Inference of population history using a likelihood approach

Genetics

Volumn 149, Issue 3, 1998, Pages 1539-1546

  Weiss, Gunter ^a   Von Haeseler, Arndt ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; DNA SEQUENCE; GENETIC MODEL; MOLECULAR EVOLUTION; POPULATION GENETICS; PRIORITY JOURNAL; STOCHASTIC MODEL;

EID: 0031827528     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (52)

1. ANDERSON, S., A. T. BANKIER, B. G. BARELL, M. H. L. DE BRUIJN, A. R. COULSON et al., 1981 Sequence and organization of the human mitochondrial genome. Nature 290: 457-465.
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. BANDELT, H. J., P. FORSTER, B. C. SYKES and M. B. RICHARDS, 1995 Mitochondrial portraits of human populations using median networks. Genetics 141: 743-753.
4. 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.
5. BERTRANPETIT, J., J. SALA, F. CALAFELL, P. A. UNDERHILL, P. MORAL, et al., 1995 Human mitochondrial DNA variation and the origin of Basques. Am. J. Hum. Genet. 59: 63-81.
6. CAVALLI-SFORZA, L. L., P. MENOZZI and A. PIAZZA, 1994 The History and Geography of Human Genes. Princeton University Press, Princeton.
7. COX, D. R., 1961 Tests of separate families of hypotheses. Proc. 4th Berkeley Symp. (Univ. California Press) 1: 105-123.
8. COX, D. R., 1962 Further results on tests of separate families of hypotheses. J. R. Stat. Soc. B 24: 406-424.
9. DONNELLY, P., and S. TAVARÉ, 1995 Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 29: 401-421.
10. FISHER, R. A., 1930 The Genetical Theory of Natural Selection. Clarendon, Oxford.
11. FU, Y.-X., 1996a New statistical tests of neutrality for DNA samples from a population. Genetics 143: 557-570.
12. FU, Y.-X., 1996b Estimating the age of the common ancestor of a DNA sample using the number of segregating sites. Genetics 144: 829-838.
13. GOLDMAN, N., 1993 Statistical tests of models of DNA substitution. J. Mol. Evol. 36: 182-198.
14. GRIFFITHS, R. C., and S. TAVARÉ, 1994a Simulating probability distributions in the coalescent. Theor. Popul. Biol. 46: 131-159.
15. GRIFFITHS, R. C., and S. TAVARÉ, 1994b Sampling theory for neutral alleles in a varying environment. Phil. Trans. R. Soc. Lond. B 344: 403-410.
16. GRIFFITHS, R. C., and S. TAVARÉ, 1994c Ancestral inference in population genetics. Stat. Sci. 9: 307-319.
17. HANDT, O., S. MEYER and A. VON HAESELER, 1998 Compilation of human mtDNA control region sequences. Nucleic Acids Res. 26: 126-130.
18. HASEGAWA, M., H. KISHINO and K. YANO, 1985 Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
19. HASEGAWA, M., A. DI RIENZO, 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.
20. HORAI, S., and K. HAYASAKA, 1990 Intraspecific nucleotide sequence differences in the major noncoding region of human mitochondrial DNA. Am. J. Hum. Genet. 46: 828-842.
21. HUDSON, R. R., 1991 Gene genealogies and the coalescent process, pp. 1-44 in Oxford Surveys in Evolutionary Biology, edited by D. FUTUYAMA and J. ANTONOVICS. Oxford University Press, Oxford.
22. JUKES, T. H., and C. R. CANTOR, 1969 Evolution of protein molecules, pp. 21-132 in Mammalian Protein Metabolism, edited by H. N. MUNRO. Academic Press, New York.
23. KIMURA, M., 1980 A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
24. KINGMAN, J. F. C., 1982a The coalescent. Stoch. Proc. Applns. 13: 235-248.
25. KINGMAN, J. F. C., 1982b On the genealogy of large populations. J. Appl. Probab. 19A: 27-43.
26. KINGMAN, J. F. C., 1982c Exchangeability and the evolution of large populations, pp. 97-112 in Exchangeability in Probability and Statistics, edited by G. KOCH and F. SPIZZICHINO. North-Holland Publishing Company, Amsterdam.
27. KOCHER, T. D., and A. C. WILSON, 1991 Sequence evolution of mitochondrial DNA in humans and chimpanzees: control region and protein coding regions, pp. 391-413 in Evolution of Life: Fossils, Molecules and Culture, edited by S. OSAWA and T. HONIO. Springer Verlag, Tokyo.
28. KOGELNIK, A. M., M. T. LOTT, M. D. BROWN, S. B. NAVATHE and D. C. WALLACE, 1997 MITOMAP: an update on the status of the human mitochondrial genome database. Nucleic Acids Res. 25: 196-199.
29. LUNDSTROM, R., S. TAVARÉ and R. H. WARD, 1992a Modelling the evolution of the human mitochondrial genome. Math. Biosci. 112: 319-335.
30. LUNDSTROM, R., S. TAVARÉ and R. H. WARD, 1992b Estimating substitution rates from molecular data using the coalescent. Proc. Natl. Acad. Sci. 89: 5961-5965.
31. MARJORAM, P., and P. DONNELLY, 1993 Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics 136: 673-683.
32. RAMBAUT, A., and N. C. GRASSLY, 1997 Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13: 235-238.
33. ROGERS, A. R., 1992 Error introduced by the infinite sites model. Mol. Biol. Evol. 9: 1181-1184.
34. ROGERS, A. R., 1995 Genetic evidence for a pleistocene population explosion. Evolution 49: 608-615.
35. 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.
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. SLATKIN, M., and R. R. HUDSON, 1991 Pairwise comparison of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
38. STRIMMER, K., and A. VON HAESELER, 1996 Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969.
39. TAJIMA, F., 1983 Evolutionary relationships of DNA sequences in finite populations. Genetics 105: 437-460.
40. TAJIMA, F., 1989a Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
41. TAJIMA, F., 1989b The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
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. TAMURA, K., and M. NEI, 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
44. TAVARÉ, S., 1984 Line-of-descent and genealogical processes, and their applications in population genetics models. Theor. Pop. Biol. 26: 119-164.
45. TAVARÉ, S., D. J. BALDING, R. C. GRIFFITHS and P. DONNELLY, 1997 Inferring coalescence times from DNA sequence data. Genetics 145: 505-518.
46. UZZEL, T., and K. W. CORBIN, 1971 Fitting discrete probability distributions to evolutionary events. Science 172: 1089-1096.
47. 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.
48. WAKELEY, J., 1993 Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37: 613-623.
49. WAKELEY, J., and J. HEY, 1997 Estimating ancestral population parameters. Genetics 145: 847-855.
50. WARD, R. H., B. L. FRAZIER, K. DEW-JAGER and S. PÄÄBO, 1991 Extensive mitochondrial diversity within a single Amerindian tribe. Nat. Acad. Sci. 88: 8720-8724.
51. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Pop. Biol. 7: 256-276.
52. WRIGHT, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.