The evolution of isochores: Evidence from SNP frequency distributions

Genetics

Volumn 162, Issue 4, 2002, Pages 1805-1810

  Lercher, Martin J ^a   Smith, Nick G C ^b   Eyre Walker, Adam ^c   Hurst, Laurence D ^a  

^a University of Bath ^*  (United Kingdom)

^b UPPSALA UNIVERSITY   (Sweden)

^c UNIVERSITY OF SUSSEX   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE; NUCLEOTIDE;

ARTICLE; GENE CONVERSION; GENE FREQUENCY; GENE MUTATION; GENETIC CODE; GENETIC MODEL; HUMAN; HUMAN GENOME; ISOCHORE; MOLECULAR EVOLUTION; NUCLEIC ACID BASE SUBSTITUTION; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; ANIMALS; BASE COMPOSITION; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; ISOCHORES; MODELS, GENETIC; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION (GENETICS);

AVES; MAMMALIA;

EID: 12244264796     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (30)

1. AKASHI, H., 1999 Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. Genetics 151: 221-238.
2. AKASHI, H., and S. W. SCHAEFFER, 1997 Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics 146: 295-307.
3. BERNARDI, G., 2000 Isochores and the evolutionary genomics of vertebrates. Gene 241: 3-17.
4. CHARLESWORTH, B., 1994 The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63: 213-227.
5. CLAY, O., S. CACCIO, S. ZOUBAK, D. MOUCHIROUD and G. BERNARDI, 1996 Human coding and noncoding DNA: compositional correlations. Mol. Phylogenet. Evol. 5: 2-12.
6. DRAKE, W., B. CHARLESWORTH, D. CHARLESWORTH and J. F. CROW, 1998 Rates of spontaneous mutation. Genetics 148: 1667-1686.
7. DURET, L., M. SENION, G. PIGANEAU, D. MOUCHIROUD and N. GALTIER, 2002 Vanishing GC-rich isochores in mammalian genomes. Genetics 162: 1837-1847.
8. EWENS, W. J., 1972 The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 3: 87-112.
9. EYRE-WALKER, A., 1997 Differentiating between selection and mutation bias. Genetics 147: 1983-1987.
10. 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.
11. EYRE-WALKER, A., and L. D. HURST, 2001 The evolution of isochores. Nat. Rev. Genet. 2: 549-555.
12. FAY, J. C., and C.-I Wu, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
13. FILIPSKI, J., 1987 Correlation between molecular clock ticking, codon usage, fidelity of DNA-repair, chromosome-banding and chromatin compactness in germline cells. FEBS Lett. 217: 184-186.
14. FRANCINO, H. P., and H. OCHMAN, 1999 Isochores result from mutation not selection. Nature 400: 30-31.
15. GALTIER, N., and D. MOUCHIROUD, 1998 Isochore evolution in mammals: a human-like ancestral structure. Genetics 150: 1577-1584.
16. IHGSC, 2001 Initial sequencing and analysis of the human genome. Nature 409: 860-921.
17. KITAMURA, M., 1983 The Neutral Theory of Evolution. Cambridge University Press, Cambridge, UK.
18. KIMURA, M., and T. OHTA, 1973 The age of a neutral mutant persisting in a finite population. Genetics 75: 199-212.
19. KLIMAN, R. M., 1999 Recent selection on synonymous codon usage in Drosophila. J. Mol. Evol. 49: 343-351.
20. LOBRY, J. R., 1997 Influence ofgenomic G+C content on average amino-acid composition of proteins from 59 bacterial species. Gene 205: 309-316.
21. NAGYLAKI, T., 1983 Evolution of a finite population under gene conversion. Proc. Natl. Acad. Sci. USA 80: 6278-6281.
22. POWELL, J. R., and E. N. MORIYAMA, 1997 Evolution of codon usage bias in Drosophila. Proc. Natl. Acad. Sci. USA 94: 7784-7790.
23. RODRIGUEZ-TRELLES, F., R. TARRIO and F. J. AYALA, 2000 Evidence for a high ancestral GC content in Drosophila. Mol. Biol. Evol. 17: 1710-1717.
24. SAWYER, S. A., and D. L. HARTL, 1992 Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
25. SAWYER, S. A., D. E. DYKHUIZEN and D. L. HARTL, 1987 Confidence interval for the number of selectively neutral amino acid polymorphisms. Proc. Natl. Acad. Sci. USA 84: 6225-6228.
26. SMITH, N. G. C., and A. EYRE-WALKER, 2001 Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans. Mol. Biol. Evol. 18: 982-986.
27. SUEOKA, N., 1988 Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85: 2653-2657.
28. WOLFE, K. H., P. M. SHARP and W.-H. LI, 1989 Mutation rates differ among regions of the mammalian genome. Nature 337: 283-285.
29. WRIGHT, S., 1937 The distribution of gene frequencies in populations. Proc. Natl. Acad. Sci. USA 23: 307-320.
30. Yu, A., C. ZHAO, Y. FAN, W. JANG, A. J. MUNGALL et al., 2001 Comparison of human genetic and sequence-based physical maps. Nature 409: 951-953.