Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics

Molecular Biology and Evolution

Volumn 16, Issue 9, 1999, Pages 1292-1299

  Whelan, Simon ^a   Goldman, Nick ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b NONE

Author keywords

Likelihood ratio tests; Markov models; Maximum likelihood; Model comparison; Molecular evolution; Phylogenetics

Indexed keywords

ARTICLE; MOLECULAR EVOLUTION; MOLECULAR MODEL; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE;

EID: 0032843848     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026219     Document Type: Article

References (21)

1. BROWN, W. M., E. M. PRAGER, A. WANG, and A. C. WILSON. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol. 18:225-239.
2. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
3. GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
4. 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.
5. HUELSENBECK, J. P., and R. NIELSEN. 1999. Variation in the pattern of nucleotide substitution across sites. J. Mol. Evol. 48:86-93.
6. HUELSENBECK, J. P., and B. RANNALA. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227-232.
7. JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. MUNRO, ed. Mammalian protein metabolism. Vol. 3. Academic Press, New York.
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. LINDGREN, B. W. 1976. Statistical theory. 3rd edition. Macmillan, New York.
10. LIÒ, P., and N. GOLDMAN. 1998. Models of molecular evolution and phylogeny. Genome Res. 8:1233-1244.
11. MIYAMOTO, M. M., J. L. SLIGHTOM, and M. GOODMAN. 1987. Phylogenetic relations of humans and African apes from DNA sequences in the ψη-globin region. Science 238:369-373.
12. SELF, S. G., and K.-L. LIANG. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J. Am. Stat. Assoc. 82:605-610.
13. SILVEY, S. D. 1975. Statistical inference. Chapman and Hall, London.
14. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, and D. M. HILLIS. 1996. Phylogenetic inference. Pp. 407-514 in D. M. HILLIS, C. MORITZ, and B. K. MABLE, eds. Molecular systematics. 2nd edition. Sinauer, Sunderland, Mass.
15. WALD, A. 1949. Note on the consistency of the maximum likelihood estimate. Ann. Math. Stat. 20:595-601.
16. YANG, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol 10:1396-1401.
17. _. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
18. _. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13:555-556.
19. _. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568-573.
20. YANG, Z., N. GOLDMAN, and A. FRIDAY. 1995. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst. Biol. 44:384-399.
21. ZHARKIKH, A. 1994. Estimation of evolutionary distances between nucleotide sequences. J. Mol. Evol. 39:315-329.