Kingman Coalescent was first proposed by Kingman [7] in population genetics to describe population's genealogical structure. Now it becomes a bench-mark model for coalescent process. Extensive studies have been conducted on Kingman coalescent. In particular, its explicit finite time distribution was obtained by Tavaré [12]. However, very few people use this explicit distribution to do analysis for it is an intractable infinite series. In this article, we are going to establish a complex integral representation for the finite time distribution, then we use steepest descent method to analyze this integral representation to obtain local central limit theorem at small time regime.
We consider both the Bolthausen-Sznitman and the Kingman coalescent restricted to the partitions of $\{1, \ldots, n\}.$ Spectral decompositions of the corresponding generators are derived. As an application we obtain a formula for the Green's functions and a short derivation of the well-known formula for the transition probabilities of the Bolthausen-Sznitman coalescent.
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 …
Consider the Markov process taking values in the partitions of N such that each pair of blocks merges at rate one, and each integer is eroded, i.e., becomes a singleton block, at rate d. This is a special case of exchangeable fragmentation-coalescence process called Kingman's coalescent with erosion. We provide a new construction of the stationary distribution of this process as a sample from a standard flow of bridges. This allows us to give a representation of the asymptotic frequencies of this stationary distribution in terms of a sequence of hierarchically independent diffusions. Moreover,…
We consider standard $\La$-coalescents (or coalescents with multiple collisions) with a non-trivial "Kingman part". Equivalently, the driving measure $Λ$ has an atom at $0$; $Λ(\{0\})=c>0$. It is known that all such coalescents come down from infinity. Moreover, the number of blocks $N_t$ is asymptotic to $v(t) = 2/(ct)$ as $t\to 0$. In the present paper we investigate the second-order asymptotics of $N_t$ in the functional sense at small times. This complements our earlier results on the fluctuations of the number of blocks for a class of regular $\La$-coalescents without the Kingman part. In…
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…
The nested Kingman coalescent describes the ancestral tree of a population undergoing neutral evolution at the level of individuals and at the level of species, simultaneously. We study the speed at which the number of lineages descends from infinity in this hierarchical coalescent process and prove the existence of an early-time phase during which the number of lineages at time $t$ decays as $ 2γ/ct^2$, where $c$ is the ratio of the coalescence rates at the individual and species levels, and the constant $γ\approx 3.45$ is derived from a recursive distributional equation for the number of lin…
In this paper we prove asymptotic normality of the total length of external branches in Kingman's coalescent. The proof uses an embedded Markov chain, which can be descriped as follows: Take an urn with n black balls. Empty it in n steps according to the rule: In each step remove a randomly chosen pair of balls and replace it by one red ball. Finally remove the last remaining ball. Then the numbers U_k, 0 \leq k \leq n, of red balls after k steps exhibits an unexpected property: (U_0,...,U_n) and (U_n,..., U_0) are equal in distribution.
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 the Kingman coalescent tree the length of order $r$ is defined as the sum of the lengths of all branches that support $r$ leaves. For $r=1$ these branches are external, while for $r\ge2$ they are internal and carry a subtree with $r$ leaves. In this paper we prove that for any $s\in\mathbb{N}$ the vector of rescaled lengths of orders $1\le r\le s$ converges to the multivariate standard normal distribution as the number of leaves of the Kingman coalescent tends to infinity. To this end we use a coupling argument which shows that for any $r\ge2$ the (internal) length of order $r$ behaves asym…
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.
The Ancestral Selection Graph (ASG) is an important genealogical process which extends the well-known Kingman coalescent to incorporate natural selection. We show that the number of lineages of the ASG with and without mutation is asymptotic to $2/t$ as $t\to 0$, in agreement with the limiting behaviour of the Kingman coalescent. We couple these processes on the same probability space using a Poisson random measure construction that allows us to precisely compare their hitting times. These comparisons enable us to characterise the speed of coming down from infinity of the ASG as well as its fl…
We consider a continuous population whose dynamics is described by the standard stationary Fleming-Viot process, so that the genealogy of $n$ uniformly sampled individuals is distributed as the Kingman $n$-coalescent. In this note, we study some genealogical properties of this population when the sample is conditioned to fall entirely into a subpopulation with most recent common ancestor (MRCA) shorter than $\varepsilon$. First, using the comb representation of the total genealogy (Lambert & Uribe Bravo 2016), we show that the genealogy of the descendance of the MRCA of the sample on the times…
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.
Full likelihood inference under Kingman's coalescent is a computationally challenging problem to which importance sampling (IS) and the product of approximate conditionals (PAC) method have been applied successfully. Both methods can be expressed in terms of families of intractable conditional sampling distributions (CSDs), and rely on principled approximations for accurate inference. Recently, more general $Λ$- and $Ξ$-coalescents have been observed to provide better modelling fits to some genetic data sets. We derive families of approximate CSDs for finite sites $Λ$- and $Ξ$-coalescents, and…
Kingman's coalescent is a random tree that arises from classical population genetic models such as the Moran model. The individuals alive in these models correspond to the leaves in the tree and the following two laws of large numbers concerning the structure of the tree-top are well-known: (i) The (shortest) distance, denoted by $T_n$, from the tree-top to the level when there are $n$ lines in the tree satisfies $nT_n \xrightarrow{n\to\infty} 2$ almost surely; (ii) At time $T_n$, the population is naturally partitioned in exactly $n$ families where individuals belong to the same family if the…
Let $\mathbb{T}^d_N$, $d\ge 2$, be the discrete $d$-dimensional torus with $N^d$ points. Place a particle at each site of $\mathbb{T}^d_N$ and let them evolve as independent, nearest-neighbor, symmetric, continuous-time random walks. Each time two particles meet, they coalesce into one. Denote by $C_N$ the first time the set of particles is reduced to a singleton. Cox [6] proved the existence of a time-scale $θ_N$ for which $C_N/θ_N$ converges to the sum of independent exponential random variables. Denote by $Z^N_t$ the total number of particles at time $t$. We prove that the sequence of Marko…
An important property of Kingman's coalescent is that, starting from a state with an infinite number of blocks, over any positive time horizon, it transitions into an almost surely finite number of blocks. This is known as `coming down from infinity'. Moreover, of the many different (exchangeable) stochastic coalescent models, Kingman's coalescent is the `fastest' to come down from infinity. In this article we study what happens when we counteract this `fastest' coalescent with the action of an extreme form of fragmentation. We augment Kingman's coalescent, where any two blocks merge at rate $…
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…
Multiple-merger coalescents, e.g. $Λ$-$n$-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 $n$-coalescent. $Λ$-$n$-coalescents can be seen as the limit process of the discrete genealogies of Cannings models with fixed population size, when time is rescaled and population size $N\to\infty$. As established for Kingman's $n$-coalescent, moderate population size fluctuations in the discrete population model should be reflected by a time-change of the limit coalescent. Fo…
We establish convergence to the Kingman coalescent for a class of age-structured population models with time-constant population size. Time is discrete with unit called a year. Offspring numbers in a year may depend on mother's age.
In the case of neutral populations of fixed sizes in equilibrium whose genealogies are described by the Kingman $N$-coalescent back from time $t$ consider the associated processes of total tree length as $t$ increases. We show that the (càdlàg) process to which the sequence of compensated tree length processes converges as $N$ tends to infinity is a process of infinite quadratic variation; therefore this process cannot be a semimartingale. This answers a question posed in Pfaffelhuber et al. (2011).
Kingman's coalescent is one of the most popular models in population genetics. It describes the genealogy of a population whose genetic composition evolves in time according to the Wright-Fisher model, or suitable approximations of it belonging to the broad class of Fleming-Viot processes. Ancestral inference under Kingman's coalescent has had much attention in the literature, both in practical data analysis, and from a theoretical and methodological point of view. Given a sample of individuals taken from the population at time $t>0$, most contributions have aimed at making frequentist or Baye…
We establish convergence to the Kingman coalescent for the genealogy of a geographically - or otherwise - structured version of the Wright-Fisher population model with fast migration. The new feature is that migration probabilities may change in a random fashion. This brings a novel formula for the coalescent effective population size (EPS). We call it a quenched EPS to emphasize the key feature of our model - random environment. The quenched EPS is compared with an annealed (mean-field) EPS which describes the case of constant migration probabilities obtained by averaging the random migration…
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.
Kingman's House-of-Cards model is a simple and celebrated model to describe the evolution of population under the competition of selection and mutation. Letting mutation probabilities vary on generations makes the model more realistic and meaningful. This paper considers the condensation phenomenon and limit fitness distribution when Kingman's model is put into a random environment consisting of i.i.d. random mutation probabilities. It turns out that the random model is completely dominated by Kingman's model in terms of condensation and fitness. Another random model where all mutation probabi…
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…
For a one-locus haploid infinite population with discrete generations, the celebrated Kingman's model describes the evolution of fitness distributions under the competition of selection and mutation, with a constant mutation probability. Letting mutation probabilities vary on generations reflects the influence of a random environment. This paper generalises Kingman's model by using a sequence of i.i.d. random mutation probabilities. For any distribution of the sequence, the weak convergence of fitness distributions to the globally stable equilibrium for any initial fitness distribution is prov…
Kingman's model describes the evolution of a one-locus haploid population of infinite size and discrete generations under the competition of selection and mutation. A random generalisation has been made in a previous paper which assumes all mutation probabilities to be i.i.d.. The weak convergence of fitness distributions to a globally stable equilibrium for any initial distribution was proved. A condensation occurs if almost surely a positive proportion of the population travels to and condensates on the largest fitness value due to the dominance of selection over mutation. A criterion of con…
The results in this paper provide new information on asymptotic properties of classical models: the neutral Kingman coalescent under a general finite-alleles, parent-dependent mutation mechanism, and its generalisation, the ancestral selection graph. Several relevant quantities related to these fundamental models are not explicitly known when mutations are parent dependent. Examples include the probability that a sample taken from a population has a certain type configuration, and the transition probabilities of their block counting jump chains. In this paper, asymptotic results are derived fo…
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…
We study several fundamental properties of a class of stochastic processes called spatial Lambda-coalescents. In these models, a number of particles perform independent random walks on some underlying graph G. In addition, particles on the same vertex merge randomly according to a given coalescing mechanism. A remarkable property of mean-field coalescent processes is that they may come down from infinity, meaning that, starting with an infinite number of particles, only a finite number remains after any positive amount of time, almost surely. We show here however that, in the spatial setting, …
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 simul…
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, we show that as the number of demes tends to infinity the limiting form of the genealogy can be described in terms of the alternation of instantaneous 'scattering' phases dominated by local demographic processes, and extended 'collecting' phases dominated by global processes. When extinction and recolonization events are local, this genealogy is given by Kin…
Let $Λ$ be a finite measure on the unit interval. A $Λ$-Fleming-Viot process is a probability measure valued Markov process which is dual to a coalescent with multiple collisions ($Λ$-coalescent) in analogy to the duality known for the classical Fleming Viot process and Kingman's coalescent, where $Λ$ is the Dirac measure in 0. We explicitly construct a dual process of the coalescent with simultaneous multiple collisions ($Ξ$-coalescent) with mutation, the $Ξ$-Fleming-Viot process with mutation, and provide a representation based on the empirical measure of an exchangeable particle system alon…
The goal of this paper is to study the lookdown model with selection in the case of a population containing two types of individuals, with a reproduction model which is dual to the $Λ$-coalescent. In particular we formulate the infinite population "$Λ$-lookdown model with selection". When the measure $Λ$ gives no mass to 0, we show that the proportion of one of the two types converges, as the population size $N$ tends to infinity, towards the solution of a stochastic differential equation driven by a Poisson point process. We show that one of the two types fixates in finite time if and only if…
We investigate a new model for populations evolving in a spatial continuum. This model can be thought of as a spatial version of the Lambda-Fleming-Viot process. It explicitly incorporates both small scale reproduction events and large scale extinction-recolonisation events. The lineages ancestral to a sample from a population evolving according to this model can be described in terms of a spatial version of the Lambda-coalescent. Using a technique of Evans(1997), we prove existence and uniqueness in law for the model. We then investigate the asymptotic behaviour of the genealogy of a finite n…
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…
Evolutionary models for populations of constant size are frequently studied using the Moran model, the Wright-Fisher model, or their diffusion limits. When evolution is neutral, a random genealogy given through Kingman's coalescent is used in order to understand basic properties of such models. Here, we address the use of a genealogical perspective for models with weak frequency-dependent selection, i.e. N s =: α is small, and s is the fitness advantage of a fit individual and N is the population size. When computing fixation probabilities, this leads either to the approach proposed by Rousset…
We consider a stochastic model describing a constant size $N$ population that may be seen as a directed polymer in random medium with $N$ sites in the transverse direction. The population dynamics is governed by a noisy traveling wave equation describing the evolution of the individual fitnesses. We show that under suitable conditions the generations are independent and the model is characterized by an extended Wright-Fisher model, in which the individual $i$ has a random fitness $η_i$ and the joint distribution of offspring $(ν_1,\ldots,ν_N)$ is given by a multinomial law with $N$ trials and …
Widely used models in genetics include the Wright-Fisher diffusion and its moment dual, Kingman's coalescent. Each has a multilocus extension but under neither extension is the sampling distribution available in closed-form, and their computation is extremely difficult. In this paper we derive two new multilocus population genetic models, one a diffusion and the other a coalescent process, which are much simpler than the standard models, but which capture their key properties for large recombination rates. The diffusion model is based on a central limit theorem for density dependent population…
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…
We identify a new natural coalescent structure, which we call the seed-bank coalescent, that describes the gene genealogy of populations under the influence of a strong seed-bank effect, where "dormant forms" of individuals (such as seeds or spores) may jump a significant number of generations before joining the "active" population. Mathematically, our seed-bank coalescent appears as scaling limit in a Wright-Fisher model with geometric seed-bank age structure if the average time of seed dormancy scales with the order of the total population size $N$. This extends earlier results of Kaj, Krone…
Consider a haploid population which has evolved through an exchangeable reproduction dynamics, and in which all individuals alive at time $t$ have a most recent common ancestor (MRCA) who lived at time $A_t$, say. As time goes on, not only the population but also its genealogy evolves: some families will get lost from the population and eventually a new MRCA will be established. For a time-stationary situation and in the limit of infinite population size $N$ with time measured in $N$ generations, i.e. in the scaling of population genetics which leads to Fisher-Wright diffusions and Kingman's c…
In this article, we derive statistical tools to analyze and distinguish the patterns of genetic variability produced by classical and recent population genetic models related to seed banks. In particular, we are concerned with models described by the Kingman coalescent (K), models exhibiting so-called weak seed banks described by a time-changed Kingman coalescent (W), models with so-called strong seed bank described by the seed bank coalescent (S) and the classical two-island model by Wright, described by the structured coalescent (TI). As the presence of a (strong) seed bank should stratify a…
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.
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 coalescent process appears in the study of the connected components of random graph processes in which connected subgraphs are added over time with probabilities that depend only on their size. First, we determine the asymptotic distribution of the coalescent time. Then, we define a Bienayme-Galton-Watson (BGW) process such that its total population size dominates t…
