Related papers: Network Models of Phage-Bacteria Coevolution

Coexistence of individuals with different species or phenotypes is often found in nature in spite of competition between them. Stable coexistence of multiple types of individuals have implications for maintenance of ecological biodiversity…

Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…

Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…

Food webs are networks describing who is eating whom in an ecological community. By now it is clear that many aspects of food-web structure are reproducible across diverse habitats, yet little is known about the driving force behind this…

Models of strategy evolution on static networks help us understand how population structure can promote the spread of traits like cooperation. One key mechanism is the formation of altruistic spatial clusters, where neighbors of a…

Fluctuating environments pose tremendous challenges to bacterial populations. It is observed in numerous bacterial species that individual cells can stochastically switch among multiple phenotypes for the population to survive in rapidly…

Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…

We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…

Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…

Apparent competition between species is believed to be one of the principle driving forces that structure ecological communities, although the precise mecha nisms have yet to be characterized. Here we develop a model system that isolates…

Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…

Reaction-diffusion waves have long been used to describe the growth and spread of populations undergoing a spatial range expansion. Such waves are generally classed as either pulled, where the dynamics are driven by the very tip of the…

Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…

A classic measure of ecological stability describes the tendency of a community to return to equilibrium after small perturbation. While many advances show how the network structure of these communities severely constrains such tendencies,…

Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…

Segregation of populations is a key question in evolution theory. One important aspect is the relation between spatial organization and the population's composition. Here we study a specific example -- sectors in expanding bacterial…

Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…

Patterns of nestedness and specialization asymmetry, where specialist species interact mainly with generalists while generalists interact with both generalists and specialists, are often observed in mutualistic and antagonistic bi-partite…

Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to…

Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…