Consider two ancestral lineages sampled from a system of two-dimensional branching random walks with logistic regulation in the stationary regime. We study the asymptotics of their coalescence time for large initial separation and find that it agrees with well known results for a suitably scaled two-dimensional stepping stone model and also with Malécot's continuous-space approximation for the probability of identity by descent as a function of sampling distance. This can be viewed as a justification for the replacement of locally fluctuating population sizes by fixed effective sizes. Our main tool is a joint regeneration construction for the spatial embeddings of the two ancestral lineages.
We give a short overview on our work on ancestral lineages in spatial population models with local regulation. We explain how an ancestral lineage can be interpreted as a random walk in a dynamic random environment. Defining regeneration times allows to prove central limit theorems for such walks. We also consider several ancestral lineages in the same population and show for one prototypical example that in one dimension the corresponding system of coalescing walks converges to the Brownian web.
We consider a branching model in discrete time where each individual has a trait in some general state space. Both the reproduction law and the trait inherited by the offsprings may depend on the trait of the mother and the environment. We study the long time behavior of the population and the ancestral lineage of typical individuals under general assumptions, which we specify for applications to some models motivated by biology. Our results focus on the growth rate, the trait distribution among the population for large time, so as local densities and the position of extremal individuals. The …
We are interested in the dynamic of a structured branching population where the trait of each individual moves according to a Markov process. The rate of division of each individual is a function of its trait and when a branching event occurs, the trait of a descendant at birth depends on the trait of the mother. We prove a law of large numbers for the empirical distribution of ancestral trajectories. It ensures that the empirical measure converges to the mean value of the spine which is a time-inhomogeneous Markov process describing the trait of a typical individual along its ancestral lineag…
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…
Empirical distribution of ancestral lineages in populations with density-dependent interactions
Centre de Mathématiques Appliquées (CMAP), Ecole Polytechnique（巴黎综合理工学院应用数学中心）；Institute of Ecology and Environmental Sciences (iEES), Sorbonne Université（索邦大学生态与环境科学研究所）
Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is heterogeneous - the expected reproductive output of ancestral cells on the lineage from time $0$ to time $T$ continuously increases. This `inspection paradox' is due to sampling bias, that cells with a larger number of offspring are more likely to have one of their descendants sampled by virtue of their prolificity, and the bias's strength grows with the random popula…
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 …
For supercritical multitype branching processes in continuous time, we investigate the evolution of types along those lineages that survive up to some time t. We establish almost-sure convergence theorems for both time and population averages of ancestral types (conditioned on non-extinction), and identify the mutation process describing the type evolution along typical lineages. An important tool is a representation of the family tree in terms of a suitable size-biased tree with trunk. As a by-product, this representation allows a `conceptual proof' (in the sense of Kurtz, Lyons, Pemantle, Pe…
Cytotoxic T lymphocytes (CTLs) are immune system cells that are thought to play an important role in controlling HIV infection. We develop a stochastic ODE model of HIV-CTL interaction that extends current deterministic ODE models. Based on this stochastic model, we consider the effect of CTL attack on intrahost HIV lineages assuming CTLs attack several epitopes with equal strength. In this setting, we introduce a limiting version of our stochastic ODE under which we show that the coalescence of HIV lineages can be described by a simple paintbox construction. Through numerical experiments, we …
We revisit the spatial $λ$-Fleming-Viot process introduced in [1]. Particularly, we are interested in the time $T_0$ to the most recent common ancestor for two lineages. We distinguish between the case where the process acts on the entire two-dimensional plane, and on a finite rectangle. Utilizing a differential equation linking $T_0$ with the physical distance between the lineages, we arrive at simple and reasonably accurate approximation schemes for both cases. Furthermore, our analysis enables us to address the question of whether the genealogical process of the model "comes down from infin…
When a beneficial mutation occurs in a population, the new, favored allele may spread to the entire population. This process is known as a selective sweep. Suppose we sample $n$ individuals at the end of a selective sweep. If we focus on a site on the chromosome that is close to the location of the beneficial mutation, then many of the lineages will likely be descended from the individual that had the beneficial mutation, while others will be descended from a different individual because of recombination between the two sites. We introduce two approximations for the effect of a selective sweep…
The nested Kingman coalescent describes the ancestral tree of a population undergoing neutral evolution at the level of individuals and at the level of species, simultaneously. We study the speed at which the number of lineages descends from infinity in this hierarchical coalescent process and prove the existence of an early-time phase during which the number of lineages at time $t$ decays as $ 2γ/ct^2$, where $c$ is the ratio of the coalescence rates at the individual and species levels, and the constant $γ\approx 3.45$ is derived from a recursive distributional equation for the number of lin…
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 …
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 present a new model for seed banks, where direct ancestors of individuals may have lived in the near as well as the very far past. The classical Wright-Fisher model, as well as a seed bank model with bounded age distribution considered by Kaj, Krone and Lascoux (2001) are special cases of our model. We discern three parameter regimes of the seed bank age distribution, which lead to substantially different behaviour in terms of genetic variability, in particular with respect to fixation of types and time to the most recent common ancestor. We prove that for age distributions with finite mean…
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.
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 t…
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 …
We consider a directed random walk on the backbone of the infinite cluster generated by supercritical oriented percolation, or equivalently the space-time embedding of the ``ancestral lineage'' of an individual in the stationary discrete-time contact process. We prove a law of large numbers and an annealed central limit theorem (i.e., averaged over the realisations of the cluster) using a regeneration approach. Furthermore, we obtain a quenched central limit theorem (i.e.\ for almost any realisation of the cluster) via an analysis of joint renewals of two independent walks on the same cluster.
We consider the backbone of the infinite cluster generated by supercritical oriented site percolation in dimension 1 +1. A directed random walk on this backbone can be seen as an "ancestral line" of an individual sampled in the stationary discrete-time contact process. Such ancestral lineages were investigated in [BCDG13] where a central limit theorem for a single walker was proved. Here, we consider infinitely many coalescing walkers on the same backbone starting at each space-time point. We show that, after diffusive rescaling, the collection of paths converges in distribution to the Brownia…
The Ancestral Selection Graph (ASG) is an important genealogical process which extends the well-known Kingman coalescent to incorporate natural selection. We show that the number of lineages of the ASG with and without mutation is asymptotic to $2/t$ as $t\to 0$, in agreement with the limiting behaviour of the Kingman coalescent. We couple these processes on the same probability space using a Poisson random measure construction that allows us to precisely compare their hitting times. These comparisons enable us to characterise the speed of coming down from infinity of the ASG as well as its fl…
We ask the question "when will natural selection on a gene in a spatially structured population cause a detectable trace in the patterns of genetic variation observed in the contemporary population?". We focus on the situation in which 'neighbourhood size', that is the effective local population density, is small. The genealogy relating individuals in a sample from the population is embedded in a spatial version of the ancestral selection graph and through applying a diffusive scaling to this object we show that whereas in dimensions at least three, selection is barely impeded by the spatial s…
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…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching process). Through a probabilistic analysis of the model, we derive sample complexity bounds for widely used quartet-based inference methods that highlight the effect of the duplication and loss rates in both subcritical and supercritical regimes.
We present a model for growth in a multi-species population. We consider two types evolving as a logistic branching process with mutation, where one of the types has a selective advantage, and are interested in the regime in which the carrying capacity of the system goes to $\infty$. We first study the genealogy of the population up until it almost reaches carrying capacity through a coupling with an independent branching process. We then focus on the phase in which the population has reached carrying capacity. After recovering a Gillespie--Wright--Fisher SDE in the infinite carrying capacity …
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 random walks in dynamic random environments, with an environment generated by the time-reversal of a Markov process from the oriented percolation universality class. If the influence of the random medium on the walk is small in space-time regions where the medium is typical, we obtain a law of large numbers and an averaged central limit theorem for the walk via a regeneration construction under suitable coarse-graining. Such random walks occur naturally as spatial embeddings of ancestral lineages in spatial population models with local regulation. We verify that our assumptions hol…
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…
We consider a stochastic individual-based population model with competition, trait-structure affecting reproduction and survival, and changing environment. The changes of traits are described by jump processes, and the dynamics can be approximated in large population by a non-linear PDE with a non-local mutation operator. Using the fact that this PDE admits a non-trivial stationary solution, we can approximate the non-linear stochastic population process by a linear birth-death process where the interactions are frozen, as long as the population remains close to this equilibrium. This allows u…
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…
