相关论文: Error thresholds in a mutation-selection model wit…

Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…

Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a…

Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (`fitness'), measured values over all possible combinations of a set of mutations yield…

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…

The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic…

In evolutionary algorithms, the fitness of a population increases with time by mutating and recombining individuals and by a biased selection of more fit individuals. The right selection pressure is critical in ensuring sufficient…

Fisher's geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic…

Using the Hamilton-Jacobi equation approach to study genomes of length $L$, we obtain 1/L corrections for the steady state population distributions and mean fitness functions for horizontal gene transfer model, as well as for the diploid…

Genetic Programming has been very successful in solving a large area of problems but its use as a machine learning algorithm has been limited so far. One of the reasons is the problem of overfitting which cannot be solved or suppresed as…

In evolution theory the concept of a fitness landscape has played an important role, evolution itself being portrayed as a hill-climbing process on a rugged landscape. In this article it is shown that in general, in the presence of other…

We consider the evolution of large but finite populations on arbitrary fitness landscapes. We describe the evolutionary process by a Markov, Moran process. We show that to $\mathcal O(1/N)$, the time-averaged fitness is lower for the finite…

The interrelationships of the fundamental biological processes natural selection, mutation, and stochastic drift are quantified by the entropy rate of Moran processes with mutation, measuring the long-run variation of a Markov process. The…

The fitness level method is a popular tool for analyzing the hitting time of elitist evolutionary algorithms. Its idea is to divide the search space into multiple fitness levels and estimate lower and upper bounds on the hitting time using…

Phenotype-switching with and without sensing environment is a ubiquitous strategy of organisms to survive in fluctuating environment. Fitness of a population of organisms with phenotype-switching may be constrained and restricted by hidden…

We analytically study the dynamics of evolving populations that exhibit metastability on the level of phenotype or fitness. In constant selective environments, such metastable behavior is caused by two qualitatively different mechanisms.…

Muller's ratchet, in its prototype version, models a haploid, asexual population whose size~$N$ is constant over the generations. Slightly deleterious mutations are acquired along the lineages at a constant rate, and individuals carrying…

We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a…

Linear mixed models (LMMs) are a powerful and established tool for studying genotype-phenotype relationships. A limiting assumption of LMMs is that the residuals are Gaussian distributed, a requirement that rarely holds in practice.…

We consider a model of a population of fixed size $N$ undergoing selection. Each individual acquires beneficial mutations at rate $\mu_N$, and each beneficial mutation increases the individual's fitness by $s_N$. Each individual dies at…

We investigate the evolutionary dynamics of a finite population of sequences adapting to NK fitness landscapes. We find that, unlike in the case of an infinite population, the average fitness in a finite population is maximized at a small…