Matthias Birkner

Computing likelihoods for coalescents with multiple collisions in the infinitely many sites model.

One of the central problems in mathematical genetics is the inference of evolutionary parameters of a population (such as the mutation rate) based on the observed genetic types in a finite DNA sample. If the population model under consideration is in the domain of attraction of the classical Fleming–Viot process, such as the Wright–Fisher- or the Moran model, then the standard means to describe its genealogy is Kingman’s coalescent. For this coalescent process, powerful inference methods are well-established. An important feature of the above class of models is, roughly speaking, that the number of offspring of each individual is small when compared to the total population size, and hence all ancestral collisions are binary only. Recently, more general population models have been studied, in particular in the domain of attraction of so-called generalised Λ-Fleming–Viot processes, as well as their (dual) genealogies, given by the so-called Λ-coalescents, which allow multiple collisions. Moreover, Eldon and Wakeley (Genetics 172:2621–2633, 2006) provide evidence that such more general coalescents might actually be more adequate to describe real populations with extreme reproductive behaviour, in particular many marine species. In this paper, we extend methods of Ethier and Griffiths (Ann Probab 15(2):515–545, 1987) and Griffiths and Tavaré (Theor Pop Biol 46:131–159, 1994a, Stat Sci 9:307–319, 1994b, Philos Trans Roy Soc Lond Ser B 344:403–410, 1994c, Math Biosci 12:77–98, 1995) to obtain a likelihood based inference method for general Λ-coalescents. In particular, we obtain a method to compute (approximate) likelihood surfaces for the observed type probabilities of a given sample. We argue that within the (vast) family of Λ-coalescents, the parametrisable sub-family of Beta(2 − α, α)-coalescents, where α ∈ (1, 2], are of particular relevance. We illustrate our method using simulated datasets, thus obtaining maximum-likelihood estimators of mutation and demographic parameters.

Annealed vs Quenched Critical Points for a Random Walk Pinning Model

We study a random walk pinning model, where conditioned on a simple random walk Y on Z d acting as a random medium, the path measure of a second independent simple random walk X up to time t is Gibbs transformed with Hamiltonian −Lt(X, Y ), where Lt(X, Y ) is the collision local time between X and Y up to time t. This model arises naturally in various contexts, including the study of the parabolic Anderson model with moving catalysts, the parabolic Anderson model with Brownian noise, and the directed polymer model. It falls in the same framework as the pinning and copolymer models, and exhibits a localization-delocalization transition as the inverse temperature β varies. We show that in dimensions d = 1,2, the annealed and quenched critical values of β are both 0, while in dimensions d ≥ 4, the quenched critical value of β is strictly larger than the annealed critical value (which is positive). This implies the existence of certain intermediate regimes for the parabolic Anderson model with Brownian noise and the directed polymer model. For d ≥ 5, the same result has recently been established by Birkner, Greven and den Hollander [BGdH08] via a quenched large deviation principle. Our proof is based on a fractional moment method used recently by Derrida, Giacomin, Lacoin and Toninelli [DGLT07] to establish the non-coincidence of annealed and quenched critical points for the pinning model in the disorder-relevant regime. The critical case d = 3 remains open.

Branching Processes in Random Environment — A View on Critical and Subcritical Cases

Branching processes exhibit a particularly rich longtime behaviour when evolving in a random environment. Then the transition from subcriticality to supercriticality proceeds in several steps, and there occurs a second ‘transition’ in the subcritical phase (besides the phase-transition from (sub)criticality to supercriticality). Here we present and discuss limit laws for branching processes in critical and subcritical i.i.d. environment. The results rely on a stimulating interplay between branching process theory and random walk theory. We also consider a spatial version of branching processes in random environment for which we derive extinction and ultimate survival criteria.

Diffraction of Stochastic Point Sets: Explicitly Computable Examples

Stochastic point processes relevant to the theory of long-range aperiodic order are considered that display diffraction spectra of mixed type, with special emphasis on explicitly computable cases together with a unified approach of reasonable generality. The latter is based on the classical theory of point processes and the Palm distribution. Several pairs of autocorrelation and diffraction measures are discussed which show a duality structure analogous to that of the Poisson summation formula for lattice Dirac combs.

Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger Coalescents?

The ability of the site-frequency spectrum (SFS) to reflect the particularities of gene genealogies exhibiting multiple mergers of ancestral lines as opposed to those obtained in the presence of population growth is our focus. An excess of singletons is a well-known characteristic of both population growth and multiple mergers. Other aspects of the SFS, in particular, the weight of the right tail, are, however, affected in specific ways by the two model classes. Using an approximate likelihood method and minimum-distance statistics, our estimates of statistical power indicate that exponential and algebraic growth can indeed be distinguished from multiple-merger coalescents, even for moderate sample sizes, if the number of segregating sites is high enough. A normalized version of the SFS (nSFS) is also used as a summary statistic in an approximate Bayesian computation (ABC) approach. The results give further positive evidence as to the general eligibility of the SFS to distinguish between the different histories.

Statistical Properties of the Site-Frequency Spectrum Associated with Lambda-Coalescents

Statistical properties of the site-frequency spectrum associated with Λ-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estimating coalescent parameters introduced by certain Λ-coalescents for data sets too large for full-likelihood methods is our focus. The recursions for the expected values we obtain can be used to find the parameter values that give the best fit to the observed frequency spectrum. The expected values are also used to approximate the probability a (derived) mutation arises on a branch subtending a given number of leaves (DNA sequences), allowing us to apply a pseudolikelihood inference to estimate coalescence parameters associated with certain subclasses of Λ-coalescents. The properties of the pseudolikelihood approach are investigated on simulated as well as real mtDNA data sets for the high-fecundity Atlantic cod (Gadus morhua). Our results for two subclasses of Λ-coalescents show that one can distinguish these subclasses from the Kingman coalescent, as well as between the Λ-subclasses, even for a moderate (maybe a few hundred) sample size.

An Ancestral Recombination Graph for Diploid Populations with Skewed Offspring Distribution

A large offspring-number diploid biparental multilocus population model of Moran type is our object of study. At each time step, a pair of diploid individuals drawn uniformly at random contributes offspring to the population. The number of offspring can be large relative to the total population size. Similar “heavily skewed” reproduction mechanisms have been recently considered by various authors (cf. e.g., Eldon and Wakeley 2006, 2008) and reviewed by Hedgecock and Pudovkin (2011). Each diploid parental individual contributes exactly one chromosome to each diploid offspring, and hence ancestral lineages can coalesce only when in distinct individuals. A separation-of-timescales phenomenon is thus observed. A result of Möhle (1998) is extended to obtain convergence of the ancestral process to an ancestral recombination graph necessarily admitting simultaneous multiple mergers of ancestral lineages. The usual ancestral recombination graph is obtained as a special case of our model when the parents contribute only one offspring to the population each time. Due to diploidy and large offspring numbers, novel effects appear. For example, the marginal genealogy at each locus admits simultaneous multiple mergers in up to four groups, and different loci remain substantially correlated even as the recombination rate grows large. Thus, genealogies for loci far apart on the same chromosome remain correlated. Correlation in coalescence times for two loci is derived and shown to be a function of the coalescence parameters of our model. Extending the observations by Eldon and Wakeley (2008), predictions of linkage disequilibrium are shown to be functions of the reproduction parameters of our model, in addition to the recombination rate. Correlations in ratios of coalescence times between loci can be high, even when the recombination rate is high and sample size is large, in large offspring-number populations, as suggested by simulations, hinting at how to distinguish between different population models.

Blow-up of semilinear pde's at the critical dimension. A probabilistic approach

We present a probabilistic approach which proves blow-up of solutions of the Fujita equation ∂w/∂t = -(-Δ) α/2 w + w 1+β in the critical dimension d = α/β. By using the Feynman-Kac representation twice, we construct a subsolution which locally grows to infinity as t → ∞. In this way, we cover results proved earlier by analytic methods. Our method also applies to extend a blow-up result for systems proved for the Laplacian case by Escobedo and Levine (1995) to the case of α-Laplacians with possibly different parameters a.

Survival and complete convergence for a spatial branching system with local regulation

We study a discrete time spatial branching system on

Random walks in dynamic random environments and ancestry under local population regulation

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