Abstract
Microsatellite loci have recently been used to date the migration Out-of-Africa of early modern humans. In this paper, an extension of the stepwise model (Zhivotovsky and Feldman 1995) is used to build a Bayesian hierarchical model for microsatellite data sampled from African and non-African populations. The prior information induced by the assumptions contained in the stepwise model is exploited to obtain the estimate of the time since the migration Out-of-Africa. The results obtained using our Bayesian model suggest that the original African populations that eventually made up the other populations could have comprised about 20,000-50,000 individuals and of these less than 15% could have migrated Out-of-Africa. The event of divergence can be dated to 100,000-300,000 years ago.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Berger, J. O. 1985. Statistical Decision Theory and Bayesian Analysis. Springer-Verlag, New York.
Best, N., M. K. Cowles, and K. Vine. 1996. CODA: Convergence Diagnosis and Output Analysis Software for Gibbs sampling output. Electronic mail: bugs@mrc-bsu.cam.ac.uk, Cambridge: MRC Biostatistic Unit.
Borland International. 1996. C++ Programmer’s Guide., CA: Borland International, Scott’s Valley.
Bernardo, J. M., and A F. M. Smith. 1994. Bayesian Theory. Wiley, New York.
Besag, J., P. Green, D. Higdon, and K. Mengersen. 1995. Bayesian computation and stochastic systems. Statistical Science 10: 3–66.
Bowcock, A. M., A Ruiz Linares, J. Tomfohrde, E. Minch, J. R. Kidd, and L. L. Cavalli-Sforza. 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 386: 455–457.
Box, G. E. P., and G. C. Tiao. 1973. Bayesian Inference in Statistical Analysis. Addison-Wesley, Reading.
Carlin, B. P., and T. A Louis. 1996. Bayes and empirical Bayes Methods for data analysis. Chapman and Hall, London.
Casella, G., and R. L. Berger. 1990. Statistical Inference. Belmont, California, Duxbury.
Casella, G., and E. I. George. 1992. Explaining the Gibbs sampler. The American Statistician 46: 167–174.
Cavalli-Sforza, L. L., P. Menozzi, and A Piazza. 1994. The History and Geography of Human Genes. Princeton University Press, Princeton.
Cowles, M K., and B. P. Carlin. 1996. Markov Chain Monte Carlo convergence diagnostics: a comparative review. Journal of the American Statistical Association 91: 883–904.
de Queiroz, A, M. J. Donoghue, and J. Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Annual Review of Ecology and Systematics 26: 657–681.
Di Rienzo, A., A. C. Peterson, J. C. Garza, A M. Valdes, M. Slatkin, and N. B. Freimer. 1994. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the U.S.A. 91: 3166–3170.
Estoup, A, L. Garnery, M. Solignac, and J. Cornuet. 1995. Microsatellite variation in Honey Bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models. Genetics 140: 679–695.
Feldman, M. W., A Bergman, D. D. Pollock, and D. B. Goldstein. 1997. Microsatellite genetic distances with range constraints: analytic description and problems of estimation. Genetics 145: 207–216.
Garza, J. C., M. Slatkin, and N. B. Freimer. 1995. Microsatellite allele frequencies in Humans and Chimpanzees, with implications for constraints on allele size. Molecular Biology and Evolution 12: 594–603.
Gelman, A., and D. B. Rubin. 1992. Inference from iterative simulation using multiple sequences. Statistical Science 7: 457–511.
Gelman, A., J. B. Carlin, H. S. Stern, and D. B. Rubin. 1995. Bayesian Data Analysis. Chapman and Hall, New York.
Geyer, C. J., and E. A Thompson. 1995. Annealing Markov Chain Monte Carlo with applications to ancestral Inference. Journal of the American Statistical Association 90: 909–920.
Gibbons, A 1995. Out of Africa-at last? Science 267: 1272–1273.
Goel, P. K. 1983. Information measures and Bayesian hierarchical models. Journal of the American Statistical Association 78, 408–410.
Goel, P. K., and M. H. DeGroot. 1981. Information about hyperparameters in hierarchical models. Journal of the American Statistical Association 76: 140–147.
Goldstein, D. B., R. A. Ruiz-Linares, L. L. Cavalli-Sforza, and M. W. Feldman. 1995a. An evaluation of genetic distances for use with microsatellite loci. Genetics 139: 463–471.
Goldstein, D. B., A Ruiz Linares, L. L. Cavalli-Sforza, and M. W. Feldman. 1995b. Genetic absolute dating based on microsatellites and the origin of modem humans. Proceedings of the National Academy of Sciences of the U.S.A 92: 6723–6727.
Goldstein, D. B., and A G. Clark. 1995. Microsatellite variation in North American populations of Drosophila melanogaster. Nucleic Acids Research 23: 3882–3886.
Goldstein, D. B., L. A Zhivotovsky, K. Nayar, A Ruiz Linares, L. L. Cavalli-Sforza, and M. W. Feldman. 1996. Statistical properties of the variation at linked microsatellite loci: implications for the history of human Y chromosomes. Molecular Biology and Evolution 13: 1213–1218.
Griffiths, R. C., and S. Tavare. 1994. Ancestral inference in population genetics. Statistical Science 9: 307–319.
Horai, S., K. Hayasaka, R. Kondo, K. Tsugane, and N. Takahata. 1995. Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proceedings of the National Academy of Sciences of the U.S.A. 92: 532–536.
Jorde, L. B., M. J. Bamshad, W. S. Watkins, R. Zenger, A. E. Fraley, P. A. Krakowiak, R. Carpenter, H. Soodyall, T. Jenkins, and A. R. Rogers. 1995. Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data. American Journal of Human Genetics 57: 523–538.
Li, S., D. K. Pearl, and H. Doss. 1996. Phylogenetic tree construction using Markov Chain Monte Carlo. The Ohio State University, Dep. of Statistics, Technical Report N.583, Columbus.
Mau, B., M. A. Newton, and B. Larget. 1996. Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods. Madison: University of Wisconsin-Madison, Dep. of Statistics. Ftp address: ftp.stat. wisc.edu/pub/newton/tr961.ps
Moran, P. A. P. 1975. Wandering Distributions and the electrophoretic profile. Theoretical Population Biology 8: 318–330.
Nauta, M. J., and F. J. Weissing. 1996. Constraints on allele size at microsatellite loci: implications for genetic differentiation. Genetics 143: 1021–1032.
Nei, M., and N. Takezaki. 1996. The root of phylogenetic tree of human populations. Molecular Biology and Evolution 13: 170–177.
Nei, M. 1995. Genetic support for the out-of-Africa theory of human evolution. Proceedings of the National Academy of Sciences of the U.S.A. 92: 6720–6722.
O’Hagan, A. 1994. Bayesian Inference. Edward Arnold, London.
Ohta, T., and M. Kimura. 1973. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetical Research 22: 201–204.
Plaschke, J., M. W. Ganal, and M. S. Roder. 1995. Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theoretical Applied Genetics 91: 1001–1007.
Pritchard, J. K., and M. W. Feldman. 1996. Statistics for microsatellite variation based on coalescence. Theoretical Population Biology 50: 325–344.
Rousset, F. 1996. Equilibrium values of measures of population subdivision for stepwise mutation process. Genetics 142: 1357–1362.
Saitou, N., and M. Nei. 1987 The neighbor-joining method: a new method for reconstructing phylog melk trees. Molecular Biology and Evolution 4: 406–425.
Shriver, M. D., L. Jin, R. Chakraborty, and E. Boerwinkle. 1993. VNTR allele frequency distribution under the stepwise mutation model: a computer simulation approach. Genetics 134: 983–993.
Shriver, M. D., L. Jin, E. Boerwinkle, R. Deka, R. E. Ferrell, and R. Chakraborty. 1995. A novel measure of genetic distance for highly polymorphic tandem repeat loci. Molecular Biology and Evolution 12: 914–920.
Sinsheimer, J. S., J. A. Lake, and R. J. A. Little. 1996. Bayesian hypothesis testing of four-taxon topologies using molecular sequence data. Biometrics 52: 193–210.
Silverman, B. W. 1992. Density Estimation for Statistics and Data Analysis. Chapman & Hall, New York.
Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457–462.
Stefanini, F. M. 1997. Metodologia Bayesiana gerarchica ed informazione evolutiva in loci genetici micrisatellite. PhD Thesis, Department of Statistics, University of Florence, Italy.
Tajima, F. 1993. Measurement of DNA polymorphism. In N. Takahata and A. G. Clark, eds., Mechanisms of Molecular Evolution, Sinauer Associates Inc Sunderland, Massachusetts, pp. 37–59.
Valdes, A. M., M. Slatkin, and N. B. Freimer. 1993. Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics 133: 737–749.
Venables, W. N., and B. D. Ripley. 1994 Modern Applied Statistics with S-Plus. Springer-Verlag, New York.
Weber, J. L., and C. Wong. 1993. Mutation of human short tandem repeats. Human Molecular Genetics 2: 1123–1128.
Yang, Z., and B. Rannala. 1997. Bayesian Phylogenetic Inference using DNA sequences: a Markov Chain Monte Carlo Method. Molecular Evolution and Biology 14: 717–724.
Zhivotovsky, L. A., and M. W. Feldman. 1995. Microsatellite variability and genetic distances. Proceedings of the National Academy of Sciences of the U.S.A. 92: 11549–11552.
Zhivotovsky, L. A., M. W. Feldman, and S. A. Grishechkin. 1997. Microsatellite evolution with biased mutations. Molecular Biology and Evolution 14: 926–933.
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1999 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Stefanini, F.M., Feldman, M.W. (1999). Microsatellite Loci and the Origin of Modern Humans: A Bayesian Analysis. In: Wasser, S.P. (eds) Evolutionary Theory and Processes: Modern Perspectives. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4830-6_15
Download citation
DOI: https://doi.org/10.1007/978-94-011-4830-6_15
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-010-6025-7
Online ISBN: 978-94-011-4830-6
eBook Packages: Springer Book Archive