Fitness conferred by replaced amino acids declines with time

Biology Letters

Volumn 8, Issue 5, 2012, Pages 825-828

  Naumenko, Sergey A ^a,b   Kondrashov, Alexey S ^b,c   Bazykin, Georgii A ^a,b  

^a INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Absent allele; Epistatic interactions; Evolution; Fitness landscape dynamics; Reversing replacement

Indexed keywords

ALLELE; AMINO ACID; EPISTASIS; FITNESS; POLYMORPHISM; PROBABILITY; PROTEIN; STEADY-STATE EQUILIBRIUM;

EID: 84866697042     PISSN: 17449561     EISSN: 1744957X     Source Type: Journal    
DOI: 10.1098/rsbl.2012.0356     Document Type: Article

References (17)

1. Mustonen, V. & Lassig, M. 2007 Adaptations to fluctuating selection in Drosophila. Proc. Natl Acad. Sci. USA 104, 2277-2282. (doi:10.1073/pnas. 0607105104)
2. Carniero, M. & Hartl, D. L. 2010 Adaptive landscapes and protein evolution. Proc. Natl Acad. Sci. USA 107, 1747-1751. (doi:10.1073/pnas. 0906192106)
3. Bazykin, G., Kondrashov, F., Brudno, M., Poliakov, A., Dubchak, I. & Kondrashov, A. 2007 Extensive parallelism in protein evolution. Biol. Direct 2, 20. (doi:10. 1186/1745-6150-2-20)
4. Rogozin, I., Thomson, K., Csü rös, M., Carmel, L. & Koonin, E. 2008 Homoplasy in genome-wide analysis of rare amino acid replacements: the molecularevolutionary basis for Vavilov's law of homologous series. Biol. Direct 3, 7. (doi:10.1186/1745-6150-3-7)
5. Rokas, A. & Carroll, S. B. 2008 Frequent and widespread parallel evolution of protein sequences. Mol. Biol. Evol. 25, 1943-1953. (doi:10.1093/molbev/ msn143)
6. Povolotskaya, I. S. & Kondrashov, F. A. 2010 Sequence space and the ongoing expansion of the protein universe. Nature 465, 922-926. (doi:10.1038/nature09105)
7. Poelwijk, F. J., Kivet, D. J., Weinreich, D. M. & Tans, S. J. 2007 Empirical fitness landscapes reveal accessible paths. Nature 445, 383-386. (doi:10.1038/ nature05451)
8. Khan, A. I., Dinh, D. M., Schneider, D., Lenski, R. E. & Cooper, T. F. 2011 Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332, 1193-1196. (doi:10.1126/science.1203801)
9. Chou, H. H., Chiu, H. C., Delaney, N. F., Segrè, D. & Marx, C. J. 2011 Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332, 1190-1192. (doi:10.1126/science.1203799)
10. Salverda, M. L. M., Dellus, E., Gorter, F. A., Debets, A. J. M., van der Oost, J., Hoekstra, R. F., Tawfik, D. S. & de Visser, J. A. G. M. 2011 Initial mutations direct alternative pathways of protein evolution. PLoS Genet. 7, e1001321. (doi:10.1371/journal.pgen.1001321)
11. Fujita, P. A. et al. 2010 The UCSC genome browser database: update 2011. Nucleic Acids Res. 39, D876-D882. (doi:10.1093/nar/gkq963)
12. Hsu, F., Kent, W. J., Clawson, H., Kuhn, R. M., Diekhans, M. & Haussler, D. 2006 The UCSC known genes. Bioinformatics 22, 1036-1046. (doi:10.1093/ bioinformatics/btl048)
13. Tweedie, S. et al. 2009 FlyBase: enhancing Drosophila gene ontology annotations. Nucleic Acids Res. 37, D555-D559. (doi:10.1093/nar/gkn788)
14. Yang, Z. 2007 PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591. (doi:10.1093/molbev/msm088)
15. Miyata, T., Miyazawa, S. & Yasunaga, T. 1979 Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12, 219-236. (doi:10.1007/bf01732340)
16. Naumenko, S. & Kondrashov, A. 2012 Rate and breadth of protein evolution are only weakly correlated. Biol. Direct 7, 8. (doi:10.1186/1745-6150- 7-8)
17. Kimura, M. 1983 The neutral theory of molecular evolution. Cambridge, UK: Cambridge University Press.