When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace their ancestral lines backwards in time, many lineages may coalesce almost instantaneously at the time of a selective sweep. We show that as the population size goes to infinity, this process converges to a coalescent process called a coalescent with multiple collisions. A better approximation for finite populations can be obtained using a coalescent with simultaneous multiple collisions. We also show how these coalescent approximations can be used to get insight into how beneficial mutations affect the behavior of statistics that have been used to detect departures from the usual Kingman's coalescent.
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…
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…
Consider a population evolving from year to year through three seasons: spring, summer and winter. Every spring starts with $N$ dormant individuals waking up independently of each other according to a given distribution. Once an individual is awake, it starts reproducing at a constant rate. By the end of spring, all individuals are awake and continue reproducing independently as Yule processes during the whole summer. In the winter, $N$ individuals chosen uniformly at random go to sleep until the next spring, and the other individuals die. We show that because an individual that wakes up unusu…
We define and analyze a coalescent process as a recursive box-filling process whose genealogy is given by an ancestral time-reversed, time-inhomogeneous Bienyamé-Galton-Watson process. Special interest is on the expected size of a typical box and its probability of being empty. Special cases leading to exact asymptotic computations are investigated when the coalescing mechanisms are either linear-fractional or quadratic.
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…
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.
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 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…
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).
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 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…
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.
At time 0, start a time-continuous binary branching process, where particles give birth to a single particle independently (at a possibly time-dependent rate) and die independently (at a possibly time-dependent and age-dependent rate). A particular case is the classical birth--death process. Stop this process at time $T>0$. It is known that the tree spanned by the $N$ tips alive at time $T$ of the tree thus obtained (called reduced tree or coalescent tree) is a coalescent point process (CPP), which basically means that the depths of interior nodes are iid. Now select each of the $N$ tips indep…
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 …
We investigate the behaviour of the genealogy of a Wright-Fisher population model under the influence of a strong seed-bank effect. More precisely, we consider a simple seed-bank age distribution with two atoms, leading to either classical or long genealogical jumps (the latter modeling the effect of seed-dormancy). We assume that the length of these long jumps scales like a power $N^β$ of the original population size $N$, thus giving rise to a `strong' seed-bank effect. For a certain range of $β$, we prove that the ancestral process of a sample of $n$ individuals converges under a non-classic…
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…
We review recent progress in the understanding of the role of multiple- and simultaneous multiple merger coalescents as models for the genealogy in idealised and real populations with exceptional reproductive behaviour. In particular, we discuss models with `skewed offspring distribution' (or under other non-classical evolutionary forces) which lead in the single locus haploid case to multiple merger coalescents, and in the multi-locus diploid case to simultaneous multiple merger coalescents. Further, we discuss inference methods under the infinitely-many sites model which allow both model sel…
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…
We consider a system of particles which perform branching Brownian motion with negative drift and are killed upon reaching zero, in the near-critical regime where the total population stays roughly constant with approximately N particles. We show that the characteristic time scale for the evolution of this population is of order $(\log N)^3$, in the sense that when time is measured in these units, the scaled number of particles converges to a variant of Neveu's continuous-state branching process. Furthermore, the genealogy of the particles is then governed by a coalescent process known as the …
We consider a model of a population of fixed size $N$ undergoing selection. Each individual acquires beneficial mutations at rate $μ_N$, and each beneficial mutation increases the individual's fitness by $s_N$. Each individual dies at rate one, and when a death occurs, an individual is chosen with probability proportional to the individual's fitness to give birth. Under certain conditions on the parameters $μ_N$ and $s_N$, we show that the genealogy of the population can be described by the Bolthausen-Sznitman coalescent. This result confirms predictions of Desai, Walczak, and Fisher (2013), a…
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…
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…
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.
When two (possibly different in distribution) continuous-state branching processes with immigration are present, we study the relative frequency of one of them when the total mass is forced to be constant at a dense set of times. This leads to a SDE whose unique strong solution will be the definition of a $Λ$-asymmetric frequency process ($Λ$-AFP). We prove that it is a Feller process and we calculate a large population limit when the total mass tends to infinity. This allows us to study the fluctuations of the process around its deterministic limit. Furthermore, we find conditions for the $Λ$…
We study the genealogy of a solvable population model with $N$ particles on the real line which evolves according to a discrete-time branching process with selection. At each time step, every particle gives birth to children around $a$ times its current position, where $a>0$ is a parameter of the model. Then, the $N$ rightmost new-born children are selected to form the next generation. We show that the genealogical trees of the process converge to those of a Beta coalescent as $N \to \infty$. The process we consider can be seen as a toy-model version of a continuous-time branching process with…
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…
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 …
Coalescents with multiple collisions (also called Lambda-coalescents or simple exchangeable coalescents) are used as models of genealogies. We study a new class of Markovian coalescent processes connected to a population model with immigration. Imagine an infinite population with immigration labelled at each generation by N:={1,2,...}. Some ancestral lineages cannot be followed backwards after some time because their ancestor is outside the population. The individuals with an immigrant ancestor constitute a distinguished family and we define exchangeable distinguished coalescent processes as a…
We study a population model of fixed size undergoing strong selection where individuals accumulate beneficial mutations, namely the Moran model with selection. In a specific setting with strong selection, Schweinsberg showed that the genealogy of the population is described by the so-called Bolthausen-Sznitman's coalescent. In this paper we sophisticate the model by splitting the population into two adversarial subgroups, that can be interpreted as two different alleles, one of which has a weak selective advantage over the other. We show that the proportion of disadvantaged individuals converg…
We present a robust method which translates information on the speed of coming down from infinity of a genealogical tree into sampling formulae for the underlying population. We apply these results to population dynamics where the genealogy is given by a Lambda-coalescent. This allows us to derive an exact formula for the asymptotic behavior of the site and allele frequency spectrum and the number of segregating sites, as the sample size tends to infinity. Some of our results hold in the case of a general Lambda-coalescent that comes down from infinity, but we obtain more precise information u…
The $N$-particle branching random walk is a discrete time branching particle system with selection. We have $N$ particles located on the real line at all times. At every time step each particle is replaced by two offspring, and each offspring particle makes a jump of non-negative size from its parent's location, independently from the other jumps, according to a given jump distribution. Then only the $N$ rightmost particles survive; the other particles are removed from the system to keep the population size constant. Inspired by work of J. Bérard and P. Maillard, we examine the long term behav…
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…
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.…
{\bf Abstract} The trajectory of the frequency of an allele which begins at $x$ at time $0$ and is known to have frequency $z$ at time $T$ can be modelled by the bridge process of the Wright-Fisher diffusion. Bridges when $x=z=0$ are particularly interesting because they model the trajectory of the frequency of an allele which appears at a time, then is lost by random drift or mutation after a time $T$. The coalescent genealogy back in time of a population in a neutral Wright-Fisher diffusion process is well understood. In this paper we obtain a new interpretation of the coalescent genealogy o…
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 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…
Consider a continuous-state branching population constructed as a flow of nested subordinators. Inverting the subordinators and reversing time give rise to a flow of coalescing Markov processes (with negative jumps) which correspond to the ancestral lineages of individuals in the current generation. The process of the ancestral lineage of a fixed individual is the Siegmund dual process of the continuous-state branching process. We study its semi-group, its long-term behavior and its generator. In order to follow the coalescences in the ancestral lineages and to describe the backward genealogy …
Consider a haploid population of fixed finite size with a finite number of allele types and having Cannings exchangeable genealogy with neutral mutation. The stationary distribution of the Markov chain of allele counts in each generation is an important quantity in population genetics but has no tractable description in general. We provide upper bounds on the distributional distance between the Dirichlet distribution and this finite population stationary distribution for the Wright-Fisher genealogy with general mutation structure and the Cannings exchangeable genealogy with parent independent …
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…
This paper extends earlier work by Cox and Durrett, who studied the coalescence times for two lineages in the stepping stone model on the two-dimensional torus. We show that the genealogy of a sample of size n is given by a time change of Kingman's coalescent. With DNA sequence data in mind, we investigate mutation patterns under the infinite sites model, which assumes that each mutation occurs at a new site. Our results suggest that the spatial structure of the human population contributes to the haplotype structure and a slower than expected decay of genetic correlation with distance reveale…
We consider a branching population where individuals live and reproduce independently. Their lifetimes are i.i.d. and they give birth at a constant rate b. The genealogical tree spanned by this process is called a splitting tree, and the population counting process is a homogeneous, binary Crump-Mode-Jagers process. We suppose that mutations affect individuals independently at a constant rate $\θ$ during their lifetimes, under the infinite-alleles assumption: each new mutation gives a new type, called allele, to his carrier. We study the allele frequency spectrum which is the numbers A(k, t) o…
We study two types of stochastic processes, a mean-field spatial system of interacting Fisher-Wright diffusions with an inferior and an advantageous type with rare mutation (inferior to advantageous) and a (mean-field) spatial system of supercritical branching random walks with an additional deathrate which is quadratic in the local number of particles. The former describes a standard two-type population under selection, mutation, the latter models describe a population under scarce resources causing additional death at high local population intensity. Geographic space is modelled by $\{1, \cd…
