Genome structure and the benefit of sex

Evolution

Volumn 65, Issue 2, 2011, Pages 523-536

  Watson, Richard A ^a   Weinreich, Daniel M ^b   Wakeley, John ^c  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b BROWN UNIVERSITY   (United States)

^c HARVARD UNIVERSITY   (United States)

Author keywords

Epistasis; Models simulations; Molecular evolution; Population genetics; Sex

Indexed keywords

ASEXUAL REPRODUCTION; EPISTASIS; FITNESS; GENETIC STRUCTURE; GENOME; MUTATION; RECOMBINATION; SEXUAL DIMORPHISM; SEXUAL REPRODUCTION;

ANIMAL; ARTICLE; ASEXUAL REPRODUCTION; BIOLOGICAL MODEL; GENETIC EPISTASIS; GENETIC SELECTION; MOLECULAR EVOLUTION; SEX;

ANIMALS; EPISTASIS, GENETIC; EVOLUTION, MOLECULAR; MODELS, GENETIC; REPRODUCTION, ASEXUAL; SELECTION, GENETIC; SEX;

EID: 79251503942     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2010.01144.x     Document Type: Article

References (74)

1. Barton, N. H., and S. P. Otto 2005. Evolution of recombination due to random drift. Genetics 169:2353-2370.
2. Barton, N. H., and B. Charlesworth 1998. Why sex and recombination? Science 281:1986-1990.
3. Barton, N. H. 1995. A general model for the evolution of recombination. Genet. Res. 65:123.
4. Charlesworth, B. 1990. Mutation selection balance and the evolutionary advantage of sex and recombination. Genet. Res. 55:199-221.
5. Culberson, J. C. 1995. Mutation-crossover isomorphism and the construction of discriminating functions. Evol. Computation 2:279.
6. Deb, K., and D. E. Goldberg 1992. Analyzing deception in trap functions. Pp. 93-108 in D. Whitley, ed. Foundations of genetic algorithms 2. Morgan Kaufmann, San Mateo, CA.
7. DePristo, M. A., D. M. Weinreich, and D. L. Hartl 2005. Missense meanderings in. sequence space: a biophysical view of protein evolution. Nat. Rev. Genet. 6:678-687.
8. Desai, M. M., D. S. Fisher, and A. W. Murray 2007. The speed of evolution and maintenance of variation in asexual populations. Curr. Biol. 17:385-394.
9. de Visser, J. A. G. M., S.-C. Park, and J. Krug 2009. Exploring the effect of sex on empirical fitness landscapes. Am. Nat. 174:S15-S30.
10. Drummond, D. A., J. J. Silberg, C. O. Wilke, M. M. Meyer, and F. H. Arnold 2005. On the conservative nature of intragenic recombination. Proc. Natl. Acad. Sci. USA 102:5380.
11. Elena, S. F., and R. E. Lenski 1997. Test of synergistic interactions between deleterious mutations in bacteria. Nature 390:395.
12. Eshel, I., and M. W. Feldman 1970. On the evolutionary effect of recombination. Theor. Popul. Biol. 1:88-100.
13. Feldman, M. W., S. P. Otto, and F. B. Christiansen 1997. Population genetic perspectives on the evolution of recombination. Annu. Rev. Genet. 30:261-295.
14. Felsenstein, J. 1974. The evolutionary advantage of recombination. Genetics 78:737-756.
15. Fisher, R. A. 1930. The genetical theory of natural selection. Oxford Univ. Press, Oxford.
16. Fontana, W., and P. Schuster 1998. Shaping space: the possible and the attainable in RNA genotype-phenotype mapping. J. Theor. Biol. 194:491-515.
17. Forrest, S., and M. Mitchell 1993. What makes a problem hard for a genetic algorithm? Some anomalous results and their explanation. Machine Learning 13:285-319.
18. Garcia-Fernandez, J. 2005. The genesis and evolution of homeobox gene clusters. Nat. Rev. Genet. 6:881-892.
19. Gerrish, P. J., and R. E. Lenski 1998. The fate of competing beneficial mutations in an asexual population. Genetica 102-103:127-144.
20. Gillespie, J. H. 1984. Molecular evolution over the mutational landscape. Evolution 38:1116-1129.
21. Goldberg, D. E. 1989. Genetic algorithms in search, optimization, and machine learning. Addison-Wesley, Reading, MA.
22. Haldane, J. B. S. 1932. A mathematical theory of natural selection. Part VIII. Metastable populations. Proceedings of the Cambridge Philosophical Society 26:137-142.
23. Hill, W. G., and A. Robertson 1966. The effects of linkage on limits to artificial selection. Genet. Res. 8:269-294.
24. Holland, J. H. 1975. Adaptation in natural and artificial systems. Univ. Michigan Press, Ann Arbor, MI.
25. Holland, J. H. 2000. Building blocks, cohort genetic algorithms, and hyperplane-defined functions. Evol. Computation 8:373.
26. Huynen, M. A. 1996. Exploring phenotype space through neutral evolution. J. Mol. Evol. 43:165-169.
27. Jansen, T., and I. Wegener 2005. Real royal road functions-where crossover provably is essential. Discrete Appl. Math. 149:111.
28. Jain, R., M. C. Rivera, and J. A. Lake 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96:3801.
29. Keightley, P. D., and S. P. Otto 2006. Interference among deleterious mutations favours sex and recombination in finite populations. Nature 443:89-92.
30. Kim, Y., and H. A. Orr 2005. Adaptation in sexuals vs. asexuals: clonal interference and the Fisher-Muller model. Genetics 171:1377-1386.
31. Kishony, R., and S. Leibler 2003. Environmental stresses can alleviate the average deleterious effect of mutations. J. Biol. 2:14.
32. Kondrashov, A. S. 1988. Deleterious mutations and the evolution of sexual reproduction. Nature 336:435-441.
33. Kondrashov, F. A., and A. S. Kondrashov 2001. Multidimensional epistasis and the disadvantage of sex. Proc. Natl Acad. Sci. USA 98:12089-12092.
34. Kouyos, R. D., S. P. Otto, and S. Bonhoeffer 2006. Effect of varying epistasis on the evolution of recombination. Genetics 173:589.
35. Lozovsky, E. R., T. Chookajorn, K. M. Brown, M. Imwong, P. J. Shaw, S. Kamchonwongpaisan, D. E. Neafsey, D. M. Weinreich, and D. L. Hartl 2009. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc. Natl. Acad. Sci. USA 106:12025-12030.
36. Macken, C. A., and A. S. Perelson 1989. Protein evolution on rugged landscapes. Proc. Natl. Acad. Sci. USA 86:6191.
37. Martin, D. P., E. Van der Walt, D. Posada, and E. P. Rybicki 2005. The evolutionary value of recombination is constrained by genome modularity. PLoS Genet. 1:e51.
38. Maynard Smith, J. 1970. Natural selection and the concept of protein space. Nature 225:563-564.
39. Meyer, M. M., J. J. Silberg, C. A. Voigt, J. B. Endelman, S. L. Mayo, Z.-G. Wang, and F. H. Arnold 2003. Library analysis of SCHEMA-guided protein recombination. Protein Science 12:1686.
40. Michalakis, Y., and M. Slatkin 1996. Interaction of selection and recombination in the fixation of negative-epistatic genes. Genet. Res. 67:257.
41. Mitchell, M., S. Forrest, and J. H. Holland 1992. The royal road for genetic algorithms: fitness landscapes and GA performance. Pp. 245-254 in F. J. Varela and P. Bourgine, eds. Procs. of first European conference on artificial life. MIT Press, Cambridge, MA.
42. Muller, H. J. 1932. Some genetic aspects of sex. Am. Nat. 66:118-138.
43. Neher, R. A., and B. I. Shraiman 2009. Competition between recombination and epistasis can cause a transition from allele to genotype selection. Proc. Natl. Acad. Sci. USA 106:6866-6871.
44. Neher, R. A., B. I. Shraiman, and D. S. Fisher 2010. Rate of adaptation in large sexual populations. Genetics 184:467-481.
45. Otto, S. P., and N. H. Barton 2001. Selection for recombination in small populations. Evolution 55:1921.
46. Otto, S. P., and M. W. Feldman 1997. Deleterious mutations, variable epistatic interactions, and the evolution of recombination. Theor. Popul. Biol. 51:134-147.
47. Otto, S. P., and T. Lenormand 2002. Resolving the paradox of sex and recombination. Nat. Rev. Genet. 3:252-261.
48. Perelson, S., and C. A. Macken 1995. Protein evolution on partially correlated landscapes. Proc. Natl. Acad. Sci. USA 92:9657.
49. Phillips, P. C. 1996. Waiting for a compensatory mutation: phase zero of the shifting-balance process. Genet. Res. 67:271.
50. Poelwijk, F. J., D. J. Kiviet, and S. J. Tans 2006. Evolutionary potential of a duplicated repressor-operator pair: simulating pathways using mutation data. PLoS Comput. Biol. 2:e58.
51. Poon, A., and L. Chao 2005. The rate of compensatory mutation in the bacteriophage φX174. Genetics 170:989-999.
52. Provine, W. B. 1986. Sewall Wright and evolutionary biology. Univ. of Chicago Press, Chicago.
53. Przeworski, M. 2005. PERSPECTIVES GENETICS: motivating hotspots. Science 310:247.
54. Rieseberg, L. H., O. Raymond, D. M. Rosenthal, Z. Lai, K. Livingstone, T. Nakazato, J. L. Durphy, A. E. Schwarzbach, L. A. Donovan, and C. Lexer 2003. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301:1189-90.
55. Rogers, A., and A. Prügel-Bennett 2001. A solvable model of a hard optimisation problem. Pp. 207-221 in L. Kallel, B. Naudts, and A. Rogers, eds. Proceedings of theoretical aspects of evolutionary computing. Springer, Berlin.
56. Rowe, W., M. Platt, D. C. Wedge, P. J. Day, D. B. Kell, and J. Knowles 2010. Analysis of a complete DNA-protein affinity landscape. J. R. Soc. Interface 7:397-408.
57. Segrè, D., A. Deluna, G. M. Church, and R. Kishony 2005. Modular epistasis in yeast metabolism. Nat. Genet. 37:77.
58. Shapiro, J. L., and A. Prügel-Bennett 1997. Genetic algorithms dynamics in two-well potentials with basins and barriers. Pp. 101-116 in R. K. Belew and M. D. Vose, eds. Foundations of genetic algorithms 4. Morgan Kaufmann, San Francisco.
59. Spears, W. M. 1992. Crossover or mutation? Pp. 221-237 in D. Whitley, ed. Foundations of genetic algorithms 2. Morgan Kaufmann, San Mateo, CA.
60. Spears, W. M. 2004. Evolutionary algorithms: the role of mutation and recombination. Springer-Verlag, Berlin.
61. Voigt, C. A., C. Martinez, Z. G. Wang, S. L. Mayo, and F. H. Arnold 2002. Protein building blocks preserved by recombination. Nat. Struct. Biol. 9:553.
62. Watson, R. A. 2001. Analysis of recombinative algorithms on a non-separable building block problem. Pp. 69-89 in W. N. Martin and W. M. Spears, eds. Foundation of genetic algorithms 6. Morgan Kaufmann, San Francisco, CA.
63. Watson, R. A. 2004. A Simple two-module problem to exemplify building-block assembly under crossover. Pp. 161-171 in X. Yao, J. A. Bullinaria, J. Rowe, P. Tiňo, and A. Kabán, eds. Parallel problem solving from nature - PPSN VIII. Springer, Berlin (LNCS 3242).
64. Watson, R. A. 2005. On the unit of selection in sexual populations. Pp. 895-905 in Advances in artificial life, eighth European conference (ECAL 2005). Springer, Berlin (LNCS 3630).
65. Watson, R. A. 2006. Compositional evolution: the impact of sex, symbiosis and modularity on the gradualist framework of evolution. MIT Press, Cambridge, MA.
66. Watson, R. A., and T. Jansen 2007. A building-block royal road where crossover is provably essential. GECCO '07: Proceedings of the 9th Annual Conference on Genetic and Evolutionary Computation 2:1452-1459.
67. Watson, R. A., D. Weinreich, and J. Wakeley 2006. Effects of intra-gene fitness interactions on the benefit of sexual recombination. Biochem. Soc. Trans. 34:560-561.
68. Weinreich, D. M., and L. Chao 2005. Rapid evolutionary escape by large populations from local fitness peaks is likely in nature. Evolution 59:1175.
69. 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.
70. Weinreich, D. M., R. A. Watson, and L. Chao 2005. Perspective: sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59:1165-1174.
71. West, S. A., A. D. Peters, and N. H. Barton 1998. Test for epistasis between deleterious mutations. Genetics 149:435.
72. Whitlock, M. C., P. C. Phillips, F. B. Moore, and S. J. Tonsor 1995. Multiple fitness peaks and epistasis. Annu. Rev. Ecol. Syst. 26:601-630.
73. Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97-159.
74. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. In Proceedings of the VI International Congress of Genetics 1:356-366.