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Volumn 332, Issue , 2013, Pages 218-227

Exact results for amplitude spectra of fitness landscapes

Author keywords

Epistasis; Experimental evolution; Fitness landscapes; Fourier decomposition; Sequence space

Indexed keywords

EPISTASIS; EVOLUTIONARY BIOLOGY; FITNESS; NUMERICAL MODEL;

EID: 84880043765     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2013.05.002     Document Type: Article
Times cited : (34)

References (57)
  • 1
    • 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
    • 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, 54:64-79.
    • (2000) Biopolymers , vol.54 , pp. 64-79
    • Aita, T.1    Uchiyama, H.2    Inaoka, T.3    Nakajima, M.4    Kokubo, T.5    Husimi, Y.6
  • 2
    • 0035178855 scopus 로고    scopus 로고
    • A cross-section of the fitness landscape of dihydrofolate reductase
    • Aita T., Iwakura M., Husimi Y. A cross-section of the fitness landscape of dihydrofolate reductase. Protein Eng. 2001, 14:633-638.
    • (2001) Protein Eng. , vol.14 , pp. 633-638
    • Aita, T.1    Iwakura, M.2    Husimi, Y.3
  • 3
    • 84880046464 scopus 로고    scopus 로고
    • NK fitness landscapes. In: Bäck, T., Fogel, D.B., Michalewicz, Z. (Eds.) Handbook of Evolutionary Computation, IOP Publishing Ltd and Oxford University Press.
    • Altenberg, L., 1997. NK fitness landscapes. In: Bäck, T., Fogel, D.B., Michalewicz, Z. (Eds.) Handbook of Evolutionary Computation, IOP Publishing Ltd and Oxford University Press.
    • (1997)
    • Altenberg, L.1
  • 4
    • 0043230411 scopus 로고
    • Spin glasses. experimental facts, theoretical concepts, and open questions
    • Binder K., Young A.P. Spin glasses. experimental facts, theoretical concepts, and open questions. Rev. Mod. Phys. 1986, 58:801-976.
    • (1986) Rev. Mod. Phys. , vol.58 , pp. 801-976
    • Binder, K.1    Young, A.P.2
  • 5
    • 78649365006 scopus 로고    scopus 로고
    • Compensatory mutations restore fitness during the evolution of dihydrofolate reductase
    • Brown K.M., Costanzo M.S., Xu W., Roy S., Lozovsky E.R., Hartl D.L. Compensatory mutations restore fitness during the evolution of dihydrofolate reductase. Mol. Biol. Evol. 2010, 27:2682-2690.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 2682-2690
    • Brown, K.M.1    Costanzo, M.S.2    Xu, W.3    Roy, S.4    Lozovsky, E.R.5    Hartl, D.L.6
  • 6
    • 0037083769 scopus 로고    scopus 로고
    • Optimal adaptive performance and delocalization in NK fitness landscapes
    • Campos P.R.A., Adami C., Wilke C.O. Optimal adaptive performance and delocalization in NK fitness landscapes. Physica A 2002, 304:495-506.
    • (2002) Physica A , vol.304 , pp. 495-506
    • Campos, P.R.A.1    Adami, C.2    Wilke, C.O.3
  • 7
    • 0037442321 scopus 로고    scopus 로고
    • Optimal adaptive performance and delocalization in NK fitness landscapes
    • (Erratum)
    • Campos P.R.A., Adami C., Wilke C.O. Optimal adaptive performance and delocalization in NK fitness landscapes. Physica A 2003, 318:637. (Erratum).
    • (2003) Physica A , vol.318 , pp. 637
    • Campos, P.R.A.1    Adami, C.2    Wilke, C.O.3
  • 8
    • 79957958115 scopus 로고    scopus 로고
    • Diminishing returns epistasis among beneficial mutations decelerates adaptation
    • Chou H.-H., Chiu H.-C., Delaney N.F., Segrè D., Marx C.J. Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 2011, 332:1190-1192.
    • (2011) Science , vol.332 , pp. 1190-1192
    • Chou, H.-H.1    Chiu, H.-C.2    Delaney, N.F.3    Segrè, D.4    Marx, C.J.5
  • 9
    • 79956356758 scopus 로고    scopus 로고
    • Fitness trade-offs in the evolution of dihydrofolate reductase and drug resistance in Plasmodium falciparum
    • Costanzo M.S., Brown K.M., Hartl D.L. Fitness trade-offs in the evolution of dihydrofolate reductase and drug resistance in Plasmodium falciparum. PLoS ONE 2011, 6:e19636.
    • (2011) PLoS ONE , vol.6
    • Costanzo, M.S.1    Brown, K.M.2    Hartl, D.L.3
  • 10
    • 84867425613 scopus 로고    scopus 로고
    • The peaks and geometry of fitness landscapes
    • Crona K., Greene D., Barlow M. The peaks and geometry of fitness landscapes. J. Theor. Biol. 2013, 317:1-10.
    • (2013) J. Theor. Biol. , vol.317 , pp. 1-10
    • Crona, K.1    Greene, D.2    Barlow, M.3
  • 11
    • 77956641491 scopus 로고    scopus 로고
    • Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region
    • da Silva J., Coetzer M., Nedellec R., Pastore C., Mosier D.E. Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region. Genetics 2010, 185:293-303.
    • (2010) Genetics , vol.185 , pp. 293-303
    • da Silva, J.1    Coetzer, M.2    Nedellec, R.3    Pastore, C.4    Mosier, D.E.5
  • 13
    • 0035296743 scopus 로고    scopus 로고
    • Biological evolution and statistical physics
    • Drossel B. Biological evolution and statistical physics. Adv. Phys. 2001, 50:209-295.
    • (2001) Adv. Phys. , vol.50 , pp. 209-295
    • Drossel, B.1
  • 15
    • 84880042363 scopus 로고    scopus 로고
    • Statistical Topography of Fitness Landscapes. Doctoral Thesis, University of Cologne.
    • Franke, J., 2012. Statistical Topography of Fitness Landscapes. Doctoral Thesis, University of Cologne.
    • (2012)
    • Franke, J.1
  • 16
    • 84866292144 scopus 로고    scopus 로고
    • Evolutionary accessibility in tunably rugged fitness landscapes
    • Franke J., Krug J. Evolutionary accessibility in tunably rugged fitness landscapes. J. Stat. Phys. 2012, 148:705-722.
    • (2012) J. Stat. Phys. , vol.148 , pp. 705-722
    • Franke, J.1    Krug, J.2
  • 19
    • 84880047293 scopus 로고    scopus 로고
    • Tables of combinatorial identities
    • Available online at
    • Gould, H.W., 2010. Tables of combinatorial identities. In: Quaintance, J. (Ed.), vol. 2. Available online at http://www.math.wvu.edu/~gould/.
    • (2010) Quaintance, J. , vol.2
    • Gould, H.W.1
  • 21
    • 77952007724 scopus 로고    scopus 로고
    • Fitness epistasis among six biosynthetic loci in the budding yeast Saccharomyces cerevisiae
    • Hall D.W., Agan M., Pope S.C. Fitness epistasis among six biosynthetic loci in the budding yeast Saccharomyces cerevisiae. J. Hered. 2010, 101:S75-S84.
    • (2010) J. Hered. , vol.101
    • Hall, D.W.1    Agan, M.2    Pope, S.C.3
  • 22
    • 59449088633 scopus 로고    scopus 로고
    • A general extreme value theory model for the adaptation of DNA sequences under strong selection and weak mutation
    • Joyce P., Rokyta D.R., Beisel C.J., Orr H.A. A general extreme value theory model for the adaptation of DNA sequences under strong selection and weak mutation. Genetics 2008, 180:1627-1643.
    • (2008) Genetics , vol.180 , pp. 1627-1643
    • Joyce, P.1    Rokyta, D.R.2    Beisel, C.J.3    Orr, H.A.4
  • 24
    • 0023647382 scopus 로고
    • Towards a general theory of adaptive walks on rugged landscapes
    • Kauffman S., Levin S. Towards a general theory of adaptive walks on rugged landscapes. J. Theor. Biol. 1987, 128:11-45.
    • (1987) J. Theor. Biol. , vol.128 , pp. 11-45
    • Kauffman, S.1    Levin, S.2
  • 25
    • 0024803111 scopus 로고
    • The NK model of rugged fitness landscapes and its application to maturation of the immune response
    • Kauffman S.A., Weinberger E.D. The NK model of rugged fitness landscapes and its application to maturation of the immune response. J. Theor. Biol. 1989, 141(2):211-245.
    • (1989) J. Theor. Biol. , vol.141 , Issue.2 , pp. 211-245
    • Kauffman, S.A.1    Weinberger, E.D.2
  • 26
    • 79957948242 scopus 로고    scopus 로고
    • Negative epistasis between beneficial mutations in an evolving bacterial population
    • Khan A.I., Dinh D.M., Schneider D., Lenski R.E., Cooper T.F. Negative epistasis between beneficial mutations in an evolving bacterial population. Science 2011, 332:1193-1196.
    • (2011) Science , vol.332 , pp. 1193-1196
    • Khan, A.I.1    Dinh, D.M.2    Schneider, D.3    Lenski, R.E.4    Cooper, T.F.5
  • 27
    • 0001503634 scopus 로고
    • A simple model for the balance between selection and mutation
    • Kingman J.F.C. A simple model for the balance between selection and mutation. J. Appl. Probab. 1978, 15:1-12.
    • (1978) J. Appl. Probab. , vol.15 , pp. 1-12
    • Kingman, J.F.C.1
  • 30
    • 4544289258 scopus 로고    scopus 로고
    • More rigorous results on the Kauffman-Levin model of evolution
    • Limic V., Pemantle R. More rigorous results on the Kauffman-Levin model of evolution. Ann. Probab. 2004, 32:2149-2178.
    • (2004) Ann. Probab. , vol.32 , pp. 2149-2178
    • Limic, V.1    Pemantle, R.2
  • 32
    • 27144538817 scopus 로고    scopus 로고
    • The biochemical architecture of an ancient adaptive landscape
    • Lunzer M., Miller S.P., Felsheim R., Dean A.M. The biochemical architecture of an ancient adaptive landscape. Science 2005, 310:499-501.
    • (2005) Science , vol.310 , pp. 499-501
    • Lunzer, M.1    Miller, S.P.2    Felsheim, R.3    Dean, A.M.4
  • 33
    • 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, 225:563-564.
    • (1970) Nature , vol.225 , pp. 563-564
    • Maynard Smith, J.1
  • 35
    • 78951475034 scopus 로고    scopus 로고
    • Mutational effects and population dynamics during viral adaptation challenge current models
    • Miller C.R., Joyce P., Wichman H.A. Mutational effects and population dynamics during viral adaptation challenge current models. Genetics 2011, 187:185-202.
    • (2011) Genetics , vol.187 , pp. 185-202
    • Miller, C.R.1    Joyce, P.2    Wichman, H.A.3
  • 36
    • 81255164432 scopus 로고    scopus 로고
    • Statistical genetics and evolution of quantitative traits
    • Neher R.A., Shraiman B.I. Statistical genetics and evolution of quantitative traits. Rev. Mod. Phys. 2011, 83:1283-1300.
    • (2011) Rev. Mod. Phys. , vol.83 , pp. 1283-1300
    • Neher, R.A.1    Shraiman, B.I.2
  • 37
    • 80054760130 scopus 로고    scopus 로고
    • Adaptive walks and extreme value theory
    • Neidhart J., Krug J. Adaptive walks and extreme value theory. Phys. Rev. Lett. 2011, 107:178102.
    • (2011) Phys. Rev. Lett. , vol.107 , pp. 178102
    • Neidhart, J.1    Krug, J.2
  • 39
    • 0036340979 scopus 로고    scopus 로고
    • The population genetics of adaptation. the adaptation of DNA sequences
    • Orr H.A. The population genetics of adaptation. the adaptation of DNA sequences. Evolution 2002, 56(7):1317-1330.
    • (2002) Evolution , vol.56 , Issue.7 , pp. 1317-1330
    • Orr, H.A.1
  • 40
    • 33748537738 scopus 로고    scopus 로고
    • The population genetics of adaptation on correlated fitness landscapes. the block model
    • Orr H.A. The population genetics of adaptation on correlated fitness landscapes. the block model. Evolution 2006, 60(6):1113-1124.
    • (2006) Evolution , vol.60 , Issue.6 , pp. 1113-1124
    • Orr, H.A.1
  • 41
    • 0028785881 scopus 로고
    • Protein evolution on partially correlated landscapes
    • Perelson A.S., Macken C.A. Protein evolution on partially correlated landscapes. Proc. Nat. Acad. Sci. 1995, 92(21):9657-9661.
    • (1995) Proc. Nat. Acad. Sci. , vol.92 , Issue.21 , pp. 9657-9661
    • Perelson, A.S.1    Macken, C.A.2
  • 42
    • 33846551980 scopus 로고    scopus 로고
    • Empirical fitness landscapes reveal accessible evolutionary paths
    • Poelwijk F.J., Kiviet D.J., Weinreich D.M., Tans S.J. Empirical fitness landscapes reveal accessible evolutionary paths. Nature 2007, 445:383-386.
    • (2007) Nature , vol.445 , pp. 383-386
    • Poelwijk, F.J.1    Kiviet, D.J.2    Weinreich, D.M.3    Tans, S.J.4
  • 43
    • 78650592680 scopus 로고    scopus 로고
    • Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes
    • Poelwijk F.J., Tǎnase-Nicola S., Kiviet D.J., Tans S.J. Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes. J. Theor. Biol. 2010, 272:141-144.
    • (2010) J. Theor. Biol. , vol.272 , pp. 141-144
    • Poelwijk, F.J.1    Tǎnase-Nicola, S.2    Kiviet, D.J.3    Tans, S.J.4
  • 44
    • 79958109129 scopus 로고    scopus 로고
    • Epistasis in a model of molecular signal transduction
    • Pumir A., Shraiman B. Epistasis in a model of molecular signal transduction. PLoS Comput. Biol. 2011, 7:e1001134.
    • (2011) PLoS Comput. Biol. , vol.7
    • Pumir, A.1    Shraiman, B.2
  • 45
    • 84880040947 scopus 로고    scopus 로고
    • Bachelor Thesis, University of Cologne.
    • Schmiegelt, B., 2012. Bachelor Thesis, University of Cologne.
    • (2012)
    • Schmiegelt, B.1
  • 46
    • 0030371056 scopus 로고    scopus 로고
    • Landscapes and their correlation functions
    • Stadler P.F. Landscapes and their correlation functions. J. Math. Chem. 1996, 20:1-45.
    • (1996) J. Math. Chem. , vol.20 , pp. 1-45
    • Stadler, P.F.1
  • 47
    • 0001092793 scopus 로고    scopus 로고
    • Random field models for fitness landscapes
    • Stadler P.F., Happel R. Random field models for fitness landscapes. J. Math. Biol. 1999, 38:435-478.
    • (1999) J. Math. Biol. , vol.38 , pp. 435-478
    • Stadler, P.F.1    Happel, R.2
  • 48
    • 84880046810 scopus 로고    scopus 로고
    • Reconstruction problems for graphs, Krawtchouk polynomials, and diophantine equations
    • Birkhäuser, Boston, M. Dehmer (Ed.)
    • Stoll T. Reconstruction problems for graphs, Krawtchouk polynomials, and diophantine equations. Structural Analysis of Complex Networks 2011, 293-317. Birkhäuser, Boston. M. Dehmer (Ed.).
    • (2011) Structural Analysis of Complex Networks , pp. 293-317
    • Stoll, T.1
  • 51
    • 79960624826 scopus 로고    scopus 로고
    • Hidden randomness between fitness landscapes limits reverse evolution
    • Tan L., Serene S., Chao H.X., Gore J. Hidden randomness between fitness landscapes limits reverse evolution. Phys. Rev. Lett. 2011, 106:198102.
    • (2011) Phys. Rev. Lett. , vol.106 , pp. 198102
    • Tan, L.1    Serene, S.2    Chao, H.X.3    Gore, J.4
  • 52
    • 0000839719 scopus 로고
    • Fourier and Taylor series on fitness landscapes
    • Weinberger E.D. Fourier and Taylor series on fitness landscapes. Biol. Cybern. 1991, 65:321-330.
    • (1991) Biol. Cybern. , vol.65 , pp. 321-330
    • Weinberger, E.D.1
  • 53
    • 0001697862 scopus 로고
    • Local properties of Kauffman's N-k model. a tunably rugged energy landscape
    • Weinberger E.D. Local properties of Kauffman's N-k model. a tunably rugged energy landscape. Phys. Rev. A 1991, 44:6399-6413.
    • (1991) Phys. Rev. A , vol.44 , pp. 6399-6413
    • Weinberger, E.D.1
  • 54
    • 21044435697 scopus 로고    scopus 로고
    • Perspective. sign epistasis and genetic constraint on evolutionary trajectories
    • Weinreich D.M., Watson R.A., Chao L. Perspective. sign epistasis and genetic constraint on evolutionary trajectories. Evolution 2005, 59:1165-1174.
    • (2005) Evolution , vol.59 , pp. 1165-1174
    • Weinreich, D.M.1    Watson, R.A.2    Chao, L.3
  • 55
    • 33645666942 scopus 로고    scopus 로고
    • Darwinian evolution can follow only very few mutational paths to fitter proteins
    • Weinreich D.M., Delaney N.F., DePristo M.A., Hartl D.L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 2006, 312:111-114.
    • (2006) Science , vol.312 , pp. 111-114
    • Weinreich, D.M.1    Delaney, N.F.2    DePristo, M.A.3    Hartl, D.L.4
  • 56
    • 15244359422 scopus 로고    scopus 로고
    • The nk model and population genetics
    • Welch J.J., Waxman D. The nk model and population genetics. J. Theor. Biol. 2005, 234:329-340.
    • (2005) J. Theor. Biol. , vol.234 , pp. 329-340
    • Welch, J.J.1    Waxman, D.2
  • 57
    • 0000907353 scopus 로고
    • The roles of mutation, inbreeding, crossbreeding and selection in evolution
    • Wright, S., 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. In: Proceedings of the Sixth International Congress of Genetics, vol. 1, pp. 356-366.
    • (1932) Proceedings of the Sixth International Congress of Genetics , vol.1 , pp. 356-366
    • Wright, S.1


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