메뉴 건너뛰기




Volumn 12, Issue 12, 2016, Pages

Beyond the Hypercube: Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks

Author keywords

[No Author keywords available]

Indexed keywords

BINARY SEQUENCES; BIOLOGY; DNA SEQUENCES; GEOMETRY; HEALTH;

EID: 85007564089     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1005218     Document Type: Article
Times cited : (34)

References (66)
  • 1
    • 0000907353 scopus 로고
    • The roles of mutation, inbreeding, crossbreeding, and selection in evolution
    • Wright S, The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the Sixth International Congress of Genetics. 1932;1:356–366.
    • (1932) Proceedings of the Sixth International Congress of Genetics , vol.1 , pp. 356-366
    • Wright, S.1
  • 3
    • 33645666942 scopus 로고    scopus 로고
    • Darwinian evolution can follow only very few mutational paths to fitter proteins
    • 16601193
    • Weinreich DM, Delaney NF, DePristo MA, Hartl DL, Darwinian evolution can follow only very few mutational paths to fitter proteins. Science. 2006;312(5770):111–114. doi: 10.1126/science.112353916601193
    • (2006) Science , vol.312 , Issue.5770 , pp. 111-114
    • Weinreich, D.M.1    Delaney, N.F.2    DePristo, M.A.3    Hartl, D.L.4
  • 5
    • 77649246045 scopus 로고    scopus 로고
    • Evolutionary trajectories of β-lactamase CTX-M-1 cluster enzymes: Predicting antibiotic resistance
    • 20107608
    • Novais Â, Comas I, Baquero F, Cantón R, Coque TM, Moya A, et al. Evolutionary trajectories of β-lactamase CTX-M-1 cluster enzymes: Predicting antibiotic resistance. PLoS Pathogens. 2010;6(1):e1000735. doi: 10.1371/journal.ppat.100073520107608
    • (2010) PLoS Pathogens , vol.6 , Issue.1 , pp. e1000735
    • Novais, Â.1    Comas, I.2    Baquero, F.3    Cantón, R.4    Coque, T.M.5    Moya, A.6
  • 6
    • 84555171441 scopus 로고    scopus 로고
    • Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
    • Toprak E, Veres A, Michel JB, Chait R, Hartl DL, Kishony R, Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nature Genetics. 2012;44(1):101–105. doi: 10.1038/ng.1034
    • (2012) Nature Genetics , vol.44 , Issue.1 , pp. 101-105
    • Toprak, E.1    Veres, A.2    Michel, J.B.3    Chait, R.4    Hartl, D.L.5    Kishony, R.6
  • 8
    • 84892555212 scopus 로고    scopus 로고
    • Small, smaller, smallest: The origins and evolution of ancient dual symbioses in a phloem-feeding insect
    • 23918810
    • Bennett GM, Moran NA, Small, smaller, smallest: The origins and evolution of ancient dual symbioses in a phloem-feeding insect. Genome Biology and Evolution. 2013;5(9):1675–1688. doi: 10.1093/gbe/evt11823918810
    • (2013) Genome Biology and Evolution , vol.5 , Issue.9 , pp. 1675-1688
    • Bennett, G.M.1    Moran, N.A.2
  • 11
    • 84902775598 scopus 로고    scopus 로고
    • Empirical fitness landscapes and the predictability of evolution
    • 24913663
    • de Visser JAGM, Krug J, Empirical fitness landscapes and the predictability of evolution. Nature Reviews Genetics. 2014;15(7):480–490. doi: 10.1038/nrg374424913663
    • (2014) Nature Reviews Genetics , vol.15 , Issue.7 , pp. 480-490
    • de Visser, J.A.G.M.1    Krug, J.2
  • 12
    • 84931274969 scopus 로고    scopus 로고
    • Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes
    • Palmer AC, Toprak E, Baym M, Kim S, Veres A, Bershtein S, et al. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nature Communications. 2015;6. doi: 10.1038/ncomms8385
    • (2015) Nature Communications , vol.6
    • Palmer, A.C.1    Toprak, E.2    Baym, M.3    Kim, S.4    Veres, A.5    Bershtein, S.6
  • 13
    • 70049100936 scopus 로고    scopus 로고
    • Interplay in the selection of fluoroquinolone resistance and bacterial fitness
    • 19662169
    • Marcusson LL, Frimodt-Møller N, Hughes D, Interplay in the selection of fluoroquinolone resistance and bacterial fitness. PLoS Pathogens. 2009;5(8):e1000541. doi: 10.1371/journal.ppat.100054119662169
    • (2009) PLoS Pathogens , vol.5 , Issue.8 , pp. e1000541
    • Marcusson, L.L.1    Frimodt-Møller, N.2    Hughes, D.3
  • 14
    • 0023648965 scopus 로고
    • A computer model of evolutionary optimization
    • 3607225
    • Fontana W, Schuster P, A computer model of evolutionary optimization. Biophysical Chemistry. 1987;26(2):123–147. doi: 10.1016/0301-4622(87)80017-03607225
    • (1987) Biophysical Chemistry , vol.26 , Issue.2 , pp. 123-147
    • Fontana, W.1    Schuster, P.2
  • 15
    • 84942935817 scopus 로고    scopus 로고
    • Lower glycolysis carries a higher flux than any biochemically possible alternative
    • 26416228
    • Court SJ, Waclaw B, Allen RJ, Lower glycolysis carries a higher flux than any biochemically possible alternative. Nature Communications. 2015;6:8427. doi: 10.1038/ncomms942726416228
    • (2015) Nature Communications , vol.6 , pp. 8427
    • Court, S.J.1    Waclaw, B.2    Allen, R.J.3
  • 17
    • 0023647382 scopus 로고
    • Towards a general theory of adaptive walks on rugged landscapes
    • 3431131
    • Kauffman S, Levin S, Towards a general theory of adaptive walks on rugged landscapes. Journal of Theoretical Biology. 1987;128(1):11–45. doi: 10.1016/S0022-5193(87)80029-23431131
    • (1987) Journal of Theoretical Biology , vol.128 , Issue.1 , pp. 11-45
    • Kauffman, S.1    Levin, S.2
  • 18
    • 0024803111 scopus 로고
    • The NK model of rugged fitness landscapes and its application to maturation of the immune response
    • 2632988
    • Kauffman SA, Weinberger ED, The NK model of rugged fitness landscapes and its application to maturation of the immune response. Journal of Theoretical Biology. 1989;141(2):211–245. doi: 10.1016/S0022-5193(89)80019-02632988
    • (1989) Journal of Theoretical Biology , vol.141 , Issue.2 , pp. 211-245
    • Kauffman, S.A.1    Weinberger, E.D.2
  • 19
    • 0034082141 scopus 로고    scopus 로고
    • Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: Application to prolyl endopeptidase and thermolysin
    • 10799982
    • Aita T, Uchiyama H, Inaoka T, Nakajima M, Kokubo T, Husimi Y, Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: Application to prolyl endopeptidase and thermolysin. Biopolymers. 2000;54(1):64–79. doi: 10.1002/(SICI)1097-0282(200007)54:1%3C64::AID-BIP70%3E3.0.CO;2-R10799982
    • (2000) Biopolymers , vol.54 , Issue.1 , pp. 64-79
    • Aita, T.1    Uchiyama, H.2    Inaoka, T.3    Nakajima, M.4    Kokubo, T.5    Husimi, Y.6
  • 20
    • 0032804774 scopus 로고    scopus 로고
    • A dynamical theory of speciation on holey adaptive landscapes
    • Gavrilets S, A dynamical theory of speciation on holey adaptive landscapes. The American Naturalist. 1999;154(1):1–22. doi: 10.1086/303217
    • (1999) The American Naturalist , vol.154 , Issue.1 , pp. 1-22
    • Gavrilets, S.1
  • 21
    • 0031556932 scopus 로고    scopus 로고
    • Percolation on the fitness hypercube and the evolution of reproductive isolation
    • 9039400
    • Gavrilets S, Gravner J, Percolation on the fitness hypercube and the evolution of reproductive isolation. Journal of Theoretical Biology. 1997;184(1):51–64. doi: 10.1006/jtbi.1996.02429039400
    • (1997) Journal of Theoretical Biology , vol.184 , Issue.1 , pp. 51-64
    • Gavrilets, S.1    Gravner, J.2
  • 23
    • 0034667684 scopus 로고    scopus 로고
    • Plasticity, evolvability, and modularity in RNA
    • 11069142
    • Ancel LW, Fontana W, Plasticity, evolvability, and modularity in RNA. Journal of Experimental Zoology. 2000;288(3):242–283. doi: 10.1002/1097-010X(20001015)288:3%3C242::AID-JEZ5%3E3.0.CO;2-O11069142
    • (2000) Journal of Experimental Zoology , vol.288 , Issue.3 , pp. 242-283
    • Ancel, L.W.1    Fontana, W.2
  • 25
    • 0014935646 scopus 로고
    • Natural selection and the concept of a protein space
    • Maynard Smith J, Natural selection and the concept of a protein space. Nature. 1970;225(5232):563–564. doi: 10.1038/225563a0
    • (1970) Nature , vol.225 , Issue.5232 , pp. 563-564
    • Maynard, S.J.1
  • 26
    • 0030625954 scopus 로고    scopus 로고
    • Neutral networks in protein space: A computational study based on knowledge-based potentials of mean force
    • 9261065
    • Babajide A, Hofacker IL, Sippl MJ, Stadler PF, Neutral networks in protein space: A computational study based on knowledge-based potentials of mean force. Folding and Design. 1997;2(5):261–269. doi: 10.1016/S1359-0278(97)00037-09261065
    • (1997) Folding and Design , vol.2 , Issue.5 , pp. 261-269
    • Babajide, A.1    Hofacker, I.L.2    Sippl, M.J.3    Stadler, P.F.4
  • 27
    • 77953718211 scopus 로고    scopus 로고
    • Sequence space and the ongoing expansion of the protein universe
    • 20485343
    • Povolotskaya IS, Kondrashov FA, Sequence space and the ongoing expansion of the protein universe. Nature. 2010;465(7300):922–926. doi: 10.1038/nature0910520485343
    • (2010) Nature , vol.465 , Issue.7300 , pp. 922-926
    • Povolotskaya, I.S.1    Kondrashov, F.A.2
  • 28
    • 0021055877 scopus 로고
    • Some properties of finite populations experiencing strong selection and weak mutation
    • Gillespie JH, Some properties of finite populations experiencing strong selection and weak mutation. The American Naturalist. 1983;121(5):691–708. doi: 10.1086/284095
    • (1983) The American Naturalist , vol.121 , Issue.5 , pp. 691-708
    • Gillespie, J.H.1
  • 29
    • 0001359641 scopus 로고
    • Molecular evolution over the mutational landscape
    • Gillespie JH, Molecular evolution over the mutational landscape. Evolution. 1984;38(5):1116–1129. doi: 10.2307/2408444
    • (1984) Evolution , vol.38 , Issue.5 , pp. 1116-1129
    • Gillespie, J.H.1
  • 30
    • 80052329913 scopus 로고    scopus 로고
    • Evolutionary accessibility of mutational pathways
    • 21876664
    • Franke J, Klözer A, de Visser JAGM, Krug J, Evolutionary accessibility of mutational pathways. PLoS computational biology. 2011;7(8):e1002134. doi: 10.1371/journal.pcbi.100213421876664
    • (2011) PLoS computational biology , vol.7 , Issue.8 , pp. e1002134
    • Franke, J.1    Klözer, A.2    de Visser, J.A.G.M.3    Krug, J.4
  • 31
    • 84901764014 scopus 로고    scopus 로고
    • On the existence of accessible paths in various models of fitness landscapes
    • Hegarty P, Martinsson A, On the existence of accessible paths in various models of fitness landscapes. The Annals of Applied Probability. 2014;24(4):1375–1395. doi: 10.1214/13-AAP949
    • (2014) The Annals of Applied Probability , vol.24 , Issue.4 , pp. 1375-1395
    • Hegarty, P.1    Martinsson, A.2
  • 34
    • 84962090322 scopus 로고    scopus 로고
    • Genetic correlations greatly increase mutational robustness and can both reduce and enhance evolvability
    • 26937652
    • Greenbury SF, Schaper S, Ahnert SE, Louis AA, Genetic correlations greatly increase mutational robustness and can both reduce and enhance evolvability. PLOS Comput Biol. 2016;12(3):e1004773. doi: 10.1371/journal.pcbi.100477326937652
    • (2016) PLOS Comput Biol , vol.12 , Issue.3 , pp. e1004773
    • Greenbury, S.F.1    Schaper, S.2    Ahnert, S.E.3    Louis, A.A.4
  • 35
    • 0032577365 scopus 로고    scopus 로고
    • Continuity in evolution: on the nature of transitions
    • 9603737
    • Fontana W, Continuity in evolution: on the nature of transitions. Science. 1998;280(5368):1451–1455. doi: 10.1126/science.280.5368.14519603737
    • (1998) Science , vol.280 , Issue.5368 , pp. 1451-1455
    • Fontana, W.1
  • 36
    • 0000135489 scopus 로고
    • Simulation of biological cell sorting using a two-dimensional extended Potts model
    • 10046374
    • Graner Fmc, Glazier JA, Simulation of biological cell sorting using a two-dimensional extended Potts model. Physical Review Letters. 1992;69:2013–2016. doi: 10.1103/PhysRevLett.69.201310046374
    • (1992) Physical Review Letters , vol.69 , pp. 2013-2016
    • Graner, F.1    Glazier, J.A.2
  • 37
    • 84877080561 scopus 로고    scopus 로고
    • Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter
    • 23650500
    • Otwinowski J, Nemenman I, Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter. PLOS ONE. 2013;8(5):e61570. doi: 10.1371/journal.pone.006157023650500
    • (2013) PLOS ONE , vol.8 , Issue.5 , pp. e61570
    • Otwinowski, J.1    Nemenman, I.2
  • 40
    • 84876138197 scopus 로고    scopus 로고
    • Accessibility percolation on n-trees
    • Nowak S, Krug J, Accessibility percolation on n-trees. EPL (Europhysics Letters). 2013;101(6):66004. doi: 10.1209/0295-5075/101/66004
    • (2013) EPL (Europhysics Letters) , vol.101 , Issue.6 , pp. 66004
    • Nowak, S.1    Krug, J.2
  • 41
    • 84958602193 scopus 로고    scopus 로고
    • The number of accessible paths in the hypercube
    • Berestycki J, Brunet E, Shi Z, The number of accessible paths in the hypercube. Bernoulli. 2016;22(2):653–680. doi: 10.3150/14-BEJ641
    • (2016) Bernoulli , vol.22 , Issue.2 , pp. 653-680
    • Berestycki, J.1    Brunet, E.2    Shi, Z.3
  • 42
    • 84885842840 scopus 로고    scopus 로고
    • Hidden specificity in an apparently nonspecific RNA-binding protein
    • 24056935
    • Guenther UP, Yandek LE, Niland CN, Campbell FE, Anderson D, Anderson VE, et al. Hidden specificity in an apparently nonspecific RNA-binding protein. Nature. 2013;502(7471):385–388. doi: 10.1038/nature1254324056935
    • (2013) Nature , vol.502 , Issue.7471 , pp. 385-388
    • Guenther, U.P.1    Yandek, L.E.2    Niland, C.N.3    Campbell, F.E.4    Anderson, D.5    Anderson, V.E.6
  • 43
    • 78049403925 scopus 로고    scopus 로고
    • Synonymous codon usage influences the local protein structure observed
    • 20530529
    • Saunders R, Deane CM, Synonymous codon usage influences the local protein structure observed. Nucleic Acids Research. 2010;38(19):6719–6728. doi: 10.1093/nar/gkq49520530529
    • (2010) Nucleic Acids Research , vol.38 , Issue.19 , pp. 6719-6728
    • Saunders, R.1    Deane, C.M.2
  • 44
    • 84867732569 scopus 로고    scopus 로고
    • Speeding with control: codon usage, tRNAs, and ribosomes
    • 22921354
    • Novoa EM, de Pouplana LR, Speeding with control: codon usage, tRNAs, and ribosomes. Trends in Genetics. 2012;28(11):574–581. doi: 10.1016/j.tig.2012.07.00622921354
    • (2012) Trends in Genetics , vol.28 , Issue.11 , pp. 574-581
    • Novoa, E.M.1    de Pouplana, L.R.2
  • 45
    • 84891871414 scopus 로고    scopus 로고
    • Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates
    • O’Brien EP, Vendruscolo M, Dobson CM, Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates. Nature Communications. 2014; 5. doi: 10.1038/ncomms3988
    • (2014) Nature Communications , vol.5
    • O’Brien, E.P.1    Vendruscolo, M.2    Dobson, C.M.3
  • 46
    • 21044435697 scopus 로고    scopus 로고
    • Perspective: sign epistasis and genetic constraint on evolutionary trajectories
    • 16050094
    • Weinreich DM, Watson RA, Chao L, Perspective: sign epistasis and genetic constraint on evolutionary trajectories. Evolution. 2005;59(6):1165–1174. doi: 10.1111/j.0014-3820.2005.tb01768.x16050094
    • (2005) Evolution , vol.59 , Issue.6 , pp. 1165-1174
    • Weinreich, D.M.1    Watson, R.A.2    Chao, L.3
  • 47
    • 78650592680 scopus 로고    scopus 로고
    • Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes
    • 21167837
    • Poelwijk FJ, Tănase-Nicola S, Kiviet DJ, Tans SJ, Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes. Journal of Theoretical Biology. 2011;272(1):141–144. doi: 10.1016/j.jtbi.2010.12.01521167837
    • (2011) Journal of Theoretical Biology , vol.272 , Issue.1 , pp. 141-144
    • Poelwijk, F.J.1    Tănase-Nicola, S.2    Kiviet, D.J.3    Tans, S.J.4
  • 48
    • 77954499525 scopus 로고    scopus 로고
    • Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape
    • 20590334
    • Dawid A, Kiviet DJ, Kogenaru M, de Vos M, Tans SJ, Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape. Chaos. 2010;20(2). doi: 10.1063/1.345360220590334
    • (2010) Chaos , vol.20 , Issue.2
    • Dawid, A.1    Kiviet, D.J.2    Kogenaru, M.3    de Vos, M.4    Tans, S.J.5
  • 49
    • 84983085001 scopus 로고    scopus 로고
    • Adaptation in protein fitness landscapes is facilitated by indirect paths
    • 27391790,.;:
    • Wu NC, Dai L, Olson CA, Lloyd-Smith JO, Sun R, Adaptation in protein fitness landscapes is facilitated by indirect paths. eLife. 2016;5:e16965. doi: 10.7554/eLife.1696527391790
    • (2016) eLife , vol.5 , pp. e16965
    • Wu, N.C.1    Dai, L.2    Olson, C.A.3    Lloyd-Smith, J.O.4    Sun, R.5
  • 52
    • 13144257707 scopus 로고    scopus 로고
    • The genetic theory of adaptation: a brief history
    • 15716908
    • Orr HA, The genetic theory of adaptation: a brief history. Nature Reviews Genetics. 2005;6(2):119–127. doi: 10.1038/nrg152315716908
    • (2005) Nature Reviews Genetics , vol.6 , Issue.2 , pp. 119-127
    • Orr, H.A.1
  • 54
    • 84887212468 scopus 로고    scopus 로고
    • Probing evolutionary repeatability: Neutral and double changes and the predictability of evolutionary adaptation
    • Roy SW, Probing evolutionary repeatability: Neutral and double changes and the predictability of evolutionary adaptation. PLoS ONE. 2009;4(2):1–6. doi: 10.1371/journal.pone.0004500
    • (2009) PLoS ONE , vol.4 , Issue.2 , pp. 1-6
    • Roy, S.W.1
  • 57
    • 34249275353 scopus 로고    scopus 로고
    • Phenotypic plasticity and the epigenetics of human disease
    • 17522677
    • Feinberg AP, Phenotypic plasticity and the epigenetics of human disease. Nature. 2007;447(7143):433–440. doi: 10.1038/nature0591917522677
    • (2007) Nature , vol.447 , Issue.7143 , pp. 433-440
    • Feinberg, A.P.1
  • 58
    • 77953809541 scopus 로고    scopus 로고
    • Constraints and plasticity in genome and molecular-phenome evolution
    • 20548290
    • Koonin EV, Wolf YI, Constraints and plasticity in genome and molecular-phenome evolution. Nature Reviews Genetics. 2010;11(7):487–498. doi: 10.1038/nrg281020548290
    • (2010) Nature Reviews Genetics , vol.11 , Issue.7 , pp. 487-498
    • Koonin, E.V.1    Wolf, Y.I.2
  • 61
    • 84923321398 scopus 로고    scopus 로고
    • Evolvability as a function of purifying selection in TEM-1 β-lactamase
    • 25723163
    • Stiffler MA, Hekstra DR, Ranganathan R, Evolvability as a function of purifying selection in TEM-1 β-lactamase. Cell. 2015;160(5):882–892. doi: 10.1016/j.cell.2015.01.03525723163
    • (2015) Cell , vol.160 , Issue.5 , pp. 882-892
    • Stiffler, M.A.1    Hekstra, D.R.2    Ranganathan, R.3
  • 63
    • 40849116411 scopus 로고    scopus 로고
    • Molecular evolution under fitness fluctuations
    • 18352233
    • Mustonen V, Lässig M, Molecular evolution under fitness fluctuations. Physical Review Letters. 2008;100:108101. doi: 10.1103/PhysRevLett.100.10810118352233
    • (2008) Physical Review Letters , vol.100 , pp. 108101
    • Mustonen, V.1    Lässig, M.2
  • 64
    • 84927973195 scopus 로고    scopus 로고
    • Quantifying the role of population subdivision in evolution on rugged fitness landscapes
    • Bitbol AF, Schwab DJ, Quantifying the role of population subdivision in evolution on rugged fitness landscapes. PLoS Computational Biology. 2014;10(8):1–15. doi: 10.1371/journal.pcbi.1003778
    • (2014) PLoS Computational Biology , vol.10 , Issue.8 , pp. 1-15
    • Bitbol, A.F.1    Schwab, D.J.2
  • 65
    • 80053144267 scopus 로고    scopus 로고
    • Acceleration of emergence of bacterial antibiotic resistance in connected microenvironments
    • 21940899
    • Zhang Q, Lambert G, Liao D, Kim H, Robin K, Tung Ck, et al. Acceleration of emergence of bacterial antibiotic resistance in connected microenvironments. Science. 2011;333(6050):1764–1767. doi: 10.1126/science.120874721940899
    • (2011) Science , vol.333 , Issue.6050 , pp. 1764-1767
    • Zhang, Q.1    Lambert, G.2    Liao, D.3    Kim, H.4    Robin, K.5    Tung, C.6
  • 66
    • 84865208085 scopus 로고    scopus 로고
    • Mutational pathway determines whether drug gradients accelerate evolution of drug-resistant cells
    • 23002776
    • Greulich P, Waclaw B, Allen RJ, Mutational pathway determines whether drug gradients accelerate evolution of drug-resistant cells. Physical Review Letters. 2012;109(8). doi: 10.1103/PhysRevLett.109.08810123002776
    • (2012) Physical Review Letters , vol.109 , Issue.8
    • Greulich, P.1    Waclaw, B.2    Allen, R.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.