Related papers: Predicting evolution and visualizing high-dimensio…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
Dynamic algorithm selection aims to exploit the complementarity of multiple optimization algorithms by switching between them during the search. While these kinds of dynamic algorithms have been shown to have potential to outperform their…
In this paper we investigate error-thresholds on dynamics fitness-landscapes. We show that there exists both lower and an upper threshold, representing limits to the copying fidelity of simple replicators. The lower bound can be expressed…
We study biological evolution on a random fitness landscape where correlations are introduced through a linear fitness gradient of strength $c$. When selection is strong and mutations rare the dynamics is a directed uphill walk that…
We propose a new procedure to monitor and forecast the onset of transitions in high dimensional complex systems. We describe our procedure by an application to the Tangled Nature model of evolutionary ecology. The quasi-stable…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…
Population structure can be modelled by evolutionary graphs, which can have a substantial, but very subtle influence on the fate of the arising mutants. Individuals are located on the nodes of these graphs, competing with each other to…
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,…
Organisms that exploit different environments may experience a stochastic delay in adjusting their fitness when they switch habitats. We study two species whose fitness is determined by the species composition of the local environment, as…
Although many phenotypic traits are determined by a large number of genetic variants, how a polygenic trait adapts in response to the changes in the environment is still poorly understood. Here we study the adaptation dynamics of a…
We consider a stochastic individual-based model of adaptive dynamics on a finite trait graph $G=(V,E)$. The evolution is driven by a linear birth rate, a density dependent logistic death rate an the possibility of mutations along the…
Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…
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…
Organisms result from adaptive processes interacting across different time scales. One such interaction is that between development and evolution. Models have shown that development sweeps over several traits in a single agent, sometimes…
Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have…
The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…
In epistatic fitness landscapes, the fitness effect of a mutation depends on the genetic background and may even switch between deleterious and beneficial depending on the presence of another mutation. Epistatic interactions may cause both…
Although there are some real world applications where the use of variable length representation (VLR) in Evolutionary Algorithm is natural and suitable, an academic framework is lacking for such representations. In this work we propose a…
Evolutionary algorithms, inspired by natural evolution, aim to optimize difficult objective functions without computing derivatives. Here we detail the relationship between population genetics and evolutionary optimization and formulate a…
Fisher's geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic…