Estimates of the Effect of Natural Selection on Protein-Coding Content

Molecular Biology and Evolution

Volumn 27, Issue 3, 2010, Pages 726-734

  Yap, Von Bing ^a   Lindsay, Helen ^b   Easteal, Simon ^b   Huttley, Gavin ^b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b Australian National University   (Australia)

Author keywords

Codon substitution models; DN dS; Maximum likelihood; Molecular evolution; Natural selection

Indexed keywords

NUCLEOTIDE; PROTEIN; TRINUCLEOTIDE; VACCINE;

ARTICLE; BACTERIAL GENE; BORRELIA BURGDORFERI; BORRELIA GARINII; CHIMPANZEE; CODON; CODON SUBSTITUTION; CONDITIONAL NUCLEOTIDE FREQUENCY; GENOME; HUMAN; INTRON; MACACA; MATHEMATICAL MODEL; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM TUBERCULOSIS; NATURAL SELECTION; NONHUMAN; NUCLEOTIDE ANALYSIS; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PLASMODIUM; PLASMODIUM FALCIPARUM; PLASMODIUM KNOWLESI; PLASMODIUM REICHENOWI; PLASMODIUM VIVAX; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SIMULATION; SYSTEMATIC ERROR;

BASE COMPOSITION; CHI-SQUARE DISTRIBUTION; CODON; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENES, PROTOZOAN; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; PLASMODIUM; SELECTION, GENETIC; SEQUENCE ALIGNMENT;

EID: 77249113749     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp232     Document Type: Article

References (32)

1. Berglund J, Pollard KS, Webster MT. 2009. Hotspots of biased nucleotide substitutions in human genes. PLoS Biol. 7(1):e26.
2. Blake RD, Hess ST, Nicholson-Tuell J. 1992. The influence of nearest neighbors on the rate and pattern of spontaneous point mutations. J Mol Evol. 34(3):189-200.
3. Carlton JM, Adams JH, Silva JC, et al. (39 co-authors). 2008. Comparative genomics of the neglected human malaria parasite Plasmod-ium vivax. Nature 455(7214):757-763.
4. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437(7055):69-87
5. dos Reis M, Wernisch L. 2009. Estimating translational selection in eukaryotic genomes. Mol Biol Evol. 26(2):451-461.
6. Duret L, Eyre-Walker A, Galtier N. 2006. A new perspective on isochore evolution. Gene. 385:71-74.
7. Elango N, Kim SH, Vigoda E, Yi SV. 2008. Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLoS Comput Biol. 4(2):e1000015.
8. Eyre-Walker A, Hurst LD. 2001. The evolution of isochores. Nat Rev Genet. 2:549-555.
9. Galtier N, Duret L, Glemin S, Ranwez V. 2009. GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet. 25(1):1-5.
10. Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol. 11(5):725-736
11. Green P, Ewing B, Miller W, Thomas PJ, Green ED. 2003. Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet. 33(4):514-517.
12. Greenbaum BD, Levine AJ, Bhanot G, Rabadan R. 2008. Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog. 4(6):e1000079.
13. Hall N, Karras M, Raine JD, et al. (30 co-authors). 2005. A comprehensive survey of the plasmodium life cycle by genomic, transcrip-tomic, and proteomic analyses. Science 307(5706):82-86.
14. Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22(2):160-174.
15. Hubbard TJP, Aken BL, Ayling S, et al. (51 co-authors). 2009. Ensembl 2009. Nucleic Acids Res. 37(Database issue):D690-D697.
16. Hughes AL, Nei M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335(6186):167-170.
17. Iversen AKN, Stewart-Jones G, Learn GH, et al. (23 co-authors). 2006. Conflicting selective forces affect T cell receptor contacts in an immunodominant human immunodeficiency virus epitope. Nat Immunol. 7(2):179-189.
18. Karlin S, Campbell AM, Mrázek J. 1998. Comparative DNA analysis across diverse genomes. Annu Rev Genet. 32:185-225.
19. Knight R, Maxwell P, Birmingham A, et al. (20 co-authors). 2007. PyCo-gent: a toolkit for making sense from sequence. Genome Biol. 8(8):R171.
20. Lanave C, Preparata G, Saccone C, Serio G. 1984. A new method for calculating evolutionary substitution rates. J Mol Evol. 20(1): 86-93.
21. Lindsay H, Yap VB, Ying H, Huttley GA. 2008. Pitfalls of the most commonly used models of context dependent substitution. Biol Direct. 3:52.
22. Liò P, Goldman N. 1998. Models of molecular evolution and phylogeny. Genome Res. 8(12):1233-1244.
23. Mes THM, van Putten JPM. 2007. Positively selected codons in immune-exposed loops of the vaccine candidate OMP-P1 of haemophilus influenzae. J Mol Evol. 64(4):411-422.
24. Messier W, Stewart CB. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385(6612):151-154.
25. Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol. 11(5):715-724.
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(3):929-936.
27. Seoighe C, Ketwaroo F, Pillay V, et al. (10 co-authors). 2007. A model of directional selection applied to the evolution of drug resistance in HIV-1. Mol Biol Evol. 24(4):1025-1031.
28. Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE. 2005. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33(4):1141-1153.
29. Siepel A, Bejerano G, Pedersen JS, et al. (15 co-authors). 2005. Evolu-tionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15(8):1034-1050.
30. Weedall GD, Polley SD, Conway DJ. 2008. Gene-specific signatures of elevated non-synonymous substitution rates correlate poorly across the plasmodium genus. PLoS One 3(5):e2281.
31. Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 19(6):908-917.
32. Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 22(12):2472-2479.