Éditeur(s) : Public Library Science
Résumé : Background: Reconstructing the history of divergence and gene flow between closely-related organisms has long been a difficult task of evolutionary genetics. Recently, new approaches based on the coalescence theory have been developed to test the existence of gene flow during the process of divergence. The deep sea is a motivating place to apply these new approaches. Differentiation by adaptation can be driven by the heterogeneity of the hydrothermal environment while populations should not have been strongly perturbed by climatic oscillations, the main cause of geographic isolation at the surface. Methodology/Principal Finding: Samples of DNA sequences were obtained for seven nuclear loci and a mitochondrial locus in order to conduct a multi-locus analysis of divergence and gene flow between two closely related and hybridizing species of hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis. The analysis revealed that (i) the two species have started to diverge approximately 0.760 million years ago, (ii) the B. azoricus population size was 2 to 5 time greater than the B. puteoserpentis and the ancestral population and (iii) gene flow between the two species occurred over the complete species range and was mainly asymmetric, at least for the chromosomal regions studied. Conclusions/Significance: A long history of gene flow has been detected between the two Bathymodiolus species. However, it proved very difficult to conclusively distinguish secondary introgression from ongoing parapatric differentiation. As powerful as coalescence approaches could be, we are left by the fact that natural populations often deviates from standard assumptions of the underlying model. A more direct observation of the history of recombination at one of the seven loci studied suggests an initial period of allopatric differentiation during which recombination was blocked between lineages. Even in the deep sea, geographic isolation may well be a crucial promoter of speciation.
Plos One (1932-6203) (Public Library Science), 2009-08 , Vol. 4 , N. 8 , P. 1-15

Droits : 2009 Faure et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
http://archimer.ifremer.fr/doc/00129/24012/21972.pdf
DOI:10.1371/journal.pone.0006485
http://archimer.ifremer.fr/doc/00129/24012/

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
ISSN: 1664-302X

hal-01546980
http://hal.upmc.fr/hal-01546980
DOI : 10.3389/fmicb.2013.00414

Résumé : La tuberculose, maladie très ancienne, est plus que jamais présentée sur la scène sanitaire mondiale avec 9 millions de nouveaux cas par an. Cette maladie, qui demeure une cause majeure de mortalité, est un des problèmes les plus difficiles à résoudre en santé publique et à échelle internationale. Les diverses programmes de lutte, lancés par l’Organisation Mondiale de la Santé (OMS), pour prévenir et garantir la guérison des patients tuberculeux, se heurtent à des difficultés qui hypothèquent leur efficacité. En effet, l'expansion du virus de rinimunodéficience humaine (VIII) et son influence néfaste sur la susceptibilité à la tuberculose, l'accroissement rapide de la tuberculose multirésistante, la pauvreté ainsi que la croissance démographique, sont un ensemble de facteurs préjudiciables à l'application des mesures préventives et curatives. Les contextes économiques difficiles conduisant indubitablement au cumul de ces facteurs, ont fait une césure entre les pays riches et les pays pauvres quant à l'incidence et la révolution de la tuberculose à échelle mondiale. Pour atténuer la disparité des résultats des luttes antituberculeuses, les méthodologies employées en épidémiologie de la tuberculose doivent s'inscrire dans une démarche d'efficacité. Les marqueurs moléculaires, indispensables à l'identification et à la classification des souches appartenant au complexe Mycobacterium tuberculosis (MTC) ont chacun des potentialités qui leur sont propres dont il convient de cerner pour une utilisation adéquate dans les études épidémiologiques et phylogénétiques. Le but de cette thèse consiste à extraire des connaissances nouvelles des résultats de génotypage stockées dans les bases de données, connaissances relatives au polymorphisme du support génomique pour estimer la contribution de chaque marqueur dans la classification de MTC. Le recours à différentes méthodes de reconstruction phylogénétique et de modélisation des données fut indispensable. A la lumière des résultats obtenus, cette thèse propose une nouvelle méthodologie de classification, pour rétablissement d'une phylogéographie robuste de MTC en relation avec l'histoire des migrations humaines qui aurait débutée en Afrique subsaharienne. Chaque méthode de génotypage ayant une efficience et un cout propres, qu'il convient de mesurer par rapport aux moyens disponibles et aux résultats escomptes, il est donc intéressant de renforcer la connaissance des marqueurs et de proposer différentes alternatives menant à la classification des mycobactéries. Ainsi, les résultats obtenus dans cette thèse apportent plus de cohérence aux solutions proposées pour la caractérisation des clones de MTC circulant dans le monde.
Tuberculosis, very old disease, is more than ever presented on the global health scene with 9 million new cases per year. This disease, which remains a major cause of mortality is one of the most intractable public health and international issues. The various control programs, launched by the World Health Organization (WHO) to prevent and guarantee the cure of tuberculosis patients face difficulties that undermine their effectiveness. Indeed, the expansion of human virus rinimunodéficience (VIII) and its negative influence on susceptibility to tuberculosis, the rapid growth of multidrug-resistant tuberculosis, poverty and population growth, are a set of factors detrimental to application of preventive and curative measures. The difficult economic circumstances undoubtedly leading to accumulation of these factors have a break between rich and poor countries about the impact and the revolution of tuberculosis worldwide. To address the disparity of the results of tuberculosis struggles, the methodologies used in epidemiology of tuberculosis must be part of a process efficiency. Molecular indispensable to the identification and classification of strains belonging to the Mycobacterium tuberculosis complex (MTC) markers each have their own potentials that need to be identified for proper use in epidemiological and phylogenetic studies. The purpose of this thesis is to extract new knowledge of the results of genotyping data stored in databases, knowledge of the polymorphism of genomic carrier to estimate the contribution of each marker in the classification of TCM. The use of different methods of phylogenetic reconstruction and modeling data was essential. In light of the results obtained, the thesis proposes a new classification methodology for a robust recovery phylogeography of TCM in connection with the history of human migration have started in sub-Saharan Africa. Each genotyping method with cost efficiency and equity, should be measured in relation to the resources available and discounts results, it is interesting to strengthen the knowledge of markers and propose alternatives leading to the classification of mycobacteria. Thus, the results obtained in this thesis bring more coherence to the proposed characterization of clones MTC circulating worldwide solutions.

http://www.theses.fr/2012AGUY0518/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The continental South Armenian Block – part of the Anatolide–Tauride South Armenian microplate – of Gondwana origin rifted from the African margin after the Triassic and collided with the Eurasian margin after the Late Cretaceous. During the Late Cretaceous, two northward dipping subduction zones were simultaneously active in the northern Neo-Tethys between the South Armenian Block in the south and the Eurasian margin in the north: oceanic subduction took place below the continental Eurasian margin and intra-oceanic subduction resulted in ophiolite obduction onto the South Armenian Block in the Late Cretaceous.The paleolatitude position of the South Armenian Block before its collision with Eurasia within paleogeographic reconstructions is poorly determined and limited to one study. This earlier study places the South Armenian Block at the African margin in the Early Jurassic. To reconstruct the paleolatitude history of the South Armenian Block, we sampled Upper Devonian–Permian and Cretaceous sedimentary rocks in Armenia. The sampled Paleozoic rocks have likely been remagnetized. Results from two out of three sites sampled in Upper Cretaceous strata pass fold tests and probably all three carry a primary paleomagnetic signal. The sampled sedimentary rocks were potentially affected by inclination shallowing. Therefore, two sites that consist of a large number of samples (> 100) were corrected for inclination shallowing using the elongation/inclination method.These are the first paleomagnetic data that quantify the South Armenian Block's position in the Tethys ocean between post-Triassic rifting from the African margin and post-Cretaceous collision with Eurasia. A locality sampled in Lower Campanian Eurasian margin sedimentary rocks and corrected for inclination shallowing, confirms that the corresponding paleolatitude falls on the Eurasian paleolatitude curve. The north–south distance between the South Armenian Block and the Eurasian margin just after Coniacian–Santonian ophiolite obduction was at most 1000 km.
ISSN: 0040-1951

hal-01365871
https://hal.archives-ouvertes.fr/hal-01365871
DOI : 10.1016/j.tecto.2015.01.012

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Resolving the early diversification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera) are the sister group to all other animals (''Porifera-sister''3 hypothesis), consistent with a single origin of the gut, nerve cells, and muscle cells in the stem lineage of eumetazoans (bilaterians + ctenophores + cnidarians). In contrast, several other studies have recovered an alternative topology in which ctenophores are the sister group to all other animals (including sponges). The ``Ctenophora-sister'' hypothesis implies that eumetazoan-specific traits, such as neurons and muscle cells, either evolved once along the metazoan stem lineage and were then lost in sponges and placozoans or evolved at least twice independently in Ctenophora and in Cnidaria + Bilateria. Here, we report on our reconstruction of deep metazoan relationships using a 1,719-gene dataset with dense taxonomic sampling of non-bilaterian animals that was assembled using a semi-automated procedure, designed to reduce known error sources. Our dataset outperforms previous metazoan gene superalignments in terms of data quality and quantity. Analyses with a best-fitting site-heterogeneous evolutionary model provide strong statistical support for placing sponges as the sister-group to all other metazoans, with ctenophores emerging as the second-earliest branching animal lineage. Only those methodological settings that exacerbated long-branch attraction artifacts yielded Ctenophora-sister. These results show that methodological issues must be carefully addressed to tackle difficult phylogenetic questions and pave the road to a better understanding of how fundamental features of animal body plans have emerged.
ISSN: 0960-9822

hal-01681528
https://hal.archives-ouvertes.fr/hal-01681528
DOI : 10.1016/j.cub.2017.02.031

Éditeur(s) : HAL CCSD
Résumé : National audience
Crustal-scale models for the Pyrenees based on ECORS reflection profileshave around 20 years now. In recent years, new understandingswere gained on the reconstruction to the preorogenic times, namelya scenario of extreme crustal attenuation and mantle exhumation ; inturn, this has implications on the interpretation of the present-day structure,as new models for the chain must consider feedbacks between themid-Cretaceous hyperextension and the Pyrenean inversion. On the WcentralPyrenean traverse, the southern part comprises 3 S-vergent basementthrust units, the Lakora, Gavarnie and Guarga units, flanked by thedetached cover of the Jaca piggyback basin and the Ebro basin, wherethe Mesozoic is thin and Late Cretaceous-Tertiary synorogenic carbonateand detrital sequences record a southward depocenter migration.To the N, the Chaînons Béarnais belt (CB) is a system of Jurassic to LowerCretaceous carbonate anticline ridges separated by synclines withthick Albian-Cenomanian flysch, covered to the north by Upper Cretaceousflysch sequences. The CB is thrust southwards together with theLakora thrust unit and northwards onto the Aquitaine basin. CB foldinglargely results from the rising and squeezing of diapirs initiated duringthe Jurassic-Early Cretaceous extension. Pieces of crust and mantle liftedin the diapirs attest that the CB derive from a Cretaceous domainof hyperextended continental crust and exhumed mantle. Moho reflectionsin the ECORS-Arzaq profile constrain the present deep structure.Restoration leads to a Mesozoic cover detachment over the N-Iberianand S-European margins. Inversion began by subduction of the exhumedmantle and folding and pop-up thrusting of the CB cover onto themargins. From the mid-late Eocene onwards, continental collision wasaccommodated by wedging and thrust stacking in the Iberian crust, involvingthe piggyback formation of S-vergent basement thrusts in theupper crust, and the northward subduction of the lower crust.
24 ème Réunion des sciences de la Terre 2014
Pau, France

insu-01080831
https://hal-insu.archives-ouvertes.fr/insu-01080831

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : Relict dune fields that are found as far south as 14 N in the modern-day African Sahel are testament to equatorward expansions of the Sahara desert during the Late Pleistocene. However, the discontinuous nature of dune records means that abrupt millennial-timescale climate events are not always resolved. High-resolution marine core studies have identified Heinrich stadials as the dustiest periods of the last glacial in West Africa although the spatial evolution of dust export on millennial timescales has so far not been investigated. We use the major-element composition of four high-resolution marine sediment cores to reconstruct the spatial extent of Saharan-dust versus river-sediment input to the continental margin from West Africa over the last 60 ka. This allows us to map the position of the sediment composition corresponding to the Sahara Sahel boundary. Our records indicate that the Sahara Sahel boundary reached its most southerly position (13 N) during Heinrich stadials and hence suggest that these were the periods when the sand dunes formed at 14 N on the continent. Heinrich stadials are associated with cold North Atlantic sea surface temperatures which appear to have triggered abrupt increases of aridity and wind strength in the Sahel. Our study illustrates the influence of the Atlantic meridional overturning circulation on the position of the Sahara Sahel boundary and on global atmospheric dust loading.
Climate Of The Past (1814-9324) (Copernicus Gesellschaft Mbh), 2013 , Vol. 9 , N. 3 , P. 1181-1191

Droits : Author(s) 2013. CC Attribution 3.0 License. Access Climate of
http://archimer.ifremer.fr/doc/00181/29240/27635.pdf
DOI:10.5194/cp-9-1181-2013
http://archimer.ifremer.fr/doc/00181/29240/

Éditeur(s) : HAL CCSD PeerJ
Résumé : International audience
Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction. How to cite this article Leray et al. (2015), Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 3:e1047
ISSN: 2167-8359

Droits : http://creativecommons.org/licenses/by/
hal-01174184
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184/file/peerj-1047.pdf
DOI : 10.7717/peerj.1047

Éditeur(s) : HAL CCSD Elsevier
Résumé : A synthesis of backscatter imagery coupled with a large 3D seismic dataset in the Lower Congo Basin (LCB) reveals a patchy distribution of features interpreted to be associated with fluid seepage from 300 m to 2500 m water depth. With the exception of one region of anomalous backscatter positive-relief mounds, all inferred seep sites occur in negative-relief pockmarks. The extensive 3D seismic dataset in the LCB offers a unique opportunity to study the plumbing system that is feeding surface cold seep systems, and in general, to reconstruct the relationship between tectonics and fluid flow in continental margins. The fluid seeps in the LCB are associated with morphologically, stratigraphically or tectonically controlled focused fluid flow. The integration of the geophysical datasets, backscatter imagery coupled to 3D seismic, clearly indicates that fluid seeps are not randomly distributed, but their seabed organization reflects 1) the location of the underlying structure (reservoir or trap) where the fluids are coming from, 2) the geometry and morphology of the reservoir/trap, and 3) the discontinuities in the sedimentary column along which fluids have migrated. In the LCB seafloor pockmarks are always associated with underlying tectonic structures (fault zones, salt diapirs, polygonal faults) or buried sedimentary bodies (turbiditic channels, erosional surfaces), whereas they never occur above sub-horizontal parallel-stratified fine-grained sediments. Even if triggering processes can not be clearly defined here, we propose a model of seafloor fluid seep organization, which represents a new tool for identifying the geometry of flow pathways and the underlying buried bodies where the fluids are originating from. This qualitative 3D model provides insight into the geohydrologic processes of continental margins.
ISSN: 0025-3227

hal-00406640
https://hal.archives-ouvertes.fr/hal-00406640
DOI : 10.1016/j.margeo.2007.06.003

Éditeur(s) : The Geological Society of London
Résumé : Conservational models, like simple shear, pure shear or polyphase models that exclude exchanges between the lower continental crust and upper mantle, are usually proposed to explain the lithospheric stretching and consequent crustal thinning of passive continental margins. These models need large amounts of horizontal movement, and have, therefore, important implications for plate kinematic reconstructions and intraplate deformation. In this paper we propose to show these implications in the Central Segment of the South Atlantic Ocean. In the Angola–Brazilian system, these models imply about 240 km of horizontal movement. This movement can be compensated by two end-member mechanisms: (1) an intraplate deformation located in Africa; and (2) an intraplate deformation located in South America. We detail for each solution the strong geological and geodynamical implications, and discuss the consequences for the genesis of passive continental margins.
Geological Society, special publication (0375-6440) (The Geological Society of London), 2012-02 , Vol. 369 , P. 75-90

Droits : The Geological Society of London 2012
http://archimer.ifremer.fr/doc/00087/19839/17757.pdf
DOI:10.1144/SP369.5
http://archimer.ifremer.fr/doc/00087/19839/

Éditeur(s) : Université Paris 7 – Denis Diderot
Résumé : Sea surface salinity (SSS) influences numerous oceanic phenomena, for instance surface water ventilation, deep water formation and thermohaline circulation. SSS also controls some ocean-atmosphere coupled processes, such as the intensity of freshwater flux and the penetration of heat flux and turbulence. Salinity is more difficult to measure than temperature from in situ surveys, which results in 20 times less data being currently available. Moreover, sea surface temperature (SST) is routinely estimated from satellites, which is not possible yet for SSS. Two space missions will fill this gap soon: SMOS from the European Space Agency and Aquarius/SAC-D from NASA and CONAE. To contribute to the SMOS project, we propose a method for estimating SSS from current satellite observations and for studying the mechanisms governing its variability. We developed a simplified model of the ocean mixed layer, based on the "slab mixed layer" formulation (Frankignoul et Hasselmann, 1977). This 2D horizontal model is implemented over the global ocean, using a near 100 km resolution, and integrated during a climatological year. Air-sea fluxes are taken from the ECMWF meteorological model (ERA40 reanalysis) and the surface currents are provided by altimeter data (SSALTO-DUACS analysis). The mixed layer depth (MLD) is derived from SST observations, using an original inversion technique. The MLD fields obtained from this inversion are well correlated to in situ estimates. This effective depth represents the air-sea fluxes penetration and ensures consistency between fluxes, les currents and SST. We first validate the simulation through examination of the heat balance in north-eastern Atlantic, by comparing to measurements and models from the POMME experiment. Then we study the salinity balance in the global domain, in terms of its geographical distribution and seasonal evolution. Equilibrium between the various processes appears generally more complex than for temperature. Noteworthy, the role of atmospheric flux is less predominant (22%), while geostrophic advection (33%) and diapycnal mixing (22%) contribute more strongly. Our results indicate this model succeeds in reconstructing SSS variability over most of the oceans. Daily SSS variations are also simulated, whereas they are not represented in current observed data at a global scale. Owing to its simplicity and fast computation, the model will be useful to the SMOS mission. It can help for the measurement calibration/validation and provide a first guess estimate to the sophisticated algorithm required for SSS restitution.
La salinité de surface des océans (SSS) influence de nombreux phénomènes océaniques, parmi lesquels la ventilation des eaux de surface, la formation d'eaux profondes et la circulation thermohaline. Elle détermine aussi certains processus couplés océan-atmosphère, notamment l'intensité du flux d'eau douce, la pénétration du flux de chaleur et de la turbulence. La mesure in situ de salinité est plus compliquée que celle de température, si bien qu'on dispose actuellement de 20 fois moins de données pour cette propriété. De plus, la température de surface (SST) est couramment estimée par satellite, ce qui n'est pas encore le cas de la SSS. Deux missions spatiales vont prochainement combler cette lacune : le satellite SMOS de l'Agence Spatiale Européenne et le satellite Aquarius/SAC-D de la NASA et de la CONAE. En préparation du projet SMOS, nous proposons une méthode pour estimer la SSS à partir des observations satellitaires actuelles et étudier les mécanismes de sa variabilité. Nous avons développé un modèle simplifié de couche mélangée océanique, basé sur la formulation "slab mixed layer" (Frankignoul et Hasselmann, 1977). Ce modèle 2D horizontal est implémenté sur l'océan global, avec une résolution proche de 100 km, et intégré au cours d'une année climatologique. Les flux air-mer proviennent du modèle météorologique ECMWF (réanalyse ERA40) et les courants de surface sont issus de l'altimétrie (analyse SSALTO-DUACS). La profondeur de la couche mélangée (MLD) est dérivée des observations de SST, grâce à une technique d'inversion originale. La MLD obtenue par inversion est bien corrélée aux estimations basées sur des données in situ. Cette profondeur effective représente la pénétration des flux air-mer et assure la cohérence entre les flux, les courants et la SST. La simulation est d'abord validée en examinant le bilan de chaleur dans l'Atlantique Nord-Est, par comparaison aux mesures et aux modèles de l'expérience POMME. Puis le bilan de salinité est étudié dans le domaine global, en termes de distribution géographique et d'évolution saisonnière. L'équilibre entre les différents processus est généralement plus complexe que pour la température. Notamment, le rôle du flux atmosphérique est moins prépondérant (22%), tandis que l'advection géostrophique (33%) et le mélange diapycnal (22%) contribuent fortement. Nos résultats montrent que ce modèle parvient à restituer la variabilité de la SSS sur la majeure partie des océans. Le modèle simule aussi les variations journalières de SSS, qui ne sont pas représentées à l'échelle globale dans les observations actuelles. Grâce à sa simplicité et à sa rapidité, le modèle pourra être utile dans le cadre de SMOS. Il pourra aider à la calibration/validation de la mesure et fournir une estimation a priori pour l'algorithme complexe nécessaire à la restitution de la SSS.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/these-2302.pdf
http://archimer.ifremer.fr/doc/00000/2302/

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) : Institut national agronomique Paris Grignon
Résumé : The flat oyster Ostrea edulis L. is the indigenous oyster of the Atlantic as well as the Mediterranean coasts of Europe. Its commercial exploitation dates back to Antiquity but its breeding is now threatened by two parasitic protozoa, among which Bonamia ostreae. Various aspects of the genetics of this species' natural and farmed populations have been studied with the aid of microsatellite markers. At first, the implementation and the screening of two partial genomic libraries made it possible to identify 28 new microsatellite loci. Analysis of the segregation of 12 of these loci and of two enzymatic loci shows that most microsatellite loci are transmitted in a Mendelian way, but some loci have significant segregation distortions. Moreover, seven linkage groups, of which four contain at least two markers, were identified in Ostrea edulis. The genetic variability of three populations selected for one or two generations for resistance to Bonamia ostreae was analysed with the aid of 5 microsatellite loci. In spite of the absence of genealogical data, we have shown that these selected populations were descended from a very low number of founding genitors (from 3 to 15 depending on the population) and for two populations, we were able to reconstruct the genealogy and the relationships between the individuals were identified. These selected populations have, in addition to a very low genetic variability, real and at times high levels of consanguinity. These results have a significant implication for the continuation of the selection programme (consanguinity management, augmentation of genetic variability by introducing wild genitors). The geographical structuring of the genetic variability of natural populations of Ostrea edulis has been analysed with the aid of 5 microsatellite loci on a sampling covering almost the entire distribution area of the species (from Norway to the Adriatic Sea). The results are consistent with those published in the literature and using enzymatic markers. The populations show a low level of differentiation that could correspond to a model of isolation by distance. The Atlantic populations, which have a reduced polymorphism, could be descended from post-glacial recolonisation from Mediterranean populations that had survived the glaciations of the Quaternary Period. The current distribution of flat oyster populations is surely also subject to anthropogenic activities. Finally, the genetic bases of the heterozygosis-growth correlation were studied in a natural population with the aid of enzymatic and microsatellite markers. Although leads favouring the direct contribution of enzymatic loci have been found, biases in the sampling design make it impossible to come to a formal conclusion. However, this study has made it possible to show that the capture of individuals over a short period (around ten days) leads to a sampling of a population descended from a very low number of founding genitors, in contradiction with the generally accepted idea that marine bivalve populations are large panmictic populations with significant, efficient numbers. These results confirm in a natural population the observations of a significant reduction of efficient sizes in hatchery populations.
L'huître plate Ostrea edulis L. est l'huître indigène des côtes européennes aussi bien atlantiques que méditerranéennes. Son exploitation commerciale remonte à l'Antiquité mais son élevage est aujourd'hui menacé par deux protozoaires parasites dont Bonamia ostreae. Différents aspects de la génétique des populations naturelles et cultivées de cette espèce ont été étudiés à l'aide de marqueurs microsatellites. Dans un premier temps, la réalisation et le criblage de deux banques génomiques partielles ont permis l'identification de 28 nouveaux locus microsatellites. L'analyse de la ségrégation de 12 de ces locus et de deux locus enzymatiques montre que la plupart des locus microsatellites sont transmis de façon mendélienne, mais certains locus présentent des distorsions de ségrégation importantes. Par ailleurs, sept groupes de liaison dont quatre contiennent au moins deux marqueurs ont été identifiés chez Ostrea edulis. La variabilité génétique de trois populations sélectionnées depuis une ou deux générations pour une résistance à Bonamia ostreae a été analysée à l'aide de 5 locus microsatellites. Malgré l'absence de données généalogiques, nous avons montré que ces populations sélectionnées étaient issues d'un très faible nombre de géniteurs fondateurs (de 3 à 15 selon les populations) et pour deux populations, la généalogie a pu être reconstituée et les liens de parenté entre les individus ont été identifiés. Ces populations sélectionnées présentent, outre une très faible variabilité génétique, des niveaux de consanguinité réels et parfois élevés. Ces résultats ont une implication importante pour la continuation du programme de sélection (gestion de la consanguinité, augmentation de la variabilité génétique par introduction de géniteurs sauvages). La structuration géographique de la variabilité génétique des populations naturelles d'Ostrea edulis a été analysée à l'aide de 5 locus microsatellites sur un échantillonnage couvrant presque toute l'aire de répartition de l'espèce (de la Norvège à la Mer Adriatique). Les résultats sont cohérents avec ceux publiés dans la littérature et utilisant des marqueurs enzymatiques. Les populations montrent un niveau de différenciation faible qui pourrait correspondre à un modèle d'isolement par la distance. Les populations atlantiques, qui présentent un polymorphisme réduit, pourraient être issues de recolonisation post-glaciaire à partir de populations méditerranéennes ayant survécu aux glaciations du Quaternaire. La répartition actuelle des populations d'huître plate est certainement aussi soumise aux actions anthropiques. Enfin, les bases génétiques de la corrélation hétérozygotie-croissance ont été étudiées dans une population naturelle à l'aide de marqueurs enzymatiques et microsatellites. Bien que des pistes en faveur de la contribution directe des locus enzymatiques aient été trouvées, des biais dans le dispositif expérimental ne permettent pas de conclure de façon formelle. Cependant, cette étude a permis de montrer que le captage d'individus sur une faible période (une dizaine de jours) conduit à l'échantillonnage d'une population issue d'un nombre très réduit de géniteurs fondateurs, en contradiction avec l'idée reçue que les populations de bivalves marins sont de larges populations panmictiques à effectif efficace important. Ces résultats confirment dans une population naturelle les observations de réduction importante des tailles efficaces dans des populations d'écloserie.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1998/these-1919.pdf
http://archimer.ifremer.fr/doc/00000/1919/

Éditeur(s) : HAL CCSD Blackwell Publishing
Résumé : International audience
The study of eight stratigraphic sections at the margin of the semi-enclosed Zsambek Basin (Hungary) allows the sedimentary anatomy of oolitic-bioclastic systems in the Sarmatian of the Central Paratethys to be reconstructed. The mollusc, foraminiferal and ostracod associations indicate that the carbonate systems are Latest Badenian to Late Sarmatian in age. The Lower-Upper Sarmatian deposits are organized in superimposed subaqueous dunes prograding towards the basin on a low-angle ramp. During the Late Sarmatian, the ramp underwent subaerial erosion linked to a moderate relative fall in sea-level. Lagoonal deposits were later formed and microbial-nubeculariid-bryozoan-serpulid buildups were emplaced. The 'abnormal' marine conditions of the Sarmatian, conducive to the development of a poorly diversified flora and fauna and dominant non-skeletal grains, are linked to fluctuating salinities, mesotrophic to eutrophic conditions and perhaps high alkalinity.
ISSN: 1469-3496

hal-00429337
https://hal.archives-ouvertes.fr/hal-00429337
DOI : 10.1111/j.1365-3091.2009.01055.x

Éditeur(s) : IEEE
Résumé : Soil Moisture and Ocean Salinity, European Space Agency, is the first satellite mission addressing the challenge of measuring sea surface salinity from space. It uses an L-band microwave interferometric radiometer with aperture synthesis (MIRAS) that generates brightness temperature images, from which both geophysical variables are computed. The retrieval of salinity requires very demanding performances of the instrument in terms of calibration and stability. This paper highlights the importance of ocean salinity for the Earth's water cycle and climate; provides a detailed description of the MIRAS instrument, its principles of operation, calibration, and image-reconstruction techniques; and presents the algorithmic approach implemented for the retrieval of salinity from MIRAS observations, as well as the expected accuracy of the obtained results.
Proceedings of the IEEE (0018-9219) (IEEE), 2010-05 , Vol. 98 , N. 5 , P. 649-665

Droits : 2010 IEEE – All Rights Reserved
http://archimer.ifremer.fr/doc/00004/11482/8066.pdf
DOI:10.1109/JPROC.2009.2033096
http://archimer.ifremer.fr/doc/00004/11482/

Éditeur(s) : Université de Pau et des Pays de l'Adour
Résumé : In a context of decline of European eel (Anguilla anguilla L.) and search for biological markers of habitat use and quality, a multidisciplinary approach was engaged on the Adour estuary and its associated wetlands. Two axes were developed. The first axe aimed at highlighting the successive presence of the species in different ecosystems based on the otolith elemental composition. The second aimed at the evaluation of the chemical pressure underwent by eels based on the contaminant bioconcentration in soft tissues and the early molecular response to the chemical stress. With a view to the analyses of otolith elemental composition taking into account the 3D structure, the low elemental concentration in the matrix and keeping the finest spatial resolution, four micro sampling strategies and multi elemental analyses using femtosecond laser ablation ICP-MS were tested (crater, 1D scan, 2D scan, flash ablation). The strategy showing the best compromise according to the objectives (continuous recording, multi elemental approach) was applied on otolith of yellow eels from the Adour. The simultaneous use of Sr and Ba profiles, after validation, represents a new tool, easy, fast and reliable for the reconstruction of freshwater and brackish ecosystems use by eel avoiding misinterpretation due to vaterite inclusions. Three major behaviors were highlighted on the Adour: a residency in brackish water, a residency in freshwater and nomad behavior. The last one is illustrated by a shift to brackish water after three to four years spent in freshwater. Simultaneously, the study of inorganic and organic contamination of eel soft tissues showed that sampled wetlands are moderately contaminated. These results were confirmed by the first estimation, in wild conditions, of the early response to the chemical stress using the hepatic expression of CYP1A1 gene measured by real time RT-PCR. Conversely, in the downstream part of the Adour estuary, Hg loads in eels, especially methyl mercury, and PCBs analyses indicate values that need further investigations considering the European norms of consumption. The comparison of the different markers used (heavy metal and organochlorinated compounds contamination of soft tissues, condition index) support a lower quality of the estuary despite higher eel growth rate on this site. This study supports the use of numerous markers in integrated studies in order to understand and specify the relationships between eels and their continental growth zones.
Dans un contexte de déclin de l'anguille européenne (Anguilla anguilla L.) et de recherche de marqueurs biologiques retraçant la fréquentation des divers habitats et renseignant sur la qualité de ceux-ci, une approche pluridisciplinaire a été mise en place sur l'estuaire de l'Adour et ses zones humides. Deux axes ont été privilégiés. Le premier cherchait à visualiser la présence successive de l'espèce dans différents écosystèmes en se basant sur la composition élémentaire des otolithes. Le deuxième avait pour but d'évaluer la pression chimique inorganique et organique subie par l'anguille dans les zones d'études en s'appuyant sur la bioconcentration des contaminants dans les tissus mous et la réponse moléculaire précoce au stress chimique. En vue des analyses de la composition élémentaire des otolithes et pour répondre au mieux à la structure en trois dimensions, à la faible concentration des éléments dans la matrice tout en conservant une résolution spatiale la plus fine possible, quatre stratégies de micro-échantillonnage et d'analyses multiélémentaires par ablation laser femtoseconde ICP-MS ont été testées (cratère, scan 1D, scan 2D, ablation flash). La méthodologie présentant le meilleur compromis par rapport aux objectifs fixés (enregistrement continu, approche multiélémentaire) a ensuite été appliquée sur les otolithes d'anguilles jaunes du Bas-Adour. L'utilisation simultanée des profils continus de Sr et de Ba, après validation, constitue un outil facile d'utilisation, rapide et fiable pour reconstruire les historiques de fréquentation des différents écosystèmes estuariens et dulçaquicoles par l'anguille tout en s'affranchissant des problèmes potentiels liés aux inclusions de vatérite, un polymorphe du carbonate de calcium. Trois grands types de comportement ont pu être mis en évidence sur l'Adour : résidence en eau saumâtre, résidence en eau douce et nomadisme. Ce dernier est plus particulièrement illustré par un mouvement marqué vers l'eau saumâtre pour des individus ayant passé de trois à quatre ans dans l'eau douce. Parallèlement, l'étude de la contamination organique et inorganique des tissus mous de l'anguille a permis de déduire à la faible contamination des zones humides échantillonnées. La première estimation en condition naturelle de la réponse précoce au stress chimique par évaluation de l'expression hépatique du gène CYP1A1 par RT-PCR en temps réel confirme ces résultats. En revanche, dans la partie estuarienne aval de l'Adour, les niveaux en Hg, présent en majorité sous sa forme méthylée dans les anguilles, et l'analyse des PCBs indiquent des valeurs qui suscitent un examen plus approfondi au regard des normes européennes en vigueur. La confrontation des différents descripteurs (contamination des tissus mous par les métaux lourds et organochlorés, indice de condition) utilisés conforte la qualité moindre de la zone estuarienne malgré des performances de croissance de l'anguille favorisées sur ces sites. Ainsi, cette étude supporte l'intérêt de la mise en oeuvre de descripteurs multiples utilisés (niveaux de métaux lourds et organochlorés dans les tissus mous, réponse moléculaire au stress chimique, microchimie de l'otolithe, indice de condition, taux de croissance) dans des approches intégrées pour comprendre et préciser les relations existantes entre l'anguille et ses zones de croissance continentales.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2009/these-7381.pdf
http://archimer.ifremer.fr/doc/00000/7381/

Éditeur(s) : Actes de colloques. Ifremer. Brest [ACTES COLLOQ. IFREMER.]. 1991
Résumé : On the bathyal slope for continental margins, steep and rocky substrates punctuated with cliffs and collapsing zones are frequently found. As survey and sampling with the classical technics from the sea surface is practically impossible in such an environment, in situ exploration with a submersible allows significant advances in ecology, with implications in paleoenvironment reconstruction. Mixing of material from shallow-water and deep-sea origins into bathyal sedimentation suggests that the so-called "fossil assemblages of outer platform" were frequently misinterpreted. Dense populations of animals closely related to fossil groups which were only considered as relict of the Past ("living fossils") and previously interpreted as shallow-water inhabitants during geological times can be discovered living in such bathyal communities. The role of bathyal ecological niches during global bioevents brings a new vision of the history of life in the Ocean through geological time and has to be further investigated. Examples from cruises monitoring the diving saucer Cyana (SP 3000) in the Bay of Biscay and off New Caledonia are given.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1990/acte-1138.pdf
http://archimer.ifremer.fr/doc/00000/1138/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The anisotropy of vibrational properties influences the acoustic behaviour of wooden pieces and their dependence on grain angle (GA). As most pieces of wood include some GA, either for technological reasons or due to grain deviations inside trunks, predicting its repercussions would be useful. This paper aims at evaluating the variability in the anisotropy of wood vibrational properties and analysing resulting trends as a function of orientation. GA dependence is described by a model based on transformation formulas applied to complex compliances, and literature data on anisotropic vibrational properties are reviewed. Ranges of variability, as well as representative sets of viscoelastic anisotropic parameters, are defined for mean hardwoods and softwoods and for contrasted wood types. GA-dependence calculations are in close agreement with published experimental results and allow comparing the sensitivity of different woods to GA. Calculated trends in damping coefficient (tanδ) and in specific modulus of elasticity (E′/ρ) allow reconstructing the general tanδ-E′/ρ statistical relationships previously reported. Trends for woods with different mechanical parameters merge into a single curve if anisotropic ratios (both elastic and of damping) are correlated between them, and with axial properties, as is indicated by the collected data. On the other hand, varying damping coefficient independently results in parallel curves, which coincide with observations on chemically modified woods, either "artificially", or by natural extractives.
ISSN: 0043-7719

hal-00804242
https://hal.archives-ouvertes.fr/hal-00804242
https://hal.archives-ouvertes.fr/hal-00804242/document
https://hal.archives-ouvertes.fr/hal-00804242/file/Anisotropy_wood_variational_properties_Bremaud_al_2011.pdf
DOI : 10.1007/s00226-010-0393-8

Éditeur(s) : HAL CCSD Geological Society
Résumé : International audience
A polyphase history of oceanic construction and consumption is documented by the distribution of the Tethyan ophiolitic suture zones in Iran. Despite the geodynamic significance of these suture zones, few modern petrological and geochronological data are available from these ophiolitic domains, hampering a full assessment of the timing, thermobaric regimes and palaeotectonic scenarios leading to oceanic suturing and continental assembly in Iran and, more in general, along the southern margin of Eurasia. In this paper, we describe a newly discovered HP ophiolite mélange within the Rasht ophiolites, at the NW termination of the Palaeo-Tethyan suture in Iran. Petrological investigations on the metamorphic units embedded within the ophiolite mélange are integrated with whole-rock geochemistry and Ar–Ar phengite geochronology to constrain the geotectonic setting of formation and to define the associated P–T–t paths. We provide evidence that the Rasht ophiolite domain corresponds to an exhumed subduction complex formed during Early Carboniferous (c. 350 Ma) subduction of a branch of the Palaeo-Tethyan oceanic realm, with peak metamorphism equilibrated under blueschist- to eclogite-facies metamorphic conditions. Implications of these data for the palaeotectonic reconstruction during closure of the Palaeo-Tethyan ocean and the terminal collisional assembly along the southern margin of the Eurasia plate are also discussed.
ISSN: 0016-7649

hal-01571998
https://hal.archives-ouvertes.fr/hal-01571998
DOI : 10.1144/jgs2016-130

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Ce texte pose les bases d’une réflexion sur les fondements de l’industrie de la croisière et sur l’importance et la portée de ce secteur d’activité. Il s’interroge notamment sur les relations entre les compagnies de croisières et le port récepteur des croisiéristes lors des excursions. Le produit croisière construit à partir des années 1970 a donné naissance à un tourisme de masse spécifique ; le bateau est à la fois le moyen de transport et la destination. Les escales n’ont qu’un rôle secondaire dans cette logique qui privilégie le gigantisme, la standardisation et l’uniformisation. Alors que le gigantisme touche certaines limites, l’offre croisière se recompose spatialement et innove sur les segments du haut de gamme et du luxe.
This paper proposes a reflection on the cruise industry, the importance and scope of this industry. One of the objectives is to examine in particular the relationship between cruise lines and ports that receive cruises and excursionists. The cruise product built from the 1970s engendred a specific mass tourism. And the boat is both the means of transport and the destination. The stops have a secondary role in this logic that favors gigantism, standardization and uniformity. While gigantism known some limits, cruise products reconstructs itself spatially and innovative segments of the high-end and luxury.

Droits : info:eu-repo/semantics/openAccess
http://journals.openedition.org/etudescaribeennes/5623