Detecting Introgression in Anopheles Mosquito Genomes using a Reconciliation-Based Approach

Introgression is an important evolutionary mechanism in insects and animals evolution. Current methods for detecting introgression rely on the analysis of phylogenetic incongruence, using either statistical tests based on expected phylogenetic patterns in small phylogenies or probabilistic modeling in a phylogenetic network context. Introgression leaves a phylogenetic signal similar to horizontal gene transfer, and it has been suggested that its detection can also be approached through the gene tree / species tree reconciliation framework, which accounts jointly for other evolutionary mechanisms such as gene duplication and gene loss. However so far the use of a reconciliation-based approach to detect introgression has not been investigated in large datasets. In this work, we apply this principle to a large dataset of Anopheles mosquito genomes. Our reconciliation-based approach recovers the extensive introgression that occurs in the gambiae complex, although with some variations compared to previous reports. Our analysis also suggests a possible ancient introgression event involving the ancestor of An. christyi

Numerical simulation evidence of dynamical transverse Meissner effect and moving Bose glass phase

We present 3D numerical simulation results of moving vortex lattices in presence of 1D correlated disorder at zero temperature. Our results with field tilting confirm the theoritical predictions of a moving Bose glass phase, characterized by transverse pinning and dynamical transverse Meissner effect, the moving flux lines being localized along the correlated disorder direction. Beyond a critical transverse field, vortex lines exhibit along all their length a "kink" structure resulting from an effective static "tin roof" pinning potential in the transverse direction.Comment: 5 pages, 4 figure

The Rooted SCJ Median with Single Gene Duplications

The median problem is a classical problem in genome rearrangements. It aims to compute a gene order that minimizes the sum of the genomic distances to  k>=3  given gene orders. This problem is intractable except in the related Single-Cut-or-Join and breakpoint rearrangement models. Here we consider the rooted median problem, where we assume one of the given genomes to be ancestral to the median, which is itself ancestral to the other genomes. We show that in the Single-Cut-or-Join model with single gene duplications, the rooted median problem is NP-hard. We also describe an Integer Linear Program for solving this problem, which we apply to simulated data, showing high accuracy of the reconstructed medians

PRINCE: Accurate approximation of the copy number of tandem repeats

Variable-Number Tandem Repeats (VNTR) are genomic regions where a short sequence of DNA is repeated with no space in between repeats. While a fixed set of VNTRs is typically identified for a given species, the copy number at each VNTR varies between individuals within a species. Although VNTRs are found in both prokaryotic and eukaryotic genomes, the methodology called multi-locus VNTR analysis (MLVA) is widely used to distinguish different strains of bacteria, as well as cluster strains that might be epidemiologically related and investigate evolutionary rates. We propose PRINCE (Processing Reads to Infer the Number of Copies via Estimation), an algorithm that is able to accurately estimate the copy number of a VNTR given the sequence of a single repeat unit and a set of short reads from a whole-genome sequence (WGS) experiment. This is a challenging problem, especially in the cases when the repeat region is longer than the expected read length. Our proposed method computes a statistical approximation of the local coverage inside the repeat region. This approximation is then mapped to the copy number using a linear function whose parameters are fitted to simulated data. We test PRINCE on the genomes of three datasets of Mycobacterium tuberculosis strains and show that it is more than twice as accurate as a previous method. An implementation of PRINCE in the Python language is freely available at https://github.com/WGS-TB/PythonPRINCE

Drift of a polymer chain in disordered media

We consider the drift of a polymer chain in a disordered medium, which is caused by a constant force applied to the one end of the polymer, under neglecting the thermal fluctuations. In the lowest order of the perturbation theory we have computed the transversal fluctuations of the centre of mass of the polymer, the transversal and the longitudinal size of the polymer, and the average velocity of the polymer. The corrections to the quantities under consideration, which are due to the interplay between the motion and the quenched forces, are controlled by the driving force and the degree of polymerization. The transversal fluctuations of the Brownian particle and of the centre of mass of the polymer are obtained to be diffusive. The transversal fluctuations studied in the present Letter may also be of relevance for the related problem of the drift of a directed polymer in disordered media and its applications.Comment: 11 pages, RevTex, Accepted for publication in Europhysics Letter

Terrain surfaces and 3-D landcover classification from small footprint full-waveform lidar data: application to badlands

This article presents the use of new remote sensing data acquired from airborne fullwaveform lidar systems. They are active sensors which record altimeter profiles. This paper introduces a set of methodologies for processing these data. These techniques 5 are then applied to a particular landscape, the badlands, but the methodologies are designed to be applied to any other landscape. Indeed, the knowledge of an accurate topography and a landcover classification is a prior knowledge for any hydrological and erosion model. Badlands tend to be the most significant areas of erosion in the world with the highest erosion rate values. Monitoring and predicting erosion within 10 badland mountainous catchments is highly strategic due to the arising downstream consequences and the need for natural hazard mitigation engineering. Additionaly, beyond the altimeter information, full-waveform lidar data are processed to extract intensity and width of echoes. They are related to the target reflectance and geometry. Wa will investigate the relevancy of using lidar-derived Digital Terrain Models (DTMs) and 15 to investigate the potentiality of the intensity and width information for 3-D landcover classification. Considering the novelty and the complexity of such data, they are presented in details as well as guidelines to process them. DTMs are then validated with field measurements. The morphological validation of DTMs is then performed via the computation of hydrological indexes and photo-interpretation. Finally, a 3-D landcover classification is performed using a Support Vector Machine classifier. The introduction of an ortho-rectified optical image in the classification process as well as full-waveform lidar data for hydrological purposes is then discussed

Functional renormalization group at large N for random manifolds

We introduce a method, based on an exact calculation of the effective action at large N, to bridge the gap between mean field theory and renormalization in complex systems. We apply it to a d-dimensional manifold in a random potential for large embedding space dimension N. This yields a functional renormalization group equation valid for any d, which contains both the O(epsilon=4-d) results of Balents-Fisher and some of the non-trivial results of the Mezard-Parisi solution thus shedding light on both. Corrections are computed at order O(1/N). Applications to the problems of KPZ, random field and mode coupling in glasses are mentioned