Related papers: Branch length statistics in phylogenetic trees und…
Continuous-time branching processes describe the evolution of a population whose individuals generate a random number of children according to a birth process. Such branching processes can be used to understand preferential attachment…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
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…
The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge,…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
In this paper, we consider time-inhomogeneous branching processes and time-inhomogeneous birth-and-death processes, in which the offspring distribution and birth and death rates (respectively) vary in time. A classical result of branching…
The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. Here, we show that parameter…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rates (speciation rate $\lambda(t)$ and extinction rate…
We consider a model of stationary population with random size given by a continuous state branching process with immigration with a quadratic branching mechanism. We give an exact elementary simulation procedure of the genealogical tree of…
Given any regularly varying dislocation measure, we identify a natural self-similar fragmentation tree as scaling limit of discrete fragmentation trees with unit edge lengths. As an application, we obtain continuum random tree limits of…
There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
The properties of randomly evolving special trees having defined and analyzed already in two earlier papers (arXiv:cond-mat/0205650 and arXiv:cond-mat/0211092) have been investigated in the case when the continuous time parameter converges…
Stochastic modeling of phylogenies raises five questions that have received varying levels of attention from quantitatively inclined biologists. 1) How large do we expect (from the model) the ration of maximum historical diversity to…
We consider a birth and death process in which death is due to both `natural death' and to competition between individuals, modelled as a quadratic function of population size. The resulting `logistic branching process' has been proposed as…
The spread of infectious disease in a human community or the proliferation of fake news on social media can be modeled as a randomly growing tree-shaped graph. The history of the random growth process is often unobserved but contains…
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 a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…