Éditeur(s) : HAL CCSD Wiley Open Access
Résumé : International audience
Plant responses to natural enemies include formation of secondary metabolites acting as direct or indirect defenses. Volatile terpenes represent one of the most diverse groups of secondary metabolites. We aimed to explore evolutionary patterns of volatile terpene emission. We measured the composition of damage-induced volatile terpenes from 202 Amazonian tree species, spanning the angiosperm phylogeny. Volatile terpenes were extracted with solid-phase micro extraction and desorbed in a gas chromatography–mass spectrometry for compound identification. The chemical diversity of the terpene blend showed a strong phylogenetic signal as closely related species emitted a similar number of compounds. Closely related species also tended to have compositionally similar blends, although this relationship was weak. Meanwhile, the ability to emit a given compound showed no significant phylogenetic signal for 200 of 286 compounds, indicating a high rate of diversification in terpene synthesis and/or great variability in their expression. Three lineages (Magnoliales, Laurales, and Sapindales) showed exceptionally high rates of terpene diversification. Of the 70 compounds found in >10% of their species, 69 displayed significant correlated evolution with at least one other compound. These results provide insights into the complex evolutionary history of volatile terpenes in angiosperms, while highlighting the need for further research into this important class of compounds.
ISSN: 2045-7758

Droits : http://creativecommons.org/licenses/by/
hal-01296640
http://hal.upmc.fr/hal-01296640
http://hal.upmc.fr/hal-01296640/document
http://hal.upmc.fr/hal-01296640/file/ece31810.pdf
DOI : 10.1002/ece3.1810

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Growth series of Palaeozoic fishes are rare because of the fragility of larval and juvenile specimens owing to their weak mineralisation and the scarcity of articulated specimens. This rarity makes it difficult to describe early vertebrate growth patterns and processes in extinct taxa. Indeed, only a few growth series of complete Palaeozoic fishes are available; however, they allow the growth of isolated elements to be described and individual growth from these isolated elements to be inferred. In addition, isolated and in situ scales are generally abundant and well-preserved, and bring information on (1) their morphology and structure relevant to phylogenetic relationships and (2) individual growth patterns and processes relative to species ontogeny. The Late Devonian acanthodian Triazeugacanthus affinis from the Miguasha Fossil-Lagerstä tte preserves one of the best known fossilised ontogenies of early vertebrates because of the exceptional preservation, the large size range, and the abundance of complete specimens. Here, we present morphological, histological, and chemical data on scales from juvenile and adult specimens (scales not being formed in lar-vae). Histologically, Triazeugacanthus scales are composed of a basal layer of acellular bone housing Sharpey's fibers, a mid-layer of mesodentine, and a superficial layer of ganoine. Developmentally, scales grow first through concentric addition of mesodentine and bone around a central primordium and then through superposition of ganoine layers. Onto-genetically, scales form first in the region below the dorsal fin spine, then squamation spreads anteriorly and posteriorly, and on fin webs. Phylogenetically, Triazeugacanthus scales show similarities with acanthodians (e.g. " box-in-box " growth), chondrichthyans (e.g. squamation pattern), and actinopterygians (e.g. ganoine). Scale histology and growth are interpreted in the light of a new phylogenetic analysis of gnathostomes supporting acantho-dians as stem chondrichthyans.
ISSN: 1932-6203

Droits : http://creativecommons.org/licenses/by/
hal-01526367
http://hal.upmc.fr/hal-01526367
http://hal.upmc.fr/hal-01526367/document
http://hal.upmc.fr/hal-01526367/file/journal.pone.0174655.pdf
DOI : 10.1371/journal.pone.0174655

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
The circumscription of Salicaceae has recently been enlarged to include a majority of the species formerly placed in the polyphyletic tropical family Flacourtiaceae. Several studies have reported a peculiar and infrequently formed multilayered structure of tension wood in four of the tropical genera. Tension wood is a tissue produced by trees to restore their vertical orientation, and most studies have focused on trees developing tension wood by means of cellulose-rich, gelatinous fibres, as is known in Populus L. and Salix L. (Salicaceae s.s.). This study aims to determine if the multilayered structure of tension wood is an anatomical characteristic common in other Salicaceae, and if so, how its distribution correlates to phylogenetic relationships. Therefore, we studied the tension wood of 14 genera of Salicaceae as well as two genera of Achariaceae, one genus of Goupiaceae, and one genus of Lacistemataceae, families closely related to Salicaceae or formerly placed in Flacourtiaceae. Opposite wood and tension wood were compared with light microscopy and 3D Laser Scanning Confocal Microscopy. The results indicate that a multilayered structure of tension wood is common in the family except in Salix, Populus, and one of their closest relatives, Idesia polycarpa Maxim. We suggest that tension wood may be a useful anatomical character in understanding phylogenetic relationships in Salicaceae. Further investigation is still needed on the tension wood of several other putatively close relatives of Salix and Populus, in particular Bennettiodendron Merr., Macrohasseltia L.O.Williams and Itoa Hemsl.
ISSN: 0024-4074

hal-01392845
https://hal.archives-ouvertes.fr/hal-01392845
https://hal.archives-ouvertes.fr/hal-01392845/document
https://hal.archives-ouvertes.fr/hal-01392845/file/GhislainEtAl2016_MultylayerTWSalicaceae_Bot_Jsur the_Lin_Soc_HALssfig.pdf
DOI : 10.1111/boj.12471

Éditeur(s) : HAL CCSD
Résumé : Ctenophores are one of the four animal phyla positioned outside from the Bilateria. Most ctenophore species are planktonic and gelatinous, and are easily recognisable by their eight comb rows used for swimming. Ctenophore systematics remains nowadays poorly understood. Anatomical characters do not help much in placing them within the animal tree, and similarly the grounds for establishment of their internal phylogeny as well as delimitation of species are notoriously weak due to a paucity of informative morpho-anatomical characters. Until now, the use of molecular data has failed to improve significantly this situation. The aim of this PhD thesis was to bring a contribution to our understanding of ctenophore evolution at different taxonomic scales. At the metazoan level, the position of ctenophores was addressed using a phylogenomic approach. Taxonomic sampling was significantly improved through sequencing and assembly of transcriptomes of 22 non-bilaterian species (belonging to ctenophores, cnidarians and sponges). Two independent datasets were analysed, one consisting in an update of an existing supermatrix of 128 genes, the other one (4235 genes) having been entirely built de novo, thanks to a newly-devised semi-automated protocol intended to eliminate all major potential causes of artefacts (contaminations, paralogies, missing data). Results clearly contradict recent phylogenomic studies which claimed Ctenophora to be the most early-diverging animal lineage, our analyses instead supporting Porifera as the sister-group to other metazoans. The exact position of ctenophores remains however uncertain at this stage, different conditions of analyses yielding three contradictory hypotheses as open possibilities. At the intra-phyletic level, analyses of a ADNr 18S and ITS (internal transcribed spacers) dataset, together with study of duplicated genes and the results of phylogenomic analyses, allowed resolving most phylogenetic relationships between ctenophore orders and families, including the placement of the ctenophore tree root. Finally, at smaller taxonomic scale, in-depth comparison between two species of the genus Pleurobrachia using immunohistochemistry demonstrates the potential of these techniques for uncovering new structural “micro-anatomical” characters useful for diagnosis and identification of ctenophore species. It is our hope that this work will contribute to improving the systematics of a poorly known phylum of great importance for understanding early animal evolution.
Les cténophores représentent l’un des quatre embranchements animaux extérieurs aux Bilateria. La majoritédes espèces sont planctoniques et gélatineuses, et sont reconnaissables à leurs huit rangées de peignes dont lebattement permet la nage. Leur systématique est encore de nos jours mal comprise. L'anatomie descténophores offre peu de caractères aussi bien pour placer la lignée dans l’arbre des métazoaires, que pourétablir les relations de parenté au sein de l’embranchement et délimiter les espèces, et jusqu’à présent lesdonnées moléculaires n’ont pas permis de résoudre ces problèmes de manière satisfaisante. L’objectif de cetravail de thèse est de contribuer à améliorer notre compréhension de l'évolution des cténophores àdifférentes échelles taxonomiques. A l’échelle des métazoaires, la position phylogénétique des cténophores aété abordée par une approche phylogénomique. Un effort significatif a été réalisé pour améliorerl’échantillonnage taxonomique à travers le séquençage et l’assemblage des transcriptomes de 22 espèces denon-Bilateria (cténophores, cnidaires, spongiaires). Deux jeux de données indépendants ont été analysés, lepremier représentant une mise à jour d’une supermatrice existante de 128 gènes ; le second (4235 gènes)ayant été entièrement construit de novo via un protocole original comportant la mise au point de nouvellesméthodes pour traiter de manière semi-automatisée les principales sources potentielles d’artéfact(contaminations, paralogies, données manquantes). Les résultats contredisent certaines études récentes enmontrant que les spongiaires et non les cténophores représentent le groupe-frère des autres métazoaires. Laposition exacte de ces derniers reste à ce stade incertaine (trois options se présentant suivant les analyses). Al’échelle intra-phylétique, l'analyse d'un jeu de données comprenant les marqueurs ADNr 18S et InternalTranscribed Spacers (ITS), associée à des analyses de gènes dupliqués chez les cténophores et aux analysesphylogénomiques précédentes, a permis de résoudre une grande partie des relations phylogénétiques entre lesordres et les familles de cténophores, tout en permettant de préciser la position de la racine. Enfin, à uneéchelle taxonomique plus fine, une comparaison approfondie entre deux espèces du genre Pleurobrachia aumoyen de marquages immunohistochimiques montre le potentiel de ces techniques comme source denouveaux caractères structuraux « micro-anatomiques » à valeur diagnostique pour la délimitation etl’identification des espèces de cténophores. En conclusion, ce travail se veut une contribution au progrès dela systématique d’un embranchement encore méconnu et d’une grande importance pour la compréhensiondes évènements anciens de l’évolution animale.
https://tel.archives-ouvertes.fr/tel-01165014

NNT : 2014PA066448
tel-01165014
https://tel.archives-ouvertes.fr/tel-01165014
https://tel.archives-ouvertes.fr/tel-01165014/document
https://tel.archives-ouvertes.fr/tel-01165014/file/these_archivage_3158995o.pdf

Éditeur(s) : Museum National d'Histoire Naturelle
Résumé : The study is based on available data of previous descriptive works dealing with the diagnostic characters of genus Thunnus seven species ; multivariable technics analysis are used for classification and ordination in order to examine the validity of specific groups usually admitted by classical technics of taxonomy analysis. Respective values of visceral, squelettic and meristic characters are reviewed. Building of a cladogram (by cladistic analysis) based on the coding of 12 characters with evolutive processes meaning leads to submit some hypothesis on phylogenetic relationships between species and group of species recognized progress of the present study. [NOT CONTROLLED OCR]
Cette étude repose exclusivement sur les données descriptives disponibles dans la littérature portant sur les caractères de diagnose spécifique des sept espèces du genre Thunnus ; elle utilise les techniques d'analyse multivariable dévelopées pour la classification (hièrarchie) et l'ordination (analyse des correspondances) afin d'examiner la validité des groupements spécifiques fréquemment reconnus à l'aide des techniques d'analyse taxinomique classiques. La valeur respective des caractères viscéraux, squelettiques et méristiques est reconnue. L'élaboration d'un cladogramme (analyse cladistique) sur la base d'un codage de 12 caractères à valeur évolutive, permet d'émettre quelques hypothèses sur les relations phylogénétiques entre les espèces et groupes d'espèces définies au cours de la présente étude. [OCR NON CONTRÔLE]
Bulletin du Museum National d'Histoire Naturelle (Museum National d'Histoire Naturelle), 1975 , Vol. 3 , N. 339 , P. 1349-1368

Droits : Museum National d'Histoire Naturelle
http://archimer.ifremer.fr/doc/1975/publication-5474.pdf
http://archimer.ifremer.fr/doc/00000/5474/

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 : Similarity-based diversity (Leinster and Cobbold 2012) encompasses classical measures of diversity, including the number of species, Shannon and Simpson diversity, and also phylogenetic and functional diversity. We derive two estimators to allow applying it to real, often under-sampled data, and its decomposition into alpha, beta and gamma diversity when an assemblage of communities is considered.
https://hal-agroparistech.archives-ouvertes.fr/hal-00989454

hal-00989454
https://hal-agroparistech.archives-ouvertes.fr/hal-00989454
https://hal-agroparistech.archives-ouvertes.fr/hal-00989454v2/document

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs 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 contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known.
ISSN: 1932-6203

hal-01190764
https://hal.archives-ouvertes.fr/hal-01190764
PRODINRA : 214530
PUBMED : 22808236
DOI : 10.1371/journal.pone.0040699

Éditeur(s) : HAL CCSD PeerJ
Résumé : International audience
The study of vertebrate ontogenies has the potential to inform us of shared developmental patterns and processes among organisms. However, fossilised ontogenies of early vertebrates are extremely rare during the Palaeozoic Era. A growth series of the Late Devonian ''acanthodian'' Triazeugacanthus affinis, from the Miguasha Fossil-Fish Lagerstätte, is identified as one of the best known early vertebrate fossilised ontogenies given the exceptional preservation, the large size range, and the abundance of specimens. Morphological, morphometric, histological and chemical data are gathered on a growth series of Triazeugacanthus ranging from 4 to 52 mm in total length. The developmental trajectory of this Devonian ''acanthodian'' is characteristic of fishes showing a direct development with alternating steps and thresholds. Larvae show no squamation but a progressive appearance of cartilaginous neurocranial and vertebral elements, and appendicular elements, whereas juveniles progress in terms of ossification and squamation. The presence of cartilaginous and bony tissues, discriminated on histological and chemical signatures, shows a progressive mineralisation of neurocranial and vertebral elements. Comparison among different body proportions for larvae, juveniles and adults suggest allometric growth in juveniles. Because of the phylogenetic position of ''acanthodians'', Triazeugacanthus ontogeny informs us about deep time developmental conditions in gnathostomes.
ISSN: 2167-8359

Droits : http://creativecommons.org/licenses/by/
hal-01633978
http://hal.upmc.fr/hal-01633978
http://hal.upmc.fr/hal-01633978/document
http://hal.upmc.fr/hal-01633978/file/peerj-3969.pdf
DOI : 10.7717/peerj.3969

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The Ras/Raf/MEK/ERK signaling pathway is involved in essential cell processes and it is abnormally activated in similar to 30 % of cancers and cognitive disorders. Two ERK isoforms have been described, ERK1 and ERK2; ERK2 being regarded by many as essential due to the embryonic lethality of ERK2 knock-out mice, whereas mice lacking ERK1 are viable and fertile. The controversial question of why we have two ERKs and whether they have differential functions or display functional redundancy has not yet been resolved. Results: To investigate this question we used a novel approach based on comparing the evolution of ERK isoforms' sequences and protein expression across vertebrates. We gathered and cloned erk1 and erk2 coding sequences and we examined protein expression of isoforms in brain extracts in all major clades of vertebrate evolution. For the first time, we measured each isoforms' relative protein level in phylogenetically distant animals using anti-phospho antibodies targeting active ERKs. We demonstrate that squamates (lizards, snakes and geckos), despite having both genes, do not express ERK2 protein whereas other tetrapods either do not express ERK1 protein or have lost the erk1 gene. To demonstrate the unexpected squamates' lack of ERK2 expression, we targeted each ERK isoform in lizard primary fibroblasts by specific siRNA-mediated knockdown. We also found that undetectable expression of ERK2 in lizard is compensated by a greater strength of lizard's erk1 promoter. Finally, phylogenetic analysis revealed that ERK1 amino acids sequences evolve faster than ERK2' s likely due to genomic factors, including a large difference in gene size, rather than from functional differences since amino acids essential for function are kept invariant. Conclusions: ERK isoforms appeared by a single gene duplication at the onset of vertebrate evolution at least 400 Mya. Our results demonstrate that tetrapods can live by expressing either one or both ERK isoforms, supporting the notion that ERK1/2 act interchangeably. Substrate recognition sites and catalytic cleft are nearly invariant in all vertebrate ERKs further suggesting functional redundancy. We suggest that future ERK research should shift towards understanding the role and regulation of total ERK quantity, especially in light of newly described erk2 gene amplification identified in tumors.
ISSN: 1471-2148

hal-01546165
https://hal.archives-ouvertes.fr/hal-01546165
DOI : 10.1186/s12862-015-0450-x

Éditeur(s) : HAL CCSD Wiley
Résumé : 1. Trade-offs among functional traits reveal major plant strategies that can give insight into species distributions and ecosystem processes. However, current identification of plant strategies lacks the integration of root structural traits together with leaf and stem traits. 2. We examined correlations among 14 traits representing leaf, stem and woody root tissues. Traits were measured on 1084 individuals representing 758 Neotropical tree species, across 13 sites representative of the environmental variation encompassed by three widespread habitats (seasonally flooded, clay terra firme and white-sand forests) at opposite ends of Amazonia (French Guiana and Peru). 3. Woody root traits were closely aligned with stem traits, but not with leaf traits. Altogether leaf, stem and woody root traits delineated two orthogonal axes of functional trade-offs: a first axis defined by leaf traits, corresponding to a leaf economics spectrum, and a second axis defined by covarying stem and woody root traits, corresponding to a wood economics spectrum. These axes remained consistent when accounting for species evolutionary history with phylogenetically independent contrasts. 4. Despite the strong species turnover across sites, the covariation among root and stem structural traits as well as their orthogonality to leaf traits were strongly consistent across habitats and regions. 5. We conclude that root structural traits mirrored stem traits rather than leaf traits in Neotropical trees. Leaf and wood traits define an integrated whole-plant strategy in lowland South American forests that may contribute to a more complete understanding of plant responses to global changes in both correlative and modelling approaches. We suggest further meta-analyses in expanded environmental and geographic zones to determine the generality of this pattern.
ISSN: 0269-8463

hal-01032415
https://hal.archives-ouvertes.fr/hal-01032415
DOI : 10.1111/j.1365-2435.2012.02020.x

Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
Sphaeroma serratum is a marine isopod species that inhabits seashores from Europe to West Africa. The individuals live under stones in direct contact with reduced sediments and harbour a diverse bacterial community on the cuticle of their pleopods. We investigated the diversity of these epibiotic bacteria on male (pubescent and senescent) and female specimens with electron microscopic obser vations and molecular tools. The microbial community of S. serratum was shown to be composed of at least 5 bacterial morphotypes observed on the pleopodal cuticle in all male specimens. Using fluorescence in situ hybridization, we identified 5 major phylogenetic groups (α-, β-, γ- and δ-Proteobacteria and Archaea) whereas denaturing gradient gel electro - phoresis (DGGE) of PCR-amplified 16S rRNA gene fragments of epibiotic bacteria revealed 50 bands. The bacterial community associated with S. serratum seems more diverse than in other marine crustaceans, such as Rimicaris. The relative diversity of this bacterial community was also studied in relation to the molt cycle. The comparison of DGGE band patterns of several individuals from female, pubescent male and senescent male groups revealed that the bacterial community diversity was dependent on the sex and the age of the individuals and more generally on the molt status.
Marine Ecology Progress Series

hal-00743743
https://hal.univ-antilles.fr/hal-00743743
DOI : 10.3354/meps09711

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

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

Éditeur(s) : Nature Publishing Group
Résumé : Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
Isme Journal (1751-7362) (Nature Publishing Group), 2013-10 , Vol. 7 , N. 10 , P. 1985-1996

Droits : 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13
http://archimer.ifremer.fr/doc/00160/27117/28369.pdf
DOI:10.1038/ismej.2013.90
http://archimer.ifremer.fr/doc/00160/27117/

Éditeur(s) : Colloque IMBC - International Marine Biotechnology Conference
Résumé : Since 1997, a new pathology seasonally occurs in new caledonian shrimp farms during the warm season. Diseased Litopenaeus stylirostris shrimp suffer from a systemic vibriosis which was attributed to highly pathogenic Vibrio nigripulchritudo. At the present time, only two farms among 17 are affected by the so called "summer syndrome". In such a context it appears urgent to develop reliable diagnostic tools to detect V. nigripulchritudo strains and to differentiate highly virulent strains from non virulent ones in order to understand the mechanisms of infection and overcome disease spreading. Multilocus Sequencing Typing (MLST) analysis on 24 bacterial strains isolated in geographically distinct shrimp farms highlighted the existence of a cluster A containing only strains displaying moderate to high virulence. Since experimental infection procedure for virulence status determination is material intensive and time consuming, and MLST method not accurate enough to inform on the virulence status of strains, it appeared of great interest to develop other diagnostic tools. Two phylogenetically closed strains, one highly virulent SFn1 and the other non-virulent SFn118 were selected in order to characterize genes specific of the virulent strain by Substractive Suppression Hybridization (SSH). Firstly, a total of 622 DNA fragments specific of SFn1 were sequenced, characterized and further used as probes in a DNA macroarray. Testing 24 strains, hybridization profiles were found to be strongly correlated with both MLST genotypes and bacterial virulence status. A total of 96 representative probes were secondly selected to validate macroarray results on 34 more additionnal strains, allowing identification of genetic markers of virulence. Most of DNA fragments specific of highly virulent strains associated to summer syndrome were found to be bore by a plasmid successfully isolated in the laboratory. In next future, these results would permit the development of relevant diagnostic tools useful for accurate epidemiological survey of the summer syndrome.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/acte-3398.pdf
http://archimer.ifremer.fr/doc/00000/3398/

Éditeur(s) : HAL CCSD
Résumé : International audience
ISSN: 1937-7835

hal-01391676
https://hal-univ-perp.archives-ouvertes.fr/hal-01391676

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : International audience
The elucidation of relationships between biodiversity and ecosystem processes has been limited by the definition of metrics of biodiversity and their integration into experimental design. Functional trait screening can strengthen the performance of these designs.* We suggest the use of Rao's quadratic entropy to measure both functional diversity and phylogenetic diversity of species mixtures proposed for an experimental design, and demonstrate how they can provide complementary information.* We also present an index assessing the statistical performance of these independent variables in different experimental designs. Measurement of independent variables as continuous vs. discrete variables reduces statistical performance, but improves the model by quantifying species differences masked by group assignments.* To illustrate these advances, we present an example from a tropical forest tree community in which we screened 38 species for nine functional traits. The proposed TropiDEP design is based on the relative orthogonality of two multivariate trait axes defined using principal component analysis.* We propose that independent variables describing functional diversity might be grouped to calculate independent variables describing suites of different traits with potentially different effects on particular ecosystem processes. In other systems these axes may differ from those reported here, yet the methods of analysis integrating functional and phylogenetic diversity into experimental design could be universal.
La compréhension des relations pouvant exister entre biodiversité et fonctionnement des écosystèmes a été longtemps limitée par la définition de méthodes de quantification de la diversité biologique et la mise en œuvre de dispositifs expérimentaux permettant sa mesure. L'identification de syndromes de traits fonctionnels clefs influençant des fonctions écosystémiques particulières peut renforcer la performance de ces dispositifs.* Nous suggérons l'utilisation de l'entropie quadratique de Rao pour mesurer la diversité fonctionnelle et phylogénétique dans des assemblages synthétiques d'espèces, et montrons comment ces mesures de diversité sont complémentaires.* Nous présentons également un indice permettant de tester la performance statistique de ces variables indépendantes dans différents modèles expérimentaux. L'utilisation de variables indépendantes continues plutôt que discrètes réduit la performance statistique mais améliore le modèle en quantifiant les différences fonctionnelles entre espèces; différences généralement masquées lors de leur assignation en groupes fonctionnels.* Pour illustrer ces avancées, nous présentons un exemple d'assemblages synthétiques à partir de 38 espèces d'arbres de forêt tropicale sélectionnées pour 9 traits fonctionnels (TropiDEP). Le plan d'expérience de TropiDEP est basé sur l'orthogonalité relative de deux axes multivariés de traits fonctionnels définis par analyse en composantes principales.* Nous proposons que les variables décrivant la diversité fonctionnelle soient groupées pour calculer des variables indépendantes, divisées en plusieurs axes décrivant des combinaisons de différents traits pouvant influencer des processus différents de l'écosystème (e.g. processus du N et du C). Dans d'autres systèmes, ces axes peuvent différer de ceux présentés ici, mais les méthodes d'analyse peuvent être universelles.
ISSN: 1286-4560

Droits : info:eu-repo/semantics/OpenAccess
hal-00883621
https://hal.archives-ouvertes.fr/hal-00883621
https://hal.archives-ouvertes.fr/hal-00883621/document
https://hal.archives-ouvertes.fr/hal-00883621/file/hal-00883621.pdf
DOI : 10.1051/forest/2009110

Résumé : La tuberculose, maladie très ancienne, est plus que jamais présentée sur la scène sanitaire mondiale avec 9 millions de nouveaux cas par an. Cette maladie, qui demeure une cause majeure de mortalité, est un des problèmes les plus difficiles à résoudre en santé publique et à échelle internationale. Les diverses programmes de lutte, lancés par l’Organisation Mondiale de la Santé (OMS), pour prévenir et garantir la guérison des patients tuberculeux, se heurtent à des difficultés qui hypothèquent leur efficacité. En effet, l'expansion du virus de rinimunodéficience humaine (VIII) et son influence néfaste sur la susceptibilité à la tuberculose, l'accroissement rapide de la tuberculose multirésistante, la pauvreté ainsi que la croissance démographique, sont un ensemble de facteurs préjudiciables à l'application des mesures préventives et curatives. Les contextes économiques difficiles conduisant indubitablement au cumul de ces facteurs, ont fait une césure entre les pays riches et les pays pauvres quant à l'incidence et la révolution de la tuberculose à échelle mondiale. Pour atténuer la disparité des résultats des luttes antituberculeuses, les méthodologies employées en épidémiologie de la tuberculose doivent s'inscrire dans une démarche d'efficacité. Les marqueurs moléculaires, indispensables à l'identification et à la classification des souches appartenant au complexe Mycobacterium tuberculosis (MTC) ont chacun des potentialités qui leur sont propres dont il convient de cerner pour une utilisation adéquate dans les études épidémiologiques et phylogénétiques. Le but de cette thèse consiste à extraire des connaissances nouvelles des résultats de génotypage stockées dans les bases de données, connaissances relatives au polymorphisme du support génomique pour estimer la contribution de chaque marqueur dans la classification de MTC. Le recours à différentes méthodes de reconstruction phylogénétique et de modélisation des données fut indispensable. A la lumière des résultats obtenus, cette thèse propose une nouvelle méthodologie de classification, pour rétablissement d'une phylogéographie robuste de MTC en relation avec l'histoire des migrations humaines qui aurait débutée en Afrique subsaharienne. Chaque méthode de génotypage ayant une efficience et un cout propres, qu'il convient de mesurer par rapport aux moyens disponibles et aux résultats escomptes, il est donc intéressant de renforcer la connaissance des marqueurs et de proposer différentes alternatives menant à la classification des mycobactéries. Ainsi, les résultats obtenus dans cette thèse apportent plus de cohérence aux solutions proposées pour la caractérisation des clones de MTC circulant dans le monde.
Tuberculosis, very old disease, is more than ever presented on the global health scene with 9 million new cases per year. This disease, which remains a major cause of mortality is one of the most intractable public health and international issues. The various control programs, launched by the World Health Organization (WHO) to prevent and guarantee the cure of tuberculosis patients face difficulties that undermine their effectiveness. Indeed, the expansion of human virus rinimunodéficience (VIII) and its negative influence on susceptibility to tuberculosis, the rapid growth of multidrug-resistant tuberculosis, poverty and population growth, are a set of factors detrimental to application of preventive and curative measures. The difficult economic circumstances undoubtedly leading to accumulation of these factors have a break between rich and poor countries about the impact and the revolution of tuberculosis worldwide. To address the disparity of the results of tuberculosis struggles, the methodologies used in epidemiology of tuberculosis must be part of a process efficiency. Molecular indispensable to the identification and classification of strains belonging to the Mycobacterium tuberculosis complex (MTC) markers each have their own potentials that need to be identified for proper use in epidemiological and phylogenetic studies. The purpose of this thesis is to extract new knowledge of the results of genotyping data stored in databases, knowledge of the polymorphism of genomic carrier to estimate the contribution of each marker in the classification of TCM. The use of different methods of phylogenetic reconstruction and modeling data was essential. In light of the results obtained, the thesis proposes a new classification methodology for a robust recovery phylogeography of TCM in connection with the history of human migration have started in sub-Saharan Africa. Each genotyping method with cost efficiency and equity, should be measured in relation to the resources available and discounts results, it is interesting to strengthen the knowledge of markers and propose alternatives leading to the classification of mycobacteria. Thus, the results obtained in this thesis bring more coherence to the proposed characterization of clones MTC circulating worldwide solutions.

http://www.theses.fr/2012AGUY0518/document

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
The shallow water bivalve Codakia orbicularis lives in symbiotic association with a sulfur-oxidizing bacterium in its gills. The endosymbiont fixes CO2 and thus generates organic carbon compounds, which support the host's growth. To investigate the uncultured symbiont's metabolism and symbiont-host interactions in detail we conducted a proteogenomic analysis of purified bacteria. Unexpectedly, our results reveal a hitherto completely unrecognized feature of the C. orbicularis symbiont's physiology: the symbiont's genome encodes all proteins necessary for biological nitrogen fixation (diazotrophy). Expression of the respective genes under standard ambient conditions was confirmed by proteomics. Nitrogenase activity in the symbiont was also verified by enzyme activity assays. Phylogenetic analysis of the bacterial nitrogenase reductase NifH revealed the symbiont's close relationship to free-living nitrogen-fixing Proteobacteria from the seagrass sediment. The C. orbicularis symbiont, here tentatively named `Candidatus Thiodiazotropha endolucinida', may thus not only sustain the bivalve's carbon demands. C. orbicularis may also benefit from a steady supply of fixed nitrogen from its symbiont-a scenario that is unprecedented in comparable chemoautotrophic symbioses.
ISSN: 2058-5276

hal-01545904
https://hal.archives-ouvertes.fr/hal-01545904
DOI : 10.1038/nmicrobiol.2016.193

Éditeur(s) : HAL CCSD Wiley
Résumé : White-sand forests represent natural laboratories of evolution over their long history throughout Amazonia and the Guiana Shield and pose significant physiological challenges to the plants and animals they host. The study of diversification in plant lineages comprising species endemic to white-sand forest can therefore give insights into processes of evolution and community assembly in tropical forests. In this article, we synthesize recent studies of white-sand forests to integrate patterns of plant species distribution with processes of lineage diversification and community assembly in the white-sand flora. We contrast lineages that have radiated uniquely in these habitats (e.g., Pagamea, Rubiaceae), with cosmopolitan lineages comprising specialists to white-sand forests and other habitats that may have arisen via ecological speciation across habitat gradients (e.g., Protium, Burseraceae). In both cases, similar suites of functional traits have evolved, including investment in dense, long-lived tissues that are well-defended structurally and chemically. White-sand endemics, therefore, play an important role in biodiversity conservation because they represent unique combinations of functional and phylogenetic diversity. Furthermore, white-sand endemics may respond differently than other tropical forest plant species to contemporary global changes because they comprise resilient functional types that may better withstand increased drought, temperature, and invasions of exotic pests in these regions.
ISSN: 0006-3606

hal-01531635
https://hal.archives-ouvertes.fr/hal-01531635
DOI : 10.1111/btp.12301
PRODINRA : 353397