Éditeur(s) : The Oceanography Society
Résumé : Data assembly and processing centers are essential elements of the operational oceanography infrastructure. They provide data and products needed by modeling and data assimilation systems; they also provide products directly usable for applications. This paper discusses the role and functions of the data centers for operational oceanography. It describes some of the main data assembly centers (Argo and in situ data, altimetry, sea surface temperature) developed during the Global Ocean Data Assimilation Experiment. An overview of other data centers (wind and fluxes, ocean color, sea ice) is also given. Much progress has been achieved over the past 10 years to validate, intercalibrate, and merge altimeter data from multiple satellites. Accuracy and timeliness of products have been improved, and new products have been developed. The same is true for sea surface temperature data through the Global High-Resolution Sea Surface Temperature Pilot Project. A breakthrough in processing, quality control, and assembly for in situ data has also been achieved through the development of the real-time and delayed-mode Argo data system. In situ and remote-sensing data are now systematically and jointly used to calibrate, validate, and monitor over the long term the quality and consistency of the global ocean observing system. Main results are illustrated. There is also a review of the development and use of products that merge in situ and remote-sensing data. Future issues and main prospects are discussed in the conclusion.
Oceanography (1042-8275) (The Oceanography Society), 2009-09 , Vol. 22 , N. 3 , P. 56-69

Droits : 2009 The Oceanography Society
http://archimer.ifremer.fr/doc/2009/publication-6879.pdf
http://archimer.ifremer.fr/doc/00000/6879/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BackgroundFor a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields.ResultsWe compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir’s drift).ConclusionsApart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to complement their studies, trying to identify cross-disciplinary and discipline-specific evolutionary processes. The fact that we found many process-based analogies favoring transfer from biology to linguistics further shows that certain biological methods and models have a broader scope than previously recognized. This opens fruitful paths for collaboration between the two disciplines.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01378396
http://hal.upmc.fr/hal-01378396
http://hal.upmc.fr/hal-01378396/document
http://hal.upmc.fr/hal-01378396/file/unity.pdf
DOI : 10.1186/s13062-016-0145-2

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Although niche-based and stochastic processes, including dispersal limitation and demographic stochasticity, can each contribute to community assembly, it is difficult to quantify the relative importance of each process in natural vegetation. Here, we extend Shipley's maxent model (Community Assembly by Trait Selection, CATS) for the prediction of relative abundances to incorporate both trait-based filtering and dispersal limitation from the larger landscape and develop a statistical decomposition of the proportions of the total information content of relative abundances in local communities that are attributable to trait-based filtering, dispersal limitation, and demographic stochasticity. We apply the method to tree communities in a mature, species-rich, tropical forest in French Guiana at 1-, 0.25- and 0.04-ha scales. Trait data consisted of species' means of 17 functional traits measured over both the entire meta-community and separately in each of nine 1-ha plots. Trait means calculated separately for each site always gave better predictions. There was clear evidence of trait-based filtering at all spatial scales. Trait-based filtering was the most important process at the 1-ha scale (34%), whereas demographic stochasticity was the most important at smaller scales (37-53%). Dispersal limitation from the meta-community was less important and approximately constant across scales (similar to 9%), and there was also an unresolved association between site-specific traits and meta-community relative abundances. Our method allows one to quantify the relative importance of local niche-based and meta-community processes and demographic stochasticity during community assembly across spatial and temporal scales.
ISSN: 0012-9658

hal-01032424
https://hal.archives-ouvertes.fr/hal-01032424

Éditeur(s) : HAL CCSD Nordic Ecological Society
Résumé : Niche differentiation and ecological filtering are primary ecological processes that shape community assembly, but their relative importance remains poorly understood. Analyses of the distributions of functional traits can provide insight into the community structure generated by these processes. We predicted the trait distributions expected under the ecological processes of niche differentiation and environmental filtering, then tested these predictions with a dataset of 4672 trees located in nine 1-ha plots of tropical rain forest in French Guiana. Five traits related to leaf function (foliar N concentration, chlorophyll content, toughness, tissue density and specific leaf area), and three traits related to stem function (trunk sapwood density, branch sapwood density, and trunk bark thickness), as well as laminar surface area, were measured on every individual tree. There was far more evidence for environmental filtering than for niche differentiation in these forests. Furthermore, we contrasted results from species-mean and individual-level trait values. Analyses that took within-species trait variation into account were far more sensitive indicators of niche differentiation and ecological filtering. Species-mean analyses, by contrast, may underestimate the effects of ecological processes on community assembly. Environmental filtering appeared somewhat more intense on leaf traits than on stem traits, whereas niche differentiation affected neither strongly. By accounting for within-species trait variation, we were able to more properly consider the ecological interactions among individual trees and between individual trees and their environment. In so doing, our results suggest that the ecological processes of niche differentiation and environmental filtering may be more pervasive than previously believed.
ISSN: 0030-1299

hal-01032397
https://hal.archives-ouvertes.fr/hal-01032397
DOI : 10.1111/j.1600-0706.2010.19110.x

Éditeur(s) : HAL CCSD Annual Reviews
Résumé : International audience
The record of the continental lithosphere is patchy and incomplete; no known rock is older than 4.02 Ga, and less than 5% of the rocks preserved are older than 3 Ga. In addition, there is no recognizable mantle lithosphere from before 3 Ga. We infer that there was lithosphere before 3 Ga and that ∼3 Ga marks the stabilization of blocks of continental lithosphere that have since survived. This was linked to plate tectonics emerging as the dominant tectonic regime in response to thermal cooling, the development of a more rigid lithosphere, and the recycling of water, which may in turn have facilitated plate tectonics. A number of models, using different approaches, suggest that at 3 Ga the volume of continental crust was ∼70% of its present-day volume and that this may be a minimum value. The continental crust before 3 Ga was on average more mafic than that generated subsequently, and this pre-3 Ga mafic new crust had fractionated Lu/Hf and Sm/Nd ratios as inferred for the sources of tonalite-trondhjemite-granodiorite and later granites. The more intermediate composition of new crust generated since 3 Ga is indicated by its higher Rb/Sr ratios. This change in composition was associated with an increase in crustal thickness, which resulted in more emergent crust available for weathering and erosion. This in turn led to an increase in the Sr isotope ratios of seawater and in the drawdown of CO2. Since 3 Ga, the preserved record of the continental crust is marked by global cycles of peaks and troughs of U-Pb crystallization ages, with the peaks of ages appearing to match periods of supercontinent assembly. There is increasing evidence that the peaks of ages represent enhanced preservation of magmatic rocks in periods leading up to and including continental collision in the assembly of supercontinents. These are times of increased crustal growth because more of the crust that is generated is retained within the crust. The rates of generation of continental crust and mantle lithosphere may have remained relatively constant at least since 3 Ga, yet the rates of destruction of continental crust have changed with time. Only relatively small volumes of rock are preserved from before 3 Ga, and so it remains difficult to establish which of these are representative of global processes and the extent to which the rock record before 3 Ga is distorted by particular biases.
ISSN: 0084-6597

hal-01622692
https://hal.archives-ouvertes.fr/hal-01622692
DOI : 10.1146/annurev-earth-063016-020525

Éditeur(s) : HAL CCSD
Résumé : Tropical forests are a biodiversity hotspot, with the coexistence of numerous species until a fine spatial scale. Particularly, 16.000 tree species coexist in Amazonia, 1.800 in Frenche Guiana and between 120 and more than 200 tree species per hectare. However, there are some uncertainties in maintaining diversity in regard to global changes. Hence before predicting the diversity evolution face of global changes, fundamental studies are needed to understand which assembly processes are involved in the maintenance of diversity. These fundamental studies still relevant given the lack of consensus on the relative importance of assembly processes. This thesis is a continuation of these fundamental studies, using innovative integrative approach, at multi-scale, to address three types of diversity: taxonomic diversity, functional and phylogenetic. Our results challenge the importance of environmental filtering for hydrological and chemical properties of soils, versus the importance of biotic interactions on community assembly. Furthermore, our results suggest that species distributions could be affected by forest dynamics related to falling trees and therefore by light availability. Finally, we have highlighted the importance of dispersal limitation on community assembly.
Les forêts tropicales représentent un ‘hotspot’ de diversité avec un nombre considérable d’espèces qui coexistent jusqu’à une échelle locale fine. Plus particulièrement, 16 000 espèces d’arbres coexistent en Amazonie, 1 800 en Guyane française et entre 120 et plus de 200 espèces d’arbres par hectare. Cependant, le maintien de cette diversité face aux changements globaux actuels et à venir (qu’ils soient anthropiques ou climatiques…) est incertain. Avant de pouvoir prédire l’évolution de la diversité face aux changements globaux, un travail fondamental est nécessaire afin de comprendre les processus d’assemblage des communautés, processus qui maintiennent cette diversité. Ce travail est réalisé depuis de nombreuses années en écologie et reste d’actualité vu l’absence de consensus quant à l’importance relative des processus d’assemblage. Cette thèse s’inscrit dans la continuité de ce travail fondamental en utilisant une approche intégrative innovante, qui aborde de manière multi-échelle trois types de diversité : diversité taxonomique, fonctionnelle et phylogénétique. Nos résultats questionnent sur l'importance du filtrage environnemental quant aux propriétés hydrologiques et chimiques des sols, et sur celle des interactions biotiques dans l’assemblage de la communauté étudiée. Par ailleurs, nos résultats suggèrent que les distributions d’espèces puissent être influencées par la dynamique forestière en lien avec les chutes d’arbres et donc avec la disponibilité en lumière. Enfin, nous avons mis en évidence l’importance de la limitation de dispersion.
https://tel.archives-ouvertes.fr/tel-01418447

NNT : 2016YANE0003
tel-01418447
https://tel.archives-ouvertes.fr/tel-01418447
https://tel.archives-ouvertes.fr/tel-01418447/document
https://tel.archives-ouvertes.fr/tel-01418447/file/these.pdf

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 Wiley
Résumé : White-sand forests represent natural laboratories of evolution over their long history throughout Amazonia and the Guiana Shield and pose significant physiological challenges to the plants and animals they host. The study of diversification in plant lineages comprising species endemic to white-sand forest can therefore give insights into processes of evolution and community assembly in tropical forests. In this article, we synthesize recent studies of white-sand forests to integrate patterns of plant species distribution with processes of lineage diversification and community assembly in the white-sand flora. We contrast lineages that have radiated uniquely in these habitats (e.g., Pagamea, Rubiaceae), with cosmopolitan lineages comprising specialists to white-sand forests and other habitats that may have arisen via ecological speciation across habitat gradients (e.g., Protium, Burseraceae). In both cases, similar suites of functional traits have evolved, including investment in dense, long-lived tissues that are well-defended structurally and chemically. White-sand endemics, therefore, play an important role in biodiversity conservation because they represent unique combinations of functional and phylogenetic diversity. Furthermore, white-sand endemics may respond differently than other tropical forest plant species to contemporary global changes because they comprise resilient functional types that may better withstand increased drought, temperature, and invasions of exotic pests in these regions.
ISSN: 0006-3606

hal-01531635
https://hal.archives-ouvertes.fr/hal-01531635
DOI : 10.1111/btp.12301
PRODINRA : 353397

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Terrane accretion and intraplate deformation are both common processes occurring during the assembly of large continental masses. The relative roles of these mechanisms are at the heart of a debate concerning the tectonic evolution of the Borborema Province, northeastern Brazil. In the Central subprovince, four terranes or domains have been proposed. In the Alto Moxotó domain, paragneiss of the Sertânia Complex were considered to record a distinct structural and geochronological evolution compared to those in the adjacent Rio Capibaribe domain, in the East. Here, we report the results of a geological study conducted in the type area of the Sertânia Complex. Kinematic criteria and metamorphic mineral assemblages indicate that the main foliation record top-to-the-W tectonic transport under upper amphibolite facies conditions (650–700 °C). The main foliation was affected by overturned folds and upright to inclined folds; the latter two formed coevally with the development of transcurrent shear zones. Samples of mafic orthogneiss and paragneiss tectonically intercalated in the same outcrop were dated by LA-ICP-MS. The orthogneiss sample yields a crystallization age of 1978 ± 8 Ma. Detrital zircons in the paragneiss sample show a multimodal pattern with a well-defined age peak at c. 700 Ma, showing that the paragneiss is younger than 700 Ma and so the main foliation is also younger than this age. In turn, these findings suggest that the occurrence of exclusively Paleoproterozoic zircons in three other dated samples of paragneiss cannot be used to accurately define the deposition age of the detritus. The structural and geochronological characteristics of the Sertânia Complex are similar to those of the Surubim Complex in the Rio Capibaribe domain. Together with previous results showing that the basement of the Alto Moxotó and Rio Capibaribe domains is also similar, we interpret these sequences as having been deposited on a once contiguous tract of continental crust. An accretionary terrane model is thus not required to account for the tectonic evolution of this portion of the Borborema Province. Instead, a model of intracontinental deformation of a preexistent continent is fully supported by the data and also by the lack of evidence for oceanic subduction.
ISSN: 0301-9268

hal-01622825
https://hal.archives-ouvertes.fr/hal-01622825
DOI : 10.1016/j.precamres.2017.07.006

Éditeur(s) : HAL CCSD
Résumé : International audience
The geology of the North Pyrenean Zone in the central Pyrenees allows for the observation in the field of theentire section of the Pyrenean rift, from the mantle to the crust and the Mesozoic cover (pre, syn and post rift).The good knowledge we have of the pre-Alpine history of the Pyrenees allows us to properly constrain the Alpinegeological evolution of the pre-Triassic rocks which record both Variscan and Alpine orogenic cycles.The mantle outcrop as kilometric to centimetric fragments of peridotite dispersed within a carbonate metamorphicbreccia. The study of peridotite serpentinisation shows several events of low-temperature serpentinisation, incontact with seawater. In some locallities, we can observe a mixture of fragments of variously serpentinizedperidotites. This suggests a tectonic context where fragments of peridotites from different structural levels weresampled more or less synchronously.The granulitic basement is characterized by a Variscan syndeformational HT event (300-280 Ma). So farwe have not found any trace of a Cretaceous HT event (> 500C). On the other hand, the basement is affectedby a regional metasomatism that began during the Jurassic and became more spatially focused with time until itwas restricted to the Pyrenean rift during the Aptien, Albian and Cenomanian. The talc-chlorite metasomatism(120-95 Ma) shows an evolution from a static toward a syn-deformation hydrothermal event, under a more or lessnormal geothermal gradient. Extensional deformation is recorded by the reworking of several inherited low-angleVariscan tectonic contacts, but also by dispersed high-angle extensional shear zones formed under greenshistconditions.The metamorphic Mesozoic cover of the basement massifs, which constitute the so-called Internal MetamorphicZone, is an allochtonous unit made of lenses of Mesozoic rocks enclosed into the breccia, whichlocally contains peridotite and basement clasts. The Mesozoic metamorphic carbonates show a first phase ofsyn-metamorphic (450-600C, P < 2 kb) ductile deformation, and subsequent phases of folding and fracturing.The datation of neoformed minerals give a 108-85 Ma time span for the metamorphism. We interpret this brecciaas an abandonment breccia which marks the emergence of the main detachment. The basal contact of the Mesozoiccover has a complex 3D geometry traced by Triassic evaporites. It corresponds to a major pre- and synorogenicpolyphased tectonic contact.All these data show a geometrically complex hyper-extended rift where the crust was not stretched under ahigh geothermal gradient but thinned by the tectonic extraction of relatively thin lenses and perhaps cut by highangle low-grade shear zones. The 3D geometry, as well as the strain records and the breccia lithologies stronglysuggest a non-cylindricity for the exhumation process, probably within a transtentional system
Geophysical Research Abstracts
Vienne, Austria

insu-01510371
https://hal-insu.archives-ouvertes.fr/insu-01510371

Éditeur(s) : HAL CCSD Wiley
Résumé : 1. Niche theory proposes that species differences underlie both coexistence within communities and the differentiation in species composition among communities via limiting similarity and environmental filtering. However, it has been difficult to extend niche theory to species-rich communities because of the empirical challenge of quantifying niches for many species. This has motivated the development of functional and phylogeny-based approaches in community ecology, which represent two different means of approximating niche attributes. 2. Here, we assess the utility of plant functional traits and phylogenetic relationships in predicting community assembly processes using the largest trait and phylogenetic data base to date for any set of species-rich communities. 3. We measured 17 functional traits for all 4672 individuals of 668 tree species co-occurring in nine tropical rain forest plots in French Guiana. Trait variation was summarized into two ordination axes that reflect species niche overlap. 4. We also generated a dated molecular phylogenetic tree based on DNA sequencing of two plastid loci (rbcL and matK) comprising 97% of the individuals and 91% of the species in the plots. 5. We found that, on average, co-occurring species had greater functional and, to a lesser extent, phylogenetic similarity than expected by chance. 6. We also found that functional traits and their ordination loadings showed significant, albeit weak, phylogenetic signal, suggesting that phylogenetic distance provides pertinent information on niche overlap in tropical tree communities. 7. Synthesis. We provide the most comprehensive examination to date of the relative importance of environmental filtering and limiting similarity in structuring tropical tree communities. Our results confirm that environmental filtering is the overriding influence on community assembly in these species-rich systems.
ISSN: 0141-6707

hal-01032423
https://hal.archives-ouvertes.fr/hal-01032423
DOI : 10.1111/j.1365-2745.2012.01966.x

Éditeur(s) : HAL CCSD
Résumé : The main objective of this thesis was to study the influence of Guianan terra firme rainforests types on medium- and large-sized vertebrates community organization. First, we choose a model species which permitted to develop an appropriate abundance estimation method which take into account the imperfect detection and temporary immigration of mobile species, and to test environmental conditions effects at different spatial scales of analysis. Second, given that bias due to animal detection can be important in the abundance estimation, we determinated the relative role of environmental conditions and species biological traits on detection probability. From this methodological framework, we studied then processes of community organization, by identifying the main determinants involved in community organization, using composition and alpha and beta diversities, and, in a complementary manner, three metrics (taxonomic, functional, and phylogenetic). We sought from these general framework to determinate the relative role of environmental conditions and historical contingency, responsible for the current community organization, and to test the forest refugia hypothesis. Finally, we downscaled the analysis to determinate, and tried to disentangle the effects of environmental conditions and interspecific interactions on species co-occurrence. We used then functional traits to test the relationship between species co-occurrence and similarities.This thesis highlights the important role of historical contingency and facilitation in the structure of regional diversity and the local assembly processes of medium- and large-sized vertebrates, respectively, in French Guiana.
Cette thèse a pour but d’étudier l'influence de l'hétérogénéité des forêts de terre ferme en Guyane sur l'organisation des communautés de moyens et grands vertébrés. Nous avons, d'abord, choisi une espèce modèle afin de déterminer une méthode adéquate d'estimation d'abondance prenant en compte la détection imparfaite et l'immigration temporaire des espèces, et de tester l'effet des conditions environnementales à différentes échelles d'analyse. Puis, partant du constat que les biais dus à la détection dans l'estimation d'abondance pouvaient être importants, nous avons déterminé l'importance relative des conditions environnementales et des traits biologiques des espèces sur la probabilité de détection. A partir de ce cadre d'étude, nous avons étudié la composition et les diversités alpha et beta en utilisant de façon complémentaire les métriques taxonomique, fonctionnelle, et phylogénétique pour déterminer le rôle relatif de l'environnement et de la contingence historique dans l'organisation des communautés, et de tester l’hypothèse des refuges forestiers. Enfin, en descendant dans l'échelle d'analyse, nous avons tenté de démêler l'effet de l'environnement et des interactions interspécifiques sur la cooccurrence des espèces, et utilisé les traits fonctionnels des espèces pour tester le lien entre cooccurrence et similitude fonctionnelle. Cette thèse met en avant les rôles prépondérants de la contingence historique et de la facilitation dans, respectivement, la structuration de la diversité régionale et les processus d’assemblages locaux des communautés de moyens et grands vertébrés en Guyane.
https://tel.archives-ouvertes.fr/tel-01537779

NNT : 2017YANE0004
tel-01537779
https://tel.archives-ouvertes.fr/tel-01537779
https://tel.archives-ouvertes.fr/tel-01537779/document
https://tel.archives-ouvertes.fr/tel-01537779/file/these_thomas_denis.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : We have studied the phase transformation of forsterite to wadsleyite under shear stress at the Earth's transition zone pressure and temperature conditions. Two-step experiments were performed using a multi-anvil press. First, we hot pressed iron-free forsterite at 6 or 11 GPa and 1100 degrees C. Then we deformed a slab of this starting material using a direct simple shear assembly at 16 GPa and 1400 degrees C for 1, 15, 35, 40, or 60 min. Both the starting material and the deformed samples were characterized using optical and scanning electron microscopy including measurements of crystal preferred orientations (CPO) by electron back scattered diffraction (EBSD), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FTIR). The phase transformation occurs very rapidly, in less than 1 min, and metastable forsterite relics are not observed after deformation. The grain size of wadsleyite is slightly smaller than the forsterite starting material. The water contents obtained from FTIR analyses in forsterite and wadsleyite are 65-124 wt ppm H2O and 114-736 wt ppm H2O, respectively, which are well below water solubility at similar conditions in the presence of free water. Wadsleyite aggregates display weak CPO patterns with [1 0 0] axes concentrated at low angle to the shear direction, [0 1 0] axes perpendicular to the shear plane and nearly random [0 0 1] axes. Only a few dislocations were observed in wadsleyite with TEM. This observation is consistent with the assumption that most dislocations formed during the initial high-stress stages of these stress-relaxation experiments, were consumed in the phase transformation, probably enhancing the transformation rate. CPO patterns vary as a function of the water content: with increasing water content the density of [1 0 0] axes parallel to the shear direction decreases, and the density of [0 0 1] axes increases. Viscoplastic self-consistent modeling of CPO evolution using previously reported glide systems for wadsleyite, i.e., [1 0 0]{0 k 1} and 1/2 (1 1 1){1 0 1}, cannot reproduce the measured CPO, unless the [0 0 1](0 1 0) system, for which dislocations have not been observed by TEM, is also activated. In addition, wadsleyite grain growth suggests the participation of diffusion-assisted processes in deformation. Calculated anisotropies for P and S-waves using measured CPO are always below 1%. This very low anisotropy is due to both the low finite strain achieved in the experiments, which leads to weak wadsleyite CPO, and to the diluting effect of added majorite. The present experiments emphasize the importance of stress, grain size evolution and water content in the forsterite to wadsleyite phase transformation and subsequent deformation in the transition zone.
ISSN: 0031-9201

hal-00617430
https://hal.archives-ouvertes.fr/hal-00617430
DOI : 10.1016/j.pepi.2010.11.001

Éditeur(s) : HAL CCSD
Résumé : International audience
In addition to soluble factors, mechanical constraints and extracellular matrix stiffness are important regulators of cell fate that are mediated by cytoskeletal modifications. The EMT (epithelial-mesenchymal transition) that occurs during normal development and malignant progression is a typical example of the phenotypic switch associated with profound actin remodelling and changes in gene expression. For instance, actin dynamics control motile cell functions in EMT, in part, through regulating the subcellular localization of the myocardin-related transcription factor MKL1 (megakaryoblastic leukaemia translocation 1), a co-activator of SRF (serum-responsive factor). In the present paper, we show that MKL1 participates also to the control of the cellular switch between growth and quiescence. Experimental disconnection between MKL1 and G-actin (globular actin), by using an MKL1 mutant or enhancing the F (filamentous)-/G-actin ratio, generates a widely open chromatin state and a global increase in biosynthetic activity, classically associated with cell growth. Conversely, G-actin accumulation favours nuclear condensation and cell quiescence. These large-scale chromatin changes rely upon extensive histone modifications, exemplified by that of H3K9 (H3 Lys9) shifting from trimethylation, a heterochromatin mark, to acetylation, a mark of euchromatin. The present study provides the first evidence for a global reversible hetero/euchromatinization phenomenon triggered by the actin/MKL1 signalling pathway.
The Biochemical Journal

hal-01063933
https://hal.archives-ouvertes.fr/hal-01063933
DOI : 10.1042/BJ20131240
PUBMED : 24762104

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Souttoufide belt is situated between the High-Atlas in the north, the Mauritanides in the south and the West African Craton as well as the Tindouf basin in the east. Thus, this belt is a part of the West African fold belt system which surrounds the West African Craton. Outcrops occur only in three areas, while the rest of the Souttoufide belt is covered by Meso- to Cenozoic sediments. These areas are, from the south to the north, the Adrar Souttouf Massif, the Smara Zemmour area, and the western part of the Anti-Atlas. Because of the continuing processing and numerous publications, the Anti-Atlas cannot be dealt with in detail. Fundamental geological work in both of the other areas was mainly done during the second third of the 20th century, followed by several decades of inactivity. Numerous studies were done in the Adrar Souttouf massif during the last decade, while the Smara-Zemmour area still remains poorly investigated. Most of them were focused on geochronological analyses and geochemistry. Accordingly, the obtained data led to a new interpretation. The Adrar Souttouf is interpreted as a Pan-African belt exhibiting a Neoproterozoic island arc reworked by the Variscan collision between the North American Craton (NAC) and the West African Craton (WAC). The Smara-Zemmour area is considered as the external part of this Variscan belt thrusted onto the Palaeozoic Tindouf basin. The western Anti-Atlas as considered as a Pan-African active margin reworked during the Variscan orogen. Together, these three areas, lead to the hypothesis of a Late Pan-African belt capped by the Early and Middle Palaeozoic covers and then affected by the Middle Carboniferous tectonic event (330 Ma) related to the Pangaean assembly. Correlations with adjacent belts (Mauritanides and Anti-Atlas) are considered.
ISSN: 0899-5362

hal-01382815
https://hal.archives-ouvertes.fr/hal-01382815
DOI : 10.1016/j.jafrearsci.2015.04.016

Éditeur(s) : HAL CCSD
Résumé : This thesis is devoted to the study of the geodynamic evolution of the panafrican belt in NW Angola, lying on the western margin of the Congo craton. This orogenic belt, resulting from the late neoproterozoic - early paleozoic convergence of the São Francisco and Congo cratons, can be subdivided into two main domains: 1) an eastern foreland made of folded neoproterozoic sediments and 2) a western hinterland made of magmatic and metamorphic rocks. Our structural, petrological, geochemical and geochronological studies lead to the recognition of two main units within this hinterland : 1) an upper eastern unit made of gneiss and micaschists (PTmax : 8-12 kbar, 650-680°C) that preserves D1 deformation structures related to the ENE transport of nappes and 2) a western lower unit made of gneiss and migmatites (P-Tmax : 7-9 kbar, 700-750°C) that were affected by a polyphased deformation. Our geochronological study shows that this belt contains ~2Ga old granites that were involved in a polyphased panafrican evolution between 540 Ma for syn-D1 peak metamorphic conditions and 480 Ma for the last stages of recrystallization and exhumation of high grade rocks. The synthesis of all data leads to a precise reconstruction of P-T-D-t paths in both tectonometamorphic units and to comparison of this panafrican belt with similar belts distributed on both sides of the Atlantic ocean. This work attests of the complexity of the geodynamic processes resulting in the Gondwana assembly and implying both large cratonic landmasses and intercalated microplates.
Cette thèse est consacrée à l'étude de l'évolution géodynamique de la chaîne panafricaine au NW de l'Angola, sur la marge occidentale du craton du Congo. Ce segment orogénique, conséquence de la convergence des cratons du São Francisco et du Congo à la fin du Néoprotérozoïque et début du Paléozoïque, peut être subdivisé en un domaine externe plissé et peu métamorphique et un domaine interne formé de roches magmatiques et métamorphiques. Les études structurales, pétrologiques, géochimiques et géochronologiques conduisent à distinguer deux unités principales dans le domaine interne : - l'unité supérieure de gneiss et micaschistes (P-Tmax : 8-12 kbar, 650-680°C) dont la déformation D1 est synchrone de la mise en place des nappes vers l'ENE; - l'unité inférieure dans la partie occidentale constituée de gneiss et migmatites (P-Tmax : 7-9 kbar, 700-750°C) affectés par une déformation polyphasée. L'étude géochronologique démontre l'existence de protolithes granitiques datés à ~2 Ga impliqués dans l'orogénèse pan africaine caractérisée par une histoire polyphasée entre 540 Ma pour le pic du métamorphisme syn-D1 et 480 Ma pour les dernières phases de recristallisation et d'exhumation des roches métamorphiques de haut grade. La synthèse des données permet ainsi de reconstruire précisément les deux chemins P-T-D-t de ces deux unités tectono-métamorphiques et de comparer ce segment panafricain à ceux présents de part et d'autre de l'Atlantique Sud. Ce travail témoigne de la complexité des processus géodynamiques de convergence amenant à l'assemblage du Gondwana impliquant à la fois de larges masses cratoniques et des microplaques intercalées entre ces masses.
https://tel.archives-ouvertes.fr/tel-00770757

Droits : info:eu-repo/semantics/OpenAccess
tel-00770757
https://tel.archives-ouvertes.fr/tel-00770757
https://tel.archives-ouvertes.fr/tel-00770757/document
https://tel.archives-ouvertes.fr/tel-00770757/file/these2012-Nsungani.pdf