Molecular population genetics of Xdh and the evolution of base composition in Drosophila

Genetics

Volumn 162, Issue 4, 2002, Pages 1725-1735

  Begun, David J ^a,b   Whitley, Penn ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; AMINO ACID; CYTOSINE; GUANINE; THYMIDINE; XANTHINE DEHYDROGENASE;

AMINO ACID COMPOSITION; ARTICLE; DNA POLYMORPHISM; DROSOPHILA; GENE LOCUS; GENE MUTATION; HETEROZYGOSITY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; PROTEIN VARIANT;

AMINO ACID SUBSTITUTION; ANIMALS; BASE COMPOSITION; DNA; DROSOPHILA; EVOLUTION, MOLECULAR; GENES, INSECT; GENETICS, POPULATION; HETEROZYGOTE; MOLECULAR BIOLOGY; MOLECULAR SEQUENCE DATA; MUTATION; POLYMORPHISM, GENETIC; SELECTION (GENETICS); SPECIES SPECIFICITY; VARIATION (GENETICS); XANTHINE DEHYDROGENASE;

ARACHNIDA; HEXAPODA;

EID: 0036964070     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (37)

1. AKASHI, H., 1995 Inferring weak selection from patterns of polymorphism and divergence at silent sites in Drosophila. Genetics 139: 1067-1076.
2. AKASHI, H., 1996 Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144: 1297-1307.
3. AKASHI, H., 1999 Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistica-power to detect directional selection under stationarity and free recombination. Genetics 151: 221-238.
4. AKASHI, H., and S. W. SCHAEFFER, 1997 Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics 146: 295-307.
5. ANDOLFATTO, P., 2001 Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol. Biol. Evol. 18: 279-290.
6. AQUADRO, C. F., K. M. LADO and W. A. NOON, 1988 The rosy region of Drosophila melanogaster and Drosophila simulans. I. Contrasting levels of naturally occurring DNA restriction map variation and divergence. Genetics 119: 875-878.
7. BEGUN, D. J., 1996 Population genetics of silent and replacement variation in Drosophila simulans and D. melanogaster: X/autosome differences? Mol. Biol. Evol. 13: 1405-1407.
8. BEGUN, D. J., 2001 The frequency distribution of nucleotide variation in Drosophila simulans. Mol. Biol. Evol. 18: 1343-1352.
9. BERGMAN, C. M., and M. KREITMAN, 2001 Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Res. 11: 13:35-1345.
10. CHERRY, J. L., 1998 Should we expect substitution rate to depend on population size? Genetics 150: 911-919.
11. CHOUDHARY, M., and R. S. SINGH, 1987 A comprehensive study of genic variation in Drosophila melanogaster III. Variations in genetic structure and their causes between Drosophila melanogaster and its sibling species Drosophila simulans. Genetics 117: 697-710.
12. FISHER, R. A., 1958 The Genetical Theory of Natural Selection. Dover Publications, New York.
13. GILLESPIE, J. H., 1999 The role of population size in molecular evolution. Theor. Popul. Biol. 55: 145-156.
14. GILLESPIE, J. H., 2000 Genetic drift in an infinite population: the pseudohitchhiking model. Genetics 155: 909-919.
15. GILLESPIE, J. H., 2001 Is the population size of a species relevant to its evolution? Evolution 55: 2161-2169.
16. GLEASON, J. M., and J. R. POWELL, 1997 Interspecific and intraspecific comparisons of the period locus in the Drosophila willistoni sibling species. Mol. Biol. Evol. 14: 741-753.
17. HEY, J., and R. M. KLIMAN, 1993 Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex. Mol. Biol. Evol. 10: 804-822.
18. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
19. KLIMAN, R. M., P. ANDOLFATTO, J. A. COYNE, F. DEPAULIS, M. KREITMAN et al., 2000 The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156: 1913-1931.
20. KREITMAN, M., and M. ANTEZANA, 2000 Population and evolutionary genetics of codon usage in Drosophila, pp. 82-101 in Evolutionary Genetics: From Molecules to Morphology, edited by R. SINGH and C. KRIMBAS. Cambridge University Press, Oxford.
21. McVEAN, G. A. T., and B. CHARLESWORTH, 1999 A population genetic model for the evolution of synonymous codon usage: patterns and predictions. Genet. Res. 74: 145-158.
22. MCVEAN, G. A. T., and J. VIEIRA, 1999 The evolution of codon preference in Drosophila: a maximum-likelihood approach to parameter estimation and hypothesis testing. J. Mol. Evol. 49: 63-75.
23. MCVEAN, G. A. T., and J. VIEIRA, 2001 Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics 157: 245-257.
24. MORIYA, E., and J. R. POWELL, 1996 Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13: 261-277.
25. OHTA, T., 1992 The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23: 263-286.
26. POWELL, J. R., 1997 Progress and Prospects in Evolutionary Biology: The Drosophila Model. Oxford University Press, New York.
27. RILEY, M. A., S. R. KAPLAN and M. VEUILLE, 1992 Nucleotide polymorphism at the xanthine dehydrogenase locus in Drosophila pseudo-obscura. Mol. Biol. Evol. 9: 56-69.
28. RODRIGUEZ-TRELLES, F., R. TARRIO and F. J. AYALA, 1999 Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group. Genetics 153: 339-350.
29. RODRIGUEZ-TRELLES, F., R. TARRIO and F. J. AYALA, 2000 Fluctuating mutation bias and the evolution of base composition in Drosophila. J. Mol. Evol. 50: 1-10.
30. ROZAS, J., and R. ROZAS, 1999 DnaSP 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
31. SKIBINSKI, D. O. F., and R. D. WARD, 1982 Correlations between heterozygosity and evolutionary rate of proteins. Nature 298: 490-492.
32. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
33. TAKANO, T. S., 1998 Rate variation of DNA sequence evolution in the Drosophila lineages. Genetics 149: 959-970.
34. TAKANO-SHIMIZU, T., 2001 Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. Mol. Biol. Evol. 18: 606-619.
35. WRIGHT, F., 1990 The effective number of codons used in a gene. Gene 87: 23-39.
36. WRIGHT, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.
37. WRIGHT, S., 1932 The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proceedings of the Sixth International Congress in Genetics, Vol 1. pp. 356-366.