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Molecular Biology and Evolution, Vol 10, 1396-1401, Copyright © 1993 by Society for Molecular Biology and Evolution

ORIGINAL ARTICLE

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

Z Yang
Department of Animal Science, Beijing Agricultural University.

Felsenstein's maximum-likelihood approach for inferring phylogeny from DNA sequences assumes that the rate of nucleotide substitution is constant over different nucleotide sites. This assumption is sometimes unrealistic, as has been revealed by analysis of real sequence data. In the present paper Felsenstein's method is extended to the case where substitution rates over sites are described by the gamma distribution. A numerical example is presented to show that the method fits the data better than do previous models.
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 ANN BOT (LOND)Home page
S. S. NEVES and M. F. WATSON
Phylogenetic Relationships in Bupleurum (Apiaceae) Based on Nuclear Ribosomal DNA ITS Sequence Data
Ann. Bot., April 1, 2004; 93(4): 379 - 398.
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 Syst BiolHome page
A. R. Lemmon and E. C. Moriarty
The Importance of Proper Model Assumption in Bayesian Phylogenetics
Syst Biol, April 1, 2004; 53(2): 265 - 277.
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 Mol Biol EvolHome page
A. Siepel and D. Haussler
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood
Mol. Biol. Evol., March 1, 2004; 21(3): 468 - 488.
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 Journal of PaleontologyHome page
SIMULATIONS OF EVOLUTIONARY RADIATIONS AND THEIR APPLICATION TO UNDERSTANDING THE PROBABILITY OF A CAMBRIAN EXPLOSION
Journal of Paleontology, January 1, 2004; 78(1): 31 - 38.


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 Mol Biol EvolHome page
M. Klinger, J. S. Taylor, T. Oertle, M. E. Schwab, C. A. O. Stuermer, and H. Diekmann
Identification of Nogo-66 Receptor (NgR) and Homologous Genes in Fish
Mol. Biol. Evol., January 1, 2004; 21(1): 76 - 85.
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 Mol Biol EvolHome page
M. P. Simmons, K. M. Pickett, and M. Miya
How Meaningful Are Bayesian Support Values?
Mol. Biol. Evol., January 1, 2004; 21(1): 188 - 199.
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 Int. J. Syst. Evol. Microbiol.Home page
J. Tapp, M. Thollesson, and B. Herrmann
Phylogenetic relationships and genotyping of the genus Streptococcus by sequence determination of the RNase P RNA gene, rnpB
Int J Syst Evol Microbiol, November 1, 2003; 53(6): 1861 - 1871.
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 Mol Biol EvolHome page
C. Seoighe, C. R. Johnston, and D. C. Shields
Significantly Different Patterns of Amino Acid Replacement After Gene Duplication as Compared to After Speciation
Mol. Biol. Evol., April 1, 2003; 20(4): 484 - 490.
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 Mol Biol EvolHome page
M. S. Rosenberg and S. Kumar
Heterogeneity of Nucleotide Frequencies Among Evolutionary Lineages and Phylogenetic Inference
Mol. Biol. Evol., April 1, 2003; 20(4): 610 - 621.
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