Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Despite a relatively 'uniform' fertile composition (Al2O3 = 2 center dot 19-4 center dot 47 wt %; Fo% = 89 center dot 2 +/- 0 center dot 3%; Cr#(Spl) = 8 center dot 9 +/- 1 center dot 5%), the Montferrier peridotite xenoliths show a wide range of S contents (22-590 ppm). Most sulphides are interstitial and show peculiar pyrrhotite-pentlandite intergrowths and low abundances of Cu-rich phases. Sulphide-rich samples are characterized by strong enrichment in the light rare earth elements and large ion lithophile elements without concomitant enrichment of the high field strength elements. Such trace-element fractionation is commonly ascribed to metasomatism by volatile-rich melts and/or carbonatitic melts. S and Se (11-67 ppb), as well as S/Se (up to approximate to 12 000), are correlated with La/Sm. Cu, however, remains broadly constant (30 +/- 5 ppm). These features strongly suggest that the percolation-reaction of such volatile-rich fluids has led to sulphide enrichment with an atypical signature marked by strong fractionation of the chalcophile elements (i.e. S vs Se and Cu). S-rich xenoliths are also characterized by high (Pd/Ir)(N) (1 center dot 2-1 center dot 9; where subscript N indicates normalized to chondrite), (Pd/Pt)(N) between 1 center dot 5 and 2 center dot 2, and (Os/Ir)(N) up to 1 center dot 85. Despite the relative uniform fertile composition of the xenoliths, Re/Os ranges between 0 center dot 02 and 0 center dot 18. Os-187/Os-188 is extremely variable even within a single sample and can be as high as 0 center dot 1756 for the most S-rich samples. Sulphides show highly fractionated and variable abundances of the highly siderophile elements (HSE) [0 center dot 03 (Pd/Ir)(N) < 1283] and Re-Os isotopic composition (0 center dot 115 < Os-187/Os-188 < 0 center dot 172). Such variation can be observed at the thin-section scale. Whole-rock and in situ sulphide data demonstrate that chalcophile and HSE systematics and the Os isotopic composition of the upper mantle could be significantly modified through metasomatism, even with volatile-rich fluids. These features highlight the complex behaviour of the HSE in fluid-rock percolation-reaction models and suggest a complex interplay between sulphide addition (crystallization or sulphidation) and partial equilibration of pre-existing sulphide. The specific fractionations observed in chemical proxies such as S and Se, Os and Ir, and Pd and Pt, as well as the low abundance of Cu-rich sulphides, suggest that sulphide addition may not have occurred via sulphide melts. Rather, we infer that S was present as a dissolved species in a (supercritical) oxidizing, volatile-rich fluid (C-O-H-S +/- Cl) along with other chalcophile and siderophile elements such as Os, Pd, Re and Au. The highly radiogenic Os composition of this fluid ( Os-187/ Os-188 > 0 center dot 17) would imply that such fluids are derived from an uncommon type of mantle source possibly related to carbonatite melts.
ISSN: 0022-3530

hal-00644524
https://hal.archives-ouvertes.fr/hal-00644524
DOI : 10.1093/petrology/egr038

Éditeur(s) : HAL CCSD
Résumé : données, méthodes disponibles auprès de l'auteur
In tropical forest communities, interspecific competition and recruitment limitation by dispersal are two general mecanisms of tree species coexistence. Their role in regeneration remains poorly known, even though it is essential to understand them to better adress the gestion of exploited forests. In this work, environemental conditions and intraspecific relations were taken into account in the analysis of juvenile distribution. Fifteen species were retained according to a gradient of shade-tolerance and various seed dispersal modes. Statistical modelling of local density was used to link the success of installation with environnemental conditions and distances to adults simultaneously. Model prediction evidenced the gradient of shade-tolerance among studied species and revealed different installation curves related to dispersal modes.
Dans les communautés de forêt tropicale humide, la compétition interspécifique et la limitation du recrutement par la dispersion ont généralement invoquées pour expliquer la coexistence de nombreuses espèces d'arbres. Le rôle de ces mécanismes dans la régénération reste peu connu, bien que leur compréhension soit essentielle pour la gestion des forêts exploitées. Dans ce travail, les conditions du milieu et les relations intraspécifiques ont été prises en compte dans l'analyse des distributions de juvéniles. Quinze espèces non pionnières ont été sélectionnées selon un gradient de tolérance à l'ombre et des modes de dispersion variés. La modélisation statistique de la densité locale a permis de relier le succès d'installation des juvéniles aux conditions du milieu et aux distances aux arbres adultes simultanément. Les prédictions des
modèles confirment le gradient de tolérance parmi les espèces étudiées et révèlent des courbes d'installation différentes selon le mode de dispersion.
https://tel.archives-ouvertes.fr/tel-00297707

tel-00297707
https://tel.archives-ouvertes.fr/tel-00297707
https://tel.archives-ouvertes.fr/tel-00297707/document
https://tel.archives-ouvertes.fr/tel-00297707/file/PhD_regeneration_Olivier_Flores.pdf

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and in silico approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp Rimicaris exoculata that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species-or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a ``domino days spreading'' branching process in which successive amplifications may interact positively.
ISSN: 1932-6203

hal-01544761
https://hal.archives-ouvertes.fr/hal-01544761
DOI : 10.1371/journal.pone.0057675

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Le Bénin, pays de l’Afrique de l’Ouest est confronté à la destruction des terres humides particulièrement dans la partie sud du pays. Les terres humides riches biodiversité sont importantes tant pour les humains que pour milieu naturel. La menace la plus importante est la pression de l’anthropique. Même si ce territoire est reconnu par la Convention Ramsar, la destruction continue. En 1995 le gouvernement a décidé de créer une aire de gestion communautaire pour ces territoires. L’objectif de cette recherche est de comprendre les grands défis liés à la mise en œuvre de la gestion communautaire des milieux humides à travers une étude de cas, en l’occurrence celui de la vallée du Sitatunga. Pour atteindre cet objectif, un séjour de 3 mois a été effectué sur le site. Des entrevues semi-dirigées ont été alors réalisées. Les résultats montrent que la vallée du Sitatunga est considérée comme inutile, voire nuisible, par les populations riveraines rencontrées dans le cadre de l’étude, qui sont davantage préoccupées à se sortir de leur état de pauvreté. Les traditions et valeurs autrefois attribuées à la conservation des milieux humides ont quasiment disparu et l’individualisme est grandissant. Il importe de tenir compte de tous ces facteurs pour espérer véritablement préserver ces milieux. D’un autre côté, parlant de gestion de l’environnement et plus particulièrement de gestion des milieux humides à l’échelle béninoise, le constat n’est pas reluisant. En effet, l’État étant donné son état de sous-développement et donc de manque de ressources, à du mal à coordonner ces activités. Il est de même pour les ONG. La situation est accentuée par l’état des relations entre ONG et structures de l’État qui se considèrent davantage comme des adversaires que comme des partenaires ce qui affecte l’efficacité des activités menées. Pour que la gestion communautaire devienne une réalité, il importe qu’un partenariat soit établi entre les différents acteurs liés à la gestion de la vallée du Sitatunga en particulier et des milieux humides en général : les ONG, l’État et les communautés locales.
Bénin, a country in West Africa is actually facing the destruction of its wetlands, especially those in the southern part of the country. The wetlands which their richness in natural resources are important for both human and wildlife are also threatened by many factors. The most important threat is population pressure. Although recognised as Ramsar sites, the destruction continues. In 1995, the Government has decided to create community protected areas in this part of the country. The objective of this research is to understand the main challenges around the community management of wetlands. The case of the Sitatunga valley, in south Bénin has been studied. The methodology used consisted on interviews with stakeholders during a period of 3 months. The results show that, although the good intentions of community management, its practical application is not easy, and reveal many difficulties in its practical application. The site although rich in biodiversity and used as refuge for several species, is regarded as useless even harmful by the bordering populations, which are more worried by their poverty state. The traditions and values formerly allotted to the wetlands almost disappeared and individualism is growing. It is important to take into account all these factors to truly hope to preserve these wetlands. The study shows that management of the wetlands on a Beninese scale is also difficult. Indeed, the government through its structures struggles to coordinate its activities. It is the same for NGOs. The situation is accentuated by the poor relations between NGOs and government institutions which consider each other more as adversaries than as partners. This affects the effectiveness of the undertaken activities. It is then important for all the stakeholders (NGOs, Government and local communities) to install a partnership to help achieve community management objectives.
Bénin

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.3630
http://journals.openedition.org/etudescaribeennes/3630

Éditeur(s) : HAL CCSD Tecpar
Résumé : International audience
The general structure and organization of the shallow water (<1.5 m) fish assemblages were studied in two southern Brazilian ecosystems, a bay and a lagoon, under different marine or continental influences. The abiotic factors were measured to define the hydrology of the sites and the biotic descriptors were evaluated to characterize the assemblage structures. Transparency, salinity and organic matter were the abiotic factors which best distinguished the sites. A total richness of 69 species was observed. Ecological guilds, density, diversity and evenness indices values were different in each site. Hydrodynamism and geomorphology determined the structure and the organization of the fish assemblages in these shallow waters. It was observed that variations in the hydrological attributes generated by the marine or continental water movements are able to alter the conditions in the lagoon more quickly and at more regular frequencies than those in the bay.
ISSN: 1516-8913

hal-00753018
https://hal.univ-antilles.fr/hal-00753018
https://hal.univ-antilles.fr/hal-00753018/document
https://hal.univ-antilles.fr/hal-00753018/file/BRAZILIAN_2010.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Ecological signs of Earth's biosphere forewarn an alarming trajectory towards a global mass-extinction. Assessing species performance and susceptibilities to decline is essential to comprehend and reverse this trend. Yet it is challenging, given difficulties associated with quantifying individual and population processes that are variable across time, space, and life-stages. We describe a new approach to estimating and comparing species performances that combines empirical data, a novel theoretical consideration of population dynamics, and modern statistics. Our approach allows for a more realistic continuous representation of individual performances along development stages while taking into account non-linearity, and natural variability as captured by spatio-temporally replicated observations. We illustrate its application in a coral meta-assemblage composed of populations of the three major reef-building taxa Acropora, Pocillopora, Porites. Using a unique set of highly replicated observations of individual coral dynamics under various environmental conditions, we show how taxa differ in their investment in recruitment and size-specific aptitude for growth and survival, notably through different use of clonal shrinkage, fragmentation, fission, and fusion processes. Our results reveal contrasting life-history trade-offs among taxa which, along with differing patterns of density-dependent recruitment, modulate species responses to decline. These differences in coral life history traits reflect opposing life-strategies, imply regulation at differing life-stages, and explain divergence in species trajectories. Our findings indicate a high potential for resilience in Pocillopora and Porites populations, thanks respectively to a sustained recruitment that promotes demographic elasticity through replacement of individuals, and a steady resistance to mortality which confers persistence through lingering of individuals. Resilience in Acropora appears more arbitrary, given high susceptibility to perturbations and dependency of recruitment on presence of established local populations. We identify management actions that can complement Acropora's life history and benefit recovery of its populations following mortality events. Our regression-modelling approach to quantifying and comparing species performances in different population processes is applicable to all taxa, as illustrated even those with complex clonal life histories, and can be implemented at wide spatio-temporal and taxonomic coverage. It can promote more accurate representation of species dynamics in both descriptive and predictive modelling approaches. The semi-parametric contrast curve method we develop facilitates comparing response variables along continuous explicative metrics while accounting for multiple sources of complexity in empirical data. It should widely benefit investigations in ecology and quantitative science.
ISSN: 1476-945X

hal-01212337
https://hal-univ-perp.archives-ouvertes.fr/hal-01212337
DOI : 10.1016/j.ecocom.2015.07.003

Éditeur(s) : ISTPM
Résumé : The Atlantic and Mediterranean members of the scorpaenidae family have always triggered numerous discussions about their reciprocious congenialities. Back in the (recent) days when the number of species known on the French coasts was still fairly low, the belonging of one species to such or such genus, as Helicolenus (Sebastes) dactylopterus DELAROCHE or Scorpaena maderensis Cuvier and Valenciennes, has been the subject of numerous articles of which the authors' conclusions might differ from one another, and even today light is still far from being shed on those topics. The difficulties met in the determination of scorpaenidae: similar general appearance, subtle differences, impossibility of comparing the samples with the types, incomplete or misinterpreted descriptions, have lead scientists to make hasty determinations resulting in: an even more complicated synonymy and incorrect data about the biogeography of the species. Thereby, the rockfish named Scorpaena rubellio by JORDAN and GUNN (I) is considered as a synonymous of S. maderensis Cuvier Valenciennes by J. R. NORMAN (2), and of S. porcus Linné by H. W. FOWLER (3). Likewise, the dispersion area of S. scrofa in Guinea, Niger and Sainte-Hélène, is caused by its confusion with other species such as S. stephanica, S. angolensis and S. scrofina. (unverified OCR)
Les représentants de la famille des Scorpénidés dans l'Atlantique et la Méditerranée ont toujours donné lieu à de nombreuses discussions au sujet de leurs affinités réciproques. A l'époque encore récente où le nombre des espèces connues des côtes de France était encore très réduit, la place dans tel ou tel genre d'espèces telles que Helicolenus (Sebastes) dactylopterus DELAROCHE ou Scorpaena maderensis Cuvier et Valenciennes, par exemple, ont provoqué des séries d'articles où les conclusions des auteurs successifs n'étaient pas toujours concordantes, et aujourd'hui encore la lumière est loin d'être faite sur bien des points. Les difficultés que l'on rencontre dans la détermination des Scorpénidés : grande ressemblance générale, différences parfois difficiles à saisir, impossibilité de comparer les échantillons d'étude aux types, obligation de se contenter de descriptions incomplètes .ou mal interprétées, ont trop souvent entraîné les chercheurs à des déterminations trop hâtives ayant comme résultats : de compliquer la synonymie et de fausser plus ou moins complètement les données acquises sur la biogéographie d'une espèce. C'est ainsi que la Scorpène appelée Scorpaena rubellio par JORDAN et GUNN (Il est considérée comme synonyme de S. maderensis Cuvier Valenciennes par J. R. NORMAN (2), et de S. porcus Linné par H. W. FOWLER (3). De même l'extension de l'aire de dispersion de S. scrofa en Guinée, au Niger et à Sainte-Hélène, est due à des confusions avec des espèces différentes telles que S. stephanica, S. angolensis et S. scrofina. (OCR non contrôlé)
Revue des Travaux de l'Institut des Pêches Maritimes (0035-2276) (ISTPM), 1943 , Vol. 13 , N. 1-4

Droits : Ifremer
http://archimer.ifremer.fr/doc/1943/publication-3420.pdf
http://archimer.ifremer.fr/doc/00000/3420/

Éditeur(s) : Elsevier
Résumé : In the Caribbean, snappers (Lutjanidae) and groupers (Serranidae) are often heavily exploited by artisanal or industrial fisheries. This paper analyzes the catches of an artisanal fishery selectively targeting these species with a moderate fishing pressure in the Bay Islands (Honduras), and discusses the implications on the understanding of the early stages of development of reef fisheries. Although snappers and groupers are targeted with handlines and spearguns in the whole archipelago, the differences in species diversity and size structure of the catch reveals various exploitation patterns. In most areas, a depletion is observed for the most vulnerable snapper and grouper species, and most other species are mainly exploited in their juvenile phase; clear signs of an intensification process are apparent in one of the areas. The comparison of the relative production in the Bay Islands with other reef fisheries in the Caribbean suggests that higher values may be related to moderate fishing pressure and appropriate combinations of fishing effort and selectivity. This example shows how fisheries strictly targeting a high quality resource with selective fishing techniques can be quite productive even at high levels of effort, but also that they are progressively lead to broaden their species range (sooner or later at the expense of the most vulnerable, often large-sized, species) while increasingly using less selective gears.
Fisheries Research (0165-7836) (Elsevier), 2005-06 , Vol. 73 , N. 1-2 , P. 159-169

Droits : 2004 Elsevier B.V. All rights reserved
http://archimer.ifremer.fr/doc/2005/publication-512.pdf
DOI:10.1016/j.fishres.2004.12.008
http://archimer.ifremer.fr/doc/00000/512/

Éditeur(s) : HAL CCSD
Résumé :   Diffusion du document : INRA Antilles-Guyane, UMR ECOFOG, 97387 Kourou, Guyane (France) Diplôme : Master Recherche
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
The gravitropic reaction is a fundamental phenomenon in the life of the young trees in under-storey of a tropical rain forest. It enables them to preserve a growth in height even after a fall of remains or a wind fallen wood had leaning them. This reaction passes mainly by the differentiation of reaction wood and the offsetting of the radial growth. The gravitropic reaction is also under the control of various parameters such as the diameter of the stems, the hardness of wood, or masses they carried. The tropical rain forest contains a great specific diversity and ecological strategies. In this work we seek to know if this diversity is reflected in the strategies of recovery of the species in particular on a level of efficiency of reaction. We compared eight species of tropical rain forest with various ecological behaviours. We studied their changes in form in the course of time, as to their growth. We showed that there are indeed interspecific differences in the gravitropic reaction. Some behaviours are specific to some species. We also showed that for the majority of the species, the deformation energy is strongly correlated with the relative growth of the species.
Le redressement gravitropique est un phénomène fondamental dans la vie des jeunes arbres en sous-bois de forêt tropicale. Il leur permet de conserver une croissance en hauteur même après avoir subi la chute de débris ou même un chablis ayant conduit à leur inclinaison. Ce redressement passe principalement par la différentiation de bois de réaction et l’excentrement de la croissance radiale. Le redressement gravitropique est également sous le contrôle de différents paramètres tels que le diamètre des tiges, la dureté du bois, ou les masse portées. La forêt tropicale humide contient une grande diversité spécifique et de stratégies écologiques. Dans ce travail nous cherchons à savoir si cette diversité se reflète dans les stratégies de redressement des espèces notamment au niveau de l’efficience de la réaction. Nous avons comparé huit espèces de forêt tropicale humide avec différents comportements écologiques. Nous avons étudié leurs changements de forme au cours du temps, ainsi que leur croissance. Nous avons réussi à montrer qu’il existe effectivement des différences interspécifiques de redressement. Des comportements particuliers à certaines espèces ont pu être dégagés. Nous avons également montré que pour la majorité des espèces, l’énergie de déformation est fortement corrélée à la croissance relative de l’espèce.
https://hal.archives-ouvertes.fr/hal-01189172

hal-01189172
https://hal.archives-ouvertes.fr/hal-01189172
PRODINRA : 11396

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Reliable assessment of fish origin is of critical importance for exploited species, since nursery areas must be identified and protected to maintain recruitment to the adult stock. During the last two decades, otolith chemical signatures (or "fingerprints") have been increasingly used as tools to discriminate between coastal habitats. However, correct assessment of fish origin from otolith fingerprints depends on various environmental and methodological parameters, including the choice of the statistical method used to assign fish to unknown origin. Among the available methods of classification, Linear Discriminant Analysis (LDA) is the most frequently used, although it assumes data are multivariate normal with homogeneous within-group dispersions, conditions that are not always met by otolith chemical data, even after transformation. Other less constrained classification methods are available, but there is a current lack of comparative analysis in applications to otolith microchemistry. Here, we assessed stock identification accuracy for four classification methods (LDA, Quadratic Discriminant Analysis [QDA], Random Forests [RF], and Artificial Neural Networks [ANN]), through the use of three distinct data sets. In each case, all possible combinations of chemical elements were examined to identify the elements to be used for optimal accuracy in fish assignment to their actual origin. Our study shows that accuracy differs according to the model and the number of elements considered. Best combinations did not include all the elements measured, and it was not possible to define an ad hoc multielement combination for accurate site discrimination. Among all the models tested, RF and ANN performed best, especially for complex data sets (e. g., with numerous fish species and/or chemical elements involved). However, for these data, RF was less time-consuming and more interpretable than ANN, and far more efficient and less demanding in terms of assumptions than LDA or QDA. Therefore, when LDA and QDA assumptions cannot be reached, the use of machine learning methods, such as RF, should be preferred for stock assessment and nursery identification based on otolith microchemistry, especially when data set include multispecific otolith signatures and/or many chemical elements.
ISSN: 1051-0761

hal-00644549
https://hal.archives-ouvertes.fr/hal-00644549
DOI : 10.1890/09-1887.1

Éditeur(s) : Academic Press Inc Elsevier Science
Résumé : Several Vibrio species are known to be pathogenic to the Pacific oyster Crassostrea gigas. Survival varies according to pathogen exposure and high mortality events usually occur in summer during gametogenesis. In order to study the effects of gametogenetic status and ploidy (a factor known to affect reproduction allocation in oysters) on vibriosis survival, we conducted two successive experiments. Our results demonstrate that a common bath challenge with pathogenic Vibrio splendidus and Vibrio aestuarianus on a mixture of mature, spawning and non-mature oysters can lead to significant mortality. Previous bath challenges, which were done using only non-mature oysters, had not produced mortality. Immunohisto-chemical analyses showed the affinity of Vibrio for gonadic tissues, highlighting the importance of sexual maturity for vibriosis infection processes in oysters. Mortality rate results showed poor repeatability between tanks, however, in this bath challenge. We then tested a standardized and repeatable injection protocol using two different doses of the same combination of two Vibrio species on related diploid and triploid oysters at four different times over a year. Statistical analyses of mortality kinetics over a 6-day period after injection revealed that active gametogenesis periods correspond to higher susceptibility to vibriosis and that there is a significant interaction of this seasonal effect with ploidy. However, no significant advantage of triploidy was observed. Triploid oysters even showed lower survival than diploid counterparts in winter. Results are discussed in relation to differing energy allocation patterns between diploid and triploid Pacific oysters. (C) 2010 Elsevier Inc. All rights reserved.
Journal Of Invertebrate Pathology (0022-2011) (Academic Press Inc Elsevier Science), 2011-02 , Vol. 106 , N. 2 , P. 179-191

Droits : 2010 Elsevier Inc. All rights reserved.
http://archimer.ifremer.fr/doc/00030/14108/11368.pdf
DOI:10.1016/j.jip.2010.09.003
http://archimer.ifremer.fr/doc/00030/14108/

Éditeur(s) : HAL CCSD
Résumé : International audience
The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification.Here, we introduce an original multi-access electronic key for the identification of 389 tree genera occurring in French Guiana terra-firme forests, based on a set of 79 morphological characters related to vegetative, floral and fruit characters. Its purpose is to help Amazonian tree identification and to support the dissemination of botanical knowledge to non-specialists, including forest workers, students and researchers from other scientific disciplines.The electronic key is accessible with the free access software Xper², and the database is publicly available on figshare: https://figshare.com/s/75d890b7d707e0ffc9bf
ISSN: 1314-2011

hal-01392306
https://hal-sde.archives-ouvertes.fr/hal-01392306
DOI : 10.3897/phytokeys.68.8707

Résumé : Selective breeding of shrimp for viral resistance is established for species like L. vannamei and L. stylirostris. However, selection for bacterial infection resistance is not documented. In New Caledonia, "Syndrome 93" is a vibriosis that affects cultured shrimps during the cool season with survival from 15 to 30%. Current practises for breeders rearing at low densities do not improve the resistance of the offsprings mainly because selection pressures for "Syndrome 93" are low. Even after the fifth generation, survival improvement is not significant.
La sélection génétique de lignées de crevettes résistantes à certains virus a démontré son efficacité en particulier chez L. vannamei et L. stylirostris. En revanche, la sélection de crevettes résistantes à une bactérie du genre Vibrio est peu documentée. En Nouvelle-Calédonie, le « Syndrome 93 », vibriose à V. penaeicida, affecte toutes les fermes de crevettes L. stylirostris lors des élevages de saison fraîche. Les survies en bassins de grossissement, de l’ordre de 40 à 60% dans un élevage sain, tombent à des valeurs de 15 à 30%. L’élevage de géniteurs à faible densité, s’il maximise les performances de reproduction, ne semble pas optimiser la qualité de la descendance du fait des faibles pressions de sélection qui s’exercent vis-à-vis du syndrome 93. Les améliorations significatives du nombre d’animaux survivant aux infections et aux épisodes de mortalité en bassin restent faibles en valeur absolue à la 5ème génération de sélection expérimentale en conditions d’élevage, mais sur le long terme la stratégie testée pourrait se révéler économiquement efficace.

Droits : 2005 Ifremer
http://archimer.ifremer.fr/doc/00117/22848/20658.pdf
http://archimer.ifremer.fr/doc/00117/22848/

Éditeur(s) : Pêche thonière et dispositifs de concentration de poissons, Caribbean-Martinique, 15-19 Oct 1999
Résumé : The original baitboat fishing technique using a permanent association between the fishing boat and the tuna school has been developed by the baitboat fleet of Dakar, Senegal and is also in use in the Canary Islands. This new fishing technique, the result of 20 years of improvements still on, has induced a dramatic increase of the catch yields which, in turn, has sustained the survival and even a recent development of the fleet. This technique is based on the aggregating behaviour of tropical tunas. However, it contains a dynamic component which is not found in tuna fishing on drifting or anchored fads. The specifications of the method, its refinement over the years and its main consequences for the fishery are described together with the school exchanges between baitboats over months even from one year to the next. Based on the analysis of 1228 recoveries from 5500 tagged fish, tuna movements among associated schools, between associated schools and free schools fished by purse seiners and movements in and out of the baitboat fishing grounds help to better understand the dynamics of tunas and schools of this peculiar tuna association. These data show a very high recovery rate, a remarkable tuna fidelity to the original school for all species, a small number of recoveries within the purse seine catch as well as the rare tuna movements outside the baitboat area. The study highlights the complexity and the numerous consequences of tuna and school behaviour.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00042/15304/12637.pdf
http://archimer.ifremer.fr/doc/00042/15304/

Éditeur(s) : Public Library Science
Résumé : Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and in silico approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp Rimicaris exoculata that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species-or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a "domino days spreading'' branching process in which successive amplifications may interact positively.
Plos One (1932-6203) (Public Library Science), 2013-03 , Vol. 8 , N. 3 , P. e57675

Droits : This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
http://archimer.ifremer.fr/doc/00185/29656/28030.pdf
DOI:10.1371/journal.pone.0057675
http://archimer.ifremer.fr/doc/00185/29656/

Éditeur(s) : Inter-Research
Résumé : Situated in the north of the Mozambique Channel, Mayotte is the easternmost island of the Comoros Archipelago. From 1998 to 2005, Grande Saziley beach was monitored daily for green turtle Chelonia mydas nesting activity. Track surveys were monitored daily on 5 other adjacent beaches. Although nesting occurs throughout the year, nesting seasonality begins at the end of the wet season and intensifies during the dry season to reach an average nesting peak in June. In order to estimate the number of females nesting in the Saziley site and population trends over the study period, incubation success and number of nests per female and per season were estimated at 0.77 (±0.05 SD) and 3.03 (±0.37) respectively. With an average of 1545 nesting turtles per year (±439), the change in nesting numbers over the study period was so small that the population can be regarded as stable, with an estimated annual mean growth rate of 0.912, confirmation that this population is both stable and in good health. Added support for this argument is demonstrated by the fact that the annual carapace size distribution of nesting females is stable, meaning that the nesting green turtle population of Mayotte is not ageing or rejuvenating. After due consideration of data on other nesting sites in the southwest Indian Ocean, the data from Mayotte emphasizes the fact that the green turtle is not an endangered species in this region. Even if it is still illegally exploited and alterations occur in their different habitats, the green turtle populations of this region seem to have successfully survived all threats during the past century.
Endangered Species Research (1613-4796) (Inter-Research), 2007-10-10 , Vol. 3 , P. 273-282

Droits : 2007 Inter-Research
http://archimer.ifremer.fr/doc/00018/12916/9873.pdf
DOI:10.3354/esr00053
http://archimer.ifremer.fr/doc/00018/12916/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Myrmecophytes offer plant-ants a nesting place in exchange for protection from their enemies, particularly defoliators. These obligate ant-plant mutualisms are common model systems for studying factors that allow horizontally transmitted mutualisms to persist since parasites of ant-myrmecophyte mutualisms exploit the rewards provided by host plants whilst providing no protection in return. In pioneer formations in French Guiana, Azteca alfari and Azteca ovaticeps are known to be mutualists of myrmecophytic Cecropia (Cecropia ants). Here, we show that Azteca andreae, whose colonies build carton nests on myrmecophytic Cecropia, is not a parasite of Azteca-Cecropia mutualisms nor is it a temporary social parasite of A. alfari; it is, however, a temporary social parasite of A. ovaticeps. Contrarily to the two mutualistic Azteca species that are only occasional predators feeding mostly on hemipteran honeydew and food bodies provided by the host trees, A. andreae workers, which also attend hemipterans, do not exploit the food bodies. Rather, they employ an effective hunting technique where the leaf margins are fringed with ambushing workers, waiting for insects to alight. As a result, the host trees' fitness is not affected as A. andreae colonies protect their foliage better than do mutualistic Azteca species resulting in greater fruit production. Yet, contrarily to mutualistic Azteca, when host tree development does not keep pace with colony growth, A. andreae workers forage on surrounding plants; the colonies can even move to a non-Cecropia tree.
ISSN: 0028-1042

hal-00818203
https://hal.archives-ouvertes.fr/hal-00818203
DOI : 10.1007/s00114-010-0710-y
PUBMED : 20730522

Éditeur(s) : Ecole Nationale Supérieure Agronomique de Rennes
Résumé : Long-line fishing has been growing on the island of La Réunion since the beginning of the 1990s. The target species is the swordfish (Xiphias gladius), fished mainly in the tropical waters surrounding the island between longitudes 45 degree E and 60 degree E, and latitudes 17 degree S and 27 degree S. From 1998 to 2000, a finalised research programme enabled the collection of precise data concerning the lines' positions and the parameters of the fishing efforts: 3,602 nettings were thus informed by the catches (in numbers of individuals caught) and 12 descriptive variables of the effort. In parallel with this collection effort, satellite maps that described the ocean's landscape of this region of the Indian Ocean exploited by La Réunion's fisheries were made available to sailors and scientists. Extractions from these environmental variables were made at the fishing lines' positions, which allowed us to propose 20 variables describing the environmental conditions of swordfish catches applied to the nettings. In an early part of this study, after a descriptive analysis and a first selection of the variables, we used several GAM (Generalised Additive Models) to model the respective effects of effort and environmental variables on the variability of swordfish catches. We thus highlighted the predominance of factors linked to fishermen (fishing effort) on oceanographic factors in the explanation of this variability. Following these results, a summary on the biology and ecology of the swordfish was proposed in order to draw up hypotheses on the characteristics of this species' population in the Indian Ocean. The aspects linked to the individual behaviour and movements of the population were particularly highlighted. In a latter part of this study and in order to complete the empirical approach by an exploratory constructivist approach, we proposed a modelling tool in order to simulate the possible movements of individuals within the oceanic landscape described by the available satellite maps. After reading in the literature about the various forms of modelling the movements of the large pelagics, we developed an original computer modelling architecture of the multi-agent type that made it possible to manipulate in a dynamic way the satellite maps (and derived products), the individual movements of "animats" whose behaviours were based on this environmental information, and agents that clarify the process of long-line fishing in a geographical way. The computer model that was implemented (MUFINS, for MUlti-Fish INdian ocean Simulator) was next used by calibrating the behaviour of the animats on the real data originally from the analysis of commercial catches proposed in the first part, using robust techniques based on fuzzy logic. The results of the simulations were compared, on the one hand, with the large-scale hypotheses of movement proposed in the first part, and, on the other hand, to swordfish catches both real and corrected for the effect of the fishing effort modelled by the GAM models. Even if the results of these simulations in this study do not allow for proposing convincing interpretations of the underlying processes, the MUFINS tool showed its ability to address questions associated with the swordfish's behaviour in the tropical oceanic landscape and to the effects of scale transfers between the individual level and the collective level. We now envisage its use in a more operational framework, as an interface for dialogue between fishermen and scientists with a goal of sustainable management of the resource.
La peche palangriere s'est developpee a l'ile de La Reunion depuis le debut des annees 1990. L'espece cible est l'espadon (Xiphias gladius), principalement exploite dans les eaux tropicales autour de l'ile entre les longitudes 45 degree E et 60 degree E, et les latitudes 17 degree S et 27 degree S. De 1998 a 2000, un programme de recherche finalisee a permis de collecter des informations precises concernant les positions des lignes et les parametres de l'effort de peche : 3602 filages sont ainsi renseignes par les captures (en nombre d'individus captures) et 12 variables descriptives de l'effort. En parallele de cet effort de collecte, des cartes satellitales ont pu etre mises a la disposition des marins et des scientifiques, decrivant le paysage oceanique de cette region de l'ocean Indien exploitee par la pecherie reunionnaise. Des extractions de ces variables environnementales ont ete effectuees aux positions des lignes de peche, nous permettant de proposer 20 variables descriptives des conditions environnementales de captures d'espadon appliquees aux filages. Dans une premiere partie de ce travail, apres une analyse descriptive et une premiere selection des variables, on a modelise par plusieurs modeles GAM (Generalized Additive Models) les effets respectifs des variables d'effort et des variables environnementales sur la variabilite des captures d'espadon. On a ainsi mis en evidence la predominance des facteurs lies aux pecheurs (effort de peche) sur les facteurs oceanographiques dans le caractere explicatif de cette variabilite. A la suite de ces resultats, une synthese sur la biologie et l'ecologie de l'espadon a ete proposee afin de degager des hypotheses sur les caracteristiques de la population de cette espece dans l'ocean Indien. Les aspects lies au comportement individuel et aux deplacements de la population ont ete particulierement mis en evidence. Dans une deuxieme partie de ce travail et afin de completer l'approche empirique par une approche constructiviste exploratoire, nous avons propose un outil de modelisation afin de simuler les deplacements possibles d'individus au sein du paysage oceanique decrit par les cartes satellitales disponibles. Apres avoir passe en revue dans la litterature les differentes formes de modelisation des deplacements des grands, pelagiques, nous avons developpe une architecture originale de modelisation informatique de type multi-agents permettant de manipuler de maniere dynamique les cartes satellitales (et les produits derives), les mouvements individuels < d'animats >, dont les comportements sont bases sur cette information environnementale, et des agents qui explicitent le processus de capture palangriere de maniere geographique. Le modele informatique ainsi implemente (MUFINS, pour MUlti-Fish INdian ocean Simulator) a ensuite ete utilise en calibrant les comportements des animats sur les donnees reelles issues de l'analyse des captures commerciales proposee en premiere partie, a partir de techniques robustes basee sur la logique floue. Les resultats des simulations ont ete confrontes d'une part aux hypotheses de deplacement a grande echelle proposees en premiere partie, et d'autre part aux captures d'espadon reelles et corrigees de l'effet de l'effort de peche modelise par les modeles GAM. Meme si les resultats de simulations presentes dans ce travail ne permettent pas de proposer d'interpretations convaincantes des processus sous-jacents, l'outil MUFINS a demontre son aptitude a aborder les questions liees au comportement de l'espadon dans le paysage oceanique tropical et aux effets des transferts d'echelle entre le niveau individuel et le niveau collectif. On envisage desormais son utilisation dans un cadre plus operationnel, comme interface de dialogue entre les pecheurs et les scientifiques a des fins de gestion durable de la ressource.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2005/these-2592.pdf
http://archimer.ifremer.fr/doc/00000/2592/

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Aims: A description of bacterial pathogens in shrimp ponds is necessary to understand their pathogenesis. Vibrio nigripulchritudo was shown to contain saprophytic and pathogenic strains among New Caledonian isolates. We established a method to map the development of V. nigripulchritudo in pond sediments at three different genetic levels: the species level, then at the pathogenic cluster level and finally at the plasmid level, present only in all highly pathogenic isolates. Methods and Results: PCR methods were applied to shrimp pond sediments both before and after a mortality outbreak. Using crude samples, the species V. nigripulchritudo is not detected at first (0/42 samples at day 56 post stocking) but appears frequently in the sediments after the mortality event (30/42 at day 107). The distribution of strains from the pathogenic cluster of V. nigripulchritudo also follows this pattern. In contrast, the pSFn1 virulence-associated plasmid was detected in one sample at day 56 and none at day 107. An enrichment method was developed to lower the detection limits of our assays. After enrichment, the species V. nigripulchritudo was detected in all samples at both dates. The number of samples positive for pSFn1 was 42/42 samples at day 56 and 29/42 at day 107. Conclusions: These results show that the sediments contain V. nigripulchritudo, notably pathogenic strains. Surprisingly, the virulence-associated plasmid pSFn1 found in all V. nigripulchritudo isolated from moribund shrimp appears less frequently in sediments, possibly being useless or even detrimental to its recipient bacteria in this environment. Significance and Impact of the Study: This study confirms the presence of pathogenic V. nigripulchritudo strains in shrimp pond sediment before a mortality outbreak complying with a previous hypothesis that sediments could be the infecting reservoir. After the outbreak, both total V. nigripulchritudo and pathogenic strains populations have largely increased, possibly contributing to the recurrent mortality observed in this shrimp vibriosis.
Journal Of Applied Microbiology (1364-5072) (Wiley-blackwell Publishing, Inc), 2010-06 , Vol. 108 , N. 6 , P. 2003-2011

Droits : 2010 The Society for Applied Microbiology - Wiley-Blackwell
http://archimer.ifremer.fr/doc/00004/11484/8177.pdf
DOI:10.1111/j.1365-2672.2009.04601.x
http://archimer.ifremer.fr/doc/00004/11484/

Éditeur(s) : HAL CCSD
Résumé : International audience
The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification.Here, we introduce an original multi-access electronic key for the identification of 389 tree genera occurring in French Guiana terra-firme forests, based on a set of 79 morphological characters related to vegetative, floral and fruit characters. Its purpose is to help Amazonian tree identification and to support the dissemination of botanical knowledge to non-specialists, including forest workers, students and researchers from other scientific disciplines.The electronic key is accessible with the free access software Xper², and the database is publicly available on figshare: https://figshare.com/s/75d890b7d707e0ffc9bf (doi: 10.6084/m9.figshare.2682550).
ISSN: 1314-2011

hal-01369143
https://hal-sde.archives-ouvertes.fr/hal-01369143
DOI : 10.3897/phytokeys.68.8707