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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…
We present a stochastic model for the size of a taxon in paleobiology, in which we allow for the evolution of new taxon members, and both individual and catastrophic extinction events. The model uses ideas from the theory of birth and death…
The Eocene--Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse…
Fluctuations in biodiversity, large and small, are pervasive in the fossil record, yet we do not understand the processes generating them. Here we extend theory from non-equilibrium statistical physics to describe the previously unaccounted…
Studies of transient dynamics captures the time history of any dramatic changes in the dynamics of a system. The transient dynamics is investigated here in a classic ecological model of a bistable tri-trophic food chain. All the species in…
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…
Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources. One way of prioritizing species is to consider their "evolutionary distinctiveness", i.e. their relative…
Stochastic models, based on random processes, may lead to power law distributions, which provide long range correlations. The observation of power law behavior and the presence of long range correlations in biological systems has been…
Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing…
The evolutionary origin of universal statistics in biochemical reaction network is studied, to explain the power-law distribution of reaction links and the power-law distributions of chemical abundances. Using cell models with catalytic…
The composition of cellular metabolism is different across species. Empirical data reveal that bacterial species contain similar numbers of metabolic reactions but that the cross-species popularity of reactions is so heterogenous that some…
When a collection of phenotypically diverse organisms compete with each other for limited resources, with competition being strongest amongst the most similar, the population can evolve into tightly localised clusters. This process can be…
Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have…
Understanding the relationship between taxonomic and morphological changes is important in identifying the reasons for accelerated morphological diversification early in the history of animal phyla. Here, a simple general model describing…
We use a generalised version of the individual-based Tangled Nature model of evolutionary ecology to study the relationship between ecosystem structure and evolutionary history. Our evolved model ecosystems typically exhibit interaction…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
The abundance of a species' population in an ecosystem is rarely stationary, often exhibiting large fluctuations over time. Using historical data on marine species, we show that the year-to-year fluctuations of population growth rate obey a…
The number of extant individuals within a lineage, as exemplified by counts of species numbers across genera in a higher taxonomic category, is known to be a highly skewed distribution. Because the sublineages (such as genera in a clade)…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
Population dynamics reflects an underlying birth-death process, where the rates associated with different events may depend on external environmental conditions and on the population density. A whole family of simple and popular…