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Nonlinear deterministic equations in biological evolution. (English) Zbl 1362.92052

Summary: We review models of biological evolution in which the population frequency changes deterministically with time. If the population is self-replicating, although the equations for simple prototypes can be linearised, nonlinear equations arise in many complex situations. For sexual populations, even in the simplest setting, the equations are necessarily nonlinear due to the mixing of the parental genetic material. The solutions of such nonlinear equations display interesting features such as multiple equilibria and phase transitions. We mainly discuss those models for which an analytical understanding of such nonlinear equations is available.

MSC:

92D15 Problems related to evolution
92D25 Population dynamics (general)

References:

[1] Akin, E., The Geometry of Population Genetics, 1979, New York: Springer, New York · Zbl 0437.92016
[2] Baake, E.; Wagner, H., Mutation-selection models solved exactly with methods of statistical mechanics, Genet. Res. Camb., 78, 93-117, 2001
[3] Baake, E.; Wiehe, T., Bifurcations in haploid and diploid sequence space models, J. Math. Biol., 35, 321-343, 1997 · Zbl 0866.92012
[4] Bellman, R., Introduction to Matrix Analysis, 1997, Philadelphia: Society for Industrial and Applied Mathematics, Philadelphia · Zbl 0872.15003
[5] Boe, L.; Danielsen, M.; Knudsen, S.; Petersen, JB; Maymann, J.; Jensen, PR, The frequency of mutators in populations of Escherichia coli, Mut. Res., 448, 47-55, 2000
[6] Brumer, Y.; Shakhnovich, EI, Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies, Phys. Rev. E, 69, 061909, 2004
[7] Bürger, R., The Mathematical Theory of Selection, Recombination, and Mutation, 2000, Chichester: Wiley, Chichester · Zbl 0959.92018
[8] Crow, JF; Kimura, M., Evolution in sexual and asexual populations, Am. Nat., 99, 439-450, 1965
[9] Crow, JF; Kimura, M., An Introduction to Population Genetics Theory, 1970, New York: Harper and Row, New York · Zbl 0246.92003
[10] Drake, JW; Charlesworth, B.; Charlesworth, D.; Crow, JF, Rates of spontaneous mutation, Genetics, 148, 1667-1686, 1998
[11] Durrett, R., Probability Models for DNA Sequence Evolution, 2002, New York: Springer, New York · Zbl 0991.92021
[12] Eigen, M., Selforganization of matter and evolution of biological macromolecules, Naturwissenchaften, 58, 465-523, 1971
[13] Eigen, M.; Schuster, P., The hypercycle, Naturwissenchaften, 64, 541-565, 1977
[14] Eshel, I.; Feldman, MW, On the evolutionary effect of recombination, Theo. Pop. Biol., 1, 88-100, 1970 · Zbl 0242.92004
[15] Ewens, WJ, Mathematical Population Genetics, 1979, Berlin: Springer, Berlin · Zbl 0422.92011
[16] D. L. Hartl and E. W. Jones, Genetics: Analysis of Genes and Genomes (Jones and Barlett Publishers, 2009).
[17] Higgs, PG, Compensatory neutral mutations and the evolution of RNA, Genetica, 102-103, 91-101, 1998
[18] Izmailian, NSh; Papoyan, VlV; Priezzhev, VB; Hu, CK, Self-organizing behavior in a lattice model for co-evolution of virus and immune systems, Phys. Rev. E, 75, 041104, 2007
[19] Jacobi, MN; Nordahl, M., Quasispecies and recombination, Theo. Pop. Biol., 70, 479-485, 2006 · Zbl 1118.92043
[20] Jain, K., Loss of least-loaded class in asexual populations due to drift and epistasis, Genetics, 179, 2125, 2008
[21] Jain, K., Time to fixation in the presence of recombination, Theo. Pop. Biol., 77, 23, 2010 · Zbl 1403.92178
[22] K. Jain and J. Krug, Evolutionary trajectories in rugged fitness landscapes, J. Stat. Mech. Theory Exp. (2005) P04008.
[23] K. Jain and J. Krug, Adaptation in simple and complex fitness landscapes, in Structural Approaches to Sequence Evolution: Molecules, Networks and Populations, eds. U. Bastolla, M. Porto, H. E. Roman and M. Vendruscolo (Springer, Berlin, 2007), pp. 299-340.
[24] Jain, K.; Krug, J., Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes, Genetics, 175, 1275, 2007
[25] Jones, B.; Enns, R.; Rangnekar, S., On the theory of selection in coupled macromolecular systems, Bull. Math. Biol., 38, 15, 1976 · Zbl 0323.92005
[26] C. Kamp and S. Bornholdt, Coevolution of quasispecies: B-cell mutation rates maximize viral error catastrophes, Phys. Rev. Lett.88(6) (2002) 068104.
[27] Kimura, M., On the evolutionary adjustment of spontaneous mutation rates, Genet. Res., 9, 23-34, 1967
[28] Komarova, NL; Niyogi, P.; Nowak, MA, The evolutionary dynamics of grammar acquisition, J. Theor. Biol., 209, 43-59, 2001
[29] Kouyos, RD; Silander, OK; Bonhoeffer, S., Epistasis between deleterious mutations and the evolution of recombination, Trends Ecol. Evol., 22, 308-315, 2007
[30] LeClerc, JE; Li, B.; Payne, WL; Cebula, TA, High mutation frequencies among Escherichia coli and Salmonella pathogens, Science, 274, 1208-1211, 1996
[31] Nagar, A.; Jain, K., Exact phase diagram of quasispecies model with mutation rate modifier, Phys. Rev. Lett., 102, 038101, 2009
[32] Nilsson, M.; Snoad, N., Error thresholds for quasispecies on dynamic fitness landscapes, Phys. Rev. Lett., 84, 191-194, 2000
[33] Nilsson, M.; Snoad, N., Quasispecies evolution on a fitness landscape with a fluctuating peak, Phys. Rev. E, 65, 031901, 2002
[34] Nowak, MA; Schuster, P., Error thresholds of replication in finite populations: mutation frequencies and the onset of Muller’s ratchet, J. Theor. Biol., 137, 375-395, 1989
[35] M. A. Nowak, Evolutionary Dynamics: Exploring the Equations of Life (Harvard University Press, 2006). · Zbl 1115.92047
[36] Nowak, MA; Komarova, NL; Niyogi, P., Evolution of universal grammar, Science, 291, 114-118, 2001 · Zbl 1226.91060
[37] Otto, SP; Feldman, MW, Deleterious mutations, variable epistatic interactions, and the evolution of recombination, Theo. Pop. Biol., 51, 134-147, 1997 · Zbl 0949.92021
[38] Park, S-C; Krug, J., Bistability in two-locus models with selection, mutation, and recombination, J. Math. Biol., 62, 763-788, 2011 · Zbl 1232.92060
[39] Perelson, AS; Macken, CA, Protein evolution on partially correlated landscapes, Proc. Natl. Acad. Sci. USA, 92, 9657-9661, 1995 · Zbl 0832.92014
[40] Quer, J.; Huerta, R.; Novella, IS; Tsimring, L.; Domingo, E.; Holland, JJ, Reproducible nonlinear population dynamics and critical points during replicative competitions of RNA virus quasispecies, J. Mol. Biol., 264, 465-471, 1996
[41] Saakian, DB; Hu, CK, Solvable biological evolution models with a parallel mutation-selection scheme, Phys. Rev. E, 69, 046121, 2004
[42] Sardanyes, J.; Sole, RV, Chaotic stability in spatially-resolved host-parasite replicators: The red queen on a lattice, Internat. J. Bifurcation Chaos, 17, 589-606, 2007 · Zbl 1137.92032
[43] Seetharaman, S.; Jain, K., Evolutionary dynamics on strongly correlated fitness landscapes, Phys. Rev. E, 82, 031109, 2010
[44] Maynard Smith, J., Natural selection and concept of a protein space, Nature, 225, 031109, 1970
[45] Sniegowski, PD; Gerrish, PJ; Lenski, RE, Evolution of high mutation rates in experimental populations of Escherichia coli, Nature, 387, 703-705, 1997
[46] A. Sorace, C. Heycock and R. Shillcock, Language Acquisition: Knowledge Representation and Processing (North Holland, 1999).
[47] Sturtevant, AH, Essays on evolution. I. On the effects of selection on the mutation rate, Q. Rev. Biol., 12, 464-476, 1937
[48] Tannenbaum, E.; Deeds, E.; Shakhnovich, EI, Equilibrium distribution of mutators in the single fitness peak model, Phys. Rev. Lett., 91, 138105, 2003
[49] Thompson, CJ; McBride, JL, On Eigen’s theory of the self-organization of matter and the evolution of biological macromolecules, Math. Biosci., 21, 127, 1974 · Zbl 0287.92005
[50] J. A. G. M. de Visser, S.-C. Park and J. Krug, Exploring the effect of sex on an empirical fitness landscape, Am. Nat.174 (2009) S15-S30.
[51] Wiehe, T., Model dependency of error thresholds: The role of fitness functions and contrasts between the finite and infinite sites models, Genet. Res. Camb., 69, 127-136, 1997
[52] Wiehe, T.; Baake, E.; Schuster, P., Error propagation in reproduction of diploid organisms: A case study on single peaked landscapes, J. Theo. Biol., 177, 1-15, 1995
[53] Wilke, CO; Ronnewinkel, C.; Martinetz, T., Dynamic fitness landscapes in molecular evolution, Phys. Rep., 349, 395-446, 2001
[54] Woodcock, G.; Higgs, PG, Population evolution on a multiplicative single-peak fitness landscape, J. Theor. Biol., 179, 61-73, 1996
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