Related papers: Distribution of phylogenetic diversity under rando…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
Knowing where a particular species can or cannot be found on Earth is crucial for ecological research and conservation efforts. By mapping the spatial ranges of all species, we would obtain deeper insights into how global biodiversity is…
We study a generic reaction-diffusion model for single-species population dynamics that includes reproduction, death, and competition. The population is assumed to be confined in a refuge beyond which conditions are so harsh that they lead…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of…
Fluctuations in diversity and extinction sizes are discussed and compared for two different, individual-based models of biological coevolution. Both models display power-law distributions for various quantities of evolutionary interest,…
Using data drawn from large-scale databases, a number of interesting trends in the fossil record have been observed in recent years. These include the average decline in extinction rates throughout the Phanerozoic, the average increase in…
We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
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…
The evolution of dispersal rate is studied with a model of several local populations linked by dispersal. Three dispersal strategies are considered where all, half, or none of the offspring disperse. The spatial scale (number of patches)…
Rooted and ranked binary trees are mathematical objects of great importance used to model hierarchical data and evolutionary relationships with applications in many fields including evolutionary biology and genetic epidemiology. Bayesian…
In a complex community, species continuously adapt to each other. On rare occasions, the adaptation of a species can lead to the extinction of others, and even its own. "Adaptive dynamics" is the standard mathematical framework to describe…
We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of…
This chapter aims to inform a practitioner about current methods for predicting potential distributions of invasive species. It mostly addresses single species models, covering the conceptual bases, touching on mechanistic models, and then…