Analysis of a Shift in Codon Usage in Drosophila

Journal of Molecular Evolution

Volumn 57, Issue SUPPL. 1, 2003, Pages

  Powell, Jeffrey R ^a   Sezzi, Erminia ^a,c   Moriyama, Etsuko N ^b   Gleason, Jennifer M ^a,d   Caccone, Adalgisa ^a  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF NEBRASKA   (United States)

^c UNIVERSITY OF TUSCIA   (Italy)

^d UNIVERSITY OF KANSAS   (United States)

Author keywords

Codon usage bias; Drosophila saltans; Drosophila willistoni; tRNA

Indexed keywords

TRANSFER RNA;

CODON; CODON USAGE; CONFERENCE PAPER; DROSOPHILA; GENE MUTATION; INTRON; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; SPECIES DIFFERENTIATION; UNINDEXED SEQUENCE;

AMINO ACIDS; ANIMALS; CODON; DROSOPHILA; EVOLUTION; INTRONS; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; RNA, TRANSFER;

DROSOPHILA MELANOGASTER; DROSOPHILA SALTANS; DROSOPHILA WILLISTONI; MELANOGASTER;

EID: 0346120050     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-0030-3     Document Type: Conference Paper

References (38)

1. Anderson CL, Carew EA, Powell JR (1993) Evolution of the Adh locus in the Drosophila willistoni group: The loss of an intron, and shift in codon usage. Mol Biol Evol 10:605-618
2. Dobzhansky TH, Powell JR (1975) The willistoni group of sibling species. In: King R (ed) Handbook of genetics, volume 3. Plenum Press, New York, pp 589-622
3. Dunn KA, Bielawski JP, Yang Z (2001) Substitution rates in Drosophila nuclear genes: Implications for translational selection. Genetics 157:295-305
4. Farris JS (1970) Methods for computing Wagner trees. Syst Zool 18:374-402
5. Farris JS, Kallersjo M, Kluge AG, Bult C (1995) Testing significance of incongruence. Cladistics 10:315-319
6. Felsestein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17:368-376
7. Gleason JM, Powell JR (1997) Interspecific and intraspecific comparisons of the period locus in the Drosophila willistoni sibling species. Mol Biol Evol 14:741-753
8. Griffith EC, Powell JR (1997) Adh nucleotide variation in Drosophila willistoni: High replacement polymorphism in an electrophoretically monomorphic protein. J Mol Evol 45:232-237
9. Hosbach HA, Kubli E (1979) Transfer RNA in aging Drosophila: II. Isoacceptor patterns. Mech Ageing Dev 10:141-149
10. Ikemura T (1992) Correlation between codon usage and tRNA content in microorganisms. In: Hatfield DL, Lee BJ, Pirtle RM (eds) Transfer RNA in protein synthesis. CRC Press, Boca Raton, pp 87-111
11. Kliman RM, Hey J (1993) Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol Biol Evol 10:1239-1258
12. Larson A (1994) The comparison of morphological and molecular data in phylogenetic systematics. In: Schierwater B, Streit B, Wagner GP, DeSalle R (eds) Molecular ecology and evolution: Approaches and applications. Birkhäuser, Basil, pp 371-390
13. Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96-99
14. His influences in vivo decoding properties. EMBO J 4:823-836
15. Moriyama EN, Hartl DL (1993) Codon usage bias and base composition of nuclear genes in Drosophila. Genetics 134:847-858
16. Moriyama EN, Petrov DA, Hartl DL (1998) Genome size and intron size in Drosophila. Mol Biol Evol 15:770-773
17. Moriyama EN, Powell JR (1996) Intraspecific nuclear DNA variation in Drosophila. Mol Biol Evol 13:261-277
18. Moriyama EN, Powell JR (1997) Codon usage bias and tRNA abundance in Drosophila. J Mol Evol 45:514-523
19. Moriyama EN, Powell JR (1997) Synonymous substitution rates of Drosophila: Mitochondrial versus nuclear genes. J Mol Evol 45:378-391
20. O'Grady PM, Kidwell MG (2002) Phylogeny of the subgenus Sophophora (Diptera: Drosophilidae) based on combined analysis of nuclear and mitocondrial sequences. Mol Phylogenet Evol 22:442-453
21. O'Grady PM, Clark JB, Kidwell MG (1998) Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences. Mol Biol Evol 15:656-664
22. Owenby RK, Stulberg MP, Jacobson KB (1979) Alteration of the Q family of transfer RNAs in adult Drosophila melanogaster as a function of age, nutrition, and genotype. Mech Ageing Dev 11:91-103
23. Powell JR, DeSalle R (1995) Drosophila molecular phylogenies and their uses. Evol Biol 28:87-138
24. Powell JR, Moriyama EN (1997) Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA 94:7784-7790
25. Rodriguez-Trelles F, Tarrio R, Ayala FJ (2000a) Evidence for a high ancestral GC content in Drosophila. Mol Biol Evol 17:1710-1717
26. Rodriguez-Trelles F, Tarrio R, Ayala FJ (2000b) Fluctuating mutation bias and the evolution of base composition in Drosophila. J Mol Evol 50:1-10
27. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
28. Sharp PM, Li W-H (1987) The codon adaptation index - A measure of directional synonymous codon usage bias. and its potential applications. Nucleic Acids Res 15:1281-1295
29. Sharp PM, Li W-H (1987) The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol 4:222-230
30. Sharp PM, Li W-H (1989) On the rate of DNA sequence evolution in Drosophila. J Mol Evol 28:398-402
31. 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
32. Swofford D (2001) PAUP*, phylogenetic analysis using parimony (* and other methods). Version 4.0b. Sinauer Associates, Sunderland, MA
33. Tamura K, Nei M (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
34. Tarrio R, Rodríguez-Trelles F, Ayala FJ (2000) Tree rooting with outgroups when they differ in their nucleotide composition from the ingroup: The Drosophila saltans and willistoni groups, a case study. Mol Phylog Evol 16:344-349
35. Templeton A (1983) Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution 37:221-244
36. Val FC, Vilela CR, Marques MD (1981) Drosophilidae of the neotropical region. In: Ashburner M, Carson HL, Thompson JN (eds) The genetics and biology of Drosophila, volume 3a. Academic Press, New York, pp 124-168
37. White BN, Tener GM, Holden J, Suzuki DT (1973) Analysis of tRNAs during the development of Drosophila. Develop Biol 33:185-195
38. Wright F (1990) The 'effective number of codons' used in a gene. Gene 87:23-29