arXiv subjects

Jochen Blath

Publications and source records attributed to Jochen Blath.

33 records · Page 2Linked to original sources

arXiv2018

The seed bank coalescent with simultaneous switching

We introduce a new Wright-Fisher type model for seed banks incorporating "simultaneous switching", which is motivated by recent work on microbial dormancy. We show that the simultaneous switching mechanism leads to a new jump-diffusion limit for the scaled frequency processes, extending the classical Wright-Fisher and seed bank diffusion limits. We further establish a new dual coalescent structure with multiple activation and deactivation events of lineages. While this seems reminiscent of multiple merger events in general exchangeable coalescents, it actually leads to an entirely new class of coalescent processes with unique qualitative and quantitative behaviour. To illustrate this, we provide a novel kind of condition for coming down from infinity for these coalescents using recent results of Griffiths.

q-bio.PE↗

arXiv2018

Structural properties of the seed bank and the two-island diffusion

We investigate various aspects of the (biallelic) Wright-Fisher diffusion with seed bank in conjunction with and contrast to the two-island model analysed e.g. in Kermany, Zhou and Hickey, 2008, and Nath and Griffiths, 1993, including moments, stationary distribution and reversibility, for which our main tool is duality. Further, we show that the Wright-Fisher diffusion with seed bank can be reformulated as a one-dimensional stochastic delay differential equation, providing an elegant interpretation of the age structure in the seed bank also forward in time in the spirit of Kaj, Krone and Lascoux, 2001. We also provide a complete boundary classification for this two-dimensional SDE using martingale-based reasoning known as McKean's argument.

math.PR↗

arXiv2016

A new coalescent for seed-bank models

We identify a new natural coalescent structure, which we call the seed-bank coalescent, that describes the gene genealogy of populations under the influence of a strong seed-bank effect, where "dormant forms" of individuals (such as seeds or spores) may jump a significant number of generations before joining the "active" population. Mathematically, our seed-bank coalescent appears as scaling limit in a Wright-Fisher model with geometric seed-bank age structure if the average time of seed dormancy scales with the order of the total population size $N$. This extends earlier results of Kaj, Krone and Lascoux [J. Appl. Probab. 38 (2011) 285-300] who show that the genealogy of a Wright-Fisher model in the presence of a "weak" seed-bank effect is given by a suitably time-changed Kingman coalescent. The qualitatively new feature of the seed-bank coalescent is that ancestral lineages are independently blocked at a certain rate from taking part in coalescence events, thus strongly altering the predictions of classical coalescent models. In particular, the seed-bank coalescent "does not come down from infinity," and the time to the most recent common ancestor of a sample of size $n$ grows like $\log\log n$. This is in line with the empirical observation that seed-banks drastically increase genetic variability in a population and indicates how they may serve as a buffer against other evolutionary forces such as genetic drift and selection.

math.PR↗

arXiv2016

The scaling limit of the interface of the continuous-space symbiotic branching model

The continuous-space symbiotic branching model describes the evolution of two interacting populations that can reproduce locally only in the simultaneous presence of each other. If started with complementary Heaviside initial conditions, the interface where both populations coexist remains compact. Together with a diffusive scaling property, this suggests the presence of an interesting scaling limit. Indeed, in the present paper, we show weak convergence of the diffusively rescaled populations as measure-valued processes in the Skorokhod, respectively the Meyer-Zheng, topology (for suitable parameter ranges). The limit can be characterized as the unique solution to a martingale problem and satisfies a "separation of types" property. This provides an important step toward an understanding of the scaling limit for the interface. As a corollary, we obtain an estimate on the moments of the width of an approximate interface.

math.PR↗

arXiv2015

A new class of large claim size distributions: Definition, properties, and ruin theory

We investigate a new natural class $\mathcal{J}$ of probability distributions modeling large claim sizes, motivated by the `principle of one big jump'. Though significantly more general than the (sub-)class of subexponential distributions $\mathcal{S}$, many important and desirable structural properties can still be derived. We establish relations to many other important large claim distribution classes (such as $\mathcal{D}$, $\mathcal{S}$, $\mathcal{L}$, $\mathcal {K}$, $\mathcal{OS}$ and $\mathcal{OL}$), discuss the stability of $\mathcal{J}$ under tail-equivalence, convolution, convolution roots, random sums and mixture, and then apply these results to derive a partial analogue of the famous Pakes-Veraverbeke-Embrechts theorem from ruin theory for $\mathcal{J}$. Finally, we discuss the (weak) tail-equivalence of infinitely-divisible distributions in $\mathcal{J}$ with their Lévy measure.

math.PR↗

arXiv2014

The largest strongly connected component in Wakeley et al's cyclical pedigree model

We establish a link between Wakeley et al's (2012) cyclical pedigree model from population genetics and a randomized directed configuration model (DCM) considered by Cooper and Frieze (2004). We then exploit this link in combination with asymptotic results for the in-degree distribution of the corresponding DCM to compute the asymptotic size of the largest strongly connected component $S^N$ (where $N$ is the population size) of the DCM resp. the pedigree. The size of the giant component can be characterized explicitly (amounting to approximately $80 \%$ of the total populations size) and thus contributes to a reduced `pedigree effective population size'. In addition, the second largest strongly connected component is only of size $O(\log N)$. Moreover, we describe the size and structure of the `domain of attraction' of $S^N$. In particular, we show that with high probability for any individual the shortest ancestral line reaches $S^N$ after $O(\log \log N)$ generations, while almost all other ancestral lines take at most $O(\log N)$ generations.

math.PR↗

arXiv2014

Genealogy of a Wright Fisher model with strong seed bank component

We investigate the behaviour of the genealogy of a Wright-Fisher population model under the influence of a strong seed-bank effect. More precisely, we consider a simple seed-bank age distribution with two atoms, leading to either classical or long genealogical jumps (the latter modeling the effect of seed-dormancy). We assume that the length of these long jumps scales like a power $N^β$ of the original population size $N$, thus giving rise to a `strong' seed-bank effect. For a certain range of $β$, we prove that the ancestral process of a sample of $n$ individuals converges under a non-classical time-scaling to Kingman's $n-$coalescent. Further, for a wider range of parameters, we analyze the time to the most recent common ancestor of two individuals analytically and by simulation.

math.PR↗

arXiv2013

Statistical properties of the site-frequency spectrum associated with Lambda-coalescents

Statistical properties of the site frequency spectrum associated with Lambda-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 Lambda-coalescents for datasets 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 which 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 pseudo-likelihood inference to estimate coalescence parameters associated with certain subclasses of Lambda coalescents. The properties of the pseudo-likelihood approach are investigated on simulated as well as real mtDNA datasets for the high fecundity Atlantic cod (\emph{Gadus morhua}). Our results for two subclasses of Lambda coalescents show that one can distinguish these subclasses from the Kingman coalescent, as well as between the Lambda-subclasses, even for moderate sample sizes.

q-bio.PE↗

arXiv2013

The ancestral process of long term seed bank models

We present a new model for seed banks, where direct ancestors of individuals may have lived in the near as well as the very far past. The classical Wright-Fisher model, as well as a seed bank model with bounded age distribution considered by Kaj, Krone and Lascoux (2001) are special cases of our model. We discern three parameter regimes of the seed bank age distribution, which lead to substantially different behaviour in terms of genetic variability, in particular with respect to fixation of types and time to the most recent common ancestor. We prove that for age distributions with finite mean, the ancestral process converges to a time-changed Kingman coalescent, while in the case of infinite mean, ancestral lineages might not merge at all with positive probability. Further, we present a construction of the forward in time process in equilibrium. The mathematical methods are based on renewal theory, the urn process introduced by Kaj et al., as well as on a paper by Hammond and Sheffield (2011).

math.PR↗

arXiv2012

Analysis of DNA sequence variation within marine species using Beta-coalescents

We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock's "reproduction sweepstakes". Besides the data analysis, in particular the inference of mutation rates and the estimation of the (real) time to the most recent common ancestor, we briefly address the question whether the genealogies might be adequately described by so-called Beta coalescents (as opposed to Kingman's coalescent), allowing multiple mergers of genealogies. The choice of the underlying coalescent model for the genealogy has drastic implications for the estimation of the above quantities, in particular the real-time embedding of the genealogy.

q-bio.PE↗

arXiv2012

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 timestep, a pair of diploid individuals drawn uniformly at random contribute offspring to the population. The number of offspring can be large relative to the total population size. Similar `heavily skewed' reproduction mechanisms have been considered by various authors recently. Each diploid parental individual contributes exactly one chromosome to each diploid offspring, and hence ancestral lineages can only coalesce 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.

q-bio.PE↗

arXiv2011

Importance sampling for Lambda-coalescents in the infinitely many sites model

We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et. al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavaré (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et. al. (2008). We conclude with a performance comparison of classical and new schemes for Beta- and Kingman coalescents.

math.PR↗

arXiv2010

On the moments and the interface of the symbiotic branching model

In this paper we introduce a critical curve separating the asymptotic behavior of the moments of the symbiotic branching model, introduced by Etheridge and Fleischmann [Stochastic Process. Appl. 114 (2004) 127--160] into two regimes. Using arguments based on two different dualities and a classical result of Spitzer [Trans. Amer. Math. Soc. 87 (1958) 187--197] on the exit-time of a planar Brownian motion from a wedge, we prove that the parameter governing the model provides regimes of bounded and exponentially growing moments separated by subexponential growth. The moments turn out to be closely linked to the limiting distribution as time tends to infinity. The limiting distribution can be derived by a self-duality argument extending a result of Dawson and Perkins [Ann. Probab. 26 (1998) 1088--1138] for the mutually catalytic branching model. As an application, we show how a bound on the 35th moment improves the result of Etheridge and Fleischmann [Stochastic Process. Appl. 114 (2004) 127--160] on the speed of the propagation of the interface of the symbiotic branching model.

math.PR↗

arXiv2008

A modified lookdown construction for the Xi-Fleming-Viot process with mutation and populations with recurrent bottlenecks

Let $Λ$ be a finite measure on the unit interval. A $Λ$-Fleming-Viot process is a probability measure valued Markov process which is dual to a coalescent with multiple collisions ($Λ$-coalescent) in analogy to the duality known for the classical Fleming Viot process and Kingman's coalescent, where $Λ$ is the Dirac measure in 0. We explicitly construct a dual process of the coalescent with simultaneous multiple collisions ($Ξ$-coalescent) with mutation, the $Ξ$-Fleming-Viot process with mutation, and provide a representation based on the empirical measure of an exchangeable particle system along the lines of Donnelly and Kurtz (1999). We establish pathwise convergence of the approximating systems to the limiting $Ξ$-Fleming-Viot process with mutation. An alternative construction of the semigroup based on the Hille-Yosida theorem is provided and various types of duality of the processes are discussed. In the last part of the paper a population is considered which undergoes recurrent bottlenecks. In this scenario, non-trivial $Ξ$-Fleming-Viot processes naturally arise as limiting models.

math.PR↗

arXiv2007

Coexistence in locally regulated competing populations and survival of branching annihilating random walk

We propose two models of the evolution of a pair of competing populations. Both are lattice based. The first is a compromise between fully spatial models, which do not appear amenable to analytic results, and interacting particle system models, which do not, at present, incorporate all of the competitive strategies that a population might adopt. The second is a simplification of the first, in which competition is only supposed to act within lattice sites and the total population size within each lattice point is a constant. In a special case, this second model is dual to a branching annihilating random walk. For each model, using a comparison with oriented percolation, we show that for certain parameter values, both populations will coexist for all time with positive probability. As a corollary, we deduce survival for all time of branching annihilating random walk for sufficiently large branching rates. We also present a number of conjectures relating to the rôle of space in the survival probabilities for the two populations.

math.PR↗