Coalescents with multiple collisions, also known as $Λ$-coalescents, were introduced by Pitman and Sagitov in 1999. These processes describe the evolution of particles that undergo stochastic coagulation in such a way that several blocks can merge at the same time to form a single block. In the case that the measure $Λ$ is the $\operatorname {Beta}(2-α,α)$ distribution, they are also known to describe the genealogies of large populations where a single individual can produce a large number of offspring. Here, we use a recent result of Birkner et al. to prove that Beta-coalescents can be embedded in continuous stable random trees, about which much is known due to the recent progress of Duquesne and Le Gall. Our proof is based on a construction of the Donnelly--Kurtz lookdown process using continuous random trees, which is of independent interest. This produces a number of results concerning the small-time behavior of Beta-coalescents. Most notably, we recover an almost sure limit theorem of the present authors for the number of blocks at small times and give the multifractal spectrum corresponding to the emergence of blocks with atypical size. Also, we are able to find exact asymptotics for sampling formulae corresponding to the site frequency spectrum and the allele frequency spectrum associated with mutations in the context of population genetics.
In this paper, we consider Beta$(2-α,α)$ (with $1<α<2$) and related $Λ$-coalescents. If $T^{(n)}$ denotes the length of an external branch of the $n$-coalescent, we prove the convergence of $n^{α-1}T^{(n)}$ when $n$ tends to $ \infty $, and give the limit. To this aim, we give asymptotics for the number $σ^{(n)}$ of collisions which occur in the $n$-coalescent until the end of the chosen external branch, and for the block counting process associated with the $n$-coalescent.
We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock's "reproduction sweepstakes". Besides the data analysis, in particular the inference of mutation rates and the estimation of the (real) time to the most recent common ancestor, we briefly address the question whether the genealogies might be adequately described by so-called Beta coalescents (as oppos…
We consider a $Λ$-coalescent and we study the asymptotic behavior of the total length $L^{(n)}_{ext}$ of the external branches of the associated $n$-coalescent. For Kingman coalescent, i.e. $Λ=δ_0$, the result is well known and is useful, together with the total length $L^{(n)}$, for Fu and Li's test of neutrality of mutations% under the infinite sites model asumption . For a large family of measures $Λ$, including Beta$(2-α,α)$ with $0<α<1$, M{ö}hle has proved asymptotics of $L^{(n)}_{ext}$. Here we consider the case when the measure $Λ$ is Beta$(2-α,α)$, with $1<α<2$. We prove that $n^{α-2}L…
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…
The Beta coalescents are stochastic processes modeling the genealogy of a population. They appear as the rescaled limits of the genealogical trees of numerous stochastic population models. In this article, we take interest in the number of blocs at small times in the Beta coalescent. Berestycki, Berestycki and Schweinsberg proved a law of large numbers for this quantity. Recently, Limic and Talarczyk proved that a functional central limit theorem holds as well. We give here a simple proof for an unidimensional version of this result, using a coupling between Beta coalescents and continuous-tim…
In mathematical population genetics, it is well known that one can represent the genealogy of a population by a tree, which indicates how the ancestral lines of individuals in the population coalesce as they are traced back in time. As the population evolves over time, the tree that represents the genealogy of the population also changes, leading to a tree-valued stochastic process known as the evolving coalescent. Here we will consider the evolving coalescent for populations whose genealogy can be described by a beta coalescent, which is known to give the genealogy of populations with very la…
We consider Beta$(2-α, α)$-coalescents with parameter range $1 <α<2$ starting from $n$ leaves. The length $\ell^{(n)}_r$ of order $r$ in the $n$-Beta$(2-α, α)$-coalescent tree is defined as the sum of the lengths of all branches that carry a subtree with $r$ leaves. We show that for any $s \in \mathbb N$ the vector of suitably centered and rescaled lengths of orders $1\le r \le s$ converges in distribution to a multivariate stable distribution as the number of leaves tends to infinity.
We consider a class of density-dependent branching processes which generalises exponential, logistic and Gompertz growth. A population begins with a single individual, grows exponentially initially, and then growth may slow down as the population size moves towards a carrying capacity. At a time while the population is still growing superlinearly, a fixed number of individuals are sampled and their coalescent tree is drawn. Taking the sampling time and carrying capacity simultaneously to infinity, we prove convergence of the coalescent tree to a limiting tree which is in a sense universal over…
We describe a simple construction of Kingman's coalescent in terms of a Brownian excursion. This construction is closely related to, and sheds some new light on, earlier work by Aldous and Warren. Our approach also yields some new results: for instance, we obtain the full multifractal spectrum of Kingman's coalescent. This complements earlier work on Beta-coalescents by the authors and Schweinsberg. Surprisingly, the thick part of the spectrum is not obtained by taking the limit as $α\to 2$ in the result for Beta-coalescents mentioned above. Other analogies and differences between the case of …
For a finite measure $\varLambda$ on $[0,1]$, the $\varLambda$-coalescent is a coalescent process such that, whenever there are $b$ clusters, each $k$-tuple of clusters merges into one at rate $\int_0^1x^{k-2}(1-x)^{b-k}\varLambda(\mathrm{d}x)$. It has recently been shown that if $1<α<2$, the $\varLambda$-coalescent in which $\varLambda$ is the $\operatorname {Beta}(2-α,α)$ distribution can be used to describe the genealogy of a continuous-state branching process (CSBP) with an $α$-stable branching mechanism. Here we use facts about CSBPs to establish new results about the small-time asymptoti…
For $1<α<2$ we derive the asymptotic distribution of the total length of {\em external} branches of a Beta$(2-α, α)$-coalescent as the number $n$ of leaves becomes large. It turns out the fluctuations of the external branch length follow those of $τ_n^{2-α}$ over the entire parameter regime, where $τ_n$ denotes the random number of coalescences that bring the $n$ lineages down to one. This is in contrast to the fluctuation behavior of the total branch length, which exhibits a transition at $α_0 = (1+\sqrt 5)/2$.
This article shows the asymptotics of distributions of various functionals of the Beta$(2-α,α)$ $n$-coalescent process with $1<α<2$ when $n$ goes to infinity. This process is a Markov process taking {values} in the set of partitions of $\{1, \dots, n\}$, evolving from the intial value $\{1\},\cdots, \{n\}$ by merging (coalescing) blocks together into one and finally reaching the absorbing state $\{1, \dots, n\}$. The minimal clade of $1$ is the block which contains $1$ at the time of coalescence of the singleton $\{1\}$. The limit size of the minimal clade of $1$ is provided. To this, we expre…
We quantify the manner in which the beta coalescent $Π=\{ Π(t), t\geq 0\},$ with parameters $a\in (0, 1),$ $b>0,$ comes down from infinity. Approximating $Π$ by its restriction $Π^n$ to $[n]\:= \{1, \ldots, n\},$ the suitably rescaled block counting process $n^{-1}\#Π^n(tn^{a-1})$ has a deterministic limit, $c(t)$, as $n\to\infty.$ An explicit formula for $c(t)$ is provided in Theorem 1. The block size spectrum $(\mathfrak{c}_{1}Π^n(t), \ldots, \mathfrak{c}_{n}Π^n(t)),$ where $\mathfrak{c}_{i}Π^n(t)$ counts the number of blocks of size $i$ in $Π^n(t),$ captures more refined information about t…
We derive the asymptotic distribution of the total length $L_n$ of a $\operatorname {Beta}(2-α,α)$-coalescent tree for $1<α<2$, starting from $n$ individuals. There are two regimes: If $α\le1/2(1+\sqrt{5})$, then $L_n$ suitably rescaled has a stable limit distribution of index $α$. Otherwise $L_n$ just has to be shifted by a constant (depending on $n$) to get convergence to a nondegenerate limit distribution. As a consequence, we obtain the limit distribution of the number $S_n$ of segregation sites. These are points (mutations), which are placed on the tree's branches according to a Poisson p…
We give the asymptotic distribution of the length of partial coalescent trees for Beta and related coalescents. This allows us to give the asymptotic distribution of the number of (neutral) mutations in the partial tree. This is a first step to study the asymptotic distribution of a natural estimator of DNA mutation rate for species with large families.
Considering a random binary tree with $n$ labelled leaves, we use a pruning procedure on this tree in order to construct a $β(3/2,1/2)$-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 $β$-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 even…
Representation of coalescent process using pruning of trees has been used by Goldschmidt and Martin for the Bolthausen-Sznitman coalescent and by Abraham and Delmas for the $β(3/2,1/2)$-coalescent. By considering a pruning procedure on stable Galton-Watson tree with $n$ labeled leaves, we give a representation of the discrete $β(1+α,1-α)$-coalescent, with $α\in [1/2,1)$ starting from the trivial partition of the $n$ first integers. The construction can also be made directly on the stable continuum L{é}vy tree, with parameter $1/α$, simultaneously for all $n$. This representation allows to use …
We study tree lengths in $Λ$-coalescents without a dust component from a sample of $n$ individuals. For the total length of all branches and the total length of all external branches we present laws of large numbers in full generality. The other results treat regularly varying coalescents with exponent 1, which cover the Bolthausen-Sznitman coalescent. The theorems contain laws of large numbers for the total length of all internal branches and of internal branches of order $a$ (i.e. branches carrying $a$ individuals out of the sample). These results transform immediately to sampling formulas i…
We consider linear preferential attachment trees which are specific scale-free trees also known as (random) plane-oriented recursive trees. Starting with a linear preferential attachment tree of size $n$ we show that repeatedly applying a so-called lifting yields a continuous-time Markov chain on linear preferential attachment trees. Each such tree induces a partition of $\{1, \ldots, n\}$ by placing labels in the same block if and only if they are attached to the same node in the tree. Our main result is that this Markov chain on linear preferential attachment trees induces a partition valued…
A well-established model for the genealogy of a large population in equilibrium is Kingman's coalescent. For the population together with its genealogy evolving in time, this gives rise to a time-stationary tree-valued process. We study the sum of the branch lengths, briefly denoted as tree length, and prove that the (suitably compensated) sequence of tree length processes converges, as the population size tends to infinity, to a limit process with cadlag paths, infinite infinitesimal variance, and a Gumbel distribution as its equilibrium.
In this paper we obtain scaling limits of $Λ$-coalescents near time zero under a regularly varying assumption. In particular this covers the case of Kingman's coalescent and beta coalescents. The limiting processes are coalescents with infinite mass, obtained geometrically as tangent cones of Evans metric space associated with the coalescent. In the case of Kingman's coalescent we are able to obtain a simple construction of the limiting space using a two-sided Brownian motion.
We study a class of coalescents derived from a sampling procedure out of N i.i.d. Pareto(alpha) random variables, normalized by their sum, including beta-size-biasing on total length effects (beta < alpha). Depending on the range of alpha, we derive the large N limit coalescents structure, leading either to a discrete-time Poisson-Dirichlet(alpha,-beta) Xi-coalescent (alpha in [0,1)), or to a family of continuous-time Beta(2-alpha,alpha-beta) Lambda-coalescents (alpha in [1,2)), or to the Kingman coalescent (alpha geq 2). We indicate that this class of coalescent processes (and their scaling l…
The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths), culminating in the $β$-family of Aldous' branching models. We next introduce real trees (trees as metric spaces) and show how to study them through their contour, provided they are properly measured and ordered. We then focus on the reduced tree, or coalescent tree, which is the tree spanned by individuals/species alive at the same fixed time. We show how red…
In this paper, we study a weak law of large numbers for the total internal length of the Bolthausen-Szmitman coalescent. As a consequence, we obtain the weak limit law of the centered and rescaled total external length. The latter extends results obtained by Dhersin & Möhle \cite{DM12}. An application to population genetics dealing with the total number of mutations in the genealogical tree is also given.
We consider the compact space of pairs of nested partitions of $\mathbb N$, where by analogy with models used in molecular evolution, we call "gene partition" the finer partition and "species partition" the coarser one. We introduce the class of nondecreasing processes valued in nested partitions, assumed Markovian and with exchangeable semigroup. These processes are said simple when each partition only undergoes one coalescence event at a time (but possibly the same time). Simple nested exchangeable coalescent (SNEC) processes can be seen as the extension of $Λ$-coalescents to nested partitio…
Formulas are provided for the cumulants and the moments of the time $T$ back to the most recent common ancestor of the Kingman coalescent. It is shown that both the $j$th cumulant and the $j$th moment of $T$ are linear combinations of the values $ζ(2m)$, $m\in\{0,\ldots,\lfloor j/2\rfloor\}$, of the Riemann zeta function $ζ$ with integer coefficients. The proof is based on a solution of a two-dimensional recursion with countably many initial values. A closely related strong convergence result for the tree length $L_n$ of the Kingman coalescent restricted to a sample of size $n$ is derived. The…
Take a continuous-time Galton-Watson tree. If the system survives until a large time $T$, then choose $k$ particles uniformly from those alive. What does the ancestral tree drawn out by these $k$ particles look like? Some special cases are known but we give a more complete answer. We concentrate on near-critical cases where the mean number of offspring is $1+μ/T$ for some $μ\in\mathbb{R}$, and show that a scaling limit exists as $T\to\infty$. Viewed backwards in time, the resulting coalescent process is topologically equivalent to Kingman's coalescent, but the times of coalescence have an inte…
The standard coalescent is widely used in evolutionary biology and population genetics to model the ancestral history of a sample of molecular sequences as a rooted and ranked binary tree. In this paper, we present a representation of the space of ranked trees as a space of constrained ordered matched pairs. We use this representation to define ergodic Markov chains on labeled and unlabeled ranked tree shapes analogously to transposition chains on the space of permutations. We show that an adjacent-swap chain on labeled and unlabeled ranked tree shapes has mixing time at least of order $n^3$, …
Incomplete lineage sorting (ILS) is a common source of gene tree incongruence in multilocus analyses. A large number of methods have been developed to infer species trees in the presence of ILS. Here we provide a mathematical analysis of several coalescent-based methods. Our analysis is performed on a three-taxon species tree and assumes that the gene trees are correctly reconstructed along with their branch lengths.
We define a multi-type coalescent point process of a general branching process with finitely many types. This multi-type coalescent fully describes the genealogy of the (quasi-stationary) standing population, providing types along ancestral lineages of all individuals in the standing population. We show that this point-process is a functional of a certain Markov chain defined by the planar embedding of the branching process. This Markov chain is further used to determine statistical properties of the ancestral tree, such as the time to the most recent common ancestor (MRCA) of two consecutive …
We give a de Finetti type representation for exchangeable random coalescent trees (formally described as semi-ultrametrics) in terms of sampling iid sequences from marked metric measure spaces. We apply this representation to define versions of tree-valued Fleming-Viot processes from a $Ξ$-lookdown model. As state spaces for these processes, we use, besides the space of isomorphy classes of metric measure spaces, also the space of isomorphy classes of marked metric measure spaces and a space of distance matrix distributions. This allows to include the case with dust in which the genealogical t…
We derive explicit formulas for the two first moments of he site frequency spectrum $(SFS_{n,b})_{1\leq b\leq n-1}$ of the Bolthausen-Sznitman coalescent along with some precise and efficient approximations, even for small sample sizes $n$. These results provide new $L_2$-asymptotics for some values of $b=o(n)$. We also study the length of internal branches carrying $b>n/2$ individuals. In this case we obtain the distribution function and a convergence in law. Our results rely on the random recursive tree construction of the Bolthausen-Sznitman coalescent.
The paper establishes a weak version of Horton self-similarity for a tree representation of Kingman's coalescent process. The proof is based on a Smoluchowski-type system of ordinary differential equations for the number of branches of a given Horton-Strahler order in a tree that represents Kingman's N-coalescent process with a constant kernel, in a hydrodynamic limit. We also demonstrate a close connection between the combinatorial Kingman's tree and the combinatorial level set tree of a white noise, which implies Horton self-similarity for the latter.
We design a theoretic tree-based functional representation of a class of Feynman-Kac particle distributions, including an extension of the Wick product formula to interacting particle systems. These weak expansions rely on an original combinatorial, and permutation group analysis of a special class of forests. They provide refined non asymptotic propagation of chaos type properties, as well as sharp $\LL\_p$-mean error bounds, and laws of large numbers for $U$-statistics. Applications to particle interpretations of the top eigenvalues, and the ground states of Schrödinger semigroups are also d…
We dedicate this paper to Sir John Kingman on his 70th Birthday. In modern mathematical population genetics the ancestral history of a population of genes back in time is described by John Kingman's coalescent tree. Classical and modern approaches model gene frequencies by diffusion processes. This paper, which is partly a review, discusses how coalescent processes are dual to diffusion processes in an analytic and probabilistic sense. Bochner (1954) and Gasper (1972) were interested in characterizations of processes with Beta stationary distributions and Jacobi polynomial eigenfunctions. We d…
Consider a population of fixed size that evolves over time. At each time, the genealogical structure of the population can be described by a coalescent tree whose branches are traced back to the most recent common ancestor of the population. As time goes forward, the genealogy of the population evolves, leading to what is known as an evolving coalescent. We will study the evolving coalescent for populations whose genealogy can be described by the Bolthausen-Sznitman coalescent. We obtain the limiting behavior of the evolution of the time back to the most recent common ancestor and the total le…
We work in the context of the infinitely many alleles model. The allelic partition associated with a coalescent process started from n individuals is obtained by placing mutations along the skeleton of the coalescent tree; for each individual, we trace back to the most recent mutation affecting it and group together individuals whose most recent mutations are the same. The number of blocks of each of the different possible sizes in this partition is the allele frequency spectrum. The celebrated Ewens sampling formula gives precise probabilities for the allele frequency spectrum associated with…
We describe a representation of the Bolthausen-Sznitman coalescent in terms of the cutting of random recursive trees. Using this representation, we prove results concerning the final collision of the coalescent restricted to [n]: we show that the distribution of the number of blocks involved in the final collision converges as n tends to infinity, and obtain a scaling law for the sizes of these blocks. We also consider the discrete-time Markov chain giving the number of blocks after each collision of the coalescent restricted to [n]; we show that the transition probabilities of the time-revers…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of the distribution and a sparse signal. Using this connection, we derive an information-theoretic trade-off between the number of genes, $m$, needed for an accurate reconstruction and the sequence length, $k$, of the genes. Specifically, we show that to detect a branch of length $f$, one needs $m = Θ(1/[f^{2} \sqrt{k}])$.
For $Λ$-$n$-coalescents with mutation, we analyse the size $O_n$ of the partition block of $i\in\{1,\ldots,n\}$ at the time where the first mutation appears on the tree that affects $i$ and is shared with any other $j\in\{1,\ldots,n\}$. We provide asymptotics of $O_n$ for $n\to\infty$ and a recursion for all moments of $O_n$ for finite $n$. This variable gives an upper bound for the minimal clade size [2], which is not observable in real data. In applications to genetics, it has been shown to be useful to lower classification errors in genealogical model selection [10].
We define a Markov process in a forward population model with backward genealogy given by the $Λ$-coalescent. This Markov process, called the fixation line, is related to the block counting process through its hitting times. Two applications are discussed. The probability that the $n$-coalescent is deeper than the $(n-1)$-coalescent is studied. The distribution of the number of blocks in the last coalescence of the $n$-$\operatorname {Beta}(2-α,α)$-coalescent is proved to converge as $n\rightarrow\infty$, and the generating function of the limiting random variable is computed.
We consider the space of complete and separable metric spaces which are equipped with a probability measure. A notion of convergence is given based on the philosophy that a sequence of metric measure spaces converges if and only if all finite subspaces sampled from these spaces converge. This topology is metrized following Gromov's idea of embedding two metric spaces isometrically into a common metric space combined with the Prohorov metric between probability measures on a fixed metric space. We show that for this topology convergence in distribution follows - provided the sequence is tight -…
The evolving Kingman coalescent is the tree-valued process which records the time evolution undergone by the genealogies of Moran populations. We consider the associated process of total external tree length of the evolving Kingman coalescent and its asymptotic behaviour when the number of leaves of the tree tends to infinity. We show that on the time-scale of the Moran model slowed down by a factor equal to the population size, the (centred and rescaled) external length process converges to a stationary Gaussian process with almost surely continuous paths and covariance function $c(s,t)=\Big(…
In these expository notes, we describe some features of the multiplicative coalescent and its connection with random graphs and minimum spanning trees. We use Pitman's proof of Cayley's formula, which proceeds via a calculation of the partition function of the additive coalescent, as motivation and as a launchpad. We define a random variable which may reasonably be called the empirical partition function of the multiplicative coalescent, and show that its typical value is exponentially smaller than its expected value. Our arguments lead us to an analysis of the susceptibility of the Erdős-Rény…
Consider a population evolving as a critical continuous-time Galton-Watson (GW) tree. Conditional on the population surviving until a large time $T$, sample $k$ individuals uniformly at random (without replacement) from amongst those alive at time $T$. What is the genealogy of this sample of individuals? In cases where the offspring distribution has finite variance, the probabilistic properties of the joint ancestry of these $k$ particles are well understood, as seen in \cite{HJR20, J19}. In the present article, we study the joint ancestry of a sample of $k$ particles under the following regim…
Rice University（莱斯大学）；Massachusetts Institute of Technology（麻省理工学院）；University of Wisconsin–Madison（威斯康星大学麦迪逊分校）
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 sequences corresponding to each gene often provide limited information about the gene trees themselves. In this paper we consider an approach to species tree reconstruction that addresses both these hurdles. Specifically, we propose an algorithm for phylogeny reconstruction under the multispecies coalescent model with a standard model of site substitution. The mu…
We introduce a colored coalescent process which recovers random colored genealogical trees. Here a colored genealogical tree has its vertices colored black or white. Moving backward along the colored genealogical tree, the color of vertices may change only when two vertice coalesce. The rule that governs the change of color involves a parameter $x$. When $x=1/2$, the colored coalescent process can be derived from a variant of the Wright-Fisher model for a haploid population in population genetics. Explicit computations of the expectation and the cumulative distribution function of the coalesce…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of reconstruction methods in this setting is based on internode distances, i.e. the average graph distance between pairs of species across gene trees. While statistical consistency in the limit of large numbers of loci has been established in some cases, little is known about the sample complexity of such methods. Here we make progress on this question by deriving …
We provide scaling limits for the block counting process and the fixation line of $Λ$-coalescents as the initial state $n$ tends to infinity under the assumption that the measure $Λ$ on $[0,1]$ satisfies $\int_{[0,1]}u^{-1}(Λ-bλ)({\rm d}u)<\infty$ for some $b>0$. Here $λ$ denotes the Lebesgue measure. The main result states that the block counting process, properly logarithmically scaled, converges in the Skorohod space to an Ornstein--Uhlenbeck type process as $n$ tends to infinity. The result is applied to beta coalescents with parameters $1$ and $b>0$. We split the generators into two parts…
We define a doubly infinite, monotone labeling of Bienayme-Galton-Watson (BGW) genealogies. The genealogy of the current generation backwards in time is uniquely determined by the coalescent point process $(A_i; i\ge 1)$, where $A_i$ is the coalescence time between individuals i and i+1. There is a Markov process of point measures $(B_i; i\ge 1)$ keeping track of more ancestral relationships, such that $A_i$ is also the first point mass of $B_i$. This process of point measures is also closely related to an inhomogeneous spine decomposition of the lineage of the first surviving particle in gene…
We derive the asymptotic behavior of the total, active and inactive branch lengths of the seed bank coalescent, when the size of the initial sample grows to infinity. Those random variables have important applications for populations evolving under some seed bank effects, such as plants and bacteria, and for some cases of structured populations like metapopulations. The proof relies on the study of the tree at a stopping time corresponding to the first time that a deactivated lineage reactivates. We also give conditional sampling formulas for the random partition and we study the system at the…
$Λ$-coalescents model the evolution of a coalescing system in which any number of blocks randomly sampled from the whole may merge into a larger block. For the coalescent restricted to initially $n$ singletons we study the collision spectrum $(X_{n,k}:2\le k\le n)$, where $X_{n,k}$ counts, throughout the history of the process, the number of collisions involving exactly $k$ blocks. Our focus is on the large $n$ asymptotics of the joint distribution of the $X_{n,k}$'s, as well as on functional limits for the bulk of the spectrum for simple coalescents. Similarly to the previous studies of the t…
Trees corresponding to $Λ$- and $Ξ$-$n$-coalescents can be both quite similar and fundamentally different compared to bifurcating tree models based on Kingman's $n$-coalescent. This has consequences for inference of a well-fitting gene genealogy as well as for assessing biological properties of species having such sample genealogies. Here, mathematical properties concerning clade sizes in the tree as well as changes of the tree when the samples are enlargened are highlighted. To be used as realistic genealogy models for real populations, an extension for changing population sizes is discussed.
