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Ecosystems, which are intricate amalgams of biological communities and their surrounding environments, continually evolve under the influence of their myriad interactions. The world is currently facing intensifying environmental…
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?…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
Models of population growth and extinction are an increasingly popular subject of study. However, consequences of stochasticity and noise in shaping distributions and outcomes are not sufficiently explored. Here we consider a distributed…
A simulation model of a population having internal (genetic) structure is presented. The population is subject to selection pressure coming from the environment which is the same in the whole system but changes in time. Reproduction has a…
We consider the optimal dynamics in the infinite population evolution models with general symmetric fitness landscape. The search of optimal evolution trajectories are complicated due to sharp transitions (like shock waves) in evolution…
Microbial populations in the natural environment are likely to experience growth conditions very different from those of a typical laboratory xperiment. In particular, removal rates of biomass and substrate are unlikely to be balanced under…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Diversity is a fundamental feature of ecosystems, even when the concept of ecosystem is extended to sociology or economics. Diversity can be intended as the count of different items, animals, or, more generally, interactions. There are two…
We present an individual based model of evolutionary ecology. The reproduction rate of individuals characterized by their genome depends on the composition of the population in genotype space. Ecological features such as the taxonomy and…
Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large species diversity on long time scales are in general…
We discuss two cases that can be connected to the dynamics of interacting populations: (I.) density waves for the case or negligible random fluctuations of the populations densities, and (II.) probability distributions connected to the…
Many species live in colonies that thrive for a while and then collapse. Upon collapse very few individuals survive. The survivors start new colonies at other sites that thrive until they collapse, and so on. We introduce spatial and…
The composition of ecological communities varies not only between different locations but also in time. Understanding the fundamental processes that drive species towards rarity or abundance is crucial to assessing ecosystem resilience and…
Despite the general acknowledgment of the role of niche and fitness differences in community dynamics, species abundance has been coined as a relevant feature not just regarding niche perspectives, but also according to neutral…
We introduce an individual-based model of a complex ecological community with random interactions. The model contains a large number of species, each with a finite population of individuals, subject to discrete reproduction and death…
In large asexual populations, multiple beneficial mutations arise in the population, compete, interfere with each other, and accumulate on the same genome, before any of them fix. The resulting dynamics, although studied by many authors, is…
Changes in human behavior are increasingly recognized as a major determinant of epidemic dynamics. Although collective activity can be modified through imposed measures to control epidemic progression, spontaneous changes can also arise as…
We consider the effect of network structure on the evolution of a population. Models of this kind typically consider a population of fixed size and distribution. Here we consider eco-evolutionary dynamics where population size and…
We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…