Related papers: A seed-diffusion model for tropical tree diversity…
We study the spreading of families in two-dimensional multispecies predator-prey systems, in which species cyclically dominate each other. In each time step randomly chosen individuals invade one of the nearest sites of the square lattice…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
Macro-level modeling is still the dominant approach in many demographic applications because of its simplicity. Individual-level models, on the other hand, provide a more comprehensive understanding of observed patterns; however, their…
A feature common to many models of vegetation pattern formation in semi-arid ecosystems is a sequence of qualitatively different patterned states, "gaps -> labyrinth -> spots", that occurs as a parameter representing precipitation…
A new family of tree models is proposed, which we call "differential trees." A differential tree model is constructed from multiple data sets and aims to detect distributional differences between them. The new methodology differs from the…
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics…
We establish a general framework using a diffusion approximation to simulate forward-in-time state counts or frequencies for cladogenetic state-dependent speciation-extinction (ClaSSE) models. We apply the framework to various two- and…
We develop an agent-based model on a lattice to investigate territorial development motivated by markings such as graffiti, generalizing a previously-published model to account for $K$ groups instead of two groups. We then analyze this…
Accelerating global biodiversity loss has highlighted the role of complex relationships and shared patterns among species in determining their responses to environmental changes. The structure of an ecological community, represented by…
Seed banks are a common characteristics to many plant species, which allow storage of genetic diversity in the soil as dormant seeds for various periods of time. We investigate an above-ground population following a Fisher-Wright model with…
An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…
We consider a stochastic susceptible-infected-recovered (SIR) model with contact tracing on random trees and on the configuration model. On a rooted tree, where initially all individuals are susceptible apart from the root which is…
We study an individual-based predator-prey model of biological coevolution, using linear stability analysis and large-scale kinetic Monte Carlo simulations. The model exhibits approximate 1/f noise in diversity and population-size…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
In this paper, we present the description of a simplified model of the dynamic of a mono-specific even-aged forest. The model studied is a tree-growth model based on a system of two ordinary differential equations concerning the tree basal…
Researchers and managers model ecological communities to infer the biotic and abiotic variables that shape species' ranges, habitat use, and co-occurrence which, in turn, are used to support management decisions and test ecological…
We analyze several florae (collections of plant species populating specific areas) in different geographic and climatic regions. For every list of species we produce a taxonomic classification tree and we consider its statistical…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
Over the last few decades, ecologists have come to appreciate that key ecological patterns, which describe ecological communities at relatively large spatial scales, are not only scale dependent, but also intimately intertwined. The…
The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to have more than one clearly different phenotypes. We present a model for…