Search

We show that genealogical trees arising from a broad class of non-neutral models of population evolution converge to the Kingman coalescent under a suitable rescaling of time. As well as non-neutral biological evolution, our results apply to genetic algorithms encompassing the prominent class of sequential Monte Carlo (SMC) methods. The time rescaling we need differs slightly from that used in classical results for convergence to the Kingman coalescent, which has implications for the performance of different resampling schemes in SMC algorithms. In addition, our work substantially simplifies earlier proofs of convergence to the Kingman coalescent, and corrects an error common to several earlier results.

Griffin, the second author, and Molnar studied coefficient duality for canonical bases for a broad range of spaces of weakly holomorphic modular forms, showing that the Fourier coefficients of canonical basis elements appear as negatives of Fourier coefficients for elements of a canonical basis of a related space of forms. We investigate the effect of the trace operator on this duality for modular forms for $\Gamma_0(N)$ of genus zero and show exactly when duality still holds after applying the trace operator., Comment: 19 pages

Wright-Fisher diffusions and their dual ancestral graphs occupy a central role in the study of allele frequency change and genealogical structure, and they provide expressions, explicit in some special cases but generally implicit, for the sampling probability, a crucial quantity in inference. Under a finite-allele mutation model, with possibly parent-dependent mutation, we consider the asymptotic regime where the selective advantage of one allele grows to infinity, while the other parameters remain fixed. In this regime, we show that the Wright-Fisher diffusion can be approximated either by a Gaussian process or by a process whose components are independent continuous-state branching processes with immigration, aligning with analogous results for Wright-Fisher models but employing different methods. While the first process becomes degenerate at stationarity, the latter does not and provides a simple, analytic approximation for the leading term of the sampling probability. Furthermore, using another approach based on a recursion formula, we characterise all remaining terms to provide a full asymptotic expansion for the sampling probability. Finally, we study the asymptotic behaviour of the rates of the block-counting process of the conditional ancestral selection graph and establish an asymptotic duality relationship between this and the diffusion., Comment: 41 pages

In this work, we develop excursion theory for the Wright-Fisher diffusion with recurrent mutation. Our construction is intermediate between the classical excursion theory where all excursions begin and end at a single point and the more general approach considering excursions of processes from general sets. Since the Wright-Fisher diffusion has two boundary points, it is natural to construct excursions which start from a specified boundary point, and end at one of two boundary points which determine the next starting point. In order to do this we study the killed Wright-Fisher diffusion, which is sent to a cemetery state whenever it hits either endpoint. We then construct a marked Poisson process of such killed paths which, when concatenated, produce a pathwise construction of the Wright-Fisher diffusion., Comment: 19 pages, 3 figures

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 at the requested sampling times from the law of the corresponding Wright--Fisher process. Output was validated by comparison to approximations of the transition density via the Kolmogorov--Smirnov test and QQ plots. All software is available at https://github.com/JaroSant/EWF, Comment: 34 pages, 12 figures

Recombination is a fundamental evolutionary force, but it is difficult to quantify because the effect of a recombination event on patterns of variation in a sample of genetic data can be hard to discern. Estimators for the recombination rate, which are usually based on the idea of integrating over the unobserved possible evolutionary histories of a sample, can therefore be noisy. Here we consider a related question: how would an estimator behave if the evolutionary history actually was observed? This would offer an upper bound on the performance of estimators used in practice. In this paper we derive an expression for the maximum likelihood estimator for the recombination rate based on a continuously observed, multi-locus, Wright--Fisher diffusion of haplotype frequencies, complementing existing work for an estimator of selection. We show that, contrary to selection, the estimator has unusual properties because the observed information matrix can explode in finite time whereupon the recombination parameter is learned without error. We also show that the recombination estimator is robust to the presence of selection in the sense that incorporating selection into the model leaves the estimator unchanged. We study the properties of the estimator by simulation and show that its distribution can be quite sensitive to the underlying mutation rates., Comment: 28 pages, 3 figures

Interacting particle systems undergoing repeated mutation and selection steps model genetic evolution, and also describe a broad class of sequential Monte Carlo methods. The genealogical tree embedded into the system is important in both applications. Under neutrality, when fitnesses of particles are independent from those of their parents, rescaled genealogies are known to converge to Kingman's coalescent. Recent work has established convergence under non-neutrality, but only for finite-dimensional distributions. We prove weak convergence of non-neutral genealogies on the space of c\`adl\`ag paths under standard assumptions, enabling analysis of the whole genealogical tree., Comment: 37 pages, 1 figure

We introduce a flexible method to simultaneously infer both the drift and volatility functions of a discretely observed scalar diffusion. We introduce spline bases to represent these functions and develop a Markov chain Monte Carlo algorithm to infer, a posteriori, the coefficients of these functions in the spline basis. A key innovation is that we use spline bases to model transformed versions of the drift and volatility functions rather than the functions themselves. The output of the algorithm is a posterior sample of plausible drift and volatility functions that are not constrained to any particular parametric family. The flexibility of this approach provides practitioners a powerful investigative tool, allowing them to posit a variety of parametric models to better capture the underlying dynamics of their processes of interest. We illustrate the versatility of our method by applying it to challenging datasets from finance, paleoclimatology, and astrophysics. In view of the parametric diffusion models widely employed in the literature for those examples, some of our results are surprising since they call into question some aspects of these models., Comment: 24 pages, 8 figures