Abstract
As in the allelic case, diversity and differentiation can be estimated at the nucleotide level, as if each nucleotide site was one locus. However, data from few sequences have been available in the past, and indirect estimates of nucleotide diversity have been obtained with restriction data. We will describe both methods, using sequence data and restriction data. The extension of the latter to random amplification data (RAPD) will also be discussed. However, contrary to the allelic approach, where most available data are from diploid genes, the investigations on nucleotide diversity concern principally haploid genomes (chioroplasts in plants and mitochondria in animals). Therefore, the methods that will be outlined refer only to haploid data.
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References
Wright S., 1943. Isolation by distance. Genetics 28: 114–138.
Weir B.S., Cockerham C.C, 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370.
Pielou E.C, 1975. Ecological diversity. Wiley, New York, USA.
Magurran A.E., 1988. Ecological diversity and its measurement. Croom Helm, Cambridge, UK.
Patil G.P., Taillie C., 1982. Diversity as a concept and its measurement. J. Amer. Stat. Assoc. 77: 548–561.
Marshall D.R. and Jain S.K., 1969. Genetic polymorphism in natural populations of Avena fatua and A. barbata. Nature 221: 276–278.
Nei M., 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Science. USA 70: 3321–3323.
Simpson E.H. 1949. Measurement of diversity. Nature 163, 688.
Lewontin R.C., 1972. The apportionment of human diversity. Evolutionary Biology. 6: 381–398.
Crow J.F., Kimura M., 1964. The number of alleles that can be maintained in a finite population. Genetics 49: 725–738.
Hattemer H.H., 1991. Measuring genetic variation. In Genetic variation in European populations of forest trees, G. Müller-Starck and M. Ziehe eds., 2–19.
Nei M., 1987. Molecular evolutionary genetics. Columbia University Press.
Gregorius H.R., 1987. The relationship between the concepts of genetic diversity and differentiation. Theoretical and Applied Genetics. 74: 397–401.
Long J.C., Smouse P.E., Wood J.W. 1987. The allelic correlation structure of Gainj- and Kalam-speaking people. II The genetic distance between population subdivisions. Genetics 117: 273–283.
Pons O., Petit R.J., 1995. Estimation, variance and optimal sampling of gene diversity. I. Haploid locus. Theoretical and Applied Genetics. 90: 462–470.
Brown A.H.D., Weir B.S., 1983. Measuring genetic variability in plant populations. In Isozymes in plant genetics and Breeding, Part A, S.D. Tanksley and T.J. Orton eds. Elsevier, Amsterdam.
Nevo E., Beiles A., Ben Shlomo R., 1984. The evolutionary significance of genetic diversity: ecological, demographic and life history correlates. In Evolutionary dynamics of genetic diversity pp 13–213. Springer Verlag, Berlin.
Hamrick J.L., Godt M.J., 1990 Allozyme diversity in plant species. In Plant population genetics, breeding and genetic resources, A.H.D. Brown, M.T. Clegg, A.L. Kahler, B.S. Weir eds, pp 43–53, Sinauer Associates, Sunderland.
Nei M., Chesser R.K., 1983. Estimation of fixation indices and gene diversities. Annals of Human Genetics. 47: 253–259.
Pons O., Chaouche K., 1995. Estimation, variance and optimal sampling of gene diversity. II. Diploid locus. Theoretical and Applied Genetics. in press.
Nei M., Roychoudhury A.K., 1974. Sampling variances of heterozygosity and genetic distance. Genetics 76: 379–380.
Zhang Q., Allard R.W., 1986. Sampling variance of the genetic diversity index. The Journal of Heredity 77: 54–55.
Chakraborty R., 1974. A note on Nei’s measure of gene diversity in a substructured population. Humangenetik 21: 85–88.
Chakraborty R., Leimar O., 1987. Genetic variation within a subdivided population. In Population genetics and fishery management, N. Ryman and F. Utter eds, pp 89–120. University of Washington Press, Seattle and London.
Nei M., Tajima R, 1981. DNA polymorphism detectable by restriction endonucleases. Genetics 97: 145–163.
Nei M., Jin L., 1989. Variances of the average numbers of nucleotide substitutions within and between populations. Molecular Biology and Evolution. 6: 290–300.
Lynch M., Crease T.J., 1990 The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution. 7: 377–394.
Nei M., 1982. Evolution of human races at the gene level. Pp. 167–181 in B. Bonne-Tamir, P. Cohen, and R. N. Goodman, eds. Human genetics, part A: the unfolding genome. Alan R. Liss, New York.
Nei M., Li W.H., 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Science. USA 35: 65–83.
Nei M., Miller J.C. 1990. A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics 125: 873–879.
Williams J.G.K., Kubelik A.R., Livak K.J., Rafalski J.A., Tingey S.V., 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research. 18: 6531–6535.
Clark A.G., Lanigan C.M.S., 1993. Prospects for estimating nucleotide divergence with RAPDs. Molecular Biology and Evolution. 10: 1096–1111.
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Karp, A., Isaac, P.G., Ingram, D.S. (1998). Diversity and Differentiation at the Nucleotide Level. In: Karp, A., Isaac, P.G., Ingram, D.S. (eds) Molecular Tools for Screening Biodiversity. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-0019-6_57
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DOI: https://doi.org/10.1007/978-94-009-0019-6_57
Publisher Name: Springer, Dordrecht
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