Consider the following stochastic model for immune response. Each pathogen gives birth to a new pathogen at rate $λ$. When a new pathogen is born, it has the same type as its parent with probability $1 - r$. With probability $r$, a mutation occurs, and the new pathogen has a different type from all previously observed pathogens. When a new type appears in the population, it survives for an exponential amount of time with mean 1, independently of all the other types. All pathogens of that type are killed simultaneously. Schinazi and Schweinsberg (2006) have shown that this model on $\Z^d$ behaves rather differently from its non-spatial version. In this paper, we show that this model on a homogeneous tree captures features from both the non-spatial version and the $\Z^d$ version. We also obtain comparison results between this model and the basic contact process on general graphs.
We are interested in the genealogical structure of alleles for a Bienaymé-Galton-Watson branching process with neutral mutations (infinite alleles model), in the situation where the initial population is large and the mutation rate small. We shall establish that for an appropriate regime, the process of the sizes of the allelic sub-families converges in distribution to a certain continuous state branching process (i.e. a Jirina process) in discrete time. Itô's excursion theory and the Léevy-Itô decomposition of subordinators provide fundamental insights for the results.
We consider supercritical Bernoulli bond percolation on a large $b$-ary tree, in the sense that with high probability, there exists a giant cluster. We show that the size of the giant cluster has non-gaussian fluctuations, which extends a result due to Schweinsberg in the case of random recursive trees. Using ideas in the recent work of Bertoin and Uribe Bravo, the approach developed in this work relies on the analysis of the sub-population with ancestral type in a system of branching processes with rare mutations, which may be of independent interest. This also allows us to establish the anal…
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 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…
We consider an initial Eve-population and a population of neutral mutants, such that the total population dies out in finite time. We describe the evolution of the Eve-population and the total population with continuous state branching processes, and the neutral mutation procedure can be seen as an immigration process with intensity proportional to the size of the population. First we establish a Williams' decomposition of the genealogy of the total population given by a continuous random tree, according to the ancestral lineage of the last individual alive. This allows us give a closed formul…
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 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.
The Fleming-Viot measure-valued diffusion is a Markov process describing the evolution of (allelic) types under mutation, selection and random reproduction. We enrich this process by genealogical relations of individuals so that the random type distribution as well as the genealogical distances in the population evolve stochastically. The state space of this tree-valued enrichment of the Fleming-Viot dynamics with mutation and selection (TFVMS) consists of marked ultrametric measure spaces, equipped with the marked Gromov-weak topology and a suitable notion of polynomials as a separating algeb…
In this paper we consider two continuous-mass population models as analogues of logistic branching random walks, one is supported on a finite trait space and the other one is supported on an infinite trait space. For the first model with nearest-neighbor competition and migration, we justify a well-described evolutionary path to the short-term equilibrium on a slow migration time scale. For the second one with an additional evolutionary mechanism-mutation, a jump process-trait substitution tree model is established under a combination of rare mutation and slow migration limits. The transition …
We consider a supercritical branching population, where individuals have i.i.d. lifetime durations (which are not necessarily exponentially distributed) and give birth (singly) at constant rate. We assume that individuals independently experience neutral mutations, at constant rate $θ$ during their lifetimes, under the infinite-alleles assumption: each mutation instantaneously confers a brand new type, called allele or haplotype, to its carrier. The type carried by a mother at the time when she gives birth is transmitted to the newborn. We are interested in the sizes and ages at time $t$ of th…
We consider a neutral dynamical model of biological diversity, where individuals live and reproduce independently. They have i.i.d. lifetime durations (which are not necessarily exponentially distributed) and give birth (singly) at constant rate b. Such a genealogical tree is usually called a splitting tree, and the population counting process (N_t;t\ge 0) is a homogeneous, binary Crump--Mode--Jagers process. We assume that individuals independently experience mutations at constant rate θduring their lifetimes, under the infinite-alleles assumption: each mutation instantaneously confers a bran…
We consider a Yule process until the total population reaches size $n\gg 1$, and assume that neutral mutations occur with high probability $1-p$ (in the sense that each child is a new mutant with probability $1-p$, independently of the other children), where $p=p_n\ll 1$. We establish a general strategy for obtaining Poisson limit laws for the number of subpopulations exceeding a given size and apply this to some mutation regimes of particular interest. Finally, we give an application to subcritical Bernoulli bond percolation on random recursive trees with percolation parameter $p_n$ tending t…
We consider branching random walks and contact processes on infinite, connected, locally finite graphs whose reproduction and infectivity rates across edges are inversely proportional to vertex degree. We show that when the ambient graph is a Galton-Watson tree then, in certain circumstances, the branching random walks and contact processes will have weak survival phases. We also provide bounds on critical values.
We study the supercritical contact process on Galton-Watson trees and periodic trees. We prove that if the contact process survives weakly then it dominates a supercritical Crump-Mode-Jagers branching process. Hence the number of infected sites grows exponentially fast. As a consequence we conclude that the contact process dies out at the critical value $λ_1$ for weak survival, and the survival probability $p(λ)$ is continuous with respect to the infection rate $λ$. Applying this fact, we show the contact process on a general periodic tree experiences two phase transitions in the sense that $λ…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data? Recently, identifiability results have appeared for networks relative to a model of sequence evolution that generalizes the standard Markov models used for phylogenetic trees. However, these results are…
In this paper we study the genealogical structure of a Galton-Watson process with neutral mutations, where the initial population is large and mutation rate is small \cite{B2}. Namely, we extend in two directions the results obtained in Bertoin's work. In the critical case, we construct the version of Bertoin's model conditioned not to be extinct, and in the case with finite variance we show convergence after normalization, of allelic sub-populations towards a tree indexed CSBP with immigration. Besides, we establish the version of the limit theorems in \cite{B2}, been for the unconditioned pr…
This paper is concerned with contact process with random vertex weights on regular trees, and study the asymptotic behavior of the critical infection rate as the degree of the trees increasing to infinity. In this model, the infection propagates through the edge connecting vertices $x$ and $y$ at rate $λρ(x)ρ(y)$ for some $λ>0$, where $\{ρ(x),{x\in T^d}\}$ are $i.i.d.$ vertex weights. We show that when $d$ is large enough there is a phase transition at $λ_c(d)\in(0,\infty)$ such that for $λ<λ_c(d)$ the contact process dies out, and for $λ>λ_c(d)$ the contact process survives with a positive pr…
A little over 25 years ago Pemantle pioneered the study of the contact process on trees, and showed that on homogeneous trees the critical values $λ_1$ and $λ_2$ for global and local survival were different. He also considered trees with periodic degree sequences, and Galton-Watson trees. Here, we will consider periodic trees in which the number of children in successive generation is $(n,a_1,\ldots, a_k)$ with $\max_i a_i \le Cn^{1-δ}$ and $\log(a_1 \cdots a_k)/\log n \to b$ as $n\to\infty$. We show that the critical value for local survival is asymptotically $\sqrt{c (\log n)/n}$ where $c=(k…
We consider a fitness-structured population model with competition and migration between nearest neighbors. Under a combination of large population and rare migration limits we are particularly interested in the asymptotic behavior of the total population partition on supporting trait sites. For the population without mutation on a finite trait space we obtain the equilibrium configuration and characterize the right time scale for fixation. For the model with mutation on an infinite trait space a jump process-trait substitution tree model is established on a rarer mutation time scale against t…
We consider the contact process with infection rate $λ$ on $\mathbb{T}_n^d$, the $d$-ary tree of height $n$. We study the extinction time $τ_{\mathbb{T}_n^d}$, that is, the random time it takes for the infection to disappear when the process is started from full occupancy. We prove two conjectures of Stacey regarding $τ_{\mathbb{T}_n^d}$. Let $λ_2$ denote the upper critical value for the contact process on the infinite $d$-ary tree. First, if $λ< λ_2$, then $τ_{\mathbb{T}_n^d}$ divided by the height of the tree converges in probability, as $n \to \infty$, to a positive constant. Second, if $λ>…
In this paper we are concerned with contact processes with random edge weights on rooted regular trees. We assign i.i.d weights on each edge on the tree and assume that an infected vertex infects its healthy neighbor at rate proportional to the weight on the edge connecting them. Under the annealed measure, we define the critical value λ_c as the maximum of the infection rate with which the process will die out and define λ_e as the maximum of the infection rate with which the process dies out at exponential rate. We show that these two critical values satisfy an identical limit theorem and gi…
We consider a random process on recursive trees, with three types of events. Vertices give birth at a constant rate (growth), each edge may be removed independently (fragmentation of the tree) and clusters (or trees) are frozen with a rate proportional to their sizes (isolation of connected component). A phase transition occurs when the isolation is able to stop the growth fragmentation process and cause extinction. When the process survives, the number of clusters increases exponentially and we prove that the normalized empirical measure of clusters a.s. converges to a limit law on recursive …
The contact process on an infinite homogeneous tree is shown to exhibit at least two phase transitions as the infection parameter lambda is varied. For small values of lambda a single infection eventually dies out. For larger lambda the infection lives forever with positive probability but eventually leaves any finite set. (The survival probability is a continuous function of lambda, and the proof of this is much easier than it is for the contact process on d-dimensional integer lattices.) For still larger lambda the infection converges in distribution to a nontrivial invariant measure. For an…
A little over 25 years ago Pemantle pioneered the study of the contact process on trees, and showed that the critical values $λ_1$ and $λ_2$ for global and local survival were different. Here, we will consider the case of trees in which the degrees of vertices are periodic. We will compute bounds on $λ_1$ and $λ_2$ and for the corresponding critical values $λ_g$ and $λ_\ell$ for branching random walk. Much of what we find for period two $(a,b)$ trees was known to Pemantle. However, two significant new results give sharp asymptotics for the critical value $λ_2$ of $(1,n)$ trees and generalize t…
We study the extinction time $\uptau$ of the contact process on finite trees of bounded degree. We show that, if the infection rate is larger than the critical rate for the contact process on $\Z$, then, uniformly over all trees of degree bounded by a given number, the expectation of $\uptau$ grows exponentially with the number of vertices. Additionally, for any sequence of growing trees of bounded degree, $\uptau$ divided by its expectation converges in distribution to the unitary exponential distribution. These also hold if one considers a sequence of graphs having spanning trees with unifor…
The key to our investigation is an improved (and in a sense sharp) understanding of the survival time of the contact process on star graphs. Using these results, we show that for the contact process on Galton-Watson trees, when the offspring distribution (i) is subexponential the critical value for local survival $λ_2=0$ and (ii) when it is geometric($p$) we have $λ_2 \le C_p$, where the $C_p$ are much smaller than previous estimates. We also study the critical value $λ_c(n)$ for "prolonged persistence" on graphs with $n$ vertices generated by the configuration model. In the case of power law …
In this paper we study threshold-one contact processes on lattices and regular trees. The asymptotic behavior of the critical infection rates as the degrees of the graphs growing to infinity are obtained. Defining λ_c as the supremum of infection rates which causes extinction of the process at equilibrium, we prove that nλ_c^{T^n}\rightarrow1 and 2dλ_c^{Z^d}\rightarrow1 as n,d\rightarrow+\infty. Our result is a development of the conclusion that λ_c^{Z^d}\leq\frac{2.18}{d} shown in \cite{Dur1991}. To prove our main result, a crucial lemma about the probability of a simple random walk on a latt…
We consider the tree-valued Fleming-Viot process, $(\mathcal X_t)_{t\geq 0}$, with mutation and selection as studied in Depperschmidt, Greven, Pfaffelhuber (2012). This process models the stochastic evolution of the genealogies and (allelic) types under resampling, mutation and selection in the population currently alive in the limit of infinitely large populations. Genealogies and types are described by (isometry classes of) marked metric measure spaces. The long-time limit of the neutral tree-valued Fleming-Viot dynamics is an equilibrium given via the marked metric measure space associated …
Recent progress in the study of the contact process [2] has verified that the extinction-survival threshold $λ_1$ on a Galton-Watson tree is strictly positive if and only if the offspring distribution $ξ$ has an exponential tail. In this paper, we derive the first-order asymptotics of $λ_1$ for the contact process on Galton-Watson trees and its corresponding analog for random graphs. In particular, if $ξ$ is appropriately concentrated around its mean, we demonstrate that $λ_1(ξ) \sim 1/\mathbb{E} ξ$ as $\mathbb{E}ξ\rightarrow \infty$, which matches with the known asymptotics on the $d$-regular…
In this paper, we consider the threshold-one contact process and the threshold-one voter model w/o spontaneous death on homogeneous trees $\mathbb{T}_d$, $d\ge 2$. Mainly inspired by the corresponding arguments for ordinary contact processes, we prove that the complete convergence theorem holds for these three systems under strong survival. When the systems survives weakly, complete convergence may also hold under certain transition and/or initial conditions.
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 …
Queensborough Community College, City University of New York（纽约城市大学皇后区社区学院）；University of Washington（华盛顿大学）
The tree reconstruction problem is to collect and analyze massive data at the $n$th level of the tree, to identify whether there is non-vanishing information of the root, as $n$ goes to infinity. Its connection to the clustering problem in the setting of the stochastic block model, which has wide applications in machine learning and data mining, has been well established. For the stochastic block model, an "information-theoretically-solvable-but-computationally-hard" region, or say "hybrid-hard phase", appears whenever the reconstruction bound is not tight of the corresponding reconstruction o…
We consider a supercritical branching process and define a contact tracing mechanism on its genealogical tree. We calculate the growth rate of the post tracing process, and give conditions under which the tracing is strong enough to drive the process to extinction.
We study the ergodic theory of a multitype contact process with equal death rates and unequal birth rates on the $d$-dimensional integer lattice and regular trees. We prove that for birth rates in a certain interval there is coexistence on the tree, which by a result of Neuhauser is not possible on the lattice. We also prove a complete convergence result when the larger birth rate falls outside of this interval.
We study the threshold $theta geq 2$ contact process on a homogeneous tree $T_b$ of degree $kappa = b + 1$, with infection parameter $lambda geq 0$ and started from a product measure with density $p$. The corresponding mean-field model displays a discontinuous transition at a critical point $lambda_c^{MF}(kappa,theta)$ and for $lambda geq lambda_c^{MF}(kappa,theta)$ it survives iff $p geq p_c^{MF}(kappa,theta,lambda)$, where this critical density satisfies $0 < p_c^{MF}(kappa,theta,lambda) < 1$, $lim_{lambda to infty} p_c^{MF}(kappa,theta,lambda) = 0$. For large $b$, we show that the process o…
We give a construction of a tree in which the contact process with any positive infection rate survives but, if a certain privileged edge $e^*$ is removed, one obtains two subtrees in which the contact process with infection rate smaller than $1/4$ dies out.
We consider the contact process with infection rate $λ$ on a random $(d+1)$-regular graph with $n$ vertices, $G_n$. We study the extinction time $τ_{G_n}$ (that is, the random amount of time until the infection disappears) as $n$ is taken to infinity. We establish a phase transition depending on whether $λ$ is smaller or larger than $λ_1(\mathbb{T}^d)$, the lower critical value for the contact process on the infinite, $(d+1)$-regular tree: if $λ< λ_1(\mathbb{T}^d)$, $τ_{G_n}$ grows logarithmically with $n$, while if $λ> λ_1(\mathbb{T}^d)$, it grows exponentially with $n$. This result differs f…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated genealogical tree is viewed both in the forward and the backward direction of time. The stationary type distribution of the reversed process, the so-called ancestral distribution, turns out as a key for the study of mutation-selection balance. This balance can be expressed in the form of a variational principle that quantifies the respective roles of reproduction and m…
We derive the asymptotic distribution of the total length $L_n$ of a $\operatorname {Beta}(2-α,α)$-coalescent tree for $1<α<2$, starting from $n$ individuals. There are two regimes: If $α\le1/2(1+\sqrt{5})$, then $L_n$ suitably rescaled has a stable limit distribution of index $α$. Otherwise $L_n$ just has to be shifted by a constant (depending on $n$) to get convergence to a nondegenerate limit distribution. As a consequence, we obtain the limit distribution of the number $S_n$ of segregation sites. These are points (mutations), which are placed on the tree's branches according to a Poisson p…
We propose the following simple stochastic model for phylogenetic trees. New types are born and die according to a birth and death chain. At each birth we associate a fitness to the new type sampled from a fixed distribution. At each death the type with the smallest fitness is killed. We show that if the birth (i.e. mutation) rate is subcritical we get a phylogenetic tree consistent with an influenza tree (few types at any given time and one dominating type lasting a long time). When the birth rate is supercritical we get a phylogenetic tree consistent with an HIV tree (many types at any given…
The existence of a weak survival region is established for the anisotropic symmetric contact process on a homogeneous tree T_{2d} of degree 2d > 2: For parameter values in a certain connected region of positive Lebesgue measure, the population survives forever with positive probability but ultimately vacates every finite subset of the tree with probability one. In this phase, infection trails must converge to the geometric boundary Ωof the tree. The random subset Λof the boundary consisting of all ends of the tree in which the infection survives, called the limit set of the process, is shown t…
We prove that the supercritical one-dimensional contact process survives in certain wedge-like space-time regions, and that when it survives it couples with the unrestricted contact process started from its upper invariant measure. As an application we show that a type of weak coexistence is possible in the nearest-neighbor ``grass-bushes-trees'' successional model introduced in Durrett and Swindle (1991).
We construct graphs (trees of bounded degree) on which the contact process has critical rate (which will be the same for both global and local survival) equal to any prescribed value between zero and $λ_c(\mathbb{Z})$, the critical rate of the one-dimensional contact process. We exhibit both graphs in which the process at this target critical value survives (locally) and graphs where it dies out (globally).
We introduce two models for multi-type random trees motivated by studies of trait dependence in the evolution of species. Our discrete time model, the multi-type ERM tree, is a generalization of Markov propagation models on a random tree generated by a binary search or `equal rates Markov' mechanism. Our continuous time model, the multi-type Yule tree with mutations, is a multi-type generalization of the tree generated by a pure birth or Yule process. We study type dependent topological properties of these two random tree models. We derive asymptotic results that allow one to infer model param…
Recently, Holmes and Perkins identified conditions which ensure that for a class of critical lattice models the scaling limit of the range is the range of super-Brownian motion. One of their conditions is an estimate on a spatial moment of order higher than four, which they verified for the sixth moment for spread-out lattice trees in dimensions $d>8$. Chen and Sakai have proved the required moment estimate for spread-out critical oriented percolation in dimensions $d+1>4+1$. We prove estimates on all moments for the spread-out critical contact process in dimensions $d>4$, which in particular …
