Ancestral inference and the study of codon bias evolution: Implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup

PLoS ONE

Volumn 2, Issue 10, 2007, Pages

  Akashi, Hiroshi ^a   Goel, Piyush ^a   John, Anoop ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CODON USAGE; COMPUTER SIMULATION; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE SEQUENCE; GENETIC LINKAGE; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENETIC TREE; PLESIOMORPHY; PROBABILITY; RELIABILITY; SUBSTITUTION LINE; SYSTEMATIC ERROR; ANIMAL; BIOLOGICAL MODEL; CELL LINEAGE; CODON; EVOLUTION; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; STATISTICAL MODEL;

DROSOPHILA MELANOGASTER; MELANOGASTER SUBGROUP;

ANIMALS; CELL LINEAGE; CODON; DNA MUTATIONAL ANALYSIS; DROSOPHILA MELANOGASTER; EVOLUTION; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; POLYMORPHISM, GENETIC; SELECTION (GENETICS); VARIATION (GENETICS);

EID: 42449105765     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001065     Document Type: Article

References (93)

1. Long M, Langley CH (1993) Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260: 91-95.
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. Eanes WF, Kirchner M, Yoon J, Biermann CH, Wang IN, et al. (1996) Historical selection, amino acid polymorphism and lineage-specific divergence at the G6pd locus in Drosophila melanogaster and D. simulans. Genetics 144: 1027-1041.
4. Fitch WM, Bush RM, Bender CA, Cox NJ (l997) Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci U S A 94: 7712-7718.
5. Messier W, Stewart GB (1997) Episodic adaptive evolution of primate iysozymes. Nature 385: 151-154.
6. Takano-Shimizu T (2001) Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. Mol Biol Evol 18: 606-619.
7. Zhang J, Zhang YP, Rosenberg HF (2002) Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet 30: 411-415.
8. Akashi H (1995) Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 139: 1067-1076.
9. 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.
10. Templeton AR (1996) Contingency tests of neutrality using intra/ interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates. Genetics 144: 1263-1270.
11. Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Mol Biol Evol 16: 1315-1328.
12. Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
13. Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, et al. (2005) Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci U S A 102: 7882-7887.
14. Kliman RM (1999) Recent selection on synonymous codon usage in Drosophila. J Mol Evol 49: 343-351.
15. Begun DJ (2001) The frequency distribution of nucleotide variation in Drosophila simulans. Mol Biol Evol 18: 1343-1352.
16. DuMont VB, Fay JC, Calabrese PP, Aquadro CF (2004) DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence. Genetics 167: 171-185.
17. Comeron JM, Guthrie TB (2005) Intragenic Hill-Robertson Interference Influences Selection Intensity on Synonymous Mutations in Drosophila. Mol Biol Evol 22: 2519-2530.
18. Presgraves DC (2005) Recombination enhances protein adaptation in Drosophila melanogaster. Curr Biol 15: 1651-1656.
19. Collins TM, Wimberger PH, Naylor GJP (1994) Compositional Bias, Character-State Bias, and Character-State Reconstruction Using Parsimony. Systematic Biology 43: 482-496.
20. Llopart A, Aguade M (1999) Synonymous rates at the RpII215 gene of Drosophila: variation among species and across the coding region. Genetics 152: 269-280.
21. McVean GA, Vieira J (1999) The evolution of codon preferences in Drosophila. a maximum-likelihood approach to parameter estimation and hypothesis testing. J Mol Evol 49: 63-75.
22. Rodriguez-Trelles F, Tarrio R, Ayala FJ (2000) Evidence for a high ancestral GC content in Drosophila. Mol Biol Evol 17: 1710-1717.
23. Rodriguez-Trelles F, Tarrio R, Ayala FJ (2000) Fluctuating mutation bias and the evolution of base composition in Drosophila. J Mol Evol 50: 1-10.
24. Begun DJ, Whitley P (2002) Molecular population genetics of Xdh and the evolution of base composition in Drosophila. Genetics 162: 1725-1735.
25. Bachtrog D (2003) Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda. Genetics 165: 1221-1232.
26. Perez JA, Munte A, Rozas J, Segarra C, Aguade M (2003) Nucleotide polymorphism in the RpII215 gene region of the insular species Drosophila guanche: reduced efficacy of weak sclection on synonymous variation. Mol Biol Evol 20: 1867-1875.
27. Powell JR, Sezzi E, Moriyama EN, Gleason JM, Caccone A (2003) Analysis of a shift in codon usage in Drosophila. J Mol Evol 57 Suppl 1: S214-225.
28. Duret L, Semon M, Piganeau G, Mouchiroud D, Galtier N (2002) Vanishing GC-rich isochores in mammalian genomes. Genetics 162: 1837-1847.
29. Smith NG, Eyre-Walker A (2002) The compositional evolution of the murid genome. J Mol Evol 55: 197-201.
30. Arndt PF, Petrov DA, Hwa T (2003) Distinct changes of genomic biases in nucleotidc substitution at the time of Mammalian radiation. Mol Biol Evol 20: 1887-1896.
31. Webster MT, Smith NG, Ellegren H (2003) Compositional evolution of noncoding DNA in the human and chimpanzee genomes. Mol Biol Evol 20: 278-286.
32. Belle EM, Duret L, Galtier N, Eyre-Walker A (2004) The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol 58: 653-660.
33. Arndt PF (2007) Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny. Gene 390: 75-83.
34. Zhang Z, Inomata N, Ohba T, Cariou ML, Yamazaki T (2002) Codon bias differentiates between the duplicated amylase loci following gene duplication in Drosophila. Genetics 161: 1187-1196.
35. Akashi H, Ko WY, Piao Sjohn A, God P, et al. (2006) Molecular evolution in the Drosophila melanogaster species subgroup: frequent parameter fluctuations on the timescale of molecular divergence. Genetics 172: 1711-1726.
36. Ko WY, Piao S, Akashi H (2006) Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome. Genetics 174: 349-362.
37. Maside X, Charlesworth B (2007) Patterns of molecular variation and evolution in Drosophila americana and its relatives. Genetics.
38. Perna NT, Kocher TD (1995) Unequal Base Frequencies and Estimation of Substitution Rates. Molecular Biology and Evolution 12: 359-361.
39. Eyre-Walker A (1998) Problems with parsimony in sequences of biased base composition. J Mol Evol 47: 686-690.
40. Galtier N, Boursot P (2000) A new method for locating changes in a tree reveals distinct nucleotide polymorphism vs. divergence patterns in mouse rnitochondrial control region. J Mol Evol 50: 224-231.
41. Alvarez-Valin F, Clay O, Cruveiller S, Bernardi G (2004) Inaccurate reconstruction of ancestral GC levels creates a "vanishing isochores" effect. Mol Phylogenet Evol 31: 788-793.
42. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
43. Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2: 13-34.
44. 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.
45. Andersson SG, Kurland CG (1990) Codon preferences in free-living microorganisms. Microbiol Rev 54: 198-210.
46. Sharp PM, Averof M, Lloyd AT, Matassi G, Peden JF (1995) DNA sequence evolution: the sounds of silence. Philos Trans R Soc Lond B Biol Sci 349: 241-247.
47. Akashi H (2001) Gene expression and molecular evolution. Curr Opin Genet Dev 11: 660-666.
48. Duret L (2002) Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 12: 640-649.
49. Kanaya S, Yamada Y, Kudo Y, Ikemura T (1999) Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238: 143-155.
50. Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T (2001) Cotton usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J Mol Evol 53: 290-298.
51. Moriyama EN, Powell JR (1997) Codon usage bias and tRNA abundance in Drosophila. J Mol Evol 45: 514-523.
52. Duret L (2000) tRNA gene number and codon usage in the C. elegans genome, are co-adapted for optimal translation of highly expressed genes. Trends Genet 16: 287-289.
53. Wright SI, Yau CB, Looseley M, Meyers BC (2004) Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol 21: 1719-1726.
54. Kurland CG (1992).Translational accuracy and the fitness of bacteria. Annu Rev Genet 26: 29-50.
55. Akashi H, Schaeffer SW (1997) Natural selection and the frequency distributions of "silent" DNA polymorphism. in Drospphila. Genetics 146: 295-307.
56. Llopart A, Aguade M (2000) Nucleotide polymorphism at the RpII215 gene in Drosophila subobscura. Weak selection on synonymous mutations. Genetics 155: 1245-1252.
57. Maside X, Lee AW, Charlesworth B (2004) Selection on codon usage in Drosophila americana. Curr Biol 14: 150-154.
58. Bartolome C, Maside X, Yi S, Grant AL, Charlesworth B (2005) Patterns of selection on synonymous and nonsynonymous variants in Drosophila miranda. Genetics 169: 1495-1507.
59. McVean GAT, Charlesworth B (l999) A population genetic model for the evolution of synonymous codon usage:. patterns and predictions. Genetical Research 74: 145-158.
60. Ko WY, David W Akashi H (2003) Molecular phylogeny of the Drosophila melanogaster species subgroup. J Mol Evol 57: 562-573.
61. Wong A, Jensen JD, Pool JE, Aquadro CF (2006) Phylogenetic incongruence in the Drosophila melanogaster species group. Mol Phylogenet Evol.
62. Pollard DA, Iyer VN, Moses AM, Eisen MB (2006) Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet 2: e173.
63. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl. Biosci 13: 555-556.
64. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.
65. Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141: 1641-1650.
66. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN, ed. Mammalian Protein Metabolism III. New York: Academic Press. pp 21-132.
67. Krishnan NM, Seligmann H, Stewart CB, De Koning AP, Pollock DD (2004) Ancestral sequence reconstruction in primate mitochondrial DNA: Compositional bias and effect on functional inference. Mol Biol Evol 21: 1871-1883.
68. Snedecor GW, Gochran WG (1989) Statistical Methods: 8th Edition. AmesIowa: Iowa State University Press. 503 p.
69. Zhang J, Nei M (1997) Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J Mol Evol 44 Suppl 1: S139-146.
70. Takano-Shimizu T (1999) Local recombination and mutation effects on molecular evolution in Drosophila. Genetics 153: 1285-1296.
71. Rodriguez-Trelles F, Tarrio R, Ayala FJ (1999) Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group. Genetics 153: 339-350.
72. Blanchette M, Green ED, Miller W, Haussler D (2004) Reconstruction large regions of an ancestral mammalian genome in silico. Genome Res 14: 2412-2423.
73. Akishi H (1994) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics. 136:927-935.
74. Moriyama EN, Powell JR (1998) Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Eschesichia coli. Nucleic Acids Res 26: 3188-3198.
75. Kliman RM, Eyre-Walker A (1998) Patterns of base composition within the genes of Drosophila melanogaster. J Mol Evol 46: 534-541.
76. Iida K, Akashi H (2000) A test of translational selection at 'silent' sites in the human genome: base-composition comparisons in alternatively spliced genes. Gene 261: 93-105.
77. Comeron JM, Kreiman M (2002) Population, evolutionary and genomic consequences of interference selection. Genetics 161: 389-410.
78. Qin H, Wu WB, Comeron JM, Kreitman M, Li WH (2004) Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes. Genetics 168:2245-2260.
79. Huelsenbeck JP, Bollback JP (2001) Empirical and hierarchical Bayesian estimation of ancestral states. Syst Biol 50: 351-366.
80. Nielsen R (2002) Mapping mutations on phylogenies. Syst Biol 51: 729-739.
81. Pagel M, Meade A, Barker D (2004) Bayesian estimation of ancestral character states on phylogenies. Syst Biol 53: 673-684.
82. Yang Z, Roberts D (1995) On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol Biol Evol 12: 451-458.
83. Galtier N, Gouy M (1998) Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol 15: 871-879.
84. Ree RH, Donoghue MJ (1998) Step matrices and the interpretation of homoplasy. Syst Biol 47: 582-588.
85. Li W-H (1997) Molecular evolution. Sunderland, Mass.: Sinauer Associates. pp xv, 487.
86. Nielsen R, Bauer DuMont VL, Hubisz MJ, Aquadro CF (2007) Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila. Mol Biol Evol 24: 228-235.
87. Hernandez RD, Williamson SH, Bustamante CD (2007) Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol Biol Evol 24: 1792-1800.
88. Sawyer SA, Dykhuizen DE, Hard DL (1987) Confidence interval for the number of selectively neutral amino acid potymorphisms. Proc Natl Acad Sci U S A 84: 6225-6228.
89. McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
90. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, et al. (2002) The cost of inbreeding in Arabidopsis. Nature 416: 531-534.
91. Bustamante CD, Wakeley J, Sawyer S, Hard DL (2001) Directional selection and the site-frequency spectrum. Genetics 159: 1779-1788.
92. Andolfatto P (2005) Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
93. Baudry E, Depaulis F (2003) Effect of misoriented sites on neutrality tests with outgroup. Genetics 165: 1619-1622.