Related papers: Co-evolution of replicators and their parasites
An object-oriented combinator chemistry was used to construct an artificial organism with a system architecture possessing characteristics necessary for organisms to evolve into more complex forms. This architecture supports modularity by…
Plant-pollinator associations are often seen as purely mutualistic, while in reality they can be more complex. Indeed they may also display a diverse array of antagonistic interactions, such as competition and victim--exploiter…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
We present a novel model that describes the within-host evolutionary dynamics of parasites undergoing antigenic variation. The approach uses a multi-type branching process with two types of entities defined according to their relationship…
When there is conspicuous under-exploitation of a limited resource, it is worth asking what mechanisms allow presumably valuable resources to be left unused? Evolutionary biologists have generated a wide range of hypotheses to explain this,…
Computer modelling for evolutionary systems consists in: 1) to store in the memory the individual features of each member of a large population; and 2) to update the whole system repeatedly, as time goes by, according to some prescribed…
Life can be viewed as a localized chemical system that sits on, or in the basin of attraction of, a metastable dynamical attractor state that remains out of equilibrium with the environment. Such a view of life allows that new living states…
If two species exhibit different nonlinear responses to a single shared resource, and if each species modifies the resource dynamics such that this favors its competitor, they may stably coexist. This coexistence mechanism, known as…
Competitive exclusion, a key principle of ecology, can be generalized to understand many other complex systems. Individuals under surviving pressure tend to be different from others, and correlations among them change correspondingly to the…
We study the probabilities of evolution based on random mutations and natural selection. We conclude that evolution to multicellular eukaryots, or even prokaryots, is unlikely to be the result of only random mutations. Complex organisms…
Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we…
Two density-dependent branching processes are considered to model predator-prey populations. For both models, preys are considered to be the main food supply of predators. Moreover, in each generation the number of individuals of each…
We consider a branching model for a population of dividing cells infected by parasites. Each cell receives parasites by inheritance from its mother cell and independent contamination from outside the population. Parasites multiply randomly…
Ecology and evolution under changing environments are important in many subfields of biology with implications for medicine. Here, we explore an example: the consequences of fluctuating environments on the emergence of antibiotic…
Predator-prey coevolution is commonly thought to result in reciprocal arms races that produce increasingly extreme and complex traits. However, such directional change is not inevitable. Here, we provide evidence for a previously…
Investigating relation between various structural patterns found in real-world networks and stability of underlying systems is crucial to understand importance and evolutionary origin of such patterns. We evolve multiplex networks,…
Interacting populations often create complicated spatiotemporal behavior, and understanding it is a basic problem in the dynamics of spatial systems. We study the two-species case by simulations of a host--parasitoid model. In the case of…
The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
Social, biological and economic networks grow and decline with occasional fragmentation and re-formation, often explained in terms of external perturbations. We show that these phenomena can be a direct consequence of simple imitation and…