Selective constraints, amino acid composition, and the rate of protein evolution

Molecular Biology and Evolution

Volumn 17, Issue 4, 2000, Pages 656-664

  Tourasse, Nicolas J ^b   Li, Wen Hsiung ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b NONE

Author keywords

Amino acid composition; Functional and structural requirements; Protein evolution; Selective constraints; Substitution rate

Indexed keywords

M PROTEIN;

AMINO ACID COMPOSITION; AMINO ACID SUBSTITUTION; ARTICLE; GENE FREQUENCY; GENETIC SELECTION; MOLECULAR EVOLUTION; PHYLOGENY; PROTEIN STRUCTURE;

MAMMALIA;

EID: 0034079112     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026344     Document Type: Article

References (27)

1. BAIROCH, A., and R. APWEILER. 1999. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res. 27:49-54.
2. CAO, Y., J. ADACHI, and M. HASEGAWA. 1994. Eutherian phylogeny as inferred from mitochondrial DNA sequence data. Jpn. J. Genet. 69:455-472.
3. DAYHOFF, M. O., R. M. SCHWARTZ, and B. C. ORCUTT. 1978. A model of evolutionary change in proteins. Pp. 345-352 in Atlas of Protein Sequence and Structure. Vol. 5, Suppl. 3. National Biomedical Research Foundation, Washington, D.C.
4. DURET, L., D. MOUCHIROUD, and M. GOUY. 1994. HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res. 22:2360-2365.
5. GATESY, J. 1997. More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene gamma-fibrinogen. Mol. Biol. Evol. 14:537-543.
6. GOODMAN, M., C. A. PORTER, J. CZELUSNIAK, S. L. PAGE, H. SCHNEIDER, J. SHOSHANI, G. F. GUNNELL, and C. P. GROVES. 1998. Toward a phylogenetic classification of Primates based on DNA evidence complemented by fossil evidence. Mol. Phylogenet. Evol. 9:585-598.
7. GRAUR, D. 1985. Amino acid composition and the evolutionary rates of protein-coding genes. J. Mol. Evol. 22:53-62.
8. GRAUR, D., L. DURET, and M. GOUY. 1996. Phylogenetic position of the order Lagomorpha. Nature 379:333-335.
9. JANKE, A., X. XU, and U. ARNASON. 1997. The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia, and Eutheria. Proc. Natl. Acad. Sci. USA 94: 1276-1281.
10. JONES, D. T., W. R. TAYLOR, and J. M. THORNTON. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
11. _. 1994. A mutation data matrix for transmembrane proteins. FEBS Lett. 339:269-275.
12. KIMURA, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England.
13. KUMA, K., and T. MIYATA. 1994. Mammalian phylogeny inferred from multiple protein data. Jpn. J. Genet. 69:555-566.
14. LI, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
15. _. 1997. Molecular evolution. Sinauer, Sunderland, Mass.
16. LI, W.-H., M. GOUY, P. M. SHARP, C. O'HUIGIN, and Y.-W. YANG. 1990. Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks. Proc. Natl. Acad. Sci. USA 87:6703-6707.
17. NEI, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
18. NIE, N. H., C. H. HULL, J. G. JENKINS, K. STEINBRENNER, and D. H. BENT. 1975. SPSS: statistical package for the social sciences. MacGraw-Hill, New York.
19. ROBINSON, M., F. CATZEFLIS, J. BRIOLAY, and D. MOUCHIROUD. 1997. Molecular phylogeny of rodents, with special emphasis on murids: evidence from nuclear gene LCAT. Mol. Phylogenet. Evol. 8:423-434.
20. SHIMAMURA, M., H. YASUE, K. OHSHIMA, H. ABE, H. KATO, T. KISHIRO, M. GOTO, I. MUNECHIKA, and N. OKADA. 1997. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388:666-670.
21. SHOSHANI, J., C. P. GROVES, E. L. SIMONS, and G. F. GUNNELL. 1996. Primate phylogeny: morphological vs. molecular results. Mol. Phylogenet. Evol. 5:102-154.
22. THOMPSON, J. D., D. G. HIGGINS, and T. J. GIBSON. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
23. URSING, B. M., and U. ARNASON. 1998. Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade. Proc. R. Soc. Lond. B Biol. Sci. 265:2251-2255.
24. YANG, Z. 1999. Phylogenetic analysis by maximum likelihood (PAML). Version 2.0. University College London, London.
25. YANG, Z., S. KUMAR, and M. NEI. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.
26. ZHANG, J., and M. NEI. 1997. Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J. Mol. Evol. 44(Suppl. 1):S139-S146.
27. ZUCKERKANDL, E., and L. PAULING. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8:357-366.