The age of the common ancestor of eukaryotes and prokaryotes: Statistical inferences

Molecular Biology and Evolution

Volumn 14, Issue 8, 1997, Pages 861-866

  Gu, Xun ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Common ancestor; Evolutionary distance; Gamma distribution; Rate variation; Substitution patterns

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; EUKARYOTE; EVOLUTION; GENE MUTATION; GENETIC VARIABILITY; NONHUMAN; PROKARYOTE; SPECIES DIFFERENTIATION;

EUKARYOTA; PROKARYOTA;

EID: 0030857505     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025827     Document Type: Article

References (37)

1. BULMER, M. 1991. Use of the method of generalized least squares in reconstructing phylogenies from sequence data. Mol. Biol. Evol. 8:868-883.
2. DAYHOFF, M. O., R. M. SCHWARTZ, and B. C. ORCUTT. 1978. A model of evolutionary changes in protein S. Pp. 345-352 in Atlas of protein sequence and structure. Vol. 5, Suppl. 3. Natural Biomedical Research Foundation, Washington, D.C.
3. DOOLITTLE, R. F., D. F. FENG, S. TSANG, G. CHO, and E. LITTLE. 1996a. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470-477.
4. _. 1996b. Dating the Cenancester of organisms. Science 274:1751-1753.
5. GOGARTEN, J. P., L. OLENDZENSKI, E. HILARIO, C. SIMON, and K. E. HOLSINGER. 1996. Dating the Cenancester of organisms. Science 274:1751-1753.
6. GU, X. 1996. Models of DNA sequence evolution. Ph.D dissertation. Graduate School of Biomedical Sciences, University of Texas at Houston.
7. Gu, X., Y. X. Fu, and W. H. LI. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557.
8. Gu, X., and W. H. LI. 1992. Higher rates of amino acid substitution in rodents than in human. Mol. Phylogenet. Evol. 1:211-214.
9. GU, X., and W. H. LI. 1996. A general additive distance with time-reversibility and rate variation among nucleotide sites. Proc. Natl. Acad. Sci. USA 93:4671-4676.
10. HASEGAWA, M., and W. M. FITCH. 1996. Dating the Cenancester of organisms. Science 274:1751-1753.
11. HEDGES, S. B., P. H. PARKER, C. G. SIBLEY, and S. KUMAR. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-229.
12. HIGGINES, D. G., A. J. BLEASBY, and R. FUCHS. 1992. CLUSTALV: improved software for multiple sequence alignment. Comput. Appl. Biosci. Comm. 8:189-191.
13. HOLMQUIST, R. M., M. GOODMAN, T. CONROY, and J. CZELUSNIAK. 1983. The spatial distribution of fixed mutations within genes coding for proteins. J. Mol. Evol. 19:437-448.
14. HORI, H., and S. OSAWA. 1979. Evolutionary changes in 5S RNA secondary structure and a phylogenetic tree of 54 5S RNA species. Proc. Natl. Acad. Sci. USA 76:381-385.
15. JIN, L., and M. NEI. 1990. Limitations of the evolutionary parsimony model of phylogenetic analysis. Mol. Biol. Evol. 7:82-102.
16. JONES, D. T., W. R. TAYLOR, and J. M. THORNTON. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
17. KIMURA, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge.
18. MCLAUGHLIN, P. J., and M. O. DAYHOFF. 1972. Evolution of species and proteins: a time scale. Pp. 47-52 in Atlas of protein sequence and structure. Natural Biomedical Research Foundation, Washington, D.C.
19. MIYAMOTO, M. M., and W. M. FITCH. 1996. Constraints on protein evolution and the age of the eubacteria/eukaryote split. Syst. Biol. 45:568-575.
20. MOOERS, A., and R. J. REDFIELD. 1996. Digging up the roots of life. Nature 379:587-588.
21. MORELL, V. 1996. Proteins 'clock' the origins of all creatures - great and small. Science 271:448.
22. NEI, M. 1987. Molecular evolutipnary genetics, Columbia University Press, New York.
23. NEI, M., R. CHAKRABORTY, and P. A. FUERST. 1976. Infinite allele model with varying mutation rate. Proc. Natl. Acad. Sci. USA 73:4164-4168.
24. OTA, T., and M. NEI. 1994. Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J. Mol. Evol. 38:642-643.
25. Russo, C. A., M. N. TAKEZAKI, and M. NET. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13:525-536.
26. RZHETSKY, A., and M. NEI. 1994. Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites. J. Mol. Evol. 38:295-299.
27. SULLIVAN, J. K., K. E. HOLSINGER, and C. SIMON. 1995. Among-site rate variation and phylogenetic analysis of 12S rRNA in Sigmontine rodents. Mol. Biol. Evol. 12:988-1001.
28. TAKEZAKI, N., A. RZHETSKY, and M. NEI. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
29. TAMURA, K., and M. NEI. 1993. Estimation of the number of nucleotide substitutions in the control of mitochondrial DNA in human and chimpanzees. Mol. Biol. Evol. 10:512-526.
30. UZZEL, T., and K. W. CORBIN. 1971. Fitting discrete probability distribution to evolutionary events. Science 172:1089-1096.
31. WAKELEY, J. 1993. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37:613-623.
32. WRAY, G. A., J. S. LEVINTON, and L. H. SHAPIRO. 1996. Molecular evidence for deep precambrian divergences among metazoan phyla. Science 274:568-573.
33. Wu, C. I., and W. H. LI. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82:1741-1745.
34. YANG, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
35. YANG, Z., and S. KUMAR. 1996. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol. Biol. Evol. 13:650-659.
36. ZHARKIKH, A. 1994. Comparison of methods of estimation of evolutionary distance between nucleotide sequences. J. Mol. Evol. 39:315-329.
37. ZUCKERKANDL, E., and L. PAULING. 1965. Evolutionary divergence and convergence in proteins. Pp. 97-166 in V. BRYSON and H. J. VOGEL, eds. Evolving genes and proteins. Academic Press, New York.