Navigating in a sea of repeats in RNA-seq without drowning

The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which transposable elements are one of the main examples. Most transcriptome assemblers are based on de Bruijn graphs and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them. The results of this work are twofold. First, we introduce a formal model for repre- senting high copy number repeats in RNA-seq data and exploit its properties for inferring a combinatorial characteristic of repeat-associated subgraphs. We show that the problem of identifying in a de Bruijn graph a subgraph with this charac- teristic is NP-complete. In a second step, we show that in the specific case of a local assembly of alternative splicing (AS) events, we can implicitly avoid such subgraphs. In particular, we designed and implemented an algorithm to efficiently identify AS events that are not included in repeated regions. Finally, we validate our results using synthetic data. We also give an indication of the usefulness of our method on real data

Spin nematic order in antiferromagnetic spinor condensates

Large spin systems can exhibit unconventional types of magnetic ordering different from the ferromagnetic or N\'eel-like antiferromagnetic order commonly found in spin 1/2 systems. Spin-nematic phases, for instance, do not break time-reversal invariance and their magnetic order parameter is characterized by a second rank tensor with the symmetry of an ellipsoid. Here we show direct experimental evidence for spin-nematic ordering in a spin-1 Bose-Einstein condensate of sodium atoms with antiferromagnetic interactions. In a mean field description this order is enforced by locking the relative phase between spin components. We reveal this mechanism by studying the spin noise after a spin rotation, which is shown to contain information hidden when looking only at averages. The method should be applicable to high spin systems in order to reveal complex magnetic phases.Comment: published versio

Recent and Ancient Signature of Balancing Selection around the S-Locus in Arabidopsis halleri and A. lyrata

Balancing selection can maintain different alleles over long evolutionary times. Beyond this direct effect on the molecular targets of selection, balancing selection is also expected to increase neutral polymorphism in linked genome regions, in inverse proportion to their genetic map distances from the selected sites. The genes controlling plant self-incompatibility are subject to one of the strongest forms of balancing selection, and they show clear signatures of balancing selection. The genome region containing those genes (the S-locus) is generally described as nonrecombining, and the physical size of the region with low recombination has recently been established in a few species. However, the size of the region showing the indirect footprints of selection due to linkage to the S-locus is only roughly known. Here, we improved estimates of this region by surveying synonymous polymorphism and estimating recombination rates at 12 flanking region loci at known physical distances from the S-locus region boundary, in two closely related self-incompatible plants Arabidopsis halleri and A. lyrata. In addition to studying more loci than previous studies and using known physical distances, we simulated an explicit demographic scenario for the divergence between the two species, to evaluate the extent of the genomic region whose diversity departs significantly from neutral expectations. At the closest flanking loci, we detected signatures of both recent and ancient indirect effects of selection on the S-locus flanking genes, finding ancestral polymorphisms shared by both species, as well as an excess of derived mutations private to either species. However, these effects are detected only in a physically small region, suggesting that recombination in the flanking regions is sufficient to quickly break up linkage disequilibrium with the S-locus. Our approach may be useful for distinguishing cases of ancient versus recently evolved balancing selection in other systems

Cocycle superrigidity from higher rank lattices to Out(FN)\mathrm{Out}(F_N)

We prove a rigidity result for cocycles from higher rank lattices to $\mathrm{Out}(F_N)$ and more generally to the outer automorphism group of a torsion-free hyperbolic group. More precisely, let $G$ be either a product of connected higher rank simple algebraic groups over local fields, or a lattice in such a product. Let $G\curvearrowright X$ be an ergodic measure-preserving action on a standard probability space, and let $H$ be a torsion-free hyperbolic group. We prove that every Borel cocycle $G\times X\to\mathrm{Out}(H)$ is cohomologous to a cocycle with values in a finite subgroup of $\mathrm{Out}(H)$. This provides a dynamical version of theorems of Farb--Kaimanovich--Masur and Bridson--Wade asserting that every morphism from $G$ to either the mapping class group of a finite-type surface or the outer automorphism group of a free group, has finite image. The main new geometric tool is a barycenter map that associates to every triple of points in the boundary of the (relative) free factor graph a finite set of (relative) free splittings.Comment: 53 page

Adaptive evolution of butterfly wing shape: from morphology to behaviour

International audienceButterflies display extreme variation in wing shape associated with tremendous ecological diversity. Disentangling the role of neutral versus adaptive processes in wing shape diversification remains a challenge for evolutionary biologists. Ascertaining how natural selection influences wing shape evolution requires both functional studies linking morphology to flight performance, and ecological investigations linking performance in the wild with fitness. However, direct links between morphological variation and fitness have rarely been established. The functional morphology of butterfly flight has been investigated but selective forces acting on flight behaviour and associated wing shape have received less attention. Here, we attempt to estimate the ecological relevance of morpho-functional links established through biomechanical studies in order to understand the evolution of butterfly wing morphology. We survey the evidence for natural and sexual selection driving wing shape evolution in butterflies, and discuss how our functional knowledge may allow identification of the selective forces involved, at both the macro-and micro-evolutionary scales. Our review shows that although correlations between wing shape variation and ecological factors have been established at the macro-evolutionary level, the underlying selective pressures often remain unclear. We identify the need to investigate flight behaviour in relevant ecological contexts to detect variation in fitness-related traits. Identifying the selective regime then should guide experimental studies towards the relevant estimates of flight performance. Habitat, predators and sex-specific behaviours are likely to be major selective forces acting on wing shape evolution in butterflies. Some striking cases of morphological divergence driven by contrasting ecology involve both wing and body morphology, indicating that their interactions should be included in future studies investigating co-evolution between morphology and flight behaviour

Utilisation de la couleur pour l'extraction de tableaux dans des images de documents

International audienceTables are complex elements that can disturb the automatic analysis of the structure of an image of a document. In this article, we present a method based on the alternation of the color of lines to extract color tables that are not materialized by physical rulings. Experimental results, obtained on a dataset of document images with various layouts, enable to validate the interest of this approach. MOTS-CLÉS : Analyse d'images de documents, extraction de tableaux, détection de couleurs dominantes, segmentation d'images, croissance de régions.Les tableaux sont des éléments complexes qui peuvent perturber l'analyse automatique de la structure d'une image de document. Dans cet article, nous présentons une méthode fondée sur l'alternance de couleurs de lignes pour extraire des tableaux colorés à bordures non matérialisées. Les résultats expérimentaux obtenus à partir d'une base d'images de documents à mise en page variée, permettent de valider l'intérêt de cette approche