Related papers: Functional bottlenecks can emerge from non-epistat…
We investigate the relationship between the average fitness decay due to single mutations and the strength of epistatic interactions in genetic sequences. We observe that epistatic interactions between mutations are correlated to the…
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.…
Every now and then the cultural paradigm of a society changes. Human history can be regarded as a sequence of long periods of cultural stasis punctuated by paradigm shifts that transform culture upside-down over the turn of a few…
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 evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
Phenotypic fluctuations and plasticity can generally affect the course of evolution, a process known as the Baldwin effect. Several studies have recast this effect and claimed that phenotypic plasticity acceler- ates evolutionary rate (the…
Approaches to gene interactions based on sign epistasis have been highly influential in recent time. Sign epistasis is useful for relating local and global properties of fitness landscapes, as well as for analyzing evolutionary trajectories…
Random walks on multidimensional nonlinear landscapes are of interest in many areas of science and engineering. In particular, properties of adaptive trajectories on fitness landscapes determine population fates and thus play a central role…
The evolutionary effect of recombination depends crucially on the epistatic interactions between linked loci. A paradigmatic case where recombination is known to be strongly disadvantageous is a two-locus fitness landscape dis- playing…
We consider the influence of disorder on the non-equilibrium steady state of a minimal model for intracellular transport. In this model particles move unidirectionally according to the \emph{totally asymmetric exclusion process} (TASEP) and…
Genetic interactions pervade every aspect of biology, from evolutionary theory where they determine the accessibility of evolutionary paths, to medicine where they contribute to complex genetic diseases. Until very recently, studies on…
The concept of fitness is introduced, and a simple derivation of the Fundamental Theorem of Natural Selection (which states that the average fitness of a population increases if its variance is nonzero) is given. After a short discussion of…
This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…
This is an introductory review of deterministic mutation-selection models for asexual populations (i.e., quasispecies theory) and related topics. First, the basic concepts of fitness, mutations, and sequence space are introduced. Different…
Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness…
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…
Statistical analysis of alignments of large numbers of protein sequences has revealed "sectors" of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein,…
We consider a stochastic individual-based model of adaptive dynamics for an asexually reproducing population with mutation. Biologically motivated by the influence of seasons or the variation of drug concentration during medical treatment,…
An important question in molecular evolution is whether an amino acid that occurs at a given position makes an independent contribution to fitness, or whether its effect depends on the state of other loci in the organism's genome, a…
Evolutionary adaptation is often likened to climbing a hill or peak. While this process is simple for fitness landscapes where mutations are independent, the interaction between mutations (epistasis) as well as mutations at loci that affect…