Related papers: Population genetics and substitution models of ada…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
To our knowledge, the populations are generally assumed to be homogeneous in the traditional approach to evolutionary game dynamics. Here, we focus on the inhomogeneous populations. A simple model which can describe the inhomogeneity of the…
In evolutionary dynamics, the probability that a mutation spreads through the whole population, having arisen in a single individual, is known as the fixation probability. In general, it is not possible to find the fixation probability…
One of the most fundamental concepts of evolutionary dynamics is the "fixation" probability, i.e. the probability that a mutant spreads through the whole population. Most natural communities are geographically structured into habitats…
In order to analyze data from cancer genome sequencing projects, we need to be able to distinguish causative, or "driver," mutations from "passenger" mutations that have no selective effect. Toward this end, we prove results concerning the…
Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, $K$, at which these substitutions accumulate in the population coincides with the…
Traditionally Genetic Algorithm has been used for optimization of unimodal and multimodal functions. Earlier researchers worked with constant probabilities of GA control operators like crossover, mutation etc. for tuning the optimization in…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But…
The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…
We give a overview of stochastic models of evolution that have found applications in genetics, ecology and linguistics for an audience of nonspecialists, especially statistical physicists. In particular, we focus mostly on neutral models in…
A key challenge to make effective use of evolutionary algorithms is to choose appropriate settings for their parameters. However, the appropriate parameter setting generally depends on the structure of the optimisation problem, which is…
Population-based evolutionary algorithms (EAs) have been widely applied to solve various optimization problems. The question of how the performance of a population-based EA depends on the population size arises naturally. The performance of…
We study a class of evolution models, where the breeding process involves an arbitrary exchangeable process, allowing for mutations to appear. The population size $n$ is fixed, hence after breeding, selection is applied. Individuals are…
The influence of migration on the stochastic dynamics of subdivided populations is still an open issue in various evolutionary models. We develop here a self-consistent mean-field-like method in order to determine the effects of migration…
We introduce and analyze a waiting time model for the accumulation of genetic changes. The continuous time conjunctive Bayesian network is defined by a partially ordered set of mutations and by the rate of fixation of each mutation. The…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Mutation has traditionally been regarded as an important operator in evolutionary algorithms. In particular, there have been many experimental studies which showed the effectiveness of adapting mutation rates for various static optimization…