Extensive parallelism in protein evolution

Biology Direct

Volumn 2, Issue , 2007, Pages

  Bazykin, Georgii A ^a,b   Kondrashov, Fyodor A ^c   Brudno, Michael ^d   Poliakov, Alexander ^e   Dubchak, Inna ^e,f   Kondrashov, Alexey S ^g  

^a INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^b PRINCETON UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF TORONTO   (Canada)

^e LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^f DOE JOINT GENOME INSTITUTE   (United States)

^g UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALIA;

AMINO ACID; PROTEIN;

ALLELE; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMAL; ARTICLE; CHEMISTRY; DOG; DROSOPHILA; GENETIC SELECTION; GENETICS; HUMAN; MOLECULAR EVOLUTION; MOUSE; PHYLOGENY; RAT; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT;

ALLELES; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMINO ACIDS; ANIMALS; DOGS; DROSOPHILA; EVOLUTION, MOLECULAR; HUMANS; MICE; PHYLOGENY; PROTEINS; RATS; SACCHAROMYCES CEREVISIAE; SELECTION (GENETICS); SEQUENCE ALIGNMENT;

EID: 35348854895     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-2-20     Document Type: Review

References (41)

1. Futuyma DJ Evolution Sunderland: Sinauer Associates; 2005.
2. Li WH Molecular Evolution Sunderland: Sinauer Associates; 1997.
3. Delsuc F Brinkmann H Philippe H Phylogenomics and the reconstruction of the tree of life Nat Rev Genet 2005, 6:361-75. 10.1038/nrg1603 15861208
4. Zhang J Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys Nat Genet 2006, 38:819-23. 10.1038/ng1812 16767103
5. Wolf YI Viboud C Holmes EC Koonin EV Lipman DJ Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus Biol Direct 2006, 1:34. 1647279 17067369 10.1186/ 1745-6150-1-34
6. Kimura M The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983.
7. Kimura M Evolutionary rate at the molecular level Nature 1968, 217:624-6. 10.1038/217624a0 5637732
8. Murphy WJ Pevzner PA O'Brien SJ Mammalian phylogenomics comes of age Trends Genet 2004, 20:631-639. 10.1016/j.tig.2004.09.005 15522459
9. Galagan JE Henn MR Ma LJ Cuomo CA Birren B Genomics of the fungal kingdom: Insights into eukaryotic biology Genome Res 2005, 15:1620-1631. 10.1101/gr.3767105 16339359
10. Gibbs RA Weinstock GM Metzker ML Muzny DM Sodergren EJ Scherer S Scott G Steffen D Worley KC Burch PE Okwuonu G Hines S Lewis L DeRamo C Delgado O Dugan-Rocha S Miner G Morgan M Hawes A Gill R Celera Holt RA Adams MD Amanatides PG Baden-Tillson H Barnstead M Chin S Evans CA Ferriera S Fosler C Glodek A Gu Z Jennings D Kraft CL Nguyen T Pfannkoch CM Sitter C Sutton GG Venter JC Woodage T Smith D Lee HM Gustafson E Cahill P Kana A Doucette-Stamm L Weinstock K Fechtel K Weiss RB Dunn DM Green ED Blakesley RW Bouffard GG De Jong PJ Osoegawa K Zhu B Marra M Schein J Bosdet I Fjell C Jones S Krzywinski M Mathewson C Siddiqui A Wye N McPherson J Zhao S Fraser CM Shetty J Shatsman S Geer K Chen Y Abramzon S Nierman WC Havlak PH Chen R Durbin KJ Egan A Ren Y Song XZ Li B Liu Y Qin X Cawley S Worley KC Cooney AJ D'Souza LM Martin K Wu JQ Gonzalez-Garay ML Jackson AR Kalafus KJ McLeod MP Milosavljevic A Virk D Volkov A Wheeler DA Zhang Z Bailey JA Eichler EE Tuzun E Birney E Mongin E Ureta-Vidal A Woodwark C Zdobnov E Bork P Suyama M Torrents D Alexandersson M Trask BJ Young JM Huang H Wang H Xing H Daniels S Gietzen D Schmidt J Stevens K Vitt U Wingrove J Camara F Mar Alba M Abril JF Guigo R Smit A Dubchak I Rubin EM Couronne O Poliakov A Hubner N Ganten D Goesele C Hummel O Kreitler T Lee YA Monti J Schulz H Zimdahl H Himmelbauer H Lehrach H Jacob HJ Bromberg S Gullings-Handley J Jensen-Seaman MI Kwitek AE Lazar J Pasko D Tonellato PJ Twigger S Ponting CP Duarte JM Rice S Goodstadt L Beatson SA Emes RD Winter EE Webber C Brandt P Nyakatura G Adetobi M Chiaromonte F Elnitski L Eswara P Hardison RC Hou M Kolbe D Makova K Miller W Nekrutenko A Riemer C Schwartz S Taylor J Yang S Zhang Y Lindpaintner K Andrews TD Caccamo M Clamp M Clarke L Curwen V Durbin R Eyras E Searle SM Cooper GM Batzoglou S Brudno M Sidow A Stone EA Venter JC Payseur BA Bourque G Lopez-Otin C Puente XS Chakrabarti K Chatterji S Dewey C Pachter L Bray N Yap VB Caspi A Tesler G Pevzner PA Haussler D Roskin KM Baertsch R Clawson H Furey TS Hinrichs AS Karolchik D Kent WJ Rosenbloom KR Trumbower H Weirauch M Cooper DN Stenson PD Ma B Brent M Arumugam M Shteynberg D Copley RR Taylor MS Riethman H Mudunuri U Peterson J Guyer M Felsenfeld A Old S Mockrin S Collins F Genome sequence of the Brown Norway rat yields insights into mammalian evolution Nature 2004, 428:493-521. 10.1038/nature02426 15057822
11. Kellis M Patterson N Endrizzi M Birren B Lander ES Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 2003, 423:241-54. 10.1038/nature01644 12748633
12. Bergman CM Pfeiffer BD Rincon-Limas DE Hoskins RA Gnirke A Mungall CJ Wang AM Kronmiller B Pacleb J Park S Stapleton M Wan K George RA de Jong PJ Botas J Rubin GM Celniker SE Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome Genome Biol 2002, 3:RESEARCH0086. 151188 12537575 10.1186/ gb-2002-3-12-research0086
13. Bulmer M The selection-mutation-drift theory of synonymous codon usage Genetics 1991, 129:97-907. 1204756 1752426
14. Kimura M Model of effectively neutral mutations in which selective constraint is incorporated Proc Natl Acad Sci USA 1979, 76:3440-3444. 383841 16592684 10.1073/pnas.76.7.3440
15. Hwang DG Green P Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution Proc Natl Acad Sci USA 2004, 101:13994-4001. 521089 15292512 10.1073/ pnas.0404142101
16. Kondrashov FA Ogurtsov AY Kondrashov AS Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites J Theor Biol 2006, 240:616-26. 10.1016/j.jtbi.2005.10.020 16343547
17. Grishin NV Wolf YI Koonin EV From complete genomes to measures of substitution rate variability within and between proteins Genome Res 2000, 10:991-1000. 310923 10899148 10.1101/gr.10.7.991
18. Yampolsky LY Kondrashov FA Kondrashov AS Distribution of the strength of selection against amino acid replacements in human proteins Hum Mol Genet 2005, 14:3191-201. 10.1093/hmg/ddi350 16174645
19. Eyre-Walker A Woolfit M Phelps T The distribution of fitness effects of new deleterious amino acid mutations in humans Genetics 2006, 173:891-900. 1526495 16547091 10.1534/genetics.106.057570
20. Ota T Nei M Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites J Mol Evol 1994, 38:642-643. 10.1007/BF00175885
21. Chen L Perlina A Lee CJ Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase J Virol 2004, 78:3722-32. 371046 15016892 10.1128/ JVI.78.7.3722-3732.2004
22. Subramanian S Kumar S Higher intensity of purifying selection on 90% of the human genes revealed by the intrinsic replacement mutation rates Mol Biol Evol 2006, 23:2283-7. 10.1093/molbev/msl123 16982819
23. Fitch WM Markowitz E An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution Biochem Genet 1970, 4:579-93. 10.1007/BF00486096 5489762
24. Bazykin GA Dushoff J Levin SA Kondrashov AS Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites Proc Natl Acad Sci USA 2006, 103:19396-401. 1698441 17164328 10.1073/pnas.0609484103
25. Ohta T Slightly deleterious mutant substitutions in evolution Nature 1973, 246:96-8. 10.1038/246096a0 4585855
26. Ohta T The nearly neutral theory of molecular evolution Annu Rev Ecol Syst 1992, 23:263-286. 10.1146/annurev.es.23.110192.001403
27. Kondrashov AS Contamination of the genome by very slightly deleterious mutations: Why have we not died 100 times over? J Theor Biol 1995, 175:583-94. 10.1006/jtbi.1995.0167 7475094
28. Sjolander K Karplus K Brown M Hughey R Krogh A Mian IS Haussler D Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology Comput Appl Biosci 1996, 12:327-45. 8902360
29. Lartillot N Philippe H A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process Mol Biol Evol 2004, 21:1095-109. 10.1093/molbev/msh112 15014145
30. Shenkin PS Erman B Mastrandrea LD Information-theoretical entropy as a measure of sequence variability Proteins 1991, 11:297-313. 10.1002/ prot.340110408 1758884
31. Pei J Grishin NV AL2CO: Calculation of positional conservation in a protein sequence alignment Bioinformatics 2001, 17:700-12. 10.1093/ bioinformatics/17.8.700 11524371
32. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25:3389-402. 146917 9254694 10.1093/nar/ 25.17.3389
33. Tatusov RL Koonin EV Lipman DJ A genomic perspective on protein families Science 1997, 278:631-7. 10.1126/science.278.5338.631 9381173
34. Wheeler DL Church DM Edgar R Federhen S Helmberg W Madden TL Pontius JU Schuler GD Schriml LM Sequeira E Suzek TO Tatusova TA Wagner L Database resources of the National Center for Biotechnology Information: Update Nucleic Acids Res 2004, 32:D35-40. 308807 14681353 10.1093/nar/gkh073
35. Benson DA Karsch-Mizrachi I Lipman DJ Ostell J Wheeler DL GenBank Nucleic Acids Res 2006, 34:D16-20. 1347519 16381837 10.1093/nar/gkj157
36. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22:4673-80. 308517 7984417 10.1093/nar/22.22.4673
37. Brudno M Malde S Poliakov A Do CB Couronne O Dubchak I Batzoglou S Glocal alignment: Finding rearrangements during alignment Bioinformatics 2003, 19(Suppl 1):i54-62. 10.1093/bioinformatics/btg1005 12855437
38. Sundararajan M Brudno M Small K Sidow A Batzoglow S Chaining algorithms for alignment of draft sequence Proceedings of the fourth Workshop on Algorithms in Bioinformatics (WABI 2004).
39. Brudno M Do CB Cooper GM Kim MF Davydov E Green ED Sidow A Batzoglou S LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA Genome Res 2003, 13:721-31. 430158 12654723 10.1101/gr.926603
40. Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 1997, 13:555-6. 9367129
41. Miyata T Miyazawa S Yasunaga T Two types of amino acid substitutions in protein evolution J Mol Evol 1979, 12:219-36. 10.1007/BF01732340 439147