Likelihood, parsimony, and heterogeneous evolution

Molecular Biology and Evolution

Volumn 22, Issue 5, 2005, Pages 1161-1164

  Spencer, Matthew ^a   Susko, Edward ^a   Roger, Andrew J ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Consistency; Heterotachy; Likelihood; Mixture models; Simulation

Indexed keywords

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; EVOLUTIONARY RATE; HETEROTACHY; MAXIMUM LIKELIHOOD METHOD; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ANIMALS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY;

EID: 17744400517     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi123     Document Type: Article

References (19)

1. Ané, C., J. G. Burleigh, M. M. McMahon, and M. J. Sanderson. 2005. Covarion structure in plastid genome evolution: a new statistical test. Mol. Biol. Evol. (in press).
2. Chang, J. T. 1996. Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Math. Biosci. 137:51-73.
3. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Mass.
4. Fitch, W. M., and E. Markowitz. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4:579-593.
5. Galtier, N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18:866-873.
6. Huelsenbeck, J. P. 2002. Testing a covariotide model of DNA substitution. Mol. Biol. Evol. 19:698-707.
7. Inagaki, Y., E. Susko, N. M. Fast, and A. J. Roger. 2004. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF1-α phylogenies. Mol. Biol. Evol. 21:1340-1349.
8. Kolaczkowski, B., and J. W. Thornton. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.
9. Lockhart, P. J., M. A. Steel, A. C. Barbrook, D. H. Huson, M. A. Charleston, and C. J. Howe. 1998. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol. Biol. Evol. 15:1183-1188.
10. Lopez, P., D. Casane, and H. Philippe. 2002. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19:1-7.
11. Pagel, M., and A. Meade. 2004. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character state data. Syst. Biol. 53:571-581.
12. Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
13. Sanderson, M. J., and J. Kim. 2000. Parametric phylogenetics? Syst. Biol. 49:817-829.
14. Steel, M., D. Huson, and P. J. Lockhart. 2000. Invariable sites models and their use in phylogeny reconstruction. Syst. Biol. 49:225-232.
15. Steel, M. A., and L. A. Székely. 2002. Inverting random functions II: explicit bounds for discrete maximum likelihood estimation, with applications. SIAM J. Discrete Math. 15:562-575.
16. Susko, E., Y. Inagaki, and A. J. Roger. 2004. On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled. Mol. Biol. Evol. 21:1629-1642.
17. Swofford, D. L. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4 beta 10. Sinauer Associates, Sunderland, Mass.
18. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. Hillis, C. Moritz, and B. Mable, eds. Molecular systematics. 2nd edition. Sinauer Associates, Sunderland, Mass.
19. Uzzell, T., and K. W. Corbin. 1971. Fitting discrete probability distributions to evolutionary events. Science 172:1089-1096.