arXiv subjects

Amaury Lambert

Publications and source records attributed to Amaury Lambert.

At least 37 records · Page 2Linked to original sources

arXiv2017

The genealogy of a sample from a binary branching process

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 independently with probability $y$ (Bernoulli sample). It is known that the tree generated by the selected tips, which we will call Bernoulli sampled CPP, is again a CPP. Now instead, select exactly $k$ tips uniformly at random among the $N$ tips ($k$-sample). We show that the tree generated by the selected tips is a mixture of Bernoulli sampled CPPs with the same parent CPP, over some explicit distribution of the sampling probability $y$. An immediate consequence is that the genealogy of a $k$-sample can be obtained by the realization of $k$ random variables, first the random sampling probability $Y$ and then the $k-1$ node depths which are iid conditional on $Y=y$.

math.PR↗

arXiv2017

Mutations on a Random Binary Tree with Measured Boundary

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 any such tree can be mapped to a random, compact ultrametric tree called coalescent point process, endowed with a `uniform' measure on its boundary which is the limit as $t\to\infty$ of the properly rescaled counting measure of the population at time $t$. We prove that the clonal (i.e., carrying the same allele as the root) part of the boundary is a regenerative set that we characterize. We then study the allelic partition of the boundary through the measures of its blocks. We also study the dynamics of the clonal subtree, which is a Markovian increasing tree process as mutations are removed.

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arXiv2017

Totally Ordered Measured Trees and Splitting Trees with Infinite Variation

Combinatorial trees can be used to represent genealogies of asexual individuals. These individuals can be endowed with birth and death times, to obtain a so-called `chronological tree'. In this work, we are interested in the continuum analogue of chronological trees in the setting of real trees. This leads us to consider totally ordered and measured trees, abbreviated as TOM trees. First, we define an adequate space of TOM trees and prove that under some mild conditions, every compact TOM tree can be represented in a unique way by a so-called contour function, which is right-continuous, admits limits from the left and has non-negative jumps. The appropriate notion of contour function is also studied in the case of locally compact TOM trees. Then we study the splitting property of (measures on) TOM trees which extends the notion of `splitting tree' studied in \cite{MR2599603}, where during her lifetime, each individual gives birth at constant rate to independent and identically distributed copies of herself. We prove that the contour function of a TOM tree satisfying the splitting property is associated to a spectrally positive Lévy process that is not a subordinator, both in the critical and subcritical cases of compact trees as well as in the supercritical case of locally compact trees.

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arXiv2017

Branching processes seen from their extinction time via path decompositions of reflected Lévy processes

We consider a spectrally positive Lévy process $X$ that does not drift to $+\infty$, viewed as coding for the genealogical structure of a (sub)critical branching process, in the sense of a contour or exploration process \cite{GaJa98,Lam10}. We denote by $I$ the past infimum process defined for each $t\geq 0$ by $I_t:= \inf_{[0,t]} X$ and we let $γ$ be the unique time at which the excursion of the reflected process $X-I$ away from 0 attains its supremum. We prove that the pre-$γ$ and the post-$γ$ subpaths of this excursion are invariant under space-time reversal, which has several other consequences in terms of duality for excursions of Lévy processes. It implies in particular that the local time process of this excursion is also invariant when seen backward from its height. As a corollary, we obtain that some (sub)critical branching processes such as the (sub)critical Crump-Mode-Jagers (CMJ) processes and the excursion away from 0 of the critical Feller diffusion, which is the width process of the continuum random tree, are invariant under time reversal from their extinction time.

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arXiv2017

Random ultrametric trees and applications

Ultrametric trees are trees whose leaves lie at the same distance from the root. They are used to model the genealogy of a population of particles co-existing at the same point in time. We show how the boundary of an ultrametric tree, like any compact ultrametric space, can be represented in a simple way via the so-called comb metric. We display a variety of examples of random combs and explain how they can be used in applications. In particular, we review some old and recent results regarding the genetic structure of the population when throwing neutral mutations on the skeleton of the tree.

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arXiv2016

Recovering the Brownian Coalescent Point Process from the Kingman Coalescent by Conditional Sampling

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 timescale $\varepsilon$ converges as $\varepsilon\to 0$. The limit is the so-called Brownian coalescent point process (CPP) stopped at an independent Gamma random variable with parameter $n$, which can be seen as the genealogy at a large time of the total population of a rescaled critical birth-death process, biased by the $n$-th power of its size. Secondly, we show that in this limit the coalescence times of the $n$ sampled individuals are i.i.d. uniform random variables in $(0,1)$. These results provide a coupling between two standard models for the genealogy of a random exchangeable population: the Kingman coalescent and the Brownian CPP.

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arXiv2016

Probabilistic Models for the (sub)Tree(s) of Life

The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths), culminating in the $β$-family of Aldous' branching models. We next introduce real trees (trees as metric spaces) and show how to study them through their contour, provided they are properly measured and ordered. We then focus on the reduced tree, or coalescent tree, which is the tree spanned by individuals/species alive at the same fixed time. We show how reduced trees, like any compact ultrametric space, can be represented in a simple way via the so-called comb metric. Beautiful examples of random combs include the Kingman coalescent and coalescent point processes. We end up displaying some recent biological applications of coalescent point processes to the inference of species diversification, to conservation biology and to epidemiology.

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arXiv2016

The comb representation of compact ultrametric spaces

We call a \emph{comb} a map $f:I\to [0,\infty)$, where $I$ is a compact interval, such that $\{f\ge \varepsilon\}$ is finite for any $\varepsilon$. A comb induces a (pseudo)-distance $\dtf$ on $\{f=0\}$ defined by $\dtf(s,t) = \max_{(s\wedge t, s\vee t)} f$. We describe the completion $\bar I$ of $\{f=0\}$ for this metric, which is a compact ultrametric space called \emph{comb metric space}. Conversely, we prove that any compact, ultrametric space $(U,d)$ without isolated points is isometric to a comb metric space. We show various examples of the comb representation of well-known ultrametric spaces: the Kingman coalescent, infinite sequences of a finite alphabet, the $p$-adic field and spheres of locally compact real trees. In particular, for a rooted, locally compact real tree defined from its contour process $h$, the comb isometric to the sphere of radius $T$ centered at the root can be extracted from $h$ as the depths of its excursions away from $T$.

math.GN↗

arXiv2015

Time reversal dualities for some random forests

We consider a random forest $\mathcal{F}^*$, defined as a sequence of i.i.d. birth-death (BD) trees, each started at time 0 from a single ancestor, stopped at the first tree having survived up to a fixed time $T$. We denote by $\left(ξ^*_t,\ 0\leq t\leq T\right)$ the population size process associated to this forest, and we prove that if the BD trees are supercritical, then the time-reversed process $\left(ξ^*_{T-t},\ 0\leq t\leq T\right)$, has the same distribution as $\left(\widetildeξ^*_t,\ 0\leq t\leq T\right)$, the corresponding population size process of an equally defined forest $\widetilde{\mathcal{F}}^*$, but where the underlying BD trees are subcritical, obtained by swapping birth and death rates or equivalently, conditioning on ultimate extinction. We generalize this result to splitting trees (i.e. life durations of individuals are not necessarily exponential), provided that the i.i.d. lifetimes of the ancestors have a specific explicit distribution, different from that of their descendants. The results are based on an identity between the contour of these random forests truncated up to $T$ and the duality property of Lévy processes. This identity allows us to also derive other useful properties such as the distribution of the population size process conditional on the reconstructed tree of individuals alive at $T$, which has potential applications in epidemiology.

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arXiv2013

Scaling limits via excursion theory: Interplay between Crump-Mode-Jagers branching processes and processor-sharing queues

We study the convergence of the $M/G/1$ processor-sharing, queue length process in the heavy traffic regime, in the finite variance case. To do so, we combine results pertaining to Lévy processes, branching processes and queuing theory. These results yield the convergence of long excursions of the queue length processes, toward excursions obtained from those of some reflected Brownian motion with drift, after taking the image of their local time process by the Lamperti transformation. We also show, via excursion theoretic arguments, that this entails the convergence of the entire processes to some (other) reflected Brownian motion with drift. Along the way, we prove various invariance principles for homogeneous, binary Crump-Mode-Jagers processes. In the last section we discuss potential implications of the state space collapse property, well known in the queuing literature, to branching processes.

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arXiv2013

Macro-evolutionary models and coalescent point processes: The shape and probability of reconstructed phylogenies

Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees (i.e., phylogenies of extant species). Alternatively, reconstructed trees can be modelled by coalescent point processes (CPP), where trees grow "horizontally" by the sequential addition of vertical edges. Each new edge starts at some random speciation time and ends at the present time; speciation times are drawn from the same distribution independently. CPP lead to extremely fast computation of tree likelihoods and simulation of reconstructed trees. Their topology always follows the uniform distribution on ranked tree shapes (URT). We characterize which forward-time models lead to URT reconstructed trees and among these, which lead to CPP reconstructed trees. We show that for any "asymmetric" diversification model in which speciation rates only depend on time and extinction rates only depend on time and on a non-heritable trait (e.g., age), the reconstructed tree is CPP, even if extant species are incompletely sampled. If rates additionally depend on the number of species, the reconstructed tree is (only) URT (but not CPP). We characterize the common distribution of speciation times in the CPP description, and discuss incomplete species sampling as well as three special model cases in detail: 1) extinction rate does not depend on a trait; 2) rates do not depend on time; 3) mass extinctions may happen additionally at certain points in the past.

q-bio.PE↗

arXiv2013

Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics

The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge, none of the epidemiological models currently used in phylogenetics can account for recovery rates and sampling rates dependent on the time elapsed since transmission. Here we introduce an epidemiological model where infectives leave the epidemic, either by recovery or sampling, after some random time which may follow an arbitrary distribution. We derive an expression for the likelihood of the phylogenetic tree of sampled infectives under our general epidemiological model. The analytic concept developed in this paper will facilitate inference of past epidemiological dynamics and provide an analytical framework for performing very efficient simulations of phylogenetic trees under our model. The main idea of our analytic study is that the non-Markovian epidemiological model giving rise to phylogenetic trees growing vertically as time goes by, can be represented by a Markovian "coalescent point process" growing horizontally by the sequential addition of pairs of coalescence and sampling times. As examples, we discuss two special cases of our general model, namely an application to influenza and an application to HIV. Though phrased in epidemiological terms, our framework can also be used for instance to fit macroevolutionary models to phylogenies of extant and extinct species, accounting for general species lifetime distributions.

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arXiv2013

Predicting the loss of phylogenetic diversity under non-stationary diversification models

For many taxa, the current high rates of extinction are likely to result in a significant loss of biodiversity. The evolutionary heritage of biodiversity is frequently quantified by a measure called phylogenetic diversity (PD). We predict the loss of PD under a wide class of phylogenetic tree models, where speciation rates and extinction rates may be time-dependent, and assuming independent random species extinctions at the present. We study the loss of PD when $K$ contemporary species are selected uniformly at random from the $N$ extant species as the surviving taxa, while the remaining $N-K$ become extinct. We consider two models of species sampling, the so-called field of bullets model, where each species independently survives the extinction event at the present with probability $p$, and a model for which the number of surviving species is fixed. We provide explicit formulae for the expected remaining PD in both models, conditional on $N=n$, conditional on $K=k$, or conditional on both events. When $N=n$ is fixed, we show the convergence to an explicit deterministic limit of the ratio of new to initial PD, as $n\to\infty$, both under the field of bullets model, and when $K=k_n$ is fixed and depends on $n$ in such a way that $k_n/n$ converges to $p$. We also prove the convergence of this ratio as $T\to\infty$ in the supercritical, time-homogeneous case, where $N$ simultaneously goes to $\infty$, thereby strengthening previous results of Mooers et al. (2012).

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arXiv2013

The weak convergence of regenerative processes using some excursion path decompositions

We consider regenerative processes with values in some Polish space. We define their ε-big excursions as excursions e such that f(e)>ε, where f is some given functional on the space of excursions which can be thought of as, e.g., the length or the height of e. We establish a general condition that guarantees the convergence of a sequence of regenerative processes involving the convergence of ε-big excursions and of their endpoints, for all εin a countable set whose closure contains 0. Finally, we provide various sufficient conditions on the excursion measures of this sequence for this general condition to hold and discuss possible generalizations of our approach to processes that can be written as the concatenation of i.i.d. paths.

math.PR↗

arXiv2013

Asymptotic behavior of local times of compound Poisson processes with drift in the infinite variance case

Consider compound Poisson processes with negative drift and no negative jumps, which converge to some spectrally positive Lévy process with non-zero Lévy measure. In this paper we study the asymptotic behavior of the local time process, in the spatial variable, of these processes killed at two different random times: either at the time of the first visit of the Lévy process to 0, in which case we prove results at the excursion level under suitable conditionings; or at the time when the local time at 0 exceeds some fixed level. We prove that finite-dimensional distributions converge under general assumptions, even if the limiting process is not càdlàg. Making an assumption on the distribution of the jumps of the compound Poisson processes, we strengthen this to get weak convergence. Our assumption allows for the limiting process to be a stable Lévy process with drift. These results have implications on branching processes and in queueing theory, namely, on the scaling limit of binary, homogeneous Crump-Mode-Jagers processes and on the scaling limit of the Processor-Sharing queue length process.

math.PR↗

arXiv2013

The peripatric coalescent

We consider a dynamic metapopulation involving one large population of size N surrounded by colonies of size \varepsilon_NN, usually called peripheral isolates in ecology, where N\to\infty and \varepsilon_N\to 0 in such a way that \varepsilon_NN\to\infty. The main population periodically sends propagules to found new colonies (emigration), and each colony eventually merges with the main population (fusion). Our aim is to study the genealogical history of a finite number of lineages sampled at stationarity in such a metapopulation. We make assumptions on model parameters ensuring that the total outer population has size of the order of N and that each colony has a lifetime of the same order. We prove that under these assumptions, the scaling limit of the genealogical process of a finite sample is a censored coalescent where each lineage can be in one of two states: an inner lineage (belonging to the main population) or an outer lineage (belonging to some peripheral isolate). Lineages change state at constant rate and inner lineages (only) coalesce at constant rate per pair. This two-state censored coalescent is also shown to converge weakly, as the landscape dynamics accelerate, to a time-changed Kingman coalescent.

math.PR↗

arXiv2013

The coalescent point process of branching trees

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 generation h in a planar BGW tree conditioned to survive h generations. The decomposition involves a point measure $ρ$ storing the number of subtrees on the right-hand side of the spine. Under appropriate conditions, we prove convergence of this point measure to a point measure on $\mathbb{R}_+$ associated with the limiting continuous-state branching (CSB) process. We prove the associated invariance principle for the coalescent point process, after we discretize the limiting CSB population by considering only points with coalescence times greater than $\varepsilon$.

math.PR↗

arXiv2013

The reconstructed tree in the lineage-based model of protracted speciation

A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree produced by a given model of diversification. Etienne & Rosindell (2012) proposed a lineage-based model of diversification, called protracted speciation, where species remain incipient during a random duration before turning good species, and showed that this can explain the slowdown in lineage accumulation observed in real phylogenies. However, they were unable to provide a general likelihood formula. Here, we present a likelihood formula for protracted speciation models, where rates at which species turn good or become extinct can depend both on their age and on time. Our only restrictive assumption is that speciation rate does not depend on species status. Our likelihood formula utilizes a new technique, based on the contour of the phylogenetic tree and first developed in Lambert (2010). We consider the reconstructed trees spanned by all extant species, by all good extant species, or by all representative species, which are either good extant species or incipient species representative of some good extinct species. Specifically, we prove that each of these trees is a coalescent point process, that is, a planar, ultrametric tree where the coalescence times between two consecutive tips are independent, identically distributed random variables. We characterize the common distribution of these coalescence times in some, biologically meaningful, special cases for which the likelihood reduces to an elegant analytical formula or becomes numerically tractable.

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