The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes

Molecular Biology and Evolution

Volumn 15, Issue 3, 1998, Pages 336-344

  Xia, Xuhua ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Codon; Mammal; Mitochondrial gene; Nonsynonymous substitution; Rate heterogeneity

Indexed keywords

MITOCHONDRIAL DNA;

AMINO ACID SUBSTITUTION; ARTICLE; CODON; EVOLUTION; GENETIC CONSERVATION; MAMMAL; NONHUMAN; PHYLOGENY;

MAMMALIA;

EID: 0031916709     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025930     Document Type: Article

References (29)

1. CAO, Y., J. ADACHI, A. JANKE, S. PÄÄBO, and M. HASEGAWA. 1994. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based of a single gene. J. Mol. Evol. 39:519-527.
2. CLARKE, B. 1970. Selective constraints on amino-acid substitutions during the evolution of proteins. Nature 228:159-160.
3. CUMMINGS, M., S. OTTO, and J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
4. EPSTEIN, C. J. 1967. Non-randomness of amino-acid changes in the evolution of homologous proteins. Nature 215:355-359.
5. FELSENSTEIN, J. 1992. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet. Res. 59:139-147.
6. _. 1993. PHYLIP (phylogeny inference package). Version 3.5. Distributed by the author. Department of Genetics, University of Washington, Seattle.
7. GRANTHAM, R. 1974. Amino acid difference formula to help explain protein evolution. Science 185:862-864.
8. GRAUR, D. 1985. Amino acid composition and the evolutionary rates of protein-coding genes. J. Mol. Evol. 22:53-62.
9. HAIG, D., and L. D. HURST. 1991. A quantitative measure of error minimization in the genetic code. J. Mol. Evol. 33: 412-417.
10. IRWIN, D. M., T. D. KOCHER, and A. C. WILSON. 1991. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32:128-144.
11. 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.
12. JOHNSON, N. L., S. KOTZ, and A. W. KEMP. 1992. Univariate discrete distributions. John Wiley & Sons, New York.
13. KIMURA, M. 1977. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267:275-276.
14. _. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England.
15. KYTE, J., and R. F. DOOLITTLE. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132.
16. LI, W.-H. 1997. Molecular evolution. Sinauer, Sunderland, Mass.
17. MIYATA, T., S. MIYAZAWA, and T. YASUNAGA. 1979. Two types of amino acid substitution in protein evolution. J. Mol. Evol. 12:219-236.
18. NEE, S., E. C. HOLMES, A. RAMBAUT, and P. H. HARVEY. 1996. Inferring population history from molecular phylogenies. Pp. 66-80 in P. H. HARVEY, A. J. L. BROWN, J. MAYNARD SMITH, and S. NEE, eds. New uses for new phylogenies. Oxford University Press, Oxford.
19. NEI, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
20. NOVACEK, M. J., A. R. WYSS, and M. MCKENNA. 1988. The major groups of eutherian mammals. Pp. 31-71 in M. J. BENTON, ed. The phylogeny and classification of the tetrapods. Vol. 2. Clarendon Press, Oxford.
21. OTTO, S. P., M. P. CUMMINGS, and J. WAKELEY. 1996. Inferring phylogenies from DNA sequence data: the effects of sampling. Pp. 103-115 in P. H. HARVEY, A. J. L. BROWN, J. MAYNARD SMITH, and S. NEE, eds. New uses for new phylogenies. Oxford University Press, Oxford.
22. SNEATH, P. H. A. 1966. Relations between chemical structure and biological activity. J. Theor. Biol. 12:157-195.
23. SWOFFORD, D. L. 1993. Phylogenetic analysis using parsimony (PAUP). University of Illinois, Champaign.
24. XIA, X., M. S. HAFNER, and P. D. SUDMAN. 1996. On transition bias in mitochondrial genes of pocket gophers. J. Mol. Evol. 43:32-40.
25. YANG, Z. 1996a. Among-site rate variation and its impact on phylogenetic analysis. TREE 11:367-372.
26. _. 1996b. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
27. _. 1996c. Phylogenetic analysis by maximum likelihood (PAML). Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park.
28. YANG, Z., S. KUMAR, and M. NEI. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.
29. ZUCKERKANDL, E., and L. PAULING. 1965. Evolutionary divergence and convergence in proteins. Pp. 97-166 in V. BRYSON and H. L. VOGEL, eds. Evolving genes and proteins. Academic Press, New York.