Related papers: Evolving generalists via dynamic sculpting of rugg…
Natural environments can present diverse challenges, but some genotypes remain fit across many environments. Such `generalists' can be hard to evolve, out-competed by specialists fitter in any particular environment. Here, inspired by the…
We propose a simple model for genetic adaptation to a changing environment, describing a fitness landscape characterized by two maxima. One is associated with "specialist" individuals that are adapted to the environment; this maximum moves…
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…
Epistatic interactions between mutations add substantial complexity to adaptive landscapes, and are often thought of as detrimental to our ability to predict evolution. Yet, patterns of global epistasis, in which the fitness effect of a…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
Epistasis occurs when the effect of a mutation depends on its carrier's genetic background. Despite increasing evidence that epistasis for fitness is common, its role during evolution is contentious. Fitness landscapes, mappings of genotype…
It has recently been noted that the relative prevalence of the various kinds of epistasis varies along an adaptive walk. This has been explained as a result of mean regression in NK model fitness landscapes. Here we show that this…
Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show…
We use fitness graphs, or directed cube graphs, for analyzing evolutionary reversibility. The main application is antimicrobial drug resistance. Reversible drug resistance has been observed both clinically and experimentally. If drug…
Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current…
Evolutionary adaptation is the process that increases the fit of a population to the fitness landscape it inhabits. As a consequence, evolutionary dynamics is shaped, constrained, and channeled, by that fitness landscape. Much work has been…
Both evolution and ecology have long been concerned with the impact of variable environmental conditions on observed levels of genetic diversity within and between species. We model the evolution of a quantitative trait under selection that…
Darwinian evolution is driven by random mutations, genetic recombination (gene shuffling) and selection that favors genotypes with high fitness. For systems where each genotype can be represented as a bitstring of length $L$, an overview of…
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…
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…
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…
Populations of replicating entities frequently experience sudden or cyclical changes in environment. We explore the implications of this phenomenon via a environmental switching parameter in several common evolutionary dynamics models…
Species sharing a habitat will co-evolve to make use of the available resources, as consumption is modulated by competition and negative feedback loops between consumers and resources. The dietary range of a given species determines the…
In classical evolutionary theory, genetic variation provides the source of heritable phenotypic variation on which natural selection acts. Against this classical view, several theories have emphasized that developmental variability and…
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…