Related papers: Randomness versus selection in genome evolution
A steady influx of a single deleterious multilocus genotype will impose genetic load on the resident population and leave multiple descendants carrying various numbers of the foreign alleles. Provided that the foreign types are rare at…
We study the simple genetic algorithm with a ranking selection mechanism (linear ranking or tournament). We denote by $\ell$ the length of the chromosomes, by $m$ the population size, by $p_C$ the crossover probability and by $p_M$ the…
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…
For a continuous state branching process with two types of individuals which are subject to selection and density dependent competition, we characterize the joint evolution of population size, type configurations and genealogies as the…
We discuss stochastic dynamics of populations of individuals playing games. Our models possess two evolutionarily stable strategies: an efficient one, where a population is in a state with the maximal payoff (fitness) and a risk-dominant…
Evolution of the reduced density matrix for a subsystem is studied to determine deviations from its Markov character for a system consisting of a closed chain of $N$ oscillators with one of them serving as a subsystem. The dependence on $N$…
Consider an advantageous allele that arises in a haploid population of size $N$ evolving in continuous time according to a skewed reproduction mechanism, which generates under neutrality genealogies lying in the domain of attraction of a…
In this paper we investigate networks whose evolution is governed by the interaction of a random assembly process and an optimization process. In the first process, new nodes are added one at a time and form connections to randomly selected…
The partially asymmetric exclusion process (PASEP) is an important model from statistical mechanics which describes a system of interacting particles hopping left and right on a one-dimensional lattice of N sites. It is partially asymmetric…
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…
We define the Sampled Moran Genealogy Process, a continuous-time Markov process on the space of genealogies with the demography of the classical Moran process, sampled through time. To do so, we begin by defining the Moran Genealogy Process…
Adaptive importance sampling is a powerful tool to sample from complicated target densities, but its success depends sensitively on the initial proposal density. An algorithm is presented to automatically perform the initialization using…
Mechanisms leading to speciation are a major focus in evolutionary biology. In this paper, we present and study a stochastic model of population where individuals, with type a or A, are equivalent from ecological, demographical and spatial…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…
Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…
Evolution occurs in populations of reproducing individuals. In stochastic descriptions of evolutionary dynamics, such as the Moran process, individuals are chosen randomly for birth and for death. If the same type is chosen for both steps,…
Markov chain sampling methods that automatically adapt to characteristics of the distribution being sampled can be constructed by exploiting the principle that one can sample from a distribution by sampling uniformly from the region under…
A branching process in a Markovian environment consists of an irreducible Markov chain on a set of "environments" together with an offspring distribution for each environment. At each time step the chain transitions to a new random…
We develop a new bidirectional algorithm for estimating Markov chain multi-step transition probabilities: given a Markov chain, we want to estimate the probability of hitting a given target state in $\ell$ steps after starting from a given…