Related papers: Interaction between directional epistasis and aver…
We analyze a model of interacting agents (e.g. prebiotic chemical species) which are represended by nodes of a network, whereas their interactions are mapped onto directed links between these nodes. On a fast time scale, each agent follows…
Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
Clonal interference, competition between multiple co-occurring beneficial mutations, has a major role in adaptation of asexual populations. We provide a simple individual based stochastic model of clonal interference taking into account a…
The nature of epistasis has important consequences for the evolutionary significance of sex and recombination. Recent efforts to find negative epistasis as source of negative linkage disequilibrium and associated long-term sex advantage…
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…
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…
Living organisms, ecosystems, and social systems are examples of complex systems in which robustness against inclusion of new elements is an essential feature. A recently proposed simple model has revealed a general mechanism by which such…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
When mutation rates are low, natural selection remains effective, and increasing the mutation rate can give rise to an increase in adaptation rate. When mutation rates are high to begin with, however, increasing the mutation rate may have a…
Affinity maturation produces antibodies that bind antigens with high specificity by accumulating mutations in the antibody sequence. Mapping out the antibody-antigen affinity landscape can give us insight into the accessible paths during…
Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…
Frequency dependent selection and demographic fluctuations play important roles in evolutionary and ecological processes. Under frequency dependent selection, the average fitness of the population may increase or decrease based on…
The Tangled Nature Model of biological and cultural evolution features interacting agents which compete for limited resources and reproduce in an error prone fashion and at a rate depending on the `tangle' of interactions they maintain with…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…
The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…
We introduce a test for the overall effect of interaction between DNA methylation and a set of single nucleotide polymorphisms (SNPs) on a quantitative phenotype. The developed inference procedure is based on a functional approach that…
Phenotypic evolution implies sequential fixations of new genomic sequences. The speed at which these mutations fixate depends, in part, on the relative fitness (selection coefficient) of the mutant vs. the ancestor. Using a simple…
We study biological evolution on a random fitness landscape where correlations are introduced through a linear fitness gradient of strength $c$. When selection is strong and mutations rare the dynamics is a directed uphill walk that…
Smoking behavior and awareness co-spread through social interactions, giving rise to coupled contagion processes on social contact networks. In addition to initiation and cessation, awareness of the harmful effects of smoking plays an…