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

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

Éditeur(s) : HAL CCSD Botanical Society of America
Résumé :  
International audience
The different hypotheses about buttress function and formation mainly involve mechanical theory. Forces were applied to two trees of Sloanea spp., a tropical genus that develops typical thin buttresses, and the three-dimensional strains were measured at different parts of the trunk base. Risks of failure were greater on the buttress sides, where shear and tangential stresses are greater, not on the ridges, in spite of high longitudinal (parallel to the grain) stresses. A simple beam model, computed from the second moment of area of digitized cross sections, is consistent with longitudinal strain variations but cannot predict accurately variations with height. Patterns of longitudinal strain variation along ridges are very different in the two individuals, owing to a pronounced lateral curvature in one specimen. The constant stress hypothesis is discussed based on these results. Without chronological data during the development of the tree, it cannot be proved that buttress formation is activated by stress or strain.
ISSN: 0002-9122

hal-01032155
https://hal.archives-ouvertes.fr/hal-01032155
https://hal.archives-ouvertes.fr/hal-01032155/document
https://hal.archives-ouvertes.fr/hal-01032155/file/Biomechanics_buttressed_trees_Clair_al_2003.pdf
DOI : 10.3732/ajb.90.9.1349

Éditeur(s) : HAL CCSD
Résumé : Gravitropism is a major process in vertical growth as it allows the positioning of plant in the gravity field and thus, for trees, it takes part in the light foraging strategies. Without any gravitropism, trees would adopt a weeping habit or fall on the ground due to the increasing with growth supported weight, especially at the advance regeneration stage (sapling stage) in the understorey, where tree are very slender and poorly stiff. Most of the gravitropic studies are made by physiologists in order to understand the process and thus are associated to complex laboratory methods (genetic engineering, anatomical studies, accurate 2D ou 3D measurements of form changes with time). In order to study the ecological relevance and the specific diversity of gravitropic performances in natural forests, we developed a framework that uses different kinds of datas. Synchronical analysis has been done i) at the population level in large sample of trees and ii) at the tree level from destructive measurement of the dissymmetry maturation strains known to be the main motor of the posture control reaction of trees. In both cases, biomechanical models allows to estimate some aspects of the dynamic gravitropic process. Diachronical analysis has been done in natural conditions on permanent plots, or in a more traditional way, by observing in greenhouse experiments the righting movements of plants artificially tilted. In the first case, the problem is the high variability of natural disturbances and the slowness of growth and movements in the dark understorey. The second choice allows a measurement of a capacity (i.e. the ability of the species to react in quite extreme conditions of verticality disturbance but good for growth light and nutrient conditions) that is more easy to analyse, but is maybe not so relevant for estimating the ecological strategy (some species could have developed a high efficience of gravitropic reaction in natural conditions by avoiding the mechanical disturbance or adapting the reaction to slow growth and changing environments in natural conditions). All approaches use the same basic biomechanical modelling, i) to analyse simultaneously the reaction and the disturbance (due to the weight increase) during growth, or ii) to combine different parameters (geometry, growth, weight, maturation strains) involved in shape changes and posture control. They give a classification of the species according to their gravitropic performances. Results on 15 species are discussed, with relation to shade-tolerance or avoidance.
6th Plant Biomechanics Conference
Cayenne, France

hal-00565956
https://hal.archives-ouvertes.fr/hal-00565956

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Cet article invite à un examen des enjeux du développement durable dans les petites économies insulaires en développement. Notre propos se décline en trois points. Après avoir rappelé les spécificités de ces entités insulaires (exiguïté, éloignement/isolement, vulnérabilité), nous analysons ensuite les caractéristiques sociétales qui leur sont couramment prêtées (qualité du substrat social : homogénéité culturelle, sociabilité, propension à l’action collective, etc.) et leur contribution à la durabilité du développement. Nous nous interrogeons dès lors sur le caractère résilient de ces déterminants sociaux dans la mesure où ils peuvent permettre la mise en place de projets et de stratégies effectives de développement durable. Enfin, notre réflexion prend appui sur quelques exemples concrets dans la Caraïbe mettant en relation le contexte social local et les actions de développement durable engagées. Selon les cas, ce socle social territorial peut être appréhendé comme un facteur de blocage ou un moteur de développement durable.
Our article deals with sustainable development in the context of small islands developping states (SIDS). Our article unfolds in three steps. First, we diagnose the disadvantages SIDS usually face to (small size, remoteness, vulnerability). Second, we analyse some societal features commonly described as strong characteristics of ‘islandness’ (social links, cultural homogeneity, sociability, propensity to collective action etc.) and their contribution to sustainable development. We then consider these social determinants as factors of resilience. Third, we discuss specific management projects in the Caribbean showing the role of local co-ordination in promoting (or hindering) effective sustainable development strategies.
Guadeloupe
Martinique
Jamaïque

Droits : info:eu-repo/semantics/openAccess
http://journals.openedition.org/etudescaribeennes/3443

Éditeur(s) : HAL CCSD
Résumé : The spectrin-based skeleton is an essential scaffold underlying different lipid bilayers in all animal cells. Spectrins (Sp), as giant extended flexible heterotetramers (αβ)2, constitute the filaments of this network, the nodes of which are cross-linked by actin filaments. The functions of the Sp-based skeleton, which are well defined in red blood cells (required for shape, resistance to shear stress and deformability) are less well understood in non-erythroid cells.The non-erythroid Sp might participate in the establishment and/or the maintenance of specialized membrane subdomains by accumulating integral membrane proteins (such as ionic channels, ionic pumps, receptors and cell adhesion molecules) as revealed by loss of the main non-erythroid β-Sp. However the effect of non-erythroid α-Sp are less well established. In mammals, α-Sp are encoded by two genes: one for αI-Sp mainly expressed in mature erythrocyte, the second one for αII-Sp which is expressed in all nucleated cells.In the pursuit of αII-Sp functions, we have checked the effect of αII-Sp knock down by siRNA melanoma human cell line. Our data revealed that spectrin depletion is associated with i) an arrest of cell cycle at G1 state ii) a loss of cell adhesion in spite of increase in some integrins iii) some modifications of actin organisation.
Le squelette dépendant de la spectrine, localisé sous la bicouche lipidique, est un échafaudage essentiel de toutes les cellules animales. La Spectrine (Sp), structure géante, robuste mais flexible d'hétéro tétramères (αβ)2, constitue les filaments de ce réseau, dont chaque nœud interagit avec des filaments d'actine. Les fonctions du squelette de Sp, qui sont bien définies dans le globule rouge (rôle dans sa forme, dans sa résistance aux forces de cisaillement et dans sa déformabilité) sont moins bien connues dans les cellules non-érythroïdes. La Sp non-érythroïde pourrait participer à l'établissement et/ou au maintien de sous-domaines membranaires spécialisés dans l'accumulation de protéines de membrane (telles que les canaux ioniques, les pompes ioniques, les récepteurs et les molécules d'adhérence) comme nous le font penser les invalidations de la Sp-β non-érythroïde. Cependant le rôle de la Sp-α non-érythroïde est moins bien établi. Chez les mammifères, la Sp-α est codée par deux gènes: un pour Sp-αI, principalement exprimée dans l'érythrocyte mature, le second pour Sp-αII qui est exprimée dans toutes les cellules nucléées. Pour étudier les fonctions de la Sp-αII, nous avons utilisé une approche de SiRNA sur des cellules de mélanome humain. Nos données montrent que la diminution de Sp-αII est associée à I) un arrêt en G1 du cycle cellulaire II) une perte d'adhérence des cellules malgré l'augmentation de quelques intégrines III) des modifications dans l'organisation du réseau d'actine.
https://tel.archives-ouvertes.fr/tel-00377569

Droits : info:eu-repo/semantics/OpenAccess
tel-00377569
https://tel.archives-ouvertes.fr/tel-00377569
https://tel.archives-ouvertes.fr/tel-00377569/document
https://tel.archives-ouvertes.fr/tel-00377569/file/these_210409_entiere.pdf
https://tel.archives-ouvertes.fr/tel-00377569/file/II-Spectrin_Is_Critical_for_Cell_Adhesion_and_Cell_Cycle.PDF

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Reliable molecular typing tools are required for a better understanding of the molecular epidemiology of Plasmodium vivax. The genes msp3a and msp1_block5 are highly polymorphic and have been used as markers in many P. vivax population studies. These markers were used to assess the genetic diversity of P. vivax strains from French Guiana (South America) and to develop a molecular typing protocol. METHODS: A total of 120 blood samples from 109 patients (including 10 patients suffered from more than one malaria episode, samples were collected during each episode) with P. vivax infection were genotyped. All samples were analysed by msp3a PCR-RFLP and msp1_b5 gene sequencing was performed on 57 samples. Genotyping protocol applied to distinguish between new infection or relapse from heterologus hypnozoites and treatment failure or relapse from homologus hypnozoites was based on analysing first msp3a by PCR-RFLP and secondly, only if the genotypes of the two samples are identical, on sequencing the msp1_b5 gene. RESULTS: msp3a alleles of three sizes were amplified by PCR: types A, B and C. Eleven different genotypes were identified among the 109 samples analysed by msp3a PCR-RFLP. In 13.8% of cases, a mixed genotype infection was observed. The sequence of msp1_b5 gene revealed 22 unique genotypes and 12.3% of cases with mixed infection. In the 57 samples analysed by both methods, 45 genotypes were found and 21% were mixed. Among ten patients with two or three malaria episodes, the protocol allowed to identify five new infections or relapses from heterologous hypnozoites and six treatment failures of relapses from homologous hypnozoites. CONCLUSION: The study showed a high diversity of msp3a and msp1_b5 genetic markers among P. vivax strains in French Guiana with a low polyclonal infection rate. These results indicated that the P. vivax genotyping protocol presented has a good discrimination power and can be used in clinical drug trials or epidemiological studies.
ISSN: 1475-2875

pasteur-00590981
https://hal-riip.archives-ouvertes.fr/pasteur-00590981
DOI : 10.1186/1475-2875-8-40
PUBMED : 19284592

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper investigates the narrative challenges and opportunities that contemporary virology offers to popular science and to fiction. The study of viruses reveals extremely complex relations, playing out over different physical and temporal scales. Viruses constitute a heterogeneous population whose interactions with living organisms occur on multiple levels, and whose numbers are vastly superior to human and even bacterial populations on earth. The resulting challenges for narration can be grouped into three main formal questions. The first is the problem of scale, since the numbers and sizes of virus and host populations are vastly different, as are the temporalities over which they transform and survive. The second is the complexity of actants, since viruses are involved in relations where destruction and mutual benefit can overlap, and genetic transformations are played out over many generations. The third is the choice of images through which to convey their behaviours: many existing metaphors in microbiology, such as “chimeras”, “parasites” or “kill-the-winner dynamics”, carry the narrative potential of a mythological and/or theatrical imagination.These questions will first be examined as challenges encountered in the narration of biology for vulgarization purposes, and effects on narrative forms will be outlined: shifts in focalization in order to create multiscalar perspectives; unstable actantial models as expressions of complex relations; and the use or resistance to narrative structures implied by several key metaphors in virological discourse. These formal characteristics will then be presented through two case studies drawn from contemporary fiction. In his “scientific fable” Conflits Intérieurs (2015), microbiologist Eric Bapteste creates a multiscalar narrative by using humans and viruses as both protagonists and narrators in a battle of ideas. In the graphic novel aâma (2011-2014), Frederik Peeters explores the ambiguous potential, both symbiotic and threatening, of a meta-organism uniting humans with microscopic agents. Both these novels play with scale, metaphor and actants so as to question the fundaments of human identity. They posit the act of narration as a defining human attribute, and consequently use the narrative voice as an arena in which we observe the weakening of the notion of the subject by microbiology.
“Narrative, Cognition & Science” Symposium
Erlangen, Germany

hal-01434744
https://hal.archives-ouvertes.fr/hal-01434744

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
To constrain the relations between deformation and metasomatism in the subcratonic lithospheric mantle, we have analyzed the microstructures and crystal preferred orientations in 50 mantle xenoliths from the Kaapvaal craton. Water contents in olivine and pyroxenes were measured in 14 samples equilibrated at different depths. Coarse-granular microstructures recording deformation by dislocation creep followed by annealing predominate. Mylonitic (sheared) peridotites with partially or totally recrystallized microstructures are however common below 140 km. Refractory compositions predominate, but multiple metasomatic events resulted in orthopyroxene enrichment or secondary crystallization of clinopyroxene and phlogopite. Coherent orthopyroxene and olivine CPO in most coarse-grained peridotites implies in pre- to syn-kinematic orthopyroxene enrichment or epitaxial growth on primary orthopyroxene. Undeformed, interstitial orthopyroxene, clinopyroxene, and phlogopite with random orientations in coarse-grained peridotites record post-kinematic modal metasomatic events. Deformation of these phases in the sheared peridotites implies that mylonitization results from a later event, which affected locally the deep cratonic lithosphere. Olivine CPO recording dominant [100] glide predominate at all depths. Only two samples, equilibrated at ~ 3.3 GPa show olivine [001] and orthopyroxene [001] axes subparallel, suggesting dominant [001] glide. Water contents in olivine are maximum (150 wt. ppm H2O) in peridotites equilibrated at ~ 160 km depth. Peridotites equilibrated below 180 km depth are, in contrast, almost dry. Lack of correlation between olivine mg# and water content indicates that the high water contents in olivine record re-hydration after the extensive partial melting, which produced the cratonic root. The vertical variation in water contents in olivine observed in the Kaapvaal peridotites may result from hydrogen addition or loss during extraction by the kimberlites. Comparison with magnetotelluric electrical conductivity data suggests, however, that the observed vertical variation of water contents in olivine may be representative of the present-day state of the Kaapvaal mantle, implying that extensive metasomatism resulted in hydration of the cratonic mantle at intermediate depths. The annealed microstructures of Kaapvaal peridotites indicate however that this metasomatism was not followed by remobilization of the cratonic root.
ISSN: 0024-4937

hal-00750328
https://hal.archives-ouvertes.fr/hal-00750328
DOI : 10.1016/j.lithos.2012.05.001

Éditeur(s) : HAL CCSD Lippincott, Williams & Wilkins
Résumé : International audience
OBJECTIVES: The ANRS-112 INTERPRIM trial assessed whether fixed-cycles of antiretroviral treatment interruption (ART-STI) combined or not with pegylated interferon alpha-2b (peg-IFN) could lower viral load and achieve a healthier immune system in patients diagnosed during primary HIV-1-infection (PHI). DESIGN AND METHODS: Patients were randomized to receive either continuous ART (cART) during 72 weeks, or cART during 36 weeks followed by three ART-STIs, or the same ART-STIs associated with peg-IFN during the first 14 weeks and each interruption (ART-STI-IFN). Treatment was stopped at week 72. Final evaluation was based on plasma HIV-RNA level 6 months after the last treatment interruption. RESULTS: Eighty-seven percent of patients achieved undetectable HIV-RNA at week 32, with no deleterious impact of sequential treatment interruptions (STIs). Viral rebounds during interruptions were lower in the ART-STI-IFN than in the ART-STI group and during the second and third interruptions compared with the first one. However, HIV-RNA levels, CD4 T-cell counts and CD4 T/CD8 T ratios were similar between groups after the 6-month interruption, with a persistent effect on CD4 T cells and total cell-associated HIV-DNA levels. Predictive factors of virological outcome were HIV-RNA and HIV-DNA levels at PHI and HIV-DNA levels at treatment interruption. HIV-specific responses did not differ between strategies and were not associated with outcome. Forty-eight percent of patients experienced treatment resumption during long-term follow-up without difference between groups. CONCLUSION: When initiated during PHI, STIs associated or not with IFN did not result in a different outcome as compared to cART. All regimens showed a high response rate and a sustained immunological benefit after cessation.
ISSN: 0269-9370

hal-00875175
https://hal.archives-ouvertes.fr/hal-00875175
DOI : 10.1097/QAD.0b013e32835844d9
PUBMED : 22842994

Éditeur(s) : HAL CCSD
Résumé : High Pressure - Low Temperature (HP-LT) rocks testify for burying and exhumation of crustal material in subduction zones. Their complete exhumation is the result of processes acting during (syn-orogenic) and after (post-orogenic) subduction is active, the latter partly obliterating the first. In the Aegean domain, the Attic-Cycladic Blueschist unit (ACBU) is a HP-LT unit exhumed in metamorphic core complexes (MCCs) in the back-arc domain of the Hellenic subduction zone. This study is an attempt to distinguish features related to syn-orogenic exhumation processes responsible for the first stages of exhumation This syn-orogenic "message" has to be read through the post-convergence structural and thermal overprint that accompanied the formation of the MCCs. Particularly, the geometry, the timing and the amount of the syn-orogenic exhumation has to be determined. We investigate these features with coupled field, metamorphic petrology and radiochronology studies First, based on observations on Ios (southern Cyclades), it has recently been proposed that syn-orogenic exhumation of the ACBU was accommodated by a basal thrust over the Cycladic Basement (CB) [Huet, et al., 2009]. The peak conditions, deduced from pseudosections calculation for the Ios main lithologies, are 500 °C-19 kbar for the ACBU and 550 °C-16 kbar for the CB. Exhumation until 400 °C-8 kbar is considered as syn-orogenic. Second, phengites populations, single grains and in situ 40Ar-39Ar geochronology has been carried out on samples from Tinos and Andros (northern Cyclades), Syros (central Cyclades) and Ios. The results gather in several clusters: 50-55 Ma, 40-45 Ma, 30-35 Ma, and 22-26 Ma. Based on these new P-T-t data and a synthesis of published data, we are able to refine the geometry and the timing of the exhumation of the ACBU. Data from the whole Cyclades exhibit little differences in ages and P-T conditions for the successive stages of exhumation. The peak of pressure (500±50 °C-18±1 kbar) has been reached at 50-55 Ma from Tinos to Ios. The onset of the exhumation occurred at 40-45 Ma in blueschist facies conditions, between a thrust at their bottom and a detachment at their top. The following decompression was accompanied by cooling until 30-35 Ma (400±50 °C-8±1 kbar). At that time, the boundary conditions switched to extension. Finally, we propose a model for the exhumation of HP-LT units accounting for these data. We also consider the rheological implications of the syn-orogenic structuration of the Aegean wedge on the post-orogenic evolution. B. Huet, L. Labrousse, and L. Jolivet [2009] Thrust or detachment? Exhumation processes in the Aegean: Insight from a field study on Ios (Cyclades, Greece), Tectonics, 28, 3, doi:10.1029/2008TC002397.
EGU General Assembly
Vienne, Austria

insu-00839054
https://hal-insu.archives-ouvertes.fr/insu-00839054
BIBCODE : 2010EGUGA..1214098H

Éditeur(s) : HAL CCSD American Institute of Physics
Résumé : International audience
In order to be able to provide valuable data in multiparameter measurement field operations, tiltmeters need to have a noise level better or equal than 10-9 rad for a period range from a few minutes to a few years and a long term stability ranging from 10-7 to 10-8 rad/yr. Tiltmeter measurements should also be as much as possible insensitive to thermal disturbances, by taking great care of the horizontality of the base line tube first. Secondly, thermal responses have been assessed. We also took great care of the coupling of our tiltmeters with the bedrock. We've designed a long base tiltmeter with sensors in silica which has a low dilatation coefficient. The linear variable displacement transducer is based on coil coupling (powered by an alternative voltage). Finally we show the results of two 100 m silica water tube tiltmeters which were installed in a mine in the French Vosges massif in the framework of a hydrology research project. These instruments show a remarkably good stability (6.5×10-9 rad/month) and a low noise level (of the order of 10-11 rad). Toroidal and spheroidal free modes of the Earth were observed after the two last major earthquakes on Sumatra.
ISSN: 0034-6748

hal-00708013
https://hal.archives-ouvertes.fr/hal-00708013
https://hal.archives-ouvertes.fr/hal-00708013/document
https://hal.archives-ouvertes.fr/hal-00708013/file/2008_RSI.pdf
BIBCODE : 2008RScI...79c4502B

Éditeur(s) : HAL CCSD
Résumé : One of the major challenges in forest ecology is to understand the ecology, physiology and potential responses of the> 250000 species of vascular plants of the planet through the categorization of this diversity into functional groups. This approach is essentially based on functional traits analysis, but few investigations were made in tropical areas. The aim of this study was to determine functional groups in two contrasted tropical ecosystems, dry (DF) and mountain rain (MRF) forest (respectively rainfall of 1 200 mm/year and 10 000 mm/year). Guadeloupe Island in FWI presents both these ecosystems spread over less 100 km. In a first time, we developed an original species typology based on 7 "soft" traits, easy to measure (stomatal density, leaf trichom density, chlorophyll content, leaf nitrogen content, specific leaf area, wood density, leaf area, plant height). The method was based on principal component analysis (PCA) and agglomerative hierarchical clustering (AHC) applied to these traits measured at the individual level (Blazy et al., 2009). In a second time, we evaluated the relevance of these soft trait-based groups compared to a typology based on 5 "hard" ecophysiological traits, more costly to quantify but with higher functional significance (difference between predawn and minimum leaf water potential, stomatal conductance, maximal carbon assimilation rate, leaf water potential at 90% of loss of stem hydraulic conductivity). When performed on the dominant canopy species in DF and MRF (a total of 13 species and 60 mature individuals), the typological approach based on soft traits seems relevant to discriminate groups with a distinct functional reality. Through both ecosystems, we obtained 4 homogenous groups. Two were exclusively composed by DF's or MRF's species, indicating that a functional strategy can be linked to specific environmental conditions. The two other groups showed a mix of DF and MRF species indicating that different functional strategies can coexist in the same environment. These mixed groups seem distinct by their ecophysiological features, particularly in term of hydraulic characteristics. One group was composed by drought tolerant species, water spender species, with a high xylem embolism resistance, whereas the second one was composed by water saver species, less resistant to embolism. Therefore, a determination of functional groups based on soft traits could be useful to model ecosystem's responses to environmental changes on a global scale.
Book of Abstracts - isem 2013 - Ecological Modelling for Ecosystem Sustainability
Toulouse, France

hal-00964668
https://hal.archives-ouvertes.fr/hal-00964668

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We experimentally studied the predatory behavior of Polybia rejecta (Vespidae, Polistinae, Epiponini) towards 2-88 mm-long insects attracted to a UV light trap. Foragers, which began to hunt at 6:30, selected 4-14 mm-long prey insects. Prey detection by sight by hovering wasps was confirmed using decoys. After the wasps landed and walked along a sinuous path, prey were detected by contact or from a distance (1-3cm). This was followed by seizure, stinging (contrarily to most other known cases), prey manipulation and retrieval. Prey that flew off might be caught in flight. The prey load, representing 30.7% of a forager's weight, was optimized by capturing up to six small prey or two medium-sized prey successively (both of which might be consumed in situ). The foragers cut off the wings of larger prey or cut them into two pieces and returned to gather the second piece. The handling time increased exponentially with the weight of the prey. Partial loading (i.e., retrieving a load much inferior to the maximum possible) was likely related to social facilitation, a form of nest-based recruitment that was demonstrated through the experimental elimination of local enhancement by removing foragers (both mechanisms favor the exploitation of favorable patches).
ISSN: 0376-6357

hal-01533217
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01533217
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01533217/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01533217/file/Dejean%20et%20al.%20-%20The%20predatory%20behavior%20of%20the%20Neotropical%20social%20w.pdf
DOI : 10.1016/j.beproc.2017.05.011

Éditeur(s) : Royal Soc
Résumé : Since its description from the Galapagos Rift in the mid-1980s, Archinome rosacea has been recorded at hydrothermal vents in the Pacific, Atlantic and Indian Oceans. Only recently was a second species described from the Pacific Antarctic Ridge. We inferred the identities and evolutionary relationships of Archinome representatives sampled from across the hydrothermal vent range of the genus, which is now extended to cold methane seeps. Species delimitation using mitochondrial cytochrome c oxidase subunit I (COI) recovered up to six lineages, whereas concatenated datasets (COI, 16S, 28S and ITS1) supported only four or five of these as clades. Morphological approaches alone were inconclusive to verify the identities of species owing to the lack of discrete diagnostic characters. We recognize five Archinome species, with three that are new to science. The new species, designated based on molecular evidence alone, include: Archinome levinae n. sp., which occurs at both vents and seeps in the east Pacific, Archinome tethyana n. sp., which inhabits Atlantic vents and Archinome jasoni n. sp., also present in the Atlantic, and whose distribution extends to the Indian and southwest Pacific Oceans. Biogeographic connections between vents and seeps are highlighted, as are potential evolutionary links among populations from vent fields located in the east Pacific and Atlantic Oceans, and Atlantic and Indian Oceans; the latter presented for the first time.
Proceedings Of The Royal Society B-biological Sciences (0962-8452) (Royal Soc), 2013-11 , Vol. 280 , N. 1770 , P. 1-9

Droits : 2013 The Author(s) Published by the Royal Society. All rights reserved.
http://archimer.ifremer.fr/doc/00157/26814/24961.pdf
DOI:10.1098/rspb.2013.1876
http://archimer.ifremer.fr/doc/00157/26814/

Résumé : In an effort to implement new fishing activities for the small scale fisheries of Reunion Island, a prospecting cruise targeting deep demersal fish (200 to 600 m) was set up on the west coast of Reunion Island in 2000. This project was carried out by the Regional Fishery Committee and the French Institute for the Exploration of the Sea (Ifremer). Large commercial stocks were identified, and numerous professional or recreational fishermen started employing electric winches to exploit these deep resources. However, the deep demersal species are a fragile resource due mainly to low growth rates and late sexual maturation. Due to the rapid increase in fishing pressure, Ifremer was asked to set up a new study and two scientific campaigns were carried out in 2011 (68 fishing trips being conducted with 559 dropline operations). The first cruise was conducted at the same sites, using the same types of fishing gear and methods used in 2000. A marked drop of greater than 90% was observed in the catches of commercial species, together with a decrease of most fish sizes, attesting the overexploitation of these stocks. Only, catches of the small non-commercial shark (Squalus megalops) remained important (50% in number and weight of total catches). The second cruise extended the prospection area to all waters surrounding Reunion Island . The overexploitation was confirmed in the west of Reunion Island, and in to a lesser degree in the north. Yields were better along the east and the south coasts. Concurrently, the efficiency of 2 hook sizes was compared : small hooks caught significantly more fish but of significantly smaller body sizes, resulting in comparable total weight of fish. We conclude that medium size hooks (i.e. type 7/0) have a significant selectivity on the fish size without loss in the global catch yield. Various types of baits were also tested with the flesh of small local pelagic fish species (Selar crumenophtalmus and Decapterus macarellus) appearing to be the most efficient. This study provides helpful indicators for the management of demersal fish stocks in Reunion island, which have been poorly surveyed and poorly regulated until now. However, the total fishing effort, especially from recreational fishermen, remains the most important factor to be quantified.
Dans la perspective de diversifier la Petite Pêche réunionnaise, une campagne de prospection des stocks de poissons démersaux profonds (200 à 600 m) avait été réalisée en 2000 par le Comité Régional des Pêches Maritimes (CRPM) et l'Institut Français de Recherche pour L'Exploitation de la Mer (Ifremer) dans l'ouest de l'île de La Réunion. Elle a montré l'existence de stocks commercialement intéressants et de nombreux pêcheurs, professionnels et plaisanciers se sont équipés en moulinets électriques pour exploiter ces ressources profondes. Cependant les poissons démersaux profonds représentent une ressource fragile du fait, notamment, de leur croissance lente et de leur maturité sexuelle tardive. Aussi, face à cette augmentation rapide de la pression de pêche, Ifremer a été sollicité pour mener une nouvelle étude ; et deux nouvelles campagnes expérimentales ont été réalisées en 2011 (68 marées ayant permis la réalisation de 559 filages). La première campagne a repris les mêmes sites de pêche, le même matériel et la même méthodologie qu’en 2000. Elle montre que les rendements en espèces commerciales ont diminué de façon très nette (plus de 90%) ainsi que la taille de certaines espèces, indicateurs caractéristiques d'une surexploitation des stocks. Seules les captures de requins zépines (Squalus megalops,) non commercialisées à La Réunion, restent comparables à celles de 2000 avec la moitié des captures totales. La 2e campagne a étendu la prospection à tout le tour de l'île. La surpêche (baisse des rendements et des tailles de poisson) est confirmée dans l'ouest et à un moindre degré sur la côte nord. Les rendements sont meilleurs dans l'est et le sud. Parallèlement, 2 tailles d'hameçons ont été comparées : les petits hameçons capturent un nombre significativement plus élevé de poissons par filage, mais de tailles plus petites, ce qui se traduit par un poids global comparable. Les hameçons de taille moyenne (type 7/0) ont donc une sélectivité significative sur la taille des poissons capturés sans nuire au rendement global. Des comparaisons ont aussi porté sur les types d'appât : Les laizes de petits pélagiques locaux (pêche-cavale et bancloche) se révèlent les plus efficaces et les plus sélectives vis-à-vis des espèces commerciales. Cette étude fournit des indicateurs utiles à la gestion des stocks démersaux jusqu'ici peu étudiés et peu encadrés. Mais la grande inconnue reste l'effort de pêche total sur cette ressource et notamment celui des pêcheurs plaisanciers.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00098/20902/18837.pdf
DOI:10.13155/20902
http://archimer.ifremer.fr/doc/00098/20902/

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 BioMed Central
Résumé : [b]Background[/b][br/] [br/] The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources.[br/] [br/] [b]Results[/b][br/] [br/] In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.[br/] [br/] [b]Conclusion[/b][br/] [br/] The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.
ISSN: 1471-2164

hal-01032439
https://hal.archives-ouvertes.fr/hal-01032439
https://hal.archives-ouvertes.fr/hal-01032439/document
https://hal.archives-ouvertes.fr/hal-01032439/file/art_10-1186_1471-2164-15-238.pdf
DOI : 10.1186/1471-2164-15-238

Éditeur(s) : HAL CCSD Elsevier
Résumé : Eperua falcata (Aublet), a late-successional species in tropical rainforest and one of the most abundant tree in French Guiana, has developed an original strategy concerning N-acquisition by largely preferring nitrate, rather than ammonium (H. Schimann, S. Ponton, S. Hattenschwiler, B. Ferry, R. Lensi, A.M. Domenach, J.C. Roggy, Differing nitrogen use strategies of two tropical rainforest tree species in French Guiana: evidence from N-15 natural abundance and microbial activities, Soil Biol, Biochem. 40 (2008) 487-494). Given the preference of this species for nitrate, we hypothesized that root exudates would promote nitrate availability by (a) enhancing nitrate production by stimulating ammonium oxidation or (b) minimizing nitrate losses by inhibiting denitrification. Root exudates were collected in situ in monospecific planted plots. The phytochemical analysis of these exudates and of several of their corresponding root extracts was achieved using UHPLC/DAD/ESI-QTOF and allowed the identification of diverse secondary metabolites belonging to the flavonoid family. Our results show that (i) the distinct exudation patterns observed are related to distinct root morphologies, and this was associated with a shift in the root flavonoid content, (ii) a root extract representative of the diverse compounds detected in roots showed a significant and selective metabolic inhibition of isolated denitrifiers in vitro, and (iii) in soil plots the abundance of nirK-type denitrifiers was negatively affected in rhizosphere soil compared to bulk. Altogether this led us to formulate hypothesis concerning the ecological role of the identified compounds in relation to N-acquisition strategy of this species. (C) 2013 Elsevier Masson SAS. All rights reserved.
ISSN: 0981-9428

hal-01032437
https://hal.archives-ouvertes.fr/hal-01032437
DOI : 10.1016/j.plaphy.2013.05.003

Éditeur(s) : Europe Aqauculture Symposium, October 14-17, San Sebastian, Spain
Résumé : Shrimp farming in New-Caledonia faces up to difficulties. A fluctuating quality of broodstock prevents sustainable production of larvae in quantity and quality. The traditional extensive rearing method of broodstock in outdoor earthen ponds used in New Caledonia raises several issues: poor water quality control and biosecurity. Therefore it is fundamental to modify the broodstock culture strategy in order to achieve an easier water quality management and maximal biosecurity. Biofloc technology (BFT) offers easier water quality management, higher natural productivity, higher level of biosecurity, and could be a good alternative. Since 2011 a R&D program started under the supervision of IFREMER in New Caledonia and French Polynesia in order to study and develop biofloc technology for rearing shrimp L. stylirostris broodstock. In a first step we showed that biofloc (BFT) improved significantly the reproductive performances of shrimps and the quality of their larvae compared to Clear Water (CW) or Earthen Pond (EP), with: • A better final survival rate of broodstock from BFT compare to CW. • Females from BFT produced more eggs per spawn and spawned more frequently compared to females from CW or EP. • The larvae from BFT females had a significantly higher survival rate compared to larvae from CW females, respectively 70% (n=4) and 45% (n=4). In a second step we studied the underlying biological mechanisms explaining the better reproductive performance and health status of the broodstock from BFT rearing system, and the better quality of their larvae. We showed that the juvenile shrimp fed actively on biofloc, which represented 60% of their whole food (40% coming from pelleted diet). Biofloc represents a significant source of essential nutrients (vitamins, antioxidants, highly unsaturated fatty acids, …) or dietary bacteria which could act as probiotic. These dietary complements could explain the improved health status (immunity and oxidative status status), the better resistance to oxidative stress and a systematically better survival rate of the shrimp reared in BFT compared to those reared in CW.

Droits : 2014 Ifremer
http://archimer.ifremer.fr/doc/00250/36084/34635.pdf
http://archimer.ifremer.fr/doc/00250/36084/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Roussillon sedimentary Basin (South France) is a complex multi-layered aquifer, close to the Mediterranean Sea facing seasonally increases of water abstraction and salinization issues. We report geochemical and isotopic vertical variability in this aquifer using groundwater sampled with a Westbay System® at two coastal monitoring sites: Barcarès and Canet. The Westbay sampling allows pointing out and explaining the variation of water quality along vertical profiles, both in productive layers and in the less permeable ones where most of the chemical processes are susceptible to take place.The aquifer layers are not equally impacted by salinization, with electrical conductivity ranging from 460 to 43,000 μS·cm− 1. The δ2H–δ18O signatures show mixing between seawater and freshwater components with long water residence time as evidenced by the lack of contribution from modern water using 3H, 14C and CFCs/SF6. S(SO4) isotopes also evidence seawater contribution but some signatures can be related to oxidation of pyrite and/or organically bounded S. In the upper layers 87Sr/86Sr ratios are close to that of seawater and then increase with depth, reflecting water–rock interaction with argillaceous formations while punctual low values reflect interaction with carbonate. Boron isotopes highlight secondary processes such as adsorption/desorption onto clays in addition to mixings. At the Barcarès site (120 m deep), the high salinity in some layers appear to be related neither to present day seawater intrusion, nor to Salses-Leucate lagoonwater intrusion. Groundwater chemical composition thus highlights binary mixing between fresh groundwater and inherited salty water together with cation exchange processes, water–rock interactions and, locally, sedimentary organic matter mineralisation probably enhanced by pyrite oxidation.Finally, combining the results of this study and those of Caballero and Ladouche (2015), we discuss the possible future evolution of this aquifer system under global change, as well as the potential management strategies needed to preserve quantitatively and qualitatively this water resource.
ISSN: 0048-9697

hal-01685219
https://hal-brgm.archives-ouvertes.fr/hal-01685219
DOI : 10.1016/j.scitotenv.2016.05.016