arXiv subjects

P. Pfaffelhuber

Publications and source records attributed to P. Pfaffelhuber.

7 recordsLinked to original sources

arXiv2019

Markov branching processes with disasters: extinction, survival and duality to p-jump processes

A $p$-jump process is a piecewise deterministic Markov process with jumps by a factor of $p$. We prove a limit theorem for such processes on the unit interval. Via duality with respect to probability generating functions, we deduce limiting results for the survival probabilities of time-homogeneous branching processes with arbitrary offspring distributions, underlying binomial disasters. Extending this method, we obtain corresponding results for time-inhomogeneous birth-death processes underlying time-dependent binomial disasters and continuous state branching processes with $p$-jumps.

math.PR↗

arXiv2012

Muller's ratchet with compensatory mutations

We consider an infinite-dimensional system of stochastic differential equations describing the evolution of type frequencies in a large population. The type of an individual is the number of deleterious mutations it carries, where fitness of individuals carrying k mutations is decreased by αk for some α>0. Along the individual lines of descent, new mutations accumulate at rate λper generation, and each of these mutations has a probability γper generation to disappear. While the case γ=0 is known as (the Fleming-Viot version of) Muller's ratchet, the case γ>0 is associated with compensatory mutations in the biological literature. We show that the system has a unique weak solution. In the absence of random fluctuations in type frequencies (i.e., for the so-called infinite population limit) we obtain the solution in a closed form by analyzing a probabilistic particle system and show that for γ>0, the unique equilibrium state is the Poisson distribution with parameter λ/(γ+α).

math.PR↗

arXiv2011

Realistic extensions of a Brownian ratchet for protein translocation

We study a model for the translocation of proteins across membranes through a nanopore using a ratcheting mechanism. When the protein enters the nanopore it diffuses in and out of the pore according to a Brownian motion. Moreover, it is bound by ratcheting molecules which hinder the diffusion of the protein out of the nanopore, i.e. the Brownian motion is reflected such that no ratcheting molecule exits the pore. New ratcheting molecules bind at rate gamma. Extending our previous approach (Depperschmidt and Pfaffelhuber, 2010) we allow the ratcheting molecules to dissociate (at rate delta) from the protein (Model I). We also provide an approximate model (Model II) which assumes a Poisson equilibrium of ratcheting molecules on one side of the current reflection boundary. Using analytical methods and simulations we show that the speed of both models are approximately the same. Our analytical results on Model II give the speed of translocation by means of a solution of an ordinary differential equation.

math.PR↗

arXiv2010

The diversity of a distributed genome in bacterial populations

The distributed genome hypothesis states that the set of genes in a population of bacteria is distributed over all individuals that belong to the specific taxon. It implies that certain genes can be gained and lost from generation to generation. We use the random genealogy given by a Kingman coalescent in order to superimpose events of gene gain and loss along ancestral lines. Gene gains occur at a constant rate along ancestral lines. We assume that gained genes have never been present in the population before. Gene losses occur at a rate proportional to the number of genes present along the ancestral line. In this infinitely many genes model we derive moments for several statistics within a sample: the average number of genes per individual, the average number of genes differing between individuals, the number of incongruent pairs of genes, the total number of different genes in the sample and the gene frequency spectrum. We demonstrate that the model gives a reasonable fit with gene frequency data from marine cyanobacteria.

math.PR↗

arXiv2007

How often does the ratchet click? Facts, heuristics, asymptotics

The evolutionary force of recombination is lacking in asexually reproducing populations. As a consequence, the population can suffer an irreversible accumulation of deleterious mutations, a phenomenon known as Muller's ratchet. We formulate discrete and continuous time versions of Muller's ratchet. Inspired by Haigh's (1978) analysis of a dynamical system which arises in the limit of large populations, we identify the parameter gamma = N*lambda/(Ns*log(N*lambda)) as most important for the speed of accumulation of deleterious mutations. Here N is population size, s is the selection coefficient and lambda is the deleterious mutation rate. For large parts of the parameter range, measuring time in units of size N, deleterious mutations accumulate according to a power law in N*lambda with exponent gamma if gamma>0.5. For gamma<0.5 mutations cannot accumulate. We obtain diffusion approximations for three different parameter regimes, depending on the speed of the ratchet. Our approximations shed new light on analyses of Stephan et al. (1993) and Gordo & Charlesworth (2000). The heuristics leading to the approximations are supported by simulations.

math.PR↗

arXiv2006

Approximating genealogies for partially linked neutral loci under a selective sweep

Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is known as a selective sweep. The fixation of the beneficial allele not only affects sequence diversity at single neutral loci but also the joint allele distribution of several partially linked neutral loci. This distribution can be studied using the ancestral recombination graph for samples of partially linked neutral loci during the selective sweep. To approximate this graph, we extend recent work by Schweinsberg & Durrett 2005 and Etheridge, Pfaffelhuber & Wakolbinger 2006 using a marked Yule tree for the genealogy at a single neutral locus linked to a strongly beneficial one. We focus on joint genealogies at two partially linked neutral loci in the case of large selection coefficients αand recombination rates ρ= O(α/\logα) between loci. Our approach leads to a full description of the genealogy with accuracy of O((\log α)^{-2}) in probability. As an application, we derive the expectation of Lewontin's D as a measure for non-random association of alleles.

q-bio.PE↗

arXiv2006

The process of most recent common ancestors in an evolving coalescent

Consider a haploid population which has evolved through an exchangeable reproduction dynamics, and in which all individuals alive at time $t$ have a most recent common ancestor (MRCA) who lived at time $A_t$, say. As time goes on, not only the population but also its genealogy evolves: some families will get lost from the population and eventually a new MRCA will be established. For a time-stationary situation and in the limit of infinite population size $N$ with time measured in $N$ generations, i.e. in the scaling of population genetics which leads to Fisher-Wright diffusions and Kingman's coalescent, we study the process $\mathcal A = (A_t)$ whose jumps form the point process of time pairs $(E,B)$ when new MRCAs are established and when they lived. By representing these pairs as the entrance and exit time of particles whose trajectories are embedded in the look-down graph of Donnelly and Kurtz (1999) we can show by exchangeability arguments that the times $E$ as well as the times $B$ from a Poisson process. Furthermore, the particle representation helps to compute various features of the MRCA process, such as the distribution of the coalescent at the instant when a new MRCA is established, and the distribution of the number of MRCAs to come that live in today's past.

math.PR↗