Éditeur(s) : Université de la Réunion
Résumé : The green turtle (Chelonia mydas) is an emblematic species of marine life. However, nowadays it is subject to many threats (poaching, by-catch). Even if there is deep growing measures for its protection, the green turtle still is an endangered species and it is listed in Appendix I of Washington Convention (CITES). In order to elaborate efficient conservation and management plans, perfect knowledge of green turtle biology, but also of its population structure and their characteristics, are needed. In this thesis, we have assessed genetic structure of green turtle populations in the South-Western Indian Ocean by using genetic tools. In all, 1551 tissue samples have been collected from our study zone and from our control site French Polynesia (37 samples). All kinds if individuals were sampled (except males in reproductive phase) from 15 sampling sites including nesting, foraging, and immature development site. We used both control region of mitochondrial DNA and 6 microsatellite loci to better infer maternal and paternal lineages. We identified 29 haplotypes in the South-Western Indian Ocean. They are distributed in 3 independent and highly divergent clades, including one composed with haplotypes from Atlantic Ocean. For 7 of these haplotypes, it was the first time they were detected in the study zone. Fifteen haplotypes were previously undescribed, distributed in all the 3 clades. These new haplotypes seem to be specific to the South-Western Indian Ocean, which is then an original zone. Besides, we found a high allelic richness. These results show the South-western Indian Ocean is rich and very diversified. This region plays an important role in the global diversity of the species. The South-Western Indian Ocean is one of the two contact zones presently known between the two metapopulations of green turtles (Atlantic-Mediterranean and Indo-Pacific). This contact induces a genetic cline based on CM8 (Atlantic) and C3 (Indo-Pacific) haplotype frequencies. Analysis of the microsatellite differentiation between individuals provides evidence of genetic exchanges between the two metapopulations in the region. The South-Western Indian Ocean participates to green turtle global genetic mixing. Studying the influence of several intrinsic and extrinsic factors on population structuring provides useful information for management plan elaboration. We found no significant difference between genetic structures of foraging females and males, contrary to immature turtles which seem to be organised in 'regional pools'. This organisation could be due to both immature natal homing and influence of oceanic currents. High mitochondrial differentiation of nesting females and low global microsatellite differentiation of our samples indicate male-mediated gene flow among populations of the study zone. The genetic composition of a sampling site presents no significant variation along the year, even if we could notice some trends. Nevertheless, it can be significantly different from a year to an other one. This may result from alternation of distinct populations on the same site. We noticed different evolution in 10 or 20 years of the genetic composition depending on the sampling site. Geographic distance seems not to have significant influence on population structuring concerning microsatellite markers. Nesting females of Saziley Beach (Mayotte Island, Comoros Archipelago) present genetic divergence from females nesting in the two other sampled beaches of this island. The observed population structure shows no contradiction with the organisation of oceanic currents in the South-Western Indian Ocean. Comparing the results from the two genetic markers used, we identified 8 genetic differentiated clusters of turtles in the study zone and at least 6 distinct populations. These clusters constitute 8 potential management units (MUs) which could serve as basis in the elaboration of conservation and management plans.
La tortue verte (Chelonia mydas) constitue l'un des espèces emblématiques de la vie marine, pourtant de nombreuses menaces pèsent de nos jours encore sur sa survie (braconnage, captures accidentelles). Ainsi, malgré l'essor de mesures de protection menées à travers pour sa sauvegarde, la tortue verte constitue une espèce 'en danger d'extinction' et figure dans l'Annexe I de la Convention de Washington (CITES). Afin d'élaborer des plans de gestion et de conservation qui soient efficaces, il est important d'avoir une parfaite connaissance de la biologie de la tortue verte, mais aussi de la structure de ses populations et de leurs caractéristiques. C'est dans ce cadre que s'inscrit la présente étude. L'objectif de cette étude était d'acquérir des connaissances sur la structure des populations de tortues vertes dans le sud-ouest de l'océan Indien grâce à l'utilisation de l'outil génétique. Au total, 1551 échantillons de tissu ont été collectés dans la zone d'étude et dans notre site témoin la Polynésie française (37 échantillons). Toutes les catégories d'individus ont été échantillonnées (excepté les mâles en phase de reproduction) et les 15 sites d'échantillonnage comprennent à la fois des sites de ponte, d'alimentation et de développement pour les immatures. Deux types de marqueurs ont été utilisés : la région contrôle de l'ADN mitochondrial et 6 loci microsatellites, afin d'appréhender au mieux l'apport des lignées maternelles et paternelles. Nous avons pu mettre en évidence la présence dans le sud-ouest de l'océan Indien de 29 haplotypes distincts, appartenant à trois clades fortement divergents dont l'un constitué d'haplotypes originaires de l'océan Atlantique. Parmi ces haplotypes, 7 ont été détectés pour la première fois dans la zone d'étude, et 15 autres n'ont jamais été précédemment décrits chez cette espèce. Ils sont présents dans chacun des 3 clades d'haplotypes. Ces nouveaux haplotypes semblent spécifiques à la région, et en font une zone originale. On observe par ailleurs une grande richesse allélique dans les effectifs analysés. Ces résultats montrent que le sud-ouest de l'océan Indien est une zone riche et très diversifiée. Cette région joue un rôle important dans la diversité génétique globale de l'espèce. Le sud-ouest de l'océan Indien constitue l'une des deux seules zones connues à l'heure actuelle de contact entre les deux métapopulations de tortues vertes (Atlantique-Méditerranée et Indo-Pacifique). Ce contact a entraîné la formation d'un cline génétique portant principalement sur les fréquences relatives des haplotypes CM8 (Atlantique) et C3 (Indo-Pacifique). Les résultats obtenus lors de l'analyse microsatellite de la différenciation entre les individus originaires des deux métapopulations montrent que le sud-ouest de l'océan Indien constitue une zone d'échanges génétiques entre les deux métapopulations, participant au brasage génétique de l'espèce. L'étude de facteurs, intrinsèques et extrinsèques, pouvant influencer la structuration des populations apportent de nombreuses informations qui pourraient s'avérer utiles lors de l'élaboration de plans de gestion. La structure des femelles et des mâles en alimentation ne diffère pas, contrairement à celle des immatures qui semble s'organiser en 'pools régionaux' qui seraient le fruit de l'interaction d'un comportement de philopatrie et d'une influence des courants océaniques. La forte différenciation mitochondriale des femelles en ponte et la très faible différenciation microsatellite observée à l'échelle de la région, indiquent l'existence de flux de gènes via les mâles. La composition génétique d'un site ne varie pas de manière significative au cours de l'année. Par contre, elle peut varier d'une année à l'autre, signifiant l'alternance dans certains sites de ponte de plusieurs populations distinctes. L'évolution de la composition génétique d'un groupe, au cours de 10 ou 20 ans, diffère selon le site considéré. La distance ne semble pas influencer de manière significative la structuration des populations au niveau microsatellite. Les femelles en ponte sur la plage de Saziley (Mayotte) diffèrent génétiquement de celles pondant sur les deux autres plages de l'île. La structure observée des populations est en accord avec l'organisation des courants océanique dans la région. La confrontation des résultats obtenus à partir des deux marqueurs génétiques utilisés, permet la détermination de 8 ensembles génétiquement différenciés dans la zone d'étude et l'identification d'au moins 6 populations distinctes. Ces ensembles constituent autant d'unités de gestion (MUs) potentielles qui pourront servir de base à l'élaboration de plans de gestion et de conservation.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/these-3532.pdf
http://archimer.ifremer.fr/doc/00000/3532/

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : Boundary Exchange (BE - exchange of elements between continental margins and the open ocean) has been emphasized as a key process in the oceanic cycle of neodymium (Nd) (Lacan and Jeandel, 2005a). Here, we use a regional eddy-permitting resolution Ocean General Circulation Model (1/4A degrees) of the North Atlantic basin to simulate the distribution of the Nd isotopic composition, considering BE as the only source. Results show good agreement with the data, confirming previous results obtained using the same parameterization of the source in a coarse resolution global model (Arsouze et al., 2007), and therefore the major control played by the BE processes in the Nd cycle on the regional scale. We quantified the exchange rate of the BE, and found that the time needed for the continental margins to significantly imprint the chemical composition of the surrounding seawater (further referred as characteristic exchange time) is of the order of 0.2 years. However, the timescale of the BE may be subject to large variations as a very short exchange time (a few days) is needed to reproduce the highly negative values of surface waters in the Labrador Sea, whereas a longer one (up to 0.5 years) is required to simulate the radiogenic influence of basaltic margins and distinguish the negative isotopic signatures of North Atlantic Deep Water from the more radiogenic southern origin water masses. This likely represents geographical variations in erosion fluxes and the subsequent particle load onto the continental margins. Although the parameterization of the BE is the same in both configurations of the model, the characteristic exchange time in the eddy-permitting configuration is significantly lower than the previous evaluations using a low resolution configuration (6 months to 10 years), but however in agreement with the available seawater Nd isotope data. This results highlights the importance of the model dynamics in simulating the BE process.
Ocean Science (1812-0784) (Copernicus Gesellschaft Mbh), 2010 , Vol. 6 , N. 3 , P. 789-797

Droits : Author(s) 2010. This work is distributed, EGU
http://archimer.ifremer.fr/doc/00013/12412/9201.pdf
DOI:10.5194/os-6-789-2010
http://archimer.ifremer.fr/doc/00013/12412/

Éditeur(s) : Inter-Research
Résumé : The spatial structure of demersal fish assemblages on the continental shelf of the NW Mediterranean Sea was examined on a large scale between the Straits of Gibraltar and the Gulf of Lions. In contrast to its predominant role in the spatial distribution of species composition, described worldwide, it seems depth has only a limited effect on the distribution patterns of the total abundance and diversity of demersal fishes. In addition, evidence is provided for the division of the whole study area into 3 geographical fish assemblages. The influence of Atlantic inputs and the semi-permanent Almena-Oran hydrographic front play a key role in defining the Alboran Sea as a specific fish fauna area. Moreover, the clear differentiation between 2 distinct assemblages in the Gulf of Lions and the Catalan Sea could be partly linked to the North Balearic front. These results contribute to the current debate on the definition of spatial units for the purpose of demersal fisheries management. They also stress the complexity of developing an ecosystem approach which deals simultaneously with species composition and biodiversity aspects of ecosystems management.
Marine Ecology Progress Series (0171-8630) (Inter-Research), 2005-08 , Vol. 297 , P. 245-257

Droits : Inter-Research 2005
http://archimer.ifremer.fr/doc/2005/publication-3623.pdf
DOI:10.3354/meps297245
http://archimer.ifremer.fr/doc/00000/3623/

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Upper-mantle flow beneath the South Pacific is investigated by analysing shear wave splitting parameters at eight permanent long-period and broad-band seismic stations and 10 broad-band stations deployed in French Polynesia from 2001 to 2005 in the framework of the Polynesian Lithosphere and Upper Mantle Experiment (PLUME). Despite the small number of eventsand the rather poor backazimuthal coverage due to the geographical distribution of the natural seismicity, upper-mantle seismic anisotropy has been detected at all stations except at Tahiti where two permanent stations with 15 yr of data show an apparent isotropy. The median value of fast polarization azimuths (N67.5°W) is parallel to the present Pacific absolute platemotion direction in French Polynesia (APM: N67°W). This suggests that the observed SKS fast polarization directions result mainly from olivine crystal preferred orientations produced by deformation in the sublithospheric mantle due to viscous entrainment by the moving Pacific Plate and preserved in the lithosphere as the plate cools. However, analysis of individualmeasurements highlights variations of splitting parameters with event backazimuth that imply an actual upper-mantle structure more complex than a single anisotropic layer with horizontal fast axis. A forward approach shows that a two-layer structure of anisotropy beneath French Polynesia better explains the splitting observations than a single anisotropic layer. Second ordervariations in the measurements may also indicate the presence of small-scale lateral heterogeneities. The influence of plumes or fracture zones within the studied area does not appear to dominate the large-scale anisotropy pattern but may explain these second-order splitting variations across the network.
ISSN: 0956-540X

hal-01249275
https://hal.archives-ouvertes.fr/hal-01249275
https://hal.archives-ouvertes.fr/hal-01249275/document
https://hal.archives-ouvertes.fr/hal-01249275/file/GJI2007SKS.pdf
DOI : 10.1111/j.1365-246X.2007.03475.x

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species.[br/] [br/] [b]Location[/b][br/] Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America.[br/] [br/] [b]Methods[/b][br/] Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH-psbA and trnC-ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times.[br/] [br/] [b]Results[/b][br/] Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal.[br/] [br/] [b]Main conclusions[/b][br/] The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.
ISSN: 0305-0270

hal-01032395
https://hal.archives-ouvertes.fr/hal-01032395
DOI : 10.1111/j.1365-2699.2011.02678.x

Éditeur(s) : Public Library Science
Résumé : Like hydrothermal vents along oceanic ridges, cold seeps are patchy and isolated ecosystems along continental margins, extending from bathyal to abyssal depths. The Atlantic Equatorial Belt (AEB), from the Gulf of Mexico to the Gulf of Guinea, was one focus of the Census of Marine Life ChEss (Chemosynthetic Ecosystems) program to study biogeography of seep and vent fauna. We present a review and analysis of collections from five seep regions along the AEB: the Gulf of Mexico where extensive faunal sampling has been conducted from 400 to 3300m, the Barbados accretionary prism, the Blake ridge diapir, and in the Eastern Atlantic from the Congo and Gabon margins and the recently explored Nigeria margin. Of the 72 taxa identified at the species level, a total of 9 species or species complexes are identified as amphi-Atlantic. Similarity analyses based on both Bray Curtis and Hellinger distances among 9 faunal collections, and principal component analysis based on presence/absence of megafauna species at these sites, suggest that within the AEB seep megafauna community structure is influenced primarily by depth rather than by geographic distance. Depth segregation is observed between 1000 and 2000m, with the middle slope sites either grouped with those deeper than 2000m or with the shallower sites. The highest level of community similarity was found between the seeps of the Florida escarpment and Congo margin. In the western Atlantic, the highest degree of similarity is observed between the shallowest sites of the Barbados prism and of the Louisiana slope. The high number of amphi-atlantic cold-seep species that do not cluster according to biogeographic regions, and the importance of depth in structuring AEB cold-seep communities are the major conclusions of this study. The hydrothermal vent sites along the Mid Atlantic Ridge (MAR) did not appear as "stepping stones" for dispersal of the AEB seep fauna, however, the south MAR and off axis regions should be further explored to more fully test this hypothesis.
Plos One (1932-6203) (Public Library Science), 2010-08 , Vol. 5 , N. 8 , P. 1-11

Droits : © 2010 Olu et al.
http://archimer.ifremer.fr/doc/00011/12207/8975.pdf
DOI:10.1371/journal.pone.0011967
http://archimer.ifremer.fr/doc/00011/12207/

Éditeur(s) : HAL CCSD BOKU - University of Natural Resources and Applied Life Sciences
Résumé : International audience
Our paper is based on the first results of a twofold interdisciplinary research project financed by the French Ministry of the Environment (DIVA2 programme) which purpose was to analyse the emergence of biodiversity conservation as a new goal set to geographical indications and to study its effects on the strategies of the various stakeholders, and their impacts on the farming practices and the...
Building sustainable rural futures: the added value of systems approaches in times of change and uncertainty. 9th European IFSA Symposium, Vienna, Austria, 4-7 July 2010.
Vienna, Austria

hal-00979640
https://hal-agroparistech.archives-ouvertes.fr/hal-00979640

Éditeur(s) : HAL CCSD Wiley
Résumé : 1. Trade-offs among functional traits reveal major plant strategies that can give insight into species distributions and ecosystem processes. However, current identification of plant strategies lacks the integration of root structural traits together with leaf and stem traits. 2. We examined correlations among 14 traits representing leaf, stem and woody root tissues. Traits were measured on 1084 individuals representing 758 Neotropical tree species, across 13 sites representative of the environmental variation encompassed by three widespread habitats (seasonally flooded, clay terra firme and white-sand forests) at opposite ends of Amazonia (French Guiana and Peru). 3. Woody root traits were closely aligned with stem traits, but not with leaf traits. Altogether leaf, stem and woody root traits delineated two orthogonal axes of functional trade-offs: a first axis defined by leaf traits, corresponding to a leaf economics spectrum, and a second axis defined by covarying stem and woody root traits, corresponding to a wood economics spectrum. These axes remained consistent when accounting for species evolutionary history with phylogenetically independent contrasts. 4. Despite the strong species turnover across sites, the covariation among root and stem structural traits as well as their orthogonality to leaf traits were strongly consistent across habitats and regions. 5. We conclude that root structural traits mirrored stem traits rather than leaf traits in Neotropical trees. Leaf and wood traits define an integrated whole-plant strategy in lowland South American forests that may contribute to a more complete understanding of plant responses to global changes in both correlative and modelling approaches. We suggest further meta-analyses in expanded environmental and geographic zones to determine the generality of this pattern.
ISSN: 0269-8463

hal-01032415
https://hal.archives-ouvertes.fr/hal-01032415
DOI : 10.1111/j.1365-2435.2012.02020.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Background : Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions.Results : Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change.Conclusions : We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time.
ISSN: 0960-9822

hal-01149637
http://hal.upmc.fr/hal-01149637
http://hal.upmc.fr/hal-01149637/document
http://hal.upmc.fr/hal-01149637/file/Logares_et_al_CurrentBiol_accepted.pdf
DOI : 10.1016/j.cub.2014.02.050

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 Elsevier
Résumé : International audience
Several studies have documented that more deprived populations tend to live in areas characterized by higher levels of environmental pollution. Yet, time trends and geographic patterns of this disproportionate distribution of environmental burden remain poorly assessed, especially in Europe. We investigated the spatial and temporal relationship between ambient air nitrogen dioxide (NO2) concentrations and socioeconomic and demographic data in four French metropolitan areas (Lille in the North, Lyon in the center, Marseille in the South, and Paris) during two different time periods. The geographical unit used was the census block. The dependent variable was the NO2 annual average concentration (μg/m(3)) per census block, and the explanatory variables were a neighborhood deprivation index and socioeconomic and demographic data derived from the national census. Generalized additive models were used to account for spatial autocorrelation. We found that the strength and direction of the association between deprivation and NO2 estimates varied between cities. In Paris, census blocks with the higher social categories are exposed to higher mean concentrations of NO2. However, in Lille and Marseille, the most deprived census blocks are the most exposed to NO2. In Lyon, the census blocks in the middle social categories were more likely to have higher concentrations than in the lower social categories. Despite a general reduction in NO2 concentrations over the study period in the four metropolitan areas, we found contrasting results in the temporal trend of environmental inequalities. There is clear evidence of city-specific spatial and temporal environmental inequalities that relate to the historical socioeconomic make-up of the cities and its evolution. Hence, general statements about environmental and social inequalities can be made.
ISSN: 0013-9351

hal-01063900
https://hal.archives-ouvertes.fr/hal-01063900
DOI : 10.1016/j.envres.2014.07.017
PUBMED : 25199972

Éditeur(s) : World Aquaculture Society, Aquaculture 2006
Résumé : Oysters are among the most familiar of all marine invertebrate taxa. However our knowledge of oyster phylogeny and systematics is fragmentary. This is principally due to the plastic growth patterns of these animals, which result in a wide range of overlapping, ecophenotypic variants that greatly reduce the value of analysis based on shell morphology. Besides that, many intentional or accidental anthropogenic transfers have emphasised this situation. In several cases of misclassification or misidentification of oysters, DNA molecular data, have provided valuable new insights on the tracing of introductions or more generally on the phylogeographic relationships between oyster species. We will illustrate this issue with recent case studies from our lab on several flat and cupped oysters: (1) the Crassostrea gigas – Crassostrea angulata couple of Asian species and their successive introductions in Europe, (2) the new species of cupped oysters, Crassostrea honkongensis, described in Hong-Kong and very divergent from the species Crassostrea gigas it was initially supposed to be, (3) the mangrove oyster Crassostrea gasar that was shown not only to be present along the coasts of Western Africa but also along the Atlantic coasts of South America, and (4) the geographic disjunction between Ostreola stentina, described in the Mediterranean Sea, and the genetically closely related species Ostrea aupouria (from New Zealand) and Ostreola equestris (from Mexico Gulf/Atlantic). At the intra specific level, we will focus on one of the main documented case in Europe, the flat oyster, Ostrea edulis. It is a marine bivalve whose natural geographical distribution ranges along the European Atlantic coast from Norway to Morocco, in addition to the Mediterranean and Black Sea. Studies of allozymes, microsatellites and mitochondrial differentiation over the whole range concluded that a significant divergence existed between Mediterranean and Atlantic populations, together with an isolation-by-distance pattern. However, the average mitochondrial haplotypic diversity displayed a high among populations variance, reflecting smaller effective population size in some locations. Additionally, a ten-fold quantitative difference was observed in the same study in Fst between the mitochondrial and the nuclear genomes, which could be due to sex biased differential reproductive success between males and females. In order to further document this hypothesis, two experiments at the population level were conducted. First, brooding females were sampled in a wild population and the number of males fertilizing a given female estimated. Then, parentage analyses were achieved under experimental conditions: successive mass spawnings were collected from a population of potential genitors kept in hatchery, whose genotypes were known, in order to infer a posteriori the relative contribution of each genitor. Moreover, we aimed to better understand the reproduction dynamics of this species. Several patterns of spawning could be distinguished: unique, successive or extended in time. The different parental contributions and reproductive behaviors observed in these experiments are discussed in the context of the hypothesis of a variance in the reproductive success of males and females and consequences in local and temporal reduced effective population sizes.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/acte-3475.pdf
http://archimer.ifremer.fr/doc/00000/3475/

Éditeur(s) : Pêche thonière et dispositifs de concentration de poissons, Caribbean-Martinique, 15-19 Oct 1999
Résumé : For most fisheries, increasing the local production of pelagic fish is the main objective of Fish Aggregating Devices (fads). This does not rule out the existence of a larger-scale impact, especially on the migratory behaviour of fish. The analysis of data collected during 25 experimental fishing surveys around Martinique between 1995 and 1997 has led to the hypothesis that fads influence the migratory behaviour of young dolphinfish. Unlike recent studies of dolphinfish migration in the Caribbean, which tend to show an annual migration pattern with a seasonal passage through the French West Indies, the experimental fishing surveys done over more than a year on a monthly basis on a single cohort, show that the migratory pattern of part of the regional stock could be disrupted. This analysis has made it possible to estimate an average growth rate for this species during the first year of life.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00042/15321/12635.pdf
http://archimer.ifremer.fr/doc/00042/15321/

Éditeur(s) : Elsevier
Résumé : Total (T-Hg) and organic (O-Hg) mercury concentrations and tissue distribution were examined in 20 species of cephalopods (n = 278) from the north eastern Atlantic waters, i.e. from the Bay of Biscay to the Faroe Islands. Concentrations of T-Hg in whole cephalopods showed elevated variations among species, i.e. from 40 to 3560ng g(-1) dwt, but a low variability within each species (mean CV%=39%). With the exception of oceanic squids, the digestive gland globally displayed higher T-Hg concentrations than the remaining tissues. In contrast, O-Hg concentrations determined in selected species were generally higher in the remaining tissues. Despite higher T-Hg concentrations, the digestive gland weakly contributed to the total body burden of both T-Hg and O-Hg (< 25% and < 15%, respectively). In fact, from 75% to 95% of the T-Hg and O-Mg were contained in the muscular remaining tissues. Therefore, O-Hg may have a strong affinity to proteins in cephalopods. Sex and size only significantly influenced the bioaccumulation of Hg for the Loliginidae family. T-Hg and O-Hg concentrations were also influenced by geographical origin: Celtic Sea > Bay of Biscay > Faroe Islands, corresponding to the seawater Hg concentrations in these areas. In the Faroe Islands and the Celtic Sea, benthic cephalopods contained significant higher Hg concentrations compared to pelagic ones. This suggests that diet is not the main pathway of Hg uptake in cephalopods as pelagic species were expected to be more exposed to O-Hg through fish consumption than benthic ones. (c) 2006 Elsevier B.V. All rights reserved.
The Science of The Total Environment (0048-9697) (Elsevier), 2006-09 , Vol. 368 , N. 2-3 , P. 585-596

Droits : 2006 Elsevier
http://archimer.ifremer.fr/doc/2006/publication-1873.pdf
DOI:10.1016/j.scitotenv.2006.01.038
http://archimer.ifremer.fr/doc/00000/1873/

Éditeur(s) : HAL CCSD
Résumé : Over the last decade, distance-based methods have been introduced and then improved in the field of spatial economics to gauge the geographic concentration of activities. There is a growing literature on this theme including new tools, discussions on their specific properties and various applications. However, there is currently no typology of distance-based methods. This paper fills that gap. The proposed classification helps understand all the properties of distance-based methods and proves that they are variations on the same framework.
https://halshs.archives-ouvertes.fr/halshs-00679993

halshs-00679993
https://halshs.archives-ouvertes.fr/halshs-00679993
https://halshs.archives-ouvertes.fr/halshs-00679993v3/document

Éditeur(s) : Elsevier Sci Ltd
Résumé : Time-series studies have reported trophic cascades in land, freshwater and marine environments in many geographic areas. However, the spatial extent of habitats, a key metric of ecosystem structure, has not been mapped in these studies. Marine reserves can provide experimental, before-after and inside-outside (control-impacted), situations for assessing the impact of fishing on ecosystems. We mapped seabed habitats and their associated communities (biotopes) in New Zealand's oldest marine reserve for comparison with pre-reserve maps created about 30 years previously. Areas grazed bare by sea urchins were entirely replaced in the centre of the reserve by kelp, or alga turf, an intermediate biotope between heavily grazed encrusting algae and lightly grazed kelp. Urchins declined following increased abundance and body size of spiny (rock) lobsters and fish (especially snapper) in the reserve but maintained bare rock outside. While this gradient in habitat change matched the gradient of predator abundance, it also matched the extent of reef habitat area. Thus the trophic cascade may be influenced by the effect of habitat on the abundance and behavioural interactions of urchins and their predators. Further ecosystem changes may arise should the abundance of mega-predators, such as seals, cetaceans and large sharks, increase in the region; if parasites become pathogenic; and/or when invasive species reach the reserve. No-take marine reserves provide real-world experiments that show the importance of species in food webs, and the consequences of fishing for ecosystems. Because these changes in ecosystem structure may continue, and will vary with environment, climate and species distributions, reserves need to be permanent and replicated geographically. Habitat maps should be produced for all reserves to enable ecological changes in the ecosystem to be spatially quantified. (C) 2012 Elsevier Ltd. All rights reserved.
Biological Conservation (0006-3207) (Elsevier Sci Ltd), 2012-10 , Vol. 155 , P. 193-201

Droits : 2012 Elsevier Ltd. All rights reserved
http://archimer.ifremer.fr/doc/00107/21842/20067.pdf
DOI:10.1016/j.biocon.2012.05.009
http://archimer.ifremer.fr/doc/00107/21842/

Éditeur(s) : Université Paris 7 – Denis Diderot
Résumé : Sea surface salinity (SSS) influences numerous oceanic phenomena, for instance surface water ventilation, deep water formation and thermohaline circulation. SSS also controls some ocean-atmosphere coupled processes, such as the intensity of freshwater flux and the penetration of heat flux and turbulence. Salinity is more difficult to measure than temperature from in situ surveys, which results in 20 times less data being currently available. Moreover, sea surface temperature (SST) is routinely estimated from satellites, which is not possible yet for SSS. Two space missions will fill this gap soon: SMOS from the European Space Agency and Aquarius/SAC-D from NASA and CONAE. To contribute to the SMOS project, we propose a method for estimating SSS from current satellite observations and for studying the mechanisms governing its variability. We developed a simplified model of the ocean mixed layer, based on the "slab mixed layer" formulation (Frankignoul et Hasselmann, 1977). This 2D horizontal model is implemented over the global ocean, using a near 100 km resolution, and integrated during a climatological year. Air-sea fluxes are taken from the ECMWF meteorological model (ERA40 reanalysis) and the surface currents are provided by altimeter data (SSALTO-DUACS analysis). The mixed layer depth (MLD) is derived from SST observations, using an original inversion technique. The MLD fields obtained from this inversion are well correlated to in situ estimates. This effective depth represents the air-sea fluxes penetration and ensures consistency between fluxes, les currents and SST. We first validate the simulation through examination of the heat balance in north-eastern Atlantic, by comparing to measurements and models from the POMME experiment. Then we study the salinity balance in the global domain, in terms of its geographical distribution and seasonal evolution. Equilibrium between the various processes appears generally more complex than for temperature. Noteworthy, the role of atmospheric flux is less predominant (22%), while geostrophic advection (33%) and diapycnal mixing (22%) contribute more strongly. Our results indicate this model succeeds in reconstructing SSS variability over most of the oceans. Daily SSS variations are also simulated, whereas they are not represented in current observed data at a global scale. Owing to its simplicity and fast computation, the model will be useful to the SMOS mission. It can help for the measurement calibration/validation and provide a first guess estimate to the sophisticated algorithm required for SSS restitution.
La salinité de surface des océans (SSS) influence de nombreux phénomènes océaniques, parmi lesquels la ventilation des eaux de surface, la formation d'eaux profondes et la circulation thermohaline. Elle détermine aussi certains processus couplés océan-atmosphère, notamment l'intensité du flux d'eau douce, la pénétration du flux de chaleur et de la turbulence. La mesure in situ de salinité est plus compliquée que celle de température, si bien qu'on dispose actuellement de 20 fois moins de données pour cette propriété. De plus, la température de surface (SST) est couramment estimée par satellite, ce qui n'est pas encore le cas de la SSS. Deux missions spatiales vont prochainement combler cette lacune : le satellite SMOS de l'Agence Spatiale Européenne et le satellite Aquarius/SAC-D de la NASA et de la CONAE. En préparation du projet SMOS, nous proposons une méthode pour estimer la SSS à partir des observations satellitaires actuelles et étudier les mécanismes de sa variabilité. Nous avons développé un modèle simplifié de couche mélangée océanique, basé sur la formulation "slab mixed layer" (Frankignoul et Hasselmann, 1977). Ce modèle 2D horizontal est implémenté sur l'océan global, avec une résolution proche de 100 km, et intégré au cours d'une année climatologique. Les flux air-mer proviennent du modèle météorologique ECMWF (réanalyse ERA40) et les courants de surface sont issus de l'altimétrie (analyse SSALTO-DUACS). La profondeur de la couche mélangée (MLD) est dérivée des observations de SST, grâce à une technique d'inversion originale. La MLD obtenue par inversion est bien corrélée aux estimations basées sur des données in situ. Cette profondeur effective représente la pénétration des flux air-mer et assure la cohérence entre les flux, les courants et la SST. La simulation est d'abord validée en examinant le bilan de chaleur dans l'Atlantique Nord-Est, par comparaison aux mesures et aux modèles de l'expérience POMME. Puis le bilan de salinité est étudié dans le domaine global, en termes de distribution géographique et d'évolution saisonnière. L'équilibre entre les différents processus est généralement plus complexe que pour la température. Notamment, le rôle du flux atmosphérique est moins prépondérant (22%), tandis que l'advection géostrophique (33%) et le mélange diapycnal (22%) contribuent fortement. Nos résultats montrent que ce modèle parvient à restituer la variabilité de la SSS sur la majeure partie des océans. Le modèle simule aussi les variations journalières de SSS, qui ne sont pas représentées à l'échelle globale dans les observations actuelles. Grâce à sa simplicité et à sa rapidité, le modèle pourra être utile dans le cadre de SMOS. Il pourra aider à la calibration/validation de la mesure et fournir une estimation a priori pour l'algorithme complexe nécessaire à la restitution de la SSS.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/these-2302.pdf
http://archimer.ifremer.fr/doc/00000/2302/

Éditeur(s) : HAL CCSD
Résumé : For a decade, distance-based methods have been largely employed and improved in the field of spatial economics. Such tools are very powerful to evaluate accurately the spatial distribution of plants or retail stores for example (Duranton and Overman, 2008; Jensen and Michel, 2011). In the present paper, we introduce a new statistic measure based on distances to evaluate the spatial concentration of economic activities. As far as we know, the m function is the first relative density function proposed in the economic literature. This tool completes the typology of distance-based methods recently drawn up by Marcon and Puech (2014). By working on several theoretical and empirical examples, we prove the advantages and the limits of the m function to gauge the spatial structures in spatial economics.
https://hal.archives-ouvertes.fr/hal-01082178

hal-01082178
https://hal.archives-ouvertes.fr/hal-01082178
https://hal.archives-ouvertes.fr/hal-01082178/document

Éditeur(s) : Institut national agronomique Paris Grignon
Résumé : The flat oyster Ostrea edulis L. is the indigenous oyster of the Atlantic as well as the Mediterranean coasts of Europe. Its commercial exploitation dates back to Antiquity but its breeding is now threatened by two parasitic protozoa, among which Bonamia ostreae. Various aspects of the genetics of this species' natural and farmed populations have been studied with the aid of microsatellite markers. At first, the implementation and the screening of two partial genomic libraries made it possible to identify 28 new microsatellite loci. Analysis of the segregation of 12 of these loci and of two enzymatic loci shows that most microsatellite loci are transmitted in a Mendelian way, but some loci have significant segregation distortions. Moreover, seven linkage groups, of which four contain at least two markers, were identified in Ostrea edulis. The genetic variability of three populations selected for one or two generations for resistance to Bonamia ostreae was analysed with the aid of 5 microsatellite loci. In spite of the absence of genealogical data, we have shown that these selected populations were descended from a very low number of founding genitors (from 3 to 15 depending on the population) and for two populations, we were able to reconstruct the genealogy and the relationships between the individuals were identified. These selected populations have, in addition to a very low genetic variability, real and at times high levels of consanguinity. These results have a significant implication for the continuation of the selection programme (consanguinity management, augmentation of genetic variability by introducing wild genitors). The geographical structuring of the genetic variability of natural populations of Ostrea edulis has been analysed with the aid of 5 microsatellite loci on a sampling covering almost the entire distribution area of the species (from Norway to the Adriatic Sea). The results are consistent with those published in the literature and using enzymatic markers. The populations show a low level of differentiation that could correspond to a model of isolation by distance. The Atlantic populations, which have a reduced polymorphism, could be descended from post-glacial recolonisation from Mediterranean populations that had survived the glaciations of the Quaternary Period. The current distribution of flat oyster populations is surely also subject to anthropogenic activities. Finally, the genetic bases of the heterozygosis-growth correlation were studied in a natural population with the aid of enzymatic and microsatellite markers. Although leads favouring the direct contribution of enzymatic loci have been found, biases in the sampling design make it impossible to come to a formal conclusion. However, this study has made it possible to show that the capture of individuals over a short period (around ten days) leads to a sampling of a population descended from a very low number of founding genitors, in contradiction with the generally accepted idea that marine bivalve populations are large panmictic populations with significant, efficient numbers. These results confirm in a natural population the observations of a significant reduction of efficient sizes in hatchery populations.
L'huître plate Ostrea edulis L. est l'huître indigène des côtes européennes aussi bien atlantiques que méditerranéennes. Son exploitation commerciale remonte à l'Antiquité mais son élevage est aujourd'hui menacé par deux protozoaires parasites dont Bonamia ostreae. Différents aspects de la génétique des populations naturelles et cultivées de cette espèce ont été étudiés à l'aide de marqueurs microsatellites. Dans un premier temps, la réalisation et le criblage de deux banques génomiques partielles ont permis l'identification de 28 nouveaux locus microsatellites. L'analyse de la ségrégation de 12 de ces locus et de deux locus enzymatiques montre que la plupart des locus microsatellites sont transmis de façon mendélienne, mais certains locus présentent des distorsions de ségrégation importantes. Par ailleurs, sept groupes de liaison dont quatre contiennent au moins deux marqueurs ont été identifiés chez Ostrea edulis. La variabilité génétique de trois populations sélectionnées depuis une ou deux générations pour une résistance à Bonamia ostreae a été analysée à l'aide de 5 locus microsatellites. Malgré l'absence de données généalogiques, nous avons montré que ces populations sélectionnées étaient issues d'un très faible nombre de géniteurs fondateurs (de 3 à 15 selon les populations) et pour deux populations, la généalogie a pu être reconstituée et les liens de parenté entre les individus ont été identifiés. Ces populations sélectionnées présentent, outre une très faible variabilité génétique, des niveaux de consanguinité réels et parfois élevés. Ces résultats ont une implication importante pour la continuation du programme de sélection (gestion de la consanguinité, augmentation de la variabilité génétique par introduction de géniteurs sauvages). La structuration géographique de la variabilité génétique des populations naturelles d'Ostrea edulis a été analysée à l'aide de 5 locus microsatellites sur un échantillonnage couvrant presque toute l'aire de répartition de l'espèce (de la Norvège à la Mer Adriatique). Les résultats sont cohérents avec ceux publiés dans la littérature et utilisant des marqueurs enzymatiques. Les populations montrent un niveau de différenciation faible qui pourrait correspondre à un modèle d'isolement par la distance. Les populations atlantiques, qui présentent un polymorphisme réduit, pourraient être issues de recolonisation post-glaciaire à partir de populations méditerranéennes ayant survécu aux glaciations du Quaternaire. La répartition actuelle des populations d'huître plate est certainement aussi soumise aux actions anthropiques. Enfin, les bases génétiques de la corrélation hétérozygotie-croissance ont été étudiées dans une population naturelle à l'aide de marqueurs enzymatiques et microsatellites. Bien que des pistes en faveur de la contribution directe des locus enzymatiques aient été trouvées, des biais dans le dispositif expérimental ne permettent pas de conclure de façon formelle. Cependant, cette étude a permis de montrer que le captage d'individus sur une faible période (une dizaine de jours) conduit à l'échantillonnage d'une population issue d'un nombre très réduit de géniteurs fondateurs, en contradiction avec l'idée reçue que les populations de bivalves marins sont de larges populations panmictiques à effectif efficace important. Ces résultats confirment dans une population naturelle les observations de réduction importante des tailles efficaces dans des populations d'écloserie.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1998/these-1919.pdf
http://archimer.ifremer.fr/doc/00000/1919/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699
Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North-South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.
ISSN: 0925-9864

hal-01032184
https://hal.archives-ouvertes.fr/hal-01032184
DOI : 10.1007/s10722-008-9375-1