Éditeur(s) : CRILLASH : Centre de Recherches Interdisciplinaires en Lettres, Langues, Arts et Sciences Humaines CRILLASH : Centre de Recherches Interdisciplinaires en Lettres, Langues, Arts et Sciences Humaines CRILLASH : Centre de Recherches Interdisciplinaires en Lettres, Langues, Arts et Sciences Humaines
Extrait de : "Criminalité, éducation et sécurité" : journée d'étude, le 28 mars 2014. Université des Antilles et de la Guyane
Résumé : "Les intervenants présentent un micro-trottoir où la population s'exprime sur la violence. Frédéric Dumesnil insiste sur la divergence des avis quant au fait de savoir s'il y a présence ou non de gang en Guadeloupe. Une divergence qui met en lumière la nuance qui existe entre "gang" et "bande". Entre le tournage du reportage et la journée d'étude, on a enregistré une baisse significative de la violence d'environ 60%."
"Les intervenants présentent un micro-trottoir où la population s'exprime sur la violence. Frédéric Dumesnil insiste sur la divergence des avis quant au fait de savoir s'il y a présence ou non de gang en Guadeloupe. Une divergence qui met en lumière la nuance qui existe entre "gang" et "bande". Entre le tournage du reportage et la journée d'étude, on a enregistré une baisse significative de la violence d'environ 60%."
Siècle(s) traité(s) : 21
Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V14146
V14146
V14146
V14146

Éditeur(s) : AMC : Association Mélanges Caraïbes
Extrait de : "Albert Camus, Aimé Césaire : poétiques de la révolte" : colloque, du 13 au 15 novembre 2013. Université des Antilles et de la Guyane
Description : Yves Ansel revient d'abord sur les différentes similitudes existant entre Césaire et Camus. Il s'intéresse ensuite aux divergences de pensées entre les deux écrivains. Des divergences qu'il attribue aux différences de positions qui prennent essence selon lui dans le bagage historique de chacun des deux écrivain.
Siècle(s) traité(s) : 21
Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V14025
V14025

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow.
ISSN: 0737-4038

hal-01032153
https://hal.archives-ouvertes.fr/hal-01032153
DOI : 10.1093/molbev/msp043

Éditeur(s) : Paris : Imprimerie de Vigor Renaudière
Extrait de : Flore médicale des Antilles, ou traité des plantes usuelles des colonies françaises, anglaises, espagnoles et portugaises. Tome premier (p. 281)
Résumé : Un Cierge Divergent avec sa fleur.
Siècle(s) traité(s) : 19
Permalien : http://www.manioc.org/images/FCL18021-0464i1
FCL18021-0464i1

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : In habitat mosaics, plant populations face environmental heterogeneity over short geographical distances. Such steep environmental gradients can induce ecological divergence. Lowland rainforests of the Guiana Shield are characterized by sharp, short-distance environmental variations related to topography and soil characteristics (from waterlogged bottomlands on hydromorphic soils to well-drained terra firme on ferralitic soils). Continuous plant populations distributed along such gradients are an interesting system to study intrapopulation divergence at highly local scales. This study tested (1) whether conspecific populations growing in different habitats diverge at functional traits, and (2) whether they diverge in the same way as congeneric species having different habitat preferences. Phenotypic differentiation was studied within continuous populations occupying different habitats for two congeneric, sympatric, and ecologically divergent tree species (Eperua falcata and E. grandiflora, Fabaceae). Over 3000 seeds collected from three habitats were germinated and grown in a common garden experiment, and 23 morphological, biomass, resource allocation and physiological traits were measured. In both species, seedling populations native of different habitats displayed phenotypic divergence for several traits (including seedling growth, biomass allocation, leaf chemistry, photosynthesis and carbon isotope composition). This may occur through heritable genetic variation or other maternally inherited effects. For a sub-set of traits, the intraspecific divergence associated with environmental variation coincided with interspecific divergence. The results indicate that mother trees from different habitats transmit divergent trait values to their progeny, and suggest that local environmental variation selects for different trait optima even at a very local spatial scale. Traits for which differentiation within species follows the same pattern as differentiation between species indicate that the same ecological processes underlie intra- and interspecific variation.
ISSN: 0305-7364

hal-01032430
https://hal.archives-ouvertes.fr/hal-01032430
DOI : 10.1093/aob/mct176

Éditeur(s) : HAL CCSD Wiley
Résumé : Unveiling the genetic basis of local adaptation to environmental variation is a major goal in molecular ecology. In rugged landscapes characterized by environmental mosaics, living populations and communities can experience steep ecological gradients over very short geographical distances. In lowland tropical forests, interspecific divergence in edaphic specialization (for seasonally flooded bottomlands and seasonally dry terra firme soils) has been proven by ecological studies on adaptive traits. Some species are nevertheless capable of covering the entire span of the gradient; intraspecific variation for adaptation to contrasting conditions may explain the distribution of such ecological generalists. We investigated whether local divergence happens at small spatial scales in two stands of Eperua falcata (Fabaceae), a widespread tree species of the Guiana Shield. We investigated Single Nucleotide Polymorphisms (SNP) and sequence divergence as well as spatial genetic structure (SGS) at four genes putatively involved in stress response and three genes with unknown function. Significant genetic differentiation was observed among sub-populations within stands, and eight SNP loci showed patterns compatible with disruptive selection. SGS analysis showed genetic turnover along the gradients at three loci, and at least one haplotype was found to be in repulsion with one habitat. Taken together, these results suggest genetic differentiation at small spatial scale in spite of gene flow. We hypothesize that heterogeneous environments may cause molecular divergence, possibly associated to local adaptation in E. falcata.
ISSN: 1010-061X

hal-01032412
https://hal.archives-ouvertes.fr/hal-01032412
DOI : 10.1111/jeb.12069

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.
Biological Journal of the Linnean Society

ird-00759711
http://hal.ird.fr/ird-00759711
http://hal.ird.fr/ird-00759711/document

Éditeur(s) : Yale University
Résumé : Sea-surface temperature images of the coastal upwelling regions off Northwest Africa show that the core of upwelling is sometimes located far from the coast. This has been documented in three regions that share a common feature, namely a wide and shallow continental shelf. This upwelling feature plays a key role in the ecology of the Canary Current System. It creates an innerfront which provides retention for biological material, e.g. fish eggs and larvae, in the highly productive nearshore environment. An analytical model has been developed based on a two dimensional extension of Ekman's solution. The linear and steady response of a homogeneous ocean forced by an upwelling-favorable wind provides a mechanism for the upwelling separation from the coast. The merging of the surface and bottom Ekman layers induces a very weak cross-shore circulation and a "kinematic barrier" for the Ekman transport divergence. In the case of an alongshore wind, the barrier is located near the isobath h ≈ 0.4D, where D is the thickness of Ekman layers. This yields an upwelling cell which is essentially concentrated in the region 0.5D < h < 1.25D, with upwelling occurring preferentially near the isobath h ≈ 0.6D. It turns out that the cross-shore width of upwelling scales with D/S, the ratio of Ekman depth to bottom topographic slope. The application of this solution to real bathymetric profiles rationalizes, not only the offshore upwelling observations in Northwest Africa, but also the influence of topography on the cross-shelf structure of a wind-driven coastal upwelling. The model also quantifies the effect of the cross-shore wind component showing how it drives the nearshore pressure gradient adjustment and how it affects the upwelling. A linear numerical experiment reproduces the theoretical steady solution, thereby allowing investigation of the transient regime. Relaxation of the hypothesis in the numerical model validates the linear assumption of the theory and then allows investigation of the sensitivity to friction parameterizations and the influence of stratification. The latter leads to an "oscillation" of the upwelling cell with seaward migration driven by outcropping and homogeneization of the water column, and, coastal incursion driven by a "boundary layers splitting" process caused by shoreward advection of the isopycnal dome and stratification of the inner shelf.
Journal of Marine Research (Yale University), 2008-09 , Vol. 66 , N. 5 , P. 589-616

Droits : 2008 Yale University
http://archimer.ifremer.fr/doc/2008/publication-6334.pdf
DOI:10.1357/002224008787536790
http://archimer.ifremer.fr/doc/00000/6334/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Background. In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic divergence has seldom been studied.[br/]Methods. We assessed the extent of within-stand neutral and environmentally-driven divergence in the Neotropical tree [i]Eperua falcate Aubl[/i]. (Fabaceae) through a genome-scan approach. Populations of this species grow in dense stands that cross the boundaries between starkly contrasting habitats. Within-stand phenotypic and candidate-gene divergence have already been proven, making this species a suitable model for the study of genome-wide microgeographic divergence. Thirty trees from each of two habitats (seasonally flooded swamps and well-drained plateaus) in two separate populations were genotyped using thousands of AFLPs markers. To avoid genotyping errors and increase marker reliability, each sample was genotyped twice and submitted to a rigorous procedure for data cleaning, which resulted in 1196 reliable and reproducible markers.[br/]Results. Despite the short spatial distances, we detected within-populations genetic divergence, probably caused by neutral processes, such as restrictions in gene flow. Moreover, habitat-structured subpopulations belonging to otherwise continuous stands also diverge in relation to environmental variability and habitat patchiness: we detected convincing evidence of divergent selection at the genome-wide level and for a fraction of the analyzed loci (comprised between 0.25% and 1.6%). Simulations showed that the levels of differentiation for these outliers are compatible with scenarios of strong divergent selection
ISSN: 1932-6203

hal-01204220
https://hal.archives-ouvertes.fr/hal-01204220
https://hal.archives-ouvertes.fr/hal-01204220/document
https://hal.archives-ouvertes.fr/hal-01204220/file/journal.pone.0121394.PDF
PRODINRA : 287494

Éditeur(s) : HAL CCSD
Résumé : East African Rift (EAR) is the divergent plate boundary. EAR exposes different stages of extension, from early stage rifting in Tanzania to oceanic accretion in Afar (Ethiopia). Manyara basin is the southernmost rift system of the east branch of EAR with recent volcanism (< 1.5 Ma) and a seismic swarm in the lower crust (20 – 40 km). Due to its location and tectonic setting, the Manyara basin offers the opportunity to study the earliest stage of rift initiation. Manyara volcanism is composed of several types of hyper-alkaline lavas as Mg-nephelinites (Mg# > 55) (Labait, Kwaraha), calciocarbonatite (Kwaraha) and evolved nephelinites (Mg# < 35) (Hanang).Mg-nephelinites (Labait and Kwaraha) are primary lavas mainly composed of olivine and clinopyroxene (cpx). Geochemical modelling from trace elements suggests that these primary magmas result from a degree of partial melting < 1 % from a CO2-garnet-phlogopite-bearing peridotite. These magmas have an asthenospheric source at depth > 120 km (lava carries xenoliths with equilibrium conditions > 4 GPa). The minerals were crystallized from a magma with a low H2O content (0.1 and 0.5 wt% H2O). The calciocarbonatite and evolved nephelinites are derived from Mg-nephelinites by fractional crystallization and immiscibility processes. Hanang nephelinites are silica- and alkaline-rich lavas (44.2 – 46.7 wt % SiO2, 9.5 –12.1 wt % Na2O+K2O, respectively) composed by cpx, Ti-garnet, nepheline, apatite and titanite. Complex zonation of cpx (e.g. abrupt change of Mg#, Nb/Ta, and H2O) and trace element patterns of nephelinites record magmatic differentiation involving open system with carbonate-silicate immiscibility and primary melt replenishment. The low H2O content of cpx (3 – 25 ppm wt. H2O) indicates that at least 0.3 wt % H2O was present at depth during carbonate-rich nephelinite crystallization at 340 – 640 MPa and 1050 – 1100 °C. The study of hosted-nepheline melt inclusions from Hanang allows constraining the late magmatic evolution of nephelinites during storage and magma ascent. Melt inclusions are composed by a silicate trachytic glass, a carbonate phase and a shrinkage bubble. Trachytic glass contains high content in CO2 (0.43 wt %, SIMS analyses), sulfur (0.21 – 0.92 wt % S), chlorine (0.28 –0.84 wt % Cl) and H2O low content (< 0.1 wt %, Raman analyses). Immiscibility process leading to the formation of carbonate occurs in a closed system during rapid magma ascent between 200 – 500 MPa. The carbonate phase is a Ca-Na-K-S-rich and anhydrous carbonate (33 wt % CaO, 20 wt % Na2O, 3 wt % K2O, and 3 wt % S). The pre-immiscible liquid has a phonolitic composition with 6 ± 1.5 wt % CO2 at 700 MPa. A preliminary study of melt inclusions by XANES spectroscopy and whole rocks by Mössbauer spectroscopy was used to determine these Manyara lavas were formed at oxidizing conditions (~ ΔFMQ +1.5).The early stage rifting volcanism (Manyara Basin) is characterized by CO2-rich and H2O-poor magmas from at least 120 km below the rift escarpment. The presence of CO2-rich magmas and the small amount of volcanic rocks erupted at the surface may indicate that the storage and percolation of these magmas at depth is a potential trigger for deep seismic swarms.
Le rift Est africain (REA) est une frontière de plaque en extension. Ce rift présente plusieurs stades d’extension, de l’initiation du rift en Tanzanie jusqu’à l’accrétion océanique en Afar. Le bassin de Manyara se situe le plus au sud de branche Est du REA. Il est caractérisé par la présence de volcanisme récent (< 1,5 Ma) et d’un essaim sismique dans la croûte inférieure (20 – 40 km). De par sa localisation et son contexte tectonique, le bassin de Manyara offre l’opportunité d’étudier le stade le plus précoce de l’initiation du rift. Le bassin de Manyara est composé de plusieurs types de laves hyperalcalines, les néphélinites magnésiennes (Mg# > 55) (Labait, Kwaraha), de calciocarbonatite (Kwaraha) et des néphélinites différenciées (Mg# < 35) (Hanang).Les néphélinites magnésiennes (Labait et Kwaraha) sont des laves primaires composées d’olivines et de clinopyroxènes (cpx). La modélisation géochimique des éléments en trace suggère que ces magmas primaires résultent d'un degré de fusion partielle ≤ 1 % à partir d'une péridotite à grenat et phlogopite. Ces magmas proviennent d’une profondeur > 120 km (présence de xénolites avec des conditions d’équilibre > 4 GPa). Les minéraux ont cristallisés à partir d’un magma pauvre en eau (0,1 et 0,5 pds % H2O). La calciocarbonatite et les néphélinites différenciés sont issues des néphélinites magnésiennes par cristallisation fractionnée et processus d’immiscibilité. Les néphélinites du Hanang sont riches en éléments alcalins (9,5 – 12,1 pds % Na2O+K2O) et en silice (44,2 – 46,7 pds% SiO2) et sont composés de cpx, grenat, néphéline, titanite et apatite. La zonation complexe dans les cpx (par exemple, changement brusque de Mg#, Nb/Ta, et H2O) implique une différenciation magmatique en système ouvert avec immiscibilité de liquide carbonaté et silicaté ainsi qu’un remplissage de la chambre magmatique avec des liquides primaires. La faible teneur en eau des cpx (3 – 25 ppm H2O) indique la présence d’un magma pauvre en eau (0,3 pds % H2O) lors de la cristallisation des cpx à des conditions crustales (340 – 640 MPa et 1050 – 1100 °C). L’étude des inclusions vitreuses dans les néphélines de Hanang permet de contraindre l'évolution magmatique tardive des néphélinites et le comportement des éléments volatils (CO2, H2O, S, F, Cl) lors du stockage et de la remontée du magma. Les inclusions vitreuses sont composées d’un verre trachytique, d’une phase carbonatée et d’une bulle de rétraction. Le verre trachytique contient du CO2 (0,43 pds % CO2, analyses SIMS), du soufre (0,21 à 0,92 pds% S), du chlore (0,28 – 0,84 pds % Cl) et très peu d’H2O (< 0,1 pds % H2O, analyses Raman). Le processus d’immiscibilité conduisant à la formation du carbonate se produit dans un système fermé pendant l'ascension rapide du magma, entre 200 – 500 MPa. La phase carbonatée est un carbonate anhydre et riche en Ca-Na-K-S (33 pds % CaO, 20 pds % Na2O, 3 pds % K2O, et 3 pds % S). Le liquide pré-immiscible a une composition phonolitique avec 6 ± 1,5 pds % CO2 à une pression de 700 MPa. Une étude préliminaire des inclusions par spectroscopie XANES et des roches par spectroscopie Mössbauer a permis de déterminer que les laves de Manyara se sont formées à conditions oxydantes (~ ∆FMQ +1,5).À l’initiation du rift, le volcanisme dans le bassin de Manyara est caractérisé par des magmas riches en CO2 et pauvres en H2O issus d’au moins 120 km de profondeur sous l'escarpement du rift. La présence de ces magmas riches en CO2 et la faible quantité de roches volcaniques émises à la surface peuvent indiquer que le piégeage et la percolation de ces magmas en profondeur est un déclencheur potentiel des essaims sismiques profonds.
https://tel.archives-ouvertes.fr/tel-01563231

NNT : 2016MONTT114
tel-01563231
https://tel.archives-ouvertes.fr/tel-01563231
https://tel.archives-ouvertes.fr/tel-01563231v2/document
https://tel.archives-ouvertes.fr/tel-01563231/file/2016_BAUDOUIN_archivage.pdf

Éditeur(s) : HAL CCSD
Résumé : il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : ACTIVITY_REPORT
Understanding genomic evolution in wild populations is of particular importance because evolution is a central process in our understanding of populations’ history and their future response to global changes. In addition to fundamental knowledge, the study of populations’ evolution has wide applications such as conservation/restoration genetics or epidemiology. Indeed, genetic diversity is the ‘fuel’ for populations’ evolution and adaptation to new conditions, and estimating the extent and the geographic structure of genetic diversity, as well as identifying the evolutionary forces behind (demography, gene flow, and adaptation) are thus major challenges in the current context of global changes. [br/]A particular attention is currently devoted to the process of genetic divergence in wild populations, with emphases on gene flow, local adaptation, and their interactions. Indeed, adaptation in wild populations is supported in many species by many kinds of experiments based on both quantitative phenotypic traits and molecular data. However, the processes governing populations’ evolution are poorly understood in the tropical rainforest of Amazonia, and the relative influence of neutral and adaptive processes are continuously discussed. [br/]I am a young scientist interested in the process of genomic divergence in wild (tree) populations. I aimed at understanding how evolution structures the genetic diversity and governs molecular divergence in wild populations, with particular emphases on gene flow and local adaptation. During five years as a young scientist, I worked on answering the following questions, focusing on two tree species occupying vulnerable areas: mainly [i]Eperua falcata[/i] in Amazonia and, to a lesser extent, [i]Abies alba[/i] in the Mediterranean area.[br/][u]Scientific questions:[/u][br/]- Which evolutionary drivers are responsible of the structure of genetic diversity in wild populations occupying wide areas? This question was addressed at different geographical scales: from large (regional) to very local (microgeographic) scales. [br/]- What is the relative influence of neutral (gene flow, inbreeding) and adaptive drivers in the process of genetic divergence?[br/]- Is microgeographic adaptation possible in spite of extensive gene flow between populations occupying the extreme boundaries of an ecological gradient? [br/]- What is the extent of natural selection in the (whole) genome of wild populations? [br/][br/]My research work is at the interface between three promising disciplines: Evolutionary genomics (i.e. the study of populations evolution and the evolutionary drivers behind), Bioinformatics (i.e. the treatment of next-generation data), and Bayesian modelling (i.e. the empirical calibration of complex mechanistic model). I intend to take advantage of the recent advances in sequencing and informatic technologies to bring up to date the field of ecological genetics and evolutionary biology, by developing modern research strategies to study the process of genomic divergence in wild populations.
https://hal.archives-ouvertes.fr/hal-01204218

hal-01204218
https://hal.archives-ouvertes.fr/hal-01204218
PRODINRA : 286326

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.
ISSN: 0024-4066

ird-00759711
http://hal.ird.fr/ird-00759711
http://hal.ird.fr/ird-00759711v2/document
http://hal.ird.fr/ird-00759711/file/FauvelotBorsa_Scomberomorus%20commerson%20p%20HAL.pdf

Éditeur(s) : HAL CCSD
Résumé : Understanding of the mechanisms driving diversification of species is a significant way to improve the management of ecosystems, predict the impacts of climate change and understand the actual and past biodiversity level. The aim of this thesis is to understand and comprehend genetic mechanisms behind the diversification of species in the presence of gene flow. This thesis is focused on the biological model Symphonia globulifera, which presents two ecotypes: the S.globulifera, specialist of seasonally flooded lowlands and S.sp1, specialist of terra firme. These two ecotypes show low genetic differentiation, despite the presence of two apparent phenotypes. A first part of this thesis was to test the presence of local adaptation of this using reciprocal transplant experiment gardens, allowing the understanding of the ecotypes distributions in their natural habitats. Then, this local adaptation in the presence of gene flow, directed me to the regulation of gene methylation in order to see the role this brand of epigenetics can have in the divergence of the ecotypes. In a third part of the thesis, new generation sequencing of the transcriptome ecotypes in reciprocal gardens transplantations allowed me to show the evidence of gene regulation to differentiate the ecotypes. This work thesis is based on phenotype records data, AFLP genotyping and high-throughput sequencing of the transcriptome, in order to show the important value of gene regulation in the divergence of the locally adapted ecotypes, and a weak role of DNA methylation in the establishment of local adaptation.
Connaitre et appréhender les mécanismes de la diversification des espèces est important pour la gestion des écosystèmes, la prévision des impacts des changements climatiques et la compréhension de la biodiversité actuelle et passée. Le but de cette thèse est de comprendre et de déceler les mécanismes génétiques à l’origine de la diversification des espèces en présence de flux de gènes. Cette thèse se focalise sur le modèle biologique Symphonia globulifera, qui compte deux écotypes : le S.globulifera spécialiste de la terra firme et le S.sp1, spécialiste des bas-fonds. Ces deux écotypes montrent une faible différenciation génétique, malgré la présence de deux phénotypes différents.Une première étape a été de mettre en évidence la présence d’une adaptation locale au sein de cette espèce, par le biais d’une expérimentation de jardins de transplantation réciproques, permettant d’expliquer la répartition des écotypes dans leur habitat naturel. Ensuite, dans le but d’identifier les mécanismes sous-jacent à cette adaptation locale, j’ai testé l’hypothèse que la méthylation des gènes pourrait être une marque de l’épigénétique contribuant à la divergence des écotypes, par l’utilisation d’enzyme sensibles à la méthylation dans un protocole de génotypage AFLP. Enfin, un séquençage haut-débit du transcriptome des écotypes en jardins de transplantation réciproques m’a permis de mettre en évidence une expression différentielle des gènes entre les écotypes, qui pourrait expliquer les différences phénotypiques observées entre les écotypes malgré une faible différentiation génétique. Ces travaux de thèse s’appuie, ainsi, sur des données de traits phénotypiques, de génotypage AFLP et de séquençage à haut débit du transcriptome pour montrer la valeur importante de la régulation des gènes dans la divergence des écotypes adaptés localement, et un faible rôle de la méthylation de l’ADN dans l’établissement cette adaptation locale.
https://tel.archives-ouvertes.fr/tel-01405400

NNT : 2015YANE0005
tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400/document
https://tel.archives-ouvertes.fr/tel-01405400/file/these_-_tinaut.pdf

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks. Results: Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain. Conclusions: Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01257771
http://hal.upmc.fr/hal-01257771
http://hal.upmc.fr/hal-01257771/document
http://hal.upmc.fr/hal-01257771/file/s13062-015-0092-3.pdf
DOI : 10.1186/s13062-015-0092-3

Éditeur(s) : CRILLASH : Centre de Recherches Interdisciplinaires en Lettres, Langues, Arts et Sciences Humaines
Extrait de : "Tracées de Jean Bernabé" : colloque international, du 25 au 27 octobre 2017. Université des Antilles
Description : La présente communication a pour origine de longues discussions entre Gerry L'Etang et Jean Bernabé. Ce dernier lui avait soumis pour avis la version d'étape d'un texte resté probablement inédit, « L'ethnonyme créole kouli, ses expansions lexicales et ses enjeux socio-symboliques ». Leurs divergences portaient sur l'interprétation du mot créole martiniquais chapé-kouli (en français créolisé : échappé-coolie ou échappé). Selon Gerry L'Etang, « par-delà la signification du terme : « métis d'Indien et de Noir », nous nous interrogions sur son étymologie, sur « qui ici a échappé à quoi ? ». Pour Bernabé, en raison même de la construction de l'expression (chapé-kouli et non kouli-chapé), c'est « le nègre (base non exprimée mais cependant présente) qui se sauve en devenant kouli ». Or les recherches que j'avais réalisées jadis sur les représentations des Indiens de Martinique, indiquaient que du point de vue de ces derniers, c'est « le kouli qui ici l'a échappé belle ». J'eus alors pour nous départager, l'idée d'une enquête dont le résultat fut inattendu. »

Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V17245
V17245

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
North Tanzanian Divergence is the first stage of continental break-up of East African Rift (<6 Ma) and is one of the most concentrated areas of carbonatite magmatism on Earth, with singular Oldoinyo Lengai and Kerimasi volcanoes. Hanang volcano is the southernmost volcano in the North Tanzanian Divergence and the earliest stage of rift initiation. Hanang volcano erupted silica-undersaturated alkaline lavas with zoned clinopyroxene, nepheline, andradite-schorlomite, titanite, apatite, and pyrrhotite. Lavas are low MgO-nephelinite with low Mg# and high silica content (Mg# = 22.4–35.2, SiO2 = 44.2–46.7 wt%, respectively), high incompatible element concentrations (e.g. REE, Ba, Sr) and display Nb–Ta fractionation (Nb/Ta = 36–61). Major elements of whole rock are consistent with magmatic differentiation by fractional crystallization from a parental melt with melilititic composition. Although fractional crystallization occurred at 9–12 km and can be considered as an important process leading to nephelinite magma, the complex zonation of cpx (e.g. abrupt change of Mg#, Nb/Ta, and H2O) and trace element patterns of nephelinites recorded magmatic differentiation involving open system with carbonate–silicate immiscibility and primary melilititic melt replenishment. The low water content of clinopyroxene (3–25 ppm wt. H2O) indicates that at least 0.3 wt% H2O was present at depth during carbonate-rich nephelinite crystallization at 340–640 MPa and 1050–1100 °C. Mg-poor nephelinites from Hanang represent an early stage of the evolution path towards carbonatitic magmatism as observed in Oldoinyo Lengai. Paragenesis and geochemistry of Hanang nephelinites require the presence of CO2-rich melilititic liquid in the southern part of North Tanzanian Divergence and carbonate-rich melt percolations after deep partial melting of CO2-rich oxidized mantle source.
ISSN: 0010-7999

hal-01467390
https://hal.archives-ouvertes.fr/hal-01467390
DOI : 10.1007/s00410-016-1273-5

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
Résumé : This study provides additional constraints on the relations between deformation, hydration and percolation of fluids and melts in the subcontinental lithospheric mantle beneath a craton and a rift, as well as their implication on its geodynamical behaviour. I have analysed the microstructures, the CPOs, and the hydrogen content of mantle xenoliths from the Kaapvaal craton, and two sets of xenoliths from different localities along the East African Rift (North Tanzanian Divergence and SE Ethiopia).The coarse-granular microstructures and the well-defined CPOs in Kaapvaal peridotites suggest a deformation followed by a long quiescence time. Orthorhombic olivine CPOs predominates, but axial-[100] and axial-[010] are also measured. Cratonic peridotites record multiple metasomatic episodes, leading to a significant compositional heterogeneity, which cannot be imaged by seismic studies. Olivine hydrogen contents are variable, but tend to increase until 150 km depth, reaching up to 50 ppm wt. H2O. The deeper samples are almost dry. Piston-cylinder experiments on hydrogen diffusion between a volatile-rich kimberlitic melt and forsterite suggest that the presence of CO2 in the system could significantly decrease water fugacity and thus forsterite hydration. These experimental results indicate that the hydrogen contents measured in olivine were acquired during a metasomatic event rather than during xenolith extraction by kimberlites. However, this metasomatism was not followed by remobilization of the cratonic root.In the North Tanzanian Divergence, localities within the rift axis and the volcanic transverse belt (Lashaine and Olmani) show significant differences in microstructures and olivine CPO patterns. In Lashaine, coarse-granular microstructures and orthorhombic to axial-[100] CPO patterns in olivine can be explained by transpressional deformation during the formation of the Mozambique belt, or by the occurrence of a remnant of a cratonic domain embedded within the Mozambique belt. Within the rift axis, porphyroclastic to mylonitic microstructures suggest a recent rift-related deformation accompanied by syn-kinematic melt-rock reactions, and followed by variable annealing. The strong heterogeneity in microstructures and olivine CPO suggests that this deformation was acquired during multiple tectonic events probably linked to episodic magma percolation, separated by quiescence episodes. The axial-[100] patterns in olivine and the oblique fast directions reported by SKS studies are coherent with transtensional deformation within the lithospheric mantle beneath the rift.The peridotites from SE Ethiopia are less recrystallized than the rift-axis Tanzanian peridotites, displaying coarse-porphyroclastic microstructures. Microstructures and orthorhombic CPOs in olivine suggest syn- to post-metasomatic deformation. S-waves polarization anisotropies calculated for these samples cannot explain alone the delay times reported by SKS studies in this part of the East-African Rift.
Les travaux réalisés durant cette thèse apportent de nouvelles contraintes sur les relations entre déformation, hydratation et percolation de fluides et/ou de magmas dans le manteau subcontinental sous un craton et sous un rift, et leurs implications sur son comportement rhéologique. Il repose sur l'analyse des microstructures, des OPRs et des teneurs en hydrogène de xénolites mantelliques du craton du Kaapvaal, et sur deux séries de xénolites provenant de différentes localités le long du rift Est-Africain (Divergence Nord Tanzanienne et SE de l'Ethiopie). Les microstructures granulaires à gros grains et les OPRs bien définies des péridotites du craton du Kaapvaal sont cohérentes avec un épisode de déformation suivi d'une longue période de quiescence. Les OPRs de l'olivine sont majoritairement à symétrie orthorhombique, mais des symétries axiale-[100] et axiale-[010] sont aussi mesurées. Les péridotites cratoniques enregistrent de multiples épisodes métasomatiques, ayant entraîné une hétérogénéité de compositions à petite échelle ne pouvant être détectée par les études sismiques. Les teneurs en hydrogène mesurées dans l'olivine sont variables, mais ont tendance à augmenter jusqu'à 150 km de profondeur, atteignant alors jusqu'à 50 ppm wt. H2O. En dessous de cette profondeur, les échantillons montrent des teneurs en hydrogène très faibles. Les expériences réalisées en piston-cylindre sur la diffusion de l'hydrogène issue d'un liquide kimberlitique vers de la forstérite suggèrent que la fugacité en eau pourrait fortement être diminuée par la présence de CO2, empêchant l'hydratation de l'olivine durant extraction des xénolites par les kimberlites. Ces résultats expérimentaux suggèrent que les teneurs en hydrogène dans l'olivine des péridotites du craton du Kaapvaal ont été acquises durant un épisode métasomatique en profondeur et non pendant leur extraction par les kimberlites. Ces teneurs n'ont toutefois pas à ce jour entraîné de remobilisation de la racine cratonique. Enfin, le calcul des propriétés sismiques des péridotites cratoniques révèle que les anisotropies générées par les OPRs de ces échantillons sont suffisantes pour expliquer les anisotropies mesurées par les ondes SKS et les ondes de surface.Les xénolites de la Divergence Nord-Tanzanienne, montrent des variations significatives de microstructures et d'OPR de l'olivine entre les péridotites des localités dans l'axe du rift et celles de la chaîne volcanique transverse (Lashaine et Olmani). A Lashaine, les microstructures granulaires à gros grains et les OPRs de type orthorhombique et axial-[010] peuvent être expliquée par une déformation en transpression liée à la formation de la chaîne Mozambique ou par la présence d'une relique d'un domaine cratonique à l'intérieur de la chaîne Mozambique. Dans l'axe du rift, les microstructures porphyroclastiques à mylonitiques suggèrent une déformation plus récente, accompagnée de réactions magma-roche sous des conditions proches du solidus, suivie d'un recuit variable. L'hétérogénéité des microstructures enregistrées par les échantillons du rift suggère de multiples épisodes de déformation localisée, probablement liés à l'injection percolation épisodique de magmas, espacés de périodes d'accalmie. Les OPRs de l'olivine de type axial-[100] et l'orientation des directions de polarisation des ondes SKS suggère que le rift s'est formé en régime de transtension Les péridotites du Sud-Est de l’Éthiopie présentent des microstructures porphyroclastiques à gros grains moins recristallisées qu'en Tanzanie. Les microstructures et les OPRs principalement de type orthorhombique suggèrent une déformation syn- à post-métasomatisme. Les anisotropies de polarisation des ondes S calculées pour ces échantillons sont insuffisantes pour expliquer à elles seules les déphasages des ondes SKS dans cette partie du rift.
https://tel.archives-ouvertes.fr/tel-01684759

Droits : info:eu-repo/semantics/OpenAccess
NNT : 2014MON20139
tel-01684759
https://tel.archives-ouvertes.fr/tel-01684759
https://tel.archives-ouvertes.fr/tel-01684759/document
https://tel.archives-ouvertes.fr/tel-01684759/file/43443_BAPTISTE_2014_archivage_cor.pdf

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : A preliminary version appeared in the 18th ACM-SIAM Symposium on Discrete Algorithms, pp. 746- 755, 2007
International audience
The Voronoi diagram of a finite set of objects is a fundamental geometric structure that subdivides the embedding space into regions, each region consisting of the points that are closer to a given object than to the others. We may define various variants of Voronoi diagrams depending on the class of objects, the distance function and the embedding space. In this paper, we investigate a framework for defining and building Voronoi diagrams for a broad class of distance functions called Bregman divergences. Bregman divergences include not only the traditional (squared) Euclidean distance but also various divergence measures based on entropic functions. Accordingly, Bregman Voronoi diagrams allow one to define information-theoretic Voronoi diagrams in sta- tistical parametric spaces based on the relative entropy of distributions. We define several types of Bregman diagrams, establish correspondences between those diagrams (using the Legendre transformation), and show how to compute them efficiently. We also introduce extensions of these diagrams, e.g. k-order and k-bag Bregman Voronoi diagrams, and introduce Bregman triangulations of a set of points and their connection with Bregman Voronoi diagrams. We show that these triangulations capture many of the properties of the celebrated Delaunay triangulation.
ISSN: 0179-5376

hal-00488441
https://hal.archives-ouvertes.fr/hal-00488441
https://hal.archives-ouvertes.fr/hal-00488441/document
https://hal.archives-ouvertes.fr/hal-00488441/file/BVD-DCG.pdf

Éditeur(s) : HAL CCSD
Résumé : The Voronoi diagram of a finite set of objects is a fundamental geometric structure that subdivides the embedding space into regions, each region consisting of the points that are closer to a given object than to the others. We may define many variants of Voronoi diagrams depending on the class of objects, the distance functions and the embedding space. In this paper, we investigate a framework for defining and building Voronoi diagrams for a broad class of distance functions called Bregman divergences. Bregman divergences include not only the traditional (squared) Euclidean distance but also various divergence measures based on entropic functions. Accordingly, Bregman Voronoi diagrams allow to define information-theoretic Voronoi diagrams in statistical parametric spaces based on the relative entropy of distributions. We define several types of Bregman diagrams, establish correspondences between those diagrams (using the Legendre transformation), and show how to compute them efficiently. We also introduce extensions of these diagrams, e.g. k-order and k-bag Bregman Voronoi diagrams, and introduce Bregman triangulations of a set of points and their connexion with Bregman Voronoi diagrams. We show that these triangulations capture many of the properties of the celebrated Delaunay triangulation. Finally, we give some applications of Bregman Voronoi diagrams which are of interest in the context of computational geometry and machine learning.
https://hal.inria.fr/inria-00137865

Report N° : RR-6154
inria-00137865
https://hal.inria.fr/inria-00137865
https://hal.inria.fr/inria-00137865v2/document
https://hal.inria.fr/inria-00137865/file/bregman.pdf