Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: Application to human mitochondrial DNA

Genetics

Volumn 152, Issue 3, 1999, Pages 1079-1089

  Schneider, Stefan ^a   Excoffier, Laurent ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; DEMOGRAPHY; DNA SEQUENCE; GENE MUTATION; GENETIC VARIABILITY; HUMAN; POPULATION DYNAMICS; PRIORITY JOURNAL; SIMULATION;

DEMOGRAPHY; DNA, MITOCHONDRIAL; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION;

EID: 0032814604     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (52)

1. AHRENS, J. H., and U. DIETER, 1974 Computer methods for sampling from gamma, beta, Poisson, and binomial distributions. Computing 12: 223-246.
2. ARIS-BROSOU, S., and L. EXCOFFIER, 1996 The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Mol. Biol. Evol. 13: 494-504.
3. BERTORELLE, G., and M. SLATKIN, 1995 The number of segregating sites in expanding human populations, with implications for estimates of demographic parameters. Mol. Biol. Evol. 12: 887-892.
4. CORNUET, J. M., and G. LUIKART, 1996 Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
5. DONNELLY, P., and S. TAVARÉ, 1997 Progress in Population Genetics and Human Evolution. Springer-Verlag, New York.
6. EFRON, B., and R. J. TIBSHIRANI, 1993 An Introduction to the Bootstrap. Chapman and Hall, London.
7. FU, Y.-X., 1997 Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
8. FU, Y. X., and W. H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
9. GRAVEN, L., G. PASSARINO, O. SEMINO, P. BOURSOT, A. S. SANTACHIARA-BENERECETTI et al., 1995 Evolutionary correlation between control region sequence and RFLP diversity pattern in the mitochondrial genome of a Senegalese sample. Mol. Biol. Evol. 12: 334-345.
10. GRIFFITHS, R. C., and S. TAVARÉ, 1994 Ancestral inference in population genetics. Stat. Sci. 9: 307-319.
11. HANDT, O., S. MEYER and A. VON HAESELER, 1998 Compilation of human mtDNA control region sequences. Nucleic Acids Res. 26: 126-129.
12. HARPENDING, H. C., M. A. BATZER, M. GURVEN, L. B. JORDE, A. R. ROGERS et al., 1998 Genetic traces of ancient demography. Proc. Natl. Acad. Sci. USA 95: 1961-1967.
13. HASEGAWA, M., A. DIRIENZO, T. D. KOCHER and A. C. WILSON, 1993 Toward a more accurate time scale for the human mitochondrial DNA tree. J. Mol. Evol. 37: 347-354.
14. HOOKE, R., and T. A. JEEVES, 1963 "Direct search" solution of numerical and statistical problem. J. Assoc. Comput. Machinery 8: 212-229.
15. HOWELL, N., I. KUBACHA and D. A. MACKEY, 1996 How rapidly does the human mitochondrial genome evolve? Am. J. Hum. Genet. 59: 501-509.
16. HUDSON, R. R., 1990 Gene genealogies and the coalescent process, pp. 1-44 in Oxford Surveys in Evolutionary Biology, edited by D. J. FUTUYMA and J. D. ANTONOVICS. Oxford University Press, New York.
17. JAZIN, E., H. SOODYALL, P. JALONEN, E. LINDHOLM, M. STONEKING et al., 1998 Mitochondrial mutation rate revisited: hot spots and polymorphism. Nat. Genet. 18: 109-110.
18. KIMURA, M., 1969 The number of heterozygous nucleotide sites maintained in a finite population due to the steady flux of mutations. Genetics 61: 893-903.
19. KIMURA, M., 1980 A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
20. KINGMAN, J. F. C., 1982 The coalescent. Stochastic Process. Appl. 13: 235-248.
21. KOCHER, T. D., and A. C. WILSON, 1991 Sequence evolution of mitochondrial DNA in humans and chimpanzees: control region and protein-coding region, pp. 391-413 in Evolution of Life: Fossils, Molecules and Culture, edited by S. OSAWA and T. HONJO. Springer-Verlag, Tokyo.
22. KOLMAN, C. J., E. BERMINGHAM, R. COOKE, R. H. WARD, T. D. ARIAS et al., 1995 Reduced mtDNA diversity in the Ngobe Amerinds of Panama. Genetics 140: 275-283.
23. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1995 Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
24. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1998 Maximum-likelihood estimation of population growth rates based on the coalescent. Genetics 149: 429-434.
25. LI, W. H., 1977 Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics 85: 331-337.
26. LUNDSTROM, R., S. TAVARÉ and R. H. WARD, 1992 Modeling the evolution of the human mitochondrial genome. Math. Biosci. 112: 319-335.
27. MEYER, S., G. WEISS and A. VON HAESELER, 1999 Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 152: 1103-1110.
28. PARSONS, T. J., and M. M. HOLLAND, 1998 Reply to Jazin et al. Nat. Genet. 18: 110.
29. PARSONS, T. J., D. S. MUNIEC, K. SULLIVAN, N. WOODYATT, R. ALLISTON-GREINER et al., 1997 A high observed substitution rate in the human mitochondrial DNA control region. Nat. Genet. 15: 363-368.
30. PIERCY, R., K. M. SULLIVAN, N. BENSON and P. GILL, 1995 The application of mitochondrial DNA typing to the study of white Caucasian genetic identification. Int. J. Legal. Med. 106: 85-90.
31. POLANSKI, A., M. KIMMEL and R. CHAKRABORTY, 1998 Application of a time-dependent coalescence process for inferring the history of population size changes from DNA sequence data. Proc. Natl. Acad. Sci. USA 95: 5456-5461.
32. RICE, J. A., 1995 Mathematical Statistics and Data Analysis. Duxburry Press, Belmont, CA.
33. ROGERS, A., 1992 Error introduced by the infinite-sites model. Mol. Biol. Evol. 9: 1181-1184.
34. ROGERS, A., 1995 Genetic evidence for a Pleistocene population explosion. Evolution 49: 608-615.
35. ROGERS, A. R., 1997 Population structure and modern humans origins, pp. 55-79 in Progress in Population Genetics and Human Evolution, edited by P. DONNELLY and S. TAVARÉ. Springer-Verlag, New York.
36. ROGERS, A. R., and H. HARPENDING, 1992 Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9: 552-569.
37. ROGERS, A. R., A. E. FRALEY, M. J. BAMSHAD, W. S. WATKINS and L. B. JORDE, 1996 Mitochondrial mismatch analysis is insensitive to the mutational process. Mol. Biol. Evol. 13: 895-902.
38. SLATKIN, M., 1994 Linkage disequilibrium in growing and stable populations. Genetics 137: 331-336.
39. SLATKIN, M., and R. R. HUDSON, 1991 Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
40. TAJIMA, F., 1989 The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
41. TAJIMA, F., 1993 Measurement of DNA polymorphism, pp. 37-59 in Mechanisms of Molecular Evolution. Introduction to Molecular Paleopopulation Biology, edited by N. TAKAHATA and A. G. CLARK. Japan Scientific Societies Press, Sinauer Associates, Tokyo/Sunderland, MA.
42. TAJIMA, F., 1996 The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites. Genetics 143: 1457-1465.
43. TAVARÉ, S., D. BALDING, R. C. GRIFFITHS and P. DONNELY, 1997 Inferring coalescence times from DNA sequence data. Genetics 145: 505-518.
44. VIGILANT, L., M. STONEKING, H. HARPENDING, K. HAWKES and A. C. WILSON, 1991 African populations and the evolution of mitochondrial DNA. Science 253: 1503-1507.
45. WAKELEY, J., 1993 Substitution rate variation among sites in hypervariable region I of human mitochondrial DNA. J. Mol. Evol. 37: 613-623.
46. WAKELEY, J., and J. HEY, 1997 Estimating ancestral population parameters. Genetics 145: 847-855.
47. WATSON, E., K. BAUER, R. AMAN, G. WEISS, A. VON HAESELER et al., 1996 mtDNA sequence diversity in Africa. Am. J. Hum. Genet. 59: 437-444.
48. WATTERSON, G., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
49. WEISS, G., and A. VON HAESELER, 1998 Inference of population history using a likelihood approach. Genetics 149: 1539-1546.
50. YANG, Z., 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39: 306-341.
51. YANG, Z., 1996 Statistical properties of a DNA sample under the finite-sites model. Genetics 144: 1941-1950.
52. YANG, Z., S. KUMAR and M. NEI, 1995 A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141: 1641-1650.