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

The Distance and Median Problems in the Single-Cut-Or-Join Model with Single-Gene Duplications

Background. In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, the problem is NP-complete for most extensions of these models accounting for duplicated genes. Moreover, problems involving more than two genomes, such as the genome median and the Small Parsimony problem, are intractable for most duplication-free models, with some exceptions, for example the Single-Cut-or-Join (SCJ) model. Results. We introduce a variant of the SCJ distance that accounts for duplicated genes, in the context of directed evolution from an ancestral genome to a descendant genome where orthology relations between ancestral genes and their descendant are known. Our model includes two duplication mechanisms: single-gene tandem duplication and the creation of single-gene circular chromosomes. We prove that in this model, computing the directed distance and a parsimonious evolutionary scenario in terms of SCJ and single-gene duplication events can be done in linear time. We also show that the directed median problem is tractable for this distance, while the rooted median problem, where we assume that one of the given genomes is ancestral to the median, is NP-complete. We also describe an Integer Linear Program for solving this problem. We evaluate the directed distance and rooted median algorithms on simulated data. Conclusion. Our results provide a simple genome rearrangement model, extending the SCJ model to account for single-gene duplications, for which we prove a mix of tractability and hardness results. For the NP-complete rooted median problem, we design a simple Integer Linear Program. Our publicly available implementation of these algorithms for the directed distance and median problems allow to solve efficiently these problems on large instances

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

Arguments hydrogéochimiques en faveur de Trias évaporitique non affleurant dans le massif du Djurdjura (dorsale kabyle, élément des Maghrébides)

L'analyse des eaux pose à nouveau la question de l'importance des faciès gypso-salifères dans le Trias de la dorsale kabyle du Djurdjura. Cette dernière est un élément de l'orogène alpin périméditerranéen où le Trias est décrit comme étant formé essentiellement de grès et de pélites avec des niveaux marneux et dolomitiques. Dans les régions telliennes, plus méridionales, il est représenté par des formations marno-gypsifères de grande épaisseur (Trias tellien), en position tectonique constamment anormale. On ne rencontre généralement pas de formations évaporitiques en surface dans le massif du Djurdjura. Les analyses chimiques de la majorité des sources le confirment. Toutefois la source de Tinzert, dont l'impluvium est constitué essentiellement de calcaires montre un cortège d'éléments d'origine évaporitique (fortes teneurs en chlorures, sodium et sulfates et la présence du strontium) et plaide pour la présence de niveaux évaporitiques du Trias, à la base de l'aquifère drainé par cette source. Le rapport Sr2+/Ca2+ (en ‰) de la source de Tinzert (3 1000 mg·l-1), sodium (> 500 mg·l-1), sulfates (> 200 mg·l-1) and potassium (> 25 mg·l-1).During flood periods, because of dilution and quick conduit flows in the upper calcareous zones, the water type becomes calcium bicarbonate. During this period, waters flowing out of the spring are traced by the limestone shallow waters (transit of epikarstic waters). On top and upstream from Tinzert, less than 20 metres to the South, Tala Agouni Lansar displays a very different chemical type, calcium bicarbonate. This fact demonstrates that Tinzert sodium chloride content is acquired by water which stays in the deep saturated zone (Figs. 3 et 4), and that longitudinal faults divide the lithological units into segments.Analyses of strontium in waters demonstrate that most of the springs (ABDESSELAM, 1995) have low Sr2+ contents (0.06-0.23 mg·l-1). Tinzert spring has a much higher content (0.35-1.83 mg·l-1 ; Table 1). The use of the Sr2+ /Ca2+ ratio (‰) enabled us to distinguish among aquifers completely developed in limestones, others related to Triassic sandstones and one related to salty layers. The map of Sr2+ /Ca2+ ratios indicates that the springs related to Triassic outcrops have the higher values (Fig. 3).According to the Sr2+ /Ca2+ ratio (‰), three groups can be distinguished:- springs related to limestones, with no relationship with Triassic formations, have a low Sr2+/Ca2+ ratio ( 5‰) classifies this water into the category of waters originating from the alpine Triassic evaporites (MEYBECK, 1984). This high ratio is coupled with the high sulfate, and especially the chloride and sodium content of these waters. This spring is situated on the trace of a north-east thrust sheet sole that probably includes Triassic in its lower part, which concerns the whole Haïzer massif of about 8 km. The water transit is probably either in the upper thrust sheet, or in the lower one, following the East-West axis lowering of the structure.The springs of the Djurdjura display well-differentiated hydrochemical responses. Several springs that only drain limestone have a standard calcium bicarbonate chemical type (Sr2+/Ca2+ < 1 ‰). Other springs (Sr2+/Ca2+ =1 - 1.5 ‰) are characteristic of waters that have flowed in the sandstone and dolomitic Triassic layers, which are observed on the outcrops. Tinzert spring at least, which drains the middle part of the limestone range (Fig. 4, Sr2+/Ca2+=3 - 8.77 ‰), is characterised by waters which have transited through the evaporitic Triassic. The waters of Tinzert spring have also high chloride, sodium and sulfate contents.In the Djurdjura, where evaporitic Triassic formations do not generally outcrop, except in very small lenses, an argument can be made for the existence of deep evaporitic Triassic deposits on the basis of the hydrochemical response of perennial springs