and Wright, J.M. 1997. Microsatellite loci reveal highly significant genetic differentiation between Atlantic salmon (Salmo salar L.) populations from the east coast of Canada. Mol. Ecol. 6: 1075-1089.
24. Michalakis, Y., and Excoffier, L. 1996. A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics, 142: 1061-1064.
25. Morin, P.A., Moore, J.J., Chakraborty, R., Jin, L., Goodall, J., and Woodruff, D.S. 1994. Kin selection, social structure, gene flow, and the evolution of chimpanzees. Science (Washington, D.C.), 265: 1193-1201.
26. Nauta, M.J., and Weissing, F.J. 1996. Constraints on allele size at microsatellite loci: implications for genetic differentiation. Genetics, 143: 1021-1032.
27. Nei, M. 1972. Genetic distance between populations. Am. Nat. 106: 283-291.
28. Nei, M., Tajima, F., and Tateno, Y. 1983. Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 19: 153-170.
29. O'Reilly, P.T., and Wright, J.M. 1995. The evolving technology of DNA fingerprinting and its application to fisheries aquaculture. J. Fish Biol. 47(Suppl. A): 29-55.
30. Paetkau, D., and Strobeck, C. 1994. Microsatellite analysis of genetic variation in black bear populations. Mol. Ecol. 3: 489-495.
31. Paetkau, D., Calvert, W., Stirling, I., and Strobeck, C. 1995. Microsatellite analysis and population structure in Canadian polar bears. Mol. Ecol. 4: 347-354.
32. Park, L.A., and Moran, P. 1994. Developments in molecular genetic techniques in fisheries. Rev. Fish Biol. Fish. 4: 272-299.
33. Queller, D.C., Strassmann, J.E., and Hughes, C.R. 1993. Microsatellites and kinship. Trends Ecol. Evol. 8: 285-288.
34. Rogers, J.S. 1972. Measures of genetic similarity and genetic distance. Stud, in Genet. No. 7213. pp. 145-153.
35. Roy, M.S., Geffen, E., Smith, D., Ostrander, E.A., and Wayne, R.K. 1994. Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci. Mol. Biol. Evol. 11: 553-570.
36. Ruzzante, D.E., Taggart, C.T., and Cook, D. 1996a. Spatial and temporal variation in the genetic composition of a larval cod (Gadus morhua) aggregation: cohort contribution and genetic stability. Can. J. Fish. Aquat. Sci. 53(12): 2695-2705.
37. Ruzzante, D.E., Taggart, C.T., Cook, D., and Goddard, S. 1996b. Genetic differentiation between inshore and offshore Atlantic cod (Gadus morhua) off Newfoundland: microsatellite DNA variation and antifreeze level. Can. J. Fish. Aquat. Sci. 53(3): 634-645.
38. Ruzzante, D.E., Taggart, C.T., Cook, D., and Goddard, S.V. 1997. Genetic differentiation between inshore and offshore Atlantic cod (Gadus morhua) off Newfoundland: a test and evidence of temporal stability. Can. J. Fish. Aquat. Sci. 54(11): 2700-2708.
39. Shriver, M.D., Jin, L., Chakraborty, R., and Boerwinkle, E. 1993. VNTR allele frequency distributions under the stepwise mutational model: a computer simulation approach. Genetics, 134: 983-993.
40. Shriver, M.D., Jin, L., Boervvinkle, E., Deka, R., Ferrell, R.E. 1995. A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol. Biol. Evol. 12(5): 914-920.
41. Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics, 139: 457-462.
42. Slatkin, M., and Barton, N.H. 1989. A comparison of three indirect methods for estimating average levels of gene flow. Evolution, 43: 1349-1368.
43. Taggart, C.T., Lochmann, S.E., Griffin, D.A., Thompson, K.R., and Maillet, G.L. 1996. Abundance distribution of larval cod (Gadus morhua) and Zooplankton in a gyre-like water mass on the Scotian Shelf. In Survival Strategies in Early Life Stages of Marine Resources. Proceedings of an International Workshop, Yokohama, Japan. Edited by Y. Watanabe, Y. Yamashita, and Y. Oozeki. Balkema Press, Rotterdam, The Netherlands, pp. 127-145.
44. Takezaki, N., and Nei, M. 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics, 144: 389-399.
45. Tautz, D. 1989. Hypervariability of simple sequences as a source for polymorphic DNA markers. Nucleic Acids Res. 17: 6463-6471.
46. Valdes, A.M., Slatkin, M., and Freimer, N.B. 1993. Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics, 133: 737-749.
47. Weber, J.L., and Wong, C. 1993. Mutation of human short tandem repeats. Hum. Mol. Genet. 2: 1123-1128.
48. Weir, B.S., and Cockerham, C.C. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38: 1358-1370.
49. Wright, S. 1951. The genetical structure of populations. Ann. Eugenics, 15: 323-354.
50. Wright, J.M. 1993. DNA fingerprinting of fishes. In Biochemistry and molecular biology of fishes. Vol. 2. Edited by P.W. Hochachka and T. Mommsen. Elsevier Science Publishers B.V. Amsterdam, The Netherlands, pp. 57-91.
51. Wright, J.M., and Bentzen, P. 1994. Microsatellites: genetic markers for the future. Rev. Fish Biol. Fish. 4: 384-388.
52. Yanisch-Perron, C., Vieira, J., and Messing, J. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of M13mp18 and puc19 vectors. Gene, 33: 103-119.