Estimating ancestral population sizes and divergence times

Genetics

Volumn 163, Issue 1, 2003, Pages 395-404

  Wall, Jeffrey D ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APE; ARTICLE; CHIMPANZEE; CONTROLLED STUDY; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC RECOMBINATION; GENETIC VARIABILITY; HUMAN; INFORMATION PROCESSING; NONHUMAN; POPULATION SIZE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES DIVERSITY;

ANIMALS; DATA INTERPRETATION, STATISTICAL; EVOLUTION; HUMANS; LIKELIHOOD FUNCTIONS; POPULATION; TIME FACTORS;

ALOCASIA MACRORRHIZOS; PAN TROGLODYTES;

EID: 0037277564     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (57)

1. BRUNET, M., F. GUY, D. PILBEAM, H. T. MACKAYE, A. LIKIUS et al., 2002 A new hominid from the Upper Miocene of Chad, Central Africa. Nature 418: 145-151.
2. CABALLERO, A., 1994 Developments in the prediction of effective population size. Heredity 73: 657-679.
3. CHEN, F.-C., and W.-H. LI, 2001 Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68: 444-456.
4. DEINARD, A., and K. KIDD, 1999 Evolution of a HOXB6 intergenic region within the great apes and humans. J. Hum. Evol. 36: 687-703.
5. EASTEAL, S., and G. HERBERT, 1997 Molecular evidence from the nuclear genome for the time frame of human evolution. J. Mol. Evol. 44: S121-S132.
6. EBERSBERGER, L., D. METZLER, C. SCHWARZ and S. PÄÄBO, 2001 Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70: 1490-1497.
7. EYRE-WALKER, A., and P. D. KEIGHTLEY, 1999 High genomic deleterious mutation rates in hominids. Nature 397: 344-347.
8. FEARNHEAD, P., and P. DONNELLY, 2002 Approximate likelihood methods for estimating local recombination rates. J. R. Stat. Soc. B 64: 657-680.
9. FRISSE, L., R. R. HUDSON, A. BARTOSZEWICZ, J. D. WALL, J. DONFACK et al., 2001 Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet. 69: 831-843.
10. GABUNIA, L., and A. VEKUA, 1995 A Plio-Pleistocene hominid from Dmanisi, East Georgia, Caucasus. Nature 373: 509-512.
11. GIANNELLI, F., T. ANAGNOSTOPOLOUS and P. M. GREEN, 1999 Mutation rates in humans. II. Sporadic mutation-specific rates and rate of detrimental human mutations inferred from hemophilia B. Am. J. Hum. Genet. 65: 1580-1587.
12. HAILE-SELASSIE, Y., 2001 Late Miocene hominids from the Middle Awash, Ethiopia. Nature 412: 178-181.
13. HARADA, K., S. KUSAKABE, T. YAMAZAKI and T. MUKAI, 1993 Spontaneous mutation rates in null and band-morph mutations of enzyme loci in Drosophila melanogaster. Jpn. J. Genet. 68: 605-616.
14. HARDING, R. M., S. M. FULLERTON, R. C. GRIFFITHS, J. BOND, M. J. COX et al., 1997 Archaic African and Asian lineages in the genetic ancestry of modern humans. Am. J. Hum. Genet. 60: 772-789.
15. HEY, J., 1994 Bridging phylogenetics and population genetics with gene tree models, pp. 435-449 in Molecular Ecology and Evolution: Approaches and Applications, edited by B. SCHIERWATER, B. STREIT, G. P. WAGNER and R. DESALLE. Birkhãuser Verlag, Basel, Switzerland.
16. 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. Proc. Nad. Acad. Sci. USA 92: 532-536.
17. HUDSON, R. R., 1983 Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23: 183-201.
18. HUDSON, R. R., 1992 Gene trees, species trees and the segregation of ancestral alleles. Genetics 131: 509-512.
19. JONES, P. A., W. M. RIDEOUT, J. C. SHEN, C. H. SPRUCK and Y. C. TSAI, 1992 Methylation, mutation and cancer. Bioessays 14: 33-36.
20. KAESSMANN, H., V. WIEBE and S. PÄÄBO, 1999 Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159-1161.
21. KAESSMANN, H., V. WIEBE, G. WEISS and S. PÄÄBO, 2001 Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat. Genet. 27: 155-156.
22. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
23. KRAWCZAK, M., and D.N. COOPER, 1991 Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environment. Hum. Genet. 86: 425-441.
24. KREITMAN, M., 1983 Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304: 412-417.
25. KUMAR, S., and B. HEDGES, 1998 A molecular timescale for vertebrate evolution. Nature 392: 917-920.
26. KUMAR, S., and S. SUBRAMANIAN, 2002 Mutation rates in mammalian genomes. Proc. Natl. Acad. Sci. USA 99: 803-808.
27. LEAKEY, M. G., C. S. FEIBEI., I. MCDOUGALI, and A. WALKER, 1995 New four-million-year-old hominid species from Kanapoi and Allia Bay, Kenya, Nature 376: 565-571.
28. NACHMAN, M. W., and S. L. CROWELL, 2000 Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297-304.
29. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
30. NIELSEN, R., and J. WAKELEY, 2001 Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158: 885-896.
31. NORDBORG, M., 2001 Coalescent theory, pp. 179-212 in Handbook of Statistical Genetics, edited by D. BALDING, M. BISHOP and C. CANNINGS. Wiley, Chichester, UK.
32. PRZEWORSKI, M., and J. D. WALL, 2001 Why is there so little intragenic linkage disequilibrium in humans? Genet. Res. 77: 143-151.
33. PRZEWORSKI, M., R. R. HUDSON and A. DI RIENZO, 2000 Adjusting the focus on human variation. Trends Genet. 16: 296-302.
34. RUVOLO, M., 1997 Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets. Mol. Biol. Evol. 14: 248-265.
35. SATTA, Y., C. O'HUIGIN, N. TAKAHATA and J. KLEIN, 1993 The synonymous substitution rate of the major histocompatibility complex loci in primates. Proc. Natl. Acad. Sci. USA 90: 7480-7484.
36. SATTA, Y., J. KLEIN and N. TAKAHATA, 2000 DNA archives and our nearest relative: the trichotomy problem revisited. Mol. Phylogenet. Evol. 14: 259-275.
37. SIGUROARDÓTTIR, S., A. HELGASON, J. R. GULCHER, K. STEFANSSON and P. DONNELLY, 2000 The mutation rate in the human mtDNA control region. Am. J. Hum. Genet. 66: 1599-1609.
38. SWISHER, C. C., G. H. CURTIS, T. JACOB, A. G. GETTY, A. SUPRIJO et al., 1994 Age of the earliest known hominids in Java, Indonesia. Science 263: 1118-1121.
39. TAKAHATA, N., 1986 An attempt to estimate the effective size of the ancestral species common to two extant species from which homologous genes are sequenced. Genet. Res. 48: 187-190.
40. TAKAHATA, N., 1991 Trans-species polymorphism of HLA molecules, founder principle, and human evolution, pp. 29-49 in Molecular Evolution of the Major Histocompatibility Complex, edited by J. KLEIN and D. KLEIN. Springer, Heidelberg, Germany.
41. TAKAHATA, N., 1993 Allelic genealogy and human evolution. Mol. Biol. Evol. 10: 2-22.
42. TAKAHATA, N., 2001 Molecular phylogeny and demographic history of humans, pp. 299-305 in Humanity From African Naissance to Coming Millennia - Colloquia in Human Biology and Palacoanthropology, edited by P. V. TOBIAS, M. A. RAATH, J. MOGGI-CECCHI and G. A. DOYLE. Firenze University Press, Firenze, Italy.
43. TAKAHATA, N., and Y. SATTA, 1997 Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences. Proc. Natl. Acad. Sci. USA 94: 4811-4815.
44. TAKAHATA, N., and Y. SATTA, 2002 Pre-speciation coalescence and the effective size of ancestral populations, pp, 52-71 in Modern Developments in Theoretical Population Genetics, edited by M. SLATKIN and M. VEUILLE. Oxford University Press, Oxford.
45. TAKAHATA, N., Y. SATTA and J. KLEIN, 1995 Divergence time and population size in the lineage leading to modern humans. Theor. Popul. Biol. 48: 198-221.
46. TEMPLETON, A. R., A. G. CLARK, K. M. WEISS, D. A. NICKERSON, E. BOERWINKLE et al., 2000 Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am. J. Hum. Genet. 66: 69-83.
47. TREMBLAY, M., and H. VÉZINA, 2000 New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am. J. Hum. Genet. 66: 651-658.
48. WAKELEY, J., and J. HEY, 1997 Estimating ancestral population parameters. Genetics 145: 847-855.
49. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
50. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
51. WEISS, G., and A. VON HAESELER, 1998 Inference of population history using a likelihood approach. Genetics 149: 1539-1546.
52. WHITE, T. D., G. SUWA and B. ASFAW, 1994 Australopithecus ramidus, a new species of early hominid from Aramis, Ethiopia. Nature 371: 306-312.
53. Wu, C.-I, 1991 Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127: 429-435.
54. Wu, C.-I, 2001 The genic view of the process of speciation. J. Evol. Biol. 14: 851-866.
55. YANG, Z., 1997 On the estimation of ancestral population sizes of modern humans. Genet. Res. 69: 111-116.
56. YANG, Z., 2002 Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162: 1811-1823.
57. Yu, A., C. ZHAO,Y. FAN, W. JANG, A.J. MUNGALI et al., 2001 Comparison of human genetic and sequence-based physical maps. Nature 409: 951-953.