Divergence population genetics of chimpanzees

Molecular Biology and Evolution

Volumn 22, Issue 2, 2005, Pages 297-307

  Won, Yong Jin ^a   Hey, Jody ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Bonobo; Chimpanzee; Gene flow; Markov chain Monte Carlo; Speciation

Indexed keywords

ARTICLE; CHIMPANZEE; CONTROLLED STUDY; DNA SEQUENCE; EFFECTIVE POPULATION SIZE; GENE LOCUS; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PROBABILITY;

ANIMALS; EVOLUTION, MOLECULAR; GENETICS, POPULATION; PAN TROGLODYTES; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

EID: 12344265079     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi017     Document Type: Article

References (50)

1. Baum, D. A. 1998. Individuality and the existence of species in time. Syst. Biol. 47:641-653.
2. Beadle, L. C. 1981. The inland waters of tropical Africa. Longman, London.
3. Boesch, C., and H. Boesch-Achermann. 2000. The Chimpanzees of the Taï forest. Oxford University Press, Oxford.
4. Bradley, B. J., and L. Vigilant. 2002. The evolutionary genetics and molecular ecology of chimpanzees and bonobos. Pp. 259-275 in C. Boesch, G. Hohmann, and L. F. Marchant, eds. Behavioural diversity in chimpanzees and bonobos. Cambridge University Press, Cambridge.
5. Brunet, M., F. Guy, D. Pilbeam et al. (38 co-authors). 2002. A new hominid from the Upper Miocene of Chad, Central Africa. Nature 418:145-151.
6. 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.
7. Clark, A. G. 1990. Inference of haplotypes of PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7:111-122.
8. Constable, J. L., M. V. Ashley, J. Goodall, and A. E. Pusey. 2001. Noninvasive paternity assignment in Gombe chimpanzees. Mol. Ecol. 10:1279-1300.
9. Deinard, A. S., and K. Kidd. 1999. Evolution of a HOXB6 intergenic region within the great apes and humans. J. Hum. Evol. 36:687-703.
10. -. 2000. Identifying conservation units within captive chimpanzee populations. Am. J. Phys. Antnropol. 111: 25-44.
11. Dobzhansky, T. 1937. Genetics and the origin of species. Columbia University Press, New York.
12. Fischer, A., V. Wiebe, S. Paabo, and M. Przeworski. 2004. Evidence for a complex demographic history of chimpanzees. Mol. Biol. Evol. 21:799-808.
13. Gagneux, P., M. K. Gonder, T. L. Goldberg, and P. A. Morin. 2001. Gene flow in wild chimpanzee populations: what genetic data tell us about chimpanzee movement over space and time. Philos. Trans. R. Soc. Lond. B Biol. Sci. 356: 889-897.
14. Gagneux, P., and A. Varki. 2001. Genetic differences between humans and great apes. Mol. Phylogenet. Evol. 18:2-13.
15. Gagneux, P., C. Wills, U. Gerloff, D. Tautz, P. A. Morin, C. Boesch, B. Fruth, G. Hohmann, O. A. Ryder, and D. S. Woodruff. 1999. Mitochondrial sequences show diverse evolutionary histories of African hominoids. Proc. Natl. Acad. Sci. USA 96:5077-5082.
16. Geyer, C. J. 1992. Practical Markov chain Monte Carlo. Stat. Sci. 7:473-511.
17. Glazko, G. V., and M. Nei. 2003. Estimation of divergence times for major lineages of primate species. Mol. Biol. Evol. 20:424-434.
18. Goldberg, T. L., and M. Ruvolo. 1997. The geographic apportionment of mitochondrial genetic diversity in east African chimpanzees, Pan troglodytes schweinfurthii. Mol. Biol. Evol. 14:976-984.
19. Gonder, M. K. 2000. Evolutionary genetics of chimpanzees in Nigeria and Cameroon. Doctoral dissertation, City University of New York, New York.
20. Gonder, M. K., J. F. Oates, T. R. Disotell, M. R. Forstner, J. C. Morales, and D. J. Melnick. 1997. A new west African chimpanzee subspecies? Nature 388:337.
21. Goodall, J. 1986. The chimpanzees of Gombe. Harvard University Press, Cambridge, Mass.
22. Groves, C. 2001. Primate taxonomy. Smithsonian Institution Press, Washington, DC.
23. Grubb, P. 1982. Refuges and dispersal in the speciation of African forest mammals. Pp. 537-553 in G. T. Prance, ed. Biological diversification in the tropics. Academic Press, New York.
24. Hamilton, A. C. 1988. Guenon evolution and forest history. Pp. 13-34 in A. Gautier-Hion, F. Bourlière, and J.-P. Gautier, eds. A primate radiation: evolutionary biology of the African guenons. Cambridge University Press, Cambridge.
25. Hey, J., and R. Nielsen. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760.
26. Hey, J., R. S. Waples, M. L. Arnold, R. K. Butlin, and R. G. Harrison. 2003. Understanding and confronting species uncertainty in biology and conservation. Trends Ecol. Evol. 18:597-603.
27. Hill, W. C. O. 1969. The nomenclature, taxonomy and distribution of chimpanzees. Pp. 22-49 in G. H. Bourne, ed. The chimpanzee. Karger, New York.
28. Hudson, R. R., and N. L. Kaplan. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147-164.
29. Irwin, D. M., T. D. Kocher, and A. C. Wilson. 1991. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32: 128-144.
30. Kaessmann, H., V. Wiebe, and S. Paabo. 1999. Extensive nuclear DNA sequence diversity among chimpanzees. Science 286:1159-1162.
31. Kaessmann, H., V. Wiebe, G. Weiss, and S. Paabo. 2001. Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat. Genet. 27:155-156.
32. Kortlandt, A. 1983. Marginal habitats of chimpanzees. J. Hum. Evol. 12:231-278.
33. Mayr, E. 1942. Systematics and the origin of species. Columbia University Press, New York.
34. Morin, P. A., J. J. Moore, R. Chakraborty, L. Jin, J. Goodall, and D. S. Woodruff. 1994. Kin selection, social structure, gene flow, and the evolution of chimpanzees. Science 265: 1193-1201.
35. Morin, P. A., J. J. Moore, and D. S. Woodruff. 1992. Identification of chimpanzee subspecies with DNA from hair and allele-specific probes. Proc. R. Soc. Lond. B Biol. Sci. 249: 293-297.
36. Nielsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885-896.
37. Ruvolo, M., D. Pan, S. Zehr, T. Goldberg, T. R. Disotell, and M. vonDornum. 1994. Gene trees and homioid phylogeny. Proc. Natl. Acad. Sci. USA 91:8900-8904.
38. Schwartz, E. 1934. On the local races of the chimpanzee. Ann. Mag. Nat. Hist. Lond. 13:576-583.
39. Shea, B. T., and H. J. Coolidge. 1988. Craniometric differentiation and systematics in the genus Pan. J. Hum. Evol. 17: 671-685.
40. Stein, R., and M. Sarnthein. 1984. Late Neogene events of atmospheric and oceanic circulation offshore Northwest Africa: high resolution record from deep-sea sediments. Palaeoecol. Africa 16:9-36.
41. Stone, A. C., R. C. Griffiths, S. L. Zegura, and M. F. Hammer. 2002. High levels of Y-chromosome nucleotide diversity in the genus Pan. Proc. Natl. Acad. Sci. USA 99:43-48.
42. Tajima, F. 1983. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
43. -. 1989. Evolutionary relationships of DNA sequences in finite populations. Genetics 105:437-460.
44. Vigilant, L., M. Hofreiter, H. Siedel, and C. Boesch. 2001. Paternity and relatedness in wild chimpanzee communities. Proc. Natl. Acad. Sci. USA 98:12890-12895.
45. Vignaud, P., P. Duringer, H. T. Mackaye et al. (21 co-authors). 2002. Geology and palaeontology of the Upper Miocene Toros-Menalla hominid locality, Chad. Nature 418:152-155.
46. Wagner, M. 1889. Die Entstehung der Arten durch räumliche Sonderung. Benno Schwalbe, Basel, Switzerland.
47. Wakeley, J., and J. Key. 1997. Estimating ancestral population parameters. Genetics 145:847-855.
48. Wang, R. L., J. Wakeley, and J. Hey. 1997. Gene flow and natural selection in the origin of Drosophila pseudoobscura and close relatives. Genetics 147:1091-1106.
49. Wildman, D. E., M. Uddin, G. Liu, L. I. Grossman, and M. Goodman. 2003. Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo. Proc. Natl. Acad. Sci. 100:7181-7188.
50. Yu, N., M. I. Jensen-Seaman, L. Chemnick, J. R. Kidd, A. S. Deinard, O. Ryder, K. K. Kidd, and W. H. Li. 2003. Low nucleotide diversity in chimpanzees and bonobos. Genetics 164:1511-1518.