Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Recent theoretical and field studies conducted in both terrestrial and marine ecosystems have suggested that diversity could be a more complex and multi-component concept than previously thought. However, it is still poorly understood to what extent the information provided by the various indices is complementary with regard to diversity, and to what extent this complementarity is reproducible in different situations or at different scales of observation. In the present work, we have analysed the reproducibility of the empirical relationships between 11 diversity indices related to four major aspects (components) of species diversity (species richness, rarity, evenness and species taxonomy) in order to determine whether there is a general pattern of redundancy or complementarity in diversity measures that holds across years, areas and spatial scales. We have applied this approach to groundfish diversity through the analysis of 2404 trawl hauls collected during the first large-scale annual surveys carried out using a single sampling design throughout the northern Mediterranean Sea (ranging from 36.3 to 45.7 degrees N, and 5.3 degrees W to 28 degrees E). Whatever the years, areas and scales studied, we found a strong reproducibility in the number and the nature of the main complementary components of diversity. The whole set of diversity indices considered may be roughly split into 6 complementary groups of descriptors. This result highlights that, in contrast to what is still the usual practice, monitoring diversity should not be based on only one or two of the most widely used components, even at large scale. Finally, in a context where developing tools for monitoring diversity is considered as a high priority worldwide, the strong reproducibility of the relationships between diversity indices we observed offers a basis for discussion of the feasibility and relevance of proposing a general shortlist of indices for monitoring diversity at different management scales.
Ecography (0906-7590) (Wiley-blackwell Publishing, Inc), 2010-12 , Vol. 33 , N. 6 , P. 1123-1135

Droits : 2010 The Authors / Ecography
http://archimer.ifremer.fr/doc/00029/14064/11382.pdf
DOI:10.1111/j.1600-0587.2009.06259.x
http://archimer.ifremer.fr/doc/00029/14064/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The full numerical simulation of turbulent flows in the context of industrial applications remains a very challenging problem. One of the difficulties is the presence of a large number of interacting scales of different orders of magnitude, ranging from the macroscopic scale to the Kolmogorov dissipation scale. In order to better understand and simulate these interactions, new algorithms of incremental type have recently been introduced, stemming from the theory of infinite-dimensional dynamical systems (see, e.g., the algorithms of Foias, Jolly et al. (1988), Foias, Manley and Temam (1988), Laminie et al. (1993, 1994), Marion and Temam (1989, 1990), and Temam (1990)). These algorithms are based on decompositions of the unknown functions into a large- and a small-scale component, one of the underlying ideas being to approximate the corresponding attractor. In the context of finite element methods, the decomposition of a solution into small- and large-scale components appears when we consider hierarchical bases (Yserentant, 1986; Zienkiewicz et al., 1982). In the present article we derive several estimates of the size of the structures for the linear and nonlinear terms which correspond to interactions of different hierarchical components of the velocity field, and also their time variation. The one-step time variation of these terms can be smaller than the expected accuracy of the computation. Using this remark, we implement an adaptive spatial and temporal multilevel algorithm which treats differently the small- and large-scale components of the flow. We derive several a priori estimates in order to study the perturbation introduced into the approximated equations. All the interaction terms between small- and large-scale structures are frozen during several time steps. Finally, we implement the multilevel method in order to simulate a bidimensional flow described by the Burgers equations. We perform a parametric study of the procedure and its efficiency. The gain in CPU time is significant and the trajectories computed by our multi-scale method remain close to the trajectories obtained with the classical Galerkin method.
ISSN: 0168-9274

hal-00730710
https://hal.archives-ouvertes.fr/hal-00730710

Éditeur(s) : Université d'Angers
Résumé : In oyster farming areas, organic matter fluxes toward sediment is increased. Pacific oysters (Crassostrea gigas) reject organic-rich faeces and pseudofaeces as a result of filtration process. Organic matter can be consumed by benthic fauna, but in excess it can entails the reduction of benthic faunal species richness, abundance and biomass. Organic matter degradation also induces hypoxic (or anoxic) conditions in the sediment, and production of ammonia and sulfides in toxic concentrations. The main objective of this study is to assess the effects of oyster farming on benthic intertidal ecosystems in the Pertuis Charentais. Benthic macrofauna, living (stained) foraminifera, and physicochemical characteristics of the water column and sediment were used as indicators to evaluate these effects. A multidisciplinary approach was conducted across the Pertuis Charentais at 3 different spatial scales: an oyster trestle (micro-scale), an oyster culture area (meso-scale) and various sites across the Pertuis Charentais (macro-scale). The study was also realised at 4 different temporal scales: some months for the spatial micro-scale, every two weeks for 2 years at meso-scale and once per season during one year at macro-scale. In this study, I found that oyster farming enriches sediment in fine particles, organic matter (up to 12 %), particulate organic carbon (15-20 µg mg 1) and leads to high microphytobenthic biomass. Moreover, the association of seasonnal warming (during spring and summer), remineralisation of accumulated organic matter and short-term hypoxic conditions leads to sulfides and ammonium production. Consequently, the benthic biodiversity decreases and the population dynamic is disturbed. The population dynamic disturbance is characterised by fast abundance rises followed by high mortality rates. In these conditions, tolerant benthic macrofaunal (Cirratulidae, Spionidae and Capitellidae) and foraminiferal (Ammonia tepida and Cribroelphidium gunteri) species are promoted. AMBI index confirms "medium" ecological quality of oyster farming areas. On the contrary, across the control sites, sensible species are maintained (Amphipods, Rosalina cf. vilardeboana). Comparison of oyster farming techniques shows that on-bottom culture is less disturbing for benthic ecosystem than off-bottom culture. Axial tomodensitometry, an innovative method, was used to describe in 3D the sedimentary column organisation. I show that oyster farming modifies the sedimentary column functioning. Indeed, the macrofaunal diversity decrease leads to the modification of the functional diversity of assemblages. Thus, the vertical distribution of living foraminifera is limited in oyster farming areas, because their distribution is tightly related to macrofaunal bioturbating modes.
Dans les zones ostréicoles, les flux de matière organique sont importants, l'huître Crasssotrea gigas rejetant sous forme de pseudo-fécès et de fécès de grandes quantités de matière organique. De ce fait, bien que cette matière organique puisse être consommée par la faune benthique, sa surabondance peut provoquer une réduction de la richesse spécifique, de l'abondance et de la biomasse et provoquer sur le plan des processus biogéochimiques des déplétions en oxygène et l'apparition de substances comme l'ammonium et les sulfures dont les concentrations peuvent devenir toxiques. L'objectif principal de cette étude était donc de déterminer l'impact de l'ostréiculture, grâce à plusieurs indicateurs, sur le compartiment benthique d'un écosystème littoral comme les pertuis charentais. Pour évaluer ces effets, la macrofaune benthique et les foraminifères vivants benthiques ont été utilisés en association avec des mesures des paramètres physico-chimiques de la colonne d'eau et du sédiment. Une approche pluridisciplinaire a ainsi été menée dans les pertuis charentais à trois échelles spatiales différentes : à l'échelle d'une table ostréicole (micro-échelle), à l'échelle d'un site ostréicole (méso-échelle) et à l'échelle des pertuis charentais (macro-échelle). Dans les trois cas, un suivi dans le temps a été associé à une étude de distribution spatiale, quelques mois à micro-échelle, tous les quinze jours pendant deux années à méso-échelle et une fois par saison pendant une année à macro-échelle. Ces différentes approches ont permis d'avoir une vision pertinente de la dynamique et de la réponse fonctionnelle de la faune benthique aux changements induits par la présence de l'ostréiculture. La présence des cultures ostréicoles dans les pertuis charentais enrichit les sédiments en particules fines, en matière organique (12 %), en carbone organique particulaire (15-20 µg mg-1) et favorise une production microphytobenthique élevée. Pendant la période chaude de l'année printemps-été, la reminéralisation de la matière organique accumulée associée à des hypoxies temporaires a favorisé la production de sulfures et d'ammonium. Dans les stations soumises à l'ostréiculture, la diversité des assemblages diminue. La dynamique des espèces est caractérisée par des augmentations rapides des abondances suivies d'épisodes de mortalité. Les espèces tolérantes de la macrofaune benthique (Cirratulidae, Spionidae et Capitellidae) et des foraminifères vivants benthiques (Ammonia tepida et Cribroelphidium gunteri) sont favorisées. Le calcul de l'indice AMBI confirme la qualité écologique moyenne de ces sites. Au contraire, dans la station témoin, les espèces sensibles sont favorisées (Amphipodes, Rosalina cf. vilardeboana). La comparaison de la technique de culture sur table et de culture à plat a montré que la culture des huîtres à plat est moins perturbante pour le milieu. L'étude de la bioturbation a montré l'influence qui existe entre le mode de bioturbation des différents groupes de la macrofaune et la répartition verticale des foraminifères vivants dans la colonne sédimentaire. La diminution de la diversité des assemblages de la macrofaune dans les zones soumises à l'ostréiculture modifient la diversité fonctionnelle de ces assemblages et affectent le fonctionnement de la colonne sédimentaire, limitant la répartition verticale des foraminifères dans ces zones.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/these-2582.pdf
http://archimer.ifremer.fr/doc/00000/2582/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: In a malaria-endemic area the distribution of patients is neither constant in time nor homogeneous in space. The WHO recommends the stratification of malaria risk on a fine geographical scale. In the village of Cacao in French Guiana, the study of the spatial and temporal distribution of malaria cases, during an epidemic, allowed a better understanding of the environmental factors promoting malaria transmission. METHODS: A dynamic cohort of 839 persons living in 176 households (only people residing permanently in the village) was constituted between January 1st, 2002 and December 31st, 2007.The information about the number of inhabitants per household, the number of confirmed cases of Plasmodium vivax and house GPS coordinates were collected to search for spatial or temporal clustering using Kurlldorff's statistical method. RESULTS: Of the 839 persons living permanently in the village of Cacao, 359 persons presented at least one vivax malaria episode between 2002 and 2007. Five temporal clusters and four spatial clusters were identified during the study period. In all temporal clusters, April was included. Two spatial clusters were localized at the north of the village near the Comté River and two others localized close to orchards. CONCLUSION: The spatial heterogeneity of malaria in the village may have been influenced by environmental disturbances due to local agricultural policies: deforestation, cultures of fresh produce, or drainage of water for agriculture. This study allowed generating behavioural, entomological, or environmental hypotheses that could be useful to improve prevention campaigns.
ISSN: 1475-2875

inserm-00849010
http://www.hal.inserm.fr/inserm-00849010
http://www.hal.inserm.fr/inserm-00849010/document
http://www.hal.inserm.fr/inserm-00849010/file/2013_Basurko_-_Deforestation_agriculture_and_farm_jobs_a_good_recipe_for_Plasmodium_vivax_in_French_Guiana.pdf
DOI : 10.1186/1475-2875-12-90

Éditeur(s) : Wiley-blackwell
Résumé : Aim The aims of this study were: (1) to identify global communities of tuna and billfish species through quantitative statistical analyses of global fisheries data; (2) to describe the spatial distribution, main environmental drivers and species composition of each community detected; and (3) to determine whether the spatial distribution of each community could be linked to the environmental conditions that affect lower trophic levels by comparing the partitions identified in this study with Longhursts biogeochemical provinces. Location The global ocean from 60 degrees S to 65 degrees N. Methods We implemented a new numerical procedure based on a hierarchical clustering method and a nonparametric probabilistic test to divide the oceanic biosphere into biomes and ecoregions. This procedure was applied to a database that comprised standardized data on commercial longline catches for 15 different species of tuna and billfish over a period of more than 50 years (i.e. 1953-2007). For each ecoregion identified (i.e. characteristic tuna and billfish community), we analysed the relationships between species composition and environmental factors. Finally, we compared the biogeochemical provinces of Longhurst with the ecoregions that we identified. Results Tuna and billfish species form nine well-defined communities across the global ocean. Each community occurs in regions with specific environmental conditions and shows a distinctive species composition. High similarity (68.8% homogeneity) between the spatial distribution of the communities of tuna and billfish and the biogeochemical provinces suggests a strong relationship between these species and the physical and chemical characteristics of the global ocean. Main conclusions Despite their high tolerance for a wide range of environmental conditions, these highly migratory species are partitioned into clear geographical communities in the ocean at a global scale. The similarity between biogeochemical and biotic divisions in the ocean suggests that the global ocean is a mosaic of large biogeographical ecosystems, each characterized by specific environmental conditions that have a strong effect on the composition of the trophic web.
Journal Of Biogeography (0305-0270) (Wiley-blackwell), 2012-01 , Vol. 39 , N. 1 , P. 114-129

Droits : 2011 Blackwell Publishing Ltd
http://archimer.ifremer.fr/doc/00060/17141/14716.pdf
DOI:10.1111/j.1365-2699.2011.02582.x
http://archimer.ifremer.fr/doc/00060/17141/

Éditeur(s) : Public Library Science
Résumé : Background: Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques - including site-based monitoring, genetic analyses, mark-recapture studies and telemetry - can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. Methodology/Principal Findings: To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine-to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally. Conclusions/Significance: The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition, the RMU framework - including maps and supporting metadata - will be an iterative, user-driven tool made publicly available in an online application for comments, improvements, download and analysis.
Plos One (1932-6203) (Public Library Science), 2010-12 , Vol. 5 , N. 12 , P. -

Droits : 2010 Plos One
http://archimer.ifremer.fr/doc/00028/13926/11308.pdf
DOI:10.1371/journal.pone.0015465
http://archimer.ifremer.fr/doc/00028/13926/

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The mantle above a subducting slab is the site of complex interactions between deformation, partial melting, fluid migration and magma transport. To constrain these interactions and their effects on olivine deformation, we analyze microstructures, crystal preferred orientations, and water contents of peridotite xenoliths entrained by andesites of the Avacha volcano, southern Kamchatka arc. These xenoliths are refractory spinel harzburgites that have coarse-grained microstructures with widely spaced subgrain boundaries and sinuous grain boundaries in olivine, consistent with deformation by dislocation creep under low deviatoric stress (< 13 MPa) and with a significant contribution from diffusional processes. Analysis of crystal preferred orientations (CPO) indicates dominant activation of high-temperature, low-stress {0kl}[100] slip systems in olivine and of(100)[001] in orthopyroxene. In most samples, coarse opx crystals, elongated parallel to the lineation, enclose small olivine grains in crystallographic continuity with neighbouring crystals, indicating crystallization of orthopyroxene at the expense of olivine as a result of reactive percolation of Si-rich fluids coeval with the high-temperature deformation. Secondary crystallization of interstitial orthopyroxene led locally to development of opx-rich lenses parallel to the foliation, characterized by a decrease in olivine grain size and dispersion of the olivine CPO without changing the dominant slip systems. Half of the samples also show acicular orthopyroxene aggregates with which is associated a fine-grained matrix composed of rounded strain-free olivine, orthopyroxene, spinel, and rare amphibole crystals. This matrix occurs pervasively along grain boundaries or forms millimeter-scale irregular lenses and anastomosing veinlets that crosscut the coarse crystals and their ductile deformation structures. Both acicular orthopyroxene and the fine-grained matrix are interpreted as resulting from reactive transport of H2O-rich fluids under static conditions, probably in the lithospheric mantle. Infrared analyses show that olivine contains 1-8 center dot 6 ppm by weight of water. These low water contents are similar to those observed in spinel peridotites from other subduction zones and probably record both the low solubility of water in olivine at low pressure and dehydration during exhumation of the xenoliths. Water contents in orthopyroxene are highly variable (25-506 ppm H2O), probably recording spatially heterogeneous interaction with fluids or melts and compositional disequilibrium in the studied samples. Change in the dominant percolation mechanism from porous flow to fracturing suggests cooling, consistent with the low temperatures estimated from pyroxene thermometry (< 800-900 degrees C). The Avacha xenoliths therefore record pervasive deformation of a region of the mantle under asthenospheric conditions, followed by its accretion to the base of the lithosphere, probably as a result of cooling of the mantle wedge. Percolation of Si-rich fluids or hydrous melts is recorded at all stages; this probably enhanced diffusion and lowered deviatoric stresses during ductile deformation, but did not change the dominant slip direction in olivine from [100] to [001].
ISSN: 0022-3530

hal-00456053
https://hal.archives-ouvertes.fr/hal-00456053
DOI : 10.1093/petrology/egp085

Résumé : L'agriculture actuelle est impliquée dans de multiples problématiques environnementales, sociales et économiques, aux échelles locales et globales. En agronomie, de nombreux travaux à l'échelle du champ et de l'exploitation visent aujourd'hui à concevoir des systèmes de culture et des systèmes de production en lien avec ces problématiques. En revanche, peu de travaux portent sur la conception et l'évaluation de systèmes agricoles à l'échelle du territoire, alors que cette échelle apparaît pourtant incontournable pour faire face à des enjeux de développement durable. Pour combler ce manque, nous proposons un ensemble méthodologique permettant i) de simuler les conséquences de scénarios de politiques agricoles sur les choix d'assolement des agriculteurs, décrits individuellement, en modélisant l'évolution de leurs système de production et ii) d'évaluer l'impact de ces changements d'assolements à l'échelle du territoire, à l'aide d'indicateurs qui apportent de l'information spatiale sur la contribution de l'agriculture au développement durable. L'ensemble méthodologique proposé débute par la construction d'une typologie des exploitations agricoles du territoire sur la base de la similarité de leur assolement. Parallèlement, l'adaptation d'indicateurs à l'échelle du territoire permet d'évaluer les impacts des externalités des systèmes de culture en mobilisant des procédures de changements d'échelles. Un modèle bioéconomique générique, multi-échelle, spatialement explicite, appelé MOSAICA, qui utilise la typologie et les indicateurs d'impact de l'agriculture à l'échelle régionale, est créé pour produire des mosaïques de systèmes de culture et évalue leur contribution au développement durable du territoire. Ce modèle, couplé à un itinéraire de définition de scénarios exploratoires et normatifs permet de tester l'impact de différents types de leviers agronomiques, socio-économiques, environnementaux, organisationnels et techniques sur les choix des exploitants et in fine sur la contribution de la mosaïque de systèmes de culture au développement durable du territoire. Nous avons appliqué cet ensemble méthodologique à la conception de scénarios de développement agricoles durables en Guadeloupe. Nous avons dans un premier temps développé une typologie des systèmes de production comprenant huit types distincts et relevant de processus décisionnel différents. Puis nous avons adapté à l'échelle du territoire 19 indicateurs pour l'évaluation des mosaïques de systèmes de culture. L’évaluation de la mosaïque actuelle nous a permis de repérer de faibles niveaux de contribution aux enjeux d’autonomie alimentaire et énergétique. Différents scénarios normatifs et exploratoires intégrant des leviers de changement de la mosaïque ont été testés avec MOSAICA. Les évaluations réalisées nous ont permis d'identifier que des leviers agronomiques comme le développement du maraîchage sans intrants chimiques et des leviers sociaux comme la formation de main-d'oeuvre supplémentaire permettraient d'améliorer la contribution de l’agriculture au développement durable du territoire Guadeloupéen. La modélisation mécaniste de l’évolution du territoire agricole permet d'intégrer des connaissances sur la localisation, les performances, les impacts des systèmes de culture et sur les processus décisionnels des exploitants régissant l’orientation productive et le fonctionnement des exploitations. Cette démarche permet de visualiser les changements de système de culture et leurs impacts de manière spatialement explicite, ce qui permet de générer des connaissances sur les leviers susceptibles de faire évoluer positivement l'agriculture du territoire. La démarche et les outils mis en oeuvre sont donc particulièrement utiles pour l'aide à la décision publique pour améliorer la durabilité de l'agriculture dans son ensemble.
Current agricultural systems are responsible for many different environmental, social and economic issues at both local and global scales. Agricultural sciences have contributed to the design of several methods at the farm and field scale in order to prototype cropping systems and farming systems to address these issues. However, few methods have been designed at the regional scale, while this scale seems to be essential in order to address these issues. In order to fill this gap, we here propose a new methodological framework for i) simulating the consequences of policy changes on farmer's cropping plan, described individually, by modeling the evolution of farming systems and to ii) assess the impacts of cropping system changes at the regional scale, with a set of indicators that generate spatially explicit information on the contribution of agriculture to sustainable development. The methodological framework starts with the design of a farm typology over the territory based on the similarity of farmer's crop acreages. In parallel, a set of indicators is adapted to the landscape scale in order to assess the impacts of cropping system externalities by integrating a set of scale change procedures. A generic, multi-scale, spatially explicit bioeconomic model called MOSAICA, which uses the farm typology and the indicators, is created for generating cropping system mosaics and assessing their contribution to sustainable development. This model coupled to a scenario approach composed of exploratory and normative scenarios can simulate the impact of several types of agronomic, socio-economic, environmental, organizational and technical levers of change on the farmer's choices in terms of cropping systems and in fine the impacts of new cropping system mosaics on the contribution to sustainable development of territories. We applied this methodological framework for building scenarios of sustainable agricultural development in Guadeloupe. We first developed a typology of farming systems encompassing eight types of farming systems that revealed several different farmer's decision processes. Then, we developed 19 indicators to assess cropping system mosaics. The assessment of the current cropping system mosaic showed low levels of response of the current mosaic to economic and social issues especially the food and energy self-sufficiency. Different normative and exploratory scenarios integrating levers of change have been simulated with MOSAICA. The assessment of cropping system mosaics from these scenarios highlighted the positive effect of agronomic levers of change such as organic crop-gardening and social levers such as the vocational training of supplementary workforce for improving the contribution of agriculture to sustainable development of the guadeloupean territory. The mechanistic modeling of the agricultural territory allows us to integrate a wide range of knowledge on the location of cropping systems, their levels of performance , their impacts and the decision process of farmer's that drive the farming system characteristics and the farm functioning. This methodological framework helps visualize the cropping system changes at the regional scale and their associated impacts at the landscape scale which is helpful in order to produce knowledge on the levers of change that can improve the response of local agriculture to local and global issues. The framework and tools designed are particularly useful for decision-aid on the future levels of contribution of agriculture to sustainable development.

http://www.theses.fr/2015AGUY0823/document

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
Many epidemiological studies examining long-term health effects of exposure to air pollutants have characterized exposure by the outdoor air concentrations at sites that may be distant to subjects' residences at different points in time. The temporal and spatial mobility of subjects and the spatial scale of exposure assessment could thus lead to misclassification in the cumulative exposure estimation. This paper attempts to fill the gap regarding cumulative exposure assessment to air pollution at a fine spatial scale in epidemiological studies investigating long-term health effects. We propose a conceptual framework showing how major difficulties in cumulative long-term exposure assessment could be surmounted. We then illustrate this conceptual model on the case of exposure to NO₂ following two steps: (i) retrospective reconstitution of NO₂ concentrations at a fine spatial scale; and (ii) a novel approach to assigning the time-relevant exposure estimates at the census block level, using all available data on residential mobility throughout a 10- to 20-year period prior to that for which the health events are to be detected. Our conceptual framework is both flexible and convenient for the needs of different epidemiological study designs
ISSN: 1660-4601

hal-01296781
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01296781
DOI : 10.3390/ijerph13030319
PUBMED : 26999170

Éditeur(s) : HAL CCSD Royal Meteorological Society
Résumé : Assessing the impact/adaptation of human activities on/to climate change is a key issue, especially in the tropics that concentrate major anthropogenic dynamics such as deforestation and nearly two-thirds of the planetary rainfall. However, this task is often made tough because human activities such as agricultural dynamics are usually analysed at local or regional scale whereas climate related studies are led at large to global scales due to a lack of reliable data, especially in the tropics. In this article we argue that the increased spatial resolution of remote sensing-based rainfall estimates enables assessing the spatiotemporal variability of rainfall regimes at regional and local scales, thus allowing fine analysis of the interactions with human activities. We processed Tropical Rainfall Measuring Mission (TRMM) 3B42 daily rainfall estimates over the state of Mato Grosso (southern Brazilian Amazon) for the 1998-2012 study period in order to compute rainfall metrics such as annual rainfall and duration, onset and end dates of the rainy season based on the Anomalous Accumulation methodology (at a 0.25◦ spatial resolution). We then crossed these metrics with agricultural maps (produced at a 250m spatial resolution) and proved that the adoption of intensive agricultural practices such as double cropping systems is partly the result of a strategy to adapt practices to local climatic conditions. Finally, we discuss how such results raise important issues regarding the sustainability of the agricultural development model in the Southern Amazon.
International Journal of Climatology

halshs-00910825
https://halshs.archives-ouvertes.fr/halshs-00910825
DOI : 10.1002/joc.3863

Éditeur(s) : HAL CCSD
Résumé : Tropical forests are a biodiversity hotspot, with the coexistence of numerous species until a fine spatial scale. Particularly, 16.000 tree species coexist in Amazonia, 1.800 in Frenche Guiana and between 120 and more than 200 tree species per hectare. However, there are some uncertainties in maintaining diversity in regard to global changes. Hence before predicting the diversity evolution face of global changes, fundamental studies are needed to understand which assembly processes are involved in the maintenance of diversity. These fundamental studies still relevant given the lack of consensus on the relative importance of assembly processes. This thesis is a continuation of these fundamental studies, using innovative integrative approach, at multi-scale, to address three types of diversity: taxonomic diversity, functional and phylogenetic. Our results challenge the importance of environmental filtering for hydrological and chemical properties of soils, versus the importance of biotic interactions on community assembly. Furthermore, our results suggest that species distributions could be affected by forest dynamics related to falling trees and therefore by light availability. Finally, we have highlighted the importance of dispersal limitation on community assembly.
Les forêts tropicales représentent un ‘hotspot’ de diversité avec un nombre considérable d’espèces qui coexistent jusqu’à une échelle locale fine. Plus particulièrement, 16 000 espèces d’arbres coexistent en Amazonie, 1 800 en Guyane française et entre 120 et plus de 200 espèces d’arbres par hectare. Cependant, le maintien de cette diversité face aux changements globaux actuels et à venir (qu’ils soient anthropiques ou climatiques…) est incertain. Avant de pouvoir prédire l’évolution de la diversité face aux changements globaux, un travail fondamental est nécessaire afin de comprendre les processus d’assemblage des communautés, processus qui maintiennent cette diversité. Ce travail est réalisé depuis de nombreuses années en écologie et reste d’actualité vu l’absence de consensus quant à l’importance relative des processus d’assemblage. Cette thèse s’inscrit dans la continuité de ce travail fondamental en utilisant une approche intégrative innovante, qui aborde de manière multi-échelle trois types de diversité : diversité taxonomique, fonctionnelle et phylogénétique. Nos résultats questionnent sur l'importance du filtrage environnemental quant aux propriétés hydrologiques et chimiques des sols, et sur celle des interactions biotiques dans l’assemblage de la communauté étudiée. Par ailleurs, nos résultats suggèrent que les distributions d’espèces puissent être influencées par la dynamique forestière en lien avec les chutes d’arbres et donc avec la disponibilité en lumière. Enfin, nous avons mis en évidence l’importance de la limitation de dispersion.
https://tel.archives-ouvertes.fr/tel-01418447

NNT : 2016YANE0003
tel-01418447
https://tel.archives-ouvertes.fr/tel-01418447
https://tel.archives-ouvertes.fr/tel-01418447/document
https://tel.archives-ouvertes.fr/tel-01418447/file/these.pdf

Éditeur(s) : HAL CCSD Oxford Journals
Résumé : International audience
Background - Several studies have investigated the implication of biological and environmental factors on geographic variations of end-stage renal disease (ESRD) incidence at large area scales, but none of them assessed the implication of neighbourhood characteristics (healthcare supply, socio-economic level and urbanization degree) on spatial repartition of ESRD. We evaluated the spatial implications of adjustment for neighbourhood characteristics on the spatial distribution of ESRD incidence at the smallest geographic unit in France.Methods - All adult patients living in Bretagne and beginning renal replacement therapy during the 2004–09 period were included. Their residential address was geocoded at the census block level. Each census block was characterized by socio-economic deprivation index, healthcare supply and rural/urban typology. Using a spatial scan statistic, we examined whether there were significant clusters of high risk of ESRD incidence.Results - The ESRD incidence was non-randomly spatially distributed, with a cluster of high risk in the western Bretagne region (relative risk, RR = 1.28, P-value = 0.0003). Adjustment for sex, age and neighbourhood characteristics induced cluster shifts. After these adjustments, a significant cluster (P = 0.013) persisted.Conclusions - Our spatial analysis of ESRD incidence at a fine scale, across a mixed rural/urban area, indicated that, beyond age and sex, neighbourhood characteristics explained a great part of spatial distribution of ESRD incidence. However, to better understand spatial variation of ESRD incidence, it would be necessary to research and adjust for other determinants of ESRD.
Clinical Kidney Journal

hal-01118626
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118626
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118626/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118626/file/Spatial%20distribution%20of%20end-stage%20renal%20disease.pdf
DOI : 10.1093/ckj/sfu131

Éditeur(s) : HAL CCSD
Résumé :   Diplôme : DEA
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
Tropical rainforests are complex ecosystems, rarely investigated from ground-level. The canopy, highest part of the cover, can on the other hand be studied by several remote sensing tools. The aim of this study is to assess in what way the canopy is related to the forest structure below and the forest dynamic. We looked for correlation between the canopy texture (crown size) observed from aerial photographs and various parameters of the forest (spatial and demographic structure, forest dynamic, floristic structure). We worked on the Paracou experimental device, in French Guiana, at two different scales. 1- At a local scale (6.5 ha ; scale of the photographs 1: 4 000), we demarcated six sub-plots with big crowns in the canopy and six with small crowns. 2- At a forest scale (approximately one hundred ha ; scale of the photograph 1: 25 000), we compared 2 forest plots: one with a rough canopy texture and one with a smooth canopy texture. We found that the size of the crowns in the canopy do not express the same characteristics of the fore according to the scale of study : at the local scale, difference in crown size means a difference in basal area but not in density, while at the forest scale it is the opposite. Several hypotheses related to the sylvigenetic cycle, the floristic structure or the nature of the substratum are suggested to explain these results.
Les forêts tropicales humides (FTH) sont des écosystèmes complexes difficiles à étudier depuis le sol. Leur canopée, partie supérieure du couvert, est en revanche abordable par divers outils de télédétection. Cette étude vise à déterminer en quoi la structure de la canopée est le reflet de la structure forestière sous-jacente et de la dynamique spatio-temporelle qui s'y exerce. Nous avons donc recherché des corrélations, entre la texture de canopée (taille des couronnes) vue sur des photographies aériennes, et différents paramètres de la forêt sous-jacente (structure spatiale et démographique, dynamique forestière, structure floristique). Ce travail a été abordé sur le dispositif expérimental forestier de Paracou, en Guyane Française, à 2 échelles différentes. 1- A l'échelle de la parcelle (6,5 ha ; photographies au 1: 4 000), nous avons délimité des placettes à grosses couronnes en canopée et des placettes à petites couronnes. 2- A l'échelle du massif forestier (une centaine d'ha ; photographies IGN au 1: 25 000) nous comparons une parcelle de texture de canopée, grossière et une parcelle de texture fine. Le résultat principal de notre étude est que la taille des couronnes en canopée ne reflète pas les mêmes caractéristiques du couvert selon l'échelle de l’étude : à l'échelle de la parcelle, des différences de taille de couronnes traduisent des différences de surface terrière mais pas de densité, tandis qu'à l'échelle du massif forestier c'est l'inverse. Plusieurs hypothèses, invoquant des différences dans le stade sylvigénétique, la composition floristique ou la nature du substrat des placettes ou parcelles comparées, sont proposées pour expliquer ces résultats.
https://hal.archives-ouvertes.fr/hal-01189180

hal-01189180
https://hal.archives-ouvertes.fr/hal-01189180
PRODINRA : 12184

Éditeur(s) : Ecole Nationale Supérieure Agronomique de Rennes (ENSAR)
Résumé : Artificial Fish Aggregating Devices (FADs) are known to concentrate tropical tunas. This aggregative behaviour drastically increases the vulnerability of these species to fishing. Alternatively, FADs can be used as oceanic observatories to study the aggregative behaviour of large pelagic fish. We conducted sea surveys in Martinique (Lesser Antilles) to i) establish a typology of the pelagic fish aggregations found around moored FADs ii) study their relations with their biotic and abiotic environment and the local fishery. The mean biomass of large pelagic fish aggregations was also estimated to provide scientific inputs to achieve a sustainable management of the moored FAD fishery. The first part presents the background of the study. We introduce the regional pelagic ecosystem, the aggregative behaviour of pelagic fish around FADs and the Martinican moored FAD fishery. The second part begins with a presentation of the conceptual framework of the study: the hierarchy theory. Observation scales and survey methodology are therefore described. Repeated echosounder surveys run in a star pattern were conducted around 2 moored FADs, in combination with underwater video observations, classical fishing experiments and CTD profiles. In the third part, the elements of the [moored FAD ¿ pelagic fish - environment - fishing] system and their interactions are numerically characterised in the vertical plane. The main type of pelagic fish aggregation was a large aggregation distributed in sub-surface (40-100 m) within a radius of 400 m of the FAD. This aggregation was mostly made of 60 cm FL blackfin tunas (Thunnus atlanticus). It appeared at sunrise and mostly spread away in the late afternoon. It was observed during all daytime surveys. The average density and the vertical structure of the micronektonic sound scattering layers (SSLs) were assessed locally around a FAD for 48h cycles. These SSLs descriptors showed positive correlation with the size and the abundance of the sub-surface tuna aggregation. Whereas this aggregation accounted for about 95% of the total biomass aggregated around a moored FAD, it was nearly unexploited by the local commercial fishermen. The fourth part focuses on the sub-surface tuna aggregation. A high variability of the spatial distribution of the aggregation was evidenced in the horizontal plane at daily, day to day and monthly temporal scales. These variations were related to fluctuations of the global abundance of the aggregation. The daytime average density of sub-surface tuna was modelled as a function of the distance to FAD, within an advection-diffusion framework. Based on these results, a universal kriging model was designed to assess the mean maximum daily biomass of the sub-surface tuna aggregation. This mean biomass estimate yielded 11 tons with an estimation error of 26%. To conclude, we present a hierarchical organization in space and time of a sub-surface tuna population distributed within a network of moored FADs, from micro to meso-scale. We suggest that the spatial distribution of tunas can be explained from fine to coarse-scales by behavioural processes (self-organization, feeding, aggregative behaviour) whereas their spatial distribution is mainly forced by environmental processes at broader scales.
L'utilisation de Dispositifs de Concentration de Poissons permet de provoquer la formation de larges agrégations de thonidés autour de dispositifs artificiels, ce qui augmente considérablement la vulnérabilité de ces ressources vis-à-vis de l'exploitation halieutique. Les DCP peuvent également être utilisés en tant qu'observatoires océaniques, afin d'étudier le comportement agrégatif du macronecton pélagique. Nous avons ainsi réalisé des observations autour de DCP ancrés en Martinique, afin de définir une typologie des agrégations de macronecton et de étudier leurs relations avec leur environnement biotique, abiotique et l'exploitation halieutique locale. Nous avons ensuite estimé la biomasse moyenne de macronecton agrégé autour d'un DCP ancré, afin de fournir des éléments scientifiques nécessaires à une gestion durable de ces ressources. La première partie présente le contexte de l'étude i.e. l'écosystème pélagique régional, le phénomène d'agrégation du macronecton autour des DCP et la pêche associée aux DCP ancrés en Martinique. La deuxième partie introduit la théorie de la hiérarchie qui a fourni le cadre conceptuel de l'étude et présente les échelles et méthodes d'observation. Le principal outil d'observation est un échosondeur scientifique, mis en oeuvre le long de parcours en étoile autour du DCP. Les prospections acoustiques ont été combinées à des observations vidéo sous marines, des pêches expérimentales et un suivi in-situ de l'environnement abiotique. La troisième partie présente une typologie des éléments constituant le système [DCP ancré - macronecton - environnement - pêche] dans le plan vertical et précise leurs interactions. Le type d'agrégation de macronecton dominant est une grande agrégation composée d'une majorité de thons noirs (Thunnus atlanticus) de taille moyenne (60 cm) distribuée en sub-surface (40-100 m), dans un rayon de 300 m autour de la tête des DCP. Cette agrégation se forme au lever du soleil et se disperse presque totalement dans l'après midi. Elle a été observée de jour lors de toutes les campagnes. Une corrélation positive entre la densité et la structure moyenne des couches micronectoniques diurnes évaluée localement autour du DCP au cours de 48 h et les dimensions et l'énergie acoustique de l'agrégation de thons de subs-surface a été mise en évidence. Malgré le fait que cette agrégation représente en moyenne 95 % de l'énergie acoustique du macronecton autour des DCP, elle est presque inexploitée par les pêcheurs artisans locaux. La quatrième partie met en évidence les fortes variations conjointes de la distribution spatiale dans le plan horizontal de la densité de l'agrégation de thons de sub-surface et de son abondance globale. Ces variations ont été observées au cours du cycle nycthéméral et aux échelles inter-journalières et mensuelles. La distribution spatiale moyenne de la densité diurne de l'agrégation en fonction de la distance au centre de gravité de l'agrégation est cependant très stable et peut être modélisée au moyen d'une équation d'advection-diffusion. Un modèle de krigeage universel, utilisant les résultats du modèle d'advection-diffusion, a permis d'évaluer la biomasse maximale journalière moyenne de l'agrégation de thons de sub-surface à une dizaine de tonnes, avec un coefficient de variation d'estimation de 26%. Nous proposons une représentation hiérarchique synthétique de la distribution spatiale d'une sous-population de thons dans un réseau de DCP ancrés de la micro à la méso-échelle. Nous suggérons que la distribution spatiale des thons est déterminée principalement à l'échelle fine (100m-1km) et à l'échelle grossière (1-10 km) par des processus comportementaux (auto-organisation, agrégation, nutrition) et par des processus environnementaux à échelle plus large.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/these-1735.pdf
http://archimer.ifremer.fr/doc/2006/sup-1735.pdf
http://archimer.ifremer.fr/doc/00000/1735/

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Seagrasses structure some of the world's key coastal ecosystems presently in decline due to human activities and global change. The ability to cope with environmental changes and the possibilities for shifts in distribution range depend largely on their evolvability and dispersal potential. As large-scale data usually show strong genetic structure for seagrasses, finer-grained work is needed to understand the local processes of dispersal, recruitment and colonization that could explain the apparent lack of exchange across large distances. We aimed to assess the fine-grained genetic structure of one of the most important and widely distributed seagrasses, Zostera marina, from seven meadows in Brittany, France. Both classic population genetics and network analysis confirmed a pattern of spatial segregation of polymorphism at both regional and local scales. One location exhibiting exclusively the variety 'angustifolia' did not appear more differentiated than the others, but instead showed a central position in the network analysis, confirming the status of this variety as an ecotype. This phenotypic diversity and the high allelic richness at nine microsatellites (2.33-9.67 alleles/locus) compared to levels previously reported across the distribution range, points to Brittany as a centre of diversity for Z. marina at both genetic and phenotypic levels. Despite dispersal potential of several 100 m, a significant pattern of genetic differentiation, even at fine-grained scale, revealed 'genetic patchiness'. Meadows seem to be composed of a mosaic of clones with distinct origins in space and time, a result that calls into question the accuracy of the concept of populations for such partially clonal species.
Molecular Ecology (0962-1083) (Wiley-blackwell Publishing, Inc), 2010-06 , Vol. 19 , N. 12 , P. 2394-2407

Droits : 2010 Blackwell Publishing Ltd
http://archimer.ifremer.fr/doc/00006/11690/8499.pdf
DOI:10.1111/j.1365-294X.2010.04649.x
http://archimer.ifremer.fr/doc/00006/11690/

Éditeur(s) : HAL CCSD
Résumé : International audience
We examined fine-scale heterogeneity of environmental conditions in a primary rain forest in French Guiana to describe variation in microhabitats that plants may experience during establishment. We characterized both the range as well as the spatial structuring of 11 environmental factors important for seedling establishment in six hexagonal sampling grids, one each in gap and understory sites at three points representing the predominant geomorphic units in this primary forest. Each grid contained 37 sampling points separated by 31 cm-20 m. Monte-Carlo tests of semivariograms against complete spatial randomness indicated that for many variables in all six sampling grids, spatial dependence did not exceed 1 m. A principal component analysis of all sampling points revealed a lack of spatial microhabitat structure, rather than homogeneous patches associated with canopy structure or geomorphology. Our results suggest that ample fine-scale spatial heterogeneity exists to support the coexistence of plant species with differential abiotic requirements for regeneration.
Botropica

halsde-00520179
https://hal.archives-ouvertes.fr/halsde-00520179
DOI : 10.1111/j.1744-7429.2009.00620.x

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Local variation in the density of Anopheles mosquitoes and the risk of exposure to bites are essential to explain the spatial and temporal heterogeneities in the transmission of malaria. Vector distribution is driven by environmental factors. Based on variables derived from satellite imagery and meteorological observations, this study aimed to dynamically model and map the densities of Anopheles darlingi in the municipality of Saint-Georges de l’Oyapock (French Guiana). Longitudinal sampling sessions of An. darlingi densities were conducted between September 2012 and October 2014. Landscape and meteorological data were collected and processed to extract a panel of variables that were potentially related to An. darlingi ecology. Based on these data, a robust methodology was formed to estimate a statistical predictive model of the spatial-temporal variations in the densities of An. darlingi in Saint-Georges de l’Oyapock. The final cross-validated model integrated two landscape variables—dense forest surface and built surface—together with four meteorological variables related to rainfall, evapotranspiration, and the minimal and maximal temperatures. Extrapolation of the model allowed the generation of predictive weekly maps of An. darlingi densities at a resolution of 10-m. Our results supported the use of satellite imagery and meteorological data to predict malaria vector densities. Such fine-scale modeling approach might be a useful tool for health authorities to plan control strategies and social communication in a cost-effective, targeted, and timely manner.
ISSN: 1932-6203

hal-01383486
https://hal.archives-ouvertes.fr/hal-01383486
https://hal.archives-ouvertes.fr/hal-01383486/document
https://hal.archives-ouvertes.fr/hal-01383486/file/Adde_et_al_PlosONE_2016.pdf
DOI : 10.1371/journal.pone.0164685

Résumé : Cette thèse concerne la modélisation des dynamiques de maladies foliaires de cultures pérennes tropicales à différentes échelles spatiales. Cette approche de modélisation est appliquée à la cercosporiose noire du bananier. Il s’agit d’explorer et de déterminer les paramètres environnementaux et de résistance de l’hôte ayant une influence significative sur la dynamique spatiotemporelle de la maladie et d’apporter des éléments associés au contrôle de la cercosporiose noire.Deux modèles ont été développés dans le cadre de cette thèse. La dynamique épidémiologique au niveau de la plante est décrite par un modèle mécaniste décomposé en un modèle de croissance de la plante et un module épidémiologique décrivant le cycle épidémique du pathogène. L’architecture du bananier est prise en compte par le biais de compartiments foliaires positionnés dans l’espace. Le modèle a été validé par un jeu de données indépendant. Les expérimentations numériques et l’analyse de sensibilité du modèle réalisées par les méthodes de Morris et de e-FAST ont permis de mieux comprendre le fonctionnement épidémique de cette maladie et d’identifier les paramètres influant le plus la dynamique épidémique en particulier la vitesse d’extension des lésions, la durée d’incubation et l’efficacité d’infection .L’approche bayésienne a permis de prendre en compte l’information a priori disponible pour ces trois paramètres sur lesquels a porté l’inférence statistique. L’analyse de sensibilité du modèle a également permis d’identifier l’influence de deux paramètres liés à la croissance de la plante : le nombre de feuilles sur une plante et le rythme d’émission foliaire Un modèle de dynamique spatio-temporelle de la cercosporiose noire a été développé à l’échelle d’un territoire à partir d’enquêtes effectuées enMartinique pendant la période d’invasion de cette maladie de septembre 2010 à mai 2012. Les données récoltées étant censurées, l’inférence des paramètres du modèle a été réalisée dans un cadre bayésien en utilisant un algorithme d’augmentation de données. Le modèle et l’inférence développés permettent de reconstruire la dynamique spatio-temporelle de l’invasion et de prédire la fin d’invasion sur le territoire.Les deux modèles de dynamiques spatio-temporelles développés à deux échelles spatiales différentes ont permis d’acquérir des informations importantes pour construire des outils de conception de méthode de contrôle de la cercosporiose noire des bananiers.
This thesis concerns the modeling of the dynamics of foliar diseases of tropical tree crops at different spatial scales. This modeling approach is applied to black Sigatoka of banana. It is to explore and determine the environmental parameters and host resistance has a significant influence on the spatiotemporal dynamics of the disease and to provide elements associated with the control of Sigatoka noire.Deux models were developed as part of this thesis. The epidemiological dynamics at the plant is described by a mechanistic model decomposed into a growth model of the plant and an epidemiological unit describing the pathogen epidemic cycle. The architecture of the banana is taken into account through foliar compartments positioned in space. The model was validated by an independent data set. Numerical experiments and model sensitivity analysis performed by the methods of Morris and e-FAST enabled to better understand the functioning of this epidemic disease and identify the parameters affecting the most dynamic epidemic especially speed extension of the lesions, the incubation period and efficiency of Bayesian .L'approche infection allowed to take into account prior information available for these three parameters that were the statistical inference. The model sensitivity analysis also identified the influence of two parameters related to plant growth: the number of leaves on a plant and rate of leaf emission A dynamic model of space-time Black Sigatoka has been developed at the scale of a territory from surveys enMartinique during the period of invasion of the disease from September 2010 to May 2012. The data collected being censored, inference of model parameters has was performed in a Bayesian framework, using a data augmentation algorithm. The model developed and inference possible to reconstruct the spatiotemporal dynamics of the invasion and predict the end of the invasion territoire.Les two spatio-temporal dynamics models developed at two different spatial scales has been gained important information for build tools design method of control of black Sigatoka of banana.

http://www.theses.fr/2015AGUY0835/document

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.
ISSN: 1932-6203

hal-01608324
https://hal.archives-ouvertes.fr/hal-01608324
DOI : 10.1371/journal.pone.0182515
PRODINRA : 403154
PUBMED : 28771629

Éditeur(s) : Styli 2003. Trente ans de crevetticulture en Nouvelle-Calédonie. Nouméa - Koné, 2-6 juin 2003. 2004. Gorarant C, Harache Y, Herbland A, Mugnier C. Ed. Ifremer, Actes de Colloque, n°38, pp.113-120
Résumé : Two oyster species are currently present along the French coasts : the indigenous European flat oyster (Ostrea edulis), and the Pacific cupped oyster (Crassostrea gigas), that has been introduced from Japan since the beginning of the 70ies. The flat oyster successively suffered from two protozoan diseases during the 60ies and its production decreased from 20 000 tons/year by that time to 1 500 tons/year nowadays. Consequently, the oyster production is principally (99%) based upon the Pacific oyster species with approximately 150 000 tons/year among which 90% are grown from the natural spat. However, the hatchery production of this species is developing and was estimated to 400 to 800 millions spat in 2002. Moreover, strengthened relationships between IFREMER and the 5 commercial hatcheries, that all joined the SYSAAF (Union of the French poultry, shellfish and fish farming selectors), allow to plan for new genetic breeding programs. At the end of the 80ies, IFREMER initiated a genetic breeding program for the resistance of the European flat oyster to the bonamiosis, and obtained strains more tolerant to this disease. After two generations of massal selection, molecular markers had identified a reduced genetic basis in this program. It was then reoriented to an intra-familial selection. However, we were confronted to a zootechnic problem to manage such a scheme and we compromised by an intra-cohorts of families selection scheme managed using molecular markers. The program has now reached the transfer level with experimentation at a professional scale. Concerning the Pacific cupped oyster, and in parallel with the obtaining and the study of polyploids, performance of different Asian cupped oyster strains were compared to the one introduced in France thirty years ago and currently suffering from summer mortalities. The local strain exhibited better performance, certainly based upon a good local adaptation. In other respects, although early growth is a relevant criteria for selection for growth to commercial stage, it is not to be privileged in the context of an oyster producing region with a limited food availability. Contrary, the spat summer mortality became a priority for numerous teams (genetic, physiology, pathology, ecology,...) joined in the MOREST program. The first results showed important survival differences between fullsib and halsib families. They indicate a genetic determinism to this character "survival" and promote for its selection.
Deux espèces d'huîtres sont aujourd'hui présentes sur les côtes françaises : l'huître plate européenne (Ostrea edulis), indigène, et l'huître creuse du Pacifique (Crassostrea gigas), introduite du Japon dans le début des années 1970. L'huître plate a subi coup sur coup, dans les années 1960, deux maladies dues à des protozoaires parasites et sa production est ainsi passée de 20 000 t/an dans les années 1960 à 1500 t/an aujourd'hui en France. Il en résulte que la filière ostréicole française repose quasiment exclusivement (99%) sur la production de l'huître creuse, C. gigas, avec 150 000 tonnes en 2000 dont environ 90% est issu du captage naturel. Cependant, la reproduction de cette espèce en écloserie est actuellement en expansion avec une estimation de 400 à 800 millions de naissains commercialisés en 2002. Des rapports renforcés entre l'IFREMER et les cinq écloseries françaises de la filière ostréicole, qui adhèrent toutes au SYSAAF (SYndicat des Sélectionneurs Avicoles et Aquacoles Français), permettent désormais d'envisager le développement de nouveaux programmes d'amélioration génétique. A la fin des années 1980, un programme de sélection pour la résistance de l'huître plate à la bonamiose a été initié au sein de l'IFREMER, et a permis d'obtenir des souches plus tolérantes à cette maladie. Après deux générations en sélection massale, les marqueurs moléculaires avaient mis en évidence une base génétique réduite au sein de ce programme qui s'était alors orienté vers une sélection intra-familiale. Devant la lourdeur zootechnique d'un tel schéma, un compromis a été trouvé en réalisant une sélection au sein de cohortes de familles biparentales, la gestion de ces cohortes étant permise par les analyses moléculaires. Le programme est maintenant dans sa phase de transfert, avec des expérimentations à plus grande échelle en partenariat avec la profession. En ce qui concerne l'huître creuse, et en parallèle de l'obtention et l'étude de polyploïdes, les performances de différentes souches d'huîtres creuses provenant d'Asie ont été comparées à celles de la souche introduite en France il y a trente ans, sujette à des mortalités estivales. La souche locale présente de meilleures performances, vraisemblablement grâce à une adaptation bien réalisée. Par ailleurs, bien que l'amélioration de la croissance jusqu'à la taille commerciale s'avère possible par une sélection précoce au stade larvaire, le critère de croissance n'est pas nécessairement à privilégier dans le contexte d'un bassin ostréicole disposant de ressources trophiques limitées. En revanche, les importantes mortalités rencontrées par le naissain en périodes estivales constituent le sujet d'étude prioritaire sur lequel se sont penchées de nombreuses équipes (génétique, physiologie, pathologie, écologie, ...) dans le cadre du grand défi MOREST. Les premiers résultats ont mis en évidence de fortes différences de survie entre des familles biparentales d'animaux indiquant un déterminisme génétique du caractère « survie », et encourageant dans la voie d'une sélection pour ce caractère.

Droits : 2004 Ifremer
http://archimer.ifremer.fr/doc/2003/acte-3491.pdf
http://archimer.ifremer.fr/doc/00000/3491/