Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01324848
http://hal.upmc.fr/hal-01324848
http://hal.upmc.fr/hal-01324848/document
http://hal.upmc.fr/hal-01324848/file/Genome%20Biol%20Evol-2014-Jachiet-2195-205.pdf
DOI : 10.1093/gbe/evu168

Éditeur(s) : HAL CCSD Springer Verlag (Germany) Springer Verlag
Résumé : International audience
Recent mathematical calculations allow us to define set fracture intensity (I), i.e., the amount of rock mass affected by fracture sets, independently of the investigation mode. This parameter, characteristic of each rock mass, is of much interest to describe the mechanical response of the rock mass to external influences. The aim of this work is to apply these mathematical equations on one site using measurements of three distinct fracture sets: (1) on a plane surface, (2) along a scanline, and (3) using borehole imaging, in order to evaluate and explain variability in collected data. Even if the three types of measurements give differences on absolute intensity values, they still define similar trends, i.e., the order of the fracturing impact of joint sets is the same from the three measurement methods, irrespective of the fact that obtained values are quite different from one survey method to another. We discuss the possible origins of these biases.
ISSN: 1435-9529

hal-01121556
https://hal.archives-ouvertes.fr/hal-01121556
DOI : 10.1007/s10064-014-0572-1

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
A network of 54 survey GPS sites, 28 continuous GPS stations and three absolute gravity (AG) observation sites have been set up in the Alborz mountain range to quantify the present-day kinematics of the range. Our results allow us to accurately estimate the motion of the South Caspian block (SCB) for the first time, and indicate rotation of the SCB relative to Eurasia, accounting for the left lateral motion in the Alborz range. In light of these new results, it clearly appears that deformation rates vary along the range, the eastern part accommodating mainly left lateral strike slip (2 mm yr(-1) south of the range and 5 mm yr(-1) north of the range) with a very low range normal shortening rate on the Khazar thrust fault (similar to 2 mm yr(-1)), and the western part accommodating range normal shortening (similar to 6 mm yr-1) on the Khazar thrust fault with a left lateral component of similar to 2 mm yr(-1) north of the range and 1 mm yr(-1) south of the range. These present-day kinematics agree with geomorphologic estimated slip rates, but not the long-term deformation, corroborating the idea that the kinematics of the range have changed recently due to the change of SCB motion.;Modelling of the interseismic deformation suggests a deep locking depth on the central-western segment of the Khazar fault (similar to 30 km) in agreement with the Baladeh earthquake rupture and aftershock ranging between 10 and 30 km. Given this unusual deep locking depth and the 34 degrees dip of the thrust, a large part of the Alborz range is located above the seismically coupled part of the fault. Based on our AG measurements this part of the range seems to uplift at a rate of 1-5 mm yr(-1), in agreement with terrace uplift.
ISSN: 0956-540X

hal-00617146
https://hal.archives-ouvertes.fr/hal-00617146
https://hal.archives-ouvertes.fr/hal-00617146v2/document
https://hal.archives-ouvertes.fr/hal-00617146/file/djamour2010.pdf
DOI : 10.1111/j.1365-246X.2010.04811.x

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
In places where sedimentation and erosion compete at fast rates, part of the record of past earthquakes on faults may be buried, hence hidden, in the first few metres below the surface. We developed a novel form of palaeoseismology, of geophysical type, based on the use of a dense pseudo-3-D Ground Penetrating Radar (GPR) survey to investigate such possible buried earthquake traces, on a long, fast-slipping strike-slip fault (Hope fault, New Zealand), at a site (Terako) where marked alluvial conditions prevail. We first used LiDAR data to analyse the ground surface morphology of the 2 km2 site at the greatest resolution. Nineteen morphological markers were observed, mainly alluvial terrace risers and small stream channels that are all dextrally offset by the fault by amounts ranging between 3 and 200 m. The measurements document about 10 past earthquake slip events with a mean coseismic slip of 3.3 +/- 1 m, with the most recent earthquake event having a slip of 3 +/- 0.5 m. We then investigated a detailed area of the site (400 x 600 m2) with pseudo-3-D GPR. We measured 56, similar to 400 m long, 510 m spaced GPR profiles (250 MHz), parallel to the fault and evenly distributed on either side. The analysis revealed the existence of a palaeosurface buried at about 3 m depth, corresponding to the top of alluvial terraces of different ages. That buried surface is incised by a dense network of stream channels that are all dextrally offset by the fault. We measured 48 lateral offsets in the buried channel network, more than twice than at the surface. These offsets range between 6 and 108 m, as observed at the surface, yet provide a more continuous record of the fault slip. The similarity of the successive slip increments suggests a slip per event averaging 4.4 +/- 1 m, fairly similar to that estimated from surface data. From the total surface and buried 67 offset collection, we infer that a minimum of 30 large earthquakes have broken the Hope fault at the Terako site in the last about 67 kyr, with an average coseismic slip of 3.2 +/- 1 m, a minimum average recurrence time of about 200 yr, and a magnitude of at least Mw 7.07.4. Our study therefore confirms that part of the record of past earthquakes may indeed reside in the first few metres below the surface, where it may be explored with geophysical, GPR-based palaeoseismology. Developing such a new palaeoseismological tool should provide rich information that may complement surface observations and help to document the past earthquakes on faults.
ISSN: 0956-540X

hal-00704560
https://hal.archives-ouvertes.fr/hal-00704560
DOI : 10.1111/j.1365-246X.2012.05366.x

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the ``good'' transcripts in the user's data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly programs. Moreover, we sequenced the transcriptome of the oomycete Achlya hypogyna and compared de novo assemblies from Velvet, ABySS, and the CLC Genomics Workbench assembly algorithms. One thousand one hundred twenty-eight of the CLC transcripts were statistically similar to the reference, compared with 49 of the Velvet transcripts and 937 of the ABySS transcripts. SCAN's strength is providing statistical support for transcript assemblies in a biological context. However, SCAN is designed to compare distinct node sets in networks, therefore it can also easily be extended to perform statistical comparisons on any network graph regardless of what the nodes represent.
ISSN: 0737-4038

hal-01544800
https://hal.archives-ouvertes.fr/hal-01544800
DOI : 10.1093/molbev/mst087

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Both oedometric and plane-strain tests were performed with parallelepipedic samples made of synthetic granular, cohesive, frictional and dilatant rock analogue material GRAM2. For the first time parallel sets of fractures that have all the characteristics of natural joints were reproduced in the laboratory. The fractures are regularly spaced, normal to σ3, and have plumose morphology very similar to that of natural joints. These fractures can form at tensile stress σ3 much smaller in magnitude than the tensile strength of material and even at slightly compressive σ3. When mean stress σ exceeds a certain value, the fractures become oblique to σ1 (the obliquity increases with σ), forming networks of conjugate shear bands/fractures. These results of plane-strain experiments are in good agreement with those of better controlled conventional axisymmetric tests on a similar material in Chemenda et al. (2011b) and are closer to real geological situations. Both types of experiments are complementary. Their results lead to the conclusion that at least certain categories of natural fractures (including joints, and conjugate shear fractures/bands) were initiated as deformation localization bands. The band orientation is defined by the constitutive properties/parameters (notably the dilatancy factor) that are sensitive to σ.
ISSN: 0040-1951

hal-00795555
https://hal.archives-ouvertes.fr/hal-00795555
DOI : 10.1016/j.tecto.2011.11.021

Éditeur(s) : HAL CCSD
Résumé : contient des versions PDF d'articles scientifiques (versions éditeur)
Spectrins are actin binding proteins that constitute the main components of membrane skeletons, the protein network located under the plasma membrane. Erythroid or non erythroid (in this case, they are called fodrins), spectrins play an important structural function in the membrane as demonstrated in the red blood cell. Spectrins are composed of two long α and β chains, associated in tetramers (αβ)2, forming the long flexible filaments of the network. Both chains are composed of repeating units which are folded in a triple helical arrangement (A, B and C helices), except for segment α10 which corresponds to a Src Homology 3 domain (SH3). The head-to-head interaction between dimers implies the N-terminal end of α chain and the C-terminal end of β chain. A model was proposed for the tetramerization site of spectrin : the two A and B helices of the last repeat of α chain interact with the C helix of the β chain in order to constitute a triple-helical structure similar to the repeats along the remainder of spectrin molecule. This model was first inferred from the relationship between the severity of the spectrin self-association defect and the location of the underlying mutations found in hereditary elliptocytosis (HE). Using recombinant peptides we defined the region, on both chains, which was sufficient and necessary to generate a fully functional tetramerization site. Producing peptides carrying a βHE mutation, we reproduced the tetramerization defect as observed in red blood cells of patients.
Finally, the presence of an SH3 domain probably gives to spectrins new functions which are different from the stability of the membrane. After contesting the existence of interaction between the fodrin SH3 domain and the α subunit of epithelial sodium channel sensitive to amiloride, we searched for partners of this domain, by screening a rat kidney library with the yeast two-hybrid system. We identified severals proteins implicated in the actin polymerization asoociated with motility or cell differenciation, suggesting that SH3 domain could play a part in this process.
Les spectrines, protéines liant l'actine, sont des constituants majeurs du squelette membranaire, réseau multiprotéique localisé sous la membrane plasmique. Érythroïdes ou non érythroïdes (dans ce cas, on les appelle fodrines), les spectrines ont un rôle structural important dans la membrane comme cela a déjà été démontré, pour la spectrine, dans le globule rouge. Elles sont constituées de deux longues chaînes a et ß associées côte à côte en tétramères (aß)2 qui forment les longs filaments du réseau. Chacune des chaînes est composée par la répétition de segments homologues, 22 pour a et 17 pour ß. Ces segments sont constitués de trois hélices a (hélices A, B et C) repliées sur elles-mêmes. Cette succession de structures trihélicoïdales est parfois interrompue par un domaine particulier comme le domaine SH3 (Src Homology 3) présent au milieu de la chaîne a. Les tétramères (aß)2 de spectrine constituent les filaments du squelette membranaire. L'interaction tête-à-tête de deux dimères aß implique les extrémités NH2 de la chaîne a et COOH de la chaîne ß. D'une part la sévérité du défaut d'auto-association et la localisation des mutations associées à celui-ci et d'autre part, les séquences en acides aminés des extrémités impliquées dans le site d'auto-association ont permis de proposer un modèle : la première hélice C isolée de la chaîne a pourrait s'associer aux deux dernières hélices A et B de la chaîne ß pour reconstituer une unité conformationnelle trihélicoïdale semblable à celles observées le long de la molécule. Un défaut dans la formation du tétramère est le support moléculaire le plus fréquemment observé dans les elliptocytoses héréditaires (HE). À l'aide de peptides recombinants, nous avons défini, sur les deux chaînes, les régions nécessaires et suffisantes possédant les caractéristiques pleinement fonctionnelles du site de tétramérisation. Nous avons ensuite, par mutagenèse dirigée, reproduit le lien entre la présence de mutations HE localisées dans les hélices A ou B et le défaut d'auto-association observé dans les globules rouges de patients HE. La présence d'un domaine SH3 localisé au milieu de la chaîne a confère probablement aux spectrine des fonctions autres que le maintien et la stabilité de la membrane. Les SH3, petits domaines protéiques, participent aux interactions protéine/protéine. Le seul partenaire connu du domaine SH3 de la fodrine était la sous-unité a du canal sodium sensible à l'amiloride (ENaC) mais la fonction de ce complexe n'était pas encore caractérisée. À l'aide de différentes méthodes, nous avons remis en cause l'interaction directe entre ENaC et le SH3 de la fodrine. La fonction de ce domaine SH3 étant liée à la nature de son ligand, nous avons donc recherché les partenaires putatifs du domaine SH3 de la fodrine par la technique du double-hybride. 29 partenaires ont été identifiés, regroupés en 19 familles et 10 clones isolés. La spécificité des interactions a été étudiée à la fois par double-hybride, à l'aide de mutants du domaine SH3 de la fodrine produits par mutagenèse dirigée. Les interactions vis-à-vis d'autres domaines SH3 (spectrine ou une protéine de levure non relatée Scd2) ont été également analysées. Enfin, la spécificité de certains partenaires a été confirmée par des études d'interactions in vitro. Deux des protéines les plus spécifiques du domaine SH3 de la fodrine sont des protéines tyrosine-phosphatase PTP. La première est l'isoforme A de PTP de faible poids moléculaire (LMPTPA) mais l'interaction n'a pas été confirmée in vitro. La deuxième, TD14, est une nouvelle PTP dont la seule fonction connue est d'inhiber la formation des foyers tumoraux des cellules surexprimant l'oncogène Ha-ras. Ces PTP pourraient soit déphosphoryler la fodrine, soit être recrutées sous la membrane pour déphosphoryler une autre cible. Nous avons également identifié trois partenaires (N-WASP, Evl et une protéine de la famille des formines) suggérant que les domaines SH3 des spectrines pourraient être impliqués dans les processus de polymérisation de l'actine liés à la mobilité ou la différenciation cellulaire. Mot clés : spectrine, fodrine, tétramérisation, SH3, double-hybride, polymérisation de l'actine
https://tel.archives-ouvertes.fr/tel-00284819

Droits : info:eu-repo/semantics/OpenAccess
tel-00284819
https://tel.archives-ouvertes.fr/tel-00284819
https://tel.archives-ouvertes.fr/tel-00284819/document
https://tel.archives-ouvertes.fr/tel-00284819/file/Nicolas_1999_-_These.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
The study of complex biological processes requires to forgo simplified models for extensive ones. Yet, these models' size and complexity place them beyond understanding. Their analysis requires new methods for identifying general patterns. The Transforming Growth Factor TGF-β is a multifunctional cytokine that regulates mammalian cell development , differentiation, and homeostasis. Depending on the context, it can play the antagonistic roles of growth inhibitor or of tumor promoter. Its context-dependent pleiotropic nature is associated with complex sig-naling pathways. The most comprehensive model of TGF-β-dependent signaling is composed of 15,934 chains of reactions (trajectories) linking TGF-β to at least one of its 159 target genes. Identifying functional patterns in such a network requires new automated methods. This article presents a framework for identifying groups of similar trajec-tories composed of the same molecules using an exhaustive and without prior assumptions approach. First, the trajectories were clustered using the Relevant Set Correlation model, a shared nearest-neighbors clustering method. Five groups of trajectories were identified. Second, for each cluster the over-represented molecules were determined by scoring the frequency of each molecule implicated in trajectories. Third, Gene set enrichment analysis on the clusters of trajectories revealed some specific TGF-β-dependent biological processes, with different clusters associated to the antagonists roles of TGF-β. This confirms that our approach yields biologically-relevant results. We developed a web interface that facilitates graph visualization and analysis. Our clustering-based method is suitable for identifying families of functionally-similar trajectories in the TGF-β signaling network. It can be generalized to explore any large-scale biological pathways.
CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology
Darmstadt, France

hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249/document
https://hal.archives-ouvertes.fr/hal-01559249/file/JeanCoquet_CMSB.pdf

Éditeur(s) : HAL CCSD
Résumé : In this paper we introduce k-laminar graphs a new class of graphs which extends the idea of Asteroidal triple free graphs. Indeed a graph is k-laminar if it admits a diametral path that is k-dominating. This bio-inspired class of graphs was motivated by a biological application dealing with sequence similarity networks of reads (called hereafter read networks for short). We briefly develop the context of the biological application in which this graph class appeared and then we consider the relationships of this new graph class among known graph classes and then we study its recognition problem. For the recognition of k-laminar graphs, we develop polynomial algorithms when k is fixed. For k=1, our algorithm improves a Deogun and Krastch's algorithm (1999). We finish by an NP-completeness result when k is unbounded.
https://hal.inria.fr/hal-01282715

hal-01282715
https://hal.inria.fr/hal-01282715
ARXIV : 1603.01179

Éditeur(s) : HAL CCSD
Résumé : Indigenous territories comprise extensive areas of tropical forest and hold significant social and conservation value. Today, they are subject to various constraints and opportunities, and face many territorial transformations. These transformations are complex and multifaceted. They involve the adoption of new production and consumption modes, the modification of forms of social organisation and identity and territorial claims. However, the links between these on-going processes are still poorly understood, and make difficult to appreciate the adaptation dynamics of indigenous common natural resources management. This thesis is particularly concerned with the territorial dynamics of the Wayãpi and Teko indigenous people of the municipality of Camopi in French Guiana. It integrates methods that include land use analysis using remotely sensed data, socio-economic and agricultural systems analysis at the household scale, and empirical analysis on the influence of identity claims, kinship networks, and conservation policies. It shows that despite the residential settlement around local towns, the growth of cash income from wage labour and welfare, associated with strong kinship networks, allows the revival of mobility and the diversification of indigenous territorialities. Environmental policies implemented on the territory involve processes of identity and territorial claims and motivate the construction of a collective project of endogenous local development. A comparative approach with the situation of the wayãpi people living in Brazil and evolving in a completely different institutional, socio-economic and environmental context shows similar dynamics. Indigenous peoples of these two sites adopt "multi-local" land use systems, allowing them to extend their territory occupation and taking part of a broader dynamic of territorial and identity affirmation. They articulate forest and local town environments. This multi-local land use system can be interpreted as a new form of environmental governance, which overcomes the access difficulties to natural resources around local towns and ensures their sovereignty over the territory.
Les territoires amérindiens couvrent de vastes étendues de forêts tropicales et possèdent une forte valeur sociale et environnementale. Soumis à des contraintes et opportunités variées, ils sont de nos jours le siège de nombreuses transformations territoriales. Ces transformations sont complexes et multiformes. Elles impliquent l'adoption de nouveaux modes de production et de consommation, le réajustement des formes d'organisation sociale et des dynamiques de réaffirmation identitaire et territoriale. Or les liens entre tous ces processus sont encore mal compris, et rendent délicate la compréhension des dynamiques d'adaptation des systèmes amérindiens de gestion des ressources communes. Cette thèse s'intéresse particulièrement aux dynamiques territoriales des Amérindiens wayãpi et teko de la commune de Camopi en Guyane française. Elle intègre des données sur l'occupation du sol obtenues par télédétection, des données socio-économiques et productives à l'échelle des ménages et des données qualitatives sur les processus identitaires, les réseaux de parenté, les politiques de conservation et la gouvernance du territoire. Elle montre que malgré la sédentarisation de l'habitat autour des bourgs locaux, la croissance des revenus monétaires issus des emplois salariés et des aides sociales, combinée avec le maintien de réseaux de parenté et d'entraide, permet une redynamisation des systèmes de mobilité et une diversification des territorialités amérindiennes. De plus, les politiques environnementales mises en place sur le territoire impliquent des processus de territorialisation et de revendications identitaires et motivent la construction collective d'un projet de développement local endogène. Une approche comparative avec la situation des Amérindiens wayãpi vivant au Brésil et évoluant dans un contexte socio-économique, institutionnel et environnemental bien différent montre des dynamiques similaires. Les Amérindiens de ces deux pays adoptent des systèmes d'exploitation du territoire multi-locaux, leur permettant d'étendre leur occupation du territoire et s'inscrivant dans une dynamique de réaffirmation identitaire et territoriale. Ils articulent ainsi les espaces de la forêt et des bourgs. Cette forme d'exploitation multi-locale du territoire peut être interprétée comme une nouvelle forme de gouvernance environnementale, qui leur permet de contourner les difficultés d'accès aux ressources naturelles autour des bourgs et d'affirmer leur souveraineté sur le territoire.
https://tel.archives-ouvertes.fr/tel-00831619

tel-00831619
https://tel.archives-ouvertes.fr/tel-00831619
https://tel.archives-ouvertes.fr/tel-00831619/document
https://tel.archives-ouvertes.fr/tel-00831619/file/These_TRITSCH_mai2013_vf.pdf

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
The outstanding exposure of deformation bands in a multilayer sequence of the Orange quarry, Provence, France, motivates a study investigating the development and controls of deformation band geometries by field mapping combined with finite element modeling. Field mapping yields new insights into angular relations between, and evolution of, the deformation bands as well as provides input parameters for the setup and boundary conditions of the numerical simulations using ADELI 2D. In particular, reverse-sense deformation bands are found to have developed within three of the four exposed layers of the multilayer stack with similar orientations to bedding, indicating layer-parallel contraction. Numerical simulations, carried out as a parametric study to investigate the influence on deformation band development and geometry, successfully reproduce the sequential development of deformation bands in the three layers as seen in the field as well as recreate the observed angular geometries of similar to 39 degrees to the maximum compression. This angular relationship is put into context with observations from other field studies and theoretical values to explore controls of deformation band orientations. Furthermore, band localization is impeded in the model by increased layer cohesive strength, demonstrating the importance of host-rock property variations on where localization of bands within the multilayer sequence. Results from both field investigation and numerical simulations are consistent with regional tectonics, where the strata underwent gentle folding due to thrust faulting at depth, and bring further insight into the development and geometry of deformation bands in both extensional and contractional tectonic regimes.
ISSN: 0148-0227

hal-00639452
https://hal.archives-ouvertes.fr/hal-00639452
DOI : 10.1029/2011JB008365

Éditeur(s) : HAL CCSD
Résumé : International audience
In this work, we propose a novel approach for the discovery of frequent patterns in a social network on the basis of both vertex attributes and link frequency. With an analogy to the traditional task of mining frequent item sets, we show that the issue addressed can be formulated in terms of a conceptual analysis that elicits conceptual links. A social-based conceptual link is a synthetic representation of a set of links between groups of vertexes that share similar internal properties. We propose a first algorithm that optimizes the search into the concept lattice of conceptual links and extracts maximal frequent conceptual links. We study the performances of our solution and give experimental results obtained on a sample example. Finally we show that the set of conceptual links extracted provides a conceptual view of the social network.
IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM)
Istanbul, Turkey

hal-00786161
https://hal.archives-ouvertes.fr/hal-00786161
DOI : 10.1109/ASONAM.2012.15

Éditeur(s) : HAL CCSD American Arachnological Society
Résumé : To obtain a reliable description of spider communities, robust sampling protocols are crucial. However, it remains unclear if descriptions of spider communities in tropical habitats require both day and night sampling. Here we tested whether sampling both day and night in high and low vegetation strata would lead to better diversity estimates of spider communities than sampling at only one period of the day. We determined spider taxonomic diversity in a network of 12 plots in French Guiana along a vegetation gradient. We found high alpha diversity of spiders as expected for a tropical area at every site. We showed strong differences in spider alpha and beta diversity between high and low vegetation strata, while they were similar between day and night sampling. Our results suggest that collecting spiders at only one period is sufficient to describe the diversity of spider communities across land use types in the neotropics.
ISSN: 0161-8202

hal-01535342
https://hal.archives-ouvertes.fr/hal-01535342
PRODINRA : 346667

Éditeur(s) : HAL CCSD
Résumé : International audience
The Corinth Rift is the most seismically active zone in Europe. Since the year 2000, the Corinth Rift Laboratory (CRL, http://crlab.eu) consisting in a multidisciplinary natural observatory, aims at understanding the mechanics of faulting and earthquake nucleation in the Rift. Recent studies have improved our view about fault geometry and mechanics within CRL but there is still a critical need for a better knowledge of the structure at depth.In this project, we aim to analyze the complete seismological database (13 years of recordings) of CRL by using recently developed methodologies of structural imaging in order to determine, with high resolution, the local 3D structure and the earthquake locations. We perform an iterative joint determination of 3D velocity model and earthquake coordinates. P and S velocity models are estimated through a first arrival traveltime tomography by using the adjoint state method proposed by Taillandier et al. (2009). It consists in the minimization of the cost function between observed and theoretical arrival times,which is achieved by estimating the gradient of the cost function. Earthquake locations are also estimated with a linearized inversion approach by computing the gradient of the misfit function. Iterations are repeated until the cost function no longer decreases. We present preliminary results consisting in: (1) the adjustment of a 1D velocity model that is used as initial model of the 3D tomography and (2) a first attempt of the joint determination of 3D velocity model and earthquake locations.We also perform a preliminary receiver function analysis of teleseismic data recorded by the broadband stations of the CRL network. The multiscale approach (Gesret et. al., 2010) analysis of teleseismic P to S converted waves allows to analyze the signal toward the higher frequencies and thus to characterize the structure at depth with a high resolution. Our multiscale approach should give us reliable depth of interfaces beneath seismometers in the CRL area. In this first attempt, we adjust the 1D velocity model that produces a synthetic RF as similar as possible to the stack of observed RF for a subset of data. The identified interfaces could then be compared with heterogeneities imaged by the tomography.
AGU Fall Meeting
San Fransico, United States

hal-01417184
https://hal-mines-paristech.archives-ouvertes.fr/hal-01417184

Résumé : Les territoires amérindiens couvrent de vastes étendues de forêts tropicales et possèdent une forte valeur sociale et environnementale, soumis à des contraintes et opportunités variées, ils sont de nos jours le siège de nombreuses transformations territoriales. Ces transformations sont complexes et multiformes. Elles impliquent l’adoption de nouveaux modes de productions et de consommation, le réajustement des formes d’organisation sociale et des dynamiques de réaffirmation identitaireet territoriale. Or les liens entre tous ces processus sont encore mal compris et rendent délicate le compréhension des dynamiques d’adaptation des systèmes amérindiens de gestion des ressources communes.Cette thèse s’intéresse particulièrement aux dynamiques territoriales des amérindiens wayapi et teko de la commune de Camopi en Guyane française. Elle intègre des données sur l’occupation de sol obtenues par télédétection, des données socio-économiques et productives à l’échelle des ménages et des données qualitatives sur les processus identitaires, les réseaux de parente, les politiques de conservation et la gouvernance du territoire. Elle montre que malgré la sédentarisation de l’habitat autour des bourgs locaux, la croissance des revenus monétaires issus des emplois salariés et des aides sociales, combinées avec le maintien des réseaux de parente et d’entraide, permet une redynamisation des systèmes de mobilité et une diversification des territoires amérindiens. De plus, les politiques environnementales mises en place sur le territoire impliquent des processus de territorialisation et de revendication identitaires et motivent la construction collective d’un projet de développement local endogène. Une approche comparative avec la situation des amérindiens wayapi vivant au Brésil et évoluant dans un contexte socio-économique, institutionnel et environnemental bien différent montre des dynamiques similaires. Les amérindiens de ces deux pays adoptent des systèmes d’exploitation du territoire multi-locaux, leur permettant d’étendre leur occupation du territoire et s’inscrivant dans une dynamique de réaffirmation identitaire et territoriale. Ils articulent ainsi les espaces de la forêt et des bourgs. Cette forme d’exploitation multi-locale du territoire peut être interprétée comme une nouvelle forme de gouvernance environnementale, qui leur permet de contourner les difficultés et d’affirmer leur souveraineté sur le territoire.
Indigenous territories comprise extensive areas of tropical forest and hold significant social and conservation value. Today, they are subject to various constraints and opportunities and face many territorial transformations. These transformations are complex and multifaceted. They involve the adoption of new production and consumption modes, the medications of forms of social organization and identity and territorial claims. However, the links between these on-going processes are still poorly understood, and make difficult to appreciate the adaptation dynamics of indigenous common natural resources management. This thesis is particularly concerned with the territorial dynamics of the wayapi and teko indigenous people of the municipality of Camopi in French Guyana. It integrates methods that include land use analysis using remotely sensed data, socio-economic and agricultural systems analysis at the household scale, and empirical analysis on the influence of identity claims, kinship networks, and conservation policies. It shows that despite the residential settlement around local towns, the growth of cash income from wage labour and welfare, associated with strong kinship networks, allows the revival of mobility and the diversification of indigenous territorialities. Environment policies implemented on the territory involve processes of identity and territorial claims and motivate the construction of a collective project of endogenous local development. A comparative approach with the situation of the Wayapi people living in Brazil, and evolving in a completely different institutional, socio-economic and environmental context shows similar dynamics. Indigenous people of these two sites adopt “multi-local” land use systems, allowing them to extend their territory occupation and taking part of a broader dynamic of territorial and identity affirmation. They articulate forest and local town environments. This multi-local land use sytem can be interpreted as a new form of environmental governance, which overcomes the difficulties access to natural resources around local towns and ensure their sovereignty over the territory.

http://www.theses.fr/2013AGUY0608/document

Éditeur(s) : HAL CCSD AGU and the Geochemical Society
Résumé : International audience
The ODP/IODP multileg campaign at ODP Site 1256 (Cocos plate, eastern equatorial Pacific) provides the first continuous in situ sampling of fast spreading ocean crust from the extrusive lavas, through the sheeted dikes and down into the uppermost gabbros. This paper focuses on a detailed petrographic and microanalytical investigation of the gabbro section drilled during IODP Expedition 312. The marked patchy and spotty features that can be observed in many Hole 1256D gabbros is mostly due to a close association of two different lithological domains in variable amounts: (1) subophitic domains and (2) a granular matrix. Major and trace element mineral compositions, geothermometry, and petrological modeling suggest that subophitic and granular domains follow one single magma evolution trend formed by in situ fractionation. The subophitic domains correspond to the relative primitive, high-temperature end-member, compositionally similar to the basalts and dikes from the extrusive unit upsection, while the granular domains fit with a magma evolution by crystal fractionation to lower temperatures, up to a degree of crystallization of similar to 80%. Our results support the following scenario for the fossilization of the axial melt lens at ODP Site 1256: relatively primitive MORB melts under near-liquidus conditions fill the melt lens and feed the upper, extrusive crust. Near the melt lens-sheeted dike boundary at lower temperatures, crystallization starts with first plagioclase before clinopyroxene in a mushy zone forming the subophitic domains. At decreasing temperatures, the subophitic domains continue to crystallize, finally forming a well-connected framework. Evolved, residual melt is finally trapped within the subophitic network, crystallizing at near-solidus conditions to the granular matrix. Another important textural feature in Hole 1256D gabbros is the presence of microgranular domains which are interpreted as relics of stoped/assimilated sheeted dikes (transformed to "granoblastic dikes" by contact metamorphism). All these different domains can be observed in close association, often at the thin section scale, demonstrating the extremely complex petrological record of combined crystallization/assimilation processes ongoing in the axial melt lens. Very similar gabbros with a marked spotty/patchy appearance, and bearing the same close association of lithological domains as observed at Site 1256, are known in the so-called "varitextured gabbro" unit from the Oman Ophiolite located at the same structural level, between cumulate gabbros and granoblastic dikes. The close petrological similarity of the gabbro/dike transition between both IODP Hole 1256D and the Oman ophiolite suggests that in situ fractionation and dike assimilation/contamination are major magmatic processes controlling the dynamics and fossilization of the axial melt lens at fast spreading oceanic ridges.
ISSN: 1525-2027

hal-00644798
https://hal.archives-ouvertes.fr/hal-00644798
DOI : 10.1029/2011GC003655

Éditeur(s) : HAL CCSD
Résumé : Evolution of organisms, genomes and genes does not strictly follow a tree-like process; symbiosis, horizontal gene transfers and gene fusions build high level composite objects with components of phylogenetically distinct origins. Such processes have been called introgressive events and are significant in evolution. They are involved in some major evolutionary transitions such as eukaryogenesis, photosynthesis acquisition in eukaryotes and the origins of major archaeal clades. Eukaryogenesis would have involved (at least) two kinds of partners: an archaeon and an alpha-proteobacterium. Photosynthetic eukaryotes arose from the integration of a cyanobacterium into a eukaryotic cell and recent findings suggested that most archaeal lineages emerged after massive acquisitions of bacterial genes. These composite lineages carry highly chimeric genomes where genes from symbiotic partners co-localize into the same genome. During my PhD thesis, I used sequence similarity networks and phylogenetic methods in order to study reticulate evolution. My research specifically focused on a previously hidden component of composite genomes: symbiogenetic genes (S genes). These chimeric genes are found in genetic mergers, and originate from the association of genes of symbiotic partners. Some association rules have been discovered. In a broad perspective, the discovery of S-genes extends the concept of genome chimerism to the within-gene level.
L'évolution des organismes, des génomes et des gènes n'est pas strictement arborescente; les symbioses, les transferts horizontaux de gènes ou encore la fusion de gènes créent des objets composites formés de parties dont les histoires évolutives sont différentes. Ces processus non arborescents sont appelés introgressifs et ont un impact non négligeable en évolution. Ils sont à l'origine de transitions évolutives majeures comme l'émergence des eucaryotes, des eucaryotes photosynthétiques ou encore de nombreux groupes d'Archaea. Dans le cas des eucaryotes, l'association et la stabilisation d'une Archaea et d'une alpha-protéobactérie a permis l'émergence d'un nouveau groupe d'organismes composites aux propriétés émergentes. L'acquisition de la photosynthèse chez les eucaryotes s'est faite via l'endosymbiose d'une cyanobactérie et, bien que débattue, l'apparition des grands groupes d'Archaea semble être concomitante avec l'acquisition de nombreux gènes d'origine bactérienne. Ces superorganismes ont la particularité d'avoir des génomes composés de gènes de différents partenaires symbiotiques. L'objectif de mon travail de thèse a constitué à étudier l'aspect introgressif de l'évolution par des méthodes de réseaux de similarité de séquence et des méthodes phylogénétiques. Je me suis particulièrement focalisé sur la détection de nouveaux gènes chimériques nommés gènes symbiogénétiques (S-gènes) car composés de parties originaires des différents partenaires symbiotiques. De tels gènes existent dans les génomes et plusieurs règles d'association ont pu être mises en évidence. Plus généralement, la présence de S-gènes étend la notion de mosaïcisme génomique au niveau infra-génique.
https://tel.archives-ouvertes.fr/tel-01536344

NNT : 2016PA066534
tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344/document
https://tel.archives-ouvertes.fr/tel-01536344/file/2016PA066534.pdf

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Patterns of connectivity and self-recruitment are recognized as key factors shaping the dynamics of marine populations. Connectivity is also essential for maintaining and restoring natural ecological processes with genetic diversity contributing to the adaptation and persistence of any species in the face of global disturbances. Estimates of connectivity are crucial to inform the design of both marine protected areas (MPAs) and MPA networks. Among several approaches, genetic structure is frequently used as a proxy for patterns of connectivity. Using 8 microsatellite loci, we investigated genetic structure of the two-banded sea bream Diplodus vulgaris, a coastal fish that is both commercially and ecologically important. Adults were sampled in 7 locations (stretches of coastline approximately 8 km long) and juveniles in 14 sites (~100 to 200 m of coastline) along 200 km of the Apulian Adriatic coast (SW Adri-atic Sea), within and outside an MPA (Torre Guaceto MPA, Italy). Our study found similar genetic diversity indices for both the MPA and the surrounding fished areas. An overall lack of genetic structure among samples suggests high gene flow (i.e. connectivity) across a scale of at least 200 km. However, some local genetic divergences found in two locations demonstrate some heterogeneity in processes renewing the population along the Apulian Adriatic coast. Furthermore, two sites appeared genetically divergent, reinforcing our observations within the genetic makeup of adults and confirming heterogeneity in early stage genetics that can come from either different supply populations or from chaotic genetic patchiness occurring under temporal variation in recruitment and in the reproductive success. While the specific role of the MPA is not entirely known in this case, these results confirm the presence of regional processes and the key role of connectivity in maintaining the local population supply.
ISSN: 1932-6203

hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/file/journal.pone.0167441.pdf
DOI : 10.1371/journal.pone.0167441.s009

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
A temporary network of 10 broad-band seismic stations has been installed in French Polynesia for the Polynesian Lithosphere and Upper Mantle Experiment (PLUME). All the seismic stations were installed either on volcanic islands or on atolls of the various archipelagos of French Polynesia in a manner which complements the geographic coverage provided by the regional permanent stations. The primary aim of PLUME is to image the upper mantle structures related to plate motion and hotspot activity. However, because of its proximity to all sites, the ocean is responsible for a high level of noise in the seismic data and we show that these data can also be used to analyse ocean wave activity. The power spectral density (PSD) analyses of the seismic data recorded in French Polynesia show clear peaks in the 0.05– 0.10 Hz band (periods between 10 and 20 s), which corresponds to swell frequencies. Clear peaks in this frequency band are also observed in infrasonic data recorded on Tahiti. Ground motion analysis shows that the swell-related seismic noise (SRSN) is linearly polarized in the horizontal plane and its amplitude decreases rapidly with the distance from the shore. The microseismic and the infrasonic 'noise' amplitudes show very similar variations from station to station and both are strongly correlated with the swell amplitudes predicted by the National Oceanic and Atmospheric Administration (NOAA), wind-forced, 'WaveWatch' models. The swell direction can be estimated from SRSN polarization analysis but this has to be done with care since, for some cases, the ground motions are strongly controlled by the islands' anisometric shapes and by swell refraction processes. We find cases, however, such as Tahiti or roughly circular Tuamotu atolls, where the azimuth of the swell is in good agreement with the seismic estimates. We, therefore, demonstrate that the SRSN and the infrasonic signal observed in French Polynesia can be used in such cases as a proxy for swell amplitude and azimuth. From the continuous analysis of the data recorded in 2003 at the permanent seismic station PPTL in Tahiti, transfer functions have been obtained. This could provide a way to quantify the swell activity during the last two decades and, therefore, assist in the investigation of climate changes.
ISSN: 0956-540X

hal-01388809
http://hal.univ-reunion.fr/hal-01388809
http://hal.univ-reunion.fr/hal-01388809/document
http://hal.univ-reunion.fr/hal-01388809/file/Barruol_swell_GJI2006.pdf
DOI : 10.1111/j.1365-246X.2006.02871.x