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 Elsevier
Résumé : International audience
The Tyrrhenian Sea is usually interpreted to be a Neogene back-arc basin that opened by continental rifting and oceanic spreading caused by the eastward migration of the Apennine subduction system during Miocene and Pliocene times. Rifting of the southern Tyrrhenian Sea started first along the Eastern Sardinian margin during the middle to late Miocene times, including the Messinian. The "METYSS" project aims at better constraining the relationships between crustal tectonics, salt tectonics and sedimentation from Messinian times to present-day. The "METYSS 1" cruise (2009) allowed to acquire about 1200 km of HR seismic-reflection profiles along the Eastern Sardinian margin, Western Tyrrhenian Sea. This data set clearly illustrates that this area has been highly dissected during the rifting stage by N-S trending normal faults delineating ridges and basins, as previously described. The Messinian seismic markers (UU and MU) locally display fan-shaped stratal geometries, but the mechanism responsible for such geometries, salt tectonics or rifting, has yet to be carefully deciphered. We also mapped the spatial distribution of the mobile salt. The highly variable thickness of the small confined salt basins may be related to the initial pre-Messinian basin geometry, to the fact that salt deposition was syn-rift or to salt movement. Southeastward, salt tectonics is vigorous in unconfined basins and appears to have started early during the UU deposition. More surprisingly, our data demonstrate that some of the major faults have been significantly reactivated during the post-rift period, up to late Quaternary time, as shown by bathymetric scarps and associated debris flows. Moreover, some of this post-rift deformation can be evidenced within the Plio-Quaternary sequence by a regional unconformity. The post-Miocene deformation style varies greatly between different areas of the margin, and can also be strongly influenced by the presence or absence of mobile Messinian salt.
ISSN: 0040-1951

hal-00996665
https://hal.archives-ouvertes.fr/hal-00996665
DOI : 10.1016/j.tecto.2013.12.015

Résumé : La distribution actuelle des espèces d’arbres des forêts tropicales humides amazoniennes est le résultat de processus dynamiques sur lesquels les perturbations passées, d’origine climatique ou anthropique, peuvent avoir jouées un rôle majeur. Des outils génétiques actuels associés à des méthodes d’analyses puissantes permettent d’inférer et de dater l’empreinte génomique des évènements démographiques subits par les populations naturelles. Le but de cette thèse est de contribuer à une vision d’ensemble de l’évolution démographique de la forêt tropicale humide du plateau des Guyanes pendant le Quaternaire. J’ai d’abord étudié les propriétés des microsatellites (répétitions simple de séquences, SSR) et les limites de leurs applications en tant que marqueurs moléculaires en phylogéographie. Plusieurs allèles SSR contenu dans diverses populations de trois genres d’arbres différents ont été séquencés et le polymorphisme, porté par chaque partie des fragments ADN contenant des SSR, a été étudié. J’ai observé que la quantité de variation génétique était aussi importante dans les régions encadrant le microsatellite que dans le SSR lui-même. Ces régions ont contribué significativement à l’information phylogénétique et ont parfois été la principale source de différenciation entre les individus et les populations. Cette expérience m’a permis de choisir la meilleure stratégie à adopter pour traiter les données de variation génétique des SSR dans des modèles démographiques. J’ai ensuite utilisé ces marqueurs SSR et des méthodes ABC pour étudier l’impact local des occupations humaines précolombiennes sur les forêts en Guyane française. Les changements démographiques subis par des populations de quatre espèces d’arbres ont été comparés entre cinq sites occupés et quatre sites non perturbés. Les perturbations naturelles et induites par l’homme ont contribué à la mise en place de la diversité observée actuellement, comme le suggère des signatures d’effet fondateur détectées sur les sites perturbés ou non. Néanmoins, la taille des populations fondatrices semble être proportionnelle à l’impact humain estimé, indiquant que les perturbations anthropique ont induit un remplacement des populations plus important que les processus écologiques naturels. Pour terminer, j’ai mené une étude de démographie comparative d’espèces d’arbres tropicaux à l’échelle régionale de la Guyane française. Cinq scénarios démographiques ont été testés pour neuf populations de huit espèces en utilisant des microsatellites nucléaires et des séquences chloroplastiques. Les changements démographiques les plus récents détectés convergent vers une signature générale d’expansion de la forêt humide depuis probablement la dernière glaciation. Cela peut suggérer, soit que la composition des forêts du plateau des Guyanes était différente, ou que le couvert forestier était moins étendu. Ce résultat constitue le premier indice de changement passé, probablement d’origine climatique, subi par les communautés forestières du plateau des Guyanes ; qui n’avait jusque-là pas pu être testé avec des méthodes standards en raison d’un manque de fossiles. En conclusion, j’ai recueilli des preuves génétiques que les perturbations, à différents échelles de temps, ont marqué la structure et la composition génétique des forêts du plateau des Guyanes. L’application de ces méthodes à d’autres régions Néotropicales pourrait contribuer, à l’avenir, à reconstruire l’histoire écologique de la forêt amazonienne de façon détaillée.
The current tree species distribution in Amazonian tropical rainforests is the outcome of dynamic processes in which past perturbations, climatic or anthropogenic, may have played a major role. Currently available genetic tools associated with powerful analytical methods allow inferring and dating the genomic imprint of demographic events undergone by natural populations. The aim of my thesis is to contribute to an overview of the demographic evolution of the tropical rainforest in the Guiana shield during the Quaternary. I have first studied the properties of microsatellites or Simple sequence repeat (SSR) and the limits in their applications as molecular markers in phylogeography. Several SSR alleles in multiple populations of three divergent tree genera have been sequenced and the sources of polymorphisms, carried by each portion of SSR-containing DNA amplicons, have been broken apart. I have observed that the amount of variation was as large in flanking regions as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations. This experiment allowed me to choose the best strategy to treat SSR variation in demographic modeling. I have subsequently used SSR markers and ABC methods to study the impact of pre-Columbian human settlements at the local level on rainforests in French Guiana. Demographic changes undergone by populations of four tree species were compared between five settled and four undisturbed sites. Both natural turnover and human-induced disturbances appeared as shaping currently observed genetic diversity, with signatures of founder effect both at disturbed and undisturbed sites. Nevertheless, the size of founding populations appeared to be proportional to the estimated human impact, suggesting that human-made disturbance caused deeper population turnover than background ecological processes. Finally, I have conducted a comparative demography study of tropical tree species at the regional level across French Guiana. Five demographic scenarios have been tested for nine populations from eight species using both nuclear microsatellites and chloroplastic sequences. The most recent demographic signals detected converge on a global signature of expansion of the rainforest since probably the last glaciation. This finding can suggest either that the composition of the Guiana shield rainforests was different, or that its global extent was smaller, during earlier epochs of the Pleistocene than today. This result is the first firm indication of changes undergone by the forest communities of the Guiana shield in the distant climatic past – something which could not be tested with standard methods due to almost complete lack of fossil evidence. In conclusion, I have gathered genetic evidence that disturbances, both in historical and geological times, have marked the structure and composition of forests in the Guiana shield.The extensive application of these methods to other regions of the Neotropics maycontribute, in the future, to the detailed reconstruction of the ecological history ofAmazonian forests.

http://www.theses.fr/2012AGUY0568/document

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
Detailed seafloor mapping in the area east of Taiwan revealed trench-parallel stretching and folding of the Ryukyu forearc and lateral motion of the accretionary wedge under oblique convergence. East of 122ø40'E, a steep accretionary wedge is elongated in an E-W direction. A major transcurrent right-lateral strike-slip fault accommodates the strain partitioning caused by an oblique convergence of 40 ø. A spectacular out-of-sequence thrust may be related to the subduction of a structural high lying in the axis of the N-S trending Gagua Ridge. This asperity is likely responsible for the uplift of the accretionary wedge and forearc basement and may have augmented strain partitioning by increasing the coupling between the two plates. West of 122ø40'E, the low-taper accretionary wedge is sheared in a direction subparallel to the convergence vector with respect to the Ryukyu Arc. The bayonet shape of the southern Ryukyu Arc slope partly results from the recent (re)opening of the southern Okinawa Trough at a rate of about 2 to 4 cm/yr. Right-lateral shearing of the sedimentary forearc with respect to the nonlinear Ryukyu backstop generates trench-parallel extension in the forearc sediment sequence at dilational jogs and trench-parallel folding at compressive jogs. The Hoping Basin lies above a diffuse trench/trench/fault (TTF) or TFF unstable triple junction moving toward the south along a N-S transform zone which accommodates the southward drift of the Ryukyu Arc with respect to Eurasia.
ISSN: 0278-7407

hal-01261555
https://hal.archives-ouvertes.fr/hal-01261555
https://hal.archives-ouvertes.fr/hal-01261555/document
https://hal.archives-ouvertes.fr/hal-01261555/file/Lallemand_et_al-1999-Tectonics.pdf
DOI : 10.1029/1998TC900011

Éditeur(s) : HAL CCSD American Geophysical Union - AGU
Résumé : IODP Expedition 335 "Superfast Spreading Rate Crust 4" returned to ODP Hole 1256D with the intent of deepening this reference penetration of intact ocean crust several hundred meters into cumulate gabbros. This was the fourth cruise of the superfast campaign to understand the formation of oceanic crust accreted at fast spreading ridges, by exploiting the inverse relationship between spreading rate and the depth to low velocity zones seismically imaged at active mid-ocean zones, thought to be magma chambers. Site 1256 is located on 15-million-year-old crust formed at the East Pacific Rise during an episode of superfast ocean spreading (>200 mm/yr full rate). Three earlier cruises to Hole 1256D have drilled through the sediments, lavas and dikes and 100 m into a complex dike-gabbro transition zone. The specific objectives of IODP Expedition 335 were to: (1) test models of magmatic accretion at fast spreading ocean ridges; (2) quantify the vigor of hydrothermal cooling of the lower crust; (3) establish the geological meaning of the seismic Layer 2-3 boundary at Site 1256; and (4) estimate the contribution of lower crustal gabbros to marine magnetic anomalies. It was anticipated that even a shortened IODP Expedition could deepen Hole 1256D a significant distance (300 m) into cumulate gabbros. Operations on IODP Expedition 335 proved challenging from the outset with almost three weeks spent re-opening and securing unstable sections of the Hole. When coring commenced, the destruction of a hard-formation C9 rotary coring bit at the bottom of the hole required further remedial operations to remove junk and huge volumes of accumulated drill cuttings. Hole-cleaning operations using junk baskets returned large samples of a contact-metamorphic aureole between the sheeted dikes and a major heat source below. These large (up to 3.5 kg) irregular samples preserve magmatic, hydrothermal and structural relationships hitherto unseen because of the narrow diameter of drill core and previous poor core recovery. Including the ~60 m-thick zone of granoblastic dikes overlying the uppermost gabbro, the dike-gabbro transition zone at Site 1256 is over 170 m thick, of which more than 100 m are recrystallized granoblastic basalts. This zone records a dynamically evolving thermal boundary layer between the principally hydrothermal domain of the upper crust and a deeper zone of intrusive magmatism. The recovered samples document a sequence of evolving geological conditions and the intimate coupling between temporally and spatially intercalated intrusive, hydrothermal, contact-metamorphic, partial melting and retrogressive processes. Despite the operational challenges, we achieved a minor depth advance to 1522 m, but this was insufficient penetration to complete any of the primary objectives. However, Hole 1256D has been thoroughly cleared of junk and drill cuttings that have hampered operations during this and previous Expeditions. At the end of Expedition 335, we briefly resumed coring and stabilized problematic intervals with cement. Hole 1256D is open to its full depth and ready for further deepening in the near future.
InterRidge News

hal-00688821
https://hal.archives-ouvertes.fr/hal-00688821

Éditeur(s) : HAL CCSD Microbiology Society
Résumé : International audience
An actinobacterial strain, designated ViU22(T), was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0-4.5 % (w/v) NaCl and at 15-37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22(T) belonged to the genus Microbacterium. It exhibited highest 16S rRNA gene sequence similarity with the type strains of Microbacterium testaceum (98.14 %) and Microbacterium binotii (98.02 %). The DNA-DNA relatedness of strains ViU22(T) with the most closely related type strains Microbacterium testaceum and Microbacterium binotii DSM 19164(T) was 20.10 % (± 0.70) and 28.05 % (± 0.35), respectively. Strain ViU22(T) possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22(T) were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other Microbacterium species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA-DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22(T) should be classified as the type strain of a novel species within the genus Microbacterium, for which the name Microbacterium lemovicicum sp. nov. is proposed. The type strain is ViU22(T) ( = ATCC BAA-2396(T) = CCUG 62198(T) = DSM 25044(T)).
ISSN: 1466-5026

hal-01561095
https://hal-amu.archives-ouvertes.fr/hal-01561095
PUBMED : 23264499
DOI : 10.1099/ijs.0.048454-0

Éditeur(s) : HAL CCSD Cold Spring Harbor Laboratory Press
Résumé : International audience
Meiotic recombination is required for the segregation of homologous chromosomes and is essential for fertility. In most mammals, the DNA double-strand breaks (DSBs) that initiate meiotic recombination are directed to a subset of genomic loci (hot spots) by sequence-specific binding of the PRDM9 protein. Rapid evolution of the DNA-binding specificity of PRDM9 and gradual erosion of PRDM9-binding sites by gene conversion will alter the recombination landscape over time. To better understand the evolutionary turnover of recombination hot spots and its consequences, we mapped DSB hot spots in four major subspecies of Mus musculus with different Prdm9 alleles and in their F1 hybrids. We found that hot spot erosion governs the preferential usage of some Prdm9 alleles over others in hybrid mice and increases sequence diversity specifically at hot spots that become active in the hybrids. As crossovers are disfavored at such hot spots, we propose that sequence divergence generated by hot spot turnover may create an impediment for recombination in hybrids, potentially leading to reduced fertility and, eventually, speciation
ISSN: 0890-9369

hal-01281480
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01281480
DOI : 10.1101/gad.270009.115
PUBMED : 26833728

Éditeur(s) : HAL CCSD Mineralogical Society of America
Résumé : International audience
To constrain the crystallization of alkaline and volatile-rich lavas present in intraplate settings, we studied the petrological features and the geochemical composition of major, trace, and volatile elements of mineral and bulk-rock of two sodalite-bearing phonolites: (1) haüyne-plagioclase-bearing Si-K-rich phonolite from Laacher See (Germany) and (2) nosean-nepheline-bearing Si-poor phonolite from Saghro (Morocco). In haüyne-bearing phonolites (55–59 wt% SiO2, K > Na, Na+K/Al = 0.96–1.08), we found that the low silica and low sodium activity promoted the early crystallization of S-rich haüyne (13.7–13.9 wt% SO3, 0.4 wt% Cl) + S-rich apatite (0.7–0.9 wt% SO3), titanite, and rare pyrrhotite followed by clinopyroxene-plagioclase-sanidine at relatively low pressure and temperature (P = 250 MPa and T = 850 °C) and oxidized condition (ΔNNO-NNO+1, where NNO is nickel-nickel oxide buffer). The crystallization of haüyne occurred at fluid-undersaturated conditions from a silicate melt with 6 wt% H2O, 0.17–0.23 wt% Cl, 0.11–0.4 wt% S, and 0.07–0.14 wt% F. Nosean-bearing phonolites from Saghro are silica-poor and peralkaline (52–54 wt% SiO2, Na > K, Na+K/Al = 1.2) and crystallized at higher P and T (300 MPa and 950 °C) and more reduced conditions (NNO) compared to haüyne-bearing phonolites. The incongruent reaction to form nosean requires high silica and Na2O activity. The mineral assemblage and composition suggest early crystallization of nepheline followed by nosean (7.8–8.8 wt% SO3; 1–1.1 wt% Cl). The sequence of crystallization is: clinopyroxene + nepheline + S-poor apatite (<0.04 wt% SO3) + pyrrhotite followed by nosean and titanite. Nosean-bearing magmas are fluid-undersaturated with relatively low volatile content (4 wt% H2O, <0.25 wt% Cl, <0.056 wt% S, 0.08–0.1 wt% F), although Cl may have exsolved during ascent and formed a fluid phase (NaCl-bearing).Both haüyne- and nosean-bearing phonolites are last equilibrated at relatively low pressure and high temperature. Haüyne and nosean crystallized at oxidized and volatile-rich pre-eruptive conditions. They record the volatile concentrations at depth and may be used as oxybarometer. The incongruent reactions involved to form haüyne and nosean suggest that phonolitic magmas became more oxidized during crystallization. The initial volatile concentrations in basanite/nephelinite magmas, from partial melting of volatile-bearing K2O-rich mantle rock, should have been one important factor influencing the crystallization of haüyne-bearing Si-K-rich phonolite and nosean-bearing Si-poor phonolite in intracontinental setting.
ISSN: 0003-004X

hal-01278067
https://hal.archives-ouvertes.fr/hal-01278067
DOI : 10.2138/am-2015-5318

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Miradouro da Lua cliffs, which are 60 km south of Luanda, record the building and uplift of the late Neogene Palaeo-Cuanza delta. The detailed study of the sedimentary architecture and stacking pattern permitted separation of the pile into five depositional units bounded by erosional surfaces and characterised by separate facies associations (genetic sequences = units in this paper). At the base of the series, aeolian deposits (Unit 1) mark the development of a possible coastal desert during the late Miocene aridification. The major Pliocene sea-level rise (Transgressive Systems Tract) led to the drowning of the continental platform into a discrete shoreface-foreshore sequence (Unit 2), followed by an expanded deltaic sequence (Unit 3) that represents the main outcrop of the area. The sedimentary fabric of this prograding wedge during the Highstand Systems Tract reveals laterally stacked pluri-hectometic mouth bars built by the abrupt switching of a bird-foot delta during the Pliocene highstand. The clinoforms are deeply incised by submarine gullies filled both by periodic river-driven turbidite and tidal currents (Unit 4) during the coeval growing of the delta. The topset of the prograding wedge and associated gullies infill is truncated by an overall erosional unconformity that marks the widespread development of an extensive braid-delta system (Unit 5) during the lower Pleistocene sea-level drop (Lowstand Systems Tract). The last 6 m of the Braid-delta unit is overprinted by a ferallitic profile, forming the surface of the plateau and indicating long-term subaerial exposure and weathering processes consistent with the maximum warming of the middle to late Pleistocene interglacial periods. The successive abrupt shifts of the depositional systems through the sedimentary pile indicate a high-amplitude sea level amplified by major coastal uplifts and the reorganisation of the fluvial network. In this context, the palaeo-Cuanza prograding wedge signals the westward tilting and 60 m total uplift of the coastal plain during the Pliocene. A new uplift pulse by differential tilt and slope increase is deduced from the widespread development of the braid-delta complex during the early Pleistocene. The last tectonic event corresponds to the 80- to 100-m uplift and ferallitic paedogenesis during the middle to late Pleistocene interglacial stages.
ISSN: 0899-5362

hal-01053716
https://hal.archives-ouvertes.fr/hal-01053716
DOI : 10.1016/j.jafrearsci.2014.01.013

Éditeur(s) : HAL CCSD Blackwell Publishing
Résumé : International audience
In the Causses platform (south-east France), Late Hettangian to Sinemurian deposits were interpreted previously as shallow-water carbonate ramp deposits. A new look at these deposits has shown a fault-controlled mosaic carbonate platform that is different from the carbonate ramp models. Within the platform mosaic, 15 lithofacies have been recognized, which are organized in four facies associations, including peritidal, restricted shallow sub-tidal, sand dunes and sub-tidal shelf facies associations. The rapid lateral and vertical facies changes, and the lack of consistent landward or seaward direction indicated by the pattern of facies changes, question the existence of a shoreline suggested by the traditional models for this region. Instead, the facies organization and cycle stacking pattern suggest deposition in a mosaic of intertidal islands between which sub-tidal restricted or open conditions could coexist in very close proximity. Such a platform mosaic would have been defined by tectonic activities along normal faults which segmented the shallow-water Causses platform. The facies and facies associations are arranged into metre-scale, peritidal and sub-tidal cycles that are also variable. Certain cycles show the same stacking pattern in all the sections and seem to be traceable over tens of kilometres. On the contrary, other cycles cannot be correlated; they are present only in specific sections and have a maximum lateral extension of 1 or 2 km. These metre-scale cycles stack to form four medium-scale cycles bounded by surfaces that display sub-aerial exposure features. Medium-scale cycles stack into two larger-scale cycles (tens of metres thick) and are bounded by well-defined karstic surfaces. Based on their lateral continuity and their stacking pattern, the metre-scale cycles are controlled probably by high frequency eustatic variations overprinting the topographic irregularities formed by differential subsidence of fault-bounded blocks. Episodic fault activities may reorganize the topography so that, even if eustatic changes may still be the major control of cycles, the expression and number of cycles could be different. Cycles of medium and large-scale are interpreted as being allogenic, controlled by changes in eustasy and/or subsidence rates as evidenced by their lateral continuity and the correlations of the large-scale cycles with third-order depositional sequences.
ISSN: 1469-3496

hal-00411940
https://hal.archives-ouvertes.fr/hal-00411940
DOI : 10.1111/j.1365-3091.2007.00896.x

Éditeur(s) : HAL CCSD Société géologique de France
Résumé : In the western Mediterranean Sea, the Liguro-Provençal Basin (LPB) is a key area for studying passive margins because of its recent formation and abundance of onshore and offshore data. The Nerthe area located in the northern margin of LPB provides the unique continuous Oligo-Miocene deposits contemporaneous of the transition rifting to drifting. However, the age of the deposits remains debated and the link between outcrops and offshore seismic data is poorly constrained. The purpose of this paper is double. First, we intend to propose a new chronostratigraphic frame based on bio- (planktonic foraminifera, calcareous nannofossils) and magneto-stratigraphy. Second, we aim to make, through the integration of new highly time-resolved seismic data and field works, a coherent onshore-offshore link concretized by a 3D geological model. The new temporal and spatial data presented in this paper allow correlating the Oligo-Miocene sequences, defining their geometry and specifying precisely the timing of syn- and post-rift stages. The first marine transgression is now precisely dated latest Chattian within the syn-rift deposits and appears to be synchronous with the first marine deposits in the offshore wells and other marginal basins. The transition from syn-rift to post-rift appears to last 3.3 Ma at maximum, between 21.8 and 18.5 Ma (late Aquitanian to early Burdigalian). It is underlined by two major erosional unconformities bearing a hiatus of around 1 Ma. The post-rift started with a major marine transgression that is now dated from middle Burdigalian, at around 18.5 Ma, as elsewhere in the LPB. Contrarily to recent proposals, the post-rift deposits are widely represented on the northeastern margin of the "Golfe du Lion". There, the subsidence of the margin was low during the syn-rift and the transitional periods and high during the post-rift. The onset of this high post-rift subsidence appears to be synchronous with the slowdown of the Corsica-Sardinia block (CSb) motion.
EISSN: 1777-5817

hal-00558497
https://hal.archives-ouvertes.fr/hal-00558497
DOI : 10.2113/gssgfbull.181.6.591

Éditeur(s) : Gauthier-Villars
Résumé : Phosphorite genesis correlates in a general way with elevated sea level and warm climate and is therefore influenced by plate tectonics and continental drift. Phosphorite genesis correlates more specifically with transgression -- a result of the interaction of continental hypsometry, tectonic perturbation and eustatic effects -- whereby a small number of shallow slope and shelf sites are available for phosphate fixation. Phosphorite genesis correlates with warm climate. Oceanic anoxic events (OAE's : episodes of world-wide deposition and preservation of organic carbon), which also correlate with particularly high sea level stands, generally do not coincide with major phosphorogenic episodes. In contrast to the assertions above, the permian Phosphoria Fromation was deposited during a marked overall global low-stand of sea level. However, the phosphatic sequences were laid down during brief transgressive episodes.
Oceanologica Acta, Special issue (0399-1784) (Gauthier-Villars), 1981

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00245/35660/34169.pdf
http://archimer.ifremer.fr/doc/00245/35660/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The identification of a large OIB-type volcanic sequence on top of an obducted nappe in the Lesser Caucaus of Armenia helps us explain the obduction processes in the Caucasus region that are related to dramatic change in the global tectonics of the Tethyan region in the late Lower Cretaceous. The ophiolitic nappe preserves three distinct magmatic series, obducted in a single tectonic slice over the South Armenian Block during the Coniacian-Santonian (88-83 Ma), the same time as the Oman ophiolite. Similar geological, petrological, geochemical and age features for various Armenian ophiolitic massifs (Sevan, Stepanavan, and Vedi) argue for the presence of a single large obducted ophiolite unit. The ophiolite, shows evidence for a slow-spreading oceanic environment in Lower to Middle Jurassic. Serpentinites, gabbros and plagiogranites were exhumed by normal faults, and covered by radiolarites. Few pillow-lava flows have infilled the rift grabens. The ophiolite lavas have hybrid geochemical composition intermediate between Arc and MORB signatures: (La/Yb)(N) = 0.6-0.9: (Nb/Th)(N) = 0.17-0.57; (Nd-143/Nd-144)(i) = 0.51273-0.51291; (Sr-87/Sr-86)(i) = 0.70370-0.70565; (Pb-207/Pb-204)(i) = 15.4587-15.5411; (Pb-208/Pb-204)(i) = 37.4053-38.2336; (Pb-206/Pb-204)(i) = 17.9195-18.4594. These compositions suggest they were probably formed in a back-arc basin by melting of a shallow asthenosphere source contaminated by a deeper mantle source modified by subducted slab-derived products. Sr-87/Sr-86 ratios and petrological evidence show that these lavas have been intensely altered by mid-oceanic hydrothermalism as well as by serpentinites, which are interpreted as exhumed mantle peridotites. The gabbros have almost the same geochemical composition as related pillow-lavas: (La/Yb)(N) = 0.2-2.3; (Nb/Th)(N) = 0.1-2.8; (Nd-143/Nd-144)(i) = 0.51264-0.51276: (Sr-87/Sr-86)(i) = 0.70386-0.70557; (Pb-207/Pb-204)(i) = 15.4888-15.5391; (Pb-208/Pb-204)(i) = 37.2729-37.8713; (Pb-206/Pb-204)(i) = 17.6296-17.9683. Plagiogranites show major and trace element features similar to other Neo-Tethyan plagiogranites (La/Yb)(N) = 1.10-7.92; (Nb/Th)(N) = 0.10-0.94; but display a less radiogenic Nd isotopic composition than basalts [(Nd-143/Nd-144)(i) = 0.51263] and more radiogenic (Sr-87/Sr-86)(i) ratios. This oceanic crust sequence is covered by variable thicknesses of unaltered pillowed OIB alkaline lavas emplaced in marine conditions. Ar-40/Ar-39 dating of a single-grain amphibole phenocryst provides a Lower Cretaceous age of 117.3 +/- 0.9 Ma, which confirms a distinct formation age of the OIB lavas. The geochemical composition of these alkaline lavas is similar to plateau-lavas [(La/Yb)(N) = 6-14; (Nb/Th)(N) = 0.23-0.76; (Nd-143/Nd-144)(i) = 0.51262-0.51271; (Sr-87/Sr-86)(i) = 0.70338-0.70551; (Pb-207/Pb-204)(i) = 15.5439-15.6158; (Pb-208/Pb-204)(i) = 38.3724-39.3623; (Pb-206/Pb-204)(i) = 18.4024-19.6744].;They have significantly more radiogenic lead isotopic compositions than phiolitic rocks, and fit the geochemical compositions of hot-spot derived lavas mixed with various proportions of oceanic mantle. In addition, this oceanic + plateau sequence is covered by Upper Cretaceous calc-alkaline lavas: (La/Yb)(N) = 2.07-2.31; (Nb/Th)(N) = 0.08-0.15; (Nd-144/Nd-143)(i) = 0.51271-0.51282; (Sr-117/Sr-116)(i) = 0.70452-0.70478), which were likely formed in a supra-subduction zone environment. During the late Lower to early Upper Cretaceous period, hot-spot related magmatism related to plateau events may have led to significant crustal thickening in various zones of the Middle-eastern Neotethys. These processes have likely hindered subduction of some of the hot and thickened oceanic crust segments, and allowed them to be obducted over small continental blocks such as the South Armenian Block.
ISSN: 0024-4937

hal-00443855
https://hal.archives-ouvertes.fr/hal-00443855
DOI : 10.1016/j.lithos.2009.02.006

Éditeur(s) : HAL CCSD BMJ Publishing Group
Résumé : International audience
OBJECTIVE:To identify local meteorological drivers of dengue fever in French Guiana, we applied an original data mining method to the available epidemiological and climatic data. Through this work, we also assessed the contribution of the data mining method to the understanding of factors associated with the dissemination of infectious diseases and their spatiotemporal spread.METHODS:We applied contextual sequential pattern extraction techniques to epidemiological and meteorological data to identify the most significant climatic factors for dengue fever, and we investigated the relevance of the extracted patterns for the early warning of dengue outbreaks in French Guiana.RESULTS:The maximum temperature, minimum relative humidity, global brilliance, and cumulative rainfall were identified as determinants of dengue outbreaks, and the precise intervals of their values and variations were quantified according to the epidemiologic context. The strongest significant correlations were observed between dengue incidence and meteorological drivers after a 4-6-week lag.DISCUSSION:We demonstrated the use of contextual sequential patterns to better understand the determinants of the spatiotemporal spread of dengue fever in French Guiana. Future work should integrate additional variables and explore the notion of neighborhood for extracting sequential patterns.CONCLUSIONS:Dengue fever remains a major public health issue in French Guiana. The development of new methods to identify such specific characteristics becomes crucial in order to better understand and control spatiotemporal transmission.Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
ISSN: 1067-5027

lirmm-01379072
https://hal-lirmm.ccsd.cnrs.fr/lirmm-01379072
DOI : 10.1136/amiajnl-2013-002348
PUBMED : 24549761

Éditeur(s) : HAL CCSD
Résumé : Evolution of organisms, genomes and genes does not strictly follow a tree-like process; symbiosis, horizontal gene transfers and gene fusions build high level composite objects with components of phylogenetically distinct origins. Such processes have been called introgressive events and are significant in evolution. They are involved in some major evolutionary transitions such as eukaryogenesis, photosynthesis acquisition in eukaryotes and the origins of major archaeal clades. Eukaryogenesis would have involved (at least) two kinds of partners: an archaeon and an alpha-proteobacterium. Photosynthetic eukaryotes arose from the integration of a cyanobacterium into a eukaryotic cell and recent findings suggested that most archaeal lineages emerged after massive acquisitions of bacterial genes. These composite lineages carry highly chimeric genomes where genes from symbiotic partners co-localize into the same genome. During my PhD thesis, I used sequence similarity networks and phylogenetic methods in order to study reticulate evolution. My research specifically focused on a previously hidden component of composite genomes: symbiogenetic genes (S genes). These chimeric genes are found in genetic mergers, and originate from the association of genes of symbiotic partners. Some association rules have been discovered. In a broad perspective, the discovery of S-genes extends the concept of genome chimerism to the within-gene level.
L'évolution des organismes, des génomes et des gènes n'est pas strictement arborescente; les symbioses, les transferts horizontaux de gènes ou encore la fusion de gènes créent des objets composites formés de parties dont les histoires évolutives sont différentes. Ces processus non arborescents sont appelés introgressifs et ont un impact non négligeable en évolution. Ils sont à l'origine de transitions évolutives majeures comme l'émergence des eucaryotes, des eucaryotes photosynthétiques ou encore de nombreux groupes d'Archaea. Dans le cas des eucaryotes, l'association et la stabilisation d'une Archaea et d'une alpha-protéobactérie a permis l'émergence d'un nouveau groupe d'organismes composites aux propriétés émergentes. L'acquisition de la photosynthèse chez les eucaryotes s'est faite via l'endosymbiose d'une cyanobactérie et, bien que débattue, l'apparition des grands groupes d'Archaea semble être concomitante avec l'acquisition de nombreux gènes d'origine bactérienne. Ces superorganismes ont la particularité d'avoir des génomes composés de gènes de différents partenaires symbiotiques. L'objectif de mon travail de thèse a constitué à étudier l'aspect introgressif de l'évolution par des méthodes de réseaux de similarité de séquence et des méthodes phylogénétiques. Je me suis particulièrement focalisé sur la détection de nouveaux gènes chimériques nommés gènes symbiogénétiques (S-gènes) car composés de parties originaires des différents partenaires symbiotiques. De tels gènes existent dans les génomes et plusieurs règles d'association ont pu être mises en évidence. Plus généralement, la présence de S-gènes étend la notion de mosaïcisme génomique au niveau infra-génique.
https://tel.archives-ouvertes.fr/tel-01536344

NNT : 2016PA066534
tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344/document
https://tel.archives-ouvertes.fr/tel-01536344/file/2016PA066534.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 Frontiers Media
Résumé : The disease, Heartwater, caused by the Anaplasmataceae E. ruminantium, represents a major problem for tropical livestock and wild ruminants. Up to now, no effective vaccine has been available due to a limited cross protection of vaccinal strains on field strains and a high genetic diversity of Ehrlichia ruminantium within geographical locations. To address this issue, we inferred the genetic diversity and population structure of 194 E. ruminantium isolates circulating worldwide using Multilocus Sequence Typing based on lipA, lipB, secY, sodB, and sucA genes. Phylogenetic trees and networks were generated using BEAST and SplitsTree, respectively, and recombination between the different genetic groups was tested using the PHI test for recombination. Our study reveals the repeated occurrence of recombination between E. ruminantium strains, suggesting that it may occur frequently in the genome and has likely played an important role in the maintenance of genetic diversity and the evolution of E. ruminantium. Despite the unclear phylogeny and phylogeography, E. ruminantium isolates are clustered into two main groups: Group 1 (West Africa) and a Group 2 (worldwide) which is represented by West, East, and Southern Africa, Indian Ocean, and Caribbean strains. Some sequence types are common between West Africa and Caribbean and between Southern Africa and Indian Ocean strains. These common sequence types highlight two main introduction events due to the movement of cattle: from West Africa to Caribbean and from Southern Africa to the Indian Ocean islands. Due to the long branch lengths between Group 1 and Group 2, and the propensity for recombination between these groups, it seems that the West African clusters of Subgroup 2 arrived there more recently than the original divergence of the two groups, possibly with the original waves of domesticated ruminants that spread across the African continent several thousand years ago.
ISSN: 2235-2988

hal-01594501
https://hal.archives-ouvertes.fr/hal-01594501
https://hal.archives-ouvertes.fr/hal-01594501/document
https://hal.archives-ouvertes.fr/hal-01594501/file/paper_MLST_ER_2016_%7B51027B58-C2C7-41C8-9746-BD8A9F387C87%7D.pdf
DOI : 10.3389/fcimb.2016.00111

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
During the GWADASEIS cruise (Lesser Antilles volcanic arc, February-March 2009) a very high resolution (VHR) seismic-reflection survey was performed in order to constrain Late Quaternary to Present faulting. The profiles we obtained evidence frequent "ponding" of reworked sediments in the deepest areas, similar to the deposition of Mediterranean "homogenites". These bodies are acoustically transparent (few ms t.w.t. thick) and are often deposited on the hanging walls of dominantly normal faults, at the base of scarps. Their thickness appears sufficient to compensate (i.e. bury) co-seismic scarps between successive earthquakes, resulting in a flat and horizontal sea floor through time. In a selected area (offshore Montserrat and Nevis islands), piston coring (4 to 7 m long) was dedicated to a sedimentological analysis of the most recent of these particular layers. It corresponds to non-stratified homogenous calcareous silty sand (reworked calcareous plankton and minor volcanoclastics). This layer can be up to 2 m thick, and overlies finegrained hemipelagites. The upper centimeters of the latter represent the normal RedOx water/sediment interface. 210Pb and 137Cs activities lack in the massive sands, while a normal profile of unsupported 210Pb decrease is observed in the hemipelagite below, together with a 137Cs peak correspond- ing to the Atmospheric Nuclear Experiments (1962). The RedOx level was thus capped by a recent instantaneous major sedimentary event considered as post-1970 AD; candidate seismic events to explain this sedimentary deposits are either the 16 March 1985 earthquake or the 8 October 1974 one (Mw=6.3 and Mw=7.4, respectively). This leads to consider that the syntectonic sedimentation in this area is not continuous but results from accumulation of thick homogenites deposited after the earthquakes (as observed in the following weeks after Haiti January 2010 event, McHugh et al., 2011). The existence of such deposits suggests that, in the area of study, vertical throw likely results from cumulated effects of separated earthquakes rather than from aseismic creep. Examination of VHR profiles shows that all major co-seismic offsets are recorded in the fault growth sequence and that co-seismic offsets can be precisely estimated. By using a sedimentation rate deduced from 210Pb decrease curve (0.5 mm yr−1) and taking into account minor reworking events detected in cores, we show that the Redonda system may have been responsible for five >M6 events during the last 34 000 yr. The approach presented in this work differs from fault activity analyses using displaced sets of isochronous surfaces and postulating co-seismic offsets. Combining VHR seismic imagery and coring we can decipher co-seismic vs. slow continuous displacement, and thus actually estimate the amplitude and the time distribution of major co-seismic offsets.
ISSN: 1561-8633

insu-00844581
https://hal-insu.archives-ouvertes.fr/insu-00844581
https://hal-insu.archives-ouvertes.fr/insu-00844581/document
https://hal-insu.archives-ouvertes.fr/insu-00844581/file/nhess-12-1755-2012.pdf
DOI : 10.5194/nhess-12-1755-2012

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Geochronological studies of samples from continuous crustal sections of fossil intra-oceanic arcs are paramount for determining the precise timing of major processes that took place during the building of an oceanic island-arc crust. In this study, laser ablation ICP-MS U-Pb zircon (and conventional Rb-Sr) analyses pinpoint the timing of major events responsible for crustal growth of the Kohistan paleo-island arc (Northern Pakistan). Inheritance in magmatic rocks is evidence for recycling of intra-arc material and indicates that the Kohistan arc may have formed as early as 135 +/- 4 Ma. One older inherited grain indicates that the arc developed on a young oceanic lithosphere whose remnants include a c. 175 Ma old component. An interesting consequence is that intra-oceanic arc magmas can yield inherited zircons, which can be much older than the arc system itself without requiring recycling back into the mantle by subduction processes. In the case of the Kohistan arc, ante-arc Neotethys oceanic lithosphere was tapped by arc magmas during their way upward into the arc crust. The oldest magmatic ages measured in this study fall in the range 101-102 Ma (100.9 +/- 0.6 and 102.1 +/- 0.4 Ma). This period corresponds to arc build-up and thickening of the arc crust. Leucogranitic melts dated at 89.9 +/- 0.4 Ma and 90.9 +/- 1.0 Ma are considered as produced by dehydration/melting reaction accompanying granulitisation of the thickened lower arc crust. A maximum age for this event is 97.7 +/- 0.7 Ma, the age of emplacement of a garnet meta-tonalite affected by granulite facies metamorphism. Magmatic activity was still ongoing during and after the granulitisation as testified by emplacement of a diorite and a gabbro dated at 89.1 +/- 0.6 and 88.2 +/- 0.9 Ma respectively. The upper part of the metaplutonic sequence contains diorite samples dated at 84.6 +/- 0.5 Ma and 84.3 +/- 0.5 Ma and as young as 81.1 +/- 0.7 Ma. During this period, and based on the present day outcropping sequences, the mean crustal growth rate varied from 32 to 65 km(3)/km/Ma (volume per unit width along the strike of the arc) which is comparable to the range for present day arcs of the Western Pacific region. The correspondence of crustal growth rates observed for present-day island arcs and the good preservation of the crustal section in the Kohistan arc, make this area an exceptional natural laboratory to study arc related processes and to check models of continental crust formation by arc accretion.
ISSN: 0012-821X

hal-00644555
https://hal.archives-ouvertes.fr/hal-00644555
DOI : 10.1016/j.epsl.2011.07.016

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : International audience
Symbioses with the dinoflagellate Symbiodinium are widespread among marine invertebrates and protists, especially in nutritionally demanding habitats, such as tropical coral reefs, where they play a major role in ecosystem survival. Moreover, apart from corals and sea anemones, many of the Symbiodinium species and clades involved in these partnerships remain to be characterized. This study provides new insights into nudibranch and sponge associations with Symbiodinium by sequencing regions of the Symbiodinium 28S rDNA and the host mitochondrial COI oxidase. Specimens were sampled between 2011 and 2013 from locations around the islands of Moorea and Tahiti, French Polynesia. Our results revealed that some of the sponges and nudibranchs harbored typical Symbiodinium from clade B or C while others harbored new, undescribed Symbiodinium-like dinoflagellates. A detailed analysis of the different life stages of the nudibranch Phestilla lugubris and of its specific coral prey, Porites rus, suggests a prey-predator horizontal transfer of the symbiont and its vertical inheritance from the parent to the eggs.
Les symbioses à zooxanthelles, dinoflagellés du genre Symbiodinium, sont largement répandues chez les invertébrés marins et les protozoaires, notamment dans les eaux oligotrophes, où ils jouent un rôle important dans la survie des récifs coralliens. De plus, excepté chez les coraux et les anémones, les différentes espèces et clades de Symbiodinium impliqués dans ces associations restent à être caractérisés. Notre étude, grâce à l’utilisation des marqueurs génétiques 28S ADNr des Symbiodinium et la sous-unité 1 de la cytochrome oxydase mitochondriale (COI) de l’hôte, procure de nouvelles données quant aux associations des éponges et des nudibranches avec les Symbiodinium. L’échantillonnage a eu lieu autour de Moorea et de Tahiti (Polynésie française), entre 2011 et 2013. Nos résultats révèlent que certaines espèces d’éponges et de nudibranches possèdent les clades B et C communément retrouvés, chez les coraux notamment, alors que d’autres présentent de nouveaux dinoflagellés « Symbiodinium-like ». Une analyses détaillée des Symbiodinium à différents stades du cycle de vie du nudibranche corallivore Phestilla lugubris et de son corail hôte Porites rus suggèrent l’existence d’un transfert horizontal de Symbiodinium proie–prédateur et un transfert vertical du parent P. lugubris à ses œufs.
ISSN: 1631-0691

hal-01145518
https://hal.archives-ouvertes.fr/hal-01145518
DOI : 10.1016/j.crvi.2015.01.005