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 (sequences differing at one site at least). It is standard to assume that mutations arrive at constant rate (on germ lines), and never hit the same site on the DNA sequence. We study the mutation pattern associated to coalescent point processes under this assumption. Here, $S_n$ and $A_n$ grow linearly as $n$ grows, with explicit rate. However, when the branch lengths have infinite expectation, $S_n$ grows more rapidly, e.g. as $n \ln(n)$ for critical birth--death processes. Then, we study the frequency spectrum of the sample, that is, the numbers of polymorphic sites/haplotypes carried by $k$ individuals in the sample. These numbers are shown to grow also linearly with sample size, and we provide simple explicit formulae for mutation frequencies and haplotype frequencies. For critical birth--death processes, mutation frequencies are given by the harmonic series and haplotype frequencies by Fisher logarithmic series.
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…
We introduce a continuous-time Markov chain describing dynamic allelic partitions which extends the branching process construction of the Pitman sampling formula in Pitman (2006) and the birth-and-death process with immigration studied in Karlin and McGregor (1967), in turn related to the celebrated Ewens sampling formula. A biological basis for the scheme is provided in terms of a population of individuals grouped into families, that evolves according to a sequence of births, deaths and immigrations. We investigate the asymptotic behaviour of the chain and show that, as opposed to the birth-a…
We consider a (sub) critical Galton-Watson process with neutral mutations (infinite alleles model), and decompose the entire population into clusters of individuals carrying the same allele. We specify the law of this allelic partition in terms of the distribution of the number of clone-children and the number of mutant-children of a typical individual. The approach combines an extension of Harris representation of Galton-Watson processes and a version of the ballot theorem. Some limit theorems related to the distribution of the allelic partition are also given.
Kingman derived the Ewens sampling formula for random partitions from the genealogy model defined by a Poisson process of mutations along lines of descent governed by a simple coalescent process. Möhle described the recursion which determines the generalization of the Ewens sampling formula when the lines of descent are governed by a coalescent with multiple collisions. In a recent work by Dong, Gnedin and Pitman, authors exploit an analogy with the theory of regenerative composition and partition structures, and provide various characterizations of the associated exchangeable random partition…
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…
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…
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…
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 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.
Kingman (1978)'s representation theorem states that any exchangeable partition of $\mathbb{N}$ can be represented as a paintbox based on a random mass-partition. Similarly, any exchangeable composition (i.e. ordered partition of $\mathbb{N}$) can be represented as a paintbox based on an interval-partition (Gnedin 1997). Our first main result is that any exchangeable coalescent process (not necessarily Markovian) can be represented as a paintbox based on a random non-decreasing process valued in interval-partitions, called nested interval-partition, generalizing the notion of comb metric space …
This paper studies the spatial coalescent on $\Z^2$. In our setting, the partition elements are located at the sites of $\Z^2$ and undergo local delayed coalescence and migration. That is, pairs of partition elements located at the same site coalesce into one partition element after exponential waiting times. In addition, the partition elements perform independent random walks. The system starts in either locally finite configurations or in configurations containing countably many partition elements per site. These two situations are relevant if the coalescent is used to study the scaling limi…
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…
Consider a random real tree whose leaf set, or boundary, is endowed with a finite mass measure. Each element of the tree is further given a type, or allele, inherited from the most recent atom of a random point measure (infinitely-many-allele model) on the skeleton of the tree. The partition of the boundary into distinct alleles is the so-called allelic partition. In this paper, we are interested in the infinite trees generated by supercritical, possibly time-inhomogeneous, binary branching processes, and in their boundary, which is the set of particles `co-existing at infinity'. We prove that…
We consider a general branching population where the lifetimes of individuals are i.i.d.\ with arbitrary distribution and where each individual gives birth to new individuals at Poisson times independently from each other. In addition, we suppose that individuals experience mutations at Poissonian rate $θ$ under the infinitely many alleles assumption assuming that types are transmitted from parents to offspring. This mechanism leads to a partition of the population by type, called the allelic partition. The main object of this work is the frequency spectrum $A(k,t)$ which counts the number of …
We study the number of collisions $X_n$ of an exchangeable coalescent with multiple collisions ($Λ$-coalescent) which starts with $n$ particles and is driven by rates determined by a finite characteristic measure $ν({\rm d}x)=x^{-2}Λ({\rm d}x)$. Via a coupling technique we derive limiting laws of $X_n$, using previous results on regenerative compositions derived from stick-breaking partitions of the unit interval. The possible limiting laws of $X_n$ include normal, stable with index $1\leα<2$ and Mittag-Leffler distributions. The results apply, in particular, to the case when $ν$ is a beta$(a-…
The generalized Fleming-Viot processes were defined in 1999 by Donnelly and Kurtz using a particle model and by Bertoin and Le Gall in 2003 using stochastic flows of bridges. In both methods, the key argument used to characterize these processes is the duality between these processes and exchangeable coalescents. A larger class of coalescent processes, called distinguished coalescents, was set up recently to incorporate an immigration phenomenon in the underlying population. The purpose of this article is to define and characterize a class of probability-measure valued processes called the gen…
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].
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…
We introduce and analyze a novel type of coalescent processes called cross-multiplicative coalescent that models a system with two types of particles, $A$ and $B$. The bonds are formed only between the pairs of particles of opposite types with the same rate for each bond, producing connected components made of particles of both types. We analyze and solve the Smoluchowski coagulation system of equations obtained as a hydrodynamic limit of the corresponding Marcus-Lushnikov process. We establish that the cross-multiplicative kernel is a gelling kernel, and find the gelation time. As an applicat…
Duality plays an important role in population genetics. It can relate results from forwards-in-time models of allele frequency evolution with those of backwards-in-time genealogical models; a well known example is the duality between the Wright-Fisher diffusion for genetic drift and its genealogical counterpart, the coalescent. There have been a number of articles extending this relationship to include other evolutionary processes such as mutation and selection, but little has been explored for models also incorporating crossover recombination. Here, we derive from first principles a new genea…
Suppose $Π$ is an exchangeable random partition of the positive integers and $Π_n$ is its restriction to $\{1, ..., n\}$. Let $K_n$ denote the number of blocks of $Π_n$, and let $K_{n,r}$ denote the number of blocks of $Π_n$ containing $r$ integers. We show that if $0 < α< 1$ and $K_n/(n^α \ell(n))$ converges in probability to $Γ(1-α)$, where $\ell$ is a slowly varying function, then $K_{n,r}/(n^α \ell(n))$ converges in probability to $αΓ(r - α)/r!$. This result was previously known when the convergence of $K_n/(n^α \ell(n))$ holds almost surely, but the result under the hypothesis of converge…
This article shows the asymptotics of distribution and moments of the size $X_n$ of the minimal clade of a randomly chosen individual in a Bolthausen-Sznitman $n$-coalescent for $n\to\infty$. The Bolthausen-Sznitman $n$-coalescent is a Markov process taking states in the set of partitions of $\left\{1,\ldots,n\right\}$, where $1,\ldots,n$ are referred to as individuals. The minimal clade of an individual is the equivalence class the individual is in at the time of the first coalescence event this individual participates in.\\ The main tool used is the connection of the Bolthausen-Sznitman $n$-…
The Ewens sampling formula was firstly introduced in the context of population genetics by Warren John Ewens in 1972, and has appeared in a lot of other scientific fields. There are abundant approximation results associated with the Ewens sampling formula especially when one of the parameters, the sample size $n$ or the mutation parameter $θ$ which denotes the scaled mutation rate, tends to infinity while the other is fixed. By contrast, the case that $θ$ grows with $n$ has been considered in a relatively small number of works, although this asymptotic setup is also natural. In this paper, whe…
In this paper, we review recent results of ours concerning branching processes with general lifetimes and neutral mutations, under the infinitely many alleles model, where mutations can occur either at birth of individuals or at a constant rate during their lives. In both models, we study the allelic partition of the population at time t. We give closed formulae for the expected frequency spectrum at t and prove pathwise convergence to an explicit limit, as t goes to infinity, of the relative numbers of types younger than some given age and carried by a given number of individuals (small famil…
In this paper we show the existence of the minimal solution to the multidimensional Lambert-Euler inversion, a multidimensional generalization of $[-e^{-1} ,0)$ branch of Lambert W function $W_0(x)$. Specifically, for a given nonnegative irreducible symmetric matrix $V \in \mathbb{R}^{k \times k}$, we show that for ${\bf u}\in(0,\infty)^k$, if equation $$y_j \exp\{-{\bf e}_j^T V {\bf y} \} = u_j ~~~~~~\forall j=1,...,k,$$ has at least one solution, it must have a minimal solution ${\bf y}^*$, where the minimum is achieved in all coordinates $y_j$ simultaneously. Moreover, such ${\bf y}^*$ is t…
We consider a population model where individuals behave independently from each other and whose genealogy is described by a chronological tree called splitting tree. The individuals have i.i.d. (non-exponential) lifetime durations and give birth at constant rate to clonal or mutant children in an infinitely many alleles model with neutral mutations. First, to study the allelic partition of the population, we are interested in its frequency spectrum, which, at a fixed time, describes the number of alleles carried by a given number of individuals and with a given age. We compute the expected val…
Similarly as in (Blancas et al. 2018) where nested coalescent processes are studied, we generalize the definition of partition-valued homogeneous Markov fragmentation processes to the setting of nested partitions, i.e. pairs of partitions $(ζ,ξ)$ where $ζ$ is finer than $ξ$. As in the classical univariate setting, under exchangeability and branching assumptions, we characterize the jump measure of nested fragmentation processes, in terms of erosion coefficients and dislocation measures. Among the possible jumps of a nested fragmentation, three forms of erosion and two forms of dislocation are …
We consider the exchangeable fragmentation-coagulation (EFC) processes, where the coagulations are multiple and not simultaneous, as in a $Λ$-coalescent, and the fragmentations dislocate at finite rate an individual block into sub-blocks of infinite size. Sufficient conditions are found for the block-counting process to explode (i.e. to reach $\infty$) or not and for infinity to be an exit boundary or an entrance boundary. In a case of regularly varying fragmentation and coagulation mechanisms, we find regimes where the boundary $\infty$ can be either an exit, an entrance or a regular boundary…
