Related papers: Recombination Rate Modifiers under Stochastic Tran…
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…
RNA viruses are a widely used tool to study evolution experimentally. Many standard protocols of virus propagation and competition are done at nominally low multiplicity of infection (m.o.i.), but lead during one passage to two or more…
Given an endogenous timescale set by invasion in a constant environment, we introduced periodic temporal variation in competitive superiority by alternating the species' propagation rates. By manipulating habitat size and introduction rate,…
A topological approach to the study of genetic recombination, based on persistent homology, was introduced by Chan, Carlsson, and Rabad\'an in 2013. This associates a sequence of signatures called barcodes to genomic data sampled from an…
Many life-history traits, like the age at maturity or adult longevity, are important determinants of the generation time. For instance, semelparous species whose adults reproduce once and die have shorter generation times than iteroparous…
Spontaneous switching events in most characterized genetic switches are rare, resulting in extremely stable epigenetic properties. We show how simple arguments lead to theories of the rate of such events much like the absolute rate theory…
We present a stochastic epidemic model to study the effect of various preventive measures, such as uniform reduction of contacts and transmission, vaccination, isolation, screening and contact tracing, on a disease outbreak in a…
Genome-wide patterns of genetic divergence reveal mechanisms of adaptation under gene flow. Empirical data show that divergence is mostly concentrated in narrow genomic regions. This pattern may arise because differentiated loci protect…
Inspired by Fisher's geometric approach to study beneficial mutations, we analyse probabilities of beneficial mutation and crossover recombination of strings in a general Hamming space with arbitrary finite alphabet. Mutations and…
We study the fixation probability of a mutant type when introduced into a resident population. As opposed to the usual assumption of constant pop- ulation size, we allow for stochastically varying population sizes. This is implemented by a…
We study a minimal stochastic individual-based model for a microbial population challenged by a persistent (lytic) virus epidemic. We focus on the situation in which the resident microbial host population and the virus population are in…
The outcome of competition among species is influenced by the spatial distribution of species and effects such as demographic stochasticity, immigration fluxes, and the existence of preferred habitats. We introduce an individual-based model…
We consider a stochastic model for a pathogen population in the presence of an immune response, in which pathogen types are partially ordered by ancestry and the immune system must eliminate ancestor types before it can eliminate their…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this paper we investigate these properties within an artificial genome model originally…
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population's limit distribution on the neutral network is solely determined by the network topology and…
Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…
Identifying and quantifying the benefits of sex and recombination is a long standing problem in evolutionary theory. In particular, contradictory claims have been made about the existence of a benefit of recombination on high dimensional…
Evolution occurs in populations of reproducing individuals. It is well known that population structure can affect evolutionary dynamics. Traditionally, natural selection is studied between mutants that differ in reproductive rate, but are…
Modern developments in population dynamics emphasize the role of the turnover of individuals. In the new approaches stable population size is a dynamic equilibrium between different mortality and fecundity factors instead of an arbitrary…
Adaptation often involves the acquisition of a large number of genomic changes which arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for…