Evolutionary accessibility of mutational pathways

PLoS Computational Biology

Volumn 7, Issue 8, 2011, Pages

  Franke, Jasper ^a   Klözer, Alexander ^a   de Visser, J Arjan G M ^b   Krug, Joachim ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EMPIRICAL DATA; EVOLUTIONARY ADAPTATION; EVOLUTIONARY SELECTION; FITNESS LANDSCAPE; MEASURED VALUES; MODEL PREDICTION; OPTIMAL STATE; PROPERTY; TOTAL EFFECT; TUNABLES;

ASPERGILLUS;

ARTICLE; ASPERGILLUS NIGER; COMPARATIVE STUDY; CONTROLLED STUDY; GENE LOCUS; GENETIC DISTANCE; GENOME ANALYSIS; GENOTYPE; HOUSE OF CARDS MODEL; LK MODEL; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; POPULATION DYNAMICS; PREDICTION; PROCESS OPTIMIZATION; REPRODUCIBILITY; ROUGH MOUNT FUJI MODEL; BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; FUNGAL GENE; GENETICS; MUTAGENESIS; MUTATION; REPRODUCTIVE FITNESS;

ASPERGILLUS NIGER; FUNGI;

ASPERGILLUS NIGER; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENES, FUNGAL; GENETIC FITNESS; MODELS, GENETIC; MUTAGENESIS; MUTATION;

EID: 80052329913     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002134     Document Type: Article

References (49)

1. Phillips PC, (2008) Epistasis- the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9: 855-867.
2. Hall BG, (2002) Predicting evolution by in vitro evolution requires determining evolutionary pathways. Antimicrob Agents Chemother 46: 3035-3038.
3. Weinreich DM, Delaney NF, DePristo MA, Hartl DM, (2006) Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312: 111-114.
4. Lozovsky ER, Chookajorn T, Brown KM, Imwong M, Shaw PJ, et al. (2009) Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci U S A 106: 12025-12030.
5. Segrè D, DeLuna A, Church GM, Kishony R, (2005) Modular epistasis in yeast metabolism. Nat Genet 37: 1.
6. Weinreich DM, Watson RA, Chao L, (2005) Perspective: Sign epistasis and genetic constraints on evolutionary trajectories. Evolution 59: 1165-1174.
7. Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ, (2007) Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445: 383-386.
8. Kvitek DJ, Sherlock G, (2011) Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLoS Genet 7: e1002056.
9. Lunzer M, Miller SP, Felsheim R, Dean AM, (2005) The biochemical architecture of an ancient adaptive landscape. Science 310: 4899-501.
10. de Visser JAGM, Park SC, Krug J, (2009) Exploring the effect of sex on empirical fitness landscapes. Am Nat 174: S15-S30.
11. Kogenaru M, de Vos MGJ, Tans SJ, (2009) Revealing evolutionary pathways by fitness landscape reconstruction. Crit Rev Biochem Mol 44: 169-174.
12. Dawid A, Kiviet DJ, Kogenaru M, de Vos M, Tans SJ, (2010) Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape. Chaos 20: 026105.
13. da Silva J, Coetzer M, Nedellec R, Pastore C, Mosier DE, (2010) Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type I protein region. Genetics 185: 293-303.
14. Tan L, Serene S, Chao HX, Gore J, (2011) Hidden randomness between fitness landscapes limits reverse evolution. Phys Rev Lett 106: 198102.
15. Chou HH, Chiu HC, Delaney NF, Segré D, Marx CJ, (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332: 1190-1192.
16. Khan AI, Dinh DM, Schneider D, Lenski RE, Cooper TF, (2011) Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332: 1193-1196.
17. de Visser JAGM, Hoekstra RF, van den Ende H, (1997) Test of interaction between genetic markers that affect fitness in Aspergillus niger. Evolution 51: 1499-1505.
18. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, et al. (2010) The genetic landscape of a cell. Science 327: 425-431.
19. Fisher RA, (1958) The genetical theory of natural selection New York Dover.
20. Wright S, (1932) The roles of mutatation, inbreeding, cross-breeding and selection in evolution. Proc Sixth Int Cong Genet 1: 356-366.
21. Kauffman SA, (1993) The Origins of Order Oxford Oxford University Press.
22. Gillespie JH, (2004) Population Genetics: A concise guide Baltimore John Hopkins University Press.
23. Hartl DL, Clark AG, (1997) Principles of Population Genetics Sunderland, Massachusetts Sinauer Associates.
24. Jain K, Krug J, (2007) Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes. Genetics 175: 1275-1288.
25. Gillespie JH, (1983) Some properties of finite populations experiencing strong selection and weak mutation. Am Nat 121: 691-708.
26. Orr HA, (2002) The population genetics of adaptation: The adaptation of DNA sequences. Evolution 56: 1317-1330.
27. Weinreich DM, Chao L, (2005) Rapid evolutionary escape by large populations from local fitness peaks is likely in nature. Evolution 59: 1175-1182.
28. Weissman DB, Desai MM, Fisher DS, Feldman MW, (2009) The rate at which asexual populations cross fitness valleys. Theor Popul Biol 75: 286-300.
29. Kauffman S, Levin S, (1987) Towards a general theory of adaptive walks on rugged landscapes. J Theor Biol 128: 11-45.
30. Gokhale CS, Iwasa Y, Nowak MA, Traulsen A, (2009) The pace of evolution across fitness valleys. J Theor Biol 259: 613-620.
31. Wagner A, (2008) Neutralism and selectionism: a network-based reconciliation. Nat Rev Genet 9: 965-974.
32. Carneiro M, Hartl DL, (2010) Adaptive landscapes and protein evolution. Proc Natl Acad Sci U S A 107: 1747-1751.
33. Kingman JFC, (1978) A simple model for the balance between mutation and selection. J Appl Prob 15: 1-12.
34. Franke J, Wergen G, Krug J, (2010) Records and sequences of records from random variables with a linear trend. J Stat Mech: Theory Exp pp. P10013.
35. Aita T, Uchiyama H, Inaoka T, Nakajima M, Kokubo T, et al. (2000) Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: Application to protyl endopeptidase and thermolysis. Biopolymers 54: 64-79.
36. Kauffman SA, Weinberger ED, (1989) The NK model of rugged fitness landscapes and its application to maturation of the immune response. J Theor Biol 141: 211-245.
37. Durrett R, Limic V, (2003) Rigorous results for the NK model. Ann Prob 31: 1713-1753.
38. Limic V, Pemantle R, (2004) More rigorous results on the Kauffman Levin model of evolution. Ann Prob 32: 2149-2178.
39. Kimura M, (1983) The neutral theory of molecular evolution Cambridge Cambridge University Press.
40. Maynard Smith J, (1970) Natural selection and the concept of a protein space. Nature 225: 563-564.
41. Gavrilets S, (2004) Fitness Landscapes and the Origin of Species Princeton Princeton University Press.
42. Stauffer D, Aharony A, (1992) Introduction to percolation theory London Taylor & Francis.
43. Gavrilets S, Gravner J, (1997) Percolation on the fitness hypercube and the evolution of reproductive isolation. J Theor Biol 184: 51-64.
44. Reidys CM, (1997) Random induced subgraphs of generalized n-cubes. Adv Appl Math 19: 360-377.
45. Miller CR, Joyce P, Wichman H, (2011) Mutational effects and population dynamics during viral adaptation challenge current models. Genetics 187: 185-202.
46. Rowe W, Platt M, Wedge DC, Day PJ, Kell DB, et al. (2010) Analysis of a complete DNA-protein affinity landscape. J R Soc Interface 7: 397-408.
47. Watson RA, Weinreich DM, Wakeley J, (2011) Genome structure and the benefit of sex. Evolution 65: 523-536.
48. Jain K, Krug J, Park SC, (2011) Evolutionary advantage of small populations on complex fitness landscapes. Evolution 65: 1945-1955.
49. Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, et al. (2011) Second-order selection for evolvability in a large Escherichia coli population. Science 331: 1433-1436.