Abstract
Different genetic identity or distance measures are compared that consider allelic variation within and between populations. Particularily we analyse those suggested by Nei ( IS, DS), Rogers (DR), Reynolds, Weir and Cockerham (Dθ), Nei, Tajima and Tateno (DA), Tomiuk and Loeschcke (ITL, DTL) and Goldstein et al. ((δμ)2). The simulations focus on the influence of non-equilibrium conditions on the stability of these measures. The degree of homozygosity of an ancestral population before it splits into two sister populations is most important for the stability of the different estimates of genetic identity. If populations are not close to their equilibrium homozygosity, a considerable bias can occur and, thereby, provide very misleading estimates of the time span since divergence. The ITL-measure based on estimates of ancestral alleles is more robust than other measures of genetic identity, especially for large population sizes and high mutation rates. For the infinite allele model, the analysis shows that more precise estimates of the frequency of ancestral alleles can greatly improve the reliability of the estimate of genetic identity in the case of ITL. For the stepwise mutation model, the TL-measure combines the attributes of the DA- and (δμ)2-measures. The TL-measure is efficient for the construction of the correct tree topology of related populations as well as for the estimation of the branch length when protein or microsatellite data are analysed.
Similar content being viewed by others
References
Bowcock, A.M., A. Ruiz-Linares, J. Tomfohrde, E. Minch, J.R. Kidd & L.L Cavalli-Sforza, 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457.
Cavalli-Sforza, L.L. & A.F.W. Edwards, 1967. Phylogenetic analysis: Models and estimation procedures. Amer. J. Hum. Genet. 19: 233-257.
Chakraborty, R. & L. Jin, 1993. A unified approach to study hypervariable polymorphisms: statistical consideration of determining relatedness and population distances, pp. 153-175 in DNA Fingerprinting: State of Science edited by S.D.J. Pena, R. Chakraborty, J.T. Epplen and A.J. Jeffreys. Birkhäuser Verlag, Basel.
Chakraborty, R. & M. Nei, 1976. Bottleneck effects on average heterozygosity and genetic distance with the stepwise mutation model. Evolution 31: 347-356.
Clark, A.G. & C.M.S. Lanigan, 1993. Prospects for estimating nucleotide divergence with RAPDs. Mol. Biol. Evol. 10: 1096- 1111.
Edwards, A.W.F., 1971. Distances between populations on the basis of gene frequencies. Biometrics 27: 873-881.
Feldman, M.W., A. Bergman, D.D. Pollock & D.B. Goldstein, 1997. Microsatellite genetic distances with range constraints: Analytic description and problems of estimation. Genetics 145: 207-216.
Fisher, R.A., 1930. The Genetical Theory of Natural Selection. Clarendon, Oxford.
Goldstein, D.B., A. Ruis Linares, L.L. Cavalli-Sforza & M.W. Feldman, 1995a. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc. Natl. Acad. Sci. USA 92: 6723-6727.
Goldstein, D.B., A. Ruis Linares, L.L. Cavalli-Sforza & M.W. Feldman, 1995b. An evaluation of genetic distances for use with mircosatellite loci. Genetics 139: 463-471.
Goldstein, D.B., L.A. Zhivotovsky, K. Nayar, A. Ruiz Linares, L.L. Cavalli-Sforza & M.W. Feldman, 1996. Statistical properities of the variation at linked microsatellite loci: Implications for the history of human Y chromosomes. Mol. Biol. Evol. 13: 1213- 1218.
Hartl, D.L. & A.G. Clark, 1989. Principles of Population Genetics. Sinauer Associates, Massachusetts.
Hasegawa, M. & H. Kishino, 1991. DNA sequence analysis and evolution of Hominoidea, pp. 303-317 in New Aspects of the Genetics of Molecular Evolution, edited by M. Kimura and N. Takahata. Japan Sci. Press, Tokyo/Springer-Verlag, Berlin.
Hedrick, P.W., 1971. A new approach to measuring genetic similarity. Evolution 25: 276-280.
Hubby, J.L. & R.C. Lewontin, 1966. A molecular approach to the study of genic heterozygosity in natural populations. I. The number of alleles at different loci in Drosophila pseudoobscura. Genetics 54: 577-594.
Hillis, D.M., 1984. Misuse and modification of Nei's genetic distance. Syst. Zool. 33: 238-240.
Langley, C.H. & Fitch, W.M., 1974. An examination of the constancy of the rate of molecular evolution. J. Mol. Evol. 3: 161-177.
Latter, B.D.H., 1973. Measures of genetic distance between individuals and populations, pp. 27-37 in Genetic Structure of Populations, edited by N.E. Morton. Univ. Press of Hawaii, Hawaii.
Li, W.H. & M. Nei, 1975. Drift variances of heterozygosity and genetic distance in transient states. Genet. Res. Camb. 25: 220- 248.
Li, W.H. & M. Tanimura, 1987. The molecular clock runs more slowly in man than in apes and monkeys. Nature 365: 93-96.
Lynch, M. & B.G. Milligan, 1994. Analysis of population genetic structure with RAPD markers. Mol. Ecol. 3: 91-99.
Nauta, M.J. & F.J. Weissing, 1996. Constraints on allele size at microsatellite loci: Implications for genetic differentiation. Genetics 143: 1021-1032.
Nei, M., 1972. Genetic distance between populations. Amer. Natur. 106: 283-292.
Nei, M., 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
Nei, M. & A.K. Roychoudhury, 1974. Sampling variance of heterozygosity and genetic distance. Genetics 76: 379-390.
Nei, M., F. Tajima & Y. Tateno, 1983. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J. Mol. Evol. 91: 153-170.
Nozawa, K., T. Shotake, Y. Ohkura & Y. Tanabe, 1977. Genetic variations within and between species of Asian macaques. Japan. J. Genet. 52: 15-30.
Ohta, T. & M. Kimura, 1973. The model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a genetic population. Genet. Res. 22: 201-204.
Pamilo, P., 1990. Statistical tests of phenograms based on genetic distances. Evolution 44: 689-697.
Pritchard, J.K. & M.W. Feldman, 1996. Statistics for microsatellite variation based on coalescence. Theor. Popl. Biol. 50: 325-344.
Reynolds, J., B.S. Weir & C.C. Cockerham, 1983. Estimation of the coancestry coefficient: Basis for a short-term genetic distance. Genetics 105: 767-779.
Rogers, J.S., 1972. Measures of genetic similarity and genetic distance. Studies in Genetics VII (Univ. Texas Publ. 7213): 145-153.
Schmitt, J., D. Graur & J. Tomiuk, 1990. Phylogenetic relationships and rates of evolution in primates: Allozymic data from Catarrhine and Platyrrhine species. Primates 31: 95-108.
Schmitt, J. & J. Tomiuk, 1994. Protein polymorphism in three cercopithecid primate species and its application for conservation. Folia Primatol. 63: 123-130.
Sanghvi, L.D., 1953. Comparison of genetical and morphological methods for a study of biological differences. Amer. J. Phys. Anthropol. 11: 385-404.
Shriver, M., L. Jin, E. Boerwinkle, R. Deka, R.E. Ferreli & R. Chakraborty, 1995. A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol. Biol. Evol. 12: 914-920.
Slatkin, M., 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462.
Takezaki, N. & M. Nei, 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144: 389-399.
Tomiuk, J. & D. Graur, 1988. Nei's modified identity and distance measure and their sampling variances. Syst. Zool. 37: 156-162.
Tomiuk, J.& V. Loeschcke, 1991. A new measure of genetic identity between populations of sexual and asexual species. Evolution 45: 1685-1694.
Tomiuk, J. & V. Loeschcke, 1992. Evolution of parthenogenesis in the Otiorhynchus scaber complex. Heredity 68: 391-397.
Tomiuk, J. & V. Loeschcke, 1995. Genetic identity combining mutation and drift. Heredity 74: 607-615.
Tomiuk, J. & V. Loeschcke, 1996. A maximum-likelihood estimator of the genetic identity between polyploid species. J. Theor. Biol. 179: 51-54.
Turner, T.R., 1981. Blood protein variation in a population of Ethiopian vervet monkeys (Cercopithecus aethiops aethiops). Amer. J. Phys. Anthropol. 55: 225-231.
Wright, S., 1931. Evolution in Mendelian populations. Genetics 16: 97-159.
Wright, S., 1951. The genetical structure ofpopulations. Ann. Eugen. 15: 323-354.
Zhivotovsky, L.A. & M.W. Feldman, 1995. Microsatellite variability and genetic distances. Proc. Natl. Acad. Sci. USA 92: 11549- 11552.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Tomiuk, J., Guldbrandtsen, B. & Loeschcke, V. Population differentiation through mutation and drift – a comparison of genetic identity measures. Genetica 102, 545–558 (1998). https://doi.org/10.1023/A:1017080119277
Issue Date:
DOI: https://doi.org/10.1023/A:1017080119277