Éditeur(s) : Taylor & Francis Ltd
Résumé : A new benthic phototrophic dinoflagellate is described from sediments of a tropical marine cove at Martinique Island and its micromorphology is studied by means of light and electron microscopy. The cell contains small golden-brown chloroplasts and the oval nucleus is posterior. It is laterally compressed, almost circular in shape when viewed laterally. It consists of a small epitheca tilted toward the right lateral side and a larger hypotheca. In the left view, the cingulum is more anterior and the epitheca is reduced. The cingulum is displaced and left-handed. This organism is peculiar in having no apical pore and its thecal plate arrangement is 2 ' 1a 7 '' 5c 3s 5 ''' 1 ''''. The plates are smooth with small groups of pores scattered on their surface. An area with 60-80 densely arranged pores is found near the centre of the 2 ''' plate, on the left lateral side. Morphologically, these features are different from all other laterally compressed benthic genera. In addition, molecular genetic sequences of SSU and partial LSU form a distinct and well-supported clade among dinoflagellates and support the erection of a new genus. However, molecular phylogenies inferred from ribosomal genes failed to confirm any clear relationship with other benthic taxa and affinity with other laterally compressed dinoflagellates has not been demonstrated. Hence, the taxonomic affinity of Madanidinium loirii with a defined order and family is unclear at the moment.
European Journal Of Phycology (0967-0262) (Taylor & Francis Ltd), 2014-04 , Vol. 49 , N. 2 , P. 165-178

Droits : 2014 British Phycological Society
http://archimer.ifremer.fr/doc/00195/30622/29458.pdf
DOI:10.1080/09670262.2014.898797
http://archimer.ifremer.fr/doc/00195/30622/

Éditeur(s) : Elsevier
Résumé : The family Kareniaceae is mostly known in France for recurrent blooms of Karenia mikimotoi in the Atlantic, English Channel, and Mediterranean Sea and for the unusual green discoloration in the saltwater lagoon of Diana (Corsica) caused by Karlodinium corsicum in April 1994. In terms of diversity, this taxonomic group was long overlooked owing to the difficult identification of these small unarmored dinoflagellates. In this study, thanks to the molecular characterization performed on single cells from field samples and cultures, twelve taxonomic units were assigned to the known genera Karenia, Karlodinium and Takayama, whereas one could not be affiliated to any described genus. The molecular phylogeny inferred from the D1–D2 region of the LSU rDNA showed that five of them formed a sister taxon of a known species, and could not be identified at species-level, on the basis of molecular analysis only. Among these latter taxa, one Karlodinium which was successfully cultured was investigated by studying the external morphological features (using two procedures for cells fixation), ultrastructure, pigment composition, and haemolytic activity. The results of our analyses corroborate the genetic results in favour of the erection of Karlodinium gentienii sp. nov., which possesses an internal complex system of trichocysts connected to external micro-processes particularly abundant in the epicone, and a peculiar pigment composition. In addition, preliminary assays showed a haemolytic activity.
Harmful Algae (1568-9883) (Elsevier), 2014-12 , Vol. 40 , P. 75-91

Droits : 2014 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00225/33611/32310.pdf
DOI:10.1016/j.hal.2014.10.006
http://archimer.ifremer.fr/doc/00225/33611/

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : The Mediterranean Sea is one of the most oligotrophic marine areas on earth where nitrogen fixation has formally believed to play an important role in carbon and nitrogen fluxes. Although this view is under debate, the diazotrophs responsible for this activity have still not been investigated in the open sea. In this study, we characterised the surface distribution and species richness of unicellular and filamentous diazotrophs across the Mediterranean Sea by combining microscopic counts with size fractionated in situ hybridization (TSA-FISH), and 16S rDNA and nifH genes phylogenies. These genetic analyses were possible owing to the development of a new PCR protocol adapted to scarce microorganisms that can detect as few as 1 cell ml(-1) in cultures. Low concentrations of diazotrophic cyanobacteria were detected and this community was dominated at 99.9% by picoplankton hybridized to the Nitro821 probe, specific for unicellular diazotrophic cyanobacteria (UCYN). Among filamentous cyanobacteria only 0.02 filament ml(-1) of Richelia were detected in the eastern basin, while small (0.7-1.5 mu m) and large (2.5-3.2 mu m) Nitro821-targeted cells were recovered at all stations with a mean concentration of 3.5 cell ml(-1). The affiliation of the small Nitro821-targeted cells to UCYN-A was confirmed by 16S and nifH phylogenies in the western Mediterranean Sea. In the central and the eastern Mediterranean Sea no 16S rDNA and nifH sequence from UCYN was obtained as cells concentration were close to, or below PCR detection limit. Bradyrhizobium sequences dominated nifH clone libraries from picoplanktonic size fractions. A few sequences of gamma-proteobacteria were also detected in the central Mediterranean Sea. While low phosphate and iron concentrations could explain the absence of Trichodesmium sp., the factors that prevent the development of UCYN-B and C remain unknown. We also propose that the dominating picoplankters probably developed specific strategies, such as associations with protists or particles, and/or photosynthetic activity, to acquire carbon for sustaining diazotrophy.
Biogeosciences (1726-4170) (Copernicus Gesellschaft Mbh), 2011 , Vol. 8 , N. 3 , P. 827-840

Droits : Author(s) 2011. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00133/24392/22416.pdf
DOI:10.5194/bg-8-827-2011
http://archimer.ifremer.fr/doc/00133/24392/

Éditeur(s) : Public Library Science
Résumé : Background: The Astrophorida (Porifera, Demospongiae(rho)) is geographically and bathymetrically widely distributed. Systema Porifera currently includes five families in this order: Ancorinidae, Calthropellidae, Geodiidae, Pachastrellidae and Thrombidae. To date, molecular phylogenetic studies including Astrophorida species are scarce and offer limited sampling. Phylogenetic relationships within this order are therefore for the most part unknown and hypotheses based on morphology largely untested. Astrophorida taxa have very diverse spicule sets that make them a model of choice to investigate spicule evolution. Methodology/Principal Findings: With a sampling of 153 specimens (9 families, 29 genera, 89 species) covering the deep- and shallow-waters worldwide, this work presents the first comprehensive molecular phylogeny of the Astrophorida, using a cytochrome c oxidase subunit I (COI) gene partial sequence and the 59 end terminal part of the 28S rDNA gene (C1-D2 domains). The resulting tree suggested that i) the Astrophorida included some lithistid families and some Alectonidae species, ii) the sub-orders Euastrophorida and Streptosclerophorida were both polyphyletic, iii) the Geodiidae, the Ancorinidae and the Pachastrellidae were not monophyletic, iv) the Calthropellidae was part of the Geodiidae clade (Calthropella at least), and finally that v) many genera were polyphyletic (Ecionemia, Erylus, Poecillastra, Penares, Rhabdastrella, Stelletta and Vulcanella). Conclusion: The Astrophorida is a larger order than previously considered, comprising ca. 820 species. Based on these results, we propose new classifications for the Astrophorida using both the classical rank-based nomenclature (i.e., Linnaean classification) and the phylogenetic nomenclature following the PhyloCode, independent of taxonomic rank. A key to the Astrophorida families, sub-families and genera incertae sedis is also included. Incongruences between our molecular tree and the current classification can be explained by the banality of convergent evolution and secondary loss in spicule evolution. These processes have taken place many times, in all the major clades, for megascleres and microscleres.
Plos One (1932-6203) (Public Library Science), 2011-04 , Vol. 6 , N. 4 , P. -

Droits : 2011 Ca´rdenas 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/00137/24817/22903.pdf
DOI:10.1371/journal.pone.0018318
http://archimer.ifremer.fr/doc/00137/24817/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Ctenophores are a phylum of non-bilaterian marine (mostly planktonic) animals, characterised by several unique synapomorphies (e.g., comb rows, apical organ). Relationships between and within the nine recognised ctenophore orders are far from understood, notably due to a paucity of phylogenetically informative anatomical characters. Previous attempts to address ctenophore phylogeny using molecular data (18S rRNA) led to poorly resolved trees but demonstrated the paraphyly of the order Cydippida. Here we compiled an updated 18S rRNA data set, notably including a few newly sequenced species representing previously unsampled families (Lampeidae, Euryhamphaeidae), and we constructed an additional more rapidly evolving ITS1 + 5.8S rRNA + ITS2 alignment. These data sets were analysed separately and in combination under a probabilistic framework, using different methods (maximum likelihood, Bayesian inference) and models (e.g., doublet model to accommodate secondary structure; data partitioning). An important lesson from our exploration of these datasets is that the fast-evolving internal transcribed spacer (ITS) regions are useful markers for reconstructing high-level relationships within ctenophores. Our results confirm the paraphyly of the order Cydippida (and thus a ``cydippid-like'' ctenophore common ancestor) and suggest that the family Mertensiidae could be the sister group of all other ctenophores. The family Lampeidae (also part of the former ``Cydippida'') is probably the sister group of the order Platyctenida (benthic ctenophores). The order Beroida might not be monophyletic, due to the position of Beroe abyssicola outside of a clade grouping the other Beroe species and members of the ``Cydippida'' family Haeckeliidae. Many relationships (e.g. between Pleurobrachiidae, Beroida, Cestida, Lobata, Thalassocalycida) remain unresolved. Future progress in understanding ctenophore phylogeny will come from the use of additional rapidly evolving markers and improvement of taxonomic sampling.
ISSN: 0944-2006

hal-01544475
https://hal.archives-ouvertes.fr/hal-01544475
DOI : 10.1016/j.zool.2014.06.004

Éditeur(s) : HAL CCSD Wiley-Blackwell Wiley
Résumé : The Late Early-to-Early Middle Eocene Zegdoumyidae are the oldest representatives of the order Rodentia to be known in Africa thus far. Despite the fragmentary nature of their fossil record, these early African rodents have been central in discussions surrounding the early evolutionary history of the Anomaluroidea clade (the living forms of which are the ‘scaly-tailed squirrels’, i.e. Anomaluridae). Here, we describe new dental remains attributable to Zegdoumys sbeitlai, a zegdoumyid from Tunisia (Djebel Chambi, CBI-1) dated at ca 50–45 Ma. The original material referred to this taxon was limited to four teeth documenting few dental loci. The new gathered material comprises practically all dental loci (except P4), thereby allowing a better description and characterization of this taxon. This Tunisian species is clearly distinct from its roughly coeval Algerian counterpart (Z. lavocati) or from the younger species recorded from Namibia (Z. namibiensis). We investigated the phylogenetic positions of Z. sbeitlai and the Zegdoumyidae in a high-level rodent phylogeny with a cladistic assessment of the dental evidence. Our results show that zegdoumyids represent the earliest offshoots (pectinately arranged) of a large clade that also encompasses the more advanced Eocene anomaluroids (here named Nementchamyidae), the Miocene Nonanomaluridae, and the stem and crown Anomaluridae. In this phylogenetic context, the species of Zegdoumys are the basalmost members of this large Anomaluroidea clade. Zegdoumyid taxa are therefore the oldest stem anomaluroid candidates, a statement which strengthens support for the hypothesis of the great antiquity of the Anomaluroidea clade in Africa. From a historical biogeography perspective, this assumption suggests that anomaluroids invaded Asia from Afro-Arabia sometime during the Middle Eocene, a dispersal event which was likely concomitant but opposite to the dispersals envisaged for the hystricognathous rodents and anthropoid primates from Asia to Afro-Arabia.
ISSN: 0300-3256

hal-01172007
https://hal.archives-ouvertes.fr/hal-01172007
DOI : 10.1111/zsc.12095

Éditeur(s) : Natl Acad Sciences
Résumé : Most marine organisms disperse via ocean currents as larvae, so it is often assumed that larval-stage duration is the primary determinant of geographic range size. However, empirical tests of this relationship have yielded mixed results, and alternative hypotheses have rarely been considered. Here we assess the relative influence of adult and larval-traits on geographic range size using a global dataset encompassing 590 species of tropical reef fishes in 47 families, the largest compilation of such data to date for any marine group. We analyze this database using linear mixed-effect models to control for phylogeny and geographical limits on range size. Our analysis indicates that three adult traits likely to affect the capacity of new colonizers to survive and establish reproductive populations (body size, schooling behavior, and nocturnal activity) are equal or better predictors of geographic range size than pelagic larval duration. We conclude that adult life-history traits that affect the postdispersal persistence of new populations are primary determinants of successful range extension and, consequently, of geographic range size among tropical reef fishes.
Proceedings Of The National Academy Of Sciences Of The United States Of America (0027-8424) (Natl Acad Sciences), 2013-10 , Vol. 110 , N. 41 , P. 16498-16502

Droits : Freely available online through the PNAS open access option.
http://archimer.ifremer.fr/doc/00161/27240/25457.pdf
DOI:10.1073/pnas.1304074110
http://archimer.ifremer.fr/doc/00161/27240/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Fish mucus has important biological and ecologicalroles such as defense against fish pathogens andchemical mediation among several species. A non-targetedliquid chromatography–mass spectrometry metabolomicapproach was developed to study gill mucus of eight butterflyfishspecies in Moorea (French Polynesia), and theinfluence of several fish traits (geographic site and reefhabitat, species taxonomy, phylogeny, diet and parasitismlevels) on the metabolic variability was investigated. Abiphasic extraction yielding two fractions (polar and apolar)was used. Fish diet (obligate corallivorous, facultativecorallivorous or omnivorous) arose as the main driver ofthe metabolic differences in the gill mucus in both fractions,accounting for 23% of the observed metabolic variabilityin the apolar fraction and 13% in the polar fraction.A partial least squares discriminant analysis allowed us toidentify the metabolites (variable important in projection,VIP) driving the differences between fish with differentdiets (obligate corallivores, facultative corallivores andomnivorous). Using accurate mass data and fragmentationdata, we identified some of these VIP as glycerophosphocholines,ceramides and fatty acids. Level of monogeneangill parasites was the second most important factor shapingthe gill mucus metabolome, and it explained 10% of themetabolic variability in the polar fraction and 5% in theapolar fraction. A multiple regression tree revealed that themetabolic variability due to parasitism in the polar fractionwas mainly due to differences between non-parasitized andparasitized fish. Phylogeny and butterflyfish species werefactors contributing significantly to the metabolic variabilityof the apolar fraction (10 and 3%, respectively) buthad a less pronounced effect in the polar fraction. Finally,geographic site and reef habitat of butterflyfish species didnot influence the gill mucus metabolome of butterflyfishes.
ISSN: 0722-4028

hal-01563312
https://hal-univ-perp.archives-ouvertes.fr/hal-01563312
DOI : 10.1007/s00338-017-1554-0

Éditeur(s) : HAL CCSD
Résumé : Designing biodiversity conservation plans requires knowledge on the biogeographic distribution of taxabut also accurate estimates of species richness and diversification processes. However, measuring the phyleticrichness can be biased by the use of inappropriate taxonomical characters, leading to erroneous speciesdelimitation and diversity estimates.This work explores the phyletic richness at several taxonomic levels (generic, specific and intraspecific) ofthe hydrozoan family Aglaopheniidae (Marktanner-Turneretscher, 1890), with a particular focus on the South-Western Indian Ocean. Firstly, using several newly constructed phylogenies based on mitochondrial andnuclear markers, this study reveals that the phyletic diversity of this family is at underestimated by at least 50%:all studied genera are polyphyletic or with doubtful monophyletic status. Then, using several speciesdelimitation methods based on molecular markers, it sheds light on the richness of cryptic diversity of thisfamily, enlightening the potential of using an integrative taxonomic approach on these morphologically simpleorganisms. Finally, the population genetics of an Aglaopheniidae brooding species shows a high populationsstructuring with pervasive pattern of isolation by distance at several geographic scales (several to thousands ofkilometres), implying a potentially high cryptic diversity existing in this family.The results of this work provide new insights on Aglaopheniidae diversity, underlining the potentialinfluence of reproductive mode on the phyletic diversity and diversification processes of brooding hydrozoanbrooders. This thesis further highlights the relevance of using several complementary
La conservation et la gestion sur le long terme de la biodiversité nécessitent une connaissance de larépartition des taxons, mais également une estimation précise de leur diversité spécifique ainsi que desprocessus de spéciation ayant permis leur formation. Cependant, la mesure de la richesse phylétique peut êtrebiaisée par l’utilisation de caractères taxinomiques ne permettant pas de délimiter les espèces de manièreappropriée.Ce travail de thèse propose d’explorer la diversité phylétique à plusieurs niveaux taxinomiques(générique, spécifique et intra-spécifique) des Aglaopheniidae, une famille d’hydrozoaires, notamment présentedans le Sud-Ouest de l’océan Indien. Dans un premier temps, en utilisant des phylogénies basées sur plusieursmarqueurs (mitochondriaux et nucléaires), ce travail démontre que la diversité phylétique de cette famille est,au minimum, sous-estimée de moitié: tous les genres de la famille sont polyphyléthiques ou présentent un statutmonophylétique restant à confirmer. Dans un deuxième temps, l’utilisation de méthodes de délimitationd’espèces basées sur des données moléculaires met en évidence la diversité cryptique très élevée des morphoespècesétudiées, révélant l’intérêt potentiel des protocoles de taxinomie intégrative chez les organismesmorphologiquement simples. Enfin, l’étude de génétique des populations d’une espèce incubatriced’Aglaopheniidae révèle l’importance de la structuration des populations et de l’isolement par la distance chezcette espèce à plusieurs échelles géographiques (de quelques kilomètres à plusieurs milliers), impliquant unepotentielle diversité cryptique extrêmement élevée chez cette famille.L’ensemble des connaissances acquises lors de ce travail de thèse fournit un nouveau regard sur ladiversité de la famille des Aglaopheniidae, soulignant le potentiel impact du cycle de reproduction sur ladiversité phylétique et les processus de spéciation des hydrozoaires incubateurs. Cette thèse met en évidence lapertinence de l’utilisation de plusieurs procédures complémentaires de délimitation d’espèces pour étudier ladiversité des organismes morphologiquement simples.
https://hal.archives-ouvertes.fr/tel-01359424

tel-01359424
https://hal.archives-ouvertes.fr/tel-01359424
https://hal.archives-ouvertes.fr/tel-01359424/document
https://hal.archives-ouvertes.fr/tel-01359424/file/These%20manuscrit%20final.pdf

Éditeur(s) : HAL CCSD Cambridge University Press (CUP)
Résumé : International audience
We studied the monogenean communities of 34 species of butterflyfish from the tropical Indo-West Pacific, identifying 13 dactylogyrid species (including two species that are presently undescribed). Monogenean assemblages differed significantly between host species in terms of taxonomic structure, intensity and prevalence. Parasite richness ranged from 0 (Chaetodon lunulatus) to 11 (C. auriga, C. citrinellus and C. lunula). Host specificity varied between the dactylogyrids species, being found on 2-29 of the 34 chaetodontid species examined. Sympatric butterflyfish species were typically parasitized by different combinations of dactylogyrid species, suggesting the existence of complex host-parasite interactions. We identified six clusters of butterflyfish species based on the similarities of their dactylogyrid communities. Dactylogyrid richness and diversity were not related to host size, diet specialization, depth range or phylogeny of butterflyfish species. However, there was a weak positive correlation between monogenean richness and diversity and host geographical range. Most communities of dactylogyrids were dominated by Haliotrema aurigae and H. angelopterum, indicating the importance of the genus Haliotrema in shaping monogenean communities of butterflyfishes. This study casts light on the structure of the monogenean communities of butterflyfishes, suggesting that the diversity and complexity of community structures arises from a combination of host species-specific parameters.
ISSN: 0031-1820

hal-01380679
https://hal-univ-perp.archives-ouvertes.fr/hal-01380679
DOI : 10.1017/S0031182016001463

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
ISSN: 1664-302X

hal-01546980
http://hal.upmc.fr/hal-01546980
DOI : 10.3389/fmicb.2013.00414

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Since the first molecular study of the suborder Notothenioidei in 1994, many phylogenetic studies have been published. Among these, those with a sufficient number of taxa have all suggested that the Nototheniidae, as currently defined, is monophyletic only with the inclusion of the Channichthyidae, Artedidraconidae, Bathydraconidae and Harpagiferidae. This is corroborated by more recent studies including more taxa, but in these studies either the number of nuclear markers or the number of taxa included remained low. We obtained sequences for a large sampling covering most nototheniid genera for five markers described previously for other samplings (COI, Rhodopsin retrogene, Pkd1, HECW2, and SSRP1) and one nuclear marker never used before in phylogenetic inference (PPM1d). The topology for the combined analysis of the nuclear coding genes, as well as the topology for SSRP1 (non-coding) and the combined analysis for all markers all support the paraphyly of Nototheniidae, the genus Notothenia (including Paranotothenia) is the sister group of the clade Channichthyidae, Artedidraconidae, Bathydraconidae and Harpagiferidae, and genus Gobionotothen is a sister group to both. As in previous studies, Trematomus, Lepidonotothen and Patagonotothen form a clade that also includes Indonotothenia cyanobrancha. The position of Pleuragramma antarctica, Dissostichus species and Aethotaxis mitopteryx remains unstable and dependant on markers and analyses. We therefore propose the inclusion of the four families of the High Antarctic clade in the Nototheniidae, and their transformation into subfamilies. We transfer Paranotothenia magellanica to the genus Notothenia, as Notothenia magellanica.
ISSN: 1874-7787

hal-01544914
https://hal.archives-ouvertes.fr/hal-01544914
DOI : 10.1016/j.margen.2012.02.003

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Bruggemann, J.H. (2016). Phylogenetic relationships within Aglaopheniidae (Cnidaria, Hydrozoa) reveal unexpected generic diversity. — Zoologica Scripta, 45, 103–114. 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-01359414
https://hal.archives-ouvertes.fr/hal-01359414
DOI : 10.1111/zsc.12135

Éditeur(s) : Society for General Microbiology
Résumé : A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16:1 omega7c, 15: 0 iso, 16: 0 and 13: 0 iso. The G + C content of the DNA was 44.9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a(T) was shown to belong to the gamma-Proteobacteria, being closely related to Shewanella putrefaciens (98%), Shewanella oneidensis (97%) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13a(T) and S. putrefaciens, S. oneidensis and S. baltica were < 20 %, indicating that strain LT13a(T) represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a(T) constitutes a novel species of the genus Shewanella, Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13a(T) (= DSM 15900(T)-JCM 12080(T)) as the type strain.
International journal of systematic and evolutionary microbiology (1466-5026) (Society for General Microbiology), 2004-11 , Vol. 54 , N. 6 , P. 1943-1949

Droits : 2004 International Union of Microbiological Societies
http://archimer.ifremer.fr/doc/2004/publication-590.pdf
DOI:10.1099/ijs.0.03007-0
http://archimer.ifremer.fr/doc/00000/590/

Éditeur(s) : Wiley-blackwell
Résumé : A new benthic dinoflagellate species, Prorocentrum bimaculatum sp. nov., is studied from Kuwaits marine sediments, based on detailed morphological and molecular data. Cells are large, oblong oval in shape. They are 49.955.3 mu m long and 38.443.2 mu m wide. The ornamentation of this new species is peculiar, and characterized by smooth valves with large pores (0.320.50 mu m) scattered on their surface, except in two circular patches of similar to 15 mu m in diameter, devoid of ornamentation and located on both sides of the valve centers. The periflagellar area is widely triangular, located in a moderate excavation of the right valve, and comprises nine platelets. The intercalary band of P. bimaculatum is smooth. The molecular phylogenetic position of this new taxon was inferred from SSU and LSU rDNA genes. In both phylogenetic analyses, P. bimaculatum branched with high support with Prorocentrum consutum and formed a clade sister to the one including P. lima and related species such as P. arenarium, P. belizeanum, P. hoffmannianum, and P. maculosum. From the phylogenetic study, since most species related to P. bimaculatum are known for their toxic effects and production of okadaic acid, this new species can be considered as a potential toxin producer, but this has to be analyzed.
Journal Of Phycology (0022-3646) (Wiley-blackwell), 2012-02 , Vol. 48 , N. 1 , P. 211-221

Droits : 2012 Phycological Society of America
http://archimer.ifremer.fr/doc/00066/17756/15698.pdf
DOI:10.1111/j.1529-8817.2011.01102.x
http://archimer.ifremer.fr/doc/00066/17756/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We explore the relationships within Serraniformes (Li et al., 2009) using a dense taxon sampling and seven nuclear markers. Six had already used been for teleost phylogeny (IRBP, MC1R, MLL4, Pkd1, Rhodopsin, and RNF213) at other scales, and one (MLL2) is new. The results corroborate the composition of Serraniformes described in previous publications (some Gasterosteiformes, Perciformes and Scorpaeniformes). Within the clade, Notothenioidei and Zoarcoidei are each monophyletic. Cottoidei was not monophyletic due to placement of the genus Ebinania (Psychrolutidae). Our independent data confirm the sister-group relationship of Percophidae and Notothenioidei as well as the division of Platycephaloidei in four different groups (Bembridae, Platycephalidae, Hoplichthyidae and Peristediidae with Triglidae). Within Cottoidei, Liparidae and Cyclopteridae formed a clade associated with Cottidae, the genus Cottunculus (Psychrolutidae), and Agonidae. Serranidae and Scorpaenidae are not monophyletic, with the Serranidae divided in two clades (Serraninae and Epinephelinae/Anthiinae) and Scorpaenidae including Caracanthidae and the genus Ebinania (Psychrolutidae). We discuss some morphological characters supporting clades within the Scorpaenidae.
ISSN: 1055-7903

hal-01544909
https://hal.archives-ouvertes.fr/hal-01544909
DOI : 10.1016/j.ympev.2012.12.020

Éditeur(s) : Springer
Résumé : Pearl oysters belonging to the genus Pinctada (Bivalvia: Pteriidae) are widely distributed between the Indo-Pacific and western Atlantic. The existence of both widely distributed and more restricted species makes this group a suitable model to study diversification patterns and prevailing modes of speciation. Phylogenies of eight out of the 11 currently recognised Pinctada species using mitochondrial (cox1) and nuclear (18S rRNA) data yielded two monophyletic groups that correspond to shell size and presence/absence of hinge teeth. Character trace of these morphological characters onto the molecular phylogeny revealed a strong correlation. Pinctada margaritifera appears polyphyletic with specimens from Mauritius grouping in a different clade from others of the French Polynesia and Japan. Hence, P. margaritifera might represent a species complex, and specimens from Mauritius could represent a different species. Regarding the putative species complex Pinctada fucata/Pinctada martensii/Pinctada radiata/Pinctada imbricata, our molecular analyses question the taxonomic validity of the morphological characters used to discriminate P. fucata and P. martensii that exhibited the lowest genetic divergence and are most likely conspecific as they clustered together. P. radiata and P. imbricata were recovered as monophyletic. The absence of overlapping distributions between sister lineages and the observed isolation by distance suggests that allopatry is the prevailing speciation mode in Pinctada. Bayesian dating analysis indicated a Miocene origin for the genus, which is consistent with the fossil record. The northward movement of the Australian plate throughout the Miocene played an important role in the diversification process within Pinctada.
Marine Biotechnology (1436-2228) (Springer), 2011-04 , Vol. 13 , N. 2 , P. 181-192

Droits : Springer Science+Business Media, LLC 2010
http://archimer.ifremer.fr/doc/00035/14635/14015.pdf
DOI:10.1007/s10126-010-9278-y
http://archimer.ifremer.fr/doc/00035/14635/

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) : HAL CCSD Wiley-Blackwell
Résumé : International audience
In this multidisciplinary study, we combined morphological, physiological, and phylogenetic approaches to identify three dominant water bloom-forming Cyanobacteria in a tropical marine mangrove in Guadeloupe (French West Indies). Phylogenetic analysis based on 16S rRNA gene sequences place these marine Cyanobacteria in the genera Oscillatoria (Oscillatoria sp. clone gwada, strain OG) or Planktothricoides (Candidatus Planktothricoides niger' strain OB and Candidatus Planktothricoides rosea' strain OP; both provisionally novel species within the genus Planktothricoides). Bioassays showed that Candidatus Planktothricoides niger' and Candidatus Planktothricoides rosea' are toxin-producing organisms. This is the first report of the characterization of Cyanobacteria colonizing periphyton mats of a tropical marine mangrove. We describe two novel benthic marine species and provide new insight into Oscillatoriaceae and their potential role in marine sulfide-rich environments such as mangroves.
ISSN: 0378-1097

hal-01536679
https://hal.archives-ouvertes.fr/hal-01536679
DOI : 10.1111/1574-6968.12551

Éditeur(s) : Gauthier-Villars
Résumé : Archaias angulatus is a soritid species found in abundance on littoral intertropical carbonate platforms. In the margino-littoral euryhaline biotopes, wedged in the neighbouring littoral marine environment, lives a distinct but similar form: Androsina lucasi. As the latter cannot migrate by sea or be transported by birds or fish, it cannot have been derived phylogenetically from an ancestral species before colonizing this wedged habitat in space and time. Only the idea of a reiterated phenomenon of speciation induced by the environment from another littoral species (Archaias angulatus) can explain its noticeable ubiquity in margino-littoral biotopes isolated from one another but each in contact with the biotopes favoured by Archaias angulatus. This interpretation is reinforced by morpho-structural, taxinomic, biological and ecological data concerning these two taxa.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1994 , Vol. 17 , N. 1 , P. 33-41

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00098/20895/18509.pdf
http://archimer.ifremer.fr/doc/00098/20895/