Mitochondrial Dna Replacement Versus Nuclear Dna Persistence

In this paper we consider two populations whose generations are not overlapping and whose size is large. The number of males and females in both populations is constant. Any generation is replaced by a new one and any individual has two parents for what concerns nuclear DNA and a single one (the mother) for what concerns mtDNA. Moreover, at any generation some individuals migrate from the first population to the second. In a finite random time $T$, the mtDNA of the second population is completely replaced by the mtDNA of the first. In the same time, the nuclear DNA is not completely replaced and a fraction $F$ of the ancient nuclear DNA persists. We compute both $T$ and $F$. Since this study shows that complete replacement of mtDNA in a population is compatible with the persistence of a large fraction of nuclear DNA, it may have some relevance for the Out of Africa/Multiregional debate in Paleoanthropology

Parameter estimation in pair hidden Markov models

This paper deals with parameter estimation in pair hidden Markov models (pair-HMMs). We first provide a rigorous formalism for these models and discuss possible definitions of likelihoods. The model being biologically motivated, some restrictions with respect to the full parameter space naturally occur. Existence of two different Information divergence rates is established and divergence property (namely positivity at values different from the true one) is shown under additional assumptions. This yields consistency for the parameter in parametrization schemes for which the divergence property holds. Simulations illustrate different cases which are not covered by our results.Comment: corrected typo

A real-time hybrid aurora alert system:combining citizen science reports with an auroral oval model

Accurately predicting when, and from where, an aurora will be visible is particularly difficult, yet it is a service much desired by the general public. Several aurora alert services exist that attempt to provide such predictions but are, generally, based upon fairly coarse estimates of auroral activity (e.g. Kp or Dst). Additionally, these services are not able to account for a potential observer's local conditions (such as cloud cover or level of darkness). Aurorasaurus, however, combines data from the well-used, solar wind driven, OVATION Prime auroral oval model with real-time observational data provided by a global network of citizen scientists. This system is designed to provide more accurate and localized alerts for auroral visibility than currently available. Early results are promising and show that over 100,000 auroral visibility alerts have been issued, including nearly 200 highly localized alerts, to over 2,000 users located right across the globe

Time-Changed Poisson Processes

We consider time-changed Poisson processes, and derive the governing difference-differential equations (DDE) these processes. In particular, we consider the time-changed Poisson processes where the the time-change is inverse Gaussian, or its hitting time process, and discuss the governing DDE's. The stable subordinator, inverse stable subordinator and their iterated versions are also considered as time-changes. DDE's corresponding to probability mass functions of these time-changed processes are obtained. Finally, we obtain a new governing partial differential equation for the tempered stable subordinator of index $0<\beta<1,$ when $\beta$ is a rational number. We then use this result to obtain the governing DDE for the mass function of Poisson process time-changed by tempered stable subordinator. Our results extend and complement the results in Baeumer et al. \cite{B-M-N} and Beghin et al. \cite{BO-1} in several directions.Comment: 18 page

Effect of selection on ancestry: an exactly soluble case and its phenomenological generalization

We consider a family of models describing the evolution under selection of a population whose dynamics can be related to the propagation of noisy traveling waves. For one particular model, that we shall call the exponential model, the properties of the traveling wave front can be calculated exactly, as well as the statistics of the genealogy of the population. One striking result is that, for this particular model, the genealogical trees have the same statistics as the trees of replicas in the Parisi mean-field theory of spin glasses. We also find that in the exponential model, the coalescence times along these trees grow like the logarithm of the population size. A phenomenological picture of the propagation of wave fronts that we introduced in a previous work, as well as our numerical data, suggest that these statistics remain valid for a larger class of models, while the coalescence times grow like the cube of the logarithm of the population size.Comment: 26 page

Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein domains

We present a combined mean-field and simulation approach to different models describing the dynamics of classes formed by elements that can appear, disappear or copy themselves. These models, related to a paradigm duplication-innovation model known as Chinese Restaurant Process, are devised to reproduce the scaling behavior observed in the genome-wide repertoire of protein domains of all known species. In view of these data, we discuss the qualitative and quantitative differences of the alternative model formulations, focusing in particular on the roles of element loss and of the specificity of empirical domain classes.Comment: 10 Figures, 2 Table

On exact time-averages of a massive Poisson particle

In this work we study, under the Stratonovich definition, the problem of the damped oscillatory massive particle subject to a heterogeneous Poisson noise characterised by a rate of events, \lambda (t), and a magnitude, \Phi, following an exponential distribution. We tackle the problem by performing exact time-averages over the noise in a similar way to previous works analysing the problem of the Brownian particle. From this procedure we obtain the long-term equilibrium distributions of position and velocity as well as analytical asymptotic expressions for the injection and dissipation of energy terms. Considerations on the emergence of stochastic resonance in this type of system are also set forth.Comment: 21 pages, 5 figures. To be published in Journal of Statistical Mechanics: Theory and Experimen

Extremal spacings between eigenphases of random unitary matrices and their tensor products

Extremal spacings between eigenvalues of random unitary matrices of size N pertaining to circular ensembles are investigated. Explicit probability distributions for the minimal spacing for various ensembles are derived for N = 4. We study ensembles of tensor product of k random unitary matrices of size n which describe independent evolution of a composite quantum system consisting of k subsystems. In the asymptotic case, as the total dimension N = n^k becomes large, the nearest neighbor distribution P(s) becomes Poissonian, but statistics of extreme spacings P(s_min) and P(s_max) reveal certain deviations from the Poissonian behavior

On the Thermodynamic Limit in Random Resistors Networks

We study a random resistors network model on a euclidean geometry \bt{Z}^d. We formulate the model in terms of a variational principle and show that, under appropriate boundary conditions, the thermodynamic limit of the dissipation per unit volume is finite almost surely and in the mean. Moreover, we show that for a particular thermodynamic limit the result is also independent of the boundary conditions.Comment: 14 pages, LaTeX IOP journal preprint style file `ioplppt.sty', revised version to appear in Journal of Physics