We derive large-sample and other limiting distributions of components of the allele frequency spectrum vector, $\mathbf{M}_n$, joint with the number of alleles, $K_n$, from a sample of n genes. Models analysed include those constructed from gamma and $\alpha$-stable subordinators by Kingman (thus including the Ewens model), the two-parameter extension by Pitman and Yor, and a two-parameter version constructed by omitting large jumps from an $\alpha$-stable subordinator. In each case the limiting distribution of a finite number of components of $\mathbf{M}_n$ is derived, joint with $K_n$. New results include that in the Poisson–Dirichlet case, $\mathbf{M}_n$ and $K_n$ are asymptotically independent after centering and norming for $K_n$, and it is notable, especially for statistical applications, that in other cases the limiting distribution of a finite number of components of $\mathbf{M}_n$, after centering and an unusual $n^{\alpha/2}$ norming, conditional on that of $K_n$, is normal.

We derive the large-sample distribution of the number of species in a version of Kingman’s Poisson–Dirichlet model constructed from an $\alpha$ -stable subordinator but with an underlying negative binomial process instead of a Poisson process. Thus it depends on parameters $\alpha\in (0,1)$ from the subordinator and $r>0$ from the negative binomial process. The large-sample distribution of the number of species is derived as sample size $n\to\infty$ . An important component in the derivation is the introduction of a two-parameter version of the Dickman distribution, generalising the existing one-parameter version. Our analysis adds to the range of Poisson–Dirichlet-related distributions available for modeling purposes.

In this paper we introduce multitype branching processes with inhomogeneous Poisson immigration, and consider in detail the critical Markov case when the local intensity r(t) of the Poisson random measure is a regularly varying function. Various multitype limit distributions (conditional and unconditional) are obtained depending on the rate at which r(t) changes with time. The asymptotic behaviour of the first and second moments, and the probability of nonextinction are investigated.

In this paper we provide an introduction to statistical inference for the classical linear birth‒death process, focusing on computational aspects of the problem in the setting of discretely observed processes. The basic probabilistic properties are given in Section 2, focusing on computation of the transition functions. This is followed by a brief discussion of simulation methods in Section 3, and of frequentist methods in Section 4. Section 5 is devoted to Bayesian methods, from rejection sampling to Markov chain Monte Carlo and approximate Bayesian computation. In Section 6 we consider the time-inhomogeneous case. The paper ends with a brief discussion in Section 7.

We consider a class of Sevastyanov branching processes with nonhomogeneous Poisson immigration. These processes relax the assumption required by the Bellman–Harris process which imposes the lifespan and offspring of each individual to be independent. They find applications in studies of the dynamics of cell populations. In this paper we focus on the subcritical case and examine asymptotic properties of the process. We establish limit theorems, which generalize classical results due to Sevastyanov and others. Our key findings include a novel law of large numbers and a central limit theorem which emerge from the nonhomogeneity of the immigration process.

Amethod for non-rigid image registration that is suitable for large deformations is presented. Conventional registration methods embed the image in a B-spline object, and the image is evolved by deforming the B-spline object. In this work, we represent the image using B-spline and deform the image using a composition approach. We also derive a computationally efficient algorithm for calculating the B-spline coefficients and gradients of the image by adopting ideas from signal processing using image filters. We demonstrate the application of our method on several different types of 2D and 3D images and compare it with existing methods.

We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein-Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the sample mean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean is approximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.

Identifiability of evolutionary tree models has been a recent topic of discussion and some models have been shown to be nonidentifiable. A coalescent-based rooted population tree model, originally proposed by Nielsen et al. (1998), has been used by many authors in the last few years and is a simple tool to accurately model the changes in allele frequencies in the tree. However, the identifiability of this model has never been proven. Here we prove this model to be identifiable by showing that the model parameters can be expressed as functions of the probability distributions of subsamples, assuming that there are at least two (haploid) individuals sampled from each population. This a step toward proving the consistency of the maximum likelihood estimator of the population tree based on this model.

We consider an inverse problem of determining unknown coefficients for a one-dimensional analogue of radiative transport equation. We show that some combination of the unknown coefficients can be uniquely determined by giving pulse-like inputs at the boundary and observing the corresponding outputs. Our result can be applied for determination of absorption and scattering properties of an optically turbid medium if the radiative transport equation is appropriate for describing the propagation of light in the medium.

The yeast Saccharomyces cerevisiae has emerged as an ideal model system to study the dynamics of prion proteins which are responsible for a number of fatal neurodegenerative diseases in humans. Within an infected cell, prion proteins aggregate in complexes which may increase in size or be fragmented and are transmitted upon cell division. Recent work in yeast suggests that only aggregates below a critical size are transmitted efficiently. We formulate a continuous-time branching process model of a yeast colony under conditions of prion curing. We generalize previous approaches by providing an explicit formula approximating prion loss as influenced by both aggregate growth and size-dependent transmission.

In the so-called lightbulb process, on days r = 1,…,n, out of n lightbulbs, all initially off, exactly r bulbs, selected uniformly and independent of the past, have their status changed from off to on, or vice versa. With X the number of bulbs on at the terminal time n, an even integer, and μ = n/2, σ2 = var(X), we have supz ∈ R | P((X - μ)/σ ≤ z) - P(Z ≤ z) | ≤ nΔ̅0/2σ2 + 1.64n/σ3 + 2/σ, where Z is a standard normal random variable and Δ̅0 = 1/2√n + 1/2n + e−n/2/3 for n ≥ 6, yielding a bound of order O(n−1/2) as n → ∞. A similar, though slightly larger bound, holds for odd n. The results are shown using a version of Stein's method for bounded, monotone size bias couplings. The argument for even n depends on the construction of a variable Xs on the same space as X that has the X-size bias distribution, that is, which satisfies E[Xg(X)] = μE[g(Xs)] for all bounded continuous g, and for which there exists a B ≥ 0, in this case B = 2, such that X ≤ Xs ≤ X + B almost surely. The argument for odd n is similar to that for even n, but one first couples X closely to V, a symmetrized version of X, for which a size bias coupling of V to Vs can proceed as in the even case. In both the even and odd cases, the crucial calculation of the variance of a conditional expectation requires detailed information on the spectral decomposition of the lightbulb chain.

Based on a simple model due to Dietz, it is shown that the size of a major epidemic of a vector-borne disease with basic reproduction ratio R0>1 is dominated by the size of a standard SIR (susceptible–infected–removed) epidemic with direct host-to-host transmission of disease and the same R0. Further bounds and numerical illustrations are provided, broadly spanning situations where the size of the epidemic is short of infecting almost all those susceptible. The total size is moderately sensitive to changes in the population parameters that contribute to R0, so that the fluctuating behaviour in ‘annual’ epidemics is not surprising.

We consider an epidemic model where the spread of the epidemic can be described by a discrete-time Galton-Watson branching process. Between times n and n + 1, any infected individual is detected with unknown probability π and the numbers of these detected individuals are the only observations we have. Detected individuals produce a reduced number of offspring in the time interval of detection, and no offspring at all thereafter. If only the generation sizes of a Galton-Watson process are observed, it is known that one can only estimate the first two moments of the offspring distribution consistently on the explosion set of the process (and, apart from some lattice parameters, no parameters that are not determined by those moments). Somewhat surprisingly, in our context, where we observe a binomially distributed subset of each generation, we are able to estimate three functions of the parameters consistently. In concrete situations, this often enables us to estimate π consistently, as well as the mean number of offspring. We apply the estimators to data for a real epidemic of classical swine fever.