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Volumn 203, Issue 3, 2016, Pages 1335-1351

Epistasis and the dynamics of reversion in molecular evolution

Author keywords

Entrenchment; Fitness landscape; Reversible Markov chain; Weak mutation

Indexed keywords

ARTICLE; EPISTASIS; GENOTYPE; HAZARD; MARKOV CHAIN; MOLECULAR EVOLUTION; MUTATION RATE; PRIORITY JOURNAL; REVERTANT; TIME; AMINO ACID SUBSTITUTION; BIOLOGICAL MODEL; GENETIC SELECTION; GENETICS; MUTATION; REPRODUCTIVE FITNESS;

EID: 84979955129     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.116.188961     Document Type: Article
Times cited : (37)

References (59)
  • 2
    • 84891364264 scopus 로고    scopus 로고
    • Mutational effects on stability are largely conserved during protein evolution
    • Ashenberg, O., L. I. Gong, and J. D. Bloom, 2013 Mutational effects on stability are largely conserved during protein evolution. Proc. Natl. Acad. Sci. USA 110: 21071–21076.
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 21071-21076
    • Ashenberg, O.1    Gong, L.I.2    Bloom, J.D.3
  • 3
    • 84943806240 scopus 로고    scopus 로고
    • Changing preferences: Deformation of single position amino acid fitness landscapes and evolution of proteins
    • Bazykin, G. A., 2015 Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins. Biol. Lett. 11: 20150315.
    • (2015) Biol. Lett , vol.11
    • Bazykin, G.A.1
  • 4
    • 84912143343 scopus 로고    scopus 로고
    • Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila
    • Bergland, A. O., E. L. Behrman, K. R. O’Brien, P. S. Schmidt, and D. A. Petrov, 2014 Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila. PLoS Genet. 10: e1004775.
    • (2014) Plos Genet , vol.10
    • Bergland, A.O.1    Behrman, E.L.2    O’Brien, K.R.3    Schmidt, P.S.4    Petrov, D.A.5
  • 7
    • 70349464621 scopus 로고    scopus 로고
    • An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
    • Bridgham, J. T., E. A. Ortlund, and J. W. Thornton, 2009 An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461: 515–519.
    • (2009) Nature , vol.461 , pp. 515-519
    • Bridgham, J.T.1    Ortlund, E.A.2    Thornton, J.W.3
  • 8
    • 76549129324 scopus 로고    scopus 로고
    • Adaptive landscapes and protein evolution
    • Carneiro, M., and D. L. Hartl, 2010 Adaptive landscapes and protein evolution. Proc. Natl. Acad. Sci. USA 107: 1747–1751.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 1747-1751
    • Carneiro, M.1    Hartl, D.L.2
  • 9
    • 53849099602 scopus 로고    scopus 로고
    • Reversing opinions on Dollo’s Law
    • Collin, R., and M. P. Miglietta, 2008 Reversing opinions on Dollo’s Law. Trends Ecol. Evol. 23: 602–609.
    • (2008) Trends Ecol. Evol , vol.23 , pp. 602-609
    • Collin, R.1    Miglietta, M.P.2
  • 10
    • 0025316459 scopus 로고
    • The geometry of evolution
    • Conrad, M., 1990 The geometry of evolution. Biosystems 24: 61– 81.
    • (1990) Biosystems , vol.24
    • Conrad, M.1
  • 12
    • 84946144214 scopus 로고    scopus 로고
    • Site-specific amino acid preferences are mostly conserved in two closely related protein homologs
    • Doud, M. B., O. Ashenberg, and J. D. Bloom, 2015 Site-specific amino acid preferences are mostly conserved in two closely related protein homologs. Mol. Biol. Evol. 33: 2944–2960.
    • (2015) Mol. Biol. Evol , vol.33 , pp. 2944-2960
    • Doud, M.B.1    Ashenberg, O.2    Bloom, J.D.3
  • 13
    • 84886298744 scopus 로고    scopus 로고
    • Selection biases the prevalence and type of epistasis along adaptive trajectories
    • Draghi, J. A., and J. B. Plotkin, 2013 Selection biases the prevalence and type of epistasis along adaptive trajectories. Evolution 67: 3120–3131.
    • (2013) Evolution , vol.67 , pp. 3120-3131
    • Draghi, J.A.1    Plotkin, J.B.2
  • 15
    • 0014860857 scopus 로고
    • An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
    • Fitch, W. M., and E. Markowitz, 1970 An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4: 579–593.
    • (1970) Biochem. Genet , vol.4 , pp. 579-593
    • Fitch, W.M.1    Markowitz, E.2
  • 16
    • 0035029534 scopus 로고    scopus 로고
    • Maximum-likelihood phylogenetic analysis under a covarion-like model
    • Galtier, N., 2001 Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18: 866–873.
    • (2001) Mol. Biol. Evol , vol.18 , pp. 866-873
    • Galtier, N.1
  • 17
    • 0031284943 scopus 로고    scopus 로고
    • Evolution and speciation on holey adaptive landscapes
    • Gavrilets, S., 1997 Evolution and speciation on holey adaptive landscapes. Trends Ecol. Evol. 12: 307–312.
    • (1997) Trends Ecol. Evol , vol.12 , pp. 307-312
    • Gavrilets, S.1
  • 18
    • 84930721455 scopus 로고    scopus 로고
    • Nonadaptive amino acid convergence rates decrease over time
    • Goldstein, R. A., S. T. Pollard, S. D. Shah, and D. D. Pollock, 2015 Nonadaptive amino acid convergence rates decrease over time. Mol. Biol. Evol. 32: 1373–1381.
    • (2015) Mol. Biol. Evol , vol.32 , pp. 1373-1381
    • Goldstein, R.A.1    Pollard, S.T.2    Shah, S.D.3    Pollock, D.D.4
  • 19
    • 0014845980 scopus 로고
    • Dollo on Dollo’s law: Irreversibility and the status of evolutionary laws
    • Gould, S. J., 1970 Dollo on Dollo’s law: irreversibility and the status of evolutionary laws. J. Hist. Biol. 3: 189–212.
    • (1970) J. Hist. Biol , vol.3 , pp. 189-212
    • Gould, S.J.1
  • 21
    • 0030574072 scopus 로고    scopus 로고
    • Compensatory nearly neutral mutations: Selection without adaptation
    • Hartl, D. L., and C. H. Taubes, 1996 Compensatory nearly neutral mutations: selection without adaptation. J. Theor. Biol. 182: 303–309.
    • (1996) J. Theor. Biol , vol.182 , pp. 303-309
    • Hartl, D.L.1    Taubes, C.H.2
  • 22
    • 0022410121 scopus 로고
    • Limits of adaptation: The evolution of selective neutrality
    • Hartl, D. L., D. E. Dykhuizen, and A. M. Dean, 1985 Limits of adaptation: the evolution of selective neutrality. Genetics 111: 655–674.
    • (1985) Genetics , vol.111 , pp. 655-674
    • Hartl, D.L.1    Dykhuizen, D.E.2    Dean, A.M.3
  • 23
    • 70350595871 scopus 로고    scopus 로고
    • Hemagglutinin receptor binding avidity drives influenza a virus antigenic drift
    • Hensley, S. E., S. R. Das, A. L. Bailey, L. M. Schmidt, H. D. Hickman et al., 2009 Hemagglutinin receptor binding avidity drives influenza a virus antigenic drift. Science 326: 734–736.
    • (2009) Science , vol.326 , pp. 734-736
    • Hensley, S.E.1    Das, S.R.2    Bailey, A.L.3    Schmidt, L.M.4    Hickman, H.D.5
  • 24
    • 0024281037 scopus 로고
    • Free fitness that always increases in evolution
    • Iwasa, Y., 1988 Free fitness that always increases in evolution. J. Theor. Biol. 135: 265–281.
    • (1988) J. Theor. Biol , vol.135 , pp. 265-281
    • Iwasa, Y.1
  • 25
    • 0000732090 scopus 로고
    • Mammalian Protein Metabolism, edited by H. N. MunroAcademic Press, New York
    • Jukes, T. H., and C. R. Cantor, 1969 Evolution of protein molecules, pp. 21–132 in Mammalian Protein Metabolism, Vol. 3, edited by H. N. Munro. Academic Press, New York.
    • (1969) Evolution of Protein Molecules , vol.3 , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 26
    • 84964972720 scopus 로고
    • Series in Probability and Mathematical Statistics, Wiley, Chichester, UK
    • Kelly, F. P., 1979 Reversibility and Stochastic Networks (Series in Probability and Mathematical Statistics). Wiley, Chichester, UK.
    • (1979) Reversibility and Stochastic Networks
    • Kelly, F.P.1
  • 27
    • 0037062936 scopus 로고    scopus 로고
    • Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors
    • Kerr, B., M. A. Riley, M. W. Feldman, and B. J. Bohannan, 2002 Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors. Nature 418: 171–174.
    • (2002) Nature , vol.418 , pp. 171-174
    • Kerr, B.1    Riley, M.A.2    Feldman, M.W.3    Bohannan, B.J.4
  • 30
    • 84920683555 scopus 로고    scopus 로고
    • Topological features of rugged fitness landscapes in sequence space
    • Kondrashov, D. A., and F. A. Kondrashov, 2015 Topological features of rugged fitness landscapes in sequence space. Trends Genet. 31: 24–33.
    • (2015) Trends Genet , vol.31 , pp. 24-33
    • Kondrashov, D.A.1    Kondrashov, F.A.2
  • 32
    • 84903291815 scopus 로고    scopus 로고
    • Global epistasis makes adaptation predictable despite sequence-level stochasticity
    • Kryazhimskiy, S., D. P. Rice, E. R. Jerison, and M. M. Desai, 2014 Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science 344: 1519–1522.
    • (2014) Science , vol.344 , pp. 1519-1522
    • Kryazhimskiy, S.1    Rice, D.P.2    Jerison, E.R.3    Desai, M.M.4
  • 33
    • 1842741699 scopus 로고    scopus 로고
    • HIV evolution: CTL escape mutation and reversion after transmission
    • Leslie, A., K. Pfafferott, P. Chetty, R. Draenert, M. Addo et al., 2004 HIV evolution: CTL escape mutation and reversion after transmission. Nat. Med. 10: 282–289.
    • (2004) Nat. Med , vol.10 , pp. 282-289
    • Leslie, A.1    Pfafferott, K.2    Chetty, P.3    Draenert, R.4    Addo, M.5
  • 34
    • 84883555753 scopus 로고    scopus 로고
    • On the findability of genotypes
    • McCandlish, D. M., 2013 On the findability of genotypes. Evolution 67: 2592–2603.
    • (2013) Evolution , vol.67 , pp. 2592-2603
    • McCandlish, D.M.1
  • 35
    • 84905454017 scopus 로고    scopus 로고
    • Modeling evolution using the probability of fixation: History and implications
    • McCandlish, D. M., and A. Stoltzfus, 2014 Modeling evolution using the probability of fixation: history and implications. Q. Rev. Biol. 89: 225–252.
    • (2014) Q. Rev. Biol , vol.89 , pp. 225-252
    • McCandlish, D.M.1    Stoltzfus, A.2
  • 37
    • 84919933295 scopus 로고    scopus 로고
    • Formal properties of the probability of fixation: Identities, inequalities and approximations
    • McCandlish, D. M., C. L. Epstein, and J. B. Plotkin, 2015a Formal properties of the probability of fixation: identities, inequalities and approximations. Theor. Popul. Biol. 99: 98–113.
    • (2015) Theor. Popul. Biol , vol.99 , pp. 98-113
    • McCandlish, D.M.1    Epstein, C.L.2    Plotkin, J.B.3
  • 38
    • 84941599641 scopus 로고    scopus 로고
    • Detecting epistasis from an ensemble of adapting populations
    • McCandlish, D. M., J. Otwinowski, and J. B. Plotkin, 2015b Detecting epistasis from an ensemble of adapting populations. Evolution 69: 2359–2370.
    • (2015) Evolution , vol.69 , pp. 2359-2370
    • McCandlish, D.M.1    Otwinowski, J.2    Plotkin, J.B.3
  • 39
    • 84979294598 scopus 로고    scopus 로고
    • Gene tree discordance causes apparent substitution rate variation
    • Mendes, F. K., and M. W. Hahn, 2016 Gene tree discordance causes apparent substitution rate variation. Syst. Biol. DOI: 10.1093/sysbio/syw018.
    • (2016) Syst. Biol.
    • Mendes, F.K.1    Hahn, M.W.2
  • 40
    • 0001250446 scopus 로고
    • Genetic variability, twin hybrids and constant hybrids, in a case of balanced lethal factors
    • Muller, H. J., 1918 Genetic variability, twin hybrids and constant hybrids, in a case of balanced lethal factors. Genetics 3: 422.
    • (1918) Genetics , vol.3 , pp. 422
    • Muller, H.J.1
  • 41
    • 84979134212 scopus 로고
    • Reversibility in evolution considered from the standpoint of genetics
    • Muller, H. J., 1939 Reversibility in evolution considered from the standpoint of genetics. Biol. Rev. Camb. Philos. Soc. 14: 261– 280.
    • (1939) Biol. Rev. Camb. Philos. Soc. , vol.14
    • Muller, H.J.1
  • 42
    • 84866697042 scopus 로고    scopus 로고
    • Fitness conferred by replaced amino acids declines with time
    • Naumenko, S. A., A. S. Kondrashov, and G. A. Bazykin, 2012 Fitness conferred by replaced amino acids declines with time. Biol. Lett. 8: 825–828.
    • (2012) Biol. Lett , vol.8 , pp. 825-828
    • Naumenko, S.A.1    Kondrashov, A.S.2    Bazykin, G.A.3
  • 43
    • 0034777365 scopus 로고    scopus 로고
    • Mathematical elegance with biochemical realism: The covarion model of molecular evolution
    • Penny, D., B. J. McComish, M. A. Charleston, and M. D. Hendy, 2001 Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J. Mol. Evol. 53: 711– 723.
    • (2001) J. Mol. Evol. , vol.53
    • Penny, D.1    McComish, B.J.2    Charleston, M.A.3    Hendy, M.D.4
  • 44
    • 84898811791 scopus 로고    scopus 로고
    • Strong evidence for protein epistasis, weak evidence against it
    • Pollock, D. D., and R. A. Goldstein, 2014 Strong evidence for protein epistasis, weak evidence against it. Proc. Natl. Acad. Sci. USA 111: E1450.
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. E1450
    • Pollock, D.D.1    Goldstein, R.A.2
  • 45
    • 84861422981 scopus 로고    scopus 로고
    • Amino acid coevolution induces an evolutionary Stokes shift
    • Pollock, D. D., G. Thiltgen, and R. A. Goldstein, 2012 Amino acid coevolution induces an evolutionary Stokes shift. Proc. Natl. Acad. Sci. USA 109: E1352–E1359.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. E1352-E1359
    • Pollock, D.D.1    Thiltgen, G.2    Goldstein, R.A.3
  • 46
    • 0141456010 scopus 로고    scopus 로고
    • Lost along the way: The significance of evolution in reverse
    • Porter, M. L., and K. A. Crandall, 2003 Lost along the way: the significance of evolution in reverse. Trends Ecol. Evol. 18: 541– 547.
    • (2003) Trends Ecol. Evol. , vol.18
    • Porter, M.L.1    Crandall, K.A.2
  • 47
    • 77953718211 scopus 로고    scopus 로고
    • Sequence space and the ongoing expansion of the protein universe
    • Povolotskaya, I. S., and F. A. Kondrashov, 2010 Sequence space and the ongoing expansion of the protein universe. Nature 465: 922–926.
    • (2010) Nature , vol.465 , pp. 922-926
    • Povolotskaya, I.S.1    Kondrashov, F.A.2
  • 48
    • 84988239865 scopus 로고    scopus 로고
    • Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history
    • Risso, V. A., F. Manssour-Triedo, A. Delgado-Delgado, R. Arco, A. Barroso-delJesus et al., 2015 Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Mol. Biol. Evol. 32: 440–455.
    • (2015) Mol. Biol. Evol , vol.32 , pp. 440-455
    • Risso, V.A.1    Manssour-Triedo, F.2    Delgado-Delgado, A.3    Arco, R.4    Barroso-Deljesus, A.5
  • 49
    • 42249084107 scopus 로고    scopus 로고
    • Homoplasy in genome-wide analysis of rare amino acid replacements: The molecular-evolutionary basis for Vavilov’s law of homologous series
    • Rogozin, I. B., K. Thomson, M. Csürös, L. Carmel, and E. V. Koonin, 2008 Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov’s law of homologous series. Biol. Direct 3: 7.
    • (2008) Biol. Direct , vol.3 , pp. 7
    • Rogozin, I.B.1    Thomson, K.2    Csürös, M.3    Carmel, L.4    Koonin, E.V.5
  • 50
    • 49749137335 scopus 로고    scopus 로고
    • Frequent and widespread parallel evolution of protein sequences
    • Rokas, A., and S. B. Carroll, 2008 Frequent and widespread parallel evolution of protein sequences. Mol. Biol. Evol. 25: 1943– 1953.
    • (2008) Mol. Biol. Evol. , vol.25
    • Rokas, A.1    Carroll, S.B.2
  • 51
    • 22144437325 scopus 로고    scopus 로고
    • The application of statistical physics to evolutionary biology
    • Sella, G., and A. E. Hirsh, 2005 The application of statistical physics to evolutionary biology. Proc. Natl. Acad. Sci. USA 102: 9541–9546.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 9541-9546
    • Sella, G.1    Hirsh, A.E.2
  • 52
    • 84934908389 scopus 로고    scopus 로고
    • Contingency and entrenchment in protein evolution under purifying selection
    • Shah, P., D. M. McCandlish, and J. B. Plotkin, 2015 Contingency and entrenchment in protein evolution under purifying selection. Proc. Natl. Acad. Sci. USA 112: E3226–E3235.
    • (2015) Proc. Natl. Acad. Sci. USA , vol.112 , pp. E3226-E3235
    • Shah, P.1    McCandlish, D.M.2    Plotkin, J.B.3
  • 54
    • 84874768052 scopus 로고    scopus 로고
    • Estimating the rate of irreversibility in protein evolution
    • Soylemez, O., and F. A. Kondrashov, 2012 Estimating the rate of irreversibility in protein evolution. Genome Biol. Evol. 4: 1213– 1222.
    • (2012) Genome Biol. Evol. , vol.4
    • Soylemez, O.1    Kondrashov, F.A.2
  • 55
    • 79960624826 scopus 로고    scopus 로고
    • Hidden randomness between fitness landscapes limits reverse evolution
    • Tan, L., S. Serene, H. X. Chao, and J. Gore, 2011 Hidden randomness between fitness landscapes limits reverse evolution. Phys. Rev. Lett. 106: 198102.
    • (2011) Phys. Rev. Lett , vol.106
    • Tan, L.1    Serene, S.2    Chao, H.X.3    Gore, J.4
  • 56
    • 0038072991 scopus 로고    scopus 로고
    • Perspective: Reverse evolution
    • Teotónio, H., and M. R. Rose, 2001 Perspective: reverse evolution. Evolution 55: 653–660.
    • (2001) Evolution , vol.55 , pp. 653-660
    • Teotónio, H.1    Rose, M.R.2
  • 58
    • 0022105767 scopus 로고
    • Heterogeneity’s ruses: Some surprising effects of selection on population dynamics
    • Vaupel, J. W., and A. I. Yashin, 1985 Heterogeneity’s ruses: some surprising effects of selection on population dynamics. Am. Stat. 39: 176–185.
    • (1985) Am. Stat , vol.39 , pp. 176-185
    • Vaupel, J.W.1    Yashin, A.I.2
  • 59
    • 84982104888 scopus 로고    scopus 로고
    • Are convergent and parallel amino acid substitutions in protein evolution more prevalent than neutral expectations?
    • Zou, Z., and J. Zhang, 2015 Are convergent and parallel amino acid substitutions in protein evolution more prevalent than neutral expectations? Mol. Biol. Evol. 32: 2085–2096.
    • (2015) Mol. Biol. Evol , vol.32 , pp. 2085-2096
    • Zou, Z.1    Zhang, J.2


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