A construction of a β\beta-coalescent via the pruning of Binary Trees

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 procedure on Aldous's continuum random tree, to construct a continuous state space process that has the same structure as the $\beta$-coalescent process up to some time change. These two constructions unable us to obtain results on the coalescent process such as the asymptotics on the number of coalescent events or the law of the blocks involved in the last coalescent event

A coalescent model for the effect of advantageous mutations on the genealogy of a population

When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace their ancestral lines backwards in time, many lineages may coalesce almost instantaneously at the time of a selective sweep. We show that as the population size goes to infinity, this process converges to a coalescent process called a coalescent with multiple collisions. A better approximation for finite populations can be obtained using a coalescent with simultaneous multiple collisions. We also show how these coalescent approximations can be used to get insight into how beneficial mutations affect the behavior of statistics that have been used to detect departures from the usual Kingman's coalescent

Coalescent histories for lodgepole species trees

Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the number of coalescent histories for gene trees and species trees affect a variety of probabilistic calculations in mathematical phylogenetics. Exact and asymptotic evaluations of the number of coalescent histories, however, are known only in a limited number of cases. Here we introduce a particular family of species trees, the \emph{lodgepole} species trees $(\lambda_n)_{n\geq 0}$, in which tree $\lambda_n$ has $m=2n+1$ taxa. We determine the number of coalescent histories for the lodgepole species trees, in the case that the gene tree matches the species tree, showing that this number grows with $m!!$ in the number of taxa $m$. This computation demonstrates the existence of tree families in which the growth in the number of coalescent histories is faster than exponential. Further, it provides a substantial improvement on the lower bound for the ratio of the largest number of matching coalescent histories to the smallest number of matching coalescent histories for trees with $m$ taxa, increasing a previous bound of $(\sqrt{\pi} / 32)[(5m-12)/(4m-6)] m \sqrt{m}$ to $[ \sqrt{m-1}/(4 \sqrt{e}) ]^{m}$. We discuss the implications of our enumerative results for phylogenetic computations

The peripatric coalescent

We consider a dynamic metapopulation involving one large population of size N surrounded by colonies of size \varepsilon_NN, usually called peripheral isolates in ecology, where N\to\infty and \varepsilon_N\to 0 in such a way that \varepsilon_NN\to\infty. The main population periodically sends propagules to found new colonies (emigration), and each colony eventually merges with the main population (fusion). Our aim is to study the genealogical history of a finite number of lineages sampled at stationarity in such a metapopulation. We make assumptions on model parameters ensuring that the total outer population has size of the order of N and that each colony has a lifetime of the same order. We prove that under these assumptions, the scaling limit of the genealogical process of a finite sample is a censored coalescent where each lineage can be in one of two states: an inner lineage (belonging to the main population) or an outer lineage (belonging to some peripheral isolate). Lineages change state at constant rate and inner lineages (only) coalesce at constant rate per pair. This two-state censored coalescent is also shown to converge weakly, as the landscape dynamics accelerate, to a time-changed Kingman coalescent.Comment: 17 pages,1 figur

A modified lookdown construction for the Xi-Fleming-Viot process with mutation and populations with recurrent bottlenecks

Let $\Lambda$ be a finite measure on the unit interval. A $\Lambda$-Fleming-Viot process is a probability measure valued Markov process which is dual to a coalescent with multiple collisions ($\Lambda$-coalescent) in analogy to the duality known for the classical Fleming Viot process and Kingman's coalescent, where $\Lambda$ is the Dirac measure in 0. We explicitly construct a dual process of the coalescent with simultaneous multiple collisions ($\Xi$-coalescent) with mutation, the $\Xi$-Fleming-Viot process with mutation, and provide a representation based on the empirical measure of an exchangeable particle system along the lines of Donnelly and Kurtz (1999). We establish pathwise convergence of the approximating systems to the limiting $\Xi$-Fleming-Viot process with mutation. An alternative construction of the semigroup based on the Hille-Yosida theorem is provided and various types of duality of the processes are discussed. In the last part of the paper a population is considered which undergoes recurrent bottlenecks. In this scenario, non-trivial $\Xi$-Fleming-Viot processes naturally arise as limiting models.Comment: 35 pages, 2 figure

On asymptotics of the beta-coalescents

We show that the total number of collisions in the exchangeable coalescent process driven by the beta $(1,b)$ measure converges in distribution to a 1-stable law, as the initial number of particles goes to infinity. The stable limit law is also shown for the total branch length of the coalescent tree. These results were known previously for the instance $b=1$, which corresponds to the Bolthausen--Sznitman coalescent. The approach we take is based on estimating the quality of a renewal approximation to the coalescent in terms of a suitable Wasserstein distance. Application of the method to beta $(a,b)$-coalescents with $0<a<1$ leads to a simplified derivation of the known $(2-a)$-stable limit. We furthermore derive asymptotic expansions for the moments of the number of collisions and of the total branch length for the beta $(1,b)$-coalescent by exploiting the method of sequential approximations.Comment: 25 pages, submitted for publicatio