Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Archaea may be involved in global energy cycles, and are known for their ability to interact with eukaryotic species (sponges, corals and ascidians) or as archaeal-bacterial consortia. The recently proposed phylum Thaumarchaeota may represent the deepest branching lineage in the archaeal phylogeny emerging before the divergence between Euryarchaeota and Crenarchaeota. Here we report the first characterization of two marine thaumarchaeal species from shallow waters that consist of multiple giant cells. One species is coated with sulfur-oxidizing g-Proteobacteria. These new uncultured thaumarchaeal species are able to live in the sulfide-rich environments of a tropical mangrove swamp, either on living tissues such as roots or on various kinds of materials such as stones, sunken woods, etc. These archaea and archaea/bacteria associations have been studied using light microscopy, transmission electron microscopy and scanning electron microscopy. Species identification of archaeons and the putative bacterial symbiont have been assessed by 16S small subunit ribosomal RNA analysis. The sulfur-oxidizing ability of the bacteria has been assessed by genetic investigation on alpha-subunit of the adenosine-5_- phosphosulfate reductase/oxidase's (AprA). Species identifications have been confirmed by fluorescence in situ hybridization using specific probes designed in this study. In this article, we describe two new giant archaeal species that form the biggest archaeal filaments ever observed. One of these species is covered by a specific biofilm of sulfur-oxidizing g-Proteobacteria. This study highlights an unexpected morphological and genetic diversity of the phylum Thaumarchaeota.
ISSN: 1462-2912

hal-00715219
https://hal.univ-antilles.fr/hal-00715219
DOI : 10.1111/j.1462-2920.2010.02309.x

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner-Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive structures for the identification of genera. This study is the most comprehensive molecular phylogeny of the Aglaopheniidae to date, including six genera and 38 species, of which 13 were investigated for the first time and sampled on tropical coral reefs throughout the Indo-Pacific region. For newly sampled individuals, we sequenced the 16S rRNA, the nuclear locus comprising the complete ITS1-5.8S rRNA gene-ITS2 and the first intron of the calmodulin nuclear gene. Phylogenetic analyses of the data revealed and confirmed a general polyphyly, or doubtful monophyly, of all sampled genera in tropical regions based on both the mitochondrial and nuclear markers. Our results revealed that several morphological characters used today are unsuited to resolve phylogenetic relationships between species and genera, as well as the high phyletic diversity within this family. Future revision of the classification of this family will require extensive geographic sampling and the use of an integrative approach.
ISSN: 0300-3256

hal-01253738
https://hal.archives-ouvertes.fr/hal-01253738
https://hal.archives-ouvertes.fr/hal-01253738/document
https://hal.archives-ouvertes.fr/hal-01253738/file/Phylogenetic%20relationships%20within%20Aglaopheniidae%20%28Cnidaria%2C._hal.pdf
DOI : 10.1111/zsc.12135

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 Public Library of Science
Résumé : International audience
The Southwest Indian Ocean (SWIO) is a striking marine biodiversity hotspot. Coral reefs in this region host a high proportion of endemics compared to total species richness and they are particularly threatened by human activities. The island archipelagos with their diverse marine habitats constitute a natural laboratory for studying diversification processes. Rocky shores in the SWIO region have remained understudied. This habitat presents a high diversity of molluscs, in particular gastropods. To explore the role of climatic and geological factors in lineage diversification within the genus Nerita, we constructed a new phylogeny with an associated chronogram from two mitochondrial genes [cytochrome oxidase sub-unit 1 and 16S rRNA], combining previously published and new data from eight species sampled throughout the region. All species from the SWIO originated less than 20 Ma ago, their closest extant relatives living in the Indo-Australian Archipelago (IAA). Furthermore, the SWIO clades within species with Indo-Pacific distribution ranges are quite recent, less than 5 Ma. These results suggest that the regional diversification of Nerita is closely linked to tectonic events in the SWIO region. The Reunion mantle plume head reached Earth's surface 67 Ma and has been stable and active since then, generating island archipelagos, some of which are partly below sea level today. Since the Miocene, sea-level fluctuations have intermittently created new rocky shore habitats. These represent ephemeral stepping-stones, which have likely facilitated repeated colonization by intertidal gastropods, like Nerita populations from the IAA, leading to allopatric speciation. This highlights the importance of taking into account past climatic and geological factors when studying diversification of highly dispersive tropical marine species. It also underlines the unique history of the marine biodiversity of the SWIO region.
ISSN: 1932-6203

hal-01185713
https://hal.archives-ouvertes.fr/hal-01185713
https://hal.archives-ouvertes.fr/hal-01185713/document
https://hal.archives-ouvertes.fr/hal-01185713/file/PLoS%20ONE%202014%20Postaire.pdf
DOI : 10.1371/journal.pone.0095040

Éditeur(s) : World Aquaculture Society, Aquaculture 2006
Résumé : Oysters are among the most familiar of all marine invertebrate taxa. However our knowledge of oyster phylogeny and systematics is fragmentary. This is principally due to the plastic growth patterns of these animals, which result in a wide range of overlapping, ecophenotypic variants that greatly reduce the value of analysis based on shell morphology. Besides that, many intentional or accidental anthropogenic transfers have emphasised this situation. In several cases of misclassification or misidentification of oysters, DNA molecular data, have provided valuable new insights on the tracing of introductions or more generally on the phylogeographic relationships between oyster species. We will illustrate this issue with recent case studies from our lab on several flat and cupped oysters: (1) the Crassostrea gigas – Crassostrea angulata couple of Asian species and their successive introductions in Europe, (2) the new species of cupped oysters, Crassostrea honkongensis, described in Hong-Kong and very divergent from the species Crassostrea gigas it was initially supposed to be, (3) the mangrove oyster Crassostrea gasar that was shown not only to be present along the coasts of Western Africa but also along the Atlantic coasts of South America, and (4) the geographic disjunction between Ostreola stentina, described in the Mediterranean Sea, and the genetically closely related species Ostrea aupouria (from New Zealand) and Ostreola equestris (from Mexico Gulf/Atlantic). At the intra specific level, we will focus on one of the main documented case in Europe, the flat oyster, Ostrea edulis. It is a marine bivalve whose natural geographical distribution ranges along the European Atlantic coast from Norway to Morocco, in addition to the Mediterranean and Black Sea. Studies of allozymes, microsatellites and mitochondrial differentiation over the whole range concluded that a significant divergence existed between Mediterranean and Atlantic populations, together with an isolation-by-distance pattern. However, the average mitochondrial haplotypic diversity displayed a high among populations variance, reflecting smaller effective population size in some locations. Additionally, a ten-fold quantitative difference was observed in the same study in Fst between the mitochondrial and the nuclear genomes, which could be due to sex biased differential reproductive success between males and females. In order to further document this hypothesis, two experiments at the population level were conducted. First, brooding females were sampled in a wild population and the number of males fertilizing a given female estimated. Then, parentage analyses were achieved under experimental conditions: successive mass spawnings were collected from a population of potential genitors kept in hatchery, whose genotypes were known, in order to infer a posteriori the relative contribution of each genitor. Moreover, we aimed to better understand the reproduction dynamics of this species. Several patterns of spawning could be distinguished: unique, successive or extended in time. The different parental contributions and reproductive behaviors observed in these experiments are discussed in the context of the hypothesis of a variance in the reproductive success of males and females and consequences in local and temporal reduced effective population sizes.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/acte-3475.pdf
http://archimer.ifremer.fr/doc/00000/3475/

Éditeur(s) : HAL CCSD Springer Verlag (Germany)
Résumé : In this paper we study merosity in the genus Urospatha within the framework of a resolved phylogeny of the Araceae. We analyse how a transition from dimerous or tetramerous merosity to pentamerous or hexamerous merosity can occur developmentally in the Lasioideae. In Urospatha, initiation of floral primordia along the inflorescence is acropetal, while development of flowers is basipetal. This indicates the presence of two distinct phases in the development of the Urospatha inflorescence. The first phase corresponds to initiation of flowers and establishment of the phyllotactic pattern, and the second phase to differentiation of floral organs. Urospatha is characterized by the presence of trimerous, tetramerous, pentamerous and rarely hexamerous flowers. In all types of flowers, the stamens are closely associated and opposite to the tepals. Pentamerous flowers are formed by addition of a sector comprising a stamen and tepal. Likewise, in the case of hexamerous flowers, two sectors are added. In the Lasioideae, the increase in the number of tepals and stamens is linked with two developmental processes that have appeared independently in the subfamily: (1) addition of one or two stamen-petal sectors (Anaphyllopsis and Urospatha), and (2) independent increase in the number of tepals and stamens on whorls, more or less organized and inserted in alternate position (Dracontium). Tetramerous whorls as they occur in basal Lasioideae would be homologous to two dimerous whorls from an evolutionary point of view.
ISSN: 0378-2697

hal-01019867
https://hal.archives-ouvertes.fr/hal-01019867
DOI : 10.1007/s00606-011-0475-6

Résumé : Ce travail de thèse intitulé «Evaluation de marqueurs génétiques du complexe Mycobacterium tuberculosis combinée à l'utilisation d'outils bioinformatiques: apport en épidémiologie et phylogénie de la tuberculose» a consisté en la sélection et l'évaluation de marqueurs minisatellites dans le cadre d'études épidémiologiques et phylogénétiques du bacille tuberculeux, Une première partie a ainsi porté sur l'épidémie de tuberculose en Guadeloupe, Martinique, et Guyane française ainsi que dans un pays continental à faible incidence de tuberculose, la Suède, Les résultats montrent les disparités existant entre les populations de patients tuberculeux des 3 départements français d'Amérique (DFA) ainsi que les similitudes génotypiques existant entre les bacilles tuberculeux. Par ailleurs le rôle majeur joué par les cas d'importation dans l'épidémie de tuberculose a été montré aussi bien dans les DFA qu'en Suède. Nous nous sommes ensuite intéressés à une utilisation optimale des minisatellites pour une meilleure discrimination de la famille génotypique émergeante « Beijing» circulant au Japon (Osaka, Kobe et Okinawa), ainsi qu'en Russie. Nous avons constaté le faible pouvoir discriminant du format classique 12-locus MIRU (Mycobacterial lnterspersed Repetitive Units) et proposons plusieurs nouvelles stratégies de typage basées plusieurs marqueurs minisatellites incluant certains locus hypervariables. Enfin, dans un troisième volet, nous avons étudié la diversité génétique des bacilles tuberculeux circulant actuellement dans la Caraïbe. laquelle semble refléter le passé historique très particulier de cette zone géographique au croisement d'une multitude de peuplements.
This thesis entitled "Evaluation of genetic markers of Mycobacterium tuberculosis combined with the use of bioinformatics tools: input for epidemiology and phylogeny of tuberculosis" deals with the selection and evaluation of minisatellite markers in the context of epidemiological and phylogenetic studies of the tubercle bacillus M. tuberculosis. The first part of the present work has focused on the epidemic of tuberculosis in Guadeloupe, Martinique and French Guiana as well as in a low incidence continental country, i.e Sweden. The results show differences between populations of TB patients in the three French Departments of America and similarities between the genotypes of the circulating tubercle bacilli Moreover, results highlight the important role played by imported cases for TB epidemic the three French departments of America and Sweden. ln a second part, minisatellite markers have been evaluated for a better discrimination of strains of the emerging genotype "Beijing" circulating in Japan (Osaka, Kobe and Okinawa), and Russia. A low discriminatory power of classical format 12-locus MIRU (Mycobacterial lnterspersed Repetitive Units) was observed and new combinations of minisatellites have also been proposed including hypervariable locus. Finally, the genetic diversity of tubercle bacilli circulating in the Caribbean was investigated which currently seem to reflect historical past of this very special region at the intersection of a multitude of cultures and peoples.

http://www.theses.fr/2011AGUY0427/document

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
ISSN: 1755-098X

hal-01149047
http://hal.upmc.fr/hal-01149047
http://hal.upmc.fr/hal-01149047/document
http://hal.upmc.fr/hal-01149047/file/Decelle_2015_PhytoREF.pdf
DOI : 10.1111/1755-0998.12401

Éditeur(s) : HAL CCSD Magnolia Press
Résumé : International audience
Hydroporus galloprovincialis sp. n. is described from Jouques, north-east of Aix-en-Provence in south-eastern France (Provence). The new species belongs to the Hydroporus memnonius-group, within which it is the only ascertained normandi-complex species of the French fauna. The habitat (small springs) and morphological features of the species suggest a semi-subterranean life style. It can be separated from the other species of the complex notably by its more elongated and parallel-sided habitus, by its wider pronotum and flatter dorsal surface, and furthermore differs from H. normandi Regimbart, 1903 by a different shape of the gonocoxa. Illustrations are provided for other described normandi-complex species and subspecies for comparison. Analyses of partial cox1 sequences indicate that the three sampled H. normandi-complex species (H. galloprovincialis sp. n., H. normandi and H. lluci Fery, 1999) diverged recently; their relationships are unresolved. H. galloprovincialis sp. n. is for the moment the only species of the genus Hydroporus Clairville, 1806 endemic to continental France.
ISSN: 1175-5326

hal-01544484
https://hal.archives-ouvertes.fr/hal-01544484
DOI : 10.11646/zootaxa.3652.4.4

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The tropical to warm-temperate marine brown macroalgal genus Lobophora (Dictyotales, Phaeophyceae) recently drew attention because of its striking regional diversity. In this study we reassess Lobophora global species diversity, and species distributions, and explore how historical factors have shaped current diversity patterns. We applied a series of algorithmic species delineation techniques on a global mitochondrial cox3 dataset of 598 specimens, resulting in an estimation of 98–121 species. This diversity by far exceeds traditional diversity estimates based on morphological data. A multi-locus time-calibrated species phylogeny using a relaxed molecular clock, along with DNA-confirmed species distribution data was used to analyse ancestral area distributions, dispersal-vicariance-founder events, and temporal patterns of diversification under different biogeographical models. The origin of Lobophora was estimated in the Upper Cretaceous (−75 to −60 MY), followed by gradual diversification until present. While most speciation events were inferred within marine realms, founder events also played a non-negligible role in Lobophora diversification. The Central Indo-Pacific showed the highest species diversity as a result of higher speciation events in this region. Most Lobophora species have small ranges limited to marine realms. Lobophora probably originated in the Tethys Sea and dispersed repeatedly in the Atlantic (including the Gulf of Mexico) and Pacific Oceans. The formation of the major historical marine barriers (Terminal Tethyan event, Isthmus of Panama, Benguela upwelling) did not act as important vicariance events. Long-distance dispersal presumably represented an important mode of speciation over evolutionary time-scales. The limited geographical ranges of most Lobophora species, however, vouch for the rarity of such events.
ISSN: 1055-7903

hal-01535635
http://hal.upmc.fr/hal-01535635
http://hal.upmc.fr/hal-01535635/document
http://hal.upmc.fr/hal-01535635/file/Vieira_2017_Historical.pdf
DOI : 10.1016/j.ympev.2017.03.007

Résumé : With the histological techniques used to study Heteropod 13, 14 larvae, the histological structures of planktonic larvae are described at a stage close to metamorphosis; species are chosen among families of Mesogastropods (Lamellariidae, Eratoidae, Cypraeidae, Naticidae) whose phylogeny is close to the Atlantacea superfamily (= Heteropoda) according to the Taylor and Sohl15 classification. The mantle, mantle cavity, foot and digestive tract are described in depth.
Avec les techniques histologiques utilisées pour l'étude des larves d'Hétéropodes 13, 14, les structures histologiques des larves planctoniques sont décrites au stade proche de la métamorphose ; les espèces sont choisies parmi les familles de Mésogastropodes (Lamellariidae, Eratoidae, Cypraeidae, Naticidae) dont la lignée phylogénique est proche de la superfamille des Atlantacea (= Heteropoda) d'après la classification de Taylor et Sohl15. Le manteau, la cavité palléale, le pied et le tube digestif sont plus particulièrement décrits. [OCR NON CONTRÔLE]
Thalassia Jugoslavica, 1974 , Vol. 10 , N. 1/2 , P. 379-399

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1974/publication-5073.pdf
http://archimer.ifremer.fr/doc/00000/5073/