Testing for differences in rates-across-sites distributions in phylogenetic subtrees

Molecular Biology and Evolution

Volumn 19, Issue 9, 2002, Pages 1514-1523

  Susko, Edward ^a   Inagaki, Yuji ^a   Field, Chris ^a   Holder, Michael E ^b   Roger, Andrew J ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b NONE

Author keywords

Covarion; Markov models; Maximum likelihood; Molecular evolution; Phylogenetics; Rates across sites

Indexed keywords

ARTICLE; GENETIC DIFFERENCE; GENETIC HETEROGENEITY; GENETIC PARAMETERS; MATHEMATICAL ANALYSIS; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENETIC TREE; PROBABILITY; REGRESSION ANALYSIS; STATISTICAL MODEL; BIOLOGICAL MODEL; CONFIDENCE INTERVAL; GENETIC PROCEDURES; GENETIC VARIABILITY; GENETICS; MUTAGENESIS; PHYLOGENY;

PROTEIN;

CONFIDENCE INTERVALS; EVOLUTION, MOLECULAR; GENETIC TECHNIQUES; MODELS, GENETIC; MUTAGENESIS; PHYLOGENY; PROTEINS; REGRESSION ANALYSIS; VARIATION (GENETICS);

EID: 0036730253     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004214     Document Type: Article

References (21)

1. CASELLA, G., and R. L. BERGER. 1990. Statistical inference. Brooks/Cole, Pacific Grove, Calif.
2. DAYHOFF, M. O., R. M. SCHWARTZ, and B. C. ORCUTT. 1979. A model of evolutionary change in proteins. Pp. 345-352 in M. O. DAYHOFF, ed. Atlas of protein sequence and structure, Vol. 5(Suppl. 3). National Biomedical Research Foundation, Silver Spring, Md.
3. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
4. -. 1993. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle.
5. 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.
6. FITCH, W. F., and E. MARKOWlTZ. 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.
7. GALTIER, N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18:866-873.
8. GAUCHER, E. A., M. M. MIYAMATO, and S. A. BENNER. 2001. Function-structure analysis of proteins using covarion-based evolutionary approaches: elongation factors. Proc. Natl. Acad. Sci. USA 98:548-552.
9. GU, X. 2001. Maximum likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18:453-464.
10. INAGAKI, Y., and W. F. DOOLITTLE. 2000. Evolution of the eukaryotic translation termination system: origins of release factors. Mol. Biol. Evol. 17:882-889.
11. KNUDSEN, B., and M. M. MIYAMATO. 2001. A likelihood ratio test of evolutionary rate shifts and functional divergence among proteins. Proc. Natl. Acad. Sci. USA 98:14512-14517.
12. LOCKHART, P. J., D. H. HUSON, U. MAIRER, M. J. FRAUNHOLZ, Y. VAN DE PEER, A. C. BARBROOK, C. J. HOWE, and M. A. STEEL. 1998. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol. Biol. Evol. 15:1183-1188.
13. -. 2000. How molecules evolve in eubacteria. Mol. Biol. Evol. 17:835-838.
14. LOPEZ, P. FORTERRE, P., and H. PHILLIPE. 1999. The root of the tree of life in the light of the covarion model. J. Mol. Evol. 49:496-508.
15. MIYAMOTO, M. M., and W. M. FITCH. 1995. Testing the covarion hypothesis of molecular evolution. Mol. Biol. Evol. 12:503-513.
16. PENNY, D., B. J. MCCOMISH, M. A. CHARLESTON, and M. D. HENDY. 2001. Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J. Mol. Evol. 53:711-723.
17. 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.
18. STRIMMER, K., and A. VON HAESELER. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
19. SUSKO, E., C. FIELD, C. BLOUIN, and A. R. ROGER. 2002. Estimation of rate distributions in phylogenetic models. Preprint.
20. TUFFLEY, C., and M. STEEL. 1998. Modeling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147:63-91.
21. YANG, Z. 1994. Maximum likelihood phylogentic estimation from DNA sequences when substitution rates differ over sites: approximate methods. J. Mol. Evol. 39:306-314.