The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents

Genetics

Volumn 153, Issue 3, 1999, Pages 1395-1402

  Smith, Nick G C ^a,b   Hurst, Laurence D ^a  

^a University of Bath ^*  (United Kingdom)

^b UNIVERSITY OF SUSSEX   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA;

ALGORITHM; ARTICLE; CORRELATION FUNCTION; DNA BASE COMPOSITION; GENETIC SELECTION; MOLECULAR EVOLUTION; MUTATION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; RNA STRUCTURE; RODENT; TANDEM REPEAT;

ALGORITHMS; ANIMALS; DNA; HUMANS; LIKELIHOOD FUNCTIONS; MAMMALS; MICE; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; RATS; RODENTIA;

MAMMALIA; RODENTIA;

EID: 0032714307     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (39)

1. AKASHI, H., and A. EYRE-WALKER, 1998 Translational selection and molecular evolution. Curr. Opin. Genet. Dev. 8: 688-693.
2. ALVAREZ-VALIN, F., K. JABBARI and G. BERNARDI, 1998 Synonymous and nonsynonymous substitutions in mammalian genes: intragenic correlations. J. Mol. Evol. 46: 37-44.
3. BERNARDI, G., D. MOUCHIROUD and C. GAUTIER, 1997 Isochores and synonymous substitutions in mammalian genes, pp. 137-168 in DNA and Protein Sequence Analysis, edited by M. J. BISHOP and C. J. RAWLINGS. Oxford University Press, Oxford.
4. COMERON, J. M., and M. AGUADE, 1996 Synonymous substitutions in the Xdh gene of Drosophila - heterogeneous distribution along the coding region. Genetics 144: 1053-1062.
5. DURET, L., D. MOUCHIROUD and M. GOUY, 1994 Hovergen - a database of homologous vertebrate genes. Nucleic Acids Res. 22: 2360-2365.
6. EYRE-WALKER, A., 1991 An analysis of codon usage in mammals: selection or mutation bias? J. Mol. Evol. 33: 442-449.
7. EYRE-WALKER, A., 1993 Recombination and mammalian genome evolution. Proc. R. Soc. Lond. Ser. B 252: 237-243.
8. EYRE-WALKER, A., 1998 Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47: 686-690.
9. EYRE-WALKER, A., 1999 Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics 152: 675-683.
10. EYRE-WALKER, A., and M. BULMER, 1993 Reduced synonymous substitution rate at the start of enterobacterial genes. Nucleic Acids Res. 21: 4599-4603.
11. GCG, 1994 Program Manual for the Wisconsin Package, Version 8. Genetics Computer Group, Madison, WI.
12. GOLDMAN, N. and Z. YANG, 1994 A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11: 725-736.
13. HUGHES, A. L., and M. YEAGER, 1997 Comparative evolutionary rates of introns and exons in murine rodents. J. Mol. Evol. 45: 125-130.
14. INA, Y., 1996a Correlation between synonymous and nonsynonymous substitutions and variation in synonymous substitution numbers, pp. 105-113 in Current Topics on Molecular Evolution, edited by M. NEI and N. TAKAHATA. Institute of Molecular Evolutionary Genetics, Penn State University, University Park, PA and The Graduate University for Advanced Studies, Hayama, Japan.
15. INA, Y., 1996b Pattern of synonymous and nonsynonymous substitutions: an indicator of mechanisms of molecular evolution. J. Genet. 75: 91-115.
16. KONDRASHOV, A. S., 1995 Modifiers of mutation-selection balance: general-approach and the evolution of mutation-rates. Genet. Res. 66: 53-69.
17. LI, W. H., 1993 Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
18. LI, W. H., 1997 Molecular Evolution. Sinauer Associates, Sunderland, MA.
19. LI, W. H., C. I. WU and C. C. LUO, 1985 A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174.
20. LIPMAN, D. J., and W. J. WILBUR, 1985 Interaction of silent and replacement changes in eukaryotic coding sequences. J. Mol. Evol. 21: 161-167.
21. MAKALOWSKI, W., and M. S. BOGUSKI, 1998a Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. USA 95: 9407-9412.
22. MAKALOWSKI, W., and M. S. BOGUSKI, 1998b Synonymous and nonsynonymous substitution distances are correlated in mouse and rat genes. J. Mol. Evol. 47: 119-121.
23. MCVEAN, G. T., and L. D. HURST, 1997a Evidence for a selectively favourable reduction in the mutation rate of the X chromosome. Nature 386: 388-392.
24. MCVEAN, G. T., and L. D. HURST, 1997b Molecular evolution of imprinted genes: no evidence for antagonistic coevolution. Proc. R. Soc. Lond. Ser. B 264: 739-746.
25. MORIYAMA, E. N., and J. R. POWELL, 1997 Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J. Mol. Evol. 45: 378-391.
26. MOUCHIROUD, D., C. GAUTIER and G. BERNARDI, 1995 Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. J. Mol. Evol. 40: 107-113.
27. OHTA, T., 1995 Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J. Mol. Evol. 40: 56-63.
28. OHTA, T., and Y. INA, 1995 Variation in synonymous substitution rates among mammalian genes and the correlation between synonymous and nonsynonymous divergences. J. Mol. Evol. 41: 717-720.
29. PESOLE, G., G. DELLISANTI, G. PREPARATA and C. SACCONE, 1995 The importance of base composition in the correct assessment of genetic distance. J. Mol. Evol. 41: 1124-1127.
30. RICE, P., 1997 Program Manual for the EGCG Package. The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, England.
31. SMITH, N. G. C., and L. D. HURST, 1998 Sensitivity of patterns of molecular evolution to alterations in methodology: a critique of Hughes and Yeager. J. Mol. Evol. 47: 493-500.
32. SMITH, N. G. C., and L. D. HURST, 1999 The causes of synonymous rate variation in the rodent genome: can substitution rates be used to estimate the sex bias in mutation rate? Genetics 152: 661-673.
33. SOKAL, R. R., and F. J. ROHLF, 1995 Biometry. W. H. Freeman and Company, New York.
34. TAMURA, K., 1992 Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C content biases. Mol. Biol. Evol. 10: 512-526.
35. TAMURA, K., and M. NEI, 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
36. THOMPSON, J. D., D. G. HIGGINS and T.J. GIBSON, 1994 ClustalW - 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.
37. WOLFE, K. H., and P. M. SHARP, 1993 Mammalian gene evolution - nucleotide sequence divergence between mouse and rat. J. Mol. Evol. 37: 441-456.
38. WOLFE, K. H., P. M. SHARP and W. H. LI, 1989 Mutation rates differ among regions of the mammalian genome. Nature 337: 283-285.
39. YANG, Z., 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.