Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as ``public goods,'' subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define `` family resemblances'' to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.
ISSN: 0737-4038

hal-01544794
https://hal.archives-ouvertes.fr/hal-01544794
DOI : 10.1093/molbev/mst228

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : The suitability of the natural 15N abundance and of total N concentration of leaves as indicators of the type of plant N nutrition in a rain forest of French Guiana were tested. Leaf samples from primary legume species, non-legumes (pioneer species) and from the non-N2-fixing species Dicorynia guianensis were analyzed. Both '15N and total leaf N varied widely (m1 r '15N (‰) r 7 and 1 r leaf N(%) r 3.2) suggesting possible distinctions between diazotrophic and non-fixing plants. The '15N also revealed two statistically distinct groups of non-N2-fixing species ('15N = 5.14 - 0.3 vs '15Nv=v1.65 - 0.17) related to the different ecological behaviors of these species in the successional processes. We conclude that the '15N signature of plant leaves combined with their total N concentration may be relevant indicators for identifying functional groups within the community of non-N2-fixing species, as well as for detecting diazotrophy. Despite the variability in the '15N of the non-N2-fixing species, N2-fixing groups can still be identified, provided that plants are simultaneously classified taxonomically, by their leaf '15N and total N concentration and by the presence or absence of nodules. The variability in the '15N of the non-fixing species is discussed.
ISSN: 0029-8549

hal-01031454
https://hal.archives-ouvertes.fr/hal-01031454
DOI : 10.1007/s004420050846

Éditeur(s) : HAL CCSD
Résumé : Fault zones are major discontinuities in sedimentary basins. Understanding their role on fluid migrations is an essential issue to (i) characterize the mechanisms and kinematics of deformation and (ii) to determine the parameters which control the distribution of energetic or mineral resources. This work applies to faulting under a temperature range of 200-250°C, corresponding to that of deeply buried reservoirs as well as potentially seismogenic fault zones. The studied faults are normal faults affecting the “Grès d’Annot” Formation, a Priabonian-Rupelian siliclastic turbidite succession of the Alpine foreland basin. They are located in two distinct areas: the Moutière-Restefond area in the eastern part of the basin and the Estrop area in the western part. Vitrinite reflectance outside fault zones indicates maximal temperatures of 240-260°C at Moutière-Restefond and 170-200°C at Estrop, i.e. burial depths around 8 km and 6 km, respectively, assuming a mean geothermal gradient of 30°C/km. Burial was due to underthrusting below the Embrunais-Ubaye Alpine nappes, the difference in burial between the two areas traducing the westward taper of the nappe front.The studied faults affect alternating arkosic sandstone beds and pelite layers with offsets from centimeters to decameters. Two types of core zones are recognized: (1) the foliated core zones of the Moutière-Restefond area, where deformation dominated by pressure solution and synkinematic phyllosilicate neoformation resulted in a foliated fabric, and (2) the core zones of the Estrop area, characterized by dilatant quartz-mineralized veins and breccia. Fault and host rock petrophysical properties were measured on drill plugs, using the water porosity technique and nitrogen permeability technique under 2 Mpa of confining pressure. In the Moutière-Restefond fault zones, plug axes were oriented in three orthogonal directions corresponding to the main deformation axes (X, Y, Z) of the foliated arkose to characterize the effect of structural anisotropy. In the Estrop fault zones, where deformation does not show equivalent anisotropy, the plug axes were oriented according to the main fault plane orientation (i.e., parallel to azimuth, parallel to dip and normal). In each fault zone, the porosity of fault rocks is equivalent to that of host rocks. In the Moutière-Restefond fault zones, the plugs parallel to the X and Z axes of deformation have a permeability similar to that of the host rocks, whereas permeability parallel to the Y axis (i.e. parallel to the foliation and the main fault plane) is one order of magnitude higher. By contrast, the permeability values in the Estrop fault zones are isotropic and equivalent to the host rock values. This study highlights the importance of various types of deformation mechanisms and related fluid-rock interactions in determining different fault rock types within a similar protolith, ultimately controlling distinct petrophysical properties of fault zones.
Les zones de failles constituent des discontinuités majeures dans la croûte supérieure. Ce mémoire s’intéresse aux failles actives à des profondeurs de 5-8 km, i.e. dans des conditions pouvant jouer un rôle important (i) sur le comportement mécanique de de la croûte, en particulier sur son potentiel sismogénique et (ii) sur la compartimentation des réservoirs géologiques profondément enfouis.Les failles étudiées sont des failles normales (rejet jusqu’à 50 mètres) affectant des alternances de bancs de grès arkosiques et de pélites dans les Grès d’Annot, une formation turbiditique d’âge priabonien-rupélien du bassin d’avant-chaine alpin. Les Grès d’Annot ont été enfouis sous les nappes de l’Embrunais-Ubaye peu de temps après leur dépôt et exhumés au Miocène moyen-supérieur. L’étude a été réalisée dans deux secteurs des Alpes de Haute-Provence, (1) le secteur de l’Estrop (chaine des Trois Evéchés, dans la partie occidentale du bassin) et (2) le secteur de Point Vert-Restefond (alentours du col de la Bonette, dans la partie orientale du bassin). La réflectance de la vitrinite dans les Grès d’Annot indique des températures maximales de 160-190°C dans le secteur (1) et de 240-260 °C dans le secteur (2) , soit des profondeurs d’enfouissement de 5-6 km et 8-10 km, respectivement, dans l’hypothèse d’un gradient géothermique moyen de 25-30°C/km. A partir des observations microstructurales, de données d’inclusions de fluides, de modélisations thermodynamiques sur chlorites syncinématiques et des indices de cristallinité de l’illite, on a établi que les failles du secteur (1) ont fonctionné à une température d’environ 200°C pour une pression de 0.6Kbar et celles du secteur (2) dans une gamme de température de 200-220°C et de pression comprise entre 0.6 et 1.1 Kba. L’activité de la faille de Point-Vert a été datée par la méthode 40Ar/39Ar au Miocène inférieur (21 Ma). Ces failles sont interprétées comme associées aux premiers stades du soulèvement résultant de l’activité des chevauchements dans le socle sous-jacent.Deux types principaux de roches de failles caractérisent les failles étudiées. Les brèches dilatantes sont majoritaires dans les zones de failles du secteur (1) alors que les arkoses foliées sont majoritaires dans les zones de failles du secteur (2). Les brèches dilatantes témoignent de mécanismes de déformation dominés par la fracturation transgranulaire et la pression-solution des silicates. Ce dernier mécanisme se manifeste principalement par d’abondantes précipitations cycliques de quartz, les stylolites restant peu développés. Les géométries structurales sont associées à l’activation de plans T de Riedel déterminant l’ouverture de relais extensifs et un régime localement dilatant. Nous associons ce type de roche de faille à une faible pression effective au cours de la déformation.La déformation cisaillante exprimée dans les arkoses foliées témoigne de mécanismes de déformation dominés par (i) la fracturation intragranulaire et transgranulaire, (ii) la pressionsolution/ précipitation des silicates, principalement le quartz, (iii) la néoformation de micas blancs liée à l’altération des feldspaths et (iv) la précipitation de chlorite. Ce travail montre également que les transformations minéralogiques liées aux interactions fluide-roche dans la zone de faille (forte augmentation de la proportion des phyllosilicates au dépend des feldspaths) changent radicalementla composition minéralogique de la roche. Nous associons ce type de roche de faille à une forte pression effective au cours de la déformation.La pétrophysique montre que les brèches de failles (secteur 1) ont une perméabilité isotrope et équivalente à celle du protolithe (10-3mD sous 2 MPa de confinement) tandis que les roches foliées (secteur 2) montrent une augmentation de perméabilité (10-2mD) selon l’axe Y de la déformation, d’un ordre de grandeur supérieure aux perméabilités suivant les axes X et Z et dans la roche hôte (10-3mD). Ce drain préférentiel potentiel est associé à l’orientation des phyllosilicates dans la foliation.
https://hal.archives-ouvertes.fr/tel-01310382

tel-01310382
https://hal.archives-ouvertes.fr/tel-01310382
https://hal.archives-ouvertes.fr/tel-01310382/document
https://hal.archives-ouvertes.fr/tel-01310382/file/Th%C3%A8seCAVAILHES2012.pdf

Résumé : L'écart de la représentation politique des femmes entre la Guadeloupe et la Martinique a été à l'origine de notre interrogation sur la socialisation politique des femmes aux Antilles françaises. En interrogeant des élus guadeloupéens et martiniquais (hommes et femmes) nous avons tenté de comprendre en quoi la socialisation politique pouvait expliquer le niveau d'engagement des femmes en politique. Le·genre étant le concept su lequel se fonde la société pour justifier la séparation et la hiérarchisation des individus masculins et féminins c'est par le biais du processus de socialisation sexué que les individus apprennent leurs rôles genrés. Si cette séparation des hommes et des femmes dans des sphères distinctes (publique et privée) tend à freiner le femmes dans leur engagement politique, les élues antillaises n'auraient pas été majoritairement touchées pas une socialisation politique sexuée. Au contraire, la matrifocalité présente aux Antilles françaises aurait permi un certain nombre de femmes d'être socialisée similairement aux hommes. Mais la société empreinte de valeurs genrées aurait tout de même freiné les femmes dans l'entame d'une carrière politique. Si la famille transmet des valeurs politiques de base, que les partis politiques n'ont qu'un rôle relatif d'agent socialisateur le monde associatif semble être un agent de socialisation déterminant en termes d'engagement politique, un révélateur et un propulseur d'hommes et de femmes dans le monde politique. Socialisés aux valeurs politiques, ces élus deviennent également des agents de socialisation politique pour les jeunes qui peuvent représenter la relève politique.
Differences in the political representation of women between Guadeloupe and Martinique were the source c our questioning about the political socialisation of women in the French West Indies. Sy interviewing elected men and women in Guadeloupe and Martinique, we tried to understand how political socialization coul explain the level of involvement of women in politics. With gender being the concept from which any societ justifies the process of separation and hierarchy between male and female individuals, it is through the sexual socialization process that individuals learn their gendered raies. If this separation between men and women in both public and private spheres tends to impede women in their political commitment, elected women of the French West Indies have not been disproportionately affected by sexual political socialization. On the contrary, the matrifocality in the French West Indies would have allowed a number of women to be socialise dsimilarly to men. However, the strong gendered values of this society would have still hampered women at the beginning of their political career. While family provides basic political values, political parties have only a relative role of socializing agent. However, associations seem to be a decisive/crucial socializing agent in terms of political commitment, acting as a career booster for men and women in politics. Socialized to political values, these elected individuals become in turn factors of political socialization for young people whe represent the next political generation.

http://www.theses.fr/2012AGUY0498/document

Résumé : À la Martinique au XVIIIe siècle, les « libres de couleur », qu’ils soient nés libres ou affranchis, noirs ou métis, forment une catégorie juridique distincte des Blancs et des esclaves. L’étude comparée, avec les territoires espagnols ou anglais, montre qu’aucune réglementation légale n’a officialisé un passage de la catégorie Libre de couleur à celle de Blanc dans les colonies françaises de la fin du XVIIe siècle à la Révolution française. Aussi, cette thèse se propose de montrer les processus officieux qui ont permis à certaines personnes – les « assimilés » – de franchir la barrière de couleur. Une réflexion a été menée sur le préjugé de couleur, système raciste dont l’idéologie, soutenue par la réglementation locale, a légitimé la construction collective d’un ordre public et social. Puis, on a examiné l’élaboration de la barrière de couleur. Les libres de couleur ont été les premiers à faire les frais de l’imperméabilisation de la ligne de démarcation et des problèmes posés par la pureté de sang ; mais les Blancs mésalliés, dans le cadre d’unions interraciales, et les Amérindiens ont aussi été visés. Enfin nous avons réfléchi à ce qui faisait la blancheur et aux stratégies adoptées pour réussir ce changement de statut. Le notariat et les 33 000 actes des registres paroissiaux traités ont donné lieu à la reconstitution de généalogies pour examiner des individus et des familles sur plusieurs générations ; on a ainsi observé l’importance du phénotype, le blanchiment, la légitimité des relations, les conjoints privilégiés, le choix des réseaux, les niveaux de fortune et l’usage de l’espace.
In Martinique in the eighteenth century, the "free people of color", both those free by birth and freedmen, black or mixed race, form a legal category, which was distinct from those of whites and slaves. Comparative studies with Spanish or English territories show that no legal regulation formalized a shift - from the category of free colored people to that of White - in the French colonies between the late seventeenth century and the French Revolution. Also, this thesis proposes to show the informal process that enabled some people - the "assimilated" - to cross the color barrier. I analysed the color prejudice, a racist system, whose ideology, supported by local regulations, legitimized the collective construction of a public and social order. In a second step, I examined the development of the color bar. The free colored people were the first to bear the brunt of the impermeability of the demarcation line and of the problems posed by the purity of blood; but some whites, through interracial unions, and Native Americans have also been targeted. Finally I thought about what made the whiteness, and the strategies to achieve whiteness, change in status. Notarial acts and 33,000 acts of parish registers treaties led to the reconstitution of genealogies, in order to examine individuals and families over generations; I observed the importance of the phenotype, whitening, legitimacy relations, privileged partners, choice of networks, wealth levels and the use of space.

http://www.theses.fr/2015AGUY0847/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : The Borborema Province, in the NE of Brazil, is a rather complex piece in the Brazil-Africa puzzle as it represents the junction of the Dahomeyide/Pharusian, Central African, Aracuai and Brasilia fold belts located between the West-African/Sao Luis, Congo/Sao Francisco and Amazonas craton. The correlation between the Dahomeyides from W-Africa (Ghana, Benin, Togo, and Mali) and the Borborema Province involves the Medio Coreau and Central Ceara domains. The inferred continuation of the main oceanic suture zone exposed in the Dahomeyides of W Africa is buried beneath the Phanerozoic Parnaiba Basin in Brazil (northwest of the Medio Coreau domain) where some high density gravity anomalies may represent hidden remnants of an oceanic suture. In addition to this major suture a narrow, nearly continuous strip composed of mainly mafic pods containing relics of eclogite-facies assemblages associated with partially migmatized granulite-facies metapelitic gneisses has been found further east in the NW Borborema Province. These high pressure mafic rocks, interpreted as retrograded eclogites, are located between the Transbrasiliano Lineament and the Santa Quiteria continental arc and comprise primitive to evolved arc-related rocks with either arc- or MORB-type imprints that can indicate either deep subduction of oceanic lithosphere or roots of continental and oceanic magmatic arcs. Average peak P-T conditions under eclogite-facies metamorphism (T=770 degrees C and P = 17.3 kbar) were estimated using garnet-clinopyroxene thermometry and Jd content in clinopyroxene. Transition to granulite-facies conditions, as well as later widespread re-equilibration under amphibolite facies, were registered both in the basic and the metapelitic rocks and suggest a clockwise P-T path characterized by an increase in temperature followed by strong decompression. A phenomenon possibly related to the exhumation of a highly thickened crust associated with the suturing of the Medio Coreau and Central Ceara domains, two distinct crustal blocks separated by the Transbrasiliano Lineament.
ISSN: 1342-937X

hal-00413584
https://hal.archives-ouvertes.fr/hal-00413584
DOI : 10.1016/j.gr.2009.01.003

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the ``good'' transcripts in the user's data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly programs. Moreover, we sequenced the transcriptome of the oomycete Achlya hypogyna and compared de novo assemblies from Velvet, ABySS, and the CLC Genomics Workbench assembly algorithms. One thousand one hundred twenty-eight of the CLC transcripts were statistically similar to the reference, compared with 49 of the Velvet transcripts and 937 of the ABySS transcripts. SCAN's strength is providing statistical support for transcript assemblies in a biological context. However, SCAN is designed to compare distinct node sets in networks, therefore it can also easily be extended to perform statistical comparisons on any network graph regardless of what the nodes represent.
ISSN: 0737-4038

hal-01544800
https://hal.archives-ouvertes.fr/hal-01544800
DOI : 10.1093/molbev/mst087

Éditeur(s) : HAL CCSD
Résumé : International audience
Human spatial motions determine geographic social contacts that influence the way an information is spread on a population or a community. As mobility is a transverse dimension to social practices it is important to better understand its role. With the Eternal-Return model we propose, we simulate an artificial world populated by heterogeneous agents who differ in their mobility. We have chosen a multi-agent framework perspective for this simulation. We endow the agents with simple rules on how to move around the space and how to establish proximity-contacts. This allows to distinguish different kinds of mobile agents, from sedentary ones to travelers. To summarize the dynamics induced by mobility over time, we define the mobility-based Social Proximity Network as being the network of all distinct contacts between agents. Its properties give insight in the process of information spreading. We conduct simulations to understand how an information can be broadcast when agent-nodes are in motion.
IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining
Niagara falls, Canada

hal-00874344
https://hal.archives-ouvertes.fr/hal-00874344

Éditeur(s) : HAL CCSD Wiley
Résumé :  
The forests in Cat Tien National Park, appear as a mosaic of different communities, distinct from each other with respect to their floristic and structural parameters. The objectives of this study are (1) to characterize the different formations occurring in the lowland part and (2) to identify the main successional trends in the area. Understanding forest succession is important for silviculture and restoration of forests and land rehabilitation, as adequate information on the ecological role of local species in the functioning of the forests is not available in Vietnam. Five plots (1 ha each) were established in the lowland part of Cat Tien National Park, where all the trees ≥ 10 cm d.b.h. (diameter at breast height) were located, measured and identified. A systematic sampling was made to assess the regeneration. Three plots (A, C and D) can be considered as secondary forests on the basis of their structural parameters. Plots A and C are dominated by Lagerstrmia calyculata and plot D by Dipterocarpus alatus. The other two plots can be regarded as mature forests. Plot B corresponds to a semideciduous formation dominated by Lagerstrmia calyculata and Fabaceae species, and plot E to an evergreen one dominated by dipterocarp species. The floristic composition of plots A and C will change in the future because dominant canopy species are rare or absent in regeneration. A correspondence analysis performed on the number of trees per species shows two kinds of successional trends: one from A to B on shallow and drier soils, and another from C to E on deeper and wetter soils.
ISSN: 0305-0270

hal-01032094
https://hal.archives-ouvertes.fr/hal-01032094
DOI : 10.1046/j.1365-2699.2000.00347.x

Résumé : Le projet de recherche actuel répond donc A un besoin d'enrichissement mutuel des approches biologiques et économiques face A un double enjeu : - socio-économique : la crise subie par un secteur représentant traditionnellement l'activité principale de certaines régions, - écologique : la survie de certaines espèces menacées par une pêche excessive, les deux enjeux étant directement liés dans de nombreux. L'idée est la suivante : à. partir des comportements de pêche observés au cours d'une année sur l'ensemble des bateaux de pêche inscrits A Boulogne-sur-Mer,essayer de définir des stratégies-types et d'isoler ainsi des groupes de bateaux aux comportements voisin. Cela devrait conduire A des distinctions de flottilles plus pertinentes que les classification : pêche industrielle, pêche au large, pêche côtière, petite pêche, qui tient compte des statuts juridiques et de la durée des marées, mais ne véhicule aucune information sur la dynamique des comportements et les choix stratégiques des navires. Avant d'aborder de façon plus détaillée l'analyse effectuée pour la mise en évidence et la compréhension des comportements de pêche, quelques éléments sur IFREMER et le SEM. Ensuite on présentera les activités de pêche A Boulogne-sur- Mer et leur évolution au cours des dernières années, la démarche suivie pour traiter les données, les résultats obtenus, les limites de l'approche. On verra enfin les développements ultérieurs possibles. [OCR NON CONTRÔLE]

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1991/rapport-4216.pdf
http://archimer.ifremer.fr/doc/00000/4216/

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
ISSN: 1664-302X

hal-01546980
http://hal.upmc.fr/hal-01546980
DOI : 10.3389/fmicb.2013.00414

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of similar to 12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.
ISSN: 0027-8424

hal-01545320
https://hal.archives-ouvertes.fr/hal-01545320
DOI : 10.1073/pnas.1509523113

Éditeur(s) : HAL CCSD
Résumé : One of the major challenges in forest ecology is to understand the ecology, physiology and potential responses of the> 250000 species of vascular plants of the planet through the categorization of this diversity into functional groups. This approach is essentially based on functional traits analysis, but few investigations were made in tropical areas. The aim of this study was to determine functional groups in two contrasted tropical ecosystems, dry (DF) and mountain rain (MRF) forest (respectively rainfall of 1 200 mm/year and 10 000 mm/year). Guadeloupe Island in FWI presents both these ecosystems spread over less 100 km. In a first time, we developed an original species typology based on 7 "soft" traits, easy to measure (stomatal density, leaf trichom density, chlorophyll content, leaf nitrogen content, specific leaf area, wood density, leaf area, plant height). The method was based on principal component analysis (PCA) and agglomerative hierarchical clustering (AHC) applied to these traits measured at the individual level (Blazy et al., 2009). In a second time, we evaluated the relevance of these soft trait-based groups compared to a typology based on 5 "hard" ecophysiological traits, more costly to quantify but with higher functional significance (difference between predawn and minimum leaf water potential, stomatal conductance, maximal carbon assimilation rate, leaf water potential at 90% of loss of stem hydraulic conductivity). When performed on the dominant canopy species in DF and MRF (a total of 13 species and 60 mature individuals), the typological approach based on soft traits seems relevant to discriminate groups with a distinct functional reality. Through both ecosystems, we obtained 4 homogenous groups. Two were exclusively composed by DF's or MRF's species, indicating that a functional strategy can be linked to specific environmental conditions. The two other groups showed a mix of DF and MRF species indicating that different functional strategies can coexist in the same environment. These mixed groups seem distinct by their ecophysiological features, particularly in term of hydraulic characteristics. One group was composed by drought tolerant species, water spender species, with a high xylem embolism resistance, whereas the second one was composed by water saver species, less resistant to embolism. Therefore, a determination of functional groups based on soft traits could be useful to model ecosystem's responses to environmental changes on a global scale.
Book of Abstracts - isem 2013 - Ecological Modelling for Ecosystem Sustainability
Toulouse, France

hal-00964668
https://hal.archives-ouvertes.fr/hal-00964668

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

Résumé : Lorsqu'on s'occupe de la classification des Échinodermes et qu'on cherche pour leurs divisions des caractères naturels et précis, on est frappé des difficultés qu'on éprouve à 'comparer d'un groupe à l'autre les mêmes éléments de leur organisation si compliquée et si variée, et l'on s'étonne de trouver des points essentiels qui, aujourd'hui encore et après tant de travaux, ont besoin d'être éclaircis et de nouveau considérés. ,C'est dans l'espoir de pouvoir combler quelques-unes de ces lacunes qu'ont été entreprises les recherches consignées dans ce mémoire 1). Si, parmi les faits auxquels elles ont conduit, il y en a qui rendent moins difficiles à saisir certaines distinctions nécessaires à la parfaite connaissance des différents types de cette classe, qui mérite à tant d'égards d'être l'objet d'.études persévérantes, la science en est en premier lieu redevable à la subvention libérale, accordée, sur la demande de l'Académie des Sciences, par le Gouvernement et par la Diète pour l'exécution des planches, sans lesquelles il aurait été impossible de faire connaître avec clarté des détails de structure pour la plupart minutieux et assez difficiles à bien décrire.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00034/14488/11789.pdf
http://archimer.ifremer.fr/doc/00034/14488/

Éditeur(s) : HAL CCSD Copernicus Publications
Résumé : International audience
During Ocean Drilling Program Leg 134, a mixed sequence of volcaniclastic and carbonate sediments was cored together with basaltic breccias and a single basalt sill in Hole 833B. In this study, data from Schlumberger's Geochemical Logging Tool, together with physical property logs, characterise part of the section and establish a complete log-derived lithostratigraphy. The major transition between the sedimentary rocks and a basaltic sill at 830 mbsf (metres below sea floor) is clearly seen as well as the distinction between the silicate-rich sediments and the carbonate-rich part of the section. The transition between the volcanic sandstone interbedded with basaltic and sed-lithic breccia of Unit III, and the volcanic sandstone of Unit IV is clearly marked by the physical property logs. The accuracy of the logging data was evaluated and discussed with an improved log versus core correlation. The cluster analysis of the complete data set shows a correlation with the data provided by the mechanical caliper device, which in turn indicates the quality of the borehole.
ISSN: 1816-8957

hal-00642165
http://hal.upmc.fr/hal-00642165
http://hal.upmc.fr/hal-00642165/document
http://hal.upmc.fr/hal-00642165/file/Rabaute_et_al-SciDrilling-1997.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
During their immature life stages, malaria mosquitoes are exposed to a wide array of microbes and contaminants from the aquatic habitats. Although prior studies have suggested that environmental exposure shapes the microbial community structure in the adult mosquito, most reports have focused on laboratory-based experiments and on a single mosquito epithelium, the gut. In this study, we investigated the influence of the breeding site on the development of the Anopheles coluzzii and Anopheles gambiae microbiota in natural conditions. We characterized bacterial communities from aquatic habitats, at surface microlayer and subsurface water levels, to freshly emerge adult mosquitoes using multiplexed 16S rRNA gene pyrosequencing and we separately analyzed the microbiota associated with the different epithelia of adult individual, midguts, ovaries and salivary glands. We found that the distribution of bacterial communities in the aquatic habitats differed according to the depth of water collections. Inter-individual variation of bacterial composition was large in larvae guts but adult mosquitoes from a same breeding site shared quite similar microbiota. Although some differences in bacterial abundances were highlighted between the different epithelia of freshly emerged An. coluzzii and An. gambiae, an intriguing feature from our study is the particular similarity of the overall bacterial communities. Our results call for further investigations on the bacterial population dynamics in the different tissues to determine the distinctive characteristics of each microbiota during the mosquito lifespan and to identify specific interactions between certain key phyla or species and the insect life history traits.
ISSN: 1567-1348

hal-01546167
https://hal.archives-ouvertes.fr/hal-01546167
DOI : 10.1016/j.meegid.2014.09.029

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Le rap a atteint un succès sans précédent auprès des jeunes urbains aux États-Unis et dans les grandes mégalopoles du monde entier. Ce genre musical, figure de proue du hip-hop, s’est affirmé dès les années 1970 comme un moyen d’expression diasporique reflétant les expériences, les rapports complexes et les interactions culturelles entre Africains-Américains, Jamaïcains et Portoricains de la diaspora vivant à New York. Cependant, le positionnement des artistes issus de la diaspora portoricaine a été peu étudié. Nourri de séjours d’observation participante et de recherches réalisées entre 2005 et 2008, ainsi que de la fréquentation assidue des concerts du collectif artistique portoricain The Terror Squad auxquels l’auteur a pu assister, cet article se propose donc d’analyser le rôle central des artistes issus de la diaspora portoricaine de New York à travers l’étude du rap, élément le plus médiatisé du hip-hop. Il devient ainsi possible de mieux entrevoir les tensions, convergences et interactions culturelles qui régissent les rapports complexes qui s’établissent entre la latinité des Portoricains et la culture africaine-américaine urbaine depuis plus d’une trentaine d’années dans le milieu du rap.
Rap music has achieved unprecedented success among urban youth in the United States and in big cities around the world. As a key element of hip-hop this musical style has been asserting its strength since the 1970s as a reflection of the diasporic experience and the complex cultural interactions between African Americans, Jamaicans and Puerto Ricans of the diaspora living in New York. However, scant research has been conducted on the role of Puerto Rican artists of the diaspora living in New York. Therefore, based on field trips and participant observation undertaken between 2005 and 2008 and the concerts of the Puerto Rican rap group The Terror Squad that the author was able to attend frequently, the purpose of this article is to analyze the central role of Puerto Rican artists located in New York through rap music, the most publicized element of hip-hop. This analysis sheds light on the tensions, commonalities and cultural interactions that govern the complex relationships between the distinctive Latin identity of Puerto Ricans and the African American urban culture, as witnessed on New York’s rap scene for more than thirty years.
New York

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.4756
http://journals.openedition.org/etudescaribeennes/4756

Éditeur(s) : HAL CCSD
Résumé : Juin 2003
Dans le contexte actuel de mondialisation, de changement climatique et de forte anthropisation de la biosphère, les Petites Antilles s'érigent en monde marginal ou encore en anti-monde. Fracturées du point de vue politique, économique, linguistique et à certains égards culturel, ces territoires insulaires du Bassin caraïbe recèlent de richesses environnementales (physiques, écosystèmiques et paysagères). Comme partout ailleurs dans le monde humanisé, la survie de ces sociétés implique le rétablissement des grands équilibres écologiques consubstantiels à une articulation efficiente entre le naturel, l'urbain et l'agricole. Compte tenu de la pression démographique, variable d'une île à l'autre, la pérennité des écosystèmes en covariance avec un développement économique profitant au plus grand nombre ne peut se concevoir à l'échelle insulaire. Il semble judicieux d'imaginer un développement à l'échelle de l'archipel basé sur la complémentarité, puisque au sein de chaque composante les diverses ressources biologiques terrestres et marines sont insuffisantes pour assurer une autosuffisance en termes de produits de premières nécessités et d'énergie. Le développement des Petites Antilles s'il doit être durable et prendre comme ossature les directives de Rio (Brésil, 1992) et de Johannesburg (Afrique du Sud, 2002), il devra s'inscrire dans une gestion administrative, scientifique, technique et agricole commune dans le cadre d'une Caraïbe fonctionnellement unifiée. A l'unité floristique, faunistique et biocénotique doivent correspondre des stratégies et donc des politiques, similaires mais diversifiées, d'utilisation des ressources abiotiques (énergie éolienne, hydroélectrique et photovoltaïque) et biotiques (écosystèmes terrestres et marins, flore, faune, sols). Malheureusement dans le présent, la compartimentation économique et politique de la Caraïbe rend ces propos profondément utopiques. Néanmoins dans le futur la survie des peuples des Petites Antilles, impliquera un développement durable signifié par des rapports équilibrés entre hommes et milieux.
–––––
In the nowadays context of "globalization", climatic variation and great anthropization of the biosphere, the Lesser Antilles appear as a marginal world. In a political point of view, those islands offer a greatly distinct and fractured image. The same fact can also be observed in an economic, linguistic and, in a certain measure, cultural perspective. Despite of such a statement, those territories of the Caribbean basin keep economic and landscape resources whom survival depends on the re-establishment of the great ecologic structures implying a productive articulation between the natural, the urban and the agricultural. It seems pertinent to imagine a development on the level of the archipelago based upon complementarity since each constituent presents a limited number of earth and marine biologic reserves which do not guarantee an autosubsistance in energy and first nessecity productivity. A lasting development of the Lesser Antilles supposes a necessary and commun administrative, scientific, technical and agricultural management within the setting of a Caribbean functionally unified. Facing the biocenotic unity, a useful strategy, based on a similar and diversified organization in the exploitation of biophisic resources, must be erected. Such statements could be considered as utopic, regarding the situation of politic and economic division in the Caribbean nowadays. However, in the future, the survival of those insular societies will imply a lasting development lying upon an efficient relationship between Man and environment.
https://halshs.archives-ouvertes.fr/halshs-00003054

Droits : info:eu-repo/semantics/OpenAccess
halshs-00003054
https://halshs.archives-ouvertes.fr/halshs-00003054
https://halshs.archives-ouvertes.fr/halshs-00003054/document
https://halshs.archives-ouvertes.fr/halshs-00003054/file/Devpt-durable_JOSEPH-PHILIPPE.pdf

Éditeur(s) : Elsevier
Résumé : Deep-sea bivalves of the subfamily Bathymodiolinae (family Mytilidae) are very widespread and form dense beds in reduced environments such as hydrothermal vents and cold seeps. Bathymodiolus mussels recently discovered on African cold seeps strangely resemble Gulf of Mexico and Barbados seep species. This raises intriguing questions regarding their taxonomic relationships and their dispersal capabilities across the Atlantic equatorial belt. The morphological study of the shell and soft parts of mussels from either sites of the Atlantic shows that they form two distinct groups: the Bathymodiolus boomerang group (also including Bathymodiolus heckerae and a species from Africa), and the Bathymodiolus childressi group (also including Bathymodiolus mauritanicus and one species from Barbados). Phylogenetic relationships inferred from the nucleotide sequences of the ribosomal DNA internal transcribed spacer (ITS-2) and mitochondrial cytochrome c oxidase subunit I (COI) confirmed morphological analyses and the existence of two amphi-Atlantic complexes of species. Both ITS2 and COI phylogenies indicate almost no difference between the two eastern Atlantic seep mussels (Bathymodiolus sp. A and B. mauritanicus) and their western Atlantic counterparts (B. boomerang and Bathymodiolus sp. B; Barbados Prism cold seeps). In the B. boomerang complex, B. heckerae seems to differ from the Barbados and the African species, whereas these latter two are not distinguishable. In the B. childressi complex, relationships are less clear and do not support the description of new species from the Barbados. Past and present-day connections across the Atlantic are discussed in the light of both larval dispersal capabilities of the mussels and the equatorial Atlantic circulation to appreciate whether these species could represent true amphi-Atlantic species.
Deep Sea Research Part I: Oceanographic Research Papers (0967-0637) (Elsevier), 2007-11 , Vol. 54 , N. 11 , P. 1890-1911

Droits : 2007 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/2007/publication-4064.pdf
DOI:10.1016/j.dsr.2007.07.004
http://archimer.ifremer.fr/doc/00000/4064/