Fluctuating mutation bias and the evolution of base composition in Drosophila

Journal of Molecular Evolution

Volumn 50, Issue 1, 2000, Pages 1-10

  Rodríguez Trelles, Francisco ^a   Tarrío, Rosa ^a   Ayala, Francisco J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Among site rate heterogeneity; Mutation bias; Nonsynonymous synonymous rate ratio; Nucleotide composition; saltans group; willistoni group

Indexed keywords

ALCOHOL DEHYDROGENASE; XANTHINE DEHYDROGENASE;

AMINO ACID SUBSTITUTION; ARTICLE; DROSOPHILA; EVOLUTION; GENETIC HETEROGENEITY; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POINT MUTATION; SEQUENCE ANALYSIS;

DROSOPHILA; DROSOPHILA SALTANS; HAWAIIA; SALTANS GROUP; WILLISTONI GROUP;

EID: 0033938993     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002399910001     Document Type: Article

References (49)

1. Akashi H (1995) Inferring weak selection from patterns of polymorphism and divergence at 'silent' sites in Drosophila DNA. 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, Schaeffer SW (1997) Natural selection and the frequency distributions of 'silent' DNA polymorphism in Drosophila. Genetics 146:295-307
4. Bernardi G (1995) The human genome: organization and evolutionary history. Annu Rev Genet 29:445-476
5. Bernardi G, Oloffsson B, Filipski J, et al. (1985) The mosaic genome of warm-blooded vertebrates. Science 228:953-958
6. Bernardi G, Mouchiroud C, Gautier C, Bernardi G (1988) Compositional patterns in vertebrate genomes: conservation and change in evolution. J Mol Evol 28:7-18
7. DeSalle R, Templeton AR (1988) Founder effects and the rate of mitochondrial DNA evolution in Hawaiian Drosophila. Evolution 42: 1076-1084
8. Feder ME (1996) Ecological and evolutionary physiology of stress proteins and the stress response: The Drosophila melanogaster model. In: Johnston IA, Bennett AF (eds) Animals and temperature. Cambridge University Press, Cambridge, pp 79-102
9. Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1-15
10. Felsenstein J (1993) PHYLIP - Phylogeny inference package, v. 3.5c. University of Washington, Seattle
11. Fitch WM, Ayala FJ (1994) The superoxide dismutase molecular clock revisited. Proc Natl Acad Sci USA 91:6802-6807
12. Francino MP, Ochman H (1999) Isochores result from mutation not selection. Nature 400:30-31
13. Galtier N, Lobry JR (1997) Relationships between genomic G+C content, RNA secondary structure and optimal growth temperature in prokaryotes. J Mol Evol 44:632-636
14. Goldman N, Yang Y (1994) A codon-based model of nucleotide substitutions for protein-coding DNA sequences. Mol Biol Evol 11: 725-736
15. Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174
16. Ikemura T (1985) Codon usage and t-RNA content in unicellular and multicellular organisms. Mol Biol Evol 2:13-34
17. Ina Y (1995) New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J Mol Evol 40:190-226
18. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. CABIOS 8:275-282
19. Kagawa YH, Nojima N, Nukiwa N, et al. (1984) High guanine plus cytosine content in the third letter of codons of an extreme thermophile. J Biol Chem 259:2956-2960
20. Kliman M, Hey J (1994) The effects of mutation and natural selection on codon bias in the genes of Drosophila. Genetics 137:1049-1056
21. Lee KY, Wahl R, Barbu E (1956) Contenu en bases puriques et pyrimidiques des acids desoxyribonucleiques des bacteries. Ann Inst Pasteur 91:212-224
22. Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitutions. J Mol Evol 36:96-99
23. Li W-H (1997) Molecular evolution. Sinauer Associates, Sunderland, MA Moriyama EN, Hartl DL (1993) Codon usage bias and basecomposition of nuclear genes in Drosophila, Genetics 134:847-858
24. Li W-H (1997) Molecular evolution. Sinauer Associates, Sunderland, MA Moriyama EN, Hartl DL (1993) Codon usage bias and base composition of nuclear genes in Drosophila, Genetics 134:847-858
25. Nei M, Gojobori T (1986) Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-426
26. Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936
27. Ohta T (1993) Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc Natl Acad Sci USA 90:4548-4551
28. Patterson JT, Stone WS (1952) Evolution in the genus Drosophila. Macmillan, New York
29. Powell JR (1997) Progress and prospects in evolutionary biology: The Drosophila model. Oxford University Press, New York
30. Powell JR, DeSalle R (1995) Drosophila molecular phylogenies and their uses. Evol Biol 28:87-138
31. Petrov DA, Hartl DL (1999) Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc Natl Acad Sci USA 96:1475-1479
32. Rodríguez-Trelles F, Tarrío R, Ayala FJ (1999a) Molecular evolution and phylogeny of the Drosophila saltans species group inferred from the Xdh gene. Mol Phylogenet Evol 13:110-121
33. Rodríguez-Trelles F, Tarrío R, Ayala FJ (1999b) Switch in codon bias and increased rates of amino acid substitution in the Drosophila sultans species group. Genetics 153:339-350
34. Shields DC, Sharp PM, Higgins DG, Wright F (1988) "Silent" sites in Drosophila genes are not neutral: Evidence of selection among synonymous codons. Mol Biol Evol 5:704-716
35. Sueoka N (1962) On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci USA 48:582-592
36. Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA 85:2653-2657
37. Sueoka N (1993) Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J Mol Evol 37:137-153
38. Tarrío R, Rodríguez-Trelles F, Ayala FJ (1998) New Drosophila introns originate by duplication. Proc Natl Acad Sci USA 95:1658-1652
39. Tatarenkov A, Kwiatowski J, Skarecky D, Barrio E, Ayala JF (1999) On the evolution of Dopa decarboxylase (Ddc) and Drosophila systematics. J Mol Evol 48:445-462
40. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
41. Throckmorton LH (1975) The phylogeny ecology and geography of Drosophila. In: King RC (ed) Handbook of genetics, Vol 3. Plenum Press, New York, pp 421-436
42. Yang Z (1994) Estimating the pattern of nucleotide substitution. J Mol Evol 39:105-111
43. Yang Z (1995) A space-time process model for the evolution of DNA sequences. Genetics 139:993-1005
44. Yang Z (1996) Maximum likelihood models for combined analyses of multiple sequence data. J Mol Evol 42:587-596
45. Yang Z (1997) PAML, a program package for phylogenetic analysis by maximum likelihood CABIOS 13:555-556
46. Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15: 568-573
47. Yang Z, Nielsen R (1998) Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol 46:409-418
48. Yang Z, Nielsen R, Hasegawa M (1998) Models of amino acid substitution and applications to mitochondrial DNA evolution. Mol Biol Evol 15:1600-1611
49. Zhang J, Gu X (1998) Correlation between the substitution rate and rate variation among sites in protein evolution. Genetics 149:1615-1625