The Kingman coalescent is a fundamental process in population genetics modelling the ancestry of a sample of individuals backwards in time. In this paper, in a large-sample-size regime, we study asymptotic properties of the coalescent under neutrality and a general finite-alleles mutation scheme, i.e. including both parent independent and parent dependent mutation. In particular, we consider a sequence of Markov chains that is related to the coalescent and consists of block-counting and mutation-counting components. We show that these components, suitably scaled, converge weakly to deterministic components and Poisson processes with varying intensities, respectively. Along the way, we develop a novel approach, based on a change of measure, to generalise the convergence result from the parent independent to the parent dependent mutation setting, in which several crucial quantities are not known explicitly.
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 …
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 thi…
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…
Kingman's model of selection and mutation studies the limit type value distribution in an asexual population of discrete generations and infinite size undergoing selection and mutation. This paper generalizes the model to analyse the long-term evolution of Escherichia. coli in Lenski experiment. Weak assumptions for fitness functions are proposed and the mutation mechanism is the same as in Kingman's model. General macroscopic epistasis are designable through fitness functions. Convergence to the unique limit type distribution is obtained.
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…
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…
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 $…
We describe the onset of condensation in the simple model for the balance between selection and mutation given by Kingman in terms of a scaling limit theorem. Loosely speaking, this shows that the wave moving towards genes of maximal fitness has the shape of a gamma distribution. We conjecture that this wave shape is a universal phenomenon that can also be found in a variety of more complex models, well beyond the genetics context, and provide some further evidence for this.
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…
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.
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…
Let $K_n$ denote the number of types of a sample of size $n$ taken from an exchangeable coalescent process ($Ξ$-coalescent) with mutation. A distributional recursion for the sequence $(K_n)_{n\in{\mathbb N}}$ is derived. If the coalescent does not have proper frequencies, i.e., if the characterizing measure $Ξ$ on the infinite simplex $Δ$ does not have mass at zero and satisfies $\int_Δ|x|Ξ(dx)/(x,x)<\infty$, where $|x|:=\sum_{i=1}^\infty x_i$ and $(x,x):=\sum_{i=1}^\infty x_i^2$ for $x=(x_1,x_2,...)\inΔ$, then $K_n/n$ converges weakly as $n\to\infty$ to a limiting variable $K$ which is charac…
Kingman derived the Ewens sampling formula for random partitions describing the genetic variation in a neutral mutation model defined by a Poisson process of mutations along lines of descent governed by a simple coalescent process, and observed that similar methods could be applied to more complex models. M{ö}hle described the recursion which determines the generalization of the Ewens sampling formula in the situation when the lines of descent are governed by a $Λ$-coalescent, which allows multiple mergers. Here we show that the basic integral representation of transition rates for the $Λ$-coa…
The star-shaped $Λ$-coalescent and corresponding $Λ$-Fleming-Viot process where the $Λ$ measure has a single atom at unity are studied in this paper. The transition functions and stationary distribution of the $Λ$-Fleming-Viot process are derived in a two-type model with mutation. The distribution of the number of non-mutant lines back in time in the star-shaped $Λ$-coalescent is found. Extensions are made to a model with $d$ types, either with parent independent mutation or general Markov mutation, and an infinitely-many-types model when $d\to \infty$. An eigenfunction expansion for the trans…
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.
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…
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…
The (Ξ, A)-Fleming-Viot process with mutation is a probability-measure-valued process whose moment dual is similar to that of the classical Fleming-Viot process except that the Kingman's coalescent is replaced by the Ξ-coalescent, the coalescent with simultaneous multiple collisions. We first prove the existence of such a process for general mutation generator A. We then investigate its reversibility. We also study both the weak and strong uniqueness of solution to the associated stochastic partial differential equation.
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…
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 consider the genealogy of a sample of individuals taken from a spatially structured population when the variance of the offspring distribution is relatively large. The space is structured into discrete sites of a graph G. If the population size at each site is large, spatial coalescents with multiple mergers, so called spatial Lambda-coalescents, for which ancestral lines migrate in space and coalesce according to some Lambda-coalescent mechanism, are shown to be appropriate approximations to the genealogy of a sample of individuals. We then consider as the graph G the two dimensional torus…
Bertoin and Le Gall (2003) introduced a certain probability measure valued Markov process that describes the evolution of a population, such that a sample from this population would exhibit a genealogy given by the so-called $Λ$-coalescent, or coalescent with multiple collisions, introduced independently by Pitman (1999) and Sagitov (1999). We show how this process can be extended to the case where lineages can experience mutations. Regenerative compositions enter naturally into this model, which is somewhat surprising, considering a negative result by M{ö}hle (2007).
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, …
Assume that individuals alive at time $t$ in some population can be ranked in such a way that the coalescence times between consecutive individuals are i.i.d. The ranked sequence of these branches is called a coalescent point process. We have shown in a previous work that splitting trees are important instances of such populations. Here, individuals are given DNA sequences, and for a sample of $n$ DNA sequences belonging to distinct individuals, we consider the number $S_n$ of polymorphic sites (sites at which at least two sequences differ), and the number $A_n$ of distinct haplotypes (sequenc…
The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to have more than one clearly different phenotypes. We present a model for analyzing quadri-allele frequency spectrum, where the ancestral population diverged into three populations at a certain divergence time and the resulting mutations on the branches of the coalescent tree gave rise to three different derived alleles, which could be observed in the present generation along with the ancestral allele. The model has been analyzed …
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…
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…
Consider a population where individuals give birth at constant rate during their lifetimes to i.i.d. copies of themselves. Individuals bear clonally inherited types, but (neutral) mutations may happen at the birth events. The smallest subtree containing the genealogy of all the extant individuals at a fixed time τ, is called the coalescent point process. We enrich this process with the history of the mutations that appeared over time, and call it the marked coalescent point process. With the help of limit theorems for Lévy processes with marked jumps established in a previous work (arXiv:1305.…
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].
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…
This article considers a model of genealogy corresponding to a regular exchangeable coalescent (also known as Xi-coalescent) started from a large finite configuration, and undergoing neutral mutations. Asymptotic expressions for the number of active lineages were obtained by the author in a previous work. Analogous results for the number of active mutation-free lineages and the combined lineage lengths are derived using the same martingale-based technique. They are given in terms of convergence in probability, while extensions to convergence in moments and convergence almost surely are discuss…
In this paper we introduce a multilocus diffusion model of a population of $N$ haploid, asexually reproducing individuals. The model includes parent-dependent mutation and interlocus selection, the latter limited to pairwise relationships but among a large number of simultaneous loci. The diffusion is expressed as a system of stochastic differential equations (SDEs) that are coupled in the drift functions through a Shahshahani gradient-like structure for interlocus selection. The system of SDEs is derived from a sequence of Markov chains by weak convergence. We find the explicit stationary (in…
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.
