Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The Southwest Indian Ocean (SWIO) is a striking marine biodiversity hotspot. Coral reefs in this region host a high proportion of endemics compared to total species richness and they are particularly threatened by human activities. The island archipelagos with their diverse marine habitats constitute a natural laboratory for studying diversification processes. Rocky shores in the SWIO region have remained understudied. This habitat presents a high diversity of molluscs, in particular gastropods. To explore the role of climatic and geological factors in lineage diversification within the genus Nerita, we constructed a new phylogeny with an associated chronogram from two mitochondrial genes [cytochrome oxidase sub-unit 1 and 16S rRNA], combining previously published and new data from eight species sampled throughout the region. All species from the SWIO originated less than 20 Ma ago, their closest extant relatives living in the Indo-Australian Archipelago (IAA). Furthermore, the SWIO clades within species with Indo-Pacific distribution ranges are quite recent, less than 5 Ma. These results suggest that the regional diversification of Nerita is closely linked to tectonic events in the SWIO region. The Reunion mantle plume head reached Earth's surface 67 Ma and has been stable and active since then, generating island archipelagos, some of which are partly below sea level today. Since the Miocene, sea-level fluctuations have intermittently created new rocky shore habitats. These represent ephemeral stepping-stones, which have likely facilitated repeated colonization by intertidal gastropods, like Nerita populations from the IAA, leading to allopatric speciation. This highlights the importance of taking into account past climatic and geological factors when studying diversification of highly dispersive tropical marine species. It also underlines the unique history of the marine biodiversity of the SWIO region.
ISSN: 1932-6203

hal-01185713
https://hal.archives-ouvertes.fr/hal-01185713
https://hal.archives-ouvertes.fr/hal-01185713/document
https://hal.archives-ouvertes.fr/hal-01185713/file/PLoS%20ONE%202014%20Postaire.pdf
DOI : 10.1371/journal.pone.0095040

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : La Balagne est un territoire rural touristique dont les restes du riche passé agropastoral sont réappropriés et réhabilités comme support de développement local. Les exploitants agricoles, en tant qu’artisans du terroir, sont au cœur de ce processus de patrimonialisation et peuvent espérer tirer profit de sa revalorisation culturelle et économique : alors qu’ils subissent la pression foncière, la demande touristique de terroir apparait comme étant une opportunité de maintien pour l’agriculture de Balagne. Or, l’enquête de terrain réalisée montre qu’elle s’avère être en réalité un puissant facteur de différenciation des exploitants entre eux et de creusement des inégalités socio-économiques. Et paradoxalement l’offre de produits du terroir et services agritouristiques n’est pas forcément accompagnée de la mise en œuvre de bonnes pratiques agricoles. Ces conclusions interrogent finalement la durabilité agricole, et plus largement celle du territoire.
Balagne is a rural touristic territory. It remains of the glorious agrarian past are restored as a resource for local development. Farmers, as artisans of the country, are at the core of this process of re-appropriation and can be pay back for this cultural and economic revalorization: whereas they are suffering the land pressure, this issue can be a way of remaining their activity. But, it is proved that it is a major factor of the farming systems differentiation. Thus, it grows bigger the socio-economic inequalities. And as a paradox, the supply of local products and/or agritourism services do not systematically implies the implementation of eco-friendly practices. Finally, the touristic valorization of the rural heritage calls into question the rural system sustainability.
Balagne
Corse

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.5407
http://journals.openedition.org/etudescaribeennes/5407

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
We studied the diversity within the former genus Gymnangium in the South West IndianOcean by using an integrative approach of both traditional (morphology-based) and modernmolecular taxonomy. Nine species were recorded in the material collected. A total of 97 16Smitochondrial DNA sequences and 54 Calmodulin nuclear sequences from eight Gymnangium/Taxella species were analyzed. We found both morphological and molecular differencesin the studied Gymnangium species that make it necessary to split the genus. It isproposed to revalidate the genus Taxella which is currently regarded as a synonym ofGymnangium. Two species of the genus Taxella (T. eximia and T. gracilicaulis), until nowregarded as distinct species based on morphological characteristics, cluster together in onephylogenetic clade. Possible explanations are discussed. Two species from Madagascarnew to science are herein described and rare species from the Indian Ocean islands are redescribed.
ISSN: 1932-6203

hal-01564043
https://hal-univ-perp.archives-ouvertes.fr/hal-01564043
DOI : 10.1371/journal.pone.0174244

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
The Pyrenean peridotites (lherzolites) form numerous small bodies of subcontinental mantle, a few meters to 3 km across, exposed within the narrow north Pyrenean zone (NPZ) of Mesozoic sediments paralleling the north Pyrenean Fault. Recent studies have shown that mantle exhumation occurred along the future NPZ during the formation of the Albian-Cenomanian Pyrenean basins in relation with detachment tectonics. This paper reviews the geological setting of the Pyrenean lherzolite bodies and reports new detailed field data from key outcrops in the Bearn region. Only two types of geological settings have to be distinguished among the Pyrenean ultramafic bodies. In the first type (sedimented type or S type), the lherzolites occur as clasts of various sizes, ranging from millimetric grains to hectometric olistoliths, within monogenic or polymictic debris flow deposits of Cretaceous age, reworking Mesozoic sediments in dominant proportions as observed around the Lherz body. In the second type (tectonic type or T type), the mantle rocks form hectometric to kilometric slices associated with crustal tectonic lenses. Both crustal and mantle tectonic lenses are in turn systematically associated with large volumes of strongly deformed Triassic rocks and have fault contacts with units of deformed Jurassic and Lower Cretaceous sediments belonging to the cover of the NPZ. These deformed Mesozoic formations are not older that the Aptian-early Albian. They are unconformably overlain by the Albian-Cenomanian flysch formations and have experienced high temperature-low pressure mid-Cretaceous metamorphism at variable grades. Such a tectonic setting characterizes most of the lherzolite bodies exposed in the western Pyrenees. These geological data first provide evidence of detachment tectonics leading to manle exhumation and second emphasize the role of gravity sliding of the Mesozoic cover in the preorogenic evolution of the Pyrenean realm. In the light of such evidence, a simple model of basin development can be inferred, involving extreme thinning of the crust, and mantle uprising along a major detachment fault. We demonstrate coeval development of a crust-mantle detachment fault and generalized gravitational sliding of the Mesozoic cover along low-angle faults involving Triassic salt deposits as a tectonic sole. This model accounts for the basic characteristics of the precollisional rift evolution in the Pyrenean realm.
ISSN: 0278-7407

hal-00512818
https://hal.archives-ouvertes.fr/hal-00512818
DOI : 10.1029/2009TC002588

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
The etiology of congenital heart defect (CHD) combines environmental and genetic factors. So far, there were studies reporting on the screening of a single gene on unselected CHD or on familial cases selected for specific CHD types. Our goal was to systematically screen a proband of familial cases of CHD on a set of genetic tests to evaluate the prevalence of disease-causing variant identification. A systematic screening of GATA4, NKX2-5, ZIC3 and Multiplex ligation-dependent probe amplification (MLPA) P311 Kit was setup on the proband of 154 families with at least two cases of non-syndromic CHD. Additionally, ELN screening was performed on families with supravalvular arterial stenosis. Twenty-two variants were found, but segregation analysis confirmed unambiguously the causality of 16 variants: GATA4 (1 x), NKX2-5 (6 x), ZIC3 (3 x), MLPA (2 x) and ELN (4 x). Therefore, this approach was able to identify the causal variant in 10.4% of familial CHD cases. This study demonstrated the existence of a de novo variant even in familial CHD cases and the impact of CHD variants on adult cardiac condition even in the absence of CHD. This study showed that the systematic screening of genetic factors is useful in familial CHD cases with up to 10.4% elucidated cases. When successful, it drastically improved genetic counseling by discovering unaffected variant carriers who are at risk of transmitting their variant and are also exposed to develop cardiac complications during adulthood thus prompting long-term cardiac follow-up. This study provides an important baseline at dawning of the next-generation sequencing era.
ISSN: 1018-4813

hal-01404211
https://hal-univ-bourgogne.archives-ouvertes.fr/hal-01404211
DOI : 10.1038/ejhg.2015.105
PUBMED : 26014430

Éditeur(s) : HAL CCSD
Résumé : International audience
Tension wood, a tissue developed by angiosperm trees to actively recover their verticality, has long been defined by the presence of an unlignified cellulosic inner layer in the cell wall of fibres, called the G-layer. Although it was known that some species have no G-layer, the definition was appropriate since it enabled easy detection of tension wood zones using various staining techniques for either cellulose or lignin. For several years now, irrespective of its anatomical structure, tension wood has been defined by its high mechanical internal tensile stress. This definition enables screening of the diversity of cell walls in tension wood fibres. Recent results obtained in tropical species with tension wood with a delay in the lignification of the G-layer opened our eyes to the effective presence of large amounts of lignin in the G-layer of some species. This led us to review older literature mentioning the presence of lignin deposits in the G-layer and give them credit. Advances in the knowledge of tension wood fibres allow us to reconsider some previous classifications of the diversity in the organisation of the fibre walls of the tension wood.
ISSN: 0928-1541

hal-01636686
https://hal.archives-ouvertes.fr/hal-01636686
https://hal.archives-ouvertes.fr/hal-01636686/document
https://hal.archives-ouvertes.fr/hal-01636686/file/2017_Ghislain-Clair_IAWAJ_DiversityOrganisationLignificationTensionWoodFibreWalls-AReview.pdf
DOI : 10.1163/22941932-20170170

Éditeur(s) : HAL CCSD American Physical Society
Résumé : 1 tex, 16 figures
International audience
We make use of a subtraction procedure, introduced to overcome double--counting problems in beyond--mean--field theories, in the second random--phase--approximation (SRPA) for the first time. This procedure guarantees the stability of SRPA (so that all excitation energies are real). We show that the method fits perfectly into nuclear density--functional theory. We illustrate applications to the monopole and quadrupole response and to low--lying $0^+$ and $2^+$ states in the nucleus $^{16}$O. We show that the subtraction procedure leads to: (i) results that are weakly cutoff dependent; (ii) a considerable reduction of the SRPA downwards shift with respect to the random--phase approximation (RPA) spectra (systematically found in all previous applications). This implementation of the SRPA model will allow a reliable analysis of the effects of 2 particle--2 hole configurations ($2p2h$) on the excitation spectra of medium--mass and heavy nuclei.
ISSN: 0556-2813

in2p3-01193119
http://hal.in2p3.fr/in2p3-01193119
DOI : 10.1103/PhysRevC.92.034303
ARXIV : 1506.05975

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Splitting of teleseismic shear waves has been measured in the Appalachians (eastern USA) and the Pyrenees (western Europe) using data recorded by permanent and portable stations. From a comparison of the results, it appears that an interpretation of the recorded seismic anisotropy in terms of geodynamics is not straightforward. Successive geodynamic events have generated structures that may have resulted in a similar pattern of mantle flow and that therefore may have contributed in the development of the recorded anisotropy. Combining geological and geophysical arguments, it appears that the mantle anisotropy measured across the Appalachians and the Pyrenees may not be systematically Appalachian or Pyrenean in age but may be mainly due to a lithospheric structure formed during earlier major tectonic events, i.e. the Grenvillian and the Hercynian orogenies, respectively. We suggest that during major episodes of continent assembly, a pervasive tectonic fabric is developed in the lithospheric mantle. In the subsequent evolution of the continent, this fabric may induce a significant mechanical anisotropy that will drastically influence the mechanical behaviour of the Iithosphere when submitted to new tectonic events.
ISSN: 0031-9201

hal-01389717
http://hal.univ-reunion.fr/hal-01389717
http://hal.univ-reunion.fr/hal-01389717/document
http://hal.univ-reunion.fr/hal-01389717/file/Vauchez_Barruol-PEPI96_hal.pdf
DOI : 10.1016/0031-9201(95)03125-1

Éditeur(s) : HAL CCSD
Résumé : Differentiation of the lithospheric mantle occurred principally through partial melting and extraction of melts. Harzburgites are generally considered as melting residues whereas lherzolites are regarded as pristine mantle weakly affected by melting. However, some orogenic peridotites show evidence of igneous refertilization. In this context, this work re-investigates the nature of the Lherz lherzolites (Pyrenees), type-locality of lherzolites, described as a piece of preserved fertile mantle. Structural and geochemical data show that these lherzolites are not pristine but formed through a refertilization reaction between MORB-like melts and refractory lithosphere. Moreover, the Lherz peridotites were partly used to infer the composition of the primitive upper mantle and these results may have important implications for the nature of the late veneer. Additionally, crystal-preferred orientations of minerals (CPO) highlight a strong feedback between melt percolation and finite strain in the percolated rocks. CPO variations are ruled by a subtle balance between instantaneous melt fraction and local strain rate. This work also investigated the effect of melt percolation on Hf, Nd and Sr isotopes. Isotope systematics in Lherz shows that strong isotopic decoupling may arise in a percolation front. The modelling suggests that decoupled isotopic signatures are generated during porous flow and governed by the melt/matrix elements concentrations, chemical diffusivities or efficiency of isotopic homogenization. Melt-rock interactions can generate “intraplate-like” isotopic signatures. This suggests that a part of isotopic signatures of mantle-related rocks could be generated by diffusional processes associated with melt transport.
La différenciation du manteau lithosphérique s'est principalement effectuée par fusion partielle et extraction de magmas. Les harzburgites sont généralement considérées comme des résidus de fusion tandis que les lherzolites représentent un manteau originel peu affecté par la fusion. Cependant, certaines péridotites orogéniques montrent des évidences de refertilisation magmatique. Dans ce contexte, ce travail remet en cause la nature primitive des lherzolites de Lherz (Pyrénées), lithotype de la lherzolite. Les données structurales et géochimiques montrent que ces lherzolites ne représentent pas du manteau préservé mais qu'elles se sont formées par une réaction de refertilisation entre un liquide de type MORB et une lithosphère réfractaire. De plus, les orientations préférentielles de réseau (OPR) des minéraux montrent une forte interdépendance entre la percolation magmatique et la déformation finie observée dans les roches percolées. Les variations d'OPR semblent contrôlées par un équilibre subtil entre fraction de liquide instantanée et taux de déformation local. Ce travail a également abordé les effets de la percolation magmatique sur la variabilité isotopique des roches mantelliques. Les résultats montrent qu'un fort découplage isotopique peut s'observer dans un front de percolation. Les modèles suggèrent que le découplage des signatures isotopiques se produit pendant la percolation, gouverné par le rapport des concentrations en éléments (magma/matrice), la diffusivité et le processus d'homogénéisation isotopique. Les réactions magma/roche peuvent générer des signatures isotopiques de type intraplaque. Ceci suggère qu'une part des signatures isotopiques des roches ou laves dérivées du manteau pourrait être produite par des processus diffusionnels associés à du transport de magma.
https://tel.archives-ouvertes.fr/tel-00431325

tel-00431325
https://tel.archives-ouvertes.fr/tel-00431325
https://tel.archives-ouvertes.fr/tel-00431325/document
https://tel.archives-ouvertes.fr/tel-00431325/file/theseleroux08.pdf

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
ISSN: 1755-098X

hal-01149047
http://hal.upmc.fr/hal-01149047
http://hal.upmc.fr/hal-01149047/document
http://hal.upmc.fr/hal-01149047/file/Decelle_2015_PhytoREF.pdf
DOI : 10.1111/1755-0998.12401

Éditeur(s) : HAL CCSD RSC Publishing
Résumé : International audience
Abstract View references (36)The size or alkyl chain length of cationic surfactants can be used to tailor both the pore morphology and the functionality or oxidation state of cobalt in silica materials. This work shows for the first time that these two mechanisms are interconnected. Cobalt oxide silica materials, with the same cobalt loading (Co:Si = 1:4), were prepared using an acid catalysed sol-gel method where the cobalt/surfactant ratio was systematically varied. The alkyl chain length of the cationic surfactant was also varied from 2 to 12 by using tetraethyl (C2-AB) ammonium bromide, and triethyl hexyl (C6-AB) and dodecyl trimethyl (C12-AB) ammonium bromides as the templating agents. Initial addition of C2-AB, C6-AB or C12-AB enhanced the oxidation of cobalt to cobalt (ii,iii) oxide in the xerogels. However, as more surfactant is added the enhancement effect is reversed and the cobalt (ii,iii) oxide content of the sample begins to decline. The point at which this transition occurs is a function of the alkyl chain length of the surfactant, with a longer chain indicating an earlier transition. Pore morphology was influenced in a similar fashion with the longer alkyl chain C12-AB surfactant undergoing an earlier transition (i.e. at lower concentrations) towards mesoporosity, than either of the smaller C2-AB and C6-AB surfactants. In both mechanisms it was the increased propensity of the C12-AB surfactant to aggregate (given its larger size and lower solubility) that was the controlling factor. This journal is © the Partner Organisations 2014.
EISSN: 2046-2069

hal-01683205
https://hal.univ-antilles.fr/hal-01683205
DOI : 10.1039/c4ra05934d

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
We present a new interpretation of anisotropy of magnetic susceptibility (AMS) fabrics in basaltic lava flows based on the detailed study of magnetic mineralogy and silicate crystallographic fabric of a Quaternary lava flow from the French Massif Central (La Palisse). We consider the model of AMS fabric imbrication between magnetic foliation and flow surface, as initially proposed for dykes. At the two sampling sites, the concordance between the flow direction deduced from the AMS foliation and that deduced from field observations indicates that the imbrication model could apply to the lava flows. However, the flow senses inferred fromAMSare systematically opposed between the two sampling sites suggesting permutations between K1 and K3 AMS axes, a configuration referred to as inverse fabric. Electron backscatter diffraction (EBSD) measurements show strong lattice-preferred orientations (LPO) for plagioclase, especially the (010) plagioclase plane, which tends to be parallel to the flow. Clinopyroxene LPO remains less marked than plagioclase LPO, whereas titanomagnetite does not display a significant LPO. Comparison between magnetic and crystallographic fabrics suggests that the AMS fabric of the lava flow results from the distribution of titanomagnetite grains, which is in turn controlled by the fabric of the silicate framework. Magnetic hysteresis parameters and anisotropy of remanent magnetization (ARM) measurements exclude a significant contribution from single-domain grains, often called upon to explain inverse magnetic fabrics. The origin of the observed inverse magnetic fabric may relate to the dip of the palaeosurface, which is the only remarkable difference between the two sampling sites. AMS appears as a good tool to determine the direction of basaltic lava flows and coupling with local crystallographic fabric data provides a valuable control of relationships between magnetic fabrics and flow and thus contributes to better constrain the AMS signature of lava flows.
ISSN: 0956-540X

hal-00903561
https://hal.archives-ouvertes.fr/hal-00903561
https://hal.archives-ouvertes.fr/hal-00903561/document
https://hal.archives-ouvertes.fr/hal-00903561/file/TB-GJI-193-2-Orig.pdf
DOI : 10.1093/gji/ggs115

Éditeur(s) : HAL CCSD World Scientific
Résumé : The present paper presents a laboratory experiment of rip current circulations over a moveable bed. The rip current characteristics over four distinct beach morphologies, exhibiting more or less developed nature-like bar-rip morphology,were investigated. For each video run, the same off shore shore-normal waves were generated by the wave maker with the same mean water level in order to study the sensitivity of the rip current characteristics as a function of the beach morphology only. In each case, a 1-hour video run was used to track a large number (~30) of drifters released within the surf zone. Image coordinates were then rectifie d to still water level Cartesian coordinates to compute drifter velocities, mean characteristics and surf zone rete ntion rates. Results show the presence of classic rip current patterns with counter-rotating cells and a relatively narrowoffshore-directed jet with, for three of the situations, a reasonably symmetric shape. Non-surprisingly, it was found that rip current intensity increases with increasing relative depth of the rip channel. The wave-driven circulations were strongly unstable. Computed standard deviation in fl ow intensity and direction provides high resolution information on the spatial variability of the rip current insta bilities with, for instance, highly-pulsating and weakly directionally variable offshore-directed flow in the rip channel. Conversely to what was previously hypothesized in the literature, there was hardly trace of vortices being shed offs hore and drifters exiting the surf zone compartment were not systematically caught by a pulsating jet. The cause for drifter exiting the semi-enclosed surf zone compartment remains, however, elusive and deserves further investigations. The computed surf zone retention rates (~90%) were of the order of those previously observed in the field, with no clear relationship with the mean rip current velocity or relative depth of the rip channel. Further video-runs will have to be analyzed to explore potential explanations
Proceedings of Coastal Dynamics 2009 Impacts of Human Activities on Dynamic Coastal Processes

ISBN : 978-981-4282-46
hal-00854534
https://hal.archives-ouvertes.fr/hal-00854534

Éditeur(s) : HAL CCSD Elsevier
Résumé : A combination of statistical studies on present-day subduction zones and three-dimensional (3D) laboratory models is performed with the aim to clarify the way that plate kinematics control the geometry of the slab and the overriding plate deformation in subduction zones. In 3D laboratory models, the analogue of a two layer linearly viscous lithosphere–upper mantle system is achieved by means of silicon putty glucose syrup tank experiment. The subducting and overriding plate velocities are systematically changed by exploring the variability field of natural plate kinematics. Both statistical and modelling approaches recognize the importance of overriding plate motion on subduction process behavior: (1) trenches migrate at a rate close to the overriding plate motion, but always move slower than the overriding plates. The mechanism at work is a direct consequence of “slab anchoring” opposed by both lithosphere and mantle viscous resistance and is responsible for overriding plate deformation and slab geometry variability. (2) An overriding plate shortens when the overriding plate moves toward the trench and conditions that are favourable for overriding plate extension are created when the overriding plate moves away from the trench. (3) Shallow and steep dips are found if the overriding plate moves toward and away from the trench, respectively.
ISSN: 0012-821X

hal-00406598
https://hal.archives-ouvertes.fr/hal-00406598
DOI : 10.1016/j.epsl.2007.02.004

Éditeur(s) : HAL CCSD
Résumé : International audience
Wound healing is important for sharks from the earliest life stages, for example, as the 'umbilical scar' in viviparous species heals, and throughout adulthood, when sharks can incur a range of external injuries from natural and anthropogenic sources. Despite anecdotal accounts of rapid healing in elasmobranchs, data regarding recovery and survival of individuals from different wound or injury types has not been systematically collected. The present study documented: (i) 'umbilical scar' healing in wild-caught, neonatal blacktip reef sharks while being reared for 30 days in flow-through laboratory aquaria in French Polynesia; (ii) survival and recovery of free-swimming blacktip reef sharks in Australia and French Polynesia following a range of injuries; and (iii) long-term survival following suspected shark-finning activities. Laboratory monitoring, tag-recapture records, telemetry data and photo-identification records suggest that blacktip reef sharks have a high capacity to survive and recover from small or even large and severe wounds. Healing rates, recovery and survival are important factors to consider when assessing impacts of habitat degradation and fishing stress on shark populations. The present study suggests that individual survival may depend more on handling practices and physiological stress rather than the extent of physical injury. These observations also contribute to discussions regarding the ethics of tagging practices used in elasmobranch research and provide baseline healing rates that may increase the accuracy in estimating reproductive timing inferred from mating scars and birth dates for neonatal sharks based on umbilical scar healing status. Cite as: Chin A, Mourier J, Rummer JL (2015) Blacktip reef sharks (Carcharhinus melanopterus) show high capacity for wound healing and recovery following injury. Conserv Physiol 3: doi:10.1093/conphys/cov062.
Conservation physiology

Droits : http://creativecommons.org/licenses/by/
hal-01250745
https://hal-univ-perp.archives-ouvertes.fr/hal-01250745
https://hal-univ-perp.archives-ouvertes.fr/hal-01250745/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01250745/file/Conserv%20Physiol-2015-Chin-.pdf
DOI : 10.1093/conphys/cov062

Éditeur(s) : HAL CCSD European Centre for Disease Prevention and Control
Résumé : International audience
Following of the emergence of Zika virus in Brazil in 2015, an epidemiological surveillance system was quickly implemented in the French overseas Territories of America (FTA) according to previous experience with dengue and chikungunya and has detected first cases of Zika. General practitioners and medical microbiologists were invited to report all clinically suspectedcases of Zika, laboratory investigations were systematically conducted (RT-PCR). On 18 December, the first autochthonous case of Zika virus infection was confirmed by RT-PCR on French Guiana and Martinique, indicating introduction of Zika virus inFTA. The viral circulation of Zika virus was then also confirmed on Guadeloupe and Saint-Martin. We report here early findings on 203 confirmed cases of Zika virus infection identified by RT-PCR or seroneutralisation on Martinique Island between 24 November 2015 and 20 January 2016. All cases were investigated. Common clinical signs were observed (maculopapularrash, arthralgia, fever, myalgia and conjunctival hyperaemia) among these patients, but the rash, the foundation of our case definition, may be absent in a significant proportion of patients (16%). These results are important for the implementation of a suspected case definition, the main tool for epidemiological surveillance, in territories that may be affected by ZIKV emergence, including Europe.
ISSN: 1025-496X

Droits : info:eu-repo/semantics/OpenAccess
inserm-01415215
http://www.hal.inserm.fr/inserm-01415215
http://www.hal.inserm.fr/inserm-01415215/document
http://www.hal.inserm.fr/inserm-01415215/file/2016%2C%20Daudens-Vaysse%20-%20Zika%20emergence%20in%20the%20French%20Territories%20of%20America%20and%20description%20of%20first%20confirmed%20cases%20of%20Zika%20virus%20infection%20on%20Martinique%20.pdf
DOI : 10.2807/1560-7917.ES.2016.21.28.30285

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Tarim and Junggar basins in central Asia are capped by a thick pile of conglomerates, called the Xiyu Formation, that are commonly linked to a change in climate and/or accelerated uplift near the Plio-Pleistocene boundary. In order to better understand their origin and significance, we carried out a combined structural and magnetostratigraphic study in the Quilitage syncline (southern Tianshan), where the base of the Xiyu conglomerates is observed at both sides of the syncline. A balanced cross-section shows that, even at a local-scale, the base of the Xiyu conglomerates cannot be regarded as a single continuous stratigraphic layer. On the southern flank of the Quilitage syncline, we collected 172 samples collected for magnetostratigraphic dating identify 17 polarity chrons that date the new section from 5.2 to ~ 1.7 Ma and constrain the base of the Xiyu conglomerate here at ~ 1.7 Ma. This is 4.2 Ma younger than the age of the Xiyu previously found on the northern limb of the same syncline. Together with other magnetostratigraphic studies carried out around the Tianshan, our study unambiguously demonstrates that the onset of deposition of the Xiyu conglomerates is diachronous, and that the conglomerates are systematically younger toward the basin. Consequently, the Xiyu Formation should not be considered as a chronostratigraphic marker related to any particular tectonic or climatic event, but is instead a prograding gravel wedge that has prograded over the underthrusting forelands. A synthesis of chronologic and structural results yields progradation rates over the last 10 Ma on the order of ~ 2.0 mm/yr and ~ 3.9 mm/yr south and north of the Tianshan Mountains respectively. These rates are comparable to the shortening rate across the Tianshan range, suggesting that underthrusting is the main factor governing the progradation rate of the Xiyu Formation.
ISSN: 0012-821X

insu-00414151
https://hal-insu.archives-ouvertes.fr/insu-00414151
https://hal-insu.archives-ouvertes.fr/insu-00414151/document
https://hal-insu.archives-ouvertes.fr/insu-00414151/file/Charreau-EPSL-2009.pdf
DOI : 10.1016/j.epsl.2009.07.035

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
We isolated and characterized 16 polymorphic microsatellite loci for Lytocarpia brevirostris (Aglaophe- niidae), a hydrozoan common in the tropical Indo-Pacific region. Four to 34 alleles per locus were detected at the Indo-Pacific scale. At the population level, observed (Ho) and expected (He) heterozygosities ranged across 0.100–0.625 and 0.097–0.597, respectively. Three markers showed significant deviation from Hardy–Weinberg equi- librium, all of them presenting null alleles. Linkage dis- equilibrium was detected in three pairs of loci among 120. These primers provide powerful tools for studying popu- lation genetic diversity and the implication of life cycle strategies on population differentiation in tropical hydro- zoans. This will be valuable for the conservation of coral reefs biodiversity and the design of marine protected areas.
ISSN: 1877-7252

hal-01185722
https://hal.archives-ouvertes.fr/hal-01185722
https://hal.archives-ouvertes.fr/hal-01185722/document
https://hal.archives-ouvertes.fr/hal-01185722/file/Postaire%20et%20al.%20-%202015%20-%20Isolation%20and%20characterisation%20of%2016%20microsatellit_hal.pdf
DOI : 10.1007/s12686-014-0407-1

Éditeur(s) : HAL CCSD HUMANA PRESS INC
Résumé : International audience
Ever since Darwin, the familiar genealogical pattern known as the Tree of Life (TOL) has been prominent in evolutionary thinking and has dominated not only systematics, but also the analysis of the units of evolution. However, recent findings indicate that the evolution of DNA, especially in prokaryotes and such DNA vehicles as viruses and plasmids, does not follow a unique tree-like pattern. Because evolutionary patterns track a greater range of processes than those captured in genealogies, genealogical patterns are in fact only a subset of a broader set of evolutionary patterns. This fact suggests that evolutionists who focus exclusively on genealogical patterns are blocked from providing a significant range of genuine evolutionary explanations. Consequently, we highlight challenges to tree-based approaches, and point the way toward more appropriate methods to study evolution (although we do not present them in technical detail). We argue that there is significant benefit in adopting wider range of models, evolutionary representations, and evolutionary explanations, based on an analysis of the full range of evolutionary processes. We introduce an ecosystem orientation into evolutionary thinking that highlights the importance of ``type 1 coalitions'' (functionally related units with genetic exchanges, aka ``friends with genetic benefits''), ``type 2 coalitions'' (functionally related units without genetic exchanges), ``communal interactions,'' and ``emergent evolutionary properties.'' On this basis, we seek to promote the study of (especially prokaryotic) evolution with dynamic evolutionary networks, which are less constrained than the TOL, and to provide new ways to analyze an expanded range of evolutionary units (genetic modules, recombined genes, plasmids, phages and prokaryotic genomes, pangenomes, microbial communities) and evolutionary processes. Finally, we discuss some of the conceptual and practical questions raised by such network-based representation.
EVOLUTIONARY GENOMICS: STATISTICAL AND COMPUTATIONAL METHODS, VOL 2

ISBN : 978-1-61779-584-8
hal-01544801
https://hal.archives-ouvertes.fr/hal-01544801
DOI : 10.1007/978-1-61779-585-5_4

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
BACKGROUND: Surveillance of HIV-1 drug resistance in treated patients with plasma viral load (VL) >50 copies/mL. METHODS: The protease and reverse transcriptase (RT) genes were systematically sequenced in samples from 756 patients with VL >50 copies/mL in 2009. The genotyping results were interpreted for each antiretroviral drug (ARV) by using the ANRS algorithm v21. Weighted analyses were used to derive representative estimates of percentages of patients. Prevalence rates were compared with those obtained in 2004 among patients with VL >1000 copies/mL. RESULTS: Sequences were obtained for 506 patients. Sequencing was successful in 45%, 80% and 96% of samples with VL of 51-500, 501-1000 and >1000 copies/mL, respectively. Resistance or possible resistance to at least one ARV was observed in 59% of samples. Overall, 0.9% of samples contained viruses resistant to all drugs belonging to at least three drug classes. All resistance prevalence rates were significantly lower in 2009 than in 2004. CONCLUSION: In France, where 86% of patients were receiving combination antiretroviral therapy in 2009, only 15.0% of patients had a VL >50 copies/mL, suggesting that only 8.9% of treated patients could potentially transmit resistant viruses. Only 0.08% of patients harboured viruses fully resistant to at least three antiretroviral drug classes. Further studies are needed to determine whether resistance continues to decline over time.
ISSN: 0305-7453

hal-00875092
https://hal.archives-ouvertes.fr/hal-00875092
DOI : 10.1093/jac/dkt033
PUBMED : 23404192