Evidence for an episodic model of protein sequence evolution

Biochemical Society Transactions

Volumn 37, Issue 4, 2009, Pages 783-786

  Studer, Romain A ^a,b   Robinson Rechavi, Marc ^a,b  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

Codon model; Functional divergence; Positive selection; Protein evolution

Indexed keywords

ALANINE; ASPARTIC ACID; LYSINE; RIBULOSEBISPHOSPHATE CARBOXYLASE; PROTEIN;

AMINO ACID SEQUENCE; CODON; CONFERENCE PAPER; DIGESTION; GENE DUPLICATION; GENE MUTATION; GENETIC IDENTIFICATION; GENETIC VARIABILITY; IMMUNITY; MOLECULAR EVOLUTION; NONHUMAN; PHOTOSYNTHESIS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; REPRODUCTION; SITE DIRECTED MUTAGENESIS; BIOLOGICAL MODEL; GENETIC SELECTION; GENETICS; REVIEW;

AMINO ACID SEQUENCE; EVOLUTION, MOLECULAR; MODELS, GENETIC; PROTEINS; SELECTION (GENETICS);

EID: 70349329176     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0370783     Document Type: Conference Paper

References (53)

1. Gillespie, J.H. (1991) The Causes of Molecular Evolution, Oxford University Press, Oxford
2. Conant, G.C. and Wolfe, K.H. (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat. Rev. Genet. 9, 938-950
3. Semon, M. and Wolfe, K.H. (2007) Consequences of genome duplication. Curr. Opin. Genet. Dev. 17, 505-512
4. Anisimova, M. and Liberles, D.A. (2007) The quest for natural selection in the age of comparative genomics. Heredity 99, 567-579
5. Liberles, D.A. (2007) Ancestral Sequence Reconstruction, Oxford University Press, Oxford
6. Pupko, T. and Galtier, N. (2002) A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proc. Biol. Sci. 269, 1313-1316
7. Gu, X. (1999) Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16, 1664-1674
8. Philippe, H., Casane, D., Gribaldo, S., Lopez, P. and Meunier, J. (2003) Heterotachy and functional shift in protein evolution. IUBMB Life 55, 257-265
9. Braasch, I., Salzburger, W. and Meyer, A. (2006) Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration. Mol. Biol. Evol. 23, 1192-1202
10. McNally, D. and Fares, M.A. (2007) In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae. BMC Evol. Biol. 7, 81
11. Penn, O., Stern, A., Rubinstein, N.D., Dutheil, J., Bacharach, E., Galtier, N. and Pupko, T. (2008) Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput. Biol. 4, e1000214
12. Gu, X. (2006) A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol. Biol. Evol. 23, 1937-1945
13. Gribaldo, S., Casane, D., Lopez, P. and Philippe, H. (2003) Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol. Biol. Evol. 20, 1754-1759
14. Seoighe, C., Johnston, C.R. and Shields, D.C. (2003) Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation. Mol. Biol. Evol. 20, 484-490
15. Fares, M.A. and McNally, D. (2006) CAPS: coevolution analysis using protein sequences. Bioinformatics 22, 2821-2822
16. Dutheil, J. (2008) Detecting site-specific biochemical constraints through substitution mapping. J. Mol. Evol. 67, 257-265
17. Dutheil, J. and Galtier, N. (2007) Detecting groups of coevolving positions in a molecule: a clustering approach. BMC Evol. Biol. 7, 242
18. Codoñer, F.M. and Fares, M.A. (2008) Why should we care about molecular coevolution? Evol. Bioinform. 4, 237-246
19. Gu, X. and Vander Velden, K. (2002) DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18, 500-501
20. Edwards, R.J. and Shields, D.C. (2005) BADASP: predicting functional specificity in protein families using ancestral sequences. Bioinformatics 21, 4190-4191
21. Yang, Z. (2006) Computational Molecular Evolution, Oxford University Press, Oxford
22. Yang, Z. (2005) The power of phylogenetic comparison in revealing protein function. Proc. Natl. Acad. Sci. U.S.A. 102, 3179-3180
23. Anisimova, M. and Kosiol, C. (2009) Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol. Biol. Evol. 26, 255-271
24. Yang, Z. (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591
25. Guindon, S., Rodrigo, A.G., Dyer, K.A. and Huelsenbeck, J.P. (2004) Modeling the site-specific variation of selection patterns along lineages. Proc. Natl. Acad. Sci. U.S.A. 101, 12957-12962
26. Stern, A., Doron-Faigenboim, A., Erez, E., Martz, E., Bacharach, E. and Pupko, T. (2007) Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res. 35, W506-W511
27. Yang, Z. (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15, 568-573
28. Zelus, D., Robinson-Rechavi, M., Delacre, M., Auriault, C. and Laudet, V. (2000) Fast evolution of interleukin-2 in mammals and positive selection in ruminants. J. Mol. Evol. 51, 234-244
29. Yang, Z. and Swanson, W.J. (2002) Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19, 49-57
30. Yang, Z. and Nielsen, R. (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19, 908-917
31. Zhang, J., Nielsen, R. and Yang, Z. (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22, 2472-2479
32. Zhang, J. (2004) Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol. 21, 1332-1339
33. Nickel, G.C., Tefft, D. and Adams, M.D. (2008) Human PAML browser: a database of positive selection on human genes using phylogenetic methods. Nucleic Acids Res. 36, D800-D808
34. Proux, E., Studer, R.A., Moretti, S. and Robinson-Rechavi, M. (2009) Selectome: a database of positive selection. Nucleic Acids Res. 37, D404-D407
35. Christin, P.A., Salamin, N., Muasya, A.M., Roalson, E.H., Russier, F. and Besnard, G. (2008) Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. Mol. Biol. Evol. 25, 2361-2368
36. Levasseur, A., Gouret, P., Lesage-Meessen, L., Asther, M., Record, E. and Pontarotti, P. (2006) Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family. BMC Evol. Biol. 6, 92
37. Aagaard, J.E., Willis, J.H. and Phillips, P.C. (2006) Relaxed selection among duplicate floral regulatory genes in Lamiales. J. Mol. Evol. 63, 493-503
38. Wong, K.M., Suchard, M.A. and Huelsenbeck, J.P. (2008) Alignment uncertainty and genomic analysis. Science 319, 473-476
39. Nuin, P.A., Wang, Z. and Tillier, E.R. (2006) The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinform. 7, 471
40. Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552
41. Talavera, G. and Castresana, J. (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564-577
42. Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U.S.A. 100, 9440-9445
43. Eyre-Walker, A. (2006) The genomic rate of adaptive evolution. Trends Ecol. Evol. 21, 569-575
44. Jorgensen, F.G., Hobolth, A., Hornshoj, H., Bendixen, C., Fredholm, M. and Schierup, M.H. (2005) Comparative analysis of protein coding sequences from human, mouse and the domesticated pig. BMC Biol. 3, 2
45. Arbiza, L., Dopazo, J. and Dopazo, H. (2006) Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput. Biol. 2, e38
46. Bakewell, M.A., Shi, P. and Zhang, J. (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc. Natl. Acad. Sci. U.S.A. 104, 7489-7494
47. Kosiol, C., Vinar, T., da Fonseca, R.R., Hubisz, M.J., Bustamante, C.D., Nielsen, R. and Siepel, A. (2008) Patterns of positive selection in six mammalian genomes. PLoS Genet. 4, e1000144
48. Studer, R.A., Penel, S., Duret, L. and Robinson-Rechavi, M. (2008) Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res. 18, 1393-1402
49. Holbrook, J.D. and Sanseau, P. (2007) Drug discovery and computational evolutionary analysis. Drug Discov. Today 12, 826-832
50. Vamathevan, J.J., Hasan, S., Emes, R.D., Amrine-Madsen, H., Rajagopalan, D., Topp, S.D., Kumar, V., Word, M., Simmons, M.D., Foord, S.M. et al. (2008) The role of positive selection in determining the molecular cause of species differences in disease. BMC Evol. Biol. 8, 273
51. Andolfatto, P. (2007) Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res. 17, 1755-1762
52. Pils, B., Copley, R.R. and Schultz, J. (2005) Variation in structural location and amino acid conservation of functional sites in protein domain families. BMC Bioinform. 6, 210
53. Seffernick, J.L., de Souza, M.L., Sadowsky, M.J. and Wackett, L.P. (2001) Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different. J. Bacteriol. 183, 2405-2410