A simple model of co-evolutionary dynamics caused by epistatic selection

Journal of Theoretical Biology

Volumn 250, Issue 1, 2008, Pages 48-65

  Schlosser, Gerhard ^a   Wagner, Günter P ^b  

^a UNIVERSITY OF BREMEN   (Germany)

^b YALE UNIVERSITY   (United States)

Author keywords

Co evolution; Epistasis; Fitness landscapes; Modularity; Molecular evolution

Indexed keywords

COEVOLUTION; EPISTASIS; MODELING; MUTATION; SELECTION;

ALLELE; ARTICLE; COVARIANCE; EPISTASIS; GENE INTERACTION; GENE LOCUS; GENE MUTATION; GENOME ANALYSIS; GENOTYPE; MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL;

ALLELES; ANIMALS; EPISTASIS, GENETIC; EVOLUTION, MOLECULAR; MODELS, GENETIC; MUTATION; SELECTION (GENETICS);

EID: 36349000660     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2007.08.033     Document Type: Article

References (46)

1. Buck M.J., and Atchley W.R. Networks of coevolving sites in structural and functional domains of serpin proteins. Mol. Biol. Evol. 22 (2005) 1627-1634
2. Chen Y., and Dokholyan N.V. The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet. 22 (2006) 416-419
3. Cheverud J., and Routman E. Epistasis and its contribution to genetic variance components. Genetics 130 (1995) 1455-1461
4. DePristo M.A., Weinreich D.M., and Hartl D.L. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat. Rev. Genet. 6 (2005) 678-687
5. Elena S.F., and Lenski R.E. Test of synergistic interactions among deleterious mutations in bacteria. Nature 390 (1997) 395-398
6. Elena S.F., and Lenski R.E. Epistasis between new mutations and genetic background and a test of genetic canalization. Evolution 55 (2001) 1746-1752
7. Fariselli P., Olmea O., Valencia A., and Casadio R. Prediction of contact maps with neural networks and correlated mutations. Protein Eng. 14 (2001) 835-843
8. Fontana W., and Schuster P. Shaping space: the possible and the attainable in RNA genotype-phenotype mapping. J. Theor. Biol. 194 (1998) 491-515
9. Fraser H.B. Coevolution, modularity and human disease. Curr. Opin. Genet. Dev. 16 (2006) 637-644
10. Gavrilets S. Fitness Landscapes and the Origin of Species (2004), Princeton University Press, Princeton and Oxford
11. Gavrilets S., and de Jong G. Pleiotropic models of polygenic variation, stabilizing selection, and epistasis. Genetics 134 (1993) 609-625
12. Gildor T., Shemer R., Atir-Lande A., and Kornitzer D. Coevolution of cyclin Pcl5 and its substrate Gcn4. Eukaryot.Cell 4 (2005) 310-318
13. Gillespie J.H. Molecular evolution over the mutational landscape. Evolution 38 (1984) 1116-1129
14. Gillespie J.H. The Causes of Molecular Evolution (1991), Oxford University Press, New York
15. Gobel U., Sander C., Schneider R., and Valencia A. Correlated mutations and residue contacts in proteins. Proteins 18 (1994) 309-317
16. Goodnight C.J. Epistasis and the effect of founder events on the additive genetic variance. Evolution 42 (1988) 441-454
17. Goodnight C.J. Epistasis and the increase in additive genetic variance: implications for phase 1 of Wright's shifting-balance process. Evolution 49 (1995) 502-511
18. Haag E.S., Wang S., and Kimble J. Rapid coevolution of the nematode sex-determining genes fem-3 and tra-2. Curr. Biol. 12 (2002) 2035-2041
19. Hansen T.F., and Wagner G.P. Modeling genetic architecture: a multilinear theory of gene interaction. Theor. Pop. Biol. 59 (2001) 61-86
20. Kauffman S.A., and Levin S. Towards a general theory of adaptive walks on rugged landscapes. J. Theor. Biol. 128 (1987) 11-45
21. Kondrashov A.S., Sunyaev S., and Kondrashov F.A. Dobzhansky-Muller incompatibilities in protein evolution. Proc. Natl. Acad. Sci. USA 99 (2002) 14878-14883
22. Kulathinal R.J., Bettencourt B.R., and Hartl D.L. Compensated deleterious mutations in insect genomes. Science 306 (2004) 1553-1554
23. Liu J.C., Makova K.D., Adkins R.M., Gibson S., and Li W.H. Episodic evolution of growth hormone in primates and emergence of the species specificity of human growth hormone receptor. Mol. Biol. Evol. 18 (2001) 945-953
24. Orr H.A. The population genetics of speciation: the evolution of hybrid incompatibilities. Genetics 139 (1995) 1805-1813
25. Orr H.A. The population genetics of adaptation: the adaptation of DNA sequences. Evolution 56 (2002) 1317-1330
26. Orr H.A., and Turelli M. The evolution of postzygotic isolation: accumulating Dobzhansky-Muller incompatibilities. Evol. Int. J. Org. Evol. 55 (2001) 1085-1094
27. Ortlund, E.A., Bridgham, J.T., Redinbo, M.R., Thornton, J.W., 2007. Crystal structure of an ancient protein: evolution by conformational epistasis. Science, doi:10.1126/science.1142819.
28. Pang P.S., Jankowsky E., Wadley L.M., and Pyle A.M. Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data. J. Exp. Zool. Part B (Mol. Dev. Evol.) 304B (2005) 50-63
29. Pazos F., Helmer-Citterich M., Ausiello G., and Valencia A. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271 (1997) 511-523
30. Peixoto A.A., Hennessy J.M., Townson I., Hasan G., Rosbash M., Costa R., and Kyriacou C.P. Molecular coevolution within a Drosophila clock gene. Proc. Natl. Acad. Sci. USA 95 (1998) 4475-4480
31. Poelwijk F.J., Kiviet D.J., Weinreich D.M., and Tans S.J. Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445 (2007) 383-386
32. Presgraves D.C. A fine-scale genetic analysis of hybrid incompatibilities in Drosophila. Genetics 163 (2003) 955-972
33. Presgraves D.C., and Stephan W. Pervasive adaptive evolution among interactors of the Drosophila hybrid inviability gene, Nup96. Mol. Biol. Evol. 24 (2007) 306-314
34. Reidys C., Stadler P.F., and Schuster P. Generic properties of combinatory maps-neutral networks of RNA secondary structure. Bull. Math. Biol. 59 (1997) 339-397
35. Schlosser G. Modularity and the units of evolution. Theory Biosci. 121 (2002) 1-80
36. Schlosser G. The role of modules in development and evolution. In: Schlosser G., and Wagner G.P. (Eds). Modularity in Development and Evolution (2004), University of Chicago Press, Chicago 519-582
37. Schuster P., Fontana W., Stadler P.F., and Hofacker I. From sequences to shapes and back: a case study in RNA secondary structure. Proc. Roy. Soc. (London) B 255 (1994) 279-284
38. Stadler P.F. Landscapes and their correlation functions. J. Math. Chem. 20 (1996) 1-45
39. Stadler P.F., Seitz R., and Wagner G.P. Population dependent Fourier decomposition of fitness landscapes over recombination spaces: evolvability of complex characters. Bull. Math. Biol. 62 (2000) 399-428
40. Stephan W. The rate of compensatory evolution. Genetics 144 (1996) 419-426
41. Taylor W.R., and Hatrick K. Compensating changes in protein multiple sequence alignments. Protein Eng. 7 (1994) 341-348
42. Wagner A., Wagner G.P., and Similion P. Epistasis can facilitate the evolution of reproductive isolation by peak shifts: a two-locus two-allele model. Genetics 138 (1994) 533-545
43. Wagner G.P., Laubichler M.D., and Bagheri-Chaichian H. Genetic measurement theory of epistatic effects. Genetica 102/103 (1998) 569-580
44. Welch J.J. Accumulating Dobzhansky-Muller incompatibilities: reconciling theory and data. Evol. Int. J. Org. Evol. 58 (2004) 1145-1156
45. Whitlock M.C., Phillips P.C., Moore F.B.-G., and Tonsor S.J. Multiple fitness peaks and epistasis. Ann. Rev. Ecol. System. 26 (1995) 601-629
46. Wright S. Evolution and the Genetics of Populations, Vol. 2: The Theory of Gene Frequencies (1969), University of Chicago Press, Chicago, IL