Modeling nucleotide evolution: A heterogeneous rate analysis

Mathematical Biosciences

Volumn 133, Issue 1, 1996, Pages 85-109

  Kelly, Colleen ^a   Rice, John ^b  

^a University of Rhode Island ^*  (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE;

ARTICLE; EVOLUTION; GENETIC DISTANCE; GENETIC HETEROGENEITY; NUCLEOTIDE SEQUENCE; PROBABILITY; STATISTICAL MODEL;

EID: 0029930086     PISSN: 00255564     EISSN: None     Source Type: Journal    
DOI: 10.1016/0025-5564(95)00083-6     Document Type: Article

References (32)

1. T. H. Jukes and C. H. Cantor, Evolution of protein molecules, in Mammalian Protein Metabolism, N. H. Munro, Ed., Academic, New York, 1969, pp. 21-123.
2. T. Miyata, Evolutionary changes and functional constraints in DNA sequences, in Molecular Evolution, Protein Polymorphism and the Neutral Allele Theory, M. Kimura, Ed., Japan Scientific Press, Tokyo, 1982, pp. 233-266.
3. W. M. Fitch and E. Margoliash, A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case, Biochem. Genet. 1:65-71 (1967).
4. W. M. Fitch, The estimate of total nucleotide substitutions from pairwise differences is biased, Phil. Trans. Roy. Soc. Lond. B 312:317-324 (1986).
5. J. S. Shoemaker and W. M. Fitch, Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated, Mol. Biol. Evol. 6(3):270-289 (1989).
6. A. Sidow, T. Nguyen, and T. Speed, Estimating the fraction of invariable codons with a capture-recapture method, J. Mol. Evol. 35:253-260 (1992).
7. M. Hasegawa, H. Kishino, and T. Yano, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, J. Mol. Evol. 26:132-147 (1985).
8. G. A. Churchill, A. von Haeseler, and W. C. Navidi, Sample size for a phylogenetic inference, Mol. Biol. Evol. 9:753-769 (1992).
9. S. R. Palumbi, Rates of molecular evolution and the fraction of nucleotide positions free to vary, J. Mol. Evol. 29:180-187 (1989).
10. D. Sankoff, Designer invariants for large phylogenies, Mol. Biol. Evol. 7(3):255-269 (1990).
11. G. B. Golding, Estimates of DNA and protein sequence divergence: an examination of some assumptions, Mol. Biol. Evol. 1:125-142 (1983).
12. L. Jin and M. M. Nei, Limitations of the evolutionary parsimony method of phylogenetic analysis, Mol. Biol. Evol. 7:82-102 (1990).
13. T. Uzzel and K. W. Corbin, Fitting discrete probability distributions to evolutionary events, Science 172:1089-1096 (1971).
14. R. M. Holmquist, The spatial distribution of fixed mutations within genes coding for proteins, J. Mol. Evol. 19:437-448 (1983).
15. N. Takahata, Overdispersed molecular clock at the major histocompatibility complex loci, Proc. Roy. Soc. Lond. B 243:13-18 (1991).
16. G. J. Olsen, Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques, Cold Spring Harbor Symp. Quant. Biol. 52:825-837 (1987).
17. J. Wakeley, Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA, J. Mol. Evol. 37:613-623 (1993).
18. C. Lanave, G. Preparata, C. Saccone, and G. Serio, A new method for calculating evolutionary substitution rates, J. Mol. Evol. 20:86-93 (1984).
19. J. Felsenstein, Phylogenies from molecular sequences: inference and reliability, Annu. Rev. Genet. 22:521-565 (1988).
20. J. Felsenstein, Evolutionary trees from DNA sequences: a maximum likelihood approach, J. Mol. Evol. 17:368-376 (1981).
21. J. Felsenstein, Statistical inference of phylogenies, J. Roy. Stat. Soc. A 146(3):246-272 (1983).
22. S. Tavaré and T. Janzen, On estimating substitution rates from pairs of nucleotide sequences, Preprint, 1985.
23. S. Tavaré, Some probabilistic and statistical problems in the analysis of DNA sequences, Lect. Math. Life Sci. 17:57-86 (1986).
24. W. B. Upholt, Estimation of DNA sequence divergence from comparison of restriction endonuclease digests, Nucleic Acids Res. 4:1257-1265 (1977).
25. M. Kimura, Estimation of evolutionary distances between homologous nucleotide sequences, Proc. Natl. Acad. Sci. USA 78(1):454-458 (1981).
26. D. Barry and J. A. Hartigan, Asynchronous distance between homologous DNA sequences, Biometrics 43:261-276 (1987).
27. J. A. Cavender and J. Felsenstein, Invariants of phylogenies in a simple case of discrete states, J. Classif. 4:57-71 (1987).
28. B. Efron, The Jackknife, the Bootstrap and Other Resampling Plans, CBMS-NSF Regional Conf. Ser. Appl. Math. Vol. 38, SIAM, Philadelphia, PA, 1982.
29. J. Chen and C. Kelly, A reexamination of DNA sequence data using a heterogeneous rate model of evolution, Unpublished, 1995.
30. G. J. Olsen, Systematic underestimation of tree branch lengths by Lake's operator metrics: an effect of position-dependent substitution rates, Mol. Biol. Evol. 8(5):592-608 (1991).
31. Z. Yang, Maximum likelihood estimation of phytogeny from DNA sequences, Mol. Biol. Evol. 10:1396-1401 (1993).
32. N. Goldman, Statistical tests of models of DNA substitution, J. Mol. Evol. 36:182-198 (1993).