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Register a new userGeneral selection models: Bernstein duality and minimal ancestral structures
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$Lambda$-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.
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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.
We consider inference about the history of a sample of DNA sequences, conditional upon the haplotype counts and the number of segregating sites observed at the present time. After deriving some theoretical results in the coalescent setting, we implement rejection sampling and importance sampling schemes to perform the inference. The importance sampling scheme addresses an extension of the Ewens Sampling Formula for a configuration of haplotypes and the number of segregating sites in the sample. The implementations include both constant and variable population size models. The methods are illustrated by two human Y chromosome data sets.
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 individuals potential ancestry back until the mutations that define the individuals type. The pruned lookdown ancestral selection graph allows one to trace the ancestry of individuals from a stationary distribution back into the distant past, thus leading to the stationary distribution of ancestral types. We illustrate the results by applying them to a prototype model for the error threshold phenomenon.
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Here we will use results of Cox, Durrett, and Perkins for voter model perturbations to study spatial evolutionary games on $Z^d$, $dge 3$ when the interaction kernel is finite range, symmetric, and has covariance matrix $sigma^2I$. The games we consider have payoff matrices of the form ${bf 1} + wG$ where ${bf 1}$ is matrix of all 1s and $w$ is small and positive. Since our population size $N=infty$, we call our selection small rather than weak which usually means $w =O(1/N)$. The key to studying these games is the fact that when the dynamics are suitably rescaled in space and time they convergence to solutions of a reaction diffusion equation (RDE). Inspired by work of Ohtsuki and Nowak and Tarnita et al we show that the reaction term is the replicator equation for a modified game matrix and the modifications of the game matrix depend on the interaction kernel only through the values of two or three simple probabilities for an associated coalescing random walk. Two strategy games lead to an RDE with a cubic nonlinearity, so we can describe the phase diagram completely. Three strategy games lead to a pair of coupled RDE, but using an idea from our earlier work, we are able to show that if there is a repelling function for the replicator equation for the modified game, then there is coexistence in the spatial game when selection is small. This enables us to prove coexistence in the spatial model in a wide variety of examples where the replicator equation of the modified game has an attracting equilibrium with all components positive. Using this result we are able to analyze the behavior of four evolutionary games that have recently been used in cancer modeling.
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