Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
The fitness landscapethe mapping between genotypes and fitnessdetermines properties of the process of adaptation. Several small genotypic fitness landscapes have recently been built by selecting a handful of beneficial mutations and measuring fitness of all combinations of these mutations. Here, we generate several testable predictions for the properties of these small genotypic landscapes under Fisher's geometric model of adaptation. When the ancestral strain is far from the fitness optimum, we analytically compute the fitness effect of selected mutations and their epistatic interactions. Epistasis may be negative or positive on average depending on the distance of the ancestral genotype to the optimum and whether mutations were independently selected, or coselected in an adaptive walk. Simulations show that genotypic landscapes built from Fisher's model are very close to an additive landscape when the ancestral strain is far from the optimum. However, when it is close to the optimum, a large diversity of landscape with substantial roughness and sign epistasis emerged. Strikingly, small genotypic landscapes built from several replicate adaptive walks on the same underlying landscape were highly variable, suggesting that several realizations of small genotypic landscapes are needed to gain information about the underlying architecture of the fitness landscape.
ISSN: 0014-3820

hal-01544760
https://hal.archives-ouvertes.fr/hal-01544760
DOI : 10.1111/evo.12545

Éditeur(s) : HAL CCSD SPRINGER
Résumé : International audience
A key question in evolutionary biology is the reproducibility of adaptation. This question can now be quantitatively analyzed using experimental evolution coupled to whole genome sequencing (WGS). With complete sequence data, one can assess convergence among replicate populations. In turn, convergence reflects the action of natural selection and also the breadth of the field of possible adaptive solutions. That is, it provides insight into how many genetic solutions or adaptive paths may lead to adaptation in a given environment. Convergence is both a property of an adaptive landscape and, reciprocally, a tool to study that landscape. In this chapter we present the links between convergence and the properties of adaptive landscapes with respect to two types of microbial experimental evolution. The first tries to reconstruct a full adaptive landscape using a handful of carefully identified mutations (the reductionist approach), while the second uses WGS of replicate experiments to infer properties of the adaptive landscape. Reductionist approaches have highlighted the importance of epistasis in shaping the adaptive landscape, but have also uncovered a wide diversity of landscape architectures. The WGS approach has uncovered a very high diversity of beneficial mutations that affect a limited set of genes or functions and also suggests some shortcomings of the reductionist approach. We conclude that convergence may be better defined at an integrated level, such as the genic level or even at a phenotypic level, and that integrated mechanistic models derived from systems biology may offer an interesting perspective for the analysis of convergence at all levels.
ECOLOGICAL GENOMICS: ECOLOGY AND THE EVOLUTION OF GENES AND GENOMES

ISBN : 978-94-007-7347-9; 978-94-007-7346-2
hal-01544757
https://hal.archives-ouvertes.fr/hal-01544757
DOI : 10.1007/978-94-007-7347-9__11

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Depuis le xviie siècle, le canal du Midi connaît des conflits d’usage et des paysages forts différents. Actuellement, les Voies Navigables de France (VNF) comme la population locale et les touristes se confrontent à une crise paysagère et environnementale majeure. La disparition des platanes centenaires à cause du champignon et de l’épidémie du chancre coloré est inéluctable. Cette crise bouleverse les niveaux d’information et de perception d’un espace touristique de première importance pour la France avec une inscription au patrimoine mondial de l’Unesco en 1996. Les arbres sont un marqueur d’une identité paysagère et de représentations touristiques très fortes. À partir d’une recherche archivistique inédite portant sur l’évolution du paysage et de l’action des acteurs, couplée à une enquête de terrain entre 2008 et 2013 sur le comportement des touristes et des promeneurs, nos résultats montrent que l’action de protection et de conservation de ce paysage rentrent dans une alliance renouvelée entre le tourisme de masse et le tourisme responsable, ils en deviennent interdépendants. La communication et la pédagogie environnementale auprès du grand public sur le degré de nature de ce site rentrent aussi dans une action à son tour résiliente et de développement durable, les ambivalences des comportements des usagers dans leur vision d’un site touristique hybride s’observent.
Since the seventeenth century, the canal du Midi known conflicts of use and a variety of landscapes. Currently, Waterways of France (VNF) as the local population and tourists are confronted with a major landscape and environmental crisis. The disappearance of the old plane because of the fungus and the epidemic of colored canker is inevitable. This crisis disrupts levels of information and perception of a tourist area of prime importance for France with an inscription on the World Heritage by UNESCO in 1996. Trees are a marker of landscape identity and tourist representations very strong. From unprecedented archival research on the changing landscape and action actors, coupled with fieldwork between 2008 and 2013 on the behavior of tourists and walkers, our results show that the action of protection and conservation of the landscape fit into a renewed relationship between mass tourism and alternative tourism alliance, they become interdependent. Communication and environmental education to the public on the state of nature of this site are also included in an action to turn its resilient and sustainable development, the ambivalences of user behavior in their vision of a hybrid attraction are observed.
Desde el siglo XVII, el canal du Midi conocido conflictos de usar y varios paisajes. Actualmente, Vías Navegables de Francia (VNF) como la población local y los turistas se enfrentan a una crisis ambiental y paisaje. La desaparición de los plátanos por el champiñón y la epidemia del cancro colorido es inevitable. Esta crisis altera los niveles de información y la percepción de una zona turística de gran importancia para Francia con una inscripción en el Patrimonio de la Humanidad por la UNESCO en 1996. Los árboles son un marcador de la identidad del paisaje y representaciones turísticas muy fuertes. De investigación de archivo original sobre la evolución del paisaje y la acción de los actores, junto con el trabajo de campo entre 2008 y 2013 en el comportamiento de los turistas y caminantes locales, nuestros resultados muestran que la acción de protección y conservación de la forma del paisaje en una renovada relación y la alianza entre el turismo de masas y el turismo alternativo, se vuelven interdependientes. Comunicación y educación ambiental al público sobre el estado de la naturaleza de este sitio se incluyen en una acción para activar su desarrollo resiliente y sostenible, las ambivalencias de comportamiento de los usuarios en su visión de un sitio turístico híbrido se observan.
France
Canal du Midi

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.7566
http://journals.openedition.org/etudescaribeennes/7566

Éditeur(s) : HAL CCSD
Résumé : In the tropical rainforest of Amazonia, the factors driving the evolution of tree species remain poorly understood, and the relative influence of neutral and adaptive processes is continuously debated. In particular, local habitat patchiness draws much attention, as profound changes in the structure and composition of forest communities occur among micro-habitats. Thus, micro-environmental variations related to topography have frequently been invoked as drivers of adaptive radiation leading to sympatric speciation in Neotropical trees. On one hand, the hypothesis of local adaptation has never been investigated at the intra-specific level, i.e. within species currently undergoing population differentiation; on the other hand, many tree species are genetically structured over local scales due to neutral processes, mainly limited gene flow (caused by restricted pollen and seed dispersal). In this study, I used populations of a common tree species of the Guiana Shield - Eperua falcata (Fabaceae) - to study how neutral and adaptive processes shape the distribution of genetic diversity across forest landscapes characterized by local micro-habitat patchiness. I asked three main questions by combining both phenotypic (quantitative genetics) and molecular (population genetics) approaches: 1) How is the genetic diversity structured in forest landscapes of French Guiana? 2) Which evolutionary drivers are relevant to explain the structure of genetic diversity at local scale? 3) Does local adaptation contribute to structure genetic diversity within continuous populations?
En forêt tropicale humide Amazonienne, les facteurs gouvernant l'évolution des espèces d'arbres restent peu connus et continuellement débattus. En particulier, les micro-variations environnementales attirent beaucoup d'attention car elles induisent de profondes modifications de structure et composition des communautés. Les variations micro-environnementales associées à la topographie ont couramment été évoquées comme facteur de radiations adaptatives chez les espèces d'arbres. Cependant, l'hypothèse de l'adaptation locale n'a jamais été testée au niveau intra-spécifique chez les arbres de forêt amazonienne alors que l'on sait que la diversité génétique des arbres tropicaux est couramment structurée à faibles échelles spatiales par des processus neutres (en particulier du fait de restrictions de flux de gènes). Dans cette étude, j'ai étudié le processus de différentiation génétique d'une espèce d'arbre (Eperua falcata, Fabaceae) dans les paysages forestiers de Guyane française grâce à la combinaison d'une approche phénotypique (génétique quantitative) et d'une approche moléculaire (génétique des populations). Je me suis attachée à répondre à trois questions principales : 1) Comment se distribue la diversité génétique dans les paysages forestiers de Guyane française ? 2) Quelles forces évolutives sont impliquées dans le processus de différentiation génétique à faible échelle spatiale ? 3) Est-ce que le processus d'adaptation locale contribue à structurer la diversité génétique à faible échelle spatiale ?
https://tel.archives-ouvertes.fr/tel-00967318

NNT : 2013LORR0188
tel-00967318
https://tel.archives-ouvertes.fr/tel-00967318
https://tel.archives-ouvertes.fr/tel-00967318/document
https://tel.archives-ouvertes.fr/tel-00967318/file/THESE_Louise_Brousseau.pdf

Éditeur(s) : HAL CCSD Springer International Publishing
Résumé : International audience
Understanding the formation processes of maritime archaeological sites and the maritime landscape in the French West Indies is a new challenge in underwater archaeology. This chapter presents an analysis of formation and conservation processes of maritime archaeological sites in Guadeloupe using evidence from both historical and archaeological research. Formation parameters include contemporary events associated with maritime loss and the in situ geophysical regime. Questions considered include: what natural and/or anthropogenic parameters best classify maritime sites in the context of the French West Indies landscape? And: how do these parameters vary by site location? Field-tested case studies are used to assess the archaeological potential for submerged shipwreck sites for three locational typologies within the landscape: submerged, coastal, and micro-island. Geomorphic parameters, including erosion, sea level evolution, and tectonic activity, are evaluated with regard to the formation of coastal Amerindian and colonial sites. The location of shipwrecks are primarily determined by historic patterns in commercial trade and by topographical constraints associated with accessibility, risk, and the presence of natural harbors, parameters important in the Caribbean. A unique feature of Guadeloupe is the high variability of the structure of the coastline through time. The recent discovery of numerous underwater prehistoric artifacts confirms that several islands, coastal areas, and their archaeological sites have been completely submerged or eroded since their formation. The characterization of these formation processes provides both academically interesting and practical information valuable in assessing the impact of development and urbanization in Guadeloupe’s maritime landscape.
Formation Processes of Maritime Archaeological Landscapes

hal-01448703
https://hal.archives-ouvertes.fr/hal-01448703

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
We studied the patterns, rates and evolution of fluvial terraces and fault system during the building process of an intracontinental transpressional mountain in the Gobi-Altay (Mongolia). By analyzing incisions and offsets of fluvial terraces and alluvial fans, we show that the massif has grown by outward migration of thrust faults through time. On the northern flank, the present bounding thrust fault began its activity ~600 ka ago, while a more internal sub-parallel fault was still active until ~200-100 ka. Vertical offset of an alluvial fan abandoned ~100 ka ago allows an estimate of 0.1 mm/yr Upper Pleistocene - Holocene uplift rate. The morphology of the catchment-piedmont system strongly suggests a periodical formation of the alluvial surfaces, controlled by the climatic pulses, at the beginning of the wet interglacial periods. The abandonment of the alluvial terraces lags by several thousand years the abandonment of the alluvial fans, showing a diachronous incision propagating upstream. The incision rate deduced from the different elevations of straths exceeds of one order of magnitude the rock uplift rate. This excess is mostly due to ongoing drainage network growth at the core of the massif, and incision due to alluvial apron entrenchment near the outlet. This implies that fluvial response is mainly controlled by drainage growth, interaction with piedmont and cyclic climatic variations, rather than by rock uplift.
ISSN: 0278-7407

hal-00323558
https://hal.archives-ouvertes.fr/hal-00323558
https://hal.archives-ouvertes.fr/hal-00323558v2/document
https://hal.archives-ouvertes.fr/hal-00323558/file/Vassallo2007.pdf
DOI : 10.1029/2006TC002081

Éditeur(s) : Université de Bretagne Occidentale
Résumé : Several small pelagic fish species contribute remarkably to world catch. Their populations are, however, characterized by large biomass fluctuations strongly affecting fisheries. The fishing gears and methods used to capture small pelagics have evolved to exploit the highly developed shoaling behavior of these species. Hence, faced to modern fishing this gregarious behavior becomes a disadvantage for fish. Fish behavior may be affected by environmental conditions and by fishing, at the same time that behavior impacts fishing. In this study, we seek to characterize the aggregative systems of small pelagic fishes inhabiting the Bay of Biscay by analyzing "acoustic images", defined as the group of echoes (planktonic layers, shoals, isolated targets) detected on a transect section of a given length. We analyzed the species composition, the spatial distribution and the evolution over time of acoustic images. We also studied the hydrological conditions of the bay, as well as the small pelagics French fishery in order to look for correlations between hydrology, commercial catch and fish aggregation patterns observed by acoustics. We observed the same species or group of species forming different types of aggregation according to habitat. Conversely, the same type of aggregation, associated with a particular habitat, can be produced by different species. The most notorious change observed during the studied period relates to small clupeoids aggregations in the vicinity of the Gironde estuary, whose structure evolved toward a greater fragmentation of shoals (a large number of small size detections) since 2000. Concerning commercial catches, pelagic trawlers fishing in pairs mainly seek for anchovy in the coastal areas, single pelagic trawlers capture mackerel and horse mackerel in deeper waters while purse seiners target mostly sardine near their fishing ports. Because of the coarse spatial resolution of commercial fishing data and the effect of the application of an international fisheries agreement limiting the fishing activity of French pelagic trawlers during spring, only small correlations between captures and types of aggregation were observed.
La participation des petits poissons pélagiques dans les captures est remarquable. Leurs populations sont cependant caractérisées par des importantes fluctuations de biomasse, impactant fortement les pêcheries. Les méthodes et appareils de pêche utilisés pour capturer ces espèces ont évolué dans le sens d'exploiter le comportement grégaire très développé des petits pélagiques. Cette tendance à former de bancs devient alors désavantageuse pour le poisson face à la pêche moderne. Les conditions environnementales et la pêche peuvent affecter le comportement du poisson, en même temps que ce dernier est susceptible d'affecter l'activité halieutique. Le but de cette étude est de caractériser les systèmes agrégatifs des petits poissons pélagiques dans le golfe de Gascogne en étudiant des « images acoustiques », définies comme l'ensemble des échos (couches planctoniques, bancs, cibles isolées) détectés sur une section de radiale de longueur donnée. Nous analysons leur composition en espèces ainsi que leur distribution spatiale et leur évolution au cours du temps. Nous étudions aussi les conditions hydrologiques du golfe, ainsi que la pêcherie française de ces espèces afin de chercher des corrélations entre l'hydrologie, la capture commerciale et les types d'agrégations observés par acoustique. Nous avons observé qu'une espèce est capable de former des agrégations différentes en fonction de l'habitat, et inversement, le même type d'agrégation, associé à un habitat particulier, peut être produit par des espèces différentes. Le changement observé le plus évident concerne les agrégations de petits clupéiformes, dont la structure a évolué vers une plus grande fragmentation des détections (des petits bancs plus nombreux) depuis 2000. Par rapport à la pêche des professionnels, les chalutiers pélagiques en boeufs recherchent en priorité l'anchois dans la zone côtière, les pélagiques simples capturent le chinchard et le maquereau au large et les senneurs recherchent principalement la sardine à proximité des ports de pêche. À cause de la résolution spatiale trop sommaire des données de pêche et l'effet de l'application des accords internationaux limitant l'activité des chalutiers pélagiques au printemps, nous n'avons observé que peu des corrélations entre les captures et les types d'agrégation établis à partir de données issues des campagnes scientifiques.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2008/these-6083.pdf
http://archimer.ifremer.fr/doc/00000/6083/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Tectonically controlled landforms develop morphologic features that provide useful markers to investigate crustal deformation and relief growth dynamics. In this paper, we present results of morphotectonic experiments obtained with an innovative approach combining tectonic and surface processes (erosion, transport, and sedimentation), coupled with accurate model monitoring techniques. This approach allows for a qualitative and quantitative analysis of landscape evolution in response to active deformation in the three end-member geological settings: compression, extension, and strike–slip.Experimental results outline first that experimental morphologies evolve significantly at a short time scale. Numerous morphologic markers form continuously, but their lifetime is generally short because erosion and sedimentation processes tend to destroy or bury them. For the compressional setting, the formation of terraces above an active thrust appears mainly controlled by narrowing and incision of the main channel through the uplifting hanging-wall and by avulsion of deposits on fan-like bodies. Terrace formation is irregular even under steady tectonic rates and erosional conditions. Terrace deformation analysis allows retrieving the growth history of the structure and the fault slip rate evolution. For the extensional setting, the dynamics of hanging-wall sedimentary filling appears to control the position of the base level, which in turn controls footwall erosion. Two phases of relief evolution can be evidenced: the first is a phase of relief growth, and the second is a phase of upstream propagation of topographic equilibrium that is reached first in the sedimentary basin. During the phase of relief growth, the formation of triangular facets occurs by degradation of the fault scarp, and their geometry (height) becomes stationary during the phase of upstream propagation of the topographic equilibrium. For the strike–slip setting, the complex morphology of the wrench zone, composed of several interacting fault segments, enhances the interactions with the drainage network. Because of the widening of the main fault zone toward the surface, a significant amount of distributed deformation is observed along the wrench zone. Locally, where two terminations of fault segments interact, less than a quarter of the far field displacement can remain measurable using fault offsets, leading to a systematic underestimation of the real fault slip rate.These different experimental examples illustrate the great potential of the approach coupling deformation mechanisms and erosion–transport–sedimentation processes to investigate qualitatively and quantitatively the morphotectonic evolution of tectonically controlled landscapes.
ISSN: 0169-555X

hal-01243587
https://hal.archives-ouvertes.fr/hal-01243587
DOI : 10.1016/j.geomorph.2015.02.011

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
Knowing the slip amplitudes that large earthquakes produced in prehistorical times is one key to anticipate the magnitude of large forthcoming events. It is long known that the morphology is preserving remnants of paleoearthquake slips in the form of fault-offset landforms. However, the measured offsets that can be attributed to the most recent paleoearthquakes are generally few along a fault, so that they rarely allow recovering the slip distributions and largest slips of these earthquakes. We acquired ~1 m resolution airborne lidar data on a 30 km stretch of a fast-slipping strike-slip fault (eastern Hope Fault, New Zealand) located in a region of high alluvial dynamics where landforms are rapidly evolving. Data analysis reveals >200 offset landforms; only 30% allow a good to moderate quality offset measurement. From these good to moderate quality measures, we recover the slip-length distributions and largest slips of the four most recent large paleoearthquakes and find evidence of 4–6 prior events. The record suggests that large earthquake slip recurred in multiples of about 4 m along the 30 km stretch. Although they have larger uncertainties, the more numerous lower-quality offsets that we also measured reveal a similar earthquake slip record. This shows that, although offset landforms are partly degraded in dynamically active landscapes, they store valuable information on paleoearthquake slips. This information might be recovered provided that the morphology is analyzed at high resolution and " continuously " over a significant fault length. Remote lidar data are powerful to perform such analyses.
ISSN: 2169-9313

insu-01469219
https://hal-insu.archives-ouvertes.fr/insu-01469219
https://hal-insu.archives-ouvertes.fr/insu-01469219/document
https://hal-insu.archives-ouvertes.fr/insu-01469219/file/Manighetti_et_al-2015-Journalsur Geophysical_Research__Solid_Earth.pdf
DOI : 10.1002/2014JB011787

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.
ISSN: 0737-4038

hal-01544755
https://hal.archives-ouvertes.fr/hal-01544755
DOI : 10.1093/molbev/msu318

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
The nine countries sharing the Amazon forest accounted for 89% of all malaria cases reported in the Americas in 2008. Remote sensing can help identify the environmental determinants of malaria transmission and their temporo-spatial evolution. Seventeen studies characterizing land cover or land use features, and relating them to malaria in the Amazon subregion, were identified. These were reviewed in order to improve the understanding of the land cover/use class roles in malaria transmission. The indicators affecting the transmission risk were summarized in terms of temporal components, landscape fragmentation and anthropic pressure. This review helps to define a framework for future studies aiming to characterize and monitor malaria.
ISSN: 1475-2875

inserm-00834790
http://www.hal.inserm.fr/inserm-00834790
http://www.hal.inserm.fr/inserm-00834790/document
http://www.hal.inserm.fr/inserm-00834790/file/1475-2875-12-192.pdf
DOI : 10.1186/1475-2875-12-192

Éditeur(s) : HAL CCSD
Résumé : Among erosion processes, river incision is classicaly described as a key process controlling erosion of landscapes. Incision efficiency is mainly influenced by climate and erodibility. This latter is not only dependent on the nature of the bedrock, but also on its past deformation, which affects its rheological effective properties, such as fracture density. The main objectives of this thesis are: (1) to better constrain the relationship between effective properties and erodibility, and (2) to quantify the influence of erodibility and erosion on both the temporal and spatial building or decay of the topography. Several numerical tools are developed. A 1D formalism of landscape evolution is introduced, including river incision with stochastic distribution of water discharge and hillslope landsliding. A new remeshing algorithm called Surface Lagrangian Remeshing (SLR) is developed as a complement to remeshing algorithms dealing with internal elements. It allows one to take into account long-term erosion into 2D Lagrangian numerical codes based on triangular finite elements. Then the potentiality of measuring erodibility in-situ using a Schmidt hammer (R) is assessed for the active orogen of Taiwan, the diagenetic Annot sandstones and St Clement fault zone. Results suggest a strong control of R by effective properties. A linear model based on effective medium theory is applied to a fault zone with an unmacthed resolution (750 measures, 25 measures per square meter). The model successfully correlates R to fracture density. These results demonstrate that effective elasticity as well as erodibility are sensitive to the density and type of fractures. Finally I focus on the erosional and rheological conditions that allows reproducing post-orogenic evolution of mountain belts. A model coupling surface erosion and regional isostatic uplift is consistent with observations. The topographic decay and decrease of the ratio of surface elevation over crustal root thickness is at first order controlled by the initial geometry of the mountain belt and erosion efficiency. This new model highlights the control ofclimate and erodibility on the topographic decay and of lithospheric rheology on the perseverance of crustal roots.
Parmi les processus d'érosion, l'incision des rivières est classiquement décrit comme un processus clé contrôlant l'érosion des paysages. L'efficacité de l'incision est principalement influencée par le climat et par l'érodabilité. Ce dernier paramètre ne dépend pas seulement de la nature du substratum rocheux, mais aussi de sa déformation passée qui affecte ses propriétés rhéologiques équivalentes. Les principaux objectifs de cette thèse sont: (1) de mieux contraindre les relations entre propriétés équivalentes et érodabilité, et (2) de quantifier l'influence de l'érosion et de l'érodabilité sur la formation ou la décadence, spatiale et temporelle, de la topographie. Plusieurs outils numériques sont développés. Un formalisme 1D d'évolution des paysages est proposé, prenant en compte simultanément l'incision des rivières avec une distribution stochastique des débits en eau et l'érosion des versants par glissements de terrain. Un nouvel algorithme de remaillage appelé Surface Lagrangian Remeshing (SLR) est développé. Il permet de prendre en compte l'érosion à long terme dans les codes numériques 2D Lagrangiens basés sur des éléments finis triangulaires. Ensuite, la possibilité de mesurer in-situ l'érodabilité avec un marteau de Schmidt (R) est évaluée pour: l'orogène actif de Taiwan, les grès diagénétiques d'Annot et la zone de faille de St Clément. Les résultats suggèrent un fort contrôle de R par les propriétés équivalentes des roches testées. Un modèle linéaire, basé sur la théorie des milieux équivalents, est appliqué à une zone de faille avec une résolution inégalée (750 mesures, 25 mesures par mètre carré). Le modèle permet de corréler avec succès la densité de fracture et R. Ces résultats démontrent empiriquement que l'élasticité équivalente ainsi que l'érodabilité sont sensibles à la densité et à la nature des fractures. Enfin j'étudie les conditions d'érosion et de rhéologie qui permettent de reproduire l'évolution des chaînes de montagnes post-orogéniques. Un modèle couplant érosion en surface et soulèvement isostatique régional est compatible avec les observations. Les taux de décroissance topographique et de diminution du rapport de l'élévation de surface sur l'épaisseur de racine crustale sont contrôlés au premier ordre par la géométrie initiale de la chaîne de montagne et par l'efficacité de l'érosion. Ce nouveau modèle met en évidence le contrôle du climat et de l'érodabilité sur la décroissance topographique et de la rhéologie lithosphérique sur la persévérance des racines crustales.
https://tel.archives-ouvertes.fr/tel-00602341

tel-00602341
https://tel.archives-ouvertes.fr/tel-00602341
https://tel.archives-ouvertes.fr/tel-00602341/document
https://tel.archives-ouvertes.fr/tel-00602341/file/thesephilippesteer.pdf

Éditeur(s) : HAL CCSD
Résumé : Staphylococcus aureus is an opportunistic pathogen of humans and warm-blooded animals. It is foundin healthy carriage and can cause a wide range of infections in its hosts. The epithelial surface is theprincipal site of staphylococcal infection. The pathogens have evolved sophisticated mechanisms tohijack the main function of the host cells, thus promoting their invasion and colonization. Amongstthese effects are, alteration of host cell apoptosis, promotion of cell proliferation or conversely,inhibition of cell growth. Using human cervix cancer HeLa and mammary gland bovine MAC-Tepithelial cells, we studied the cytopathic effect of S. aureus and its ability to affect host cell cycle.Using microscopic examination, we found that S. aureus induced the cytopathic effect resulting in theenlargement of the host cells 72 hours post infection. Our experiments showed that the proliferationrate of the epithelial cells was slowed down in S. aureus-infected culture. Three different S. aureusstrains from human and animal origins were used and showed similar effect on both human and bovinecells. Microscopic analysis of DAPI-stained cells revealed huge decrease of mitotic indexes in infectedHeLa and Mac-T cells, synchronized by Double Thymidine Block. Using flow cytometry analysis, wefound that S. aureus induces G2/M phase delay in synchronous HeLa cells. By Western blot analysis,we showed that the G2/M phase delay was associated with accumulation of inactive phosphorylatedcyclin-dependent kinase Cdk1/cdc2, a key inducer of mitosis entry, and dephosphorylation of corehistone H3, an important component of the epigenetic landscape.These results suggest that the delay in G2/M phase transition of the infected epithelial cells may beone of the mechanisms employed by S. aureus to survive and to propagate inside the host. A fullcomprehension of the mechanisms associated to S. aureus-host cell interactions will undoubtedly helpto discover novel targets to treat staphylococcal infections.
EMBO
Villars sur Ollon, Switzerland

hal-01454214
https://hal.archives-ouvertes.fr/hal-01454214
PRODINRA : 171657

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a similar to 6-km transect, to evaluate dispersal ability, and between paired bank populations along a similar to 65-km stretch of the Approuague river, to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale, and conclude that the species has a restricted dispersal ability that is probably tied to its life-history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river, and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is the result of restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life-history traits comparable with A. andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 356373.
ISSN: 0024-4066

hal-01032422
https://hal.archives-ouvertes.fr/hal-01032422
DOI : 10.1111/j.1095-8312.2012.01871.x

Résumé : L'agriculture actuelle est impliquée dans de multiples problématiques environnementales, sociales et économiques, aux échelles locales et globales. En agronomie, de nombreux travaux à l'échelle du champ et de l'exploitation visent aujourd'hui à concevoir des systèmes de culture et des systèmes de production en lien avec ces problématiques. En revanche, peu de travaux portent sur la conception et l'évaluation de systèmes agricoles à l'échelle du territoire, alors que cette échelle apparaît pourtant incontournable pour faire face à des enjeux de développement durable. Pour combler ce manque, nous proposons un ensemble méthodologique permettant i) de simuler les conséquences de scénarios de politiques agricoles sur les choix d'assolement des agriculteurs, décrits individuellement, en modélisant l'évolution de leurs système de production et ii) d'évaluer l'impact de ces changements d'assolements à l'échelle du territoire, à l'aide d'indicateurs qui apportent de l'information spatiale sur la contribution de l'agriculture au développement durable. L'ensemble méthodologique proposé débute par la construction d'une typologie des exploitations agricoles du territoire sur la base de la similarité de leur assolement. Parallèlement, l'adaptation d'indicateurs à l'échelle du territoire permet d'évaluer les impacts des externalités des systèmes de culture en mobilisant des procédures de changements d'échelles. Un modèle bioéconomique générique, multi-échelle, spatialement explicite, appelé MOSAICA, qui utilise la typologie et les indicateurs d'impact de l'agriculture à l'échelle régionale, est créé pour produire des mosaïques de systèmes de culture et évalue leur contribution au développement durable du territoire. Ce modèle, couplé à un itinéraire de définition de scénarios exploratoires et normatifs permet de tester l'impact de différents types de leviers agronomiques, socio-économiques, environnementaux, organisationnels et techniques sur les choix des exploitants et in fine sur la contribution de la mosaïque de systèmes de culture au développement durable du territoire. Nous avons appliqué cet ensemble méthodologique à la conception de scénarios de développement agricoles durables en Guadeloupe. Nous avons dans un premier temps développé une typologie des systèmes de production comprenant huit types distincts et relevant de processus décisionnel différents. Puis nous avons adapté à l'échelle du territoire 19 indicateurs pour l'évaluation des mosaïques de systèmes de culture. L’évaluation de la mosaïque actuelle nous a permis de repérer de faibles niveaux de contribution aux enjeux d’autonomie alimentaire et énergétique. Différents scénarios normatifs et exploratoires intégrant des leviers de changement de la mosaïque ont été testés avec MOSAICA. Les évaluations réalisées nous ont permis d'identifier que des leviers agronomiques comme le développement du maraîchage sans intrants chimiques et des leviers sociaux comme la formation de main-d'oeuvre supplémentaire permettraient d'améliorer la contribution de l’agriculture au développement durable du territoire Guadeloupéen. La modélisation mécaniste de l’évolution du territoire agricole permet d'intégrer des connaissances sur la localisation, les performances, les impacts des systèmes de culture et sur les processus décisionnels des exploitants régissant l’orientation productive et le fonctionnement des exploitations. Cette démarche permet de visualiser les changements de système de culture et leurs impacts de manière spatialement explicite, ce qui permet de générer des connaissances sur les leviers susceptibles de faire évoluer positivement l'agriculture du territoire. La démarche et les outils mis en oeuvre sont donc particulièrement utiles pour l'aide à la décision publique pour améliorer la durabilité de l'agriculture dans son ensemble.
Current agricultural systems are responsible for many different environmental, social and economic issues at both local and global scales. Agricultural sciences have contributed to the design of several methods at the farm and field scale in order to prototype cropping systems and farming systems to address these issues. However, few methods have been designed at the regional scale, while this scale seems to be essential in order to address these issues. In order to fill this gap, we here propose a new methodological framework for i) simulating the consequences of policy changes on farmer's cropping plan, described individually, by modeling the evolution of farming systems and to ii) assess the impacts of cropping system changes at the regional scale, with a set of indicators that generate spatially explicit information on the contribution of agriculture to sustainable development. The methodological framework starts with the design of a farm typology over the territory based on the similarity of farmer's crop acreages. In parallel, a set of indicators is adapted to the landscape scale in order to assess the impacts of cropping system externalities by integrating a set of scale change procedures. A generic, multi-scale, spatially explicit bioeconomic model called MOSAICA, which uses the farm typology and the indicators, is created for generating cropping system mosaics and assessing their contribution to sustainable development. This model coupled to a scenario approach composed of exploratory and normative scenarios can simulate the impact of several types of agronomic, socio-economic, environmental, organizational and technical levers of change on the farmer's choices in terms of cropping systems and in fine the impacts of new cropping system mosaics on the contribution to sustainable development of territories. We applied this methodological framework for building scenarios of sustainable agricultural development in Guadeloupe. We first developed a typology of farming systems encompassing eight types of farming systems that revealed several different farmer's decision processes. Then, we developed 19 indicators to assess cropping system mosaics. The assessment of the current cropping system mosaic showed low levels of response of the current mosaic to economic and social issues especially the food and energy self-sufficiency. Different normative and exploratory scenarios integrating levers of change have been simulated with MOSAICA. The assessment of cropping system mosaics from these scenarios highlighted the positive effect of agronomic levers of change such as organic crop-gardening and social levers such as the vocational training of supplementary workforce for improving the contribution of agriculture to sustainable development of the guadeloupean territory. The mechanistic modeling of the agricultural territory allows us to integrate a wide range of knowledge on the location of cropping systems, their levels of performance , their impacts and the decision process of farmer's that drive the farming system characteristics and the farm functioning. This methodological framework helps visualize the cropping system changes at the regional scale and their associated impacts at the landscape scale which is helpful in order to produce knowledge on the levers of change that can improve the response of local agriculture to local and global issues. The framework and tools designed are particularly useful for decision-aid on the future levels of contribution of agriculture to sustainable development.

http://www.theses.fr/2015AGUY0823/document

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Le tourisme balnéaire joue un rôle fondamental dans le développement économique des pays des deux rives du bassin méditerranéen. Climat tempéré, plages sablonneuses et beauté du paysage naturel côtier représentent le support à cette nouvelle activité. Si dans beaucoup de pays, comme l’Espagne, le Maroc, la Tunisie, la France, etc., une large surface du littoral est mise en tourisme, les aménagements touristiques restent en Algérie très ponctuels et en décalage avec la demande réelle de la population. La volonté de l’Etat algérien de faire du tourisme balnéaire une activité génératrice de richesse dans l’objectif d’atténuer la dépendance de l’économie au secteur des hydrocarbures, rencontre beaucoup de difficultés telles la question des enjeux fonciers et les dysfonctionnements entre les outils d’aménagement et ceux de protection de la nature. Dans cet article, l’objectif est, à travers le cas du littoral mostaganemois, d’analyser l’évolution des dispositions institutionnelles en matière du tourisme balnéaire et de leurs mises en œuvre sur le terrain toute en analysant les spécificités du contexte socioéconomique et naturel à une échelle locale.
The seaside tourism plays a fundamental role in the economic development of the Mediterranean countries. Temperate climate, sandy beaches and natural coastal landscape are the support to this new activity. If in many countries such as Spain, Morocco, Tunisia and France, etc., the tourism development is diffused over a wide area of the coast, it remains very limited phenomenon in Algeria and out of step with real request of the population. The will of the Algerian state to make of the seaside tourism a generative financial activity with the objective to limit the dependence of the energy income, faced many difficulties such land issues and dysfunctions between development tools and those of nature protection.In this article, the objective is, through the case of the Mostaganem coast, to discuss the evolution of the institutional capacities regarding the seaside tourism and his implementation on the ground while analyzing the specifities of socioeconomic and natural context in a local scale.
Algérie
Monstaganem

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.9305
http://journals.openedition.org/etudescaribeennes/9305

Éditeur(s) : HAL CCSD Wiley
Résumé : Clay shale landscapes are sensitive to landslide, erosion, and re-sedimentation processes. In this context, tectonized clay shales have peculiar hydrological and mechanical behaviours. In order to improve our understanding of the processes involved in such systems, an experimental site has been settled in the Draix Observatory (ORE DRAIX) on a black marl hill slope of the Southern Alps (France) in the framework of the ECOU-PREF project. The site is a natural laboratory to study the evolution of clay shale landscapes at several scales (regional to µm). In this study, we aim to characterize the internal structure and fissure patterns of a stable interfluve, in order to locate preferential water flows within the system, and anticipate its evolution. This work is based on a series of mutli-disciplinary approaches including petrophysical analyses, well pulse injection tests and downhole geophysical measurements. Borehole geophysical results were combined with laboratory measurements on core plugs (permeability, density, porosity, and acoustic velocity). Optical and acoustical images have been used as an original tool for internal discontinuities characterisation and potential active flow path detection. They allowed the identification of three main lithological units interpreted as several stages of shale alteration. In addition, several main structural plane discontinuities (open fractures, schistosity planes, and fractures infilled with calcite or clays) were identified from the images and their potential transmissivity discussed with regard to piezometric and tracer measurements. In all, the integration of measurements leads to propose a simple scenario of fluid circulation and chemical alteration of the interfluve.
ISSN: 0885-6087

hal-00757581
https://hal.archives-ouvertes.fr/hal-00757581
DOI : 10.1002/hyp.7997

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We developed a new granular material (MatIV) to study experimentally landscape evolution in active mountain belt piedmonts. Its composition and related physical properties have been determined using empirical criteria derived from the scaling of deformation, erosion-transport and sedimentation natural processes. MatIV is a water-saturated composite material made up with 4 granular components (silica powder, glass microbeads, plastic powder and graphite) whose physical, mechanical and erosion-related properties were measured with different laboratory tests. Mechanical measurements were made on a modified Hubbert-type direct shear apparatus. Erosion-related properties were determined using an experimental set-up that allows quantifying the erosion/sedimentation budget from tilted relaxation topographies. For MatIV, we also investigated the evolution of mean erosion rates and stream power erosion law exponents in 1D as a function of slope.;Our results indicate that MatIV satisfies most of the defined criteria. It deforms brittlely according to the linear Mohr-Coulomb failure criterion and localizes deformation along discrete faults. Its erosion pattern is characterized by realistic hillslope and channelized processes (slope diffusion, mass wasting, channel incision). During transport, eroded particles are sorted depending on their density and shape, which results in stratified alluvial deposits displaying lateral fades variations. To evaluate the degree of similitude between model and nature, we used a new experimental device that combines accretionary wedge deformation mechanisms and surface runoff erosion processes. Results indicate that MatIV succeeded in producing detailed morphological and sedi-mentological features (drainage basin, channel network, terrace, syntectonic alluvial fan). Geometric, kinematic and dynamic similarity criteria have been investigated to compare precisely model to nature. Although scaling is incomplete, it yields particularly informative orders of magnitude. With all these characteristics, MatIV appears as a very promising material to investigate experimentally a wide range of scientific questions dealing with relief dynamics and interactions between tectonics, erosion and sedimentation processes.
ISSN: 0040-1951

hal-00669904
https://hal.archives-ouvertes.fr/hal-00669904
DOI : 10.1016/j.tecto.2011.09.029

Éditeur(s) : HAL CCSD Endocrine Society
Résumé : International audience
Sertoli cells (SCs), the only somatic cells within seminiferous tubules, associate intimately with developing germ cells. They not only provide physical and nutritional support but also secrete factors essential to the complex developmental processes of germ cell proliferation and differentiation. The SC transcriptome must therefore adapt rapidly during the different stages of spermatogenesis. We report comprehensive genome-wide expression profiles of pure populations of SCs isolated at 5 distinct stages of the first wave of mouse spermatogenesis, using RNA sequencing technology. We were able to reconstruct about 13 901 high-confidence, nonredundant coding and noncoding transcripts, characterized by complex alternative splicing patterns with more than 45% comprising novel isoforms of known genes. Interestingly, roughly one-fifth (2939) of these genes exhibited a dynamic expression profile reflecting the evolving role of SCs during the progression of spermatogenesis, with stage-specific expression of genes involved in biological processes such as cell cycle regulation, metabolism and energy production, retinoic acid synthesis, and blood-testis barrier biogenesis. Finally, regulatory network analysis identified the transcription factors endothelial PAS domain-containing protein 1 (EPAS1/Hif2α), aryl hydrocarbon receptor nuclear translocator (ARNT/Hif1β), and signal transducer and activator of transcription 1 (STAT1) as potential master regulators driving the SC transcriptional program. Our results highlight the plastic transcriptional landscape of SCs during the progression of spermatogenesis and provide valuable resources to better understand SC function and spermatogenesis and its related disorders, such as male infertility.
ISSN: 0888-8809

hal-01146846
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146846
DOI : 10.1210/me.2014-1356
PUBMED : 25710594

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
S U M M A R Y Over the last decade, thermomechanical models have revealed the control of both tectonics and erosion on the morphology of continental plateaus margins. However, unravelling the specific effects of these two coupled processes has been difficult in practice. Here, to assess the control of erosion, we investigate the dynamics of the eastern and the northern borders of the Tibetan Plateau, which are characterized by a low convergence rate and a steep topographic escarpment adjacent to the Sichuan and Tarim basins, respectively. Thermomechanical modelling of continental lithosphere coupled with fluvial denudation reveals that important crustal deformation with large-scale horizontal displacements can occur, without any convergence, as a response to mass transfer due to gravitational collapse and to erosional unloading. These processes are sensitive to crustal structure, geothermal gradient as well as surface erosion. At a timescale of several million years, our results suggest that this denudation-triggered deformation exerts a primary control on the evolution of those plateau margins by counterbalancing the mass removal due to erosion and stabilizing the topographic escarpment. This finding supports a possible explanation for the morphology of the Longmen Shan, eastern Tibet, in which the paradoxical combination of persistent high-topographic gradients close to the foreland and low convergence rates can be related to the influence of erosion on deformation patterns.
ISSN: 0956-540X

hal-01577060
https://hal-amu.archives-ouvertes.fr/hal-01577060
https://hal-amu.archives-ouvertes.fr/hal-01577060/document
https://hal-amu.archives-ouvertes.fr/hal-01577060/file/godard2009erosional.pdf
DOI : 10.1111/j.1365-246X.2009.04324.x