Nucleotide Polymorphism in the RpII215 Gene Region of the Insular Species Drosophila guanche: Reduced Efficacy of Weak Selection on Synonymous Variation

Molecular Biology and Evolution

Volumn 20, Issue 11, 2003, Pages 1867-1875

  Pérez, José A ^a,b   Munté, Agustí ^a   Rozas, Julio ^a   Segarra, Carmen ^a   Aguadé, Montserrat ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

^b UNIVERSIDAD DE LA LAGUNA   (Spain)

Author keywords

Codon bias; Drosophila guanche; Drosophila subobscura; Effective population size; Weak selection

Indexed keywords

ARTICLE; CODON; COMPARATIVE STUDY; DNA POLYMORPHISM; DROSOPHILA; DROSOPHILA GUANCHE; DROSOPHILA SUBOBSCURA; EFFECTIVE POPULATION SIZE; FEMALE; GENE; GENE SEQUENCE; GENETIC SELECTION; GENETIC VARIABILITY; MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; RPII215 GENE; SPECIES DIFFERENCE; SPECIES ENDEMICITY;

ANIMALS; BASE SEQUENCE; CODON; DROSOPHILA; GENES, INSECT; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; SPECIES SPECIFICITY; VARIATION (GENETICS);

DROSOPHILA GUANCHE; DROSOPHILA SUBOBSCURA;

EID: 0242582368     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg199     Document Type: Article

References (52)

1. Akashi, H. 1994. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136:927-935.
2. -. 1995. Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 139:1067-1076.
3. -. 1997. Distinguishing the effects of mutational biases and natural selection on DNA sequence variation. Genetics 147:1989-1991.
4. -. 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.
5. Akashi, H., and S. W. Schaeffer. 1997. Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics 146:295-307.
6. Ashbumer, M. 1989. Drosophila, a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
7. Begun, D. J. 2002. Protein variation in Drosophila simulans, and comparison of genes from centromeric versus noncentromeric regions of chromosome 3. Mol. Biol. Evol. 19:201-203.
8. Bulmer, M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907.
9. Comeron, J. M., and M. Kreitman. 2002. Population, evolutionary and genomic consequences of interference selection. Genetics 161:389-410.
10. Comeron, J. M., M. Kreitman, and M. Aguadé. 1999. Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 151:239-249.
11. Duret, L., and D. Mouchiroud. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc. Natl. Acad. Sci. USA 96:4482-4487.
12. Eyre-Walker, A. 1997. Differentiating between selection and mutation bias. Genetics 147:1983-1987.
13. Gillespie, J. H. 2000. Genetic drift in an infinite population: the pseudohitchhiking model. Genetics 155:909-919.
14. -. 2001. Is the population size of a species relevant to its evolution? Evolution 55:2161-2169.
15. Hagemann, T. L., and S. P. Kwan. 1997. SeqEd: manipulation of sequence data and chromatograms from the ABI DNA sequencer analysis files. Methods Mol. Biol. 70:55-63.
16. Harti, D. L., E. N. Moriyama, and S. A. Sawyer. 1994. Selection intensity for codon bias. Genetics 138:227-234.
17. Hey, J., and R. M. Kliman. 2002. Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160:595-608.
18. Hudson, R. R. 2000. A new statistic for detecting genetic differentiation. Genetics 155:2011-2014.
19. Hudson, R. R., D. D. Boos, and N. L. Kaplan. 1992. A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9:138-151.
20. Hudson, R. R., and N. L. Kaplan. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147-164.
21. Jokerst, R. S., J. R. Weeks, W. A. Zehring, and A. L. Greenleaf. 1989. Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila. Mol. Gen. Genet. 215:266-275.
22. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-123 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
23. Kelly, J. K. 1997. A test of neutrality based on interlocus associations. Genetics 146:1197-1206.
24. Kliman, R. M. 1999. Recent selection on synonymous codon usage in Drosophila. J. Mol. Evol. 49:343-351.
25. Kliman, R. M., and J. Hey. 1993. Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol. Biol. Evol. 10:1239-1258.
26. -. 1994. The effects of mutation and natural selection on codon bias in the genes of Drosophila. Genetics 137:1049-1056.
27. Kreitman, M., and M. Antezana. 2000. The population and evolutionary genetics of codon bias. Pp. 82-101 in R. S. Singh and C. B. Krimbas, eds. Evolutionary genetics: from molecules to morphology, Cambridge University Press, Cambridge.
28. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
29. Lewontin, R. C. 1974. The genetic basis of evolutionary change. Columbia University Press, New York.
30. Li, W.-H. 1987. Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J. Mol. Evol. 24:337-345.
31. Llopart, A., and M. Aguadé. 1999. Synonymous rates at the RpII215 gene of Drosophila: variation among species and across the coding region. Genetics 152:269-280.
32. -. 2000. Nucleotide polymorphism at the RpII215 gene in Drosophila subobscura: weak selection on synonymous mutations. Genetics 155:1245-1252.
33. Maddison, W. P., and D. R. Maddison. 1992. MacClade: analysis of phylogeny and character evolution. Version 3.0. Sinauer Associates, Sunderland, Mass.
34. McVean, G. A., and B. Charlesworth. 2000. The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 155:929-944.
35. Moriyama, E. N., and D. L. Hartl. 1993. Codon usage bias and base composition of nuclear genes in Drosophila. Genetics 134:847-858.
36. Munté, A., M. Aguadé, and C. Segarra. 1997. Divergence of the yellow gene between Drosophila melanogaster and D. subobscura: recombination rate, codon bias and synonymous substitutions. Genetics 147:165-175.
37. -. 2001. Changes in the recombinational environment affect divergence in the yellow gene of Drosophila. Mol. Biol. Evol. 18:1045-1056.
38. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
39. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
40. Ohta, T. 1972. Evolutionary rate of cistrons and DNA divergence. J. Mol. Evol. 1:150-157.
41. Ohta, T., and M. Kimura. 1971. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1:18-25.
42. Petrov, D. A., and D. L. Hartl. 1999. Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc. Natl. Acad. Sci. USA 96:1475-1479.
43. Ramos-Onsins, S., C. Segarra, J. Rozas, and M. Aguadé. 1998. Molecular and chromosomal phylogeny in the obscura group of Drosophila inferred from sequences of the rp49 gene region. Mol. Phylogenet. Evol. 9:33-41.
44. Rozas, J., and R. Rozas. 1999. DnaSP: an integrated program for molecular population genetics and molecular evolution analysis. Version 3. Bioinformatics. 15:174-175.
45. Rozas, J., M. Gullaud, G. Blandin, and M. Aguadé. 2001. DNA variation at the rp49 gene region of Drosophila simulans: evolutionary inferences from an unusual haplotype structure. Genetics 158:1147-1155.
46. Saitou, N., and M. Nei. 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
47. Sawyer, S. A., and D. L. Hartl. 1992. Population genetics of polymorphism and divergence. Genetics 132:1161-1176.
48. Segarra, C., and M. Aguadé. 1992. Molecular organization of the X chromosome in different species of the obscura group of Drosophila. Genetics 130:513-521.
49. Shields, D. C., P. M. Sharp, D. G. Higgins, and F. Wright. 1988. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol. 5:704-716.
50. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
51. Takano-Shimizu, T. 1999. Local recombination and mutation effects on molecular evolution in Drosophila. Genetics 153:1285-1296.
52. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: 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.