Solving the recombination equation has been a long-standing challenge of \emph{deterministic} population genetics. We review recent progress obtained by introducing ancestral processes, as traditionally used in the context of \emph{stochastic} models of population genetics, into the deterministic setting. With the help of an ancestral partitioning process, which is obtained by letting population size tend to infinity (without rescaling parameters or time) in an ancestral recombination graph, we obtain the solution to the recombination equation in a transparent form.
Recently, the selection-recombination equation with a single selected site and an arbitrary number of neutral sites was solved by means of the ancestral selection-recombination graph. Here, we introduce a more accessible approach, namely the ancestral initiation graph. The construction is based on a discretisation of the selection-recombination equation. We apply our method to systematically explain a long-standing observation concerning the dynamics of linkage disequilibrium between two neutral loci hitchhiking along with a selected one. In particular, this clarifies the nontrivial dependence…
Known results on the moments of the distribution generated by the two-locus Wright-Fisher diffusion model and a duality between the diffusion process and the ancestral process with recombination are briefly summarized. A numerical methods for computing moments by a Markov chain Monte Carlo and a method to compute closed-form expressions of the moments are presented. By using the duality argument properties of the ancestral recombination graph are studied in terms of the moments.
We consider the Wright-Fisher model for a population of $N$ individuals, each identified with a sequence of a finite number of sites, and single-crossover recombination between them. We trace back the ancestry of single individuals from the present population. In the $N \to \infty$ limit without rescaling of parameters or time, this ancestral process is described by a random tree, whose branching events correspond to the splitting of the sequence due to recombination. With the help of a decomposition of the trees into subtrees, we calculate the probabilities of the topologies of the ancestral …
A large offspring number diploid biparental multilocus population model of Moran type is our object of study. At each timestep, a pair of diploid individuals drawn uniformly at random contribute offspring to the population. The number of offspring can be large relative to the total population size. Similar `heavily skewed' reproduction mechanisms have been considered by various authors recently. Each diploid parental individual contributes exactly one chromosome to each diploid offspring, and hence ancestral lineages can only coalesce when in distinct individuals. A separation of timescales ph…
We consider a Moran model with recombination in a haploid population of size $N$. At each birth event, with probability $1-ρ_N R$ the offspring copies one parent's chromosome, and with probability $ρ_N R$ she inherits a chromosome that is a mosaic of both parental chromosomes. We assume that at time $0$ each individual has her chromosome painted in a different color and we study the color partition of the chromosome that is asymptotically fixed in a large population, when we look at a portion of the chromosome such that $ρ:= \lim_{N\to \infty} \frac{ρ_N N}{2}\to \infty$. To do so, we follow ba…
The Moran model with recombination is considered, which describes the evolution of the genetic composition of a population under recombination and resampling. There are $n$ sites (or loci), a finite number of letters (or alleles) at every site, and we do not make any scaling assumptions. In particular, we do not assume a diffusion limit. We consider the following marginal ancestral recombination process. Let $S = \{1,...,n\}$ and $\mathcal A=\{A_1, ..., A_m\}$ be a partition of $S$. We concentrate on the joint probability of the letters at the sites in $A_1$ in individual $1$, $...$, and at th…
The genealogy at a single locus of a constant size $N$ population in equilibrium is given by the well-known Kingman's coalescent. When considering multiple loci under recombination, the ancestral recombination graph encodes the genealogies at all loci in one graph. For a continuous genome $G$, we study the tree-valued process $(T^N_u)_{u\in G}$ of genealogies along the genome in the limit $N\to\infty$. Encoding trees as metric measure spaces, we show convergence to a tree-valued process with cadlag paths. In addition, we study mixing properties of the resulting process for loci which are far a…
We review recent progress on ancestral processes related to mutation-selection models, both in the deterministic and the stochastic setting. We mainly rely on two concepts, namely, the killed ancestral selection graph and the pruned lookdown ancestral selection graph. The killed ancestral selection graph gives a representation of the type of a random individual from a stationary population, based upon the individual's potential ancestry back until the mutations that define the individual's type. The pruned lookdown ancestral selection graph allows one to trace the ancestry of individuals from …
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 reconsider the deterministic haploid mutation-selection equation with two types. This is an ordinary differential equation that describes the type distribution (forward in time) in a population of infinite size. This paper establishes ancestral (random) structures inherent in this deterministic model. In a first step, we obtain a representation of the deterministic equation's solution (and, in particular, of its equilibrium) in terms of an ancestral process called the killed ancestral selection graph. This representation allows one to understand the bifurcations related to the error thresho…
The ancestral selection graph in population genetics was introduced by KroneNeuhauser (1997) as an analogue of the coalescent genealogy of a sample of genes from a neutrally evolving population. The number of particles in this graph, followed backwards in time, is a birth and death process with quadratic death and linear birth rates. In this paper an explicit form of the probability distribution of the number of particles is obtained by using the density of the allele frequency in the corresponding diffusion model obtained by Kimura (1955). It is shown that the process of fixation of the allel…
We reconsider the Moran model in continuous time with population size $N$, two allelic types, and selection. We introduce a new particle representation, which we call the labelled Moran model, and which has the same distribution of type frequencies as the original Moran model, provided the initial values are chosen appropriately. In the new model, individuals are labelled $1,2, \dots, N$; neutral resampling events may take place between arbitrary labels, whereas selective events only occur in the direction of increasing labels. With the help of elementary methods only, we not only recover fixa…
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…
Widely used models in genetics include the Wright-Fisher diffusion and its moment dual, Kingman's coalescent. Each has a multilocus extension but under neither extension is the sampling distribution available in closed-form, and their computation is extremely difficult. In this paper we derive two new multilocus population genetic models, one a diffusion and the other a coalescent process, which are much simpler than the standard models, but which capture their key properties for large recombination rates. The diffusion model is based on a central limit theorem for density dependent population…
Duality plays an important role in population genetics. It can relate results from forwards-in-time models of allele frequency evolution with those of backwards-in-time genealogical models; a well known example is the duality between the Wright-Fisher diffusion for genetic drift and its genealogical counterpart, the coalescent. There have been a number of articles extending this relationship to include other evolutionary processes such as mutation and selection, but little has been explored for models also incorporating crossover recombination. Here, we derive from first principles a new genea…
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…
We consider a multi-type Moran model (in continuous time) with selection and type-dependent mutation. This paper is concerned with the evolution of genealogical information forward in time. For this purpose we define and analytically characterize a path-valued Markov process that contains in its state at time $t$ the extended ancestral lines (adding genealogical distances) of the population alive at time $t$. The main result is a representation for the conditional distribution of the extended ancestral lines of a subpopulation alive at a fixed time $T$ (present time) given the type information…
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）
Wright-Fisher diffusions describe the evolution of the type composition of an infinite haploid population with two types (say type $0$ and type $1$) subject to neutral reproductions, and possibly selection and mutations. In the present paper we study a Wright-Fisher diffusion in a Lévy environment that gives a selective advantage to sometimes one type, sometimes the other. Classical methods using the Ancestral Selection Graph (ASG) fail in the study of this model because of the complexity, resulting from the two-sided selection, of the structure of the information contained in the ASG. We prop…
The distributed genome hypothesis states that the set of genes in a population of bacteria is distributed over all individuals that belong to the specific taxon. It implies that certain genes can be gained and lost from generation to generation. We use the random genealogy given by a Kingman coalescent in order to superimpose events of gene gain and loss along ancestral lines. Gene gains occur at a constant rate along ancestral lines. We assume that gained genes have never been present in the population before. Gene losses occur at a rate proportional to the number of genes present along the a…
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 …
Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity of recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them used simulations of fixed size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use non-linear Markov chains to describe a bacterial population evolving under mutation and recombination processes. We consider a population as a space of genomes and a probability measure on it. Thus, …
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 construct the non-linear Markov process connected with biological model of bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory.
