Related papers: The coalescent point process of branching trees
We propose a general method to study dependent data in a binary tree, where an individual in one generation gives rise to two different offspring, one of type 0 and one of type 1, in the next generation. For any specific characteristic of…
We introduce and study a model of plane random trees generalizing the famous Bienaym\'e--Galton--Watson model but where births and deaths are locally correlated. More precisely, given a random variable $(B,H)$ with values in $\{1,2,3,…
The aim of this lecture is to give an overview of old and new resultson Bienaym\'e-Galton-Watson (BGW) trees. After introducing the framework of discretetrees, we first give alternative proofs of classical results on theextinction…
Coalescent models of bifurcating genealogies are used to infer evolutionary parameters from molecular data. However, there are many situations where bifurcating genealogies do not accurately reflect the true underlying ancestral history of…
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…
Two sequentially Markov coalescent models (SMC and SMC') are available as tractable approximations to the ancestral recombination graph (ARG). We present a Markov process describing coalescence at two fixed points along a pair of sequences…
In population genetics, extant samples are usually used for inference of past population genetic forces. With the Kingman coalescent and the backward diffusion equation, inference of the marginal likelihood proceeds from an extant sample…
We code Galton-Walton trees by a continuous height process, in order to give a precise meaning to the convergence of forests of trees. This allows us to establish the convergence of the forest of genealogical trees of the branching process…
Studying how diverse human populations are related is of historical and anthropological interest, in addition to providing a realistic null model for testing for signatures of natural selection or disease associations. Furthermore,…
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume…
We consider a model of a population in which individuals are sampled from different species. The Yule-Kingman nested coalescent describes the genealogy of the sample when each species merges with another randomly chosen species with a…
We revisit certain decompositions of continuous-state branching processes (CSBPs), commonly referred to as skeletal decompositions, through the lens of intertwining of semi-groups. Precisely, we associate to a CSBP $X$ with branching…
In phylogenomics, species-tree methods must contend with two major sources of noise; stochastic gene-tree variation under the multispecies coalescent model (MSC) and finite-sequence substitutional noise. Fast agglomerative methods such as…
Understanding the evolution of binary traits, which affects the birth and survival of species and also the rate of molecular evolution, remains challenging. A typical example is the evolution of mating systems in plant species. In this…
Multiple-merger coalescents, e.g. $\Lambda$-$n$-coalescents, have been proposed as models of the genealogy of $n$ sampled individuals for a range of populations whose genealogical structures are not captured well by Kingman's…
We define the Sampled Moran Genealogy Process, a continuous-time Markov process on the space of genealogies with the demography of the classical Moran process, sampled through time. To do so, we begin by defining the Moran Genealogy Process…
We consider two versions of stochastic population models with mutation and selection. The first approach relies on a multitype branching process; here, individuals reproduce and change type (i.e., mutate) independently of each other,…
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…
We establish sufficient conditions for exponential convergence to a unique quasi-stationary distribution in the total variation norm. These conditions also ensure the existence and exponential ergodicity of the Q-process, the process…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…