The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism.

In order to study the effect of mutation rate heterogeneity on patterns of DNA polymorphism, we simulated samples of DNA sequences with gamma-distributed nucleotide substitution rates in stationary and expanding populations. We find that recent population expansions and mutation rate heterogeneity have similar effects on several polymorphism indicators, like the shape and the mean of the observed pairwise difference distribution, or the number of segregating sites. The inferred size of population expansion thus appears overestimated if nucleotides have dissimilar substitution rates. Interestingly, population expansion and uneven mutation rates have contrasting effects on Tajima's D statistic when acting separately, and the consequence on the associated test of selective neutrality is investigated. The patterns of polymorphism of several human populations analyzed for the mitochondrial control region are examined, mainly showing the difficulty in quantifying the respective contribution of past demographic history and uneven mutation rates from a single sampled evolutionary process. However, substitution rates appear more heterogeneous in the second hypervariable segment of the control region than in the first segment.

[1]  Thomas Uzzell,et al.  Fitting Discrete Probability Distributions to Evolutionary Events , 1971, Science.

[2]  W. Fitch.  Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .

[3]  W. Ewens.  The sampling theory of selectively neutral alleles. , 1972, Theoretical population biology.

[4]  G. A. Watterson.  On the number of segregating sites in genetical models without recombination. , 1975, Theoretical population biology.

[5]  R. Griffiths.  Exact sampling distributions from the infinite neutral alleles model , 1979, Advances in Applied Probability.

[6]  F. Tajima.  Evolutionary relationship of DNA sequences in finite populations. , 1983, Genetics.

[7]  William H. Press,et al.  Numerical recipes in C. The art of scientific computing , 1987 .

[8]  William H. Press,et al.  Book-Review - Numerical Recipes in Pascal - the Art of Scientific Computing , 1989 .

[9]  M Slatkin,et al.  A cladistic measure of gene flow inferred from the phylogenies of alleles. , 1989, Genetics.

[10]  F. Tajima.  Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[11]  A. Wilson,et al.  Mitochondrial DNA sequences in single hairs from a southern African population. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[12]  F. Tajima.  The effect of change in population size on DNA polymorphism. , 1989, Genetics.

[13]  S. Horai,et al.  Intraspecific nucleotide sequence differences in the major noncoding region of human mitochondrial DNA. , 1990, American journal of human genetics.

[14]  R. Hudson.  Gene genealogies and the coalescent process. , 1990 .

[15]  A. Wilson,et al.  Sequence Evolution of Mitochondrial DNA in Humans and Chimpanzees: Control Region and a Protein-Coding Region , 1991 .

[16]  M. Slatkin,et al.  Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. , 1991, Genetics.

[17]  S. Pääbo,et al.  Extensive mitochondrial diversity within a single Amerindian tribe. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[18]  大沢 省三,et al.  Evolution of life : fossils, molecules, and culture , 1991 .

[19]  A. Di Rienzo,et al.  Branching pattern in the evolutionary tree for human mitochondrial DNA. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[20]  S. Tavaré,et al.  Modeling the evolution of the human mitochondrial genome. , 1992, Mathematical biosciences.

[21]  Error introduced by the infinite-site model. , 1992, Molecular biology and evolution.

[22]  H. Harpending,et al.  Population growth makes waves in the distribution of pairwise genetic differences. , 1992, Molecular biology and evolution.

[23]  William H. Press,et al.  The Art of Scientific Computing Second Edition , 1998 .

[24]  L. Excoffier,et al.  Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. , 1992, Genetics.

[25]  Stephen T. Sherry,et al.  The Genetic Structure of Ancient Human Populations , 1993, Current Anthropology.

[26]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[27]  John C. Avise,et al.  Molecular Markers, Natural History and Evolution , 1993, Springer US.

[28]  John C. Avise.  Molecular Markers, Natural History and Evolution , 1994, Springer US.

[29]  J. Wakeley,et al.  Substitution-rate variation among sites and the estimation of transition bias. , 1994, Molecular biology and evolution.

[30]  P. Donnelly,et al.  Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. , 1994, Genetics.

[31]  M. Slatkin,et al.  The number of segregating sites in expanding human populations, with implications for estimates of demographic parameters. , 1995, Molecular biology and evolution.

[32]  M Slatkin,et al.  A measure of population subdivision based on microsatellite allele frequencies. , 1995, Genetics.

[33]  A. Rogers.  GENETIC EVIDENCE FOR A PLEISTOCENE POPULATION EXPLOSION , 1995, Evolution; international journal of organic evolution.

[34]  L. Jorde,et al.  Genetic evidence on modern human origins. , 1995, Human biology.

[35]  L. Excoffier,et al.  Evolutionary correlation between control region sequence and restriction polymorphisms in the mitochondrial genome of a large Senegalese Mandenka sample. , 1995, Molecular biology and evolution.