Related papers: Species Abundance Patterns in Complex Evolutionary…
Lotka-Volterra (LV) equations play a key role in the mathematical modeling of various ecological, biological and chemical systems. When the number of species (or, depending on the viewpoint, chemical components) becomes large, basic but…
Stochastic, spatially extended models for predator-prey interaction display spatio-temporal structures that are not captured by the Lotka-Volterra mean-field rate equations. These spreading activity fronts reflect persistent correlations…
In ecology, the description of species composition and biodiversity calls for statistical methods that involve estimating features of interest in unobserved samples based on an observed one. In the last decade, the Bayesian nonparametrics…
Biological networks of interacting agents exhibit similar topological properties for a wide range of scales, from cellular to ecological levels, suggesting the existence of a common evolutionary origin. A general evolutionary mechanism…
Introducing the effect of extinction into the so-called replicator equations in mathematical biology, we construct a general model of ecosystems. The present model shows mass extinction by its own extinction dynamics when the system…
Higher-order interactions are increasingly recognized as a key component of ecological dynamics. However, we show that higher-order Lotka-Volterra dynamics can, in some scenarios, be accurately reproduced by effective pairwise models fitted…
We introduce a multi-species generalization of the symmetric simple exclusion process with open boundaries. This model possesses the property of being integrable and appears as physically relevant because the boundary conditions can be…
Several diseases related to cell proliferation are characterized by the accumulation of somatic DNA changes, with respect to wildtype conditions. Cancer and HIV are two common examples of such diseases, where the mutational load in the…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…
Statistical inference on biodiversity has a rich history going back to RA Fisher. An influential ecological theory suggests the existence of a fundamental biodiversity number, denoted $\alpha$, which coincides with the precision parameter…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
We have generalized our ``unified'' model of evolutionary ecology by taking into account the possible movements of the organisms from one ``patch'' to another within the same eco-system. We model the spatial extension of the eco-system…
The statistical properties of an ecosystem composed of species interacting via pairwise, random interactions and deterministic, concentration limiting self-interaction are studied analytically with tools of equilibrium statistical mechanics…
We build networks of genetic similarity in which the nodes are organisms sampled from biological populations. The procedure is illustrated by constructing networks from genetic data of a marine clonal plant. An important feature in the…
Population dynamics in systems composed of cyclically competing species has been of increasing interest recently. Here, we investigate a system with four or more species. Using mean field theory, we study in detail the trajectories in…
Explaining the wide range of dynamics observed in ecological communities is challenging due to the large number of species involved, the complex network of interactions among them, and the influence of multiple environmental variables.…
Applying the concepts and formalisms from Evolutionary Game Theory to the data regime, the fundamental paradigms of Evolutionary Data Theory are introduced. Interpreting data in matrix form as evolutionary entities, input data is mapped to…
In the framework of the generalized Lotka Volterra model, solutions representing multispecies sequencial competition can be predictable with high probability. In this paper, we show that it occurs because the corresponding "heteroclinic…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…