Inferring the mode of speciation from genomic data: A study of the great apes

Genetics

Volumn 169, Issue 1, 2005, Pages 259-264

  Osada, Naoki ^a   Wu, Chung I ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ALLOPATRY; APE; ARTICLE; CHIMPANZEE; CONTROLLED STUDY; DNA SEQUENCE; GENE SEQUENCE; GENETIC VARIABILITY; NONHUMAN; PREVALENCE; PRIORITY JOURNAL; SPECIES DIFFERENTIATION;

ANIMALS; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENOME; GORILLA GORILLA; HUMANS; OPEN READING FRAMES; PAN TROGLODYTES; TIME; VARIATION (GENETICS);

ALOCASIA MACRORRHIZOS; PAN TROGLODYTES;

EID: 13744253303     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.029231     Document Type: Article

References (31)

1. BUTLIN, R., 1998 What do hybrid zones in general, and the Chorthippus parallelus Zone in particular, tell us about speciation?, pp. 367-378 in Endless Forms: Species and Speciation, edited by D. HOWARD and S. BERLOCHERS. Oxford University Press, Oxford.
2. 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.
3. CLARK, A. G., S. GLANOWSKI, R. NIELSEN, P. D. THOMAS, A. KEJARIWAL et al., 2003 Inferring nonneutral evolution from human-chimpmouse orthologous gene trios. Science 302: 1960-1963.
4. COYNE, J., and T. D. PRICE, 2000 Little evidence for sympatric speciation in island birds. Evolution 54: 2166-2171.
5. DIECKMANN, U., and M. DOEBELI, 1999 On the origin of species by sympatric speciation. Nature 400: 354-357.
6. ENDLER, J. A., 1977 Geographic variation, speciation, and clines. Monogr. Popul. Biol. 10: 1-246.
7. HELLMANN, I., S. ZOLLNER, W. ENARD, I. EBERSBERGER, B. NICKEL et al., 2003 Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13: 831-837.
8. KIMURA, M., 1980 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
9. KLIMAN, R. M., P. ANDOLFATTO, J. A. COYNE, F. DEPAULIS, M. KREITMAN et al., 2000 The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156: 1913-1921.
10. KONDRASHOV, S., and F. A. KONDRASHOV, 1999 Interactions among quantitative traits in the course of sympatric speciation. Nature 400: 351-354.
11. LEAKEY, M. G., F. SPOOR, F. H. BROWN, P. N. GATHOGO, C. KIARIE et al., 2001 New hominin genus from eastern Africa shows diverse middle Pliocene lineages. Nature 410: 433-440.
12. LI, W.-H., 1993 Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
13. LU, J., W.-H. LI and C.-I WU, 2003 Comment on chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes. Science 302: 988.
14. MACHADO, C. A., R. M. KLIMAN, J. A. MARKERT and J. HEY, 2002 Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Mol. Biol. Evol. 19: 472-488.
15. MAYR, E., 1963 Animal Species and Evolution. Belknap Press, Cambridge, MA.
16. NAVARRO, A., and N. H. BARTON, 2003 Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes. Science 300: 321-324.
17. NAVARRO, A., T. MARQUES-BONET and N. H. BARTON, 2003 Response to comment on chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes. Science 302: 988.
18. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
19. PAMILO, P., and N. O. BIANCHI, 1993 Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol. Biol. Evol. 10: 271-281.
20. PLUZHNIKOV, A., A. D. RIENZO and R. R. HUDSON, 2002 Inferences about human demography based on multilocus analyses of noncoding sequences. Genetics 161: 1209-1218.
21. RUVOLO, M., 1997 Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets. Mol. Biol. Evol. 14: 248-265.
22. SAKATE, R., N. OSADA, M. HIDA, S. SUGANO, I. HAYASAKA et al., 2003 Analysis of 5′-end sequences of chimpanzee cDNAs. Genome Res. 13: 1022-1026.
23. SATTA, Y., H. KUPFERMANN, Y. J. LI and N. TAKAHATA, 1999 Molecular clock and recombination in primate Mhc genes. Immunol. Rev. 167: 367-379.
24. TING, T., S. C. TSAUR and C.-I WU, 2000 The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus. Proc. Natl. Acad. Sci. USA 97: 5313-5316.
25. 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.
26. THOMPSON, J. D., D. G. HIGGINS and T. J. GIBSON, 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
27. WAKELEY, J., and J. HEY, 1997 Estimating ancestral population parameters. Genetics 145: 847-855.
28. WALL, J. D., 2003 Estimating ancestral population sizes and divergence times. Genetics 163: 395-404.
29. WU, C.-I, 1991 Inferences of species phylogeny in relation to segregation of ancient polymorphism. Genetics 127: 429-435.
30. WU, C.-I, and C. T. TING, 2004 Genes and speciation. Nat. Rev. Genet. 5: 114-122.
31. YANG, Z., 2002 Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162: 1811-1823.