Near-neutrality, robustness, and epigenetics

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 1034-1038

  Ohta, Tomoko ^a  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Epigenetics; Near neutrality; Robustness

Indexed keywords

DNA;

ANIMAL; ARTICLE; DNA METHYLATION; DNA SEQUENCE; EPIGENETICS; GENETIC DRIFT; GENETIC EPIGENESIS; GENETIC POLYMORPHISM; GENETIC SELECTION; HUMAN; HUMAN GENOME; METHODOLOGY; MOLECULAR EVOLUTION; MUTATION; PHENOTYPE;

ANIMALS; DNA; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; EVOLUTION, MOLECULAR; GENETIC DRIFT; GENOME, HUMAN; HUMANS; MUTATION; PHENOTYPE; POLYMORPHISM, GENETIC; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84856134667     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr012     Document Type: Article

References (30)

1. Bedford T, Hartl DL. 2009. Optimization of gene expression by natural selection. Proc Natl Acad Sci U S A. 106:1133-1138.
2. Beltrao P, Cagney G, Krogan NJ. 2010. Quantitative genetic interactions reveal biological modularity. Cell 141:739-745.
3. Bonasio R, Tu S, Reinberg D. 2010. Molecular signals of epigenetic states. Science. 330:612-616.
4. The Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87.
5. Elyashiv E, et al. 2010. Shifts in the intensity of purifying selection: an analysis of genome-wide polymorphism data from two closely related yeast species. Genome Res. doi: 10.1101/gr.108993.110.
6. The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
7. Feinberg AP, Irizarry RA. 2010. Stochastic epigenetic variation as a driving force of development, evolutionary adaptation and disease. Proc Natl Acad Sci U S A. 107:1757-1767.
8. Hornstein E, Shomron N. 2006. Canalization of development by microRNAs. Nat Genet. 38:S20-S24.
9. Hughes AL, et al. 2003. Widespread purifying selection at polymorphic sites in human protein coding loci. Proc Natl Acad Sci U S A. 100:15754-15757. (Pubitemid 38021062)
10. Jablonka E, Lamb MJ. 2002. The changing concept of epigenetics. Ann New York Acad Sci. 981:82-96. (Pubitemid 36127087)
11. Kaneko K. 2007. Evolution of robustness to noise and mutation in gene expression dynamics. PLoS One. 2(5):e434.
12. Khaitovich P, Enard W, Lachman M, Paabo S. 2006. Evolution of primate gene expression. Nat Rev Genet. 7:693-702. (Pubitemid 44260005)
13. Lehner B. 2010. Genes confer similar robustness to environmental, stochastic and genetic perturbations in yeast. PLoS One. 5(2):e9035.
14. Ludwig MZ, Bergman C, Patel NH, Kreitman M. 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403:564-567. (Pubitemid 30082204)
15. Lunzer M, Golding GB, Dean AM. 2010. Pervasive cryptic epistasis in molecular evolution. PLoS Genet. 6(10):e1001162.
16. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654. (Pubitemid 21896661)
17. Ohta T. 1972. Population size and rate of evolution. J Mol Evol. 1:305-314.
18. Ohta T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246:96-98.
19. Ohta T. 1992. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst. 23:263-286. (Pubitemid 24412250)
20. Ohta T. 1995. Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol. 40:56-63.
21. Ohta T. 2002. Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci U S A. 99:16134-16137. (Pubitemid 35462761)
22. Roguev A, et al. 2008. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 322:405-410.
23. Rutherford SL, Lindquist S. 1998. Hsp90 as a capacitor for morphological evolution. Nature 396:336-342. (Pubitemid 28557387)
24. Sawyer SA, Parsch J, Zhang Z, Hartl DL. 2007. Prevalence of positive selection among nearly neutral amino acid replacement in Drosophila. Proc Natl Acad Sci U S A. 104:6504-6510. (Pubitemid 47175532)
25. Slatkin M. 2009. Epigenetic inheritance and the missing heritability problem. Genetics 182:845-850.
26. Smith NGC, Eyre-Walker A. 2002. Adaptive protein evolution in Drosophila. Nature 415:1022-1024. (Pubitemid 34193448)
27. Suzuki MM, Bird A. 2008. DNA methylation landscape: provocative insight from epigenomics. Nat Rev Genet. 9:465-476. (Pubitemid 351693975)
28. Tischler J, Lerner B, Fraser AG. 2008. Evolutionary plasticity of genetic interaction networks. Nat Genet. 40:390-391. (Pubitemid 351450883)
29. Wagner A. 2005. Distributed robustness versus redundancy as causes of mutational robustness. BioEssays 27:176-188. (Pubitemid 40292389)
30. West-Eberhard MJ. 2003. Developmental plasticity and evolution. New York: Oxford University Press.