Molecular Biology and Evolution 18:691-699 (2001)
© 2001 Society for Molecular Biology and Evolution
ARTICLE |
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
Department of Zoology, University of Cambridge, Cambridge, England
Phylogenetic inference from amino acid sequence data uses mainly empirical models of amino acid replacement and is therefore dependent on those models. Two of the more widely used models, the Dayhoff and JTT models, are estimated using similar methods that can utilize large numbers of sequences from many unrelated protein families but are somewhat unsatisfactory because they rely on assumptions that may lead to systematic error and discard a large amount of the information within the sequences. The alternative method of maximum-likelihood estimation may utilize the information in the sequence data more efficiently and suffers from no systematic error, but it has previously been applicable to relatively few sequences related by a single phylogenetic tree. Here, we combine the best attributes of these two methods using an approximate maximum-likelihood method. We implemented this approach to estimate a new model of amino acid replacement from a database of globular protein sequences comprising 3,905 amino acid sequences split into 182 protein families. While the new model has an overall structure similar to those of other commonly used models, there are significant differences. The new model outperforms the Dayhoff and JTT models with respect to maximum-likelihood values for a large majority of the protein families in our database. This suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates. Potentially, this matrix, and the methods used to generate it, may also be useful in other areas of research, such as biological sequence database searching, sequence alignment, and protein structure prediction, for which an accurate description of amino acid replacement is required.
Key Words: amino acid replacement • general reversible model • maximum likelihood • protein evolution
Key Words: amino acid replacement • general reversible model • maximum likelihood • protein evolution
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S. O. Sassi, E. L. Braun, and S. A. Benner The Evolution of Seminal Ribonuclease: Pseudogene Reactivation or Multiple Gene Inactivation Events? Mol. Biol. Evol., April 1, 2007; 24(4): 1012 - 1024. [Abstract] [Full Text] [PDF]
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S. Richardt, D. Lang, R. Reski, W. Frank, and S. A. Rensing PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins Plant Physiology, April 1, 2007; 143(4): 1452 - 1466. [Abstract] [Full Text] [PDF]
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 J. M. Fitzpatrick, Y. Hirai, H. Hirai, and K. F. Hoffmann Schistosome egg production is dependent upon the activities of two developmentally regulated tyrosinases FASEB J, March 1, 2007; 21(3): 823 - 835. [Abstract] [Full Text] [PDF]
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N. Rodriguez-Ezpeleta, H. Philippe, H. Brinkmann, B. Becker, and M. Melkonian Phylogenetic Analyses of Nuclear, Mitochondrial, and Plastid Multigene Data Sets Support the Placement of Mesostigma in the Streptophyta Mol. Biol. Evol., March 1, 2007; 24(3): 723 - 731. [Abstract] [Full Text] [PDF]
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B. Brindefalk, J. Viklund, D. Larsson, M. Thollesson, and S. G. E. Andersson Origin and Evolution of the Mitochondrial Aminoacyl-tRNA Synthetases Mol. Biol. Evol., March 1, 2007; 24(3): 743 - 756. [Abstract] [Full Text] [PDF]
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M. L. Sanderson-Smith, M. Dowton, M. Ranson, and M. J. Walker The Plasminogen-Binding Group A Streptococcal M Protein-Related Protein Prp Binds Plasminogen via Arginine and Histidine Residues J. Bacteriol., February 15, 2007; 189(4): 1435 - 1440. [Abstract] [Full Text] [PDF]
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A. Doron-Faigenboim and T. Pupko A Combined Empirical and Mechanistic Codon Model Mol. Biol. Evol., February 1, 2007; 24(2): 388 - 397. [Abstract] [Full Text] [PDF]
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R. Bredemeier, T. Schlegel, F. Ertel, A. Vojta, L. Borissenko, M. T. Bohnsack, M. Groll, A. von Haeseler, and E. Schleiff Functional and Phylogenetic Properties of the Pore-forming beta-Barrel Transporters of the Omp85 Family J. Biol. Chem., January 19, 2007; 282(3): 1882 - 1890. [Abstract] [Full Text] [PDF]
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D. Baurain, H. Brinkmann, and H. Philippe Lack of Resolution in the Animal Phylogeny: Closely Spaced Cladogeneses or Undetected Systematic Errors? Mol. Biol. Evol., January 1, 2007; 24(1): 6 - 9. [Abstract] [Full Text] [PDF]
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S. L. Kosakovsky Pond, F. V. Mannino, M. B. Gravenor, S. V. Muse, and S. D. W. Frost Evolutionary Model Selection with a Genetic Algorithm: A Case Study Using Stem RNA Mol. Biol. Evol., January 1, 2007; 24(1): 159 - 170. [Abstract] [Full Text] [PDF]
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M. L. Porter, T. W. Cronin, D. A. McClellan, and K. A. Crandall Molecular Characterization of Crustacean Visual Pigments and the Evolution of Pancrustacean Opsins Mol. Biol. Evol., January 1, 2007; 24(1): 253 - 268. [Abstract] [Full Text] [PDF]
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 T. H. Shafer, M. A. McCartney, and L. M. Faircloth Identifying exoskeleton proteins in the blue crab from an expressed sequence tag (EST) library Integr. Comp. Biol., December 1, 2006; 46(6): 978 - 990. [Abstract] [Full Text] [PDF]
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M. Gray-Mitsumune, M. O'Brien, C. Bertrand, F. Tebbji, A. Nantel, and D. P. Matton Loss of ovule identity induced by overexpression of the fertilization-related kinase 2 (ScFRK2), a MAPKKK from Solanum chacoense J. Exp. Bot., December 1, 2006; 57(15): 4171 - 4187. [Abstract] [Full Text] [PDF]
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S. B. Gould, M. S. Sommer, P. G. Kroth, G. H. Gile, P. J. Keeling, and U.-G. Maier Nucleus-to-Nucleus Gene Transfer and Protein Retargeting into a Remnant Cytoplasm of Cryptophytes and Diatoms Mol. Biol. Evol., December 1, 2006; 23(12): 2413 - 2422. [Abstract] [Full Text] [PDF]
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J. Savard, D. Tautz, S. Richards, G. M. Weinstock, R. A. Gibbs, J. H. Werren, H. Tettelin, and M. J. Lercher Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects Genome Res., November 1, 2006; 16(11): 1334 - 1338. [Abstract] [Full Text] [PDF]
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R. E. Baker and K. Rogers Phylogenetic Analysis of Fungal Centromere H3 Proteins Genetics, November 1, 2006; 174(3): 1481 - 1492. [Abstract] [Full Text] [PDF]
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