Related papers: Unifying Theories of Molecular, Community and Netw…

We consider the population dynamics of a set of species whose network of catalytic interactions is described by a directed graph. The relationship between the attractors of this dynamics and the underlying graph theoretic structures like…

Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…

Cooperation is a widespread natural phenomenon yet current evolutionary thinking is dominated by the paradigm of selfish competition. Recent advanced in many fronts of Biology and Non-linear Physics are helping to bring cooperation to its…

Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…

We construct a model of speciation from evolution in an ecosystem consisting of a limited amount of energy recources. The species posses genetic information, which is inherited according to the rules of the Penna model of genetic evolution.…

What determines biodiversity in nature is a prominent issue in ecology, especially in biotic resource systems that are typically devoid of cross-feeding. Here, we show that by incorporating pairwise encounters among consumer individuals…

Evolution in finite populations is often modelled using the classical Moran process. Over the last ten years this methodology has been extended to structured populations using evolutionary graph theory. An important question in any such…

Predator-prey networks originating from different aqueous and terrestrial environments are compared to assess if the difference in environments of these networks produce any significant difference in the structure of such predator-prey…

Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…

Commonly recognized evolutionarily relevant effects of sexual reproduction include increased diversity, accelerated adaptation, and constrained accumulation of deleterious mutations, along with a secondary effect of species genotype…

Evolution algebras are a new type of non-associative algebras which are inspired from biological phenomena. A special class of such algebras, called Markov evolution algebras, is strongly related to the theory of discrete time Markov…

Evolutionary game dynamics in structured populations has been extensively explored in past decades. However, most previous studies assume that payoffs of individuals are fully determined by the strategic behaviors of interacting parties and…

The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…

A detailed analysis of three species-rich ecosystem food webs has shown that they display scale-free distributions of connections. Such graphs of interaction are in fact shared by a number of biological and technological networks, which…

We introduce a simple computational model that, with a microscopic dynamics driven by natural selection and mutation alone, allows the description of true speciation events. A statistical analysis of the so generated evolutionary tree…

Current theories about mechanisms promoting species co-existence in diverse communities assume that species only interact ecologically. Species are treated as discrete evolutionary entities, even though abundant empirical evidence indicates…

Species sharing a prey or a predator species may go extinct due to exploitative or apparent competition. We examine whether evolution of the shared species acts as a coexistence mechanism and to what extent the answer depends on the genetic…

Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…

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,…

Until recently, much of the microbial world was hidden from view. A global research effort has changed this, unveiling and quantifying microbial diversity across enormous range of critically-important contexts, from the human microbiome, to…