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Logarithmic growth-rates are fundamental observables for describing ecological systems and the characterization of their distributions with analytical techniques can greatly improve their comprehension. Here a neutral model based on a…
Evolutionary hypotheses to explain the greater numbers of species in the tropics than the temperate zone include greater age and area, higher temperature and metabolic rates, and greater ecological opportunity. These ideas make contrasting…
Expression level is known to be a strong determinant of a protein's rate of evolution. But the converse can also be true: evolutionary dynamics can affect expression levels of proteins. Having implications in both directions fosters the…
Eco-evolutionary dynamics, or eco-evolution for short, are thought to involve rapid demography (ecology) and equally rapid phenotypic changes (evolution) leading to novel, emergent system behaviours. This focus on contemporary dynamics is…
This paper explores a number of questions regarding optimal strategies evolved by viruses upon entry into a vertebrate host. The infected cell life cycle consists of a non-productively infected stage in which it is producing virions but not…
Population dynamics and evolutionary genetics underly the structure of ecosystems, changing on the same timescale for interacting species with rapid turnover, such as virus (e.g. HIV) and immune response. Thus, an important problem in…
Many biological systems are governed by difference equations and exhibit discrete-time dynamics. Examples include the size of a population when generations are non-overlapping, and the incidence of a disease when infections are recorded at…
Predicting evolution of expanding populations is critical to control biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of…
Understanding the conditions of feasibility and stability in ecological systems is a major challenge in theoretical ecology. The seminal work of May in 1972 and recent developments based on the theory of random matrices have shown the…
To understand biological diversification, it is important to account for large-scale processes that affect the evolutionary history of groups of co-distributed populations of organisms. Such events predict temporally clustered divergences…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
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…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…
Social dilemmas are an integral part of social interactions. Cooperative actions, ranging from secreting extra-cellular products in microbial populations to donating blood in humans, are costly to the actor and hence create an incentive to…
Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed, diluted cultures routinely used in microbial research, bacteria in a…
Species interactions (ranging from direct predator prey relationships to indirect effects mediated by the environment) are central to ecosystem balance and biodiversity. While empirical methods for measuring these interactions exist, their…
We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an…
Aim: Spatio-temporal processes play a key role in ecology, from genes to large-scale macroecological and biogeographical processes. Existing methods studying such spatio-temporally structured data either simplify the dynamic structure or…
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…
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.…