The causes of epistasis in genetic networks

Evolution

Volumn 66, Issue 2, 2012, Pages 586-596

  Macía, Javier ^a   Solé, Ricard V ^a,b   Elena, Santiago F ^b,c  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b SANTA FE INSTITUTE   (United States)

^c Ciudad Politécnica de la Innovación   (Spain)

Author keywords

Complexity; Degeneracy; Feedback loops; Redundancy; Robustness

Indexed keywords

CORRELATION; EPISTASIS; GENE EXPRESSION; GENETIC ANALYSIS; PHENOTYPE;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; ESCHERICHIA COLI; GENE REGULATORY NETWORK; GENETIC EPISTASIS; GENETICS; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; EPISTASIS, GENETIC; ESCHERICHIA COLI; GENE REGULATORY NETWORKS; MODELS, GENETIC; SACCHAROMYCES CEREVISIAE;

EID: 84856305258     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2011.01451.x     Document Type: Article

References (43)

1. Albert, R., H. Jeong, and A. L. Barabási. 2000. Error and attack tolerance of complex networks. Nature 406:378-382.
2. Aldana, M., and P. Cluzel. 2003. A natural class of robust networks. Proc. Natl. Acad. Sci. USA 100:8710-8714.
3. Alon, U. 2007. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8:450-461.
4. Ash, R. B. 1990. Information theory. Dover Publications, New York.
5. Azevedo, R. B. R., R. Lohaus, S. Srinivasan, K. K. Dang, and C. L. Burch. 2006. Sexual reproduction selects for robustness and negative epistasis in artificial gene networks. Nature 440:87-90.
6. Bagheri, H. C., and G. P. Wagner. 2004. Evolution of dominance in metabolic pathways. Genetics 168:1716-1735.
7. Barabási, A. L., and Z. N. Oltvai. 2004. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5:101-114.
8. Barkai, N., and S. Leibler. 1997. Robustness in simple biochemical networks. Nature 387:913-917.
9. Bateson, W. 1909. Mendel's principles of heredity. Cambridge Univ. Press, Cambridge.
10. Bershtein, S., M. Segal, R. Bekerman, N. Tokuriki, and D. S. Tawfik. 2006. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444:929-932.
11. Bonhoeffer, S., C. Chappey, N. T. Parkin, J. M. Whitcomb, and C. J. Petropoulos. 2004. Evidence for positive epistasis in HIV-1. Science 306:1547-1550.
12. Ciliberti, S., O. C. Martin, and A. Wagner. 2007. Innovation and robustness in complex regulatory gene networks. Proc. Natl. Acad. Sci. USA 104:13591-13596.
13. Cordell, H. J. 2002. Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum. Mol. Genet. 11:2463-2468.
14. Coyne, J. A. 1992. Genetics and speciation. Nature 355:511-515.
15. Crow, J. F. 2010. On epistais: why it is unimportant in polygenic directional selection. Phil. Trans. R. Soc. B 365:1241-1244.
16. De la Iglesia, F., and S. F. Elena. 2007. Fitness declines in Tobacco etch virus upon serial bottlenecks transfers. J. Virol. 81:4941-4947.
17. De Visser, J. A. G. M., J. Hermisson, G. P. Wagner, L. Ancel-Meyers, H. Bagheri-Chaichian, J. L. Blanchard, L. Chao, J. M. Cheverud, S. F. Elena, W. Fontana, et al. 2003. Perspective: evolution and detection of genetic robustness. Evolution 57:1959-1972.
18. De Visser, J. A. G. M., and S. F. Elena. 2007. The evolution of sex: empirical insights into the roles of epistasis and drift. Nat. Rev. Genet. 8:139-149.
19. De Visser, J. A. G. M., R. F. Hoekstra, and H. van den Ende. 1997a. An experimental test for synergistic epistasis and its application in Chlamydomonas. Genetics 145:815-819.
20. De Visser, J. A. G. M., R. F. Hoekstra, and H. van den Ende. 1997b. Test of interaction between genetic markers that affect fitness in Aspergillus niger. Evolution 51:1499-1505.
21. Desai, M. M., D. Weissman, and M. W. Feldman. 2007. Evolution can favor antagonistic epistasis. Genetics 177:1001-1010.
22. Elena, S. F., and R. E. Lenski. 1997. Test of synergistic interactions among deleterious mutations in bacteria. Nature 390:395-398.
23. Fisher, R. A. 1918. The correlation between relatives on the supposition of Mendelian inheritance. Trans. R. Soc. Edin. 52:399-433.
24. He, X., W. Qian, Z. Wang, Y. Li, and J. Zhang. 2010. Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks. Nat. Genet. 42:272-276.
25. Kondrashov, A. S. 1994. Muller's ratchet under epistatic selection. Genetics 136:1469-1473.
26. Kondrashov, A. S., and J. F. Crow. 1991. Haploidy or diploidy: which is better. Nature 351:314-315.
27. Lenski, R. E., C. Ofria, T. C. Collier, and C. Adami. 1999. Genome complexity, robustness and genetic interactions in digital organisms. Nature 400:661-664.
28. Macía, J., and R. V. Solé. 2009. Distributed robustness in cellular networks: insights from synthetic evolved circuits. J. R. Soc. Interface 6:393-400.
29. Parera, M., N. Pérez-Álvarez, B. Clotet, and M. A. Martínez. 2009. Epistasis among deleterious mutations in the HIV-1 protease. J. Mol. Biol. 392:243-250.
30. Poelwijk, F. J., D. J. Kiviet, D. M. Weinreich, and S. J. Tans. 2007. Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445:383-386.
31. Proulx, S. R., and P. C. Phillips. 2005. The opportunity for canalization and the evolution of genetic networks. Am. Nat. 165:147-162.
32. Sanjuán, R., and S. F. Elena. 2006. Epistasis correlates to genome complexity. Proc. Natl. Acad. Sci. USA 103:14402-14405.
33. Sanjuán, R., A. Moya, and S. F. Elena. 2004. The contribution of epistasis to the architecture of fitness in an RNA virus. Proc. Natl. Acad. Sci. USA 10:15376-15379.
34. Sanjuán, R., and M. R. Nebot. 2008. A network model for the correlation between epistasis and genomic complexity. PLoS ONE 3:e2663.
35. Siegal, M. L., and A. Bergman. 2002. Waddington's canalization revisited: developmental stability and evolution. Proc. Natl. Acad. Sci. USA 99:10528-10532.
36. Tononi, G., O. Sporns, and G. M. Edelman. 1999. Measures of degeneracy and redundancy in biological networks. Proc. Natl. Acad. Sci. USA 96:3257-3262.
37. Wagner, A. 1996. Does evolutionary plasticity evolve? Evolution 50:1008-1023.
38. Wagner, A.. 2005. Distributed robustness versus redundancy as causes of mutational robustness. BioEssays 27:176-188.
39. Wagner, G. P., G. Booth, and H. Bagheri-Chaichian. 1997. A population genetic theory of canalization. Evolution 51:329-347.
40. Weinreich, D. M., N. F. Delaney, M. A. DePristo, and D. L. Hartl. 2006. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312:111-114.
41. Whitlock, M. C., and D. Bourguet. 2000. Factors affecting the genetic load in Drosophila: synergistic epistasis and correlations among fitness components. Evolution 54:1654-1660.
42. Wilke, C. O., and C. Adami. 2001. Interaction between direction epistasis and average mutational effect. Proc. R. Soc. B 268:1469-1474.
43. Yukilevich, R., J. Lachance, F. Aoki, and J. R. True. 2008. Long-term adaptation of epistatic genetic networks. Evolution 62:2215-2235.