相关论文: Irreversible evolution, obstacles in fitness lands…

We study the evolutionary dynamics of a maladapted population of self-replicating sequences on strongly correlated fitness landscapes. Each sequence is assumed to be composed of blocks of equal length and its fitness is given by a linear…

Bacterial growth environment strongly influences the efficacy of antibiotic treatment, with slow growth often being associated with decreased susceptibility. Yet in many cases the connection between antibiotic susceptibility and pathogen…

Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting…

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…

The fitness landscape encodes the mapping of genotypes to fitness and provides a succinct representation of possible trajectories followed by an evolving population. Evolutionary accessibility is quantified by the existence of…

Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…

Models of bacterial growth tend to be `irreversible', allowing for the number of bacteria in a colony to increase but not to decrease. By contrast, models of molecular self-assembly are usually `reversible', allowing for addition and…

The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence…

A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the…

We consider the directed evolution of a population after an intervention that has significantly altered the underlying fitness landscape. We model the space of genotypes as a distributive lattice; the fitness landscape is a real-valued…

Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness…

The tempo and mode of an adaptive process is strongly determined by the structure of the fitness landscape that underlies it. In order to be able to predict evolutionary outcomes (even on the short term), we must know more about the nature…

Reversibility of state transitions is intensively studied topic in many scientific disciplines over many years. In cell biology, it plays an important role in epigenetic variation of phenotypes, known as phenotypic plasticity. More…

The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…

We consider the evolutionary trajectories traced out by an infinite population undergoing mutation-selection dynamics in static, uncorrelated random fitness landscapes. Starting from the population that consists of a single genotype, the…

Since penicillin was discovered about 90 years ago, we have become used to using drugs to eradicate unwanted pathogenic cells. However, using drugs to kill bacteria, viruses or cancer cells has the serious side effect of selecting for…

Mutational robustness quantifies the effect of random mutations on fitness. When mutational robustness is high, most mutations do not change fitness or have only a minor effect on it. From the point of view of fitness landscapes, robust…

Fitness landscapes are a useful concept to study the dynamics of meta-heuristics. In the last two decades, they have been applied with success to estimate the optimization power of several types of evolutionary algorithms, including genetic…

Practically, all chemotherapeutic agents lead to drug resistance. Clinically, it is a challenge to determine whether resistance arises prior to, or as a result of, cancer therapy. Further, a number of different intracellular and…

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…