Biological Evolution and Statistical Physics

Abstract

This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. Throughout the review, attention is paid to giving the necessary biological information, and to pointing out the assumptions underlying the models, and their limits of validity.

Review article accepted for publication in Advances in Physics. 106 pages

Cited by in corpus (120)

• Evolutionary games on graphs
• Life is physics: evolution as a collective phenomenon far from equilibrium
• Stochastic Models of Evolution in Genetics, Ecology and Linguistics
• The context-dependence of mutations: a linkage of formalisms
• The speed of evolution in large asexual populations
• Extinction Rates for Fluctuation-Induced Metastabilities : A Real-Space WKB Approach
• Péclet number governs transition to acceleratory restart in drift-diffusion
• Phase transition and selection in a four-species cyclic Lotka-Volterra model
• Sequence Space Localization in the Immune System Response to Vaccination and Disease
• Species lifetime distribution for simple models of ecologies
• Networks of Recurrent Events, a Theory of Records, and an Application to Finding Causal Signatures in Seismicity
• Breaking records in the evolutionary race
• Evolutionary food web model based on body masses gives realistic networks with permanent species turnover
• Evolution in a Changing Environment
• Punctuated equilibria and 1/f noise in a biological coevolution model with individual-based dynamics
• Exactly solvable dynamics of the Eigen and the Crow-Kimura models
• The Nonequilibrium Nature of Culinary Evolution
• Competing associations in six-species predator-prey models
• Exact Results for Amplitude Spectra of Fitness Landscapes
• Adaptive walks in a gene network model of morphogenesis: insights into the Cambrian explosion
• Evolutionary trajectories in rugged fitness landscapes
• The Tangled Nature model as an evolving quasi-species model
• Brownian motion: a paradigm of soft matter and biological physics
• The Self-Organization of Interaction Networks for Nature-Inspired Optimization
• Power of the power-laws: lessons from unification of small and large time scales for evolution
• The species-area relationship and evolution
• Quasispecies evolution in general mean-field landscapes
• Oscillations and dynamics in a two-dimensional prey-predator system
• Evolution and non-equilibrium physics. A study of the Tangled Nature Model
• Evolutionary accessibility in tunably rugged fitness landscapes
• Fitness landscape of the cellular automata majority problem: View from the Olympus
• Quantum dynamics with stochastic gauge simulations
• The intermediate evolution phase in case of truncated selection
• Dynamics of Competitive Evolution on a Smooth Landscape
• Fluctuations and correlations in an individual-based model of biological coevolution
• Evolutionary ecology in-silico:evolving foodwebs, migrating population and speciation
• An individual-based predator-prey model for biological coevolution: Fluctuations, stability, and community structure
• Genetic flow directionality and geographical segregation in a Cymodocea nodosa genetic diversity network
• The Renormalization Group and the Dynamics of Genetic Systems
• Generalized Voter-like model on activity driven networks with attractiveness
• Heterogenous mean-field analysis of a generalized voter-like model on networks
• Frequency-dependent fitness induces multistability in coevolutionary dynamics
• Power Law Distribution of the Frequency of Demises of U.S Firms
• Effects of correlated interactions in a biological coevolution model with individual-based dynamics
• Extinction dynamics of Lotka-Volterra ecosystems on evolving networks
• A food-web based unified model of "macro"- and "micro-" evolution
• Drift reversal in asymmetric coevolutionary conflicts: Influence of microscopic processes and population size
• Simple model for the Darwinian transition in early evolution
• Periodicity of mass extinctions without an extraterrestrial cause
• Gompertz law in simple computer model of aging of biological population
• Tail-behavior roadmap for sharp restart
• Elementary Components of the Quadratic Assignment Problem
• Computer simulations of history of life: speciation, emergence of complex species from simpler organisms, and extinctions
• Cultural Evolution as a Non-Stationary Stochastic Process
• Analytical solution of a generalized Penna model
• Biological Evolution in a Multidimensional Fitness Landscape
• Who runs fastest in an adaptive landscape: Sexual versus asexual reproduction
• Correlations in the T Cell Response to Altered Peptide Ligands
• Gompertz mortality law and scaling behaviour of the Penna model
• Strategies for the evolution of sex
• Discrete stochastic processes, replicator and Fokker-Planck equations of coevolutionary dynamics in finite and infinite populations
• Extinction risk and structure of a food web model
• Unified "micro"- and "macro-" evolution of eco-systems: Self-organization of a dynamic network
• Dynamics and energy landscape of the jammed spin-liquid
• Delays in fitness adjustment can lead to coexistence of hierarchically interacting species
• Thermodynamic selection: mechanisms and scenarios
• Are Triggering Rates of Labquakes Universal? Inferring Triggering Rates From Incomplete Information
• A Comprehensive Empirical Evaluation of Generating Test Suites for Mobile Applications with Diversity
• The Tangled Nature Model of evolutionary dynamics reconsidered: structural and dynamical effects of trait inheritance
• Evolving eco-system: a network of networks
• Lane formation and critical coarsening in a model of bacterial competition
• The Complexity of Biological Ageing
• On singular probability densities generated by extremal dynamics
• Population size effects in evolutionary dynamics on neutral networks and toy landscapes
• Interplay of spatial dynamics and local adaptation shapes species lifetime distributions and species-area relationships
• Fate of Duplicated Neural Structures
• Modelling Food Webs
• Speciational view of macroevolution: are micro and macroevolution decoupled?
• Sole-Manrubia model of biological evolution: some new insights
• Risk of Population Extinction from Periodic and Abrupt Changes of Environment
• Survival-extinction phase transition in a bit-string population with mutation
• On-Chart Success Dynamics of Popular Songs
• Chaotic itinerancy, temporal segmentation and spatio-temporal combinatorial codes
• Adaptation in simple and complex fitness landscapes
• Universal Mortality Law, Life Expectancy and Immortality
• A Selective Advantage for Conservative Viruses
• Possible Origin of Stagnation and Variability of Earth's Biodiversity
• Asymmetric dynamics and critical behavior in the Bak-Sneppen model
• Positive mutations and mutation-dependent Verhulst factor in Penna ageing model
• How the Quasispecies Evolution Depends on the Topology of the Genome Space
• Evolution of Spatially Inhomogeneous Eco-Systems: An Unified Model Based Approach
• Stochastic delocalization of finite populations
• Ranking Competitors Using Degree-Neutralized Random Walks
• Population Dynamics in the Penna Model
• Absorbing-state phase transitions with extremal dynamics
• Density outbursts in a food web model with closed nutrient cycle
• Analytical results on the Muller's ratchet effect in growing populations
• Kinetic theory of decentralized learning for smart active matter
• Perceptual Rationality: An Evolutionary Game Theory of Perceptually Rational Decision-Making
• Role of detritus in a spatial food web model with diffusion
• Hidden Thermodynamic Information in Protein Amino Acid Mutation Tables
• Degree Correlations in a Dynamically Generated Model Food Web
• A short-ranged memory model with preferential growth
• Food Web Structure and the Evolution of Ecological Communities
• Large deviations for singular and degenerate diffusion models in adaptive evolution
• Fermi and Lotka: The Long Odds of Survival in a Dangerous Universe
• Complex Behavior in Simple Models of Biological Coevolution
• Information theory, predictability, and the emergence of complex life
• Evolutionary ecology in-silico: Does mathematical modelling help in understanding the "generic" trends?
• System Fitness and the Extinction Patterns of Firms under Pure Economic Competition
• A p-Spin Interaction Ashkin-Teller Spin-Glass Model
• Social Effects in Simple Computer Model of Ageing
• Complexity in the Immune System
• Explanation, Evolution and Subjective Probability in Everett Quantum Mechanics with Positive Preclusion
• The dauer mutation of the caenorhabditis elegans, simulated with the Penna and the Stauffer model
• Non-local Potts model on random lattice and chromatic number of a plane
• The Tangled nature model with inheritance and constraint: Evolutionary ecology restricted by a conserved resource
• An energy-based natural selection model
• Evidence of coevolution in multi-objective evolutionary algorithms
• The optimization and shock waves in evolution dynamics