Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Seagrasses structure some of the world's key coastal ecosystems presently in decline due to human activities and global change. The ability to cope with environmental changes and the possibilities for shifts in distribution range depend largely on their evolvability and dispersal potential. As large-scale data usually show strong genetic structure for seagrasses, finer-grained work is needed to understand the local processes of dispersal, recruitment and colonization that could explain the apparent lack of exchange across large distances. We aimed to assess the fine-grained genetic structure of one of the most important and widely distributed seagrasses, Zostera marina, from seven meadows in Brittany, France. Both classic population genetics and network analysis confirmed a pattern of spatial segregation of polymorphism at both regional and local scales. One location exhibiting exclusively the variety 'angustifolia' did not appear more differentiated than the others, but instead showed a central position in the network analysis, confirming the status of this variety as an ecotype. This phenotypic diversity and the high allelic richness at nine microsatellites (2.33-9.67 alleles/locus) compared to levels previously reported across the distribution range, points to Brittany as a centre of diversity for Z. marina at both genetic and phenotypic levels. Despite dispersal potential of several 100 m, a significant pattern of genetic differentiation, even at fine-grained scale, revealed 'genetic patchiness'. Meadows seem to be composed of a mosaic of clones with distinct origins in space and time, a result that calls into question the accuracy of the concept of populations for such partially clonal species.
Molecular Ecology (0962-1083) (Wiley-blackwell Publishing, Inc), 2010-06 , Vol. 19 , N. 12 , P. 2394-2407

Droits : 2010 Blackwell Publishing Ltd
http://archimer.ifremer.fr/doc/00006/11690/8499.pdf
DOI:10.1111/j.1365-294X.2010.04649.x
http://archimer.ifremer.fr/doc/00006/11690/

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
Nucleation mechanisms occurring during dynamic recrystallization play a crucial role in the evolution of microstructures and textures during high temperature deformation. In polycrystalline ice, the strong viscoplastic anisotropy induces high strain heterogeneities between grains which control the recrystallization mechanisms. Here, we study the nucleation mechanisms occurring during creep tests performed on polycrystalline columnar ice at high temperature and stress (T=−5°C;σ=0.5 MPa) by post-mortem analyses of deformation microstructures using cryogenic electron backscatter diffraction. The columnar geometry of the samples enables discrimination of the nuclei from the initial grains. Various nucleation mechanisms are deduced from the analysis of the nuclei relations with the dislocation sub-structures within grains and at grain boundaries. Tilt sub-grain boundaries and kink bands are the main structures responsible for development of polygonization and mosaic sub-structures. Nucleation by bulging at serrated grain boundaries is also an efficient nucleation mechanism near the grain boundaries where strain incompatibilities are high. Observation of nuclei with orientations not related to the ‘parent’ ones suggests the possibility of ‘spontaneous’ nucleation driven by the relaxation of the dislocation-related internal stress field. The complexity of the nucleation mechanisms observed here emphasizes the impact of stress and strain heterogeneities on dynamic recrystallization mechanisms.This article is part of the themed issue ‘Microdynamics of ice’.
ISSN: 1364-503X

hal-01467152
https://hal.archives-ouvertes.fr/hal-01467152
DOI : 10.1098/rsta.2015.0345

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01324848
http://hal.upmc.fr/hal-01324848
http://hal.upmc.fr/hal-01324848/document
http://hal.upmc.fr/hal-01324848/file/Genome%20Biol%20Evol-2014-Jachiet-2195-205.pdf
DOI : 10.1093/gbe/evu168

Éditeur(s) : Geological Soc Amer, Inc
Résumé : Pockmarks are seafloor depressions commonly associated with fluid escape from the seabed and are believed to contribute noticeably to the transfer of methane into the ocean and ultimately into the atmosphere. They occur in many different areas and geological contexts, and vary greatly in size and shape. Nevertheless, the mechanisms of pockmark growth are still largely unclear. Still, seabed methane emissions contribute to the global carbon budget, and understanding such processes is critical to constrain future quantifications of seabed methane release at local and global scales. The giant Regab pockmark (9 degrees 42.6' E, 5 degrees 47.8' S), located at 3160 m water depth near the Congo deep-sea channel (offshore southwestern Africa), was investigated with state-of-the-art mapping devices mounted on IFREMER's (French Research Institute for Exploitation of the Sea) remotely operated vehicle (ROV) Victor 6000. ROV-borne micro-bathymetry and backscatter data of the entire structure, a high-resolution photo-mosaic covering 105,000 m(2) of the most active area, sidescan mapping of gas emissions, and maps of faunal distribution as well as of carbonate crust occurrence are combined to provide an unprecedented detailed view of a giant pockmark. All data sets suggest that the pockmark is composed of two very distinctive zones in terms of seepage intensity. We postulate that these zones are the surface expression of two fluid flow regimes in the subsurface: focused flow through a fractured medium and diffuse flow through a porous medium. We conclude that the growth of giant pockmarks is controlled by self-sealing processes and lateral spreading of rising fluids. In particular, partial redirection of fluids through fractures in the sediments can drive the pockmark growth in preferential directions.
Geology (0091-7613) (Geological Soc Amer, Inc), 2014-01 , Vol. 42 , N. 1 , P. 63-66

Droits : 2013 Geological Society of America
http://archimer.ifremer.fr/doc/00186/29731/28293.pdf
DOI:10.1130/G34801.1
http://archimer.ifremer.fr/doc/00186/29731/

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
We report on microstructural data obtained by optical microscopy and transmission electron microscopy concerning the crystallographic relationships of serpentine minerals with their host olivine in two contrasting situations. In the first case, mesh-textured lizardite (liz) is developed in a standard 60% serpentinized oceanic harzburgite from the Oman ophiolite where olivine converts to columnar lizardite. The joined columns are perpendicular to the basal plane (001)(liz), corresponding to the pseudofibres observed optically. The plane (001)(liz) is locally parallel to the narrow boundary ol-liz; thus column orientations register the interface of serpentinization. The ol-liz relationships are not strictly topotactic, but reflect preferred cracking orientations in olivine, parallel to (010)(ol). In the second case, antigorite (atg) develops in a rare sample of antigorite schist in a kimberlite from Moses Rock (Colorado Plateau), representative of a suprasubduction-zone mantle wedge. High-resolution transmission electron microscopy (HRTEM) images along [010](atg) show domains of very regular modulation with a 43 center dot 5 A wavelength (m = 17, where m is the number of silicate tetrahedra along the wave), with few defects, indicative of HP-HT antigorite, and also heavily kinked regions as fingerprints of strong tectonic shear. TEM imaging and electron diffraction patterns reveal two topotactic relationships between antigorite and olivine: [100](atg)//[010](ol) and < 100 >(atg)//< 100 >(ol); the planes in contact are (001)(atg)//(100)(ol) and (001)(atg)//(010)(ol), respectively. The [010](atg)//[001](ol) and antigorite lamellae are parallel to the forsterite b-axis. In both cases, the topography of olivine-serpentine interfaces is controlled by open fluid pathways along microcracks oriented according to the anisotropy of the olivine aggregate. In the cases studied, the serpentine aggregate exhibits a preferred orientation inherited from that of the peridotite. These results have some relevance to the seismic anisotropy of serpentinized mantle. Anisotropy of propagation of seismic waves as a result of the olivine fabric is maintained and reinforced with the development of lizardite. Conversely, the development of antigorite produces a trench-parallel fast S-wave polarization and an anisotropy that is lowered at low degrees of serpentinization and then increased with increasing serpentinization.
ISSN: 0022-3530

hal-00456061
https://hal.archives-ouvertes.fr/hal-00456061
DOI : 10.1093/petrology/egp049

Éditeur(s) : HAL CCSD Museum Nationale d'Histoire Naturelle Paris
Résumé : International audience
ISSN: 1280-9551

hal-01084016
https://hal-agroparistech.archives-ouvertes.fr/hal-01084016
DOI : 10.5252/z2009n4a8

Éditeur(s) : HAL CCSD
Résumé : International audience
The core of South East Asia is composed of a mosaic of continental blocks, among which the Indochina and theSouth China blocks (present day northern Vietnam), amalgamated during the Permian and/or the Triassic. LatePermian to Late Triassic geodynamic evolution of these two blocks remains controversial. The main discussionpoints concern the existence and the closure of an oceanic domain separating the Indochina and the South Chinablocks during this period. Especially, the polarity and the timing of the subduction zone that led to the collisionbetween the blocks as well as the present location of the suture delimiting them are a matter of debate. Despite thevaluable information they can provide, the sedimentary basins from northern Vietnam have been neglected in theprevious studies dealing with the geodynamic evolution of South East Asia.To determine the geodynamic evolution of the area, the basins of Sam Nua and Song Da, presently locatedin North Vietnam, have been investigated using a combined approach involving sedimentology, geochronology(U-Pb/zircon) and geochemistry (whole-rock major and trace elements composition of both volcanic and volcaniclasticrocks). The palaeoenvironment evolution, the main unconformities, their age and the tectonic affinitiesof the interbedded volcanic and volcaniclastics series have been characterized for these two basins. Our resultsdemonstrate (i) that the Song Da Basin exhibits a palaeogeographic affinity with the South China block, (ii) theoccurrence of extensive calk-alkaline volcanism and associated volcaniclastic deposits in the Sam Nua Basin,related to the existence of an active magmatic arc during the Early and the lower Middle Triassic, (iii) a Southdipping (present day coordinate) oceanic lithosphere beneath the Indochina block, deduced from the location ofthe magmatic arc south of the potential suture zones, (iv) that an angular unconformity postdates the lower MiddleTriassic volcaniclastic deposits in the Sam Nua basin. This unconformity, crosscutting the subduction relateddeposits, is interpreted as the result of the collision between the Indochina and the South China blocks.
European Geoscience Union General Assembly 2015
Vienne, Austria

insu-01137675
https://hal-insu.archives-ouvertes.fr/insu-01137675

Éditeur(s) : HAL CCSD Société géologique de France
Résumé : International audience
New geodynamical data from West Africa bring consistent informations on the pre-Mesozoic reconstruction within a large area running from the western Sahara to the Colombian cordillera. These new data support a Neoproterozoic Ocean (WANO) between the Amazonian (AMC) and West African (WAC) cratons previously to the Iapetus and Rheic oceans. We delineate 31 blocs detached from the surrounding three continents: NAC (North American Craton), AMC and WAC. 7 came from the WAC margin, 7 from the NAC, 6 from the AMC and 11 from an intermediate volcano sedimentary domain (COB) built on a 1200-1000 Ma oceanic crust. These imbricated blocks formed a tight mosaic by the Hercynian/Alleghanian tectonic event which gave way to the Pangea super-continent. But, during the Atlantic Ocean opening these blocks began to move. They were separated by new oceanic basins. However, previously to the Pangea, blocks from the COB domain formed two sets of garlands located on the northwestern Gondwana margin. The northern one moved to the North until the Silurian to collide the NAC (Taconic tectonic event) meanwhile the southern one remains on the Gondwana margin. All together were gathered by the Carboniferous/Permian time. Then, the framework for the opening of the Atlantic Ocean was not totally disconnected from the "Variscan" collage and many variscan weakness zones were re-used as initial breaking zones. Beyond this tectonic impact, the pre-mesozoic assemblage allows us to compare this "Caribbean" island arc with another one: the Indonesian "Banda" arc. Thus, West Africa is a geological key area for correlations between the Caribbean, the Appalachian, the Brazilian "Nordeste" and the West European domains and for the understanding of the Atlantic Ocean opening process.
EISSN: 1777-5817

hal-00842747
https://hal.archives-ouvertes.fr/hal-00842747
DOI : 10.2113/gssgfbull.184.1-2.5

Éditeur(s) : HAL CCSD
Résumé : International audience
In this paper, we use a multifractal approach based on the computation of two spectrums for image analysis and texture segmentation problems. The two spectrums are the Legendre Spectrum, determined by classical methods, and the Large Deviation Spectrum, determined by kernel density estimation. We propose a way for the fusion of these two spectrums to improve textured image segmentation results. An unsupervised k-means is used as clustering approach for the texture classification. The algorithm is applied on mosaic image built using IKONOS images and various natural textures from the Brodatz album. The segmentation obtained with our approach gives better results than the application of each spectrum separately.
CIARP Proceedings
Cancun, Mexico

hal-00602268
https://hal.archives-ouvertes.fr/hal-00602268

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Although advanced anthropoid primates (i.e., Simiiformes) are recorded at the end of the Eocene in North Africa (Proteopithecidae, Parapithecidae, and Oligopithecidae), the origin and emergence of this group has so far remained undocumented. The question as to whether these primates are the result of a monophyletic radiation of endemic anthropoids in Africa, or several Asian clades colonizing Africa, is a current focus of paleoprimatology. In this article, we report the discovery of a new anthropoid from Djebel el Kébar in central Tunisia, dating from the late middle Eocene (Bartonian). This taxon, Amamria tunisiensis, new genus and species, currently known by only one isolated upper molar, is among the most ancient anthropoids to be recorded in Africa thus far. Amamria displays a suite of dental features that are primarily observed in Eosimiiformes (stem Anthropoidea). However, it is not allocated to any known family of that group (i.e., Asian Eosimiidae and Afro-Asian Afrotarsiidae) inasmuch as it develops some dental traits that are unknown among eosimiiforms, but can be found in African simiiform anthropoids such as proteopithecids and oligopithecids. With such a mosaic of dental traits, Amamria appears to be a structural intermediate, and as such it could occupy a key position, close to the root of the African simiiforms. Given its antiquity and its apparent pivotal position, the possibility exists that Amamria could have evolved in Africa from Asian eosimiiform or Asian "proto"-simiiform ancestors, which would have entered Africa sometime during the middle Eocene. Amamria could then represent one of the earliest offshoots of the African simiiform radiation. This view would then be rather in favor of the hypothesis of a monophyletic radiation of endemic simiiform anthropoids in Africa. Finally, these new data suggest that there must have been at least two Asian anthropoid colonizers of Africa: the afrotarsiids and the ancestor of Amamria.
ISSN: 0002-9483

hal-01053704
https://hal.archives-ouvertes.fr/hal-01053704
DOI : 10.1002/ajpa.22523

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.
ISSN: 2041-1723

hal-01545322
https://hal.archives-ouvertes.fr/hal-01545322
DOI : 10.1038/ncomms3091

Éditeur(s) : HAL CCSD
Résumé : Poster
The Lesser Caucasus in Armenia is an active volcanic and tectonic zone which resulted from the collision of the Arabian and the Eurasian plates since Neogene times. The During Quaternary, Lesser Caucasus was uplifted (0.3 mm/yr; Mitchell and Westaway, 1999) and experienced extensional tectonics times. Large lakes developed in graben structures. The diatomitic sequences of the Shamb paleo-lake (South Armenia) offer a rare opportunity to give new insights of Western Asia paleo-climate. Based on macroflora analysis, Bruch and Gabrielyan (2002) proposed a cooling and drying general climate trend through Pleistocene times in relation with a general uplift of the chain. Several questions have to be answer for this poorly investigated region. Did the climate record humid glacials and arid interglacials as suggested northward in Kazakhstan? What are the vegetation and climate responses to orbital parameters and to the monsoon? Moreover the lesser Caucasus is known as the entrance way used by the first hominids in Eurasia during Pleistocene time. How was the environment at this time? We present an integrated palynological, 40Ar/39Ar isotopic and magnetostratigraphic study for the most complete section (Joannin et al., in press). 40Ar/39Ar dating of two volcaniclastic layers provided ages of 1.24 ± 0.03 and 1.16 ± 0.02 Ma (2. Magnetostratigraphic data show that the entire Shamb section is of reversed polarity which correlates with part of the Matuyama period (1.785-1.070 Ma). Pollen assemblages and macroremains diversity revealed an alternation of glacial and interglacial phases that are compared with climate changes inferred from the global isotopic curve. The Shamb section ranges from approximately 1.300 to 1.080 Ma in age (marine isotopic stages 40 to 31). The vegetation of the Lesser Caucasus developed in a mosaic pattern in a Pleistocene continental, mostly arid climate, similar to the present-day climate. The vegetation changes record a dominant climate response to the obliquity orbital parameter. The influence of precession could not be established from the Shamb data. Pollen and macroflora both indicate that glacial periods were cold and dry and that interglacials were warm with local humidity. The early Pleistocene climatic model for Western Asia is thus similar to the climatic model for the Mediterranean area. Bruch, A., Gabrielyan, I.G., 2002. Quantitative data of the Neogene climatic development in Armenia and Nakhichevan. Acta Universitatis Carolinae – Geologica 46, 41–48. Joannin, S., Cornée, J.J., Münch, P., Fornari, M., Vasiliev, J., Krijgsman, W., Nahapetyan, S., Gabrielyan, Y., Ollivier, V., Roiron, P., Chataîgnier, C. In press. Early Pleistocene climatic cycles in continental deposits of the Lesser Caucasus of Armenia inferred from palynology, magnetostratigraphy, and 40Ar/39Ar dating. Earth and Planetary Science Letters. Mitchell, J., Westaway, R., 1999. Chronology of Neogene and Quaternary uplift and magmatism in the Caucasus: constraints from K-Ar dating of volcanism in Armenia. Tectonophysics 304, 157–186.
EGU Eurasian Climate and Tectonics
Vienne, Austria

hal-00481799
https://hal.archives-ouvertes.fr/hal-00481799