Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleurenComment: 6 pages, 3 figures, accepted at BIBE 2017. Minor modifications to the text due to reviewer feedback and fixed typo

Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites

BACKGROUND: The molecular operational taxonomic unit(MOTU)has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of "reverse taxonomy" has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of "reverse taxonomy" has not been sufficiently evaluated. Therefore, the practical applicability of "reverse taxonomy" is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts. METHODOLOGY: Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types (= MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified. CONCLUSIONS: That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.Natsumi Kanzaki, Robin M. Giblin-Davis, Rudolf H. Scheffrahn, Hisatomo Taki, Alejandro Esquivel, Kerrie A. Davies and E. Allen Herr

Weaning Weight Summary for South Dakota Livestock Production Records Association Member Herds Using Crossbreeding

The primary objective of this study was to provide members of the Production Records Association an analysis of the weaning weights of various crossbreds produced in member herds. The results should form an important part of the total information needed by members and other cattlemen to formulate individual breeding programs

Disturbance alters beta-diversity but not the relative importance of community assembly mechanisms

Ecological disturbances are often hypothesized to alter community assembly processes that influence variation in community composition (β-diversity). Disturbance can cause convergence in community composition (low β-diversity) by increasing niche selection of disturbance-tolerant species. Alternatively, disturbance can cause divergence in community composition (high β-diversity) by increasing habitat filtering across environmental gradients. However, because disturbance may also influence β-diversity through random sampling effects owing to changes in the number of individuals in local communities (community size) or abundances in the regional species pool, observed patterns of β-diversity alone cannot be used to unambiguously discern the relative importance of community assembly mechanisms. We compared β-diversity of woody plants and inferred assembly mechanisms among unburned forests and forests managed with prescribed fires in the Missouri Ozarks, USA. Using a null-model approach, we compared how environmental gradients influenced β-diversity after controlling for differences in local community size and regional species abundances between unburned and burned landscapes. Observed β-diversity was higher in burned landscapes. However, this pattern disappeared or reversed after controlling for smaller community size in burned landscapes. β-diversity was higher than expected by chance in both landscapes, indicating an important role for processes that create clumped species distributions. Moreover, fire appeared to decrease clumping of species at broader spatial scales, suggesting homogenization of community composition through niche selection of disturbance-tolerant species. Environmental variables, however, explained similar amounts of variation in β-diversity in both landscapes, suggesting that disturbance did not alter the relative importance of habitat filtering. Our results indicate that contingent responses of communities to fire reflect a combination of fire-induced changes in local community size and scale-dependent effects of fire on species clumping across landscapes. Synthesis. Although niche-based mechanisms of community assembly are often invoked to explain changes in community composition following disturbance, our results suggest that these changes also arise through random sampling effects owing to the influence of disturbance on community size. Comparative studies of these processes across disturbed ecosystems will provide important insights into the ecological conditions that determine when disturbance alters the interplay of deterministic and stochastic processes in natural and human-modified landscapes

Fast computation of Bernoulli, Tangent and Secant numbers

We consider the computation of Bernoulli, Tangent (zag), and Secant (zig or Euler) numbers. In particular, we give asymptotically fast algorithms for computing the first n such numbers in O(n^2.(log n)^(2+o(1))) bit-operations. We also give very short in-place algorithms for computing the first n Tangent or Secant numbers in O(n^2) integer operations. These algorithms are extremely simple, and fast for moderate values of n. They are faster and use less space than the algorithms of Atkinson (for Tangent and Secant numbers) and Akiyama and Tanigawa (for Bernoulli numbers).Comment: 16 pages. To appear in Computational and Analytical Mathematics (associated with the May 2011 workshop in honour of Jonathan Borwein's 60th birthday). For further information, see http://maths.anu.edu.au/~brent/pub/pub242.htm

On the Path Integral in Imaginary Lobachevsky Space

The path integral on the single-sheeted hyperboloid, i.e.\ in $D$-dimensional imaginary Lobachevsky space, is evaluated. A potential problem which we call ``Kepler-problem'', and the case of a constant magnetic field are also discussed.Comment: 16 pages, LATEX, DESY 93-14

Geometric approach to nonvariational singular elliptic equations

In this work we develop a systematic geometric approach to study fully nonlinear elliptic equations with singular absorption terms as well as their related free boundary problems. The magnitude of the singularity is measured by a negative parameter $(\gamma -1)$, for $0 < \gamma < 1$, which reflects on lack of smoothness for an existing solution along the singular interface between its positive and zero phases. We establish existence as well sharp regularity properties of solutions. We further prove that minimal solutions are non-degenerate and obtain fine geometric-measure properties of the free boundary $\mathfrak{F} = \partial \{u > 0 \}$. In particular we show sharp Hausdorff estimates which imply local finiteness of the perimeter of the region $\{u > 0 \}$ and $\mathcal{H}^{n-1}$ a.e. weak differentiability property of $\mathfrak{F}$.Comment: Paper from D. Araujo's Ph.D. thesis, distinguished at the 2013 Carlos Gutierrez prize for best thesis, Archive for Rational Mechanics and Analysis 201

A Computer-Assisted Uniqueness Proof for a Semilinear Elliptic Boundary Value Problem

A wide variety of articles, starting with the famous paper (Gidas, Ni and Nirenberg in Commun. Math. Phys. 68, 209-243 (1979)) is devoted to the uniqueness question for the semilinear elliptic boundary value problem -{\Delta}u={\lambda}u+u^p in {\Omega}, u>0 in {\Omega}, u=0 on the boundary of {\Omega}, where {\lambda} ranges between 0 and the first Dirichlet Laplacian eigenvalue. So far, this question was settled in the case of {\Omega} being a ball and, for more general domains, in the case {\lambda}=0. In (McKenna et al. in J. Differ. Equ. 247, 2140-2162 (2009)), we proposed a computer-assisted approach to this uniqueness question, which indeed provided a proof in the case {\Omega}=(0,1)x(0,1), and p=2. Due to the high numerical complexity, we were not able in (McKenna et al. in J. Differ. Equ. 247, 2140-2162 (2009)) to treat higher values of p. Here, by a significant reduction of the complexity, we will prove uniqueness for the case p=3

Dynamical response of the "GGG" rotor to test the Equivalence Principle: theory, simulation and experiment. Part I: the normal modes

Recent theoretical work suggests that violation of the Equivalence Principle might be revealed in a measurement of the fractional differential acceleration $\eta$ between two test bodies -of different composition, falling in the gravitational field of a source mass- if the measurement is made to the level of $\eta\simeq 10^{-13}$ or better. This being within the reach of ground based experiments, gives them a new impetus. However, while slowly rotating torsion balances in ground laboratories are close to reaching this level, only an experiment performed in low orbit around the Earth is likely to provide a much better accuracy. We report on the progress made with the "Galileo Galilei on the Ground" (GGG) experiment, which aims to compete with torsion balances using an instrument design also capable of being converted into a much higher sensitivity space test. In the present and following paper (Part I and Part II), we demonstrate that the dynamical response of the GGG differential accelerometer set into supercritical rotation -in particular its normal modes (Part I) and rejection of common mode effects (Part II)- can be predicted by means of a simple but effective model that embodies all the relevant physics. Analytical solutions are obtained under special limits, which provide the theoretical understanding. A simulation environment is set up, obtaining quantitative agreement with the available experimental data on the frequencies of the normal modes, and on the whirling behavior. This is a needed and reliable tool for controlling and separating perturbative effects from the expected signal, as well as for planning the optimization of the apparatus.Comment: Accepted for publication by "Review of Scientific Instruments" on Jan 16, 2006. 16 2-column pages, 9 figure

Traveling Wave Solutions of Advection-Diffusion Equations with Nonlinear Diffusion

We study the existence of particular traveling wave solutions of a nonlinear parabolic degenerate diffusion equation with a shear flow. Under some assumptions we prove that such solutions exist at least for propagation speeds c {\in}]c*, +{\infty}, where c* > 0 is explicitly computed but may not be optimal. We also prove that a free boundary hy- persurface separates a region where u = 0 and a region where u > 0, and that this free boundary can be globally parametrized as a Lipschitz continuous graph under some additional non-degeneracy hypothesis; we investigate solutions which are, in the region u > 0, planar and linear at infinity in the propagation direction, with slope equal to the propagation speed.Comment: 40 pages, 1 figur