相关论文: Interaction between directional epistasis and aver…

Antagonistic interactions in biological systems, which occur when one perturbation blunts the effect of another, are typically interpreted as evidence that the two perturbations impact the same cellular pathway or function. Yet, this…

We propose a minimal model to simulate long waiting times followed by evolutionary bursts on rugged landscapes. It combines point and inversions-like mutations as sources of genetic variation. The inversions are intended to simulate one of…

The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the Random Energy Model…

The Lenski experiment investigates the long-term evolution of bacterial populations. Its design allows the direct comparison of the reproductive fitness of an evolved strain with its founder ancestor. It was observed by Wiser et al. (2013)…

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,…

Methods for predicting the probability and timing of a species' extinction are typically based on a combination of theoretical models and empirical data, and focus on single species population dynamics. Of course, species also interact with…

Mutations are typically classified by their effects on the nucleotide sequence and by their size. Here, we argue that if our main aim is to understand the effect of mutations on evolutionary outcomes (such as adaptation or speciation), we…

The contact structure of the population shapes the progression of epidemics. Nonetheless, the joint evolution of individual behavioral adaptations and disease dynamics on networks remains poorly understood. We use a…

The concept of a fitness landscape is a powerful metaphor that offers insight into various aspects of evolutionary processes and guidance for the study of evolution. Until recently, empirical evidence on the ruggedness of these landscapes…

Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…

We report on both analytical and numerical results concerning stochastic Hopfield--like neural automata exhibiting the following (biologically inspired) features: (1) Neurons and synapses evolve in time as in contact with respective baths…

There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…

A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of…

We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…

The genotype-fitness map plays a fundamental role in shaping the dynamics of evolution. However, it is difficult to directly measure a fitness landscape in practice, because the number of possible genotypes is astronomical. One approach is…

Defining the extent of epistasis - the non-independence of the effects of mutations - is essential for understanding the relationship of genotype, phenotype, and fitness in biological systems. The applications cover many areas of biological…

Intraspecific trait variation has been increasingly recognized as an important factor in determining species interaction and diversity. Eco-evolutionary models have studied the distribution of trait values within a population that changes…

When beneficial mutations are rare, they accumulate by a series of selective sweeps. But when they are common, many beneficial mutations will occur before any can fix, so there will be many different mutant lineages in the population…

We study the competition between several advantageous mutants in an asexual population (clonal interference) as a function of the time between the appearance of the mutants, their selective advantages, and the rate of deleterious mutations.…

Dynamical properties of the transcriptional regulatory network of {\it Escherichia coli} and {\it Saccharomyces cerevisiae} are studied within the framework of random Boolean functions. The dynamical response of these networks to a single…