Related papers: The Network Species Model
Identifying the rank of species in a social or ecological network is a difficult task, since the rank of each species is invariably determined by complex interactions stipulated with other species. Simply put, the rank of a species is a…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life.' In this paper we use an…
Recent studies uncovered important core/periphery network structures characterizing complex sets of cooperative and competitive interactions between network nodes, be they proteins, cells, species or humans. Better characterization of the…
We study the statistics of ecosystems with a variable number of co-evolving species. The species interact in two ways: by prey-predator relationships and by direct competition with similar kinds. The interaction coefficients change slowly…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
While the study of a single network is well-established, technological advances now allow for the collection of multiple networks with relative ease. Increasingly, anywhere from several to thousands of networks can be created from brain…
We incorporate the generic hierarchical architecture of foodwebs into a "{\it unified}" model that describes both "micro" and "macro" evolutions within a single theoretical framework. This model describes the "micro" -evolution in detail by…
We present a novel approach to represent ecological systems using reaction networks, and show how a particular framework called Chemical Organization Theory (COT) sheds new light on the longstanding complexity-stability debate. Namely, COT…
Reconstructing network connectivity from the collective dynamics of a system typically requires access to its complete continuous-time evolution although these are often experimentally inaccessible. Here we propose a theory for revealing…
On a global level, ecological communities are being perturbed at an unprecedented rate by human activities and environmental instabilities. Yet, we understand little about what factors facilitate or impede long-term persistence of these…
In this working paper, we present a simple theoretical framework based on network theory to study how speciation, the process by which new species appear, shapes spatial patterns of diversity. We show that this framework can be expanded to…
Complex networks are universal, arising in fields as disparate as sociology, physics, and biology. In the past decade, extensive research into the properties and behaviors of complex systems has uncovered surprising commonalities among the…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
Standard techniques for studying biological systems largely focus on their dynamical, or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
We present a simple discrete model for the non-linear spatial interaction of different kinds of ``subpopulations'' composed of identical moving entities like particles, bacteria, individuals, etc. The model allows to mimic a variety of…
We do not attempt to provide yet another definition of selforganization, but explore the conditions under which we can model a system as self-organizing. These involve the dynamics of entropy, and the purpose, aspects, and description level…
We examine the global organization of heterogeneous equilibrium networks consisting of a number of well distinguished interconnected parts--``communities'' or modules. We develop an analytical approach allowing us to obtain the statistics…
We study a version of the Tangled Nature model of evolutionary ecology redefined in a phenotype space where mutants have properties correlated to their parents. The model has individual-based dynamics whilst incorporating species scale…