A Fast Method for Approximating Maximum Likelihoods of Phylogenetic Trees from Nucleotide Sequences

Systematic Biology

Volumn 47, Issue 1, 1998, Pages 77-89

  Rogers, James S ^a   Swofford, David L ^b  

^a UNIVERSITY OF NEW ORLEANS   (United States)

^b SMITHSONIAN INSTITUTION   (United States)

Author keywords

Approximations; Maximum likelihood; Parsimony; Tree searching

Indexed keywords

DNA; RIBOSOME DNA; RIBOSOME RNA;

ANIMAL; ARTICLE; CHEMISTRY; DECISION TREE; GENETICS; INVERTEBRATE CHORDATA; NUCLEOTIDE SEQUENCE; PHYLOGENY; REGRESSION ANALYSIS; REPRODUCIBILITY; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; CHORDATA, NONVERTEBRATE; DECISION TREES; DNA; DNA, RIBOSOMAL; LIKELIHOOD FUNCTIONS; PHYLOGENY; REGRESSION ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL;

EID: 0032025769     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351598261049     Document Type: Article

References (33)

1. ADACHI, J., AND M. HASEGAWA. 1995. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Institute of Statistical Mathematics, Tokyo.
2. Barry, D., and J. A. Hartigan. 1987. Statistical analysis of hominoid molecular evolution. Stat. Sci. 2:191-210.
3. DEBRY, R. W., AND L. G. ABELE. 1995. The relationship between parsimony and maximum-likelihood analyses: Tree scores and confidence estimates for three real data sets. Mol. Biol. Evol. 12:291-297.
4. FARRIS, J. S. 1973. A probability model for inferring evolutionary trees. Syst. Zool. 22:250-256.
5. FARRIS, J. S. 1977. Phylogenetic analysis under Dollo's law. Syst. Zool. 26:77-88.
6. FELSENSTEIN, J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22:240-249.
7. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
8. FELSENSTEIN, J. 1993. PHYLIP (Phylogenetic inference package), version 3.5p. Univ. Washington, Seattle.
9. FITCH, W. M. 1971. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20:406-416.
10. 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.
11. HARTIGAN, J. A. 1973. Minimum mutation fits to a given tree. Biometrics 29:53-65.
12. HASEGAWA, M., H. KISHINO, AND T. YANO. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
13. HAYASAKA, K., T. GOJOBORI, AND S. HORAI. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol. 5:626-644.
14. HELM-BYCHOWSKI, K., AND J. CRACRAFT. 1993. Recovering phylogenetic signal from DNA sequences: Relationships within the corvine assemblage (class Aves) as inferred from complete sequences of the mitochondrial cytochrome-b gene. Mol. Biol. Evol. 10:1196-1214.
15. HILLIS, D. M., J. P. HUELSENBECK, AND C. W. CUNNINGHAM. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
16. HILLIS, D. M., C. MORITZ, AND B. K. MABLE (eds.). 1996. Molecular systematics, 2nd edition. Sinauer, SunderLand, Massachusetts.
17. HUELSENBECK, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
18. HUELSENBECK, J. P., AND D. M. HILLIS. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-264.
19. JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
20. KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
21. KISHINO, H., AND M. HASLGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29: 170-179.
22. KUHNER, M. K., AND J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-168.
23. MAIDAK, B. L., N. LARSEN, M. J. MCCAUGHEY, R. OVERBEEK, G. J. OLSEN, K. FOGEL, J. BLANDY, AND C. R. WOESE. 1994. The ribosomal database project. Nucleic Acids Res. 22:3485-3487.
24. 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.
25. PATTON, J. L., AND M. F. SMITH. 1994. Paraphyly, polyphyly, and the nature of species boundaries in pocket gophers (genus Thomomys). Syst. Biol. 143:11-26.
26. STEEL, M. 1994. The maximum likelihood point for a phylogenetic tree is not unique. Syst. Biol. 43:560-564.
27. SWOFFORD, D. L., AND W. P. MADDISON. 1992. Parsimony, character-state reconstructions, and evolutionary inferences. Pages 186-223 in Systematics, historical ecology and North American freshwater fishes (R. L. Mavden, ed.). Stanford Univ. Press, Stanford, California.
28. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition. (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
29. TATENO, Y., N. T. TAKEZAKI, AND M. NEI. 1994. Relative efficiencies or the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11:261-277.
30. WADDELL, P. J. 1995. Statistical methods of phylogenetic analysis, including Hadamard conjugations, LogDet transforms and maximum likelihood. Ph. D. Dissertation, Massey Univ., New Zealand.
31. YANG, Z. 1994. Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Syst. Biol. 43:329-342.
32. 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.
33. YANG, Z., S. KUMAR, AND M. NEI. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.