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Register a new userPartitioning, duality, and linkage disequilibria in the Moran model with recombination
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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 the sites in $A_m$ in individual $m$, where the individuals are sampled from the current population without replacement. Following the ancestry of these sites backwards in time yields a process on the set of partitions of $S$, which, in the diffusion limit, turns into a marginalised version of the $n$-locus ancestral recombination graph. With the help of an inclusion-exclusion principle, we show that the type distribution corresponding to a given partition may be represented in a systematic way, with the help of so-called recombinators and sampling functions. The same is true of correlation functions (known as linkage disequilibria in genetics) of all orders. We prove that the partitioning process (backward in time) is dual to the Moran population process (forward in time), where the sampling function plays the role of the duality function. This sheds new light on the work of Bobrowski, Wojdyla, and Kimmel (2010). The result also leads to a closed system of ordinary differential equations for the expectations of the sampling functions, which can be translated into expected type distributions and expected linkage disequilibria.
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Moran or Wright-Fisher processes are probably the most well known model to study the evolution of a population under various effects. Our object of study will be the Simpson index which measures the level of diversity of the population, one of the key parameter for ecologists who study for example forest dynamics. Following ecological motivations, we will consider here the case where there are various species with fitness and immigration parameters being random processes (and thus time evolving). To measure biodiversity, ecologists generally use the Simpson index, who has no closed formula, except in the neutral (no selection) case via a backward approach, and which is difficult to evaluate even numerically when the population size is large. Our approach relies on the large population limit in the weak selection case, and thus to give a procedure which enable us to approximate, with controlled rate, the expectation of the Simpson index at fixed time. Our approach will be forward and valid for all time, which is the main difference with the historical approach of Kingman, or Krone-Neuhauser. We will also study the long time behaviour of the Wright-Fisher process in a simplified setting, allowing us to get a full picture for the approximation of the expectation of the Simpson index.
$Lambda$-Wright--Fisher processes provide a robust framework to describe the type-frequency evolution of an infinite neutral population. We add a polynomial drift to the corresponding stochastic differential equation to incorporate frequency-dependent selection. A decomposition of the drift allows us to approximate the solution of the stochastic differential equation by a sequence of Moran models. The genealogical structure underlying the Moran model leads in the large population limit to a generalisation of the ancestral selection graph of Krone and Neuhauser. Building on this object, we construct a continuous-time Markov chain and relate it to the forward process via a new form of duality, which we call Bernstein duality. We adapt classical methods based on the moment duality to determine the time to absorption and criteria for the accessibility of the boundaries; this extends a recent result by Gonzalez Casanova and Span`o. An intriguing feature of the construction is that the same forward process is compatible with multiple backward models. In this context we introduce suitable notions for minimality among the ancestral processes and characterise the corresponding parameter sets. In this way we recover classic ancestral structures as minimal ones.
We consider the mutation--selection differential equation with pairwise interaction (or, equivalently, the diploid mutation--selection equation) and establish the corresponding ancestral process, which is a random tree and a variant of the ancestral selection graph. The formal relation to the forward model is given via duality. To make the tree tractable, we prune branches upon mutations, thus reducing it to its informative parts. The hierarchies inherent in the tree are encoded systematically via tripod trees with weighted leaves; this leads to the stratified ancestral selection graph. The latter also satisfies a duality relation with the mutation--selection equation. Each of the dualities provides a stochastic representation of the solution of the differential equation. This allows us to connect the equilibria and their bifurcations to the long-term behaviour of the ancestral process. Furthermore, with the help of the stratified ancestral selection graph, we obtain explicit results about the ancestral type distribution in the case of unidirectional mutation.
We study ancestral structures for the two-type Moran model with two-way mutation and frequency-dependent selection that follows the nonlinear dominance or fittest-type-wins scheme. Both schemes lead, in distribution, to the same type-frequency process. Reasoning through the mutation structure on the ancestral selection graph (ASG), we derive processes suitable to determine the type distribution of the present and ancestral population, leading to, respectively, the killed and pruned lookdown ASG. To this end, we establish factorial moment dualities to the Moran model and a relative thereof, respectively. Finally, we extend the results to the diffusion limit.
We consider a spatial model of cancer in which cells are points on the $d$-dimensional torus $mathcal{T}=[0,L]^d$, and each cell with $k-1$ mutations acquires a $k$th mutation at rate $mu_k$. We will assume that the mutation rates $mu_k$ are increasing, and we find the asymptotic waiting time for the first cell to acquire $k$ mutations as the torus volume tends to infinity. This paper generalizes results on waiting for $kgeq 3$ mutations by Foo, Leder, and Schweinsberg, who considered the case in which all of the mutation rates $mu_k$ were the same. In addition, we find the limiting distribution of the spatial distances between mutations for certain values of the mutation rates.
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