Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant

Molecular Biology and Evolution

Volumn 16, Issue 6, 1999, Pages 719-723

  Lobry, J R ^a   Lobry, C ^b  

^a UNIVERSITÉ LYON 1   (France)

^b Ctr Intl Mathematiques Pures Appl   (France)

Author keywords

Base composition skew; DNA base composition; GC content; Mathematical model; Molecular evolution; Parity rules

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; DNA BASE COMPOSITION; DNA SEQUENCE; GENETIC CODE; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE;

EID: 0032976213     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026156     Document Type: Article

References (23)

1. BLATTNER, F. R., G. PLUNKETT III, C. A. BLOCH et al. (14 co-authors). 1997. The complete genome sequence of Escherichia coli K12. Science 277:1453-1462.
2. FILIPSKI, J. 1990. Evolution of DNA sequence, contributions of mutational bias and selection to the origin of chromosomal compartments. Pp. 1-54 in G. OLE, ed. Advances in mutagenesis research 2. Springer-Verlag, Berlin.
3. FRANCINO, M. P., and H. OCHMAN. 1997. Strand asymmetries in DNA evolution. Trends Genet. 13:240-245.
4. FREEMAN, J. M., T. N. PLASTERER, T. F. SMITH, and S. C. MOHR. 1998. Patterns of genome organization in bacteria. Science 279:1827a.
5. GRIGORIEV, A. 1998. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 26:2286-2290.
6. JERMIIN, L. S., D. GRAUR, and R. H. CROZIER. 1995. Evidence from analyses of intergenic region for strand-specific directional mutation pressure in metazoan mitochondrial DNA. Mol. Biol. Evol. 12:558-563.
7. KUNST, F., N. OGASAWARA, I. MOSZER et al. (149 co-authors). 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249-256.
8. KYTE, J., and R. F. DOOLITTLE. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132.
9. LI, W.-H. 1997. Molecular evolution. Sinauer, Sunderland Mass.
10. LOBRY, C., A. SCIANDRA, and P. NIVAL. 1994. Paradoxal effects on growth and competition induced by fluctuations in environment. C. R. Acad. Sci. Life Sci. 317:102-107.
11. LOBRY, J. R. 1995. Properties of a general model of DNA evolution under no-strand-bias conditions. J. Mol. Evol. 40: 326-330 (erratum in J. Mol. Evol. 41:680).
12. _. 1996a. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13:660-665.
13. _. 1996b. Origin of replication of Mycoplasma genitalium. Science 272:745-746.
14. MRÁZEK, J., and S. KARLIN. 1998. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95:3720-3725.
15. REYES. A., C. GISSI, G. PESOLE, and C. SACCONE. 1998. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol. Biol. Evol. 15:957-966.
16. RODRÍGUEZ, E, J. L. OLIVER, A. MARÍN, and J. R. MEDINA. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142:485-501.
17. Aγ fetal globin region. Cell 26:345-353.
18. SUEOKA, N. 1961. Variation and heterogeneity of base composition of deoxyribonucleic acids: a compilation of old and new data. J. Mol. Biol. 3:31-40.
19. _. 1962. On the genetic basis of variation and heterogeneity of DNA base composition. Proc. Natl. Acad. Sci. USA 48:582-592.
20. _. 1995. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J. Mol. Evol. 40:318-325 (erratum in J. Mol. Evol. 42:323).
21. TANAKA, M., and T. OZAWA. 1994. Strand asymmetry in human mitochondrial DNA mutations. Genomics 22:327-335.
22. WU, C.-I., and N. MAEDA. 1987. Inequality in mutation rates of the two strands of DNA. Nature 327:169-170.
23. ZHARKIKH, A. 1994. Estimation of evolutionary distances between nucleotide sequences. J. Mol. Evol. 39:315-329.