Related papers: Trees within trees: Simple nested coalescents
Bipartition cover probabilities quantify whether a collection of gene trees contains every bipartition of the underlying species tree, a condition that underlies finite-sample guarantees for summary methods such as ASTRAL. We study this…
Considering a random binary tree with $n$ labelled leaves, we use a pruning procedure on this tree in order to construct a $\beta(3/2,1/2)$-coalescent process. We also use the continuous analogue of this construction, i.e. a pruning…
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,…
We revisit the discrete additive and multiplicative coalescents, starting with $n$ particles with unit mass. These cases are known to be related to some "combinatorial coalescent processes": a time reversal of a fragmentation of Cayley…
We define a Markov process on the partitions of $[n]=\{1,\ldots,n\}$ by drawing a sample in $[n]$ at each time of a Poisson process, by merging blocks that contain one of these points and by leaving all other blocks unchanged. This…
We study coalescent processes conditional on the population pedigree under the exchangeable diploid bi-parental population model of \citet{BirknerEtAl2018}. While classical coalescent models average over all reproductive histories, thereby…
We investigate the infinitely many demes limit of the genealogy of a sample of individuals from a subdivided population subject to sporadic mass extinction events. By exploiting a separation of timescales property of Wright's island model,…
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common…
In this paper we study the homogenization of a stochastic process and its associated evolution equations in which we mix a local part (given by a Brownian motion with a reflection on the boundary) and a nonlocal part (given by a jump…
We define a new class of $\Xi$-coalescents characterized by a possibly infinite measure over the non negative integers. We call them symmetric coalescents since they are the unique family of exchangeable coalescents satisfying a symmetry…
We study a model of a population with individuals sampled from different species. The Yule-$\Lambda$ nested coalescent describes the genealogy of the sample when each species merges with another randomly chosen species with a constant rate…
In a coalescing random walk, a set of particles make independent random walks on a graph. Whenever one or more particles meet at a vertex, they unite to form a single particle, which then continues the random walk through the graph.…
Consider a random real tree whose leaf set, or boundary, is endowed with a finite mass measure. Each element of the tree is further given a type, or allele, inherited from the most recent atom of a random point measure…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
We consider a zero-range process with two species of interacting particles. The steady state phase diagram of this model shows a variety of condensate phases in which a single site contains a finite fraction of all the particles in the…
For stacked simplicial complexes, (special subclasses of such are: trees, triangulations of polygons, stacked polytopes), we give an explicit bijection between partitions of facets (for trees: edges), and partitions of vertices into…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
We consider the class of exchangeable fragmentation-coagulation (EFC) processes where coagulations are multiple and not simultaneous, as in a $\Lambda$-coalescent, and fragmentation dislocates at finite rate an individual block into…
Probability modelling for DNA sequence evolution is well established and provides a rich framework for understanding genetic variation between samples of individuals from one or more populations. We show that both classical and more recent…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…