We study two types of stochastic processes, a mean-field spatial system of interacting Fisher-Wright diffusions with an inferior and an advantageous type with rare mutation (inferior to advantageous) and a (mean-field) spatial system of supercritical branching random walks with an additional deathrate which is quadratic in the local number of particles. The former describes a standard two-type population under selection, mutation, the latter models describe a population under scarce resources causing additional death at high local population intensity. Geographic space is modelled by $\{1, \cdots, N\}$. The first process starts in an initial state with only the inferior type present or an exchangeable configuration and the second one with a single initial particle. {This material is a special case of the theory developed in \cite{DGsel}.}
We study the behaviour in two time windows, first between time 0 and $T$ and secondly after a large time when in the Fisher-Wright model the rare mutants succeed respectively in the branching random walk the particle population reaches a positive spatial intensity. It is shown that the second phase for both models sets in after time $α^{-1} \log N$, if $N$ is the size of geographic space and $N^{-1}$ the rare mutation rate and $α\in (0, \infty)$ depends on the other parameters. We identify the limit dynamics in both time windows and for both models as a nonlinear Markov dynamic (McKean-Vlasov dynamic) respectively a corresponding random entrance law from time $-\infty$ of this dynamic.
Finally we explain that the two processes are just two sides of the very same coin, a fact arising from duality, in particular the particle model generates the genealogy of the Fisher-Wright diffusions with selection and mutation. We discuss the extension of this duality relation to a multitype model with more than two types.
One-dimensional Fisher-Wright diffusion process on the interval $(0,1)$ with mutations is considered. This is a widely known model in population genetics. The goal of the paper is an exponential recurrence of the process, which also implies exponential rate of convergence towards the invariant measure.
In this paper we introduce a multilocus diffusion model of a population of $N$ haploid, asexually reproducing individuals. The model includes parent-dependent mutation and interlocus selection, the latter limited to pairwise relationships but among a large number of simultaneous loci. The diffusion is expressed as a system of stochastic differential equations (SDEs) that are coupled in the drift functions through a Shahshahani gradient-like structure for interlocus selection. The system of SDEs is derived from a sequence of Markov chains by weak convergence. We find the explicit stationary (in…
Let $Z = (Z_t)_{t\in[0,\infty)}$ be an ergodic Markov process and, for every $n\in\mathbb{N}$, let $Z^n = (Z_{n^2 t})_{t\in[0,\infty)}$ drive a process $X^n$. Classical results show under suitable conditions that the sequence of non-Markovian processes $(X^n)_{n\in\mathbb{N}}$ converges to a Markov process and give its infinitesimal characteristics. Here, we consider a general sequence $(Z^n)_{n\in\mathbb{N}}$. Using a general result on stochastic averaging from [Kur92], we derive conditions which ensure that the sequence $(X^n)_{n\in\mathbb{N}}$ converges as in the classical case. As an appli…
We study a family of n-dimensional diffusions, taking values in the unit simplex of vectors with nonnegative coordinates that add up to one. These processes satisfy stochastic differential equations which are similar to the ones for the classical Wright-Fisher diffusions, except that the "mutation rates" are now nonpositive. This model, suggested by Aldous, appears in the study of a conjectured diffusion limit for a Markov chain on Cladograms. The striking feature of these models is that the boundary is not reflecting, and we kill the process once it hits the boundary. We derive the explicit e…
We consider the classical Wright-Fisher model with mutation and selection. Mutations occur independently in each locus, and selection is performed according to the sharp peak landscape. In the asymptotic regime studied in [3], a quasispecies is formed. We find explicitly the distribution of this quasispecies, which turns out to be the same distribution as for the Moran model.
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…
We consider a population evolving under mutation and selection. The genotype of an individual is a word of length $\ell$ over a finite alphabet. Mutations occur during reproduction, independently on each locus; the fitness depends on the Hamming class (the distance to a reference sequence $w^*$). Evolution is driven according to the classical Wright--Fisher process. We focus on the proportion of the different classes under the invariant measure of the process. We consider the regime where the length of the genotypes $\ell$ goes to infinity, and both the population size and the inverse of the m…
In [arXiv:1906.10951 (forthcoming on Advances in Applied Probability),arXiv:2011.05933 (published on PLOS ONE)] the authors introduce, study and apply a new variant of the Eggenberger-Polya urn, called the "Rescaled" Polya urn, which, for a suitable choice of the model parameters, is characterized by the following features: (i) a "local" reinforcement, i.e. a reinforcement mechanism mainly based on the last observations, (ii) a random persistent fluctuation of the predictive mean, and (iii) a long-term almost sure convergence of the empirical mean to a deterministic limit, together with a chi-…
Consider a haploid population of fixed finite size with a finite number of allele types and having Cannings exchangeable genealogy with neutral mutation. The stationary distribution of the Markov chain of allele counts in each generation is an important quantity in population genetics but has no tractable description in general. We provide upper bounds on the distributional distance between the Dirichlet distribution and this finite population stationary distribution for the Wright-Fisher genealogy with general mutation structure and the Cannings exchangeable genealogy with parent independent …
We introduce a multi-allele Wright-Fisher model with non-recurrent, reversible mutation and directional selection. In this setting, the allele frequencies at a single locus track the path of a hybrid jump-diffusion process with state space given by the vertex and edge set of a graph. Vertices represent monomorphic population states and edge-positions mark the biallelic proportions of ancestral and derived alleles during polymorphic segments. We derive the stationary distribution in mutation-selection-drift equilibrium and obtain the expected allele frequency spectrum under large population siz…
The eigenfunction expansion by Gegenbauer polynomials for the diffusion on a hypersphere is transformed into the diffusion for the Wright-Fisher model with a particular mutation rate. We use the Ito calculus considering stochastic differential equations. The expansion gives a simple interpretation of the Griffiths eigenfunction expansion for the Wright-Fisher model. Our representation is useful to simulate the Wright-Fisher model as well as Brownian motion on a hypersphere.
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 study a population model of fixed size undergoing strong selection where individuals accumulate beneficial mutations, namely the Moran model with selection. In a specific setting with strong selection, Schweinsberg showed that the genealogy of the population is described by the so-called Bolthausen-Sznitman's coalescent. In this paper we sophisticate the model by splitting the population into two adversarial subgroups, that can be interpreted as two different alleles, one of which has a weak selective advantage over the other. We show that the proportion of disadvantaged individuals converg…
The Wright--Fisher diffusion is important in population genetics in modelling the evolution of allele frequencies over time subject to the influence of biological phenomena such as selection, mutation, and genetic drift. Simulating paths of the process is challenging due to the form of the transition density. We present EWF, a robust and efficient sampler which returns exact draws for the diffusion and diffusion bridge processes, accounting for general models of selection including those with frequency-dependence. Given a configuration of selection, mutation, and endpoints, EWF returns draws a…
We consider a multi-colony version of the Wright-Fisher model with seed-bank that was recently introduced by Blath et al. Individuals live in colonies and change type via resampling and mutation. Each colony contains a seed-bank that acts as a genetic reservoir. Individuals can enter the seed-bank and become dormant or can exit the seed-bank and become active. In each colony at each generation a fixed fraction of individuals swap state, drawn randomly from the active and the dormant population. While dormant, individuals suspend their resampling. While active, individuals resample from their o…
A number of discrete time, finite population size models in genetics describing the dynamics of allele frequencies are known to converge (subject to suitable scaling) to a diffusion process in the infinite population limit, termed the Wright-Fisher diffusion. In this article we show that the diffusion is ergodic uniformly in the selection and mutation parameters, and that the measures induced by the solution to the stochastic differential equation are uniformly locally asymptotically normal. Subsequently these two results are used to analyse the statistical properties of the Maximum Likelihood…
{\bf Abstract} The trajectory of the frequency of an allele which begins at $x$ at time $0$ and is known to have frequency $z$ at time $T$ can be modelled by the bridge process of the Wright-Fisher diffusion. Bridges when $x=z=0$ are particularly interesting because they model the trajectory of the frequency of an allele which appears at a time, then is lost by random drift or mutation after a time $T$. The coalescent genealogy back in time of a population in a neutral Wright-Fisher diffusion process is well understood. In this paper we obtain a new interpretation of the coalescent genealogy o…
We consider diffusion processes x_{t} on the unit interval. Doob-transformation techniques consist of a selection of x_{t}-paths procedure. The law of the transformed process is the one of a branching diffusion system of particles, each diffusing like a new process tilde{x}_{t}, superposing an additional drift to the one of x_{t}. Killing and/or branching of tilde{x}_{t}-particles occur at some space-dependent rate lambda. For this transformed process, so in the class of branching diffusions, the question arises as to whether the particle system is sub-critical, critical or super-critical. In …
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 results in this paper provide new information on asymptotic properties of classical models: the neutral Kingman coalescent under a general finite-alleles, parent-dependent mutation mechanism, and its generalisation, the ancestral selection graph. Several relevant quantities related to these fundamental models are not explicitly known when mutations are parent dependent. Examples include the probability that a sample taken from a population has a certain type configuration, and the transition probabilities of their block counting jump chains. In this paper, asymptotic results are derived fo…
We consider a meanfield system of interacting Fisher-Wright diffusions with selection and rare mutation on the geographic space $\{1,2,...,N\}$. The type 1 has fitness 0, type 2 has fitness 1 and (rare) mutation occurs from type 1 to 2 at rate $m...N^{-1}$, selection is at rate $s>0$. The system starts in the state concentrated on type 1, the state of low fitness. We investigate this system for $N \to \infty$ on the original and large time scales. We show that for some $α\in (0,s)$ at times $α^{-1} \log N+t, t \in \R, N \to \infty$ the emergence of type 2 (positive global type-2 intensity) at …
We provide a general theorem bounding the error in the approximation of a random measure of interest--for example, the empirical population measure of types in a Wright-Fisher model--and a Dirichlet process, which is a measure having Poisson-Dirichlet distributed atoms with i.i.d. labels from a diffuse distribution. The implicit metric of the approximation theorem captures the sizes and locations of the masses, and so also yields bounds on the approximation between the masses of the measure of interest and the Poisson-Dirichlet distribution. We apply the result to bound the error in the approx…
In the context of population genetics, active information can be extended to measure the change of information of a given event (e.g., fixation of an allele) from a neutral model in which only genetic drift is taken into account to a non-neutral model that includes other sources of frequency variation (e.g., selection and mutation). In this paper we illustrate active information in population genetics through the Wright-Fisher model.
We consider the sensitivity, with respect to a parameter θ, of parametric families of operators A_θ, vectors π_θ corresponding to the adjoints A_θ^{*} of A_θ via A_θ^{*}π_θ=0 and one parameter semigroups t\mapsto e^{tA_θ}. We display formulas relating weak differentiability of θ\mapsto π_θ (at θ=0) to weak differentiability of θ\mapsto A_θ^{*}π_{0} and [e^{A_θt}]^{*}π_{0}. We give two applications: The first one concerns the sensitivity of the Ornstein--Uhlenbeck process with respect to its location parameter. The second one provides new insights regarding the Wright--Fisher diffusion for smal…
The d-dimensional Lambda-Fleming-Viot generator acting on functions g(x), with x being a vector of d allele frequencies, can be written as a Wright-Fisher generator acting on functions g with a modified random linear argument of x induced by partitioning occurring in the Lambda-Fleming-Viot process. The eigenvalues and right polynomial eigenvectors are easy to see from this representation. The two-dimensional process, which has a one-dimensional generator, is considered in detail. A non-linear equation is found for the Green's function. In a model with genic selection a proof is given that the…
We extend the ideas of (Barbour 1990) and use Stein's method to obtain a bound on the distance between a scaled time-changed random walk and a time-changed Brownian Motion. We then apply this result to bound the distance between a time-changed compensated scaled Poisson process and a time-changed Brownian Motion. This allows us to bound the distance between a process whose dynamics resemble those of the Moran model with mutation and a process whose dynamics resemble those of the Wright-Fisher diffusion with mutation upon noting that the former may be expressed as a difference of two time-chang…
Characterizing time-evolution of allele frequencies in a population is a fundamental problem in population genetics. In the Wright-Fisher diffusion, such dynamics is captured by the transition density function, which satisfies well-known partial differential equations. For a multi-allelic model with general diploid selection, various theoretical results exist on representations of the transition density, but finding an explicit formula has remained a difficult problem. In this paper, a technique recently developed for a diallelic model is extended to find an explicit transition density for an …
The recently introduced two-parameter Poisson-Dirichlet diffusion extends the infinitely-many-neutral-alleles model, related to Kingman's distribution and to Fleming-Viot processes. The role of the additional parameter has been shown to regulate the clustering structure of the population, but is yet to be fully understood in the way it governs the reproductive process. Here we shed some light on these dynamics by providing a finite-population construction, with finitely-many species, of the two-parameter infinite-dimensional diffusion. The costruction is obtained in terms of Wright-Fisher chai…
In a (two-type) Wright-Fisher diffusion with directional selection and two-way mutation, let $x$ denote today's frequency of the beneficial type, and given $x$, let $h(x)$ be the probability that, among all individuals of today's population, the individual whose progeny will eventually take over in the population is of the beneficial type. Fearnhead [Fearnhead, P., 2002. The common ancestor at a nonneutral locus. J. Appl. Probab. 39, 38-54] and Taylor [Taylor, J. E., 2007. The common ancestor process for a Wright-Fisher diffusion. Electron. J. Probab. 12, 808-847] obtained a series representat…
We pursue the task of developing a finite population counterpart to Eigen's model. We consider the classical Wright-Fisher model describing the evolution of a population of size $m$ of chromosomes of length $\ell$ over an alphabet of cardinality $κ$. The mutation probability per locus is $q$. The replication rate is $σ>1$ for the master sequence and $1$ for the other sequences. We study the equilibrium distribution of the process in the regime where $\ell\to+\infty$, $m\to+\infty$, $q\to0$, $\ell q\to a\in\,]0,+\infty[$, $\frac{m}{\ell}\toα\in [0,+\infty]$. We obtain an equation $αψ(a)=\lnκ$ i…
The goal of cancer genome sequencing projects is to determine the genetic alterations that cause common cancers. Many malignancies arise during the clonal expansion of a benign tumor which motivates the study of recurrent selective sweeps in an exponentially growing population. To better understand this process, Beerenwinkel et al. [PLoS Comput. Biol. 3 (2007) 2239--2246] consider a Wright--Fisher model in which cells from an exponentially growing population accumulate advantageous mutations. Simulations show a traveling wave in which the time of the first $k$-fold mutant, $T_k$, is approximat…
The stationary asymptotic properties of the diffusion limit of a multi-type branching process with neutral mutations are studied. For the critical and subcritical processes the interesting limits are those of quasi-stationary distributions conditioned on non-extinction. Pedagogical derivations are given for known results that the limiting distributions for supercritical and critical processes are found to collapse onto rays aligned with stationary eigenvectors of the mutation rate matrix, in agreement with discrete multi-type branching processes. For the sub-critical process the previously uns…
The two-parameter Poisson--Dirichlet diffusion, introduced in 2009 by Petrov, extends the infinitely-many-neutral-alleles diffusion model, related to Kingman's one-parameter Poisson--Dirichlet distribution and to certain Fleming--Viot processes. The additional parameter has been shown to regulate the clustering structure of the population, but is yet to be fully understood in the way it governs the reproductive process. Here we shed some light on these dynamics by formulating a $K$-allele Wright--Fisher model for a population of size $N$, involving a uniform mutation pattern and a specific sta…
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 …
In this paper, we consider a mathematical model for the evolution of neutral genetic diversity in a spatial continuum including mutations, genetic drift and either short range or long range dispersal. The model we consider is the spatial $ Λ$-Fleming-Viot process introduced by Barton, Etheridge and Véber, which describes the state of the population at any time by a measure on $ \R^d \times [0,1] $, where $ \R^d $ is the geographical space and $ [0,1] $ is the space of genetic types. In both cases (short range and long range dispersal), we prove a functional central limit theorem for the proces…
A forward diffusion equation describing the evolution of the allele frequency spectrum is presented. The influx of mutations is accounted for by imposing a suitable boundary condition. For a Wright-Fisher diffusion with or without selection and varying population size, the boundary condition is $\lim_{x \downarrow 0} x f(x,t)=θρ(t)$, where $f(\cdot,t)$ is the frequency spectrum of derived alleles at independent loci at time $t$ and $ρ(t)$ is the relative population size at time $t$. When population size and selection intensity are independent of time, the forward equation is equivalent to the …
We apply our general method of duality, introduced in [Giardina', Kurchan, Redig, J. Math. Phys. 48, 033301 (2007)], to models of population dynamics. The classical dualities between forward and ancestral processes can be viewed as a change of representation in the classical creation and annihilation operators, both for diffusions dual to coalescents of Kingman's type, as well as for models with finite population size. Next, using SU(1,1) raising and lowering operators, we find new dualities between the Wright-Fisher diffusion with $d$ types and the Moran model, both in presence and absence of…
The paper reviews the results obtained for spatial population models and the evolution of the genealogies of these populations during the last decade by the author and his coworkers. The focus is on their large scale behaviour and on the analysis of universality classes of large scale behaviour via the methods of the hierarchical mean-field limit or via the spatial continuum limit and from another angel, the finite system scheme . We use genealogical information to analyze the type and location structure and vice versa. To apply this approach and to explain effects in biological situations we …
