Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis

Molecular Biology and Evolution

Volumn 15, Issue 7, 1998, Pages 871-879

  Galtier, Nicolas ^a,b   Gouy, Manolo ^a  

^a UNIVERSITÉ LYON 1   (France)

^b UNIV MONTPELLIER   (France)

Author keywords

G+C content; Maximum likelihood; Molecular phylogeny; Nonhomogeneous model

Indexed keywords

ARTICLE; DNA SEQUENCE; EVOLUTION; MAXIMUM LIKELIHOOD METHOD; MODEL; NUCLEOTIDE SEQUENCE; PHYLOGENY;

EID: 0031829758     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025991     Document Type: Article

References (45)

1. BERNARDI, G. 1993. The vertebrate genome: isochores and evolution. Mol. Biol. Evol. 10:186-204.
2. CAVALLI-SFORZA, L. L., and A. W. EDWARDS. 1967. Phylogenetic analysis. Model and estimation procedures. Am. J. Hum. Genet. 19:223.
3. EDWARDS, A. W. F. 1972. Likelihood. Cambridge University Press, Cambridge, England.
4. _. 1996. Assessing molecular phylogenies. Science 267: 253.
5. EISEN, J. A. 1995. The recA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of recAs and 16S rRNAs from the same species. J. Mol. Evol. 41:1105-1123.
6. FELSENSTEIN, J. 1973a. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25:471-492.
7. _. 1973b. Maximum-likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22:240-249.
8. _. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
9. _. 1988. Phylogenies from molecular sequences: inferences and reliability. Annu. Rev. Genet. 22:521-565.
10. _. 1993. PHYLIP: phylogeny inference package. Version 3.5. Distributed by the author, Department of Genetics, University of Washington, Seattle.
11. FELSENSTEIN, J., and G. A. CHURCHILL. 1996. A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:93-104.
12. FITCH, W. M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:406-416.
13. GALTIER, N., and M. GOUY. 1994. Eubacterial phylogeny: a new multiple-tree analysis method applied to 15 sequence data sets questions the monophyly of Gram-positive bacteria. Res. Microbiol. 145:531-541.
14. _. 1995. Inferring phylogenies from sequences of unequal base compositions. Proc. Natl. Acad. Sci. USA 92: 11317-11321.
15. GOLDMAN, N. 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses. Syst. Zool. 39:345-361.
16. HASEGAWA, M., H. KISHINO, and T. YANO. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
17. HILLIS, D. M., and J. P. HUELSENBECK. 1996. Assessing molecular phylogenies. Science 267:255-256.
18. JERMIIN, L. S., D. GRAUR, R. M. LOWE, and R. H. CROZIER. 1994. Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes. J. Mol. Evol. 39:160-173.
19. 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.
20. KISHINO, H., and M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequences data, and the branching order in Hominoidae. J. Mol. Evol. 29:170-179.
21. KUHNER, M. K., and J. FELSENSTEIN. 1994. A simulation of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
22. LAKE, J. A. 1994. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc. Natl. Acad. Sci. USA 91:1455-1459.
23. LLOYD, A. T., and P. M. SHARP. 1993. Evolution of the recA gene and the molecular phylogeny of Bacteria. J. Mol. Evol. 37:399-407.
24. LOBRY, J. R. 1995. Properties of a general model of DNA evolution under no-strand-bias conditions. J. Mol. Evol. 40: 326-330.
25. LOCKHART, P. J., C. J. HOWE, D. A. BRYANT, T. J. BEANLAND, and A. W. D. LARKUM. 1992. Substitutional bias confounds inference of cyanelle origins from sequence data. J. Mol. Evol. 34:153-162.
26. LOCKHART, P. J., M. A. STEEL, M. D. HENDY, and D. PENNY. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612.
27. MOUCHIROUD, D., G. D'ONOFRIO, B. AISSANI, G. MACAYA, C. GAUTIER, and G. BERNARDI. 1991. The distribution of genes in the human genome. Gene 100:181-187.
28. MOUCHIROUD, D., C. GAUTIER, and G. BERNARDI. 1988. The compositional distribution of coding sequences and DNA molecules in humans and murids. J. Mol. Evol. 27:311-320.
29. OLSEN, G. J., H. MATSUDA, R. HAGSTROM, and R. OVERBEEK. 1994. fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10:41-48.
30. OLSEN, G. J., C. R. WOESE, and R. OVERBEEK. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6.
31. SAITOU, N. 1988. Property and efficiency of the maximum likelihood method for molecular phylogeny. J. Mol. Evol. 27: 261-273.
32. SAITOU, N., and M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
33. STEEL, M. A. 1993. Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett. 7: 19-23.
34. SUEOKA, N. 1961. Variation and heterogeneity of base composition of deoxyribonucleic acids: a compilation of old and new data. J. Mol. Biol. 3:31-40.
35. TAMURA, K. 1992. Estimation of the number of nucleotide substitutions when there are strong transitition-transversion and G+C-content biases. Mol. Biol. Evol. 9:678-687.
36. TOURASSE, N. J., and M. GOUY. 1997. Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony. Mol. Biol. Evol. 14:287-298.
37. VAN DE PEER, Y., I. VAN DEN BROECK, P. DE RIJK, and R. DE WACHTER. 1994. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 22:3488-3494.
38. WAKELEY, J. 1996. The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance. TREE 11:158-163.
39. WOESE, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221-271.
40. WOLFE, K. H., W.-H. LI, and P. M. SHARP. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA 84:9054-9058.
41. YANG, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
42. _. 1995. Phylogenetic analysis by maximum likelihood (PAML). Version 1.1. Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park.
43. _. 1996. Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42:294-307.
44. YANG, Z., N. GOLDMAN, and A. FRIDAY. 1994. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11:316-324.
45. YANG, Z., and D. ROBERTS. 1995. On the use of nucleic acid sequences to infer branchings in the tree of life. Mol. Biol. Evol. 12:451-458.