Related papers: Simulating short- and long-term evolutionary dynam…
In epistatic fitness landscapes, the fitness effect of a mutation depends on the genetic background and may even switch between deleterious and beneficial depending on the presence of another mutation. Epistatic interactions may cause both…
We consider a stochastic individual-based model of adaptive dynamics for an asexually reproducing population with mutation. Biologically motivated by the influence of seasons or the variation of drug concentration during medical treatment,…
Evolutionary adaptation is the process that increases the fit of a population to the fitness landscape it inhabits. As a consequence, evolutionary dynamics is shaped, constrained, and channeled, by that fitness landscape. Much work has been…
Evolutionary branching is analysed in a stochastic, individual-based population model under mutation and selection. In such models, the common assumption is that individual reproduction and life career are characterised by values of a…
Community assembly is studied using individual-based multispecies models. The models have stochastic population dynamics with mutation, migration, and extinction of species. Mutants appear as a result of mutation of the resident species,…
This Letter studies the quasispecies dynamics of a population capable of genetic repair evolving on a time-dependent fitness landscape. We develop a model that considers an asexual population of single-stranded, conservatively replicating…
Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current…
Evolutionary algorithms have long been used for optimization problems where the appropriate size of solutions is unclear a priori. The applicability of this methodology is here investigated on the problem of designing a nano-particle (NP)…
On rugged fitness landscapes where sign epistasis is common, adaptation can often involve either individually beneficial "uphill" mutations or more complex mutational trajectories involving fitness valleys or plateaus. The dynamics of the…
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and…
This is an introductory review of deterministic mutation-selection models for asexual populations (i.e., quasispecies theory) and related topics. First, the basic concepts of fitness, mutations, and sequence space are introduced. Different…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
Agent-based stochastic models for finite populations have recently received much attention in the game theory of evolutionary dynamics. Both the ultimate fixation and the pre-fixation transient behavior are important to a full understanding…
In this paper we consider two continuous-mass population models as analogues of logistic branching random walks, one is supported on a finite trait space and the other one is supported on an infinite trait space. For the first model with…
Frequency-dependent selection reflects the interaction between different species as they battle for limited resources in their environment. In a stochastic evolutionary game the species relative fitnesses guides the evolutionary dynamics…
Population dynamics on a rugged landscape is studied analytically and numerically within a simple discrete model for evolution of N individuals in one-dimensional fitness space. We reduce the set of master equations to a single Fokker-Plank…
We study the evolutionary dynamics of a maladapted population of self-replicating sequences on strongly correlated fitness landscapes. Each sequence is assumed to be composed of blocks of equal length and its fitness is given by a linear…
We re-examine the evolutionary dynamics of RNA secondary structures under directional selection towards an optimum RNA structure. We find that the punctuated equilibria lead to a very slow approach to the optimum, following on average an…
We consider an asexual population under strong selection-weak mutation conditions evolving on rugged fitness landscapes with many local fitness peaks. Unlike the previous studies in which the initial fitness of the population is assumed to…
In both natural and artificial studies, evolution is often seen as synonymous to natural selection. Individuals evolve under pressures set by environments that are either reset or do not carry over significant changes from previous…