Related papers: Inferring resource competition in microbial commun…
A challenging problem in the study of complex systems is that of resolving, without prior information, the emergent, mesoscopic organization determined by groups of units whose dynamical activity is more strongly correlated internally than…
Feed-forward dynamics, which is well-known to have several important implications in nonlinear dynamical systems, frequently occurs in gene expression motifs, and has been well explored experimentally and mathematically. However, dependency…
It is well-known that population structure is a catalyst for the evolution of cooperation since individuals can reciprocate with their neighbors through local interactions defined by network structures. Previous research typically relies on…
Ecological networks are theoretical abstractions that represent ecological communities. These networks are usually defined as static entities, in which the occurrence of a particular interaction between species is considered fixed despite…
Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We…
Explaining how competing species coexist remains a central question in ecology. The well-known competitive exclusion principle (CEP) states that two species competing for the same resource cannot stably coexist, and more generally, that the…
In mutualisms where there is exchange of resources for resources, or resources for services, the resources are typically short lived compared with the lives of the organisms that produce and make use of them. This fact allows a separation…
Natural ecosystems are characterized by striking diversity of form and functions and yet exhibit deep symmetries emerging across scales of space, time and organizational complexity. Species-area relationships and species-abundance…
We present a new algorithm for community detection. The algorithm uses random walks to embed the graph in a space of measures, after which a modification of $k$-means in that space is applied. The algorithm is therefore fast and easily…
Using a set of heterogeneous competing systems with intra-system cooperation and inter-system aggression, we show how the coevolution of the system parameters (degree of organization and conditions for aggression) depends on the rate of…
Conflict destabilizes social interactions and impedes cooperation at multiple scales of biological organization. Of fundamental interest are the causes of turbulent periods of conflict. We analyze conflict dynamics in a monkey society model…
We introduce an approach to partitioning networks into communities that not only determines the best community structure, but also provides a range of characterization techniques to assess how significant that structure is. We study the…
The goal of community detection algorithms is to identify densely-connected units within large networks. An implicit assumption is that all the constituent nodes belong equally to their associated community. However, some nodes are more…
Effective multicellularity requires both cooperation and competition between constituent cells. Cooperation involves sacrificing individual fitness in favor of that of the community, but excessive cooperation makes the community susceptible…
The human body consists of microbiomes associated with the development and prevention of several diseases. These microbial organisms form several complex interactions that are informative to the scientific community for explaining disease…
In order to better understand the interplay of partnership and competition in population dynamics we study a family of generalized May-Leonard models with $N$ species. These models have a very rich structure, characterized by different…
Natural ecosystems, in particular on the microbial scale, are inhabited by a large number of species. The population size of each species is affected by interactions of individuals with each other and by spatial and temporal changes in…
Noise and spatial degrees of freedom characterize most ecosystems. Some aspects of their influence on the coevolution of populations with cyclic interspecies competition have been demonstrated in recent experiments [e.g. B. Kerr et al.,…
High-diversity assemblages are very common in nature, and yet the factors allowing for the maintenance of biodiversity remain obscure. The competitive exclusion principle and May's complexity-diversity puzzle both suggest that a community…
Evolutionary game dynamics in structured populations are strongly affected by updating rules. Previous studies usually focus on imitation-based rules, which rely on payoff information of social peers. Recent behavioral experiments suggest…