Related papers: Neutral phylogenetic models and their role in tree…
We develop an theoretical approach for predicting biodiversity in multi-dimensional niche spaces, arising due to ecological drivers such as competitive exclusion. The novelty of our approach relies on the fact that ecological niches are…
The robustness of an ecological network quantifies the resilience of the ecosystem it represents to species loss. It corresponds to the proportion of species that are disconnected from the rest of the network when extinctions occur…
The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions…
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…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…
In this paper we present a new way to understand the timing of branching events in phylogenetic trees. Our method explicitly considers the relative timing of diversification events between sister clades; as such it is complimentary to…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
We propose the following model for speciation and extinction. Birth and deaths occur according to spatially inhomogeneous contact rates. We assume that the ratio of the birth rate over the death rate at a site converges to some limit as the…
A demographic Allee effect occurs when individual fitness, at low densities, increases with population density. Coupled with environmental fluctuations in demographic rates, Allee effects can have subtle effects on population persistence…
Frequency-dependent selection reflects the interaction between different species as they battle for limited resources in their environment. In a stochastic evolutionary game the species relative fitnesses guides the evolutionary dynamics…
Spatial metapopulation models are fundamental to theoretical ecology, enabling to study how landscape structure influences global species dynamics. Traditional models, including recent generalizations, often rely on the deterministic limit…
The role of forest heterogeneity in the long-term, large-scale dynamics of forest fires is investigated by means of a cellular automata model and mean field approximation. Heterogeneity was conceived as trees (or acres of forest) with…
Mitochondrial genetic material is widely used for phylogenetic reconstruction and as a barcode for species identification. Here we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial…
Species' interactions are shaped by their traits. Thus, we expect traits -- in particular, trait (dis)similarity -- to play a central role in determining whether a particular set of species coexists. Traits are, in turn, the outcome of an…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
We study the stochastic evolution of four species in cyclic competition in a well mixed environment. In systems composed of a finite number $N$ of particles these simple interaction rules result in a rich variety of extinction scenarios,…
The stability and ability of an ecosystem to withstand climate change is directly linked to its biodiversity. Dead trees are a key indicator of overall forest health, housing one-third of forest ecosystem biodiversity, and constitute 8%of…
Density dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can…