相关论文: On the accessibility of adaptive phenotypes of a b…
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 adaptive evolution of a population under the influence of mutation and selection is strongly influenced by the structure of the underlying fitness landscape, which encodes the interactions between mutations at different genetic loci.…
All possible phenotypes are not equally accessible to evolving populations. In fact, only phenotypes of large size, i.e. those resulting from many different genotypes, are found in populations of sequences, presumably because they are…
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…
Even closely related prokaryotes show an astounding diversity in their ability to grow in different nutritional environments. Mechanistically, this diversity arises predominantly through horizontal gene transfer, the exchange of DNA between…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
Background: A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism…
Genetic redundancy is ubiquitous and can be found in any organism. However, it has been argued that genetic redundancy reduces total population fitness, and therefore, redundancy is unlikely to evolve. In this letter, we study an…
Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Cells generally change their internal state to adapt to an environmental change, and accordingly evolve in response to the new conditions. This process involves phenotypic changes that occur over several different time scales, ranging from…
The evolutionary dynamics of molecular populations are strongly dependent on the structure of genotype spaces. The map between genotype and phenotype determines how easily genotype spaces can be navigated and the accessibility of…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to…
The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
1) Micro-evolutionary predictions are complicated by ecological feedbacks like density dependence, while ecological predictions can be complicated by evolutionary change. A widely used approach in micro-evolution, quantitative genetics,…
Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is essential for…
We study the evolution of large but finite asexual populations evolving in fitness landscapes in which all mutations are either neutral or strongly deleterious. We demonstrate that despite the absence of higher fitness genotypes, adaptation…