Dynamics of the Eigen and the Crow-Kimura models for molecular evolution.

We introduce an alternative way to study molecular evolution within well-established Hamilton-Jacobi formalism, showing that for a broad class of fitness landscapes it is possible to derive dynamics analytically within the 1N accuracy, where N is the genome length. For a smooth and monotonic fitness function this approach gives two dynamical phases: smooth dynamics and discontinuous dynamics. The latter phase arises naturally with no explicite singular fitness function, counterintuitively. The Hamilton-Jacobi method yields straightforward analytical results for the models that utilize fitness as a function of Hamming distance from a reference genome sequence. We also show the way in which this method gives dynamical phase structure for multipeak fitness.

[1]  Eigen model as a quantum spin chain: exact dynamics. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[2]  Chin-Kun Hu,et al.  Solvable biological evolution models with general fitness functions and multiple mutations in parallel mutation-selection scheme. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[3]  D. Saakian A New Method for the Solution of Models of Biological Evolution: Derivation of Exact Steady-State Distributions , 2007 .

[4]  Richard H. Enns,et al.  On the theory of selection of coupled macromolecular systems , 1976 .

[5]  Kessler,et al.  RNA virus evolution via a fitness-space model. , 1996, Physical review letters.

[6]  M. Baake,et al.  Ising quantum chain is equivalent to a model of biological evolution , 1997 .

[7]  G. M.,et al.  Partial Differential Equations I , 2023, Applied Mathematical Sciences.

[8]  J. Hermisson,et al.  Four-State Quantum Chain as a Model of Sequence Evolution , 2000, cond-mat/0008123.

[9]  M. Eigen,et al.  The molecular quasi-species , 2007 .

[10]  Joachim Hermisson,et al.  Mutation-selection balance: ancestry, load, and maximum principle. , 2002, Theoretical population biology.

[11]  H. Georgii,et al.  Mutation, selection, and ancestry in branching models: a variational approach , 2006, Journal of mathematical biology.

[12]  Chin-Kun Hu,et al.  Solvable biological evolution model with a parallel mutation-selection scheme. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[13]  S. Wright Evolution in mendelian populations , 1931 .

[14]  K. Kaneko,et al.  Evolution equation of phenotype distribution: general formulation and application to error catastrophe. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[15]  S Wright,et al.  The Differential Equation of the Distribution of Gene Frequencies. , 1945, Proceedings of the National Academy of Sciences of the United States of America.

[16]  E. Baake,et al.  Mutation-selection models solved exactly with methods of statistical mechanics. , 2001, Genetical research.

[17]  Terence Hwa,et al.  On the Selection and Evolution of Regulatory DNA Motifs , 2001, Journal of Molecular Evolution.

[18]  Colin J. Thompson,et al.  On Eigen's theory of the self-organization of matter and the evolution of biological macromolecules , 1974 .

[19]  J. Coffin,et al.  The solitary wave of asexual evolution , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[20]  M. Kimura,et al.  An introduction to population genetics theory , 1971 .

[21]  B. Drossel Biological evolution and statistical physics , 2001, cond-mat/0101409.

[22]  Terence Hwa,et al.  Dynamics of competitive evolution on a smooth landscape. , 2002, Physical review letters.

[23]  Arik Melikyan,et al.  Generalized characteristics of first order PDEs , 1998 .

[24]  M. Eigen Selforganization of matter and the evolution of biological macromolecules , 1971, Naturwissenschaften.

[25]  Chin-Kun Hu,et al.  Exact solution of the Eigen model with general fitness functions and degradation rates. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Franco Bagnoli,et al.  Speciation as Pattern Formation by Competition in a Smooth Fitness Landscape , 1997, cond-mat/9708101.