Extending the applicability of Thermal Dynamics to Evolutionary Biology

In the past years, a remarkable mapping has been found between the dynamics of a population of M individuals undergoing random mutations and selection, and that of a single system in contact with a thermal bath with temperature 1/M. This correspondence holds under the somewhat restrictive condition that the population is dominated by a single type at almost all times, punctuated by rare successive mutations. Here we argue that such thermal dynamics will hold more generally, specifically in systems with rugged fitness landscapes. This includes cases with strong clonal interference, where a number of concurrent mutants dominate the population. The problem becomes closely analogous to the experimental situation of glasses subjected to controlled variations of parameters such as temperature, pressure or magnetic fields. Non-trivial suggestions from the field of glasses may be thus proposed for evolutionary systems - including a large part of the numerical simulation procedures - that in many cases would have been counter intuitive without this background.

[1]  Luca Peliti,et al.  Introduction to the statistical theory of Darwinian evolution , 1997, cond-mat/9712027.

[2]  Michael M. Desai,et al.  Beneficial Mutation–Selection Balance and the Effect of Linkage on Positive Selection , 2006, Genetics.

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

[4]  A. J. Kovacs,et al.  Transition vitreuse dans les polymères amorphes. Etude phénoménologique , 1964 .

[5]  N. Shoresh,et al.  Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations , 2014, Nature.

[6]  B. Derrida Random-Energy Model: Limit of a Family of Disordered Models , 1980 .

[7]  K. Jain,et al.  Evolutionary dynamics on strongly correlated fitness landscapes. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[8]  M. Lynch The Lower Bound to the Evolution of Mutation Rates , 2011, Genome biology and evolution.

[9]  T. R. Kirkpatrick,et al.  Scaling concepts for the dynamics of viscous liquids near an ideal glassy state. , 1989, Physical review. A, General physics.

[10]  S. Leibler,et al.  Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments , 2005, Science.

[11]  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.

[12]  Chiara Cammarota,et al.  Spontaneous energy-barrier formation in entropy-driven glassy dynamics. , 2014, Physical review. E, Statistical, nonlinear, and soft matter physics.

[13]  P. Sibani,et al.  Evolution dynamics in terraced NK landscapes , 1999, adap-org/9904004.

[14]  Memory and Chaos Effects in Spin Glasses , 1998, cond-mat/9806134.

[15]  M. Lässig,et al.  Stochastic evolution of transcription factor binding sites , 2022 .

[16]  C. Wilke,et al.  The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation. , 2007, Theoretical population biology.

[17]  Maurizio Serva,et al.  Diffusion reproduction processes , 1990 .

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

[19]  L. Struik On the rejuvenation of physically aged polymers by mechanical deformation , 1997 .

[20]  Meyer,et al.  Clustering of independently diffusing individuals by birth and death processes. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[21]  T. Hwa,et al.  On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient , 2012, Proceedings of the National Academy of Sciences.

[22]  P. Sibani,et al.  The long time behavior of the rate of recombination , 1981 .

[23]  V. Pande,et al.  On the application of statistical physics to evolutionary biology. , 2009, Journal of theoretical biology.

[24]  M. Lässig,et al.  Molecular evolution under fitness fluctuations. , 2008, Physical review letters.

[25]  S. Kauffman Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

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

[27]  Michael W Deem,et al.  Parallel tempering: theory, applications, and new perspectives. , 2005, Physical chemistry chemical physics : PCCP.

[28]  M. Mézard,et al.  Emergence of clones in sexual populations , 2012, 1205.2059.

[29]  Johannes Berg,et al.  Adaptive evolution of transcription factor binding sites , 2003, BMC Evolutionary Biology.

[30]  Debra J. Searles,et al.  The Fluctuation Theorem , 2002 .

[31]  D. Nelson,et al.  Genetic drift at expanding frontiers promotes gene segregation , 2007, Proceedings of the National Academy of Sciences.

[32]  S. Sastry,et al.  Encoding of memory in sheared amorphous solids. , 2014, Physical review letters.

[33]  M. Lässig,et al.  Fitness flux and ubiquity of adaptive evolution , 2010, Proceedings of the National Academy of Sciences.

[34]  J. Fontanari,et al.  Evolutionary dynamics on rugged fitness landscapes: exact dynamics and information theoretical aspects. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[35]  Andrea Montanari,et al.  Gibbs states and the set of solutions of random constraint satisfaction problems , 2006, Proceedings of the National Academy of Sciences.

[36]  Evolution on a Smooth Landscape: The Role of Bias , 1998 .

[37]  L. Laloux,et al.  Phase space geometry and slow dynamics , 1995, cond-mat/9510079.

[38]  Benjamin H. Good,et al.  Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations , 2012, Proceedings of the National Academy of Sciences.

[39]  R. Lenski,et al.  Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation , 2003, Nature Reviews Genetics.

[40]  A. W. F. Edwards,et al.  The statistical processes of evolutionary theory , 1963 .

[41]  R. Axelrod,et al.  Evolutionary Dynamics , 2004 .

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

[43]  Lev Tsimring,et al.  Evolution on a smooth landscape , 1996, cond-mat/9607174.