GENE GENEALOGY AND VARIANCE OF INTERPOPULATIONAL NUCLEOTIDE DIFFERENCES

Naoyuki Takahata ¹ and Masatoshi Nei ¹

¹ Center for Demographic and Population Genetics, University of Texas at Houston, Houston, Texas 77225

A mathematical theory is developed for computing the probability that m genes sampled from one population (species) and n genes sampled from another are derived from l genes that existed at the time of population splitting. The expected time of divergence between the two most closely related genes sampled from two different populations and the time of divergence (coalescence) of all genes sampled are studied by using this theory. It is shown that the time of divergence between the two most closely related genes can be used as an approximate estimate of the time of population splitting (T) only when T t/(2 N) is small, where t and N are the number of generations and the effective population size, respectively. The variance of Nei and Li's estimate (d) of the number of net nucleotide differences between two populations is also studied. It is shown that the standard error ( s_d) of d is larger than the mean when T is small (T << 1). In this case, s_d is reduced considerably by increasing sample size. When T is large (T > 1), however, a large proportion of the variance of d is caused by stochastic factors, and increase in the sample size does not help to reduce s_d. To reduce the stochastic variance of d, one must use data from many independent unlinked gene loci.

This article has been cited by other articles:

				T. Stadler, U. Arunyawat, and W. Stephan Population Genetics of Speciation in Two Closely Related Wild Tomatoes (Solanum Section Lycopersicon) Genetics, January 1, 2008; 178(1): 339 - 350. [Abstract] [Full Text] [PDF]

				M. D. Carling and R. T. Brumfield Integrating Phylogenetic and Population Genetic Analyses of Multiple Loci to Test Species Divergence Hypotheses in Passerina Buntings Genetics, January 1, 2008; 178(1): 363 - 377. [Abstract] [Full Text] [PDF]

				A. Abe, Y. Oda, K. Asano, and T. Sone Rhizopus delemar is the proper name for Rhizopus oryzae fumaric-malic acid producers. Mycologia, September 1, 2007; 99(5): 714 - 722. [Abstract] [Full Text] [PDF]

				M. G. B. Blum and N. A. Rosenberg Estimating the Number of Ancestral Lineages Using a Maximum-Likelihood Method Based on Rejection Sampling Genetics, July 1, 2007; 176(3): 1741 - 1757. [Abstract] [Full Text] [PDF]

				K. Yamane and T. Kawahara Intra- and interspecific phylogenetic relationships among diploid Triticum-Aegilops species (Poaceae) based on base-pair substitutions, indels, and microsatellites in chloroplast noncoding sequences Am. J. Botany, November 1, 2005; 92(11): 1887 - 1898. [Abstract] [Full Text] [PDF]

				J. Hey and R. Nielsen Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis Genetics, June 1, 2004; 167(2): 747 - 760. [Abstract] [Full Text] [PDF]

				M. F. Hammer, F. Blackmer, D. Garrigan, M. W. Nachman, and J. A. Wilder Human Population Structure and Its Effects on Sampling Y Chromosome Sequence Variation Genetics, August 1, 2003; 164(4): 1495 - 1509. [Abstract] [Full Text] [PDF]

				A. Loytynoja and M. C. Milinkovitch Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: The Plantae/Fungi/Metazoa trichotomy revisited PNAS, August 17, 2001; (2001) 181187698. [Abstract] [Full Text] [PDF]

				B. F. McAllister and G. A. T. McVean Neutral Evolution of the Sex-Determining Gene transformer in Drosophila Genetics, April 1, 2000; 154(4): 1711 - 1720. [Abstract] [Full Text]

				J. Wakeley Nonequilibrium Migration in Human History Genetics, December 1, 1999; 153(4): 1863 - 1871. [Abstract] [Full Text]

				B. F. McAllister and B. Charlesworth Reduced Sequence Variability on the Neo-Y Chromosome of Drosophila americana americana Genetics, September 1, 1999; 153(1): 221 - 233. [Abstract] [Full Text]

				G. Bertorelle and B. Rannala Using rare mutations to estimate population divergence times: A maximum likelihood approach PNAS, December 22, 1998; 95(26): 15452 - 15457. [Abstract] [Full Text] [PDF]

				S. Nagl, H. Tichy, W. E. Mayer, N. Takahata, and J. Klein Persistence of neutral polymorphisms in Lake Victoria cichlid fish PNAS, November 24, 1998; 95(24): 14238 - 14243. [Abstract] [Full Text] [PDF]

				J. C. Avise and K. Wollenberg Phylogenetics and the origin of species PNAS, July 22, 1997; 94(15): 7748 - 7755. [Abstract] [Full Text] [PDF]

				F. J. Ayala Association Affairs|The Myth of Eve: Molecular Biology and Human Origins: F. J. Ayala Science, December 22, 1995; 270(5244): 1930 - 1936. [PDF]

				A. Loytynoja and M. C. Milinkovitch Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: The Plantae/Fungi/Metazoa trichotomy revisited PNAS, August 28, 2001; 98(18): 10202 - 10207. [Abstract] [Full Text] [PDF]