Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Le violent séisme qui a secoué Haïti et sa capitale le 12 janvier 2010 dernier a laissé des séquelles au sein de la population haïtienne déjà fragilisée par la violence, la pauvreté et aussi par des catastrophes naturelles répétées (ouragans, inondations, érosion, etc.). Ce séisme, aussi prévisible qu’il soit, est une catastrophe naturelle et humanitaire sans précédent dont les principales causes sont l’absence de constructions et d’infrastructures solides, bâties selon les normes parasismiques, l’occupation anarchique de l’espace urbain par les populations et les nombreuses irrégularités incontestées observées dans le domaine de l’urbanisme. En outre, ce séisme s’est produit à un moment où l’on commençait à observer dans le pays un élan de stabilisation sur le plan politique, un mouvement de croissance économique ainsi qu’un début d’amélioration des conditions de vie des populations. La catastrophe est venue freiner cette dynamique socioéconomique tout en amplifiant les problèmes existants et en engendrant d’autres difficultés et d’autres défis. Cet article analyse, à travers des témoignages de première main et un état des lieux, les différents impacts de cette catastrophe sur la population locale ainsi que les interrogations et les incertitudes diverses de cette population concernant son avenir.
On January the twelfth 2010, Haiti and its capital have been devastated by a very strong earthquake that has provoked many aftereffects among the local population since that population had already been weakened before by street violence, poverty and by frequent natural disasters such as hurricanes, floods... That earthquake, even foreseeable, has given way to an important disaster whose causes are the absence of well built infrastructures and buildings, the anarchic use of urban spaces by the population, and multiple irregularities in town planning issues. Furthermore, that earthquake took place in a moment when that population was on its way of improvement politically, socially and economically. The disaster has stopped that dynamic, intensifying the existing problems and challenges, and creating new ones. This article analyze – through first hand testimonies, statements and observations – the impacts of such a disaster on the local population as well as diverse inquiries and doubts of that population on its future.
Haïti

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.4842
http://journals.openedition.org/etudescaribeennes/4842

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been described, the interpenetration of both environments leads to hybridization between strains that may be at risk for human health.
ISSN: 1567-1348

pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/document
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/file/Mercier_et_al_IGE2011.pdf
DOI : 10.1016/j.meegid.2011.05.003

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

Éditeur(s) : HAL CCSD NRC Research Press
Résumé : Molecular, cytological, and morphological data support the existence of a hybrid population between Schoenus nigricans and Schoenus ferrugineus. This population was found in northeastern Italy, where S. nigricans is central with respect to its natural range and S. ferrugineus is marginal, being most common in the Alps and in central and northern Europe. Molecular marker data show that the putative hybrid population is genetically intermediate between nearby populations of the parent species. Cytological evidence confirmed the hybrid nature of this population, as does the almost complete sterility of plants within the population. Although no seeds were produced by the hybrid population, some possibly fertile pollen grains were produced; this suggests that the possibility of introgression between the two species through the hybrids cannot completely be excluded.
ISSN: 0831-2796

hal-01032047
https://hal.archives-ouvertes.fr/hal-01032047
DOI : 10.1139/G01-138

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Le patrimoine et le tourisme sont des facteurs avérés de développement. De leur bonne exploitation peut contribuer à l’amélioration des conditions d’existence des populations locales. L’Est-Cameroun est le fief de ressources naturelles et culturelles d’une étonnante diversité pouvant impulser une forte activité touristique. Cependant, même si cette région reçoit chaque année des touristes nationaux et étrangers, elle ne peut pas se targuer de faire profiter sa population des effets directs, indirects et induits qu’engendrerait une activité touristique convenablement menée. Le présent article expose, dans une perspective historique (1980-2010), les raisons pour lesquelles, le tourisme et le développement de l’Est-Cameroun piétinent en dépit de ses nombreuses ressources patrimoniales.La collecte des données (écrites, orales, iconographiques, électroniques) sur le terrain de recherche associée à l’observation permet de constater que le tourisme fut très vite relégué au second plan. L’exploitation minière et forestière intensive, au lieu de faciliter l’émergence de la région, a plutôt hypothéquée son avenir. Le rôle des agences chargées de la gestion du tourisme à l’Est-Cameroun s’est limité à l’inventaire des sites touristiques, l’aménagement sporadique de quelques-uns et la mise en œuvre d’actions promotionnelles approximatives. La négligence du tourisme par les autorités camerounaises n’est pas une nouveauté ; elle a pour corollaire l’apparition de difficultés diverses (braconnage, manque de personnel, insécurité…).
Heritage and tourism are recognized factors of development. Their good exploitation can contribute to the improvement of the conditions of existence of local populations. East-Cameroon is the fief of natural and cultural resources which can stimulate tourism. Although even if this region receives every year domestic and foreign tourists, its population cannot profit from direct, indirect and induced effects which would engender a suitably led tourist activity. The present article exposes, in a historical perspective (1980-2010), reasons why, tourism and development of East-Cameroon tramples in spite of its numerous heritage resources. The data collection (written, oral, iconographic, electronic…) on the research filed and personal observation allow to notice that tourism was very fast relegated in East-Cameroon. The intensive mining and forest exploitation have hypothecated the future of this area instead of developing it. Moreover, the role of tourism agencies in eastern Cameroon is limited itself to inventory of places of interest, sporadic development and approximate promotional actions. The negligence of tourism by the Cameroon authorities is not novelty; it has for corollary appearance of difficulties (as poaching, lack of personal, insecurity).
Cameroun

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.9453
http://journals.openedition.org/etudescaribeennes/9453

Éditeur(s) : Inter-research
Résumé : Environmental conditions experienced by aquatic organisms are archived in biogenic carbonates such as fish otoliths, bivalve shells and coral skeletons. These calcified structures present an accretionary growth and variations in optical properties - color or opacity - that are used to reconstruct time. Full and reliable exploitation of the information extracted from these structures is, however, often limited as the metabolic processes that control their growth and their optical properties are poorly understood. Here, we propose a new modeling framework that couples both the growth of a biogenic carbonate and its optical properties with the metabolism of the organism. The model relies on well-tested properties of Dynamic Energy Budget (DEB) theory. It is applied to otoliths of the Bay of Biscay anchovy (Engraulis encrasicolus) for which a DEB model has been previously developed. The model reproduces well-known otolith patterns and thus provides us with mechanisms for the metabolic control of otolith size and opacity at the scale of an individual lifespan. Two original contributions using this framework are demonstrated. First, the model can be used to reconstruct the temporal variations in the food assimilated by an individual fish. Reconstructing food conditions of past and present aquatic species in their natural environment is key ecological information to better understand population dynamics. Second, we show that non-seasonal checks can be discriminated from seasonal checks, which is a well-recognized problem when interpreting fish otoliths. We discuss further developments of the model and the experimental settings required to test this new promising framework.
Marine Ecology-progress Series (0171-8630) (Inter-research), 2012 , Vol. 447 , P. 151-164

Droits : 2012 Inter-Research
http://archimer.ifremer.fr/doc/00060/17082/14593.pdf
DOI:10.3354/meps09492
http://archimer.ifremer.fr/doc/00060/17082/

Éditeur(s) : Natl Shellfisheries Assoc
Résumé : The pearl industry in French Polynesia is based on exploitation of natural stocks of the black-lip pearl oyster (Pinctada margaritifera); it generates an annual turnover of 90 million euros. Improvements in pearl quality need genetic studies to improve the populations. This pearl oyster is a protandric species, where the sex-ratio normally is biased towards males. There is an increasing interest in gender control to find the mechanisms to augment female proportions for management purposes. This review summarizes information on exogenous and endogenous factors regulating gender in this and other bivalves and concludes that P. margaritifera is a protandric hermaphrodite, developing as a male during the first two years and without evidence of an effect from abiotic and biotic factors on gender during this phase. Later, pearl oysters progressively change to females, reaching a sex ratio close to 1:1 in specimens >8 years; at this stage, gender is apparently influenced by environmental parameters, but particularly by stress. Future research should seek to accurately determine the effect of temperature and food on sex ratios. Studies should be performed to characterize genes responsible for expression of gender. The use of hormones is a path that might be explored to influence the gender of pearl oysters.
Journal Of Shellfish Research (0730-8000) (Natl Shellfisheries Assoc), 2011-08 , Vol. 30 , N. 2 , P. 231-240

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00040/15100/12543.pdf
DOI:10.2983/035.030.0206
http://archimer.ifremer.fr/doc/00040/15100/

Éditeur(s) : Gauthier-Villars
Résumé : The tropical alga Caulerpa taxifolia (Vahl) C. Agardh has been displayed over the last fifteen years in tropical aquaria at the Oceanographic Museum, Monaco. Its accidental introduction into the natural environment dates from 1984. It developed first in the sea immediately below the museum, and resisted winter temperatures of 11 to 13-degrees-C. Gradually the population spread over all types of substrate, including rock, sand and mud, and over a wide range of depth, 3 to 35 m, on this relatively exposed site. In summer 1990 we became aware of its presence both to the east and to the west of Monaco. To the east, it now occurs on the whole of the eastern side of Cap Martin (3 km from Monaco) and is spreading over the west face. To the west we have observed it 150 km from Monaco near Toulon. In those sites which it colonized three years ago, its coverage now reaches 100 % over extensive areas in depths between 5 and 25 m. Areas supporting stands of Cymodocea nodosa and Posidonia oceanica are covered by fronds of C. taxifolia, which measure up to 45 cm in length. The development characteristics of the species in the Mediterranean, such as population density and frond length, are different from those in its native tropical areas. The rapid spreading of this alga is probably due both to sexual reproduction and to efficient vegetative reproduction. At the rate of spreading observed at present, further rapid extension of its range is to be feared. Moreover, wherever it becomes established, it considerably modifies the vegetal communities in the infralittoral zone. This species, like most of those in the genus Caulerpa, contains the toxin, caulerpenyn, which may play a role against other organisms such as grazers, epiphytes and competitors. This alga will be eaten only by certain animals such as the Mediterranean bream or saupe, Sarpa salpa. The toxin accumulated by fish which eat Caulerpa can render them unsuitable for human consumption, as their ingestion produces symptoms similar to those of Ciguatera poisoning. Never has a species so potentially harmful to the marine population been introduced into the Mediterranean. This biological pollution raises the major international problem of direct discharge of water having passed through aquaria or mariculture installations containing exotic species. As importing exotic marine species becomes technically easier, the lack of regulation risks further similar accidents concerning not only algae, but also metazoa and micro-organisms.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1991 , Vol. 14 , N. 4 , P. 415-426

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00101/21268/18879.pdf
http://archimer.ifremer.fr/doc/00101/21268/

Éditeur(s) : Springer
Résumé : The great fecundity and very high larval mortality of most marine invertebrates and fish make possible substantial variance in the number of offspring contributed by adults to subsequent generations. The reproductive success of such organisms may thus resemble a sweepstakes lottery, in which a minority of progenitors succeeds in replacing an entire population, while the majority fails to procreate. One specific prediction of this hypothesis, that genetic diversity of newly settled cohorts should be less than that of the adult population, is tested in the present study. Microsatellite DNA markers were examined in naturally spawned juvenile European flat oysters Ostrea edulis (L.), collected over a 12-day period in 1993 from the western Mediterranean Sea, near Sete, France (43 degrees 32'N, 3 degrees 56'E) and grown out for a period of up to 10 months. Variation in these juveniles was compared to that in a pooled sample of adults collected in 1994 from two locations (Thau Lagoon and Port St. Louis) that had statistically homogeneous allelic frequencies. Though nearly twice as large as the pooled adult sample, the juvenile sample had only 60% of the adult allelic diversity. Analyses of linkage disequilibrium and kinship, as well as estimation of the effective number of parents, suggested that 10-20 adults produced this juvenile cohort. This observation supports the hypothesis of sweepstakes reproductive success and suggests that partial inbreeding may occur even in species with large populations and dispersing planktonic larvae.
Marine Biology (0025-3162) (Springer), 2007-03 , Vol. 150 , N. 6 , P. 1173-1182

Droits : 2007 Springer
http://archimer.ifremer.fr/doc/2007/publication-2616.pdf
DOI:10.1007/s00227-006-0441-y
http://archimer.ifremer.fr/doc/00000/2616/

Éditeur(s) : Public Library Science
Résumé : Background: Reconstructing the history of divergence and gene flow between closely-related organisms has long been a difficult task of evolutionary genetics. Recently, new approaches based on the coalescence theory have been developed to test the existence of gene flow during the process of divergence. The deep sea is a motivating place to apply these new approaches. Differentiation by adaptation can be driven by the heterogeneity of the hydrothermal environment while populations should not have been strongly perturbed by climatic oscillations, the main cause of geographic isolation at the surface. Methodology/Principal Finding: Samples of DNA sequences were obtained for seven nuclear loci and a mitochondrial locus in order to conduct a multi-locus analysis of divergence and gene flow between two closely related and hybridizing species of hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis. The analysis revealed that (i) the two species have started to diverge approximately 0.760 million years ago, (ii) the B. azoricus population size was 2 to 5 time greater than the B. puteoserpentis and the ancestral population and (iii) gene flow between the two species occurred over the complete species range and was mainly asymmetric, at least for the chromosomal regions studied. Conclusions/Significance: A long history of gene flow has been detected between the two Bathymodiolus species. However, it proved very difficult to conclusively distinguish secondary introgression from ongoing parapatric differentiation. As powerful as coalescence approaches could be, we are left by the fact that natural populations often deviates from standard assumptions of the underlying model. A more direct observation of the history of recombination at one of the seven loci studied suggests an initial period of allopatric differentiation during which recombination was blocked between lineages. Even in the deep sea, geographic isolation may well be a crucial promoter of speciation.
Plos One (1932-6203) (Public Library Science), 2009-08 , Vol. 4 , N. 8 , P. 1-15

Droits : 2009 Faure et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
http://archimer.ifremer.fr/doc/00129/24012/21972.pdf
DOI:10.1371/journal.pone.0006485
http://archimer.ifremer.fr/doc/00129/24012/

Éditeur(s) : HAL CCSD SpringerLink
Résumé : Trinucleotide microsatellites have proven to be the markers of choice in human genetic analysis because they are easier to genotype than dinucleotides. Their development can be more time-consuming due to their lower abundance in the genome. We isolated trinucleotide microsatellites in Norway spruce (Picea abies K.) using an enrichment procedure for the genomic-library construction. Here we report on the characterisation of 85 ATC microsatellite-containing clones, from which 39 markers were developed. Many of the clones showed the occurrence of tandem repeats of higher order than the trinucleotide ones, often resembling minisatellite repeats. The sequencing of a sample of the alleles at one of the loci revealed size homoplasy due to base substitutions within the microsatellite region. The presence of ATC motifs within repetitive sequence families was observed. We found a significant relationship between the level of polymorphism and the length of the microsatellite. The levels of variability for ATC trinucleotide markers were lower than those for dinucleotides, both when tested on all loci in a set of six individuals and on a subset of loci in four natural populations. This difference is most likely attributable to lower mutation rates for trinucleotide than for dinucleotide loci. The availability of markers with different mutation rates allows one to select the proper marker set to investigate population processes on different time scales.
Theoretical and Applied Genetics

hal-01032029
https://hal.archives-ouvertes.fr/hal-01032029
DOI : 10.1007/s00122-002-0986-1

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism.
ISSN: 2045-2322

hal-01469339
https://hal-univ-perp.archives-ouvertes.fr/hal-01469339
https://hal-univ-perp.archives-ouvertes.fr/hal-01469339/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01469339/file/population%20expansions.pdf
DOI : 10.1038/srep40519

Éditeur(s) : HAL CCSD
Résumé : International audience
Introduction: Diabetes mellitus results from the loss of tolerance to insulin and alters glycemia and the glycogen content. Oxidative stress and inflammation are linked to theses alterations, especially with insulin-resistance. The therapy management of diabetes includes nutritional recommendations. Several nutrients are developed to improve glycemia, oxidative stress, inflammation and glycogen content. More interestingly, ?-GOS exhibits anti-inflammatory and insulin-sensitive effects in vitro (Efstathiou and Fathi 2010) and in vivo (Boucher et al. 2003). Thus, ?-GOS is a potential functional food for the treatment of diabetes. But, less is known about the in vivo effect of ?-GOS on inflammatory, glycoxidation markers and glycogen content in diabetes. In this context, the aim of this work was to study the effect of ?-GOS developed by Sojasun technologies (from fermented soy product) compared to a synthetic ?-GOS produced by Sigma on inflammatory, glycoxidation markers and glycogen content in a streptozotocin-induced diabetic rat model. Methods: Twenty-four male Wistar streptozotocin-diabetic rat (STZ) were divided into three group: control group, supplemented with natural ?-GOS (20 mg/kg/day) group and supplemented with synthetic ?-GOS (20 mg/kg/day). The supplementation protocol duration was 8 weeks. At the end of the protocol, blood and skeletal muscle (gastrocnemius) were obtained to measure glucose , insulin, fructosamine in plasma and N-(carboxymethyl)lysine, glycogen synthase activity and glycogen content, in muscle. Results-Discussion: Diabetes was confirmed with the measure of insuline and glucose levels. All the diabetic groups had significantly higher glucose and insuline levels compared to control healthy group (data not shown). Insuline level in plasma and storage of glycogen in muscle were increased only in both ?-GOS groups. Fructosamine, TNF?and glycogen synthase activity was also decreased in the two supplemented groups (synthetic ?-GOS and natural ?-GOS). CML remained unchanged in all groups. Natural ?-OGT and synthetic ?-OGT only differed on muscular glucose level: only natural ?-OGT induced a significant decrease in muscular glucose. To conclude, our results suggest that ?-GOS alters positively glucose level, increases the glycogen content in diabetique population, improves glycemic control in the long term and decreases the inflammatory effects in streptozotocin-diabetic rat . Keywords: ?-GOS, inflammatory and glycoxidation markers, diabetes. Acknowledgment : Brittany region References Efstathiou, T. and D. Fathi. Sojasun Technologies. 2010 Boucher J et al. J Physiol Biochem. 59(3):169-73, 2003
5e congrès international de "Nutrition, Oxygen Biology and Medicine", Paris 5-7 juin 2013
Paris, France

hal-01159375
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01159375

Éditeur(s) : HAL CCSD Paris : Muséum national d'histoire naturelle
Résumé : International audience
Coral reefs are one of the most diverse ecosystems on Earth and sustain millions of people worldwide.However, coral reefs are temporally dynamic and fragile systems subject to ever increasing disturbancesof anthoropogenic and natural origins. Understanding the patterns and trajectories of changes through time isurgently needed to estimate the resilience of coral reefs. To ascertain these patterns, we depend on the availabilityof long-term datasets, which are seldom available. In this study, we present the data set which allowed us to analysethe long-term trends of coral and fish assemblages for the island of Moorea (French Polynesia) from 1983to 2014, a dataset spanning 32 years, comprising two Acanthaster planci outbreaks (1987 and 2006) and severalhurricanes (1982, 1983, 1991 and 2010), on three permanent monitoring sites (quadrats of 50 × 2 m2) located onboth fringing and barrier reefs as well as on the outer slope. Coral cover oscillated significantly over time, particularlyon the outer slope where it suffered greatly from the effects of A. planci outbreaks and hurricanes. Totalfish and commercial fish abundances varied significantly across the three habitats. Prior to 2000, both total fishand herbivorous fish abundances increased on the barrier reef while after this time, numbers began to drop significantlyalong the outer slope. Species richness for total, commercialized and herbivorous fish increased over thesampling period for all three habitats. There were varied responses amongst species to disturbances on the outerslope over the sampling period: while some tended to disappear for a while before reappearing, others showed apeak in abundance in the middle of the sampling period, and still others increased or decreased continuously orwere stable over time. Our results support the view that coral reefs are highly dynamic systems and that differentfunctional groups show different temporal trajectories. While disturbance is probably the major driver for coralcover dynamics, its impact is less obvious for fish, possibly due to their mobility and population dynamics whichmay mask the effect of disturbance.
Les récifs coralliens sont des systèmes dynamiques et diversifiés régulièrement soumis à des perturbationsnaturelles et anthropiques, sources d’hétérogénéité spatiale et temporelle dans la structure et la dynamique deces communautés d’organismes que sont, entre autres, les poissons et les coraux. Récemment, il a été démontréque les activités humaines pouvaient modifier les régimes naturels de perturbations des récifs coralliens en transformantles événements ponctuels en perturbations persistantes ou en stress chronique, soit en introduisant denouveaux types de perturbations, soit en ajoutant ou altérant certaines perturbations naturelles nécessaires au bonmaintien de la dynamique inhérente aux récifs. Dans cette étude, nous présentons la base de données qui nouspermettra d’analyser les tendances à long-terme des assemblages de poissons et de coraux de l’île de Moorea(Polynésie française) entre 1983 et 2014 sur une période de 32 ans, comprenant deux proliférations d’Acanthasterplanci (1987 et 2006) et plusieurs cyclones (1982, 1983, 1991 et 2010), sur trois sites de suivi permanents(quadrats de 50 × 2 m2) sur les récifs barrière et frangeant ainsi que sur la pente externe. La couverture corallienneprésente de fortes oscillations, en particulier sur la pente externe où elle a répondu fortement à la proliférationd’A. planci et des cyclones. Les abondances des poissons totaux et des poissons commercialisés montrent destendances contrastées sur les trois habitats, avec, plus particulièrement, une augmentation sur le récif barrière etune diminution sur la pente externe après 2000. Ces tendances se retrouvent chez les poissons herbivores dansces deux habitats. La richesse spécifique des poissons totaux, commerciaux et herbivores, augmente de façoncontinue au cours de la période d’étude dans les trois habitats. Des groupes particuliers d’espèces répondentdifféremment aux perturbations de la pente externe au cours du suivi : alors que certaines espèces ont tendanceà disparaître pendant quelques années avant de réapparaître, d’autres présentent un pic en terme d’abondanceen milieu de suivi ; d’autres espèces ont des abondances qui augmentent ou diminuent de façon continue, etd’autres encore montrent des abondances stables. Ceci indique que les récifs coralliens sont des systèmes trèsdynamiques dans lesquels les perturbations naturelles peuvent affecter les espèces de façon différente. Alors quele régime de perturbations naturelles semble être important pour la dynamique de la couverture corallienne danscertains habitats, cela se retrouve beaucoup moins pour les poissons. Cette atténuation des fluctuations spatialeset temporelles peut être due aux aptitudes de dispersion de nombreuses espèces de poissons, capables de chercherun autre habitat favorable en cas de perturbation de l’habitat corallien d’origine.
ISSN: 0399-0974

hal-01282378
https://hal-univ-perp.archives-ouvertes.fr/hal-01282378

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) : Université de Bretagne Occidentale
Résumé : The stock of Lambi, Strombus gigas (gastropod: strombidae), coastal benthic resource, has been exploited artisanally since the prehistoric period in Martinique. Nowadays, three lines of work exploit the species: free diving, nets (since the middle of the century) and scuba diving since 1985. This report presents the activity of each line of work, surveyed directly from 1986 to 1987: fishing zones and resource allocation, production, effort and performance, detail of catches (by length). The socio economic characteristics of the lambi fishermen are studied. The significant production of leisure fishing is also estimated. The decrease in the production and performance, as well as the lowering of the size of the first catch for about thirty years show that the stock is overexploited. The biological phenomenon of the stock: growth of the shell (length and shell lip), growth in weight, acquiring of sexual maturity, natural mortality are studied. The factors of mortality through fishing are estimated by class of length for the current exploitation regime by pseudo-cohort analysis. If the results confirm that the stock is overexploited, the level of overexploitation of the stock cannot be specified because of the presence of a number of lipped adults not yet too exploited in water deeper than 20 metres. The analysis of the dynamic process of the exploited population indicates two ways to the production of the stock: the forcing of the recruitment and the regulation of the exploitation regime. The lack of economic profitability of the production of juveniles over 30 mm and the difficulties raised by their collection in their natural habitat lead to the rationalization of the exploitation. The production and performance (by recruits) simulations performed for different exploitation regimens indicate that the only two conceivable options are the introduction of a minimum catch size, i.e. lambi with forming lip, and the regulation of the fishing effort. The socio-economic implications of the introduction of the determined management measures show that their applicability level is very low, because of the Martinique fishermen polyactivity, their low socio-economic level and mostly because of the free access to the resource. As a consequence, it is suggested to create new professional structures with a wide jurisdiction, in order to locally manage the marine areas, their use and their resources. (unverified OCR)
Le stock de lambi, Strombus gigas (gastéropode: strombidae), ressource benthique côtière, est exploitée artisanalement depuis l'époque préhistorique en Martinique. Trois métiers exploitent actuellement l'espèce: plongée libre, filets (depuis le milieu du siècle) et plongée en scaphandre autonome depuis 1985. Ce rapport présente l'activité de chaque métier, suivie de 1986 à 1987 par une enquête directe: zones de pêche et allocation de la ressource, productions, efforts et rendements, composition en longueur des captures. Les caractéristiques socioéconomiques des pêcheurs de lambi sont étudiées. La production d'une pêche plaisancière non négligeable est estimée. La diminution de la production, des rendements et l'abaissement de la taille de première capture depuis une trentaine d'années révèlent que le stock est surexploité. Les phénomènes biologiques du stock: croissance de la coquille (longueur et pavillon), croissance en poids, acquisition de la maturité sexuelle, mortalité naturelle sont étudiés. Les coefficients de mortalité par pêche sont estimés par classe de longueur pour le régime d'exploitation actuel par l'analyse de pseudo-cohorte. Si les résultats confirment l'état surexploité du stock, le niveau de surexploitation ne peut être précisé en raison de l'existence d'adultes pavillonnés encore peu exploités sur les fonds de plus de 20 mètres. L'analyse des processus dynamiques de la population exploitée indique deux voies pour restaurer la production du stock: le forçage du recrutement et la régulation du régime d'exploitation. Le manque de rentabilité économique de l'élevage des juvéniles au-delà de 30 mm et les difficultés pour leur collecte dans le milieu naturel conduisent à rechercher la rationalisation de l'exploitation. Les simulations de la production et du rendement par recrue réalisées pour différents régimes d'exploitation indiquent que seule la mise en place d'une taille minimale de capture, i.e le lambi au pavillon en formation, et une régulation de l'effort de pêche sont envisageables. Les implications socio-économiques de la mise en oeuvre des mesures de gestion déterminées montrent que leur niveau d'applicabilité est très faible, en raison de la polyactivité des pêcheurs martiniquais, de leur faible niveau socioéconomique et surtout, du régime de libre accès à la ressource. Aussi, il est proposé la création de nouvelles structures professionnelles aux compétences larges, qui permettraient, pour chacun des bourgs, une gestion locale de l'espace marin, des usages et des ressources. OCR NON CONTRÔLE

Droits : 1993 UBO
http://archimer.ifremer.fr/doc/1993/these-3751.PDF
http://archimer.ifremer.fr/doc/00000/3751/

Éditeur(s) : HAL CCSD Instituto Oswaldo Cruz, Ministério da Saúde
Résumé : International audience
Leishmania are protozoan parasites that show remarkable diversity, as revealed by the various clinical forms of leishmaniasis, which can range from mild skin lesions to severe metastatic cutaneous/mucosal lesions. The exact nature and extent of Leishmania phenotypic diversity in establishing infection is not fully understood. In order to try to understand some aspects of this diversity, we subcutaneously infected BALB/c mice with first and second generation subclones of a L. amazonensis strain isolated from a patient (BA125) and examined in vivo lesion growth rate and antimony susceptibility. In vivo fast-, medium- and slow-growing subclones were obtained; moreover, fast-growing subclones could generate slow-growing subclones and inversely, revealing the continuous generation of diversity after passage into mice. No antimony-resistant subclone appeared, probably a rare occurrence. By tagging subclone cells with a L. amazonensis genomic cosmid library, we found that only a very small number of founding cells could produce lesions. Leishmania clones transfected with in vivo selected individual cosmids were also diverse in terms of lesion growth rate, revealing the cosmid-independent intrinsic characteristics of each clone. Our results suggest that only a few of the infecting parasites are able to grow and produce lesions; later, within the cell mixture of each lesion, there coexist several parasite populations with different potentialities to grow lesions during the next infection round. This may reflect a sort of programmed heterogeneity of individual parasites, favoring the survival of some individuals in various environmental conditions.
ISSN: 0074-0276

hal-01489008
https://hal-univ-perp.archives-ouvertes.fr/hal-01489008

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Herbivores are often implicated in the generation of the extraordinarily diverse tropical flora. One hypothesis linking enemies to plant diversification posits that the evolution of novel defenses allows plants to escape their enemies and expand their ranges. When range expansion involves entering a new habitat type, this could accelerate defense evolution if habitats contain different assemblages of herbivores and/or divergent resource availabilities that affect plant defense allocation. We evaluated this hypothesis by investigating two sister habitat specialist ecotypes of Protium subserratum (Burseraceae), a common Amazonian tree that occurs in white-sand and terra firme forests. We collected insect herbivores feeding on the plants, assessed whether growth differences between habitats were genetically based using a reciprocal transplant experiment, and sampled multiple populations of both lineages for defense chemistry. Protium subserratum plants were attacked mainly by chrysomelid beetles and cicadellid hemipterans. Assemblages of insect herbivores were dissimilar between populations of ecotypes from different habitats, as well as from the same habitat 100 km distant. Populations from terra firme habitats grew significantly faster than white-sand populations; they were taller, produced more leaf area, and had more chlorophyll. White-sand populations expressed more dry mass of secondary compounds and accumulated more flavone glycosides and oxidized terpenes, whereas terra firme populations produced a coumaroylquinic acid that was absent from white-sand populations. We interpret these results as strong evidence that herbivores and resource availability select for divergent types and amounts of defense investment in white-sand and terra firme lineages of Protium subserratum, which may contribute to habitat-mediated speciation in these trees.
ISSN: 0012-9658

hal-01032403
https://hal.archives-ouvertes.fr/hal-01032403
DOI : 10.1890/12-1920.1

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : Elsevier
Résumé : In order to provide reliable scientific advice and support for fisheries management, it is necessary to evaluate the biological and economic sustainability of complex fisheries, such as multi-species multi-fleet fisheries. Existing policy-screening modelling tools are not fully suitable in this purpose due to either an over-simplified description of population dynamics, or due to the lack of consideration of economic aspects. In this paper, we present a package that enables quantitative bioeconomic assessment of management scenarios. Population dynamics is described through spatially- and seasonally-explicit models. Exploitation dynamics is characterized by several fishing activities with specific spatial and seasonal features, and practiced by several kinds of vessels with specific technical characteristics. Exploitation costs and revenues are considered at several levels: the fishing trip, the fishing unit (vessel and crew), and the vessel owner. The model is generic and can be used for different types of fisheries. A database is attached to the software for the storage and updating of information for each fishery. This includes the specification of model dimensions and of the parameters describing populations and exploitation. Several model assumptions regarding either population or exploitation may be adapted to suit a specific fishery. Both policies and corresponding fishers' response may be interactively specified through JAVA (TM) scripts. This version of ISIS-Fish allows for the calculation of biological and economic consequences of a range of policies, including conventional ones like catch and effort controls, and alternative policies such as marine protected areas. To facilitate policy-screening in a high-dimension parameter space, the software includes features, like interfaces for sensitivity analysis and simulation queues. (C) 2009 Elsevier B.V. All rights reserved.
Ecological Modelling (0304-3800) (Elsevier), 2009-04 , Vol. 220 , N. 7 , P. 1013-1033

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6782.pdf
DOI:10.1016/j.ecolmodel.2009.01.007
http://archimer.ifremer.fr/doc/00000/6782/