Éditeur(s) : Elsevier Science Bv
Résumé : Academia and management agencies show a growing interest for ecosystem-based fishery management (EBFM). However, the way to operationalize this approach remains challenging. The present paper illustrates how the concepts of stochastic co-viability, which accounts for dynamic complexities, uncertainties, risk and sustainability constraints, can be useful for the implementation of EBFM. In the present case, this concept is used to identify fishing strategies that satisfy both ecological conservation and economic sustainability in a multi-species, multi-fleet context. Economic Viability Analysis (EVA) and the broader Co-Viability Analysis (CVA), are proposed to expand the usual Population Viability Analysis (PVA) and precautionary approach. An illustration is proposed, using data on the fisheries of Bay of Biscay (France) exploiting the stocks of nephrops and hake. Stochastic simulations show how CVA can guarantee both ecological (stock) and economic (profit) sustainability. Using 2008 as a baseline, the model is used to identify fishing efforts that ensure such co-viability. (C) 2012 Elsevier B.V. All rights reserved.
Ecological Economics (0921-8009) (Elsevier Science Bv), 2012-03 , Vol. 75 , P. 32-42

Droits : 2012 Elsevier Science Bv
http://archimer.ifremer.fr/doc/00074/18571/16153.pdf
DOI:10.1016/j.ecolecon.2012.01.005
http://archimer.ifremer.fr/doc/00074/18571/

Éditeur(s) : HAL CCSD EDP Sciences
Résumé : International audience
This study determined the movements of a Giant Grouper, Epinephelus lanceolatus, in which an acoustictag was surgically implanted and monitored by an array of six VR2W acoustic receiver units from August 2010 toJanuary 2013 in the remote, uninhabited Chesterfield Islands, Coral Sea (800 km West of New Caledonia). Our datarevealed a home reef area (residency rate of 44.9%) with an increased activity revealed by movements at dawn anddusk toward and between two adjacent reef passages, probably for foraging. The fish was absent from its residentreef between October and December 2010 and 2012, corresponding to the time known for spawning aggregationsof this species in New Caledonia. A skipped spawning seems to have occurred in 2011. We hope these data will becomplemented in the future by locating the spawning site or sites and thus provide adequate conservation measures.The Coral Sea links two World Heritage Sites, the Australian Great Barrier Reefs and the New Caledonian coral reefs.It would be fitting to create a Marine Protected Area for the Chesterfield Islands between these two major conservationareas of the sea.
ISSN: 0990-7440

hal-01238809
https://hal-univ-perp.archives-ouvertes.fr/hal-01238809
DOI : 10.1051/alr/2015006

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The separation of the germ line from the soma is a classic concept in animal biology, and depending on species is thought to involve fate determination either by maternally localized germ plasm (''preformation'' or ``maternal inheritance'') or by inductive signaling (classically termed ``epigenesis'' or ``zygotic induction''). The latter mechanism is generally considered to operate in non-bilaterian organisms such as cnidarians and sponges, in which germ cell fate is determined at adult stages from multipotent stem cells. We have found in the hydrozoan cnidarian Clytia hemisphaerica that the multipotent ``interstitial'' cells (i-cells) in larvae and adult medusae, from which germ cells derive, express a set of conserved germ cell markers: Vasa, Nanos1, Piwi and PL10. In situ hybridization analyses unexpectedly revealed maternal mRNAs for all these genes highly concentrated in a germ plasm-like region at the egg animal pole and inherited by the i-cell lineage, strongly suggesting i-cell fate determination by inheritance of animal-localized factors. On the other hand, experimental tests showed that i-cells can form by epigenetic mechanisms in Clytia, since larvae derived from both animal and vegetal blastomeres separated during cleavage stages developed equivalent i-cell populations. Thus Clytia embryos appear to have maternal germ plasm inherited by i-cells but also the potential to form these cells by zygotic induction. Reassessment of available data indicates that maternally localized germ plasm molecular components were plausibly present in the common cnidarian/bilaterian ancestor, but that their role may not have been strictly deterministic.
ISSN: 0012-1606

hal-01544487
https://hal.archives-ouvertes.fr/hal-01544487
DOI : 10.1016/j.ydbio.2012.01.018

Résumé : Le mérou géant, Epinephelus itajara, espèce en danger critique d’extinction au niveau mondial, est présent dans les eaux turbides et saumâtres de la Guyane française où l’espèce est exploitée par une pêcherie côtière. Dans la partie est du plateau continental guyanais, les mérous géants se localisent autour de tous les sites rocheux marins où ils se répartissent en fonction de la profondeur et du faciès (éboulis ou tombant). Les analyses des isotopes stables du carbone et de l’azote suggèrent qu’environ 30 % des mérous géants < 115 cm présents sur ces sites rocheux, proviendraient des mangroves alentours. Les analyses de contenus stomacaux révèlent un changement ontogénétique du régime alimentaire. Les petits individus (< 90 cm) s’alimentent principalement de Crustacés puis intègrent progressivement les poissons à leur alimentation jusqu’à devenir essentiellement piscivores au-delà de 140 cm. La population de Guyane est principalement composée d’individus juvéniles : seulement 8,5 % des individus capturés en Guyane a plus de 6 ans. Ces jeunes mérous sont très territoriaux durant les 4-5 premières années de leur vie puis ne sont plus retrouvés sur les sites rocheux. Le devenir de ces juvéniles est incertain, soit ils sont pêchés, soit ils migrent vers d’autres sites ou vers les agrégations de reproduction. Cependant, les mérous géants ne semblent pas se reproduire en Guyane. Il est possible que les conditions environnementales (forte turbidité et température) ne favorisent pas le développement gonadique, ce qui engendrerait une omission totale de reproduction. Le suivi par tags satellite suggère que les mérous géants migrent dans le sens des courants marins vers Trinidad-et-Tobago, potentiellement pour la reproduction. Aucun mouvement vers le Brésil n’a été mis en évidence bien que les stocks de mérous géants du Brésil et de Guyane semblent liés. En effet, ces deux stocks évoluent conjointement avec un déclin des populations au début des années 90. Le maintien de la population de mérou géant en Guyane se ferait grâce à l’apport de larves des sites d’agrégation du Brésil par le courant marin. La mortalité totale des mérous géants (0,65) est aussi élevée au sein de la réserve marine ainsi que sur les sites de pêche. Cela suggère que l’interdiction de pêche à la réserve n’est pas respectée et que les grands individus quittent la réserve pour des sites plus spacieux. En supposant que la population de mérous géants adultes a été réduite à cause de la pêche, une protection régionale des individus > 150 cm doit être instaurée afin de régénérer le stock d’individus matures. Il semble nécessaire de développer une politique de gestion internationale de l’espèce, surtout entre la Guyane et le Brésil, afin de conserver les populations de mérous géants d’Amérique du Sud.
The critically endangered Goliath Grouper, Epinephelus itajara, is found in the turbid and brackish waters of French Guiana, where the species is subject to a coastal fishery. Goliath Grouper populations inhabit all rocky habitats and exhibit increasing abundance with depth. Around 30% of individuals less than 115 cm may derive from the abundant mangrove habitat along the french Guiana coast. There is a ontogenetic shift of the diet, primarily crustacivorous, individuals >140 cm become piscivorous. The Goliath Grouper population in French Guiana is composed primarily og juvelines. The fate of the juvelines is unknonw, some may be caught in the fishery, others may move to other habitat. No evidence of spawning or gonadal readiness was found in french Guiana. it is possible that environmental conditions (high turbidity and temperature) are not conducive to reproductive activity. Goliath Grouper may migrate down current from French Guiana to Trinidad and Tobago or further. No movement of Goliath Grouper was found against the current toward Brazil. French Guiana juveniles may be derived from spawns occuring off Brazil. Calculated total mortality of Goliath Grouper off French Guiana is high (0.65) in both fished and protected areas suggesting that illegal fishing is occuring within the protected area, or that emigration rates are high. Assuming that the adult population of Goliath Grouper in French Guiana has been reduced due to fishing, protection of spawning-size adults (larger than about 150 cm TL) should be instated.

http://www.theses.fr/2014AGUY0721/document

Éditeur(s) : HAL CCSD Paris : Muséum national d'histoire naturelle
Résumé : International audience
The chromosomal diversity within six species of Mormyridae belonging to six different genera (Gnathonemus petersii, Marcusenius moorii, Ivindomyrus obdenboschi, Brienomyrus sp., Stomatorhinus walkeri and Petrocephalus microphthalmus) is investigated for the first time. These species have a conserved diploid chromosome number of 2n = 50 (except G. petersii 2n = 48) but different chromosome formulae, essentially involving pericentric inversions. C-banding has been used for the localization of heterochromatin. For a deeper interspecific comparison, several molecular markers were localized in the chromosomes by fluorescence in situ hybridization (FISH): a 18S rDNA probe; a microsatellite probe (GAA)(10), and a telomeric probe (TTAGGG)(7). The distribution of the 18S rDNA patterns, in particular, shows an amazing specific diversity, confirming a rapid radiation accompanied by major chromosome rearrangements.
ISSN: 0399-0974

hal-01544756
https://hal.archives-ouvertes.fr/hal-01544756

Éditeur(s) : HAL CCSD CSIRO Publishing
Résumé : International audience
The present study assessed the occurrence of multiple paternity in four litters of bull shark Carcharhinus leucas (n¼5, 8, 9 and 11 embryos) sampled at Reunion Island in the Western Indian Ocean. Using 21 microsatellite loci, we revealed that two litters were generated from two sires each, demonstrating for the first time multiple paternity for this species. We also reported a high paternal skew (10 : 1 in Litter 1 and 7 : 1 in Litter 3), which may be because of postcopulatory or post-zygotic selection processes. These results contribute to a better understanding of the reproductive behaviour of the bull shark, which remains poorly documented. The present study must be expanded to assess the frequency of multiple paternity in this species, and to test for genetic or cryptic benefits (convenience polyandry), which is important for long-term conservation and management plans.
ISSN: 1323-1650

hal-01253775
https://hal.archives-ouvertes.fr/hal-01253775
https://hal.archives-ouvertes.fr/hal-01253775/document
https://hal.archives-ouvertes.fr/hal-01253775/file/Pirog%20et%20al.%20-%202015%20-%20First%20evidence%20of%20multiple%20paternity%20in%20the%20bull%20s_hal.pdf
DOI : 10.1071/mf15255

Résumé : Le maintien de ressources génétiques suffisamment larges est nécessaire pour assurer la viabilité et le potentiel évolutif des populations naturelles. Cette thèse a le principal objectif de caractériser la diversité et la variabilité génétique chez le genre Virola (Myristicaceae) pour décrire les processus évolutifs qui en sont à l'origine. Premièrement,une étude de la régénération d'un échantillonnage exhaustif de V. michelii a été menée dans une parcelle du dispositif expérimental de Paracou ayant subi une exploitation forestière de faible intensité et comparée à une parcelle témoin. La diversité génétique mesurée à partir de marqueurs AFLP (Amplified Fragment-Length Polymorphism, N=229) en zones perturbées s'est révélée être plis grande qu'en zone non-perturbées. Puis, l'adaptation locale a été étudiée à travers ces mêmes individus et certains loci (AFLP) montrent une sélection divergente pour des environnements contrastés, indiquant un signe d'adaptation. Enfin, l'étude des niveaux de divergence génétique chez trois espèces de Virola du bouclier guyanais (V. michelii, V. surinamensis et V. kwatae) montrent que deux d'entre elles (V. surinamensis et V. kwatae) montrent de fortes similarités génétiques malgré leur distribution sur des environnements contrastés. des Flux de gènes intersécifiques ont été mis en évidence chez ces deux espèces-soeurs et l'hypothèse d'une spéciation écologique est avancée. Ce travail a permis d'aborder différents processus évolutifs à l'origine de la diversité génétique actuelle chez ces espèces forestières tropicales et peut fournir une contribution pour appréhender le devenir des populations.
Genetic diversity is an essential component of biodiversity. The maintenance of sufficient genetic resources is needed to ensure the adaptive potential and the viability of natural populations. In the current context of global changes, the study of adaptation in living organisms is a key task, particularly for tropical forest trees that are dominant components (in terms of biomass and as ecological drivers) of some of the most diverse ecosystems on Earth. The main objective of this thesis is to characterize genetic diversity and genetic variability to understand the evolutionary processes that act on them. This ecological-genetic study was carried out at the interspecific and intraspecific level in the Virola genus.If overall high levels of genetic diversity are a guarantee of prosperity for the future of the species, it seems essential to perform studies on the impact of environmental disturbance on genetic diversity. In the first section, the genetic consequences of regeneration dynamics were studied in an exhaustive sample of V. michelii in a low-intensity logging plot and in a control plot at the Paracou experimental site. A greater genetic diversity, measured from AFLP markers (Amplified Fragment Length Polymorphism, N = 229), was found in perturbed areas. Because studying genetic diversity within species may be useful for understanding species adaptation to environmental changes, in the second section. I studied local adaptation in a population of V. michelii on the Paracou experimental site. A genome scan approach with AFLPs (N = 229) was conducted on 77 adult individuals and 401 juveniles to identify genetic differences between populations associated to contrasting conditions for an array of environmental variables. Some loci (N = 2) were found to be subject to divergent selection, indicating adaptation to contrasting habitats.In the third section, the study of levels of genetic divergence in three Virola species of the Guiana Shield (V. michelii, V. surinamensis and V. kwatae) was investigated for nuclear and chloroplast molecular markers. V. surinamensis and V. kwatae showed strong genetic similarities despite their contrasting habitats preferences. Coalescent analyses have revealed, on one hand, a recent divergence between these two species suggesting an ecological speciation, and one the other hand that interspecific gene flow occurs between these sister-species.This work focuses on understanding evolutionary processes shaping genetic diversity and provides a useful contribution for biodiversity conservation programs.

http://www.theses.fr/2011AGUY0480/document

Éditeur(s) : Academic Press Ltd- Elsevier Science Ltd
Résumé : Over the last decade, RNA interference pathways have emerged in eukaryotes as critical regulators of many diverse biological functions including, among others, transcriptional gene regulation, post-transcriptional gene silencing, heterochromatin remodelling, suppression of transposon activity, and antiviral defences. Although this gene silencing process has been reported to be relatively well conserved in species of different phyla, there are important discrepancies between plants, invertebrates and mammals. In penaeid shrimp, the existence of an intact and functional RNAi machinery is supported by a rapidly growing body of evidence. However, the extent to which this process participates to the host immune responses remains poorly defined in this non-model organism. This review summarizes our current knowledge of RNAi mechanisms in shrimp and focuses on their implication in antiviral activities and shrimp immune defences.
Fish & Shellfish Immunology (1050-4648) (Academic Press Ltd- Elsevier Science Ltd), 2013-04 , Vol. 34 , N. 4 , P. 1002-1010

Droits : 2012 Elsevier Ltd. Published by Elsevier Ltd
http://archimer.ifremer.fr/doc/00119/23063/20899.pdf
DOI:10.1016/j.fsi.2012.06.008
http://archimer.ifremer.fr/doc/00119/23063/

Éditeur(s) : Elsevier Science Bv
Résumé : Underwater video techniques are increasingly used in marine ecology studies. Technological progress regarding video cameras, sensors (such as sounders), battery life and information storage make these techniques now accessible to a majority of users. However, diver-based underwater visual censuses, and catch and effort data, remain the most commonly used for observing coastal biodiversity and species. In this paper, we review the underwater video techniques that have been developed since the 1950s to investigate and/or monitor coastal biodiversity. Techniques such as remote underwater video, whether baited or not, diver-operated video and towed video are described, along with corresponding applications in the field. We then analyse the complementary of techniques, first from studies comparing video techniques with other observation techniques, whether video-based or not, and second by documenting their respective cost efficiencies. These findings are discussed with respect to current challenges in monitoring and investigating coastal biodiversity. Video should be more often considered and used, either in addition to or as an alternative to diver-based, fishing and acoustic techniques, as it may be particularly suited for monitoring coastal biodiversity in a variety of areas and on larger scales than hitherto and within an ecosystem-based approach to management and conservation.
Fisheries Research (0165-7836) (Elsevier Science Bv), 2014-06 , Vol. 154 , P. 44-62

Droits : 2014 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00181/29274/27901.pdf
DOI:10.1016/j.fishres.2014.01.019
http://archimer.ifremer.fr/doc/00181/29274/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Signalling through the Wnt family of secreted proteins originated in a common metazoan ancestor and greatly influenced the evolution of animal body plans. In bilaterians, Wnt signalling plays multiple fundamental roles during embryonic development and in adult tissues, notably in axial patterning, neural development and stem cell regulation. Studies in various cnidarian species have particularly highlighted the evolutionarily conserved role of the Wnt/b-catenin pathway in specification and patterning of the primary embryonic axis. However in another key non-bilaterian phylum, Ctenophora, Wnts are not involved in early establishment of the body axis during embryogenesis. We analysed the expression in the adult of the ctenophore Pleurobrachia pileus of 11 orthologues of Wnt signalling genes including all ctenophore Wnt ligands and Fz receptors and several members of the intracellular b-catenin pathway machinery. All genes are strongly expressed around the mouth margin at the oral pole, evoking the Wnt oral centre of cnidarians. This observation is consistent with primary axis polarisation by the Wnts being a universal metazoan feature, secondarily lost in ctenophores during early development but retained in the adult. In addition, local expression of Wnt signalling genes was seen in various anatomical structures of the body including in the locomotory comb rows, where their complex deployment suggests control by the Wnts of local comb polarity. Other important contexts of Wnt involvement which probably evolved before the ctenophore/ cnidarian/bilaterian split include proliferating stem cells and progenitors irrespective of cell types, and developing as well as differentiated neuro-sensory structures.
ISSN: 1932-6203

hal-01544483
https://hal.archives-ouvertes.fr/hal-01544483
DOI : 10.1371/journal.pone.0084363

Résumé : The tropical seabass Lates calcarifer was introduced in Tahiti in 1984 and then was domesticated without other introduction. Three successive generations have been obtained in captivity. Tissue samples of the 38 animaIs which represent the total Tahitian broodstock were preserved in alcohol to be genotyped with four microsatellite markers (Yue et al., 2001). Three of four described markers were successfully transferred to the laboratory of genetics of Tahiti (marker LcaM01, LcaM02, LcaM03), as the revelation technology available locally did not allow the use of LcaM04 in routine. The results show that the genetic diversity of the tahitian broodstock is not equivalent of the one of the species, which could be explained by the small size of the founder population, which is consistant with the history of the Tahitian population. The structuration of the 4th generation into several batches obtained from different parents appears to be the minimum management procedure to limit inbreeding.
Le loup tropical Lates calcarifer a été introduit à Tahiti en 1984 puis domestiqué sans apport d'animaux extérieurs. Trois générations successives ont été obtenues en captivité. Des prélèvements de tissus sur les 38 géniteurs qui constituent l'intégralité du stock de reproducteurs tahitiens sont conservés dans l'alcool pour être génotypés à l'aide de quatre marqueurs microsatellites (Yue et al., 2001). Trois des quatre marqueurs décrits ont pu être transférés avec succès au laboratoire de génétique de Tahiti (marqueurs LcaM01, LcaM02, LcaM03), la technique de révélation disponible localement ne permettant pas d'utiliser LcaM04 en routine. Les résultats montrent qu'on ne dispose pas à Tahiti de toute la variabilité génétique de l'espèce, ce qui pourrait s'expliquer, compte tenu de l'histoire de cette population, par un faible nombre de géniteurs fondateurs. La structuration de la 4ème génération en plusieurs lots issus de parents différents apparaît comme la mesure de gestion minimale pour limiter la consanguinité au sein de cette population.

Droits : 2003 Ifremer
http://archimer.ifremer.fr/doc/00142/25300/23372.pdf
http://archimer.ifremer.fr/doc/00142/25300/

Éditeur(s) : PSIC 11 - 11th Pacific Science Inter-Congress : Pacific Countries and their Ocean: Facing Local and Global Changes / 2nd Symposium on French Research in the Pacific. March 2 - 6, 2009 Tahiti, French Polynesia
Résumé : Shrimp farming in New Caledonia relies on the culture of a domesticated strain of Litopenaeus stylirostris introduced from Mexico at a time when genetic principles were of little or no consideration. Since then, advances in agriculture and for some aquatic species of importance led caledonian shrimp farmers to reconsider the appropriateness of a genetic improvement strategy adapted to local biotechnical and economical constraints. This questioning involves many different and interrelated aspects: scientific and technologic (genetics, biosecurity, quarantine, ), economic and organizational (financing, diffusion of genetic improvement) and pedagogic (awareness of farmers). Local institutions, producers associations, research centre and sanitary services associated to carry on the test of a first improvement strategy based on the crossing of different strains of L. stylirostris. This conceptually simple approach aimed at eliminating inbreeding, the first genetic limitating factor of improvement in captive populations. A second domesticated strain was obtained from Hawaii by the caledonian farmers, imported through a quarantine under the control of the zoosanitary local authorities, and reproduced and tested as pure or crossbred stocks by Ifremer within the framework of an interdisciplinary research project financed by caledonian institutions. Present results for hybrids (better growth and survival in the absence of virus) demonstrate the validity of this approach. They also bring out the importance to simultaneously integrate in a development scheme, a breeding centre to maintain and reproduce disease free breeders. This strategy and organization, tested in New Caledonia, could possibly be of benefit to other small scale aquaculture activities in the pacific islands.
La filière crevetticole de Nouvelle-Calédonie s’est développée jusqu’à aujourd’hui à partir d’un stock domestiqué de Litopenaeus stylirostris introduit d’Amérique à une époque où les principes de base en génétique n’étaient pas ou peu appliqués en aquaculture. Les avancées récentes en agriculture et chez quelques espèces aquacoles d’importance mondiale ont conduit les acteurs de cette filière à se poser la question de la mise en place d’une stratégie d’amélioration génétique adaptée aux contraintes biotechniques et économiques locales. Cette réflexion comportait à la fois des aspects scientifiques et technologiques (génétique, biosécurité, quarantaine, conservatoire), économiques et organisationnels (coût de l’opération, modalité de diffusion du progrès attendu), pédagogiques (sensibilisation des fermiers). Des acteurs d’horizons différents (institutions locales, association de producteurs, centre de recherche, police zoosanitaire) se sont associés pour monter une opération de testage d’une première stratégie d’amélioration par croisement de souches de la même espèce. Cette stratégie conceptuellement simple visait l’élimination du premier facteur génétique de limitation des performances d’élevage d’une population captive, à savoir une consanguinité d’autant plus élevée que le nombre de géniteurs fondateurs était faible. Une seconde souche domestiquée a ainsi été acquise à Hawaii par les producteurs calédoniens, contrôlée en quarantaine par les services vétérinaires calédoniens en charge de la réglementation sanitaire, reproduite et testée pure et en croisement par l’Ifremer dans le cadre d’un projet de recherche pluridisciplinaire plus large financé par les institutions du Pays. Les résultats obtenus démontrent l’intérêt de la démarche (meilleure croissance, meilleure survie en l’absence de virus). Mais ils montrent aussi l’utilité d’intégrer simultanément dans le plan de développement de la filière une stratégie de conservation des souches parentales afin de disposer de géniteurs exempts de pathogènes. Cette stratégie et cette organisation testées en Nouvelle-Calédonie pourraient vraisemblablement être profitables à d’autres filières aquacoles modestes, en particulier dans les pays insulaires du Pacifique.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00198/30879/29247.pdf
http://archimer.ifremer.fr/doc/00198/30879/

Éditeur(s) : Pêche thonière et dispositifs de concentration de poissons, Caribbean-Martinique, 15-19 Oct 1999
Résumé : In recent years, the use of fads in Martinique has evolved from an experimental stage to a productive one. This transformation results in the pitching up of operational device park by the regional fishery committee. Nevertheless, this technical change in fishing practices is not implemented in a homogeneous way all around the island; some differences exist especially between the Atlantic and the Caribbean coasts. From surveys carried out during an annual cycle on two main landing sites, this study describes the pelagic fishing activity around fads and in the open sea. A comparison of fishing strategies adopted in different places as well as an analysis of the results obtained by the fishing units in terms of species (size of catches and daily yields) allow to describe the progress made in the implementation adoption of this new fishing practice. For several fishermen, fishing around fads has become an exclusive job, practised all year round. For others, fads is used in addition to traditional fishing activity on flotsam, "Miquelon" fishing and keeps a seasonal character.Original Abstract: Au cours des recentes annees, l'utilisation des DCP en Martinique est passee du stade experimental au stade operationnel. Cette mutation se traduit par la prise en charge du parc de dispositifs operationnels par le comite regional des peches. Toutefois, l'adoption de cette nouvelle technique d'exploitation ne s'effectue pas de facon homogene dans toutes les communes de l'ile, des differences existent notamment entre les cotes Atlantique et Caraibe. A partir d'enquetes effectuees pendant un cycle annuel, sur deux principaux points de debarquement, cette etude decrit l'activite de peche des poissons pelagiques avec ou sans DCP. Une comparaison des strategies de peche developpees dans les differents sites ainsi qu'une analyse des resultats obtenus par les unites de peche en termes d'especes, de taille des captures, de rendement journalier permettent de decrire la progression differenciee de l'adoption de cette nouvelle activite halieutique. Pour certains pecheurs, la peche sous DCP est devenue un metier exclusif, pratique tout au long de l'annee. Pour d'autres, le DCP est utilise en complement de l'activite traditionnelle de peche sous bois derivants, " peche a Miquelon ", et conserve un caractere saisonnier.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00042/15298/12657.pdf
http://archimer.ifremer.fr/doc/00042/15298/

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

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

Éditeur(s) : HAL CCSD Sociedade Entomológica do Brasil
Résumé : Variations in diel activity among hyperdiverse tropical communities of moths, despite representing a key component of niche partitioning between species, have barely been studied so far. Using light trapping from dawn to sunset over a 1-year period in French Guiana, we investigated these variations within and between two families of moths (Sphingidae and Saturniidae). Our results revealed contrasting patterns in flight activity at night between Sphingidae and Saturniidae. Sphingidae reached their peak in species richness and abundance between 7:00 and 8:00 p.m., followed by a decrease around 11:00 p.m. to midnight, whereas Saturniidae were continuously present throughout the night, with a peak around midnight. In addition, we found changes in diel activity among some of the most common genera in each family, highlighting distinct behavioral, physiological, and functional traits among taxa. Given differences in flight activity at different taxonomic levels, it is strongly recommended to monitor by light trapping throughout the night to effectively sample saturniid and sphingid assemblages, even though the activity of Sphingidae sharply declines after midnight. These results improve the general natural history information of tropical moths and reinforce the need of further research on the ecological and taxonomic consequences of differences in diel activity.
ISSN: 1519-566X

hal-01536447
https://hal.archives-ouvertes.fr/hal-01536447
DOI : 10.1007/s13744-014-0264-3
PRODINRA : 320714

Éditeur(s) : HAL CCSD Elsevier
Résumé : Analyses of tree diversity and community composition in tropical rain forests are usually based either on general herbarium data or on a restricted number of botanical plots. Despite their high taxonomic accuracy, both types of data are difficult to extrapolate to landscape scales. Meanwhile, forestry surveys provide quantitative occurrence data on large areas, and are thus increasingly used for landscape-scale analyses of tree diversity. However, the reliability of these approaches has been challenged because of the ambiguity of the common (vernacular) names used by foresters and the complexity of tree taxonomy in those hyper-diverse communities.We developed and tested a novel approach to evaluate taxonomic reliability of forestry surveys and to propagate the resulting uncertainty in the estimates of several diversity indicators (alpha and beta entropy, Fisher-alpha and Sørensen similarity). Our approach is based on Monte-Carlo processes that simulate communities by taking into account the expected accuracy and reliability of common names. We tested this method in French Guiana, on 9 one-hectare plots (4279 trees – DBH ⩾ 10 cm) for which both common names and standardized taxonomic determinations were available. We then applied our method of community simulation on large forestry inventories (560 ha) at the landscape scale and compared the diversity indices obtained for 10 sites with those computed from precise botanical determination situated at the same localities.We found that taxonomic reliability of forestry inventories varied from 22% (species level) to 83% (family level) in this Amazonian region. Indices computed directly with raw forestry data resulted in incorrect values, except for Gini–Simpson beta-diversity. On the contrary, our correction method provides more accurate diversity estimates, highly correlated with botanical measurements, for almost all diversity indices at both regional and local scales. We obtained a robust ranking of sites consistent with those shown by botanical inventories.These results show that (i) forestry inventories represent a significant part of taxonomic information, (ii) the relative diversity of regional sites can be successfully ranked using forestry inventory data using our method and (iii) forestry inventories can valuably contribute to the detection of large-scale diversity patterns when biases are well-controlled and corrected.The tools we developed as R-functions are available in supplementary material and can be adapted with local parameters to be used for forest management and conservation issues in other regional contexts
ISSN: 0378-1127

hal-01204219
https://hal.archives-ouvertes.fr/hal-01204219
DOI : 10.1016/j.foreco.2014.05.045
PRODINRA : 286554

Éditeur(s) : HAL CCSD Nordic Ecological Society
Résumé : Beta diversity is among the most employed theoretical concepts in ecology and biodiversity conservation. Up to date, a self-contained definition of it, with no reference to alpha and gamma diversity, has never been proposed. Using Kullback-Leibler divergence, we present the explicit formula of Shannon's beta entropy, a bias correction for its estimator and a confidence interval. We also provide the mathematical framework to decompose Shannon diversity into several hierarchical nested levels. From botanical inventories of tropical forest plots in French Guiana, we estimate Shannon diversity at the plot, forest and regional level. We believe this is a complete and usefulness toolbox for ecologists interested in partitioning biodiversity.
ISSN: 0030-1299

hal-01032426
https://hal.archives-ouvertes.fr/hal-01032426
DOI : 10.1111/j.1600-0706.2011.19267.x

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

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

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
While the populations of large herbivores are being depleted in many tropical rainforests, the importance of their trophic role in the ecological functioning and biodiversity of these ecosystems is still not well evaluated. This is due to the outstanding plant diversity that they feed upon and the inherent difficulties involved in observing their elusive behaviour. Classically, the diet of elusive tropical herbivores is studied through the observation of browsing signs and macroscopic analysis of faeces or stomach contents. In this study, we illustrate that the original coupling of classic methods with genetic and ethnobotanical approaches yields information both about the diet diversity, the foraging modalities and the potential impact on vegetation of the largest terrestrial mammal of Amazonia, the lowland tapir. The study was conducted in the Guianan shield, where the ecology of tapirs has been less investigated. We identified 92 new species, 51 new genera and 13 new families of plants eaten by tapirs. We discuss the relative contribution of our different approaches, notably the contribution of genetic barcoding, used for the first time to investigate the diet of a large tropical mammal, and how local traditional ecological knowledge is accredited and valuable for research on the ecology of elusive animals.
ISSN: 1932-6203

halsde-00676374
https://hal.archives-ouvertes.fr/halsde-00676374
DOI : 10.1371/journal.pone.0025850
PUBMED : 21991372

Éditeur(s) : Wiley-blackwell
Résumé : In bird species that have a high movement capacity, dispersal may connect subpopulations over vast geographical regions, with important consequences for the design of conservation management strategies. Here we used a molecular approach to infer the patterns and rates of dispersal among eight Mediterranean subpopulations of the endangered Bonelli's Eagle, based on 245 individuals screened at 17 microsatellite loci. There was moderate genetic differentiation between subpopulations sampled in the western (Iberia and Morocco) and eastern (Cyprus) Mediterranean, whereas differentiation among subpopulations in the former region was weak to moderate and followed a pattern of isolation by distance. Within the western Mediterranean, the small, peripheral and ecologically unique population of southwest Portugal had the lowest genetic diversity and the highest differentiation. The remaining subpopulations formed two loose clusters, one including Morocco and southwest and eastern Spain, and the other northeast Portugal and western and central Spain. Few recent migrants were detected, and they originated primarily from adjacent subpopulations. Our findings suggest that western Mediterranean Bonelli's Eagles may have a large-scale metapopulation structure, with subpopulations connected to some extent by distance-dependent dispersal, probably influenced by natal philopatry and the geographical configuration of subpopulations. The combination of marked ecological and genetic divergence suggests that the peripheral subpopulation of southwest Portugal may be regarded as a distinct management unit.
Ibis (0019-1019) (Wiley-blackwell), 2013-07 , Vol. 155 , N. 3 , P. 485-498

Droits : 2013 British Ornithologists’ Union
http://archimer.ifremer.fr/doc/00148/25924/24018.pdf
DOI:10.1111/ibi.12065
http://archimer.ifremer.fr/doc/00148/25924/