Related papers: Simulating short- and long-term evolutionary dynam…
A biologically motivated individual-based framework for evolution in network-structured populations is developed that can accommodate eco-evolutionary dynamics. This framework is used to construct a network birth and death model. The…
The fitness contribution of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations under selection, and can shape the…
Granular simulations are used to probe the particle scale dynamics at short, intermediate, and long time scales for gravity driven, dense granular flows down an inclined plane. On approach to the angle of repose, where motion ceases, the…
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…
Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant…
The coupling between evolutionary and ecological changes (eco-evolutionary dynamics) has been shown to be relevant among diverse species, and is also of interest outside of ecology, i.e. in cancer evolution. These dynamics play an important…
We study self-replicating molecules under externally varying conditions. Changing conditions such as temperature variations and/or alterations in the environment's resource composition lead to both non-constant replication and decay rates…
The influence of time-dependent fitnesses on the infinite population dynamics of simple genetic algorithms (without crossover) is analyzed. Based on general arguments, a schematic phase diagram is constructed that allows one to characterize…
In evolution theory the concept of a fitness landscape has played an important role, evolution itself being portrayed as a hill-climbing process on a rugged landscape. In this article it is shown that in general, in the presence of other…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
We consider a trait-structured population subject to mutation, birth and competition of logistic type, where the number of coexisting types may fluctuate. Applying a limit of rare mutations to this population while keeping the population…
Spatial extent is a complicating factor in mathematical biology. The possibility that an action at point A cannot immediately affect what happens at point B creates the opportunity for spatial nonuniformity. This nonuniformity must change…
We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic…
In this paper we are concerned with the learnability of energies from data obtained by observing time evolutions of their critical points starting at random initial equilibria. As a byproduct of our theoretical framework we introduce the…
We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…
A novel mathematical framework is proposed to describe the ecological and evolutionary consequences of consumer--resource interactions. Both the consumer and resource are assumed to consist of several (sub)species, which interact between…
Background: The accumulation of deleterious mutations of a population directly contributes to the fate as to how long the population would exist. Muller's ratchet provides a quantitative framework to study the effect of accumulation.…
Natural selection acts on traits at different scales, often with opposing consequences. This article identifies the particular forces that act at each scale and how those forces combine to determine the overall evolutionary outcome. A…
We study a fundamental instability mechanism in nonlinear, nonlocal dynamical systems arising from the interaction of long-range memory and stochastic regime switching. The dynamics are governed by network-coupled, operator-valued Volterra…