Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Coupled-mode equations and gap solitons in a two-dimensional nonlinear elliptic problem with a separable periodic potential

We address a two-dimensional nonlinear elliptic problem with a finite-amplitude periodic potential. For a class of separable symmetric potentials, we study the bifurcation of the first band gap in the spectrum of the linear Schr\"{o}dinger operator and the relevant coupled-mode equations to describe this bifurcation. The coupled-mode equations are derived by the rigorous analysis based on the Fourier--Bloch decomposition and the Implicit Function Theorem in the space of bounded continuous functions vanishing at infinity. Persistence of reversible localized solutions, called gap solitons, beyond the coupled-mode equations is proved under a non-degeneracy assumption on the kernel of the linearization operator. Various branches of reversible localized solutions are classified numerically in the framework of the coupled-mode equations and convergence of the approximation error is verified. Error estimates on the time-dependent solutions of the Gross--Pitaevskii equation and the coupled-mode equations are obtained for a finite-time interval.Comment: 32 pages, 16 figure

No cosmological domain wall problem for weakly coupled fields

After inflation occurs, a weakly coupled scalar field will in general not be in thermal equilibrium but have a distribution of values determined by the inflationary Hubble parameter. If such a field subsequently undergoes discrete symmetry breaking, then the different degenerate vacua may not be equally populated so the domain walls which form will be `biased' and the wall network will subsequently collapse. Thus the cosmological domain wall problem may be solved for sufficiently weakly coupled fields in a post-inflationary universe. We quantify the criteria for determining whether this does happen, using a Higgs-like potential with a spontaneously broken $Z_2$ symmetry.Comment: 17 pages, 4 figures (Revtex), clarifying Comments added in Introduction; to appear in Phys. Rev

Solar Wakes of Dark Matter Flows

We analyze the effect of the Sun's gravitational field on a flow of cold dark matter (CDM) through the solar system in the limit where the velocity dispersion of the flow vanishes. The exact density and velocity distributions are derived in the case where the Sun is a point mass. The results are extended to the more realistic case where the Sun has a finite size spherically symmetric mass distribution. We find that regions of infinite density, called caustics, appear. One such region is a line caustic on the axis of symmetry, downstream from the Sun, where the flow trajectories cross. Another is a cone-shaped caustic surface near the trajectories of maximum scattering angle. The trajectories forming the conical caustic pass through the Sun's interior and probe the solar mass distribution, raising the possibility that the solar mass distribution may some day be measured by a dark matter detector on Earth. We generalize our results to the case of flows with continuous velocity distributions, such as that predicted by the isothermal model of the Milky Way halo.Comment: 30 pages, 8 figure

Phenomenology of Λ\Lambda-CDM model: a possibility of accelerating Universe with positive pressure

Among various phenomenological $\Lambda$ models, a time-dependent model $\dot \Lambda\sim H^3$ is selected here to investigate the $\Lambda$-CDM cosmology. Using this model the expressions for the time-dependent equation of state parameter $\omega$ and other physical parameters are derived. It is shown that in $H^3$ model accelerated expansion of the Universe takes place at negative energy density, but with a positive pressure. It has also been possible to obtain the change of sign of the deceleration parameter $q$ during cosmic evolution.Comment: 16 Latex pages, 11 figures, Considerable modifications in the text; Accepted in IJT

Fertility, Living Arrangements, Care and Mobility

There are four main interconnecting themes around which the contributions in this book are based. This introductory chapter aims to establish the broad context for the chapters that follow by discussing each of the themes. It does so by setting these themes within the overarching demographic challenge of the twenty-first century – demographic ageing. Each chapter is introduced in the context of the specific theme to which it primarily relates and there is a summary of the data sets used by the contributors to illustrate the wide range of cross-sectional and longitudinal data analysed

Dark matter and Colliders searches in the MSSM

We study the complementarity between dark matter experiments (direct detection and indirect detections) and accelerator facilities (the CERN LHC and a $\sqrt{s}= 1$ TeV $e^+e^-$ Linear Collider) in the framework of the constrained Minimal Supersymmetric Standard Model (MSSM). We show how non--universality in the scalar and gaugino sectors can affect the experimental prospects to discover the supersymmetric particles. The future experiments will cover a large part of the parameter space of the MSSM favored by WMAP constraint on the relic density, but there still exist some regions beyond reach for some extreme (fine tuned) values of the supersymmetric parameters. Whereas the Focus Point region characterized by heavy scalars will be easily probed by experiments searching for dark matter, the regions with heavy gauginos and light sfermions will be accessible more easily by collider experiments. More informations on both supersymmetry and astrophysics parameters can be thus obtained by correlating the different signals.Comment: 25 pages, 10 figures, corrected typos and reference adde

Atmospheric Heating and Wind Acceleration: Results for Cool Evolved Stars based on Proposed Processes

A chromosphere is a universal attribute of stars of spectral type later than ~F5. Evolved (K and M) giants and supergiants (including the zeta Aurigae binaries) show extended and highly turbulent chromospheres, which develop into slow massive winds. The associated continuous mass loss has a significant impact on stellar evolution, and thence on the chemical evolution of galaxies. Yet despite the fundamental importance of those winds in astrophysics, the question of their origin(s) remains unsolved. What sources heat a chromosphere? What is the role of the chromosphere in the formation of stellar winds? This chapter provides a review of the observational requirements and theoretical approaches for modeling chromospheric heating and the acceleration of winds in single cool, evolved stars and in eclipsing binary stars, including physical models that have recently been proposed. It describes the successes that have been achieved so far by invoking acoustic and MHD waves to provide a physical description of plasma heating and wind acceleration, and discusses the challenges that still remain.Comment: 46 pages, 9 figures, 1 table; modified and unedited manuscript; accepted version to appear in: Giants of Eclipse, eds. E. Griffin and T. Ake (Berlin: Springer

The modulation effect for supersymmetric dark matter detection with asymmetric velocity dispersion

The detection of the theoretically expected dark matter is central to particle physics cosmology. Current fashionable supersymmetric models provide a natural dark matter candidate which is the lightest supersymmetric particle (LSP). Such models combined with fairly well understood physics like the quark substructure of the nucleon and the nuclear form factor and the spin response function of the nucleus, permit the evaluation of the event rate for LSP-nucleus elastic scattering. The thus obtained event rates are, however, very low or even undetectable. So it is imperative to exploit the modulation effect, i.e. the dependence of the event rate on the earth's annual motion. In this review we study such a modulation effect in directional and undirectional experiments. We calculate both the differential and the total rates using symmetric as well as asymmetric velocity distributions. We find that in the symmetric case the modulation amplitude is small, less than 0.07. There exist, however, regions of the phase space and experimental conditions such that the effect can become larger. The inclusion of asymmetry, with a realistic enhanced velocity dispersion in the galactocentric direction, yields the bonus of an enhanced modulation effect, with an amplitude which for certain parameters can become as large as 0.46.Comment: 35 LATEX pages, 7 Tables, 8 PostScript Figures include

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss

Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While duplication–loss (DL) reconciliation leads to a unique maximum-parsimony solution, duplication-transfer-loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult to infer the true evolutionary history of the gene family. This problem is further exacerbated by the fact that different event cost assignments yield different sets of optimal reconciliations. Here, we present an effective, efficient, and scalable method for dealing with these fundamental problems in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We show that even gene trees with only a few dozen genes often have millions of optimal reconciliations and present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn[superscript 2]) time per sample, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mappings and event assignments and to investigate the impact of varying event costs. We apply our method to a biological dataset of approximately 4700 gene trees from 100 taxa and observe that 93% of event assignments and 73% of mappings remain consistent across different multiple optima. Our analysis represents the first systematic investigation of the space of optimal DTL reconciliations and has many important implications for the study of gene family evolution.National Science Foundation (U.S.) (CAREER Award 0644282)National Institutes of Health (U.S.) (Grant RC2 HG005639)National Science Foundation (U.S.). Assembling the Tree of Life (Program) (Grant 0936234