If we follow an asexually reproducing population through time, then the amount of time that has passed since the most recent common ancestor (MRCA) of all current individuals lived will change as time progresses. The resulting "MRCA age" process has been studied previously when the population has a constant large size and evolves via the diffusion limit of standard Wright--Fisher dynamics. For any population model, the sample paths of the MRCA age process are made up of periods of linear upward drift with slope +1 punctuated by downward jumps. We build other Markov processes that have such paths from Poisson point processes on $\mathbb{R}_{++}\times\mathbb{R}_{++}$ with intensity measures of the form $λ\otimesμ$ where $λ$ is Lebesgue measure, and $μ$ (the "family lifetime measure") is an arbitrary, absolutely continuous measure satisfying $μ((0,\infty))=\infty$ and $μ((x,\infty))<\infty$ for all $x>0$. Special cases of this construction describe the time evolution of the MRCA age in $(1+β)$-stable continuous state branching processes conditioned on nonextinction--a particular case of which, $β=1$, is Feller's continuous state branching process conditioned on nonextinction. As well as the continuous time process, we also consider the discrete time Markov chain that records the value of the continuous process just before and after its successive jumps. We find transition probabilities for both the continuous and discrete time processes, determine when these processes are transient and recurrent and compute stationary distributions when they exist.
We present an elementary model of random size varying population given by a stationary continuous state branching process. For this model we compute the joint distribution of: the time to the most recent common ancestor, the size of the current population and the size of the population just before the most recent common ancestor (MRCA). In particular we show a natural mild bottleneck effect as the size of the population just before the MRCA is stochastically smaller than the size of the current population. We also compute the number of old families which corresponds to the number of individual…
We consider a stationary continuous model of random size population with non-neutral mutations using a continuous state branching process with non-homogeneous immigration. We assume the type (or mutation) of the immigrants is random given by a constant mutation rate measure. We determine some genealogical properties of this process such as: distribution of the time to the most recent common ancestor (MRCA), bottleneck effect at the time to the MRCA (which might be drastic for some mutation rate measures), favorable type for the MRCA, asymptotics of the number of ancestors.
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…
Genetic contribution of advantaged ancestors in the biparental Moran model -- finite selection
Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay（巴黎萨克雷大学、农业巴黎技术学院、法国国家农业食品环境研究院）；Université Paris-Saclay, CNRS, Laboratoire de mathématiques d’Orsay（巴黎萨克雷大学、法国国家科学研究中心）
Using graphical methods based on a `lookdown' and pruned version of the {\em ancestral selection graph}, we obtain a representation of the type distribution of the ancestor in a two-type Wright-Fisher population with mutation and selection, conditional on the overall type frequency in the old population. This extends results from Lenz, Kluth, Baake, and Wakolbinger (Theor. Pop. Biol., 103 (2015), 27-37) to the case of heavy-tailed offspring, directed by a reproduction measure $Λ$. The representation is in terms of the equilibrium tail probabilities of the line-counting process $L$ of the graph…
Consider the population model with infinite size associated to subcritical continuous-state branching processes (CSBP). Individuals reproduce independently according to the same subcritical offspring distribution. We study the long-term behaviour of the ancestral lineages as time goes to the past and show that the flow of ancestral lineages, properly renormalized, converges almost surely to the inverse of a drift-free subordinator whose Laplace exponent is explicit in terms of the branching mechanism. We provide an interpretation in terms of the genealogy of the population. In particular, we s…
Perfect simulation of an one-dimensional loss network on $\R$ with length distribution $π$ and cable capacity $C$ is performed using the clan of ancestors method. Domination of the clan of ancestors by a branching process with longer memory improves the sufficient conditions for the perfect scheme to be applicable.
We consider the Moran model in continuous time with two types, mutation, and selection. We concentrate on the ancestral line and its stationary type distribution. Building on work by Fearnhead (J. Appl. Prob. 39 (2002), 38-54) and Taylor (Electron. J. Probab. 12 (2007), 808-847), we characterise this distribution via the fixation probability of the offspring of all individuals of favourable type (regardless of the offspring's types). We concentrate on a finite population and stay with the resulting discrete setting all the way through. This way, we extend previous results and gain new insight …
Critical branching processes in a varying environment behave much the same as critical Galton-Watson processes. In this note we like to confirm this finding with regard to the underlying genealogical structures. In particular, we consider the most recent common ancestor given survival and the corresponding reduced branching processes, in the spirit of Zubkov (1975) and Fleischmann and Siegmund-Schultze (1977).
This paper considers the relative frequencies of distinct types of individuals in multitype branching processes. We prove that the frequencies are asymptotically multivariate normal when the initial number of ancestors is large and the time of observation is fixed. The result is valid for any branching process with a finite number of types; the only assumption required is that of independent individual evolutions. The problem under consideration is motivated by applications in the area of cell biology. Specifically, the reported limiting results are of advantage in cell kinetics studies where …
Coalescence processes have received a lot of attention in the context of conditional branching processes with fixed population size and non-overlapping generations. Here we focus on similar problems in the context of the standard unconditional Bienaymé-Galton-Watson branching processes, either (sub)-critical or supercritical. Using an analytical tool, we derive the structure of some counting aspects of the ancestral genealogy of such processes, including: the transition matrix of the ancestral count process and an integral representation of various coalescence times distributions, such as the …
We study the common ancestor type distribution in a $2$-type Moran model with population size $N$, mutation and selection, and in the deterministic limit regime arising in the former when $N$ tends to infinity, without any rescaling of parameters or time. In the finite case, we express the common ancestor type distribution as a weighted sum of combinatorial terms, and we show that the latter converges to an explicit function. Next, we recover the previous results through pruning of the ancestral selection graph (ASG). The notions of relevant ASG, finite and asymptotic pruned lookdown ASG permi…
Motivated as a null model for comparison with data, we study the following model for a phylogenetic tree on $n$ extant species. The origin of the clade is a random time in the past, whose (improper) distribution is uniform on $(0,\infty)$. After that origin, the process of extinctions and speciations is a continuous-time critical branching process of constant rate, conditioned on having the prescribed number $n$ of species at the present time. We study various mathematical properties of this model as $n \to \infty$ limits: time of origin and of most recent common ancestor; pattern of divergenc…
We consider the population model associated to continuous state branching processes and we are interested in the so-called Eve property that asserts the existence of an ancestor with an overwhelming progeny at large times, and more generally, in the possible behaviours of the frequencies among the population at large times. In this paper, we classify all the possible behaviours according to the branching mechanism of the continuous state branching process.
We prove the existence of the total length process for the genealogical tree of a population model with random size given by a quadratic stationary continuous-state branching processes. We also give, for the one-dimensional marginal, its Laplace transform as well as the fluctuation of the corresponding convergence. This result is to be compared with the one obtained by Pfaffelhuber and Wakolbinger for constant size population associated to the Kingma coalescent. We also give a time reversal property of the number of ancestors process at all time, and give a description of the so-called lineage…
We encode the genealogy of a continuous-state branching process associated with a branching mechanism $Ψ$ - or $Ψ$-CSBP in short - using a stochastic flow of partitions. This encoding holds for all branching mechanisms and appears as a very tractable object to deal with asymptotic behaviours and convergences. In particular we study the so-called Eve property - the existence of an ancestor from which the entire population descends asymptotically - and give a necessary and sufficient condition on the $Ψ$-CSBP for this property to hold. Finally, we show that the flow of partitions unifies the loo…
Consider a population of fixed size that evolves over time. At each time, the genealogical structure of the population can be described by a coalescent tree whose branches are traced back to the most recent common ancestor of the population. As time goes forward, the genealogy of the population evolves, leading to what is known as an evolving coalescent. We will study the evolving coalescent for populations whose genealogy can be described by the Bolthausen-Sznitman coalescent. We obtain the limiting behavior of the evolution of the time back to the most recent common ancestor and the total le…
We provide sufficient conditions for polynomial rate of convergence in the weak law of large numbers for supercritical general indecomposable multi-type branching processes. The main result is derived by investigating the embedded single-type process composed of all individuals having the same type as the ancestor. As an important intermediate step, we determine the (exact) polynomial rate of convergence of Nerman's martingale in continuous time to its limit. The techniques used also allow us to give streamlined proofs of the weak and strong laws of large numbers and ratio convergence for the …
We continue our study of the distribution of the maximal number $X^{\ast}_k$ of offsprings amongst all individuals in a critical Galton-Watson process started with $k$ ancestors, treating the case when the reproduction law has a regularly varying tail $\bar F$ with index $-α$ for $α>2$ (and hence finite variance). We show that $X^{\ast}_k$ suitably normalized converges in distribution to a Frechet law with shape parameter $α/2$; this contrasts sharply with the case $1<α<2$ when the variance is infinite. More generally, we obtain a weak limit theorem for the offspring sequence ranked in the dec…
We define a multi-type coalescent point process of a general branching process with finitely many types. This multi-type coalescent fully describes the genealogy of the (quasi-stationary) standing population, providing types along ancestral lineages of all individuals in the standing population. We show that this point-process is a functional of a certain Markov chain defined by the planar embedding of the branching process. This Markov chain is further used to determine statistical properties of the ancestral tree, such as the time to the most recent common ancestor (MRCA) of two consecutive …
We provide a many-to-few formula in the general setting of non-local branching Markov processes. This formula allows one to compute expectations of k-fold sums over functions of the population at k different times. The result generalises [14] to the non-local setting, as introduced in [11] and [8]. As an application, we consider the case when the branching process is critical, and conditioned to survive for a large time. In this setting, we prove a general formula for the limiting law of the death time of the most recent common ancestor of two particles selected uniformly from the population a…
The objective of this paper is the study of the equilibrium behavior of a population on the hierarchical group $Ω_N$ consisting of families of individuals undergoing critical branching random walk and in addition these families also develop according to a critical branching process. Strong transience of the random walk guarantees existence of an equilibrium for this two-level branching system. In the limit $N\to\infty$ (called the hierarchical mean field limit), the equilibrium aggregated populations in a nested sequence of balls $B^{(N)}_\ell$ of hierarchical radius $\ell$ converge to a backw…
Let $\{\mm_n, n=0,1,...\}$ be the supercritical branching random walk starting with one initial ancestor located at the origin of the real line. For $n=0,1,...$ let $W_n$ be the moment generating function of $\mm_n$ normalized by its mean. Denote by $AW_n$ any of the following random variables: maximal function, square function, $L_1$ and a.s. limit $W$, $\su |W-W_n|$, $\su |W_{n+1}-W_n|$. Under mild moment restrictions and the assumption that $\rP\{W_1>x\}$ regularly varies at $\infty$ it is proved that $\rP\{AW_n>x\}$ regularly varies at $\infty$ with the same exponent. All the proofs given …
A decomposable strongly critical Galton-Watson branching process with $N$ types of particles labelled $1,2,...,N$ is considered in which a type~$i$ parent may produce individuals of types $j\geq i$ only. This model may be viewed as a stochastic model for the sizes of a geographically structured population occupying $N$ islands, the location of a particle being considered as its type. The newborn particles of island $i\leq N-1$ either stay at the same island or migrate, just after their birth to the islands $% i+1,i+2,...,N$. Particles of island $N$ do not migrate. We investigate the structure …
We consider the diffusion approximation of branching processes in random environment (BPREs). This diffusion approximation is similar to and mathematically more tractable than BPREs. We obtain the exact asymptotic behavior of the survival probability. As in the case of BPREs, there is a phase transition in the subcritical regime due to different survival opportunities. In addition, we characterize the process conditioned to never go extinct and establish a backbone construction. In the strongly subcritical regime, mean offspring numbers are increased but still subcritical in the process condit…
Conditions for almost sure extinction are studied in discrete time branching processes with an infinite number of types. It is not assumed that the expected number of children is a bounded function of the parent's type. There might also be no integer m such that there is a lower positive bound, uniform over the ancestor's type, for the probability that a population is extinct at the m-th generation. A weaker condition than the existence of such an m is seen to lead to extinction almost surely if the sequence of expected generation sizes does not tend to infinity. Some criteria for a positive p…
We associate with a Bienayme-Galton-Watson branching process a family tree rooted at the ancestor. For a positive integer N, define a complete N-ary tree to be the family tree of a deterministic branching process with offspring generating function s^N. We study the random variables V(N,n) and V(N) counting the number of disjoint complete N-ary subtrees, rooted at the ancestor, and having height n and infinity, respectively. Dekking (1991) and Pakes and Dekking (1991) find recursive relations for Pr(V(N,n)>0) and Pr(V(N)>0) involving the offspring probability generation function (pgf) and its d…
Quasispecies theory predicts that there is a critical mutation probability above which a viral population will go extinct. Above this threshold the virus loses the ability to replicate the best adapted genotype, leading to a population composed of low replicating mutants that is eventually doomed. We propose a new branching model that shows that this is not necessarily so. That is, a population composed of ever changing mutants may survive.
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 consider a class of density-dependent branching processes which generalises exponential, logistic and Gompertz growth. A population begins with a single individual, grows exponentially initially, and then growth may slow down as the population size moves towards a carrying capacity. At a time while the population is still growing superlinearly, a fixed number of individuals are sampled and their coalescent tree is drawn. Taking the sampling time and carrying capacity simultaneously to infinity, we prove convergence of the coalescent tree to a limiting tree which is in a sense universal over…
We study the evolution of the population genealogy in the classic neutral Moran Model of finite size and in discrete time. The stochastic transformations that shape a Moran population can be realized directly on its genealogy and give rise to a process with a state space consisting of the finite set of Yule trees of a certain size. We derive a number of properties of this process, and show that they are in agreement with existing results on the infinite-population limit of the Moran Model. Most importantly, this process admits time reversal, which gives rise to another tree-valued Markov Chain…
We consider a birth and death process in which death is due to both `natural death' and to competition between individuals, modelled as a quadratic function of population size. The resulting `logistic branching process' has been proposed as a model for numbers of individuals in populations competing for some resource, or for numbers of species. However, because of the quadratic death rate, even if the intrinsic growth rate is positive, the population will, with probability one, die out in finite time. There is considerable interest in understanding the process conditioned on non-extinction. In…
Branching Processes in Random Environment (BPREs) $(Z_n:n\geq0)$ are the generalization of Galton-Watson processes where in each generation the reproduction law is picked randomly in an i.i.d. manner. In the supercritical case, the process survives with positive probability and then almost surely grows geometrically. This paper focuses on rare events when the process takes positive but small values for large times. We describe the asymptotic behavior of $\mathbb{P}(1 \leq Z_n \leq k|Z_0=i)$, $k,i\in\mathbb{N}$ as $n\rightarrow \infty$. More precisely, we characterize the exponential decrease o…
We consider a Galton-Watson process $\mathbf{Z}% (n)=(Z_{1}(n),Z_{2}(n))$ with two types of particles. Particles of type 2 may produce offspring of both types while particles of type 1 may produce particles of their own type only. Let $Z_{i}(m,n)$ be the number of particles of type $i$ at time $m<n$ having offspring at time $n$. Assuming that the process is critical and that the variance of the offspring distribution may be infinite we describe the asymptotic behavior, as $m,n\rightarrow \infty $ of the law of $\mathbf{Z}(m,n)=(Z_1(m,n),Z_2(m,n))$ given $\mathbf{Z}(n)\neq \mathbf{0}$. We find …
We consider two versions of stochastic population models with mutation and selection. The first approach relies on a multitype branching process; here, individuals reproduce and change type (i.e., mutate) independently of each other, without restriction on population size. We analyze the equilibrium behaviour of this model, both in the forward and in the backward direction of time; the backward point of view emerges if the ancestry of individuals chosen randomly from the present population is traced back into the past. The second approach is the Moran model with selection. Here, the population…
In this paper, we investigate the consequences of dormancy in the `rare mutation' and `large population' regime of stochastic adaptive dynamics. Starting from an individual-based micro-model, we first derive the polymorphic evolution sequence of the population, based on previous work by Baar and Bovier (2018). After passing to a second `small mutations' limit, we arrive at the canonical equation of adaptive dynamics, and state a corresponding criterion for evolutionary branching, extending a previous result of Champagnat and Méléard (2011). The criterion allows a quantitative and qualitative a…
We consider a branching process with Poissonian immigration where individuals have inheritable types. At rate theta, new individuals singly enter the total population and start a new population which evolves like a supercritical, homogeneous, binary Crump-Mode-Jagers process: individuals have i.i.d. lifetimes durations (non necessarily exponential) during which they give birth independently at constant rate b. First, using spine decomposition, we relax previously known assumptions required for a.s. convergence of total population size. Then, we consider three models of structured populations: …
Branching Brownian Motion describes a system of particles which diffuse in space and split into offsprings according to a certain random mechanism. In virtue of the groundbreaking work by M. Bramson on the convergence of solutions of the Fisher-KPP equation to traveling waves, the law of the rightmost particle in the limit of large times is rather well understood. In this work, we address the full statistics of the extremal particles (first-, second-, third- etc. largest). In particular, we prove that in the large $t-$limit, such particles descend with overwhelming probability from ancestors h…
We study a universal object for the genealogy of a sample in populations with mutations: the critical birth-death process with Poissonian mutations, conditioned on its population size at a fixed time horizon. We show how this process arises as the law of the genealogy of a sample in a large class of critical branching populations with mutations at birth, namely populations converging, in a large population asymptotic, towards the continuum random tree. We extend this model to populations with random foundation times, with (potentially improper) prior distributions g_i: x\mapsto x^{-i}, i\in\Z_…
Under the assumption that the initial population size of a Galton-Watson branching process increases to infinity, the paper studies asymptotic behavior of the population size before extinction. More specifically, we establish asymptotic properties of the conditional moments (which are exactly defined in the paper).
Identifying the critical domain size necessary for a population to persist is an important question in ecology. Both demographic and environmental stochasticity impact a population's ability to persist. Here we explore ways of including this variability. We study populations which have traditionally been modelled using a deterministic integrodifference equation (IDE) framework, with distinct dispersal and sedentary stages. Individual based models (IBMs) are the most intuitive stochastic analogues to IDEs but yield few analytic insights. We explore two alternate approaches; one is a scaling up …
In this paper we study a two-level branching model for virus populations under cell division. We assume that the cells are carrying virus populations which evolve as a branching particle system with competition, while the cells split according to a Yule process thereby dividing their virus populations into two independently evolving sub-populations. We then assume that sizes of the virus populations are huge and characterize the fast branching rate and huge population density limit as the solution of a well-posed martingale problem. While verifying tightness is quite standard, we provide a Fey…
We consider a continuous-time branching random walk on a multidimensional lattice in a random branching medium. It is theoretically known that, in such branching random walks, large rare fluctuations of the medium may lead to anomalous properties of a particle field, e.g., such as intermittency. However, the time intervals on which this intermittency phenomenon can be observed are very difficult to estimate in practice. In this paper, branching media containing only a finite and non-finite number of branching sources are considered. The evolution of the mean number of particles with a random p…
We obtain a representation of Feller's branching diffusion with logistic growth in terms of the local times of a reflected Brownian motion $H$ with a drift that is affine linear in the local time accumulated by $H$ at its current level. As in the classical Ray-Knight representation, the excursions of $H$ are the exploration paths of the trees of descendants of the ancestors at time $t=0$, and the local time of $H$ at height $t$ measures the population size at time $t$ (see e.g. \cite{LG4}). We cope with the dependence in the reproduction by introducing a pecking order of individuals: an indivi…
The paper has four goals. First, we want to generalize the classical concept of the branching property so that it becomes applicable for historical and genealogical processes (using the coding of genealogies by ($V$-marked) ultrametric measure spaces leading to state spaces $\mathbb{U}$ resp. $\mathbb{U}^V$). The processes are defined by well-posed martingale problems. In particular we want to complement the corresponding concept of infinite divisibility developed in \cite{infdiv} for this context. Second one of the two main points, we want to find a corresponding characterization of the gener…
We construct a modified continuous-state branching process whose Malthusian parameter is replaced by another when passing below a certain level. The construction is obtained via a Lamperti-like transform applied to a refracted Lévy process. Infinitesimal generator, probability of vanishing at infinity, of explosion and some path properties are also provided.
We study the maximal displacement and related population for a branching Brownian motion in Euclidean space in terms of the principal eigenvalue of an associated Schrödinger type operator. We first determine their growth rates on the survival event. We then establish the upper deviation for the maximal displacement under the possibility of extinction. Under the non-extinction condition, we further discuss the decay rate of the upper deviation probability and the population growth at the critical phase.
In this note we consider a branching Brownian motion (BBM) on $\mathbb{R}$ in which a particle at spatial position $y$ splits into two at rate $βy^2$, where $β>0$ is a constant. This is a critical breeding rate for BBM in the sense that the expected population size blows up in finite time while the population size remains finite, almost surely, for all time. We find an asymptotic for the almost sure rate of growth of the population.
Motivated by sample path decomposition of the stationary continuous state branching process with immigration, a general population model is considered using the idea of immortal individual. We compute the joint distribution of the random variables: the time to the most recent common ancestor (MRCA), the size of the current population and the size of the population just before MRCA. We obtain the bottleneck effect as well. The distribution of the number of the oldest families is also established.
We consider a model of stationary population with random size given by a continuous state branching process with immigration with a quadratic branching mechanism. We give an exact elementary simulation procedure of the genealogical tree of $n$ individuals randomly chosen among the extant population at a given time. Then, we prove the convergence of the renormalized total length of this genealogical tree as $n$ goes to infinity, see also Pfaffelhuber, Wakolbinger and Weisshaupt (2011) in the context of a constant size population. The limit appears already in Bi and Delmas (2016) but with a diff…
We use a multitype continuous time Markov branching process model to describe the dynamics of the spread of parasites of two types that can mutate into each other in a common host population. Instead of using a single virulence characteristic which is typical of most mathematical models for infectious diseases, our model uses a combination of two characteristics: lethality and transmissibility. This makes the model capable of reproducing the empirically observed fact that the increase in the host density can lead to the prevalence of the more virulent pathogen type. We provide some numerical i…
