Éditeur(s) : ISTPM
Résumé : I.S.T.P.M. lab of La Reunion (Indian Ocean) studies L. enigmaticus, its taxonomy, morphology, ecology, biology, feeding, reproduction and growth, and its fishing in the La Reunion and Mauritius Islands area.
Revue des Travaux de l'Institut des Pêches Maritimes (0035-2276) (ISTPM), 1975-12 , Vol. 39 , N. 4 , P. 415-442

Droits : Ifremer
http://archimer.ifremer.fr/doc/1975/publication-2030.pdf
http://archimer.ifremer.fr/doc/00000/2030/

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) : HAL CCSD Wiley
Résumé : International audience
Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September-October (autumn) and lowest in April-May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3-5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. See also the Perspective by Massana
ISSN: 0962-1083

hal-01545321
https://hal.archives-ouvertes.fr/hal-01545321
DOI : 10.1111/mec.13160

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) : HAL CCSD Elsevier
Résumé : International audience
Marine Protected Areas (MPAs) are increasingly used for biodiversity conservation and the management of sustainable fisheries. The use of taxonomic surrogates in routine monitoring of the reserve effects on fish assemblages may represent a promising method due to its substantial technical and economic benefits. However, higher taxonomic ranks should be used as surrogates with caution, especially for fish, where the approach is still virtually undocumented. This study aims to shed light on relationships between taxonomic relatedness and ecological similarity, which is crucial to assess the relevance of species surrogacy to reflect species-level information and detect changes in fish related to protection regimes. By analyzing data from a Mediterranean MPA, we show that rather being related to taxonomic relationships, the ability of higher taxa to reflect species-level patterns was explained in terms of aggregation level and distribution of species within taxa. Null models using random aggregations of species were created to identify the best surrogates able to depict changes in responses of assemblages to protection observed at the species-level. Comparison of null model predictions with the more classical higher-taxon approach revealed that the latter was not reliable because, unlike null model outcomes, surrogates determined empirically were not relevant for other subsequent independent monitoring. The effectiveness of species surrogates to depict changes in responses of assemblages to protection observed at the species-level depended (1) on the numerical resolution of the aggregation and (2) the magnitude of differences between protected and unprotected locations. Such findings suggest that surrogacy approaches may be applied for routine monitoring of Mediterranean reef fish communities, although mere empirical determinations of sufficient taxonomy seems to be not reliable, legitimizing the use of alternative methods based on null models. Guidelines for the careful use of species surrogacy in the ecological evaluation of MPAs on fish assemblages are provided.
ISSN: 0006-3207

hal-01174428
https://hal-univ-perp.archives-ouvertes.fr/hal-01174428
DOI : 10.1016/j.biocon.2015.06.002

Éditeur(s) : HAL CCSD Wiley
Résumé : 1. Considerable debate surrounds the extent to which tropical forests can be managed for resource extraction while conserving biodiversity and ecosystem properties, which depend on functional composition. Here we evaluate the compatibility of these aims by examining the effects of logging on taxonomic and functional diversity and composition in a tropical forest. 2. Twenty years after selective logging, we inventoried 4140 stems regenerating in logging gaps and adjacent undisturbed areas, and we integrated a database of 13 functional traits describing leaf and wood economics of tropical trees. 3. We found no differences in taxonomic and functional richness among habitats, but logging gaps had significantly higher taxonomic and functional evenness. 4. Logging also effected striking, long-term changes in both species and functional composition. In particular, the xylem density of recruits in logging gaps was 6% less than in unlogged forests, leaves were 11% less tough and had 613% greater mineral nutrient concentrations. 5. Synthesis and applications. Our results suggest that managers of tropical forests should limit overall surface area converted to logging gaps by creating fewer, larger gaps during selective logging, to reduce impacts on the taxonomic and functional composition of the regenerating stand.
ISSN: 0021-8901

hal-01032420
https://hal.archives-ouvertes.fr/hal-01032420
DOI : 10.1111/j.1365-2664.2012.02164.x

Éditeur(s) : Oxford Univ Press
Résumé : The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssurrna. org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of hightroughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.
Nucleic Acids Research (0305-1048) (Oxford Univ Press), 2013-01 , Vol. 41 , N. D1 , P. D597-D604

Droits : The Author(s) 2012. Published by Oxford University Press.
http://archimer.ifremer.fr/doc/00114/22492/20174.pdf
DOI:10.1093/nar/gks1160
http://archimer.ifremer.fr/doc/00114/22492/

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) : Station Biologique de Roscoff
Résumé : The hydrothermal vent shrimp genus Mirocaris is reviewed. Morphological comparison between the two nominal species in the genus, M. fortunata and M. keldyshi, was made based on the re-examination of the holotype and paratypes of Mirocarisfortunata and the paratypes of M. keldyshi. Samples newly collected from various sites on the Mid-Atlantic Ridge were also examined. The validity of the genus Mirocaris has been confirmed. However, our study has revealed that the supposed morphological characters distinguishing M. fortunata and M. keldyshi do not provide significant taxonomic differences and further comparison failed to detect morphological differences between the two taxa. Thus M. keldyshi is synonymized with M. fortunata, and so there is only one single species in the genus Mirocaris. This supports the suggestion by Shank et al. (1999), based on a molecular study, that the two taxa might be conspecific. A redescription of M. fortunata is provided to better establish the morphology of the species. The clarification led us to improve the morphological descriptions of the caridean species associated with vent or seep environments and to reassess the relationships among Mirocaris and the other shrimp taxa in the superfamily Bresilioidea. The generic diagnosis of Mirocaris is emended. Because a number of presumably apomorphic characters are shared by Mirocaris and other alvinocaridid genera, the genus Mirocaris is now assigned to the family Alvinocarididae. The family Mirocarididae is synonymized with the Alvinocarididae and the diagnosis of this family is emended.
Révision du genre Mirocaris, crevette des sources hydrothermales océaniques, redescription de M. fortunata et réexamen du statut de la famille des Alvinocarididae. Le genre Mirocaris, créé pour des crevettes hydrothermales, est révisé. Une étude morphologique comparative des deux espèces Mirocaris fortunata et M. keldyshi, basée sur le réexamen des holo-types et paratypes et sur l'étude de nombreux échantillons provenant de divers sites hydrothermaux de la dorsale médio-atlantique, a été effectuée. La validité du genre Mirocaris est confirmée. Il apparaît que les caractères qui distinguent M. keldyshi et M.fortunata ne sont pas des critères taxonomiques suffisants et une étude morphologique plus poussée n'a pas révélé de différences morphologiques entre les deux taxa. Ceci est en accord avec l'interprétation de Shank et al. (1999) qui, à la suite d'une étude moléculaire, suggèrent la synonymie des deux espèces. Une redescription détaillée de M. fortunata est donnée et les relations entre Mirocaris et les autres genres de la superfamille des Bresilioidea sont discutées. La diagnose générique de Mirocaris est modifiée. Comme plusieurs caractères apomorphes sont partagés par Mirocaris et les autres genres de la famille des Alvinocarididae, le genre Mirocaris est maintenant affecté à cette famille. La famille des Mirocarididae est mise en synonymie avec celle des Alvinocarididae dont la diagnose est modifiée.
CBM - Cahiers de Biologie Marine (0007-9723) (Station Biologique de Roscoff), 2003-03 , Vol. 44 , N. 2 , P. 199-215

Droits : 2003 Station Biologique de Roscoff
http://archimer.ifremer.fr/doc/2003/publication-883.pdf
http://archimer.ifremer.fr/doc/00000/883/

Éditeur(s) : Public Library Science
Résumé : Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.
Plos One (1932-6203) (Public Library Science), 2014-08 , Vol. 9 , N. 8 , P. e104427

Droits : This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
http://archimer.ifremer.fr/doc/00203/31408/29801.pdf
DOI:10.1371/journal.pone.0104427
http://archimer.ifremer.fr/doc/00203/31408/

Éditeur(s) : HAL CCSD Elsevier
Résumé : Analyses of tree diversity and community composition in tropical rain forests are usually based either on general herbarium data or on a restricted number of botanical plots. Despite their high taxonomic accuracy, both types of data are difficult to extrapolate to landscape scales. Meanwhile, forestry surveys provide quantitative occurrence data on large areas, and are thus increasingly used for landscape-scale analyses of tree diversity. However, the reliability of these approaches has been challenged because of the ambiguity of the common (vernacular) names used by foresters and the complexity of tree taxonomy in those hyper-diverse communities.We developed and tested a novel approach to evaluate taxonomic reliability of forestry surveys and to propagate the resulting uncertainty in the estimates of several diversity indicators (alpha and beta entropy, Fisher-alpha and Sørensen similarity). Our approach is based on Monte-Carlo processes that simulate communities by taking into account the expected accuracy and reliability of common names. We tested this method in French Guiana, on 9 one-hectare plots (4279 trees – DBH ⩾ 10 cm) for which both common names and standardized taxonomic determinations were available. We then applied our method of community simulation on large forestry inventories (560 ha) at the landscape scale and compared the diversity indices obtained for 10 sites with those computed from precise botanical determination situated at the same localities.We found that taxonomic reliability of forestry inventories varied from 22% (species level) to 83% (family level) in this Amazonian region. Indices computed directly with raw forestry data resulted in incorrect values, except for Gini–Simpson beta-diversity. On the contrary, our correction method provides more accurate diversity estimates, highly correlated with botanical measurements, for almost all diversity indices at both regional and local scales. We obtained a robust ranking of sites consistent with those shown by botanical inventories.These results show that (i) forestry inventories represent a significant part of taxonomic information, (ii) the relative diversity of regional sites can be successfully ranked using forestry inventory data using our method and (iii) forestry inventories can valuably contribute to the detection of large-scale diversity patterns when biases are well-controlled and corrected.The tools we developed as R-functions are available in supplementary material and can be adapted with local parameters to be used for forest management and conservation issues in other regional contexts
ISSN: 0378-1127

hal-01204219
https://hal.archives-ouvertes.fr/hal-01204219
DOI : 10.1016/j.foreco.2014.05.045
PRODINRA : 286554

Éditeur(s) : HAL CCSD Springer Verlag (Germany)
Résumé : International audience
Mass bleaching events resulting in coral mortality are among the greatest threats to coral reefs, and are projected to increase in frequency and intensity with global warming. Achieving a better understanding of the consistency of the response of coral assemblages to thermal stress, both spatially and temporally, is essential to determine which reefs are more able to tolerate climate change. We compared variations in spatial and taxonomic patterns between two bleaching events at the scale of an island (Moorea Island, French Polynesia). Despite similar thermal stress and light conditions, bleaching intensity was significantly lower in 2007 (approximately 37 % of colonies showed signs of bleaching) than in 2002, when 55 % of the colonies bleached. Variations in the spatial patterns of bleaching intensity were consistent between the two events. Among nine sampling stations at three locations and three depths, the stations at which the bleaching response was lowest in 2002 were those that showed the lowest levels of bleaching in 2007. The taxonomic patterns of susceptibility to bleaching were also consistent between the two events. These findings have important implications for conservation because they indicate that corals are capable of acclimatization and/or adaptation and that, even at small spatial scales, some areas are consistently more susceptible to bleaching than others.
ISSN: 0167-6369

hal-00905944
https://hal.archives-ouvertes.fr/hal-00905944
DOI : 10.1007/s10661-012-2923-3

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) : 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) : 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
ISSN: 0006-3207

hal-01090646
https://hal-agroparistech.archives-ouvertes.fr/hal-01090646
DOI : 10.1016/j.biocon.2010.07.034

Éditeur(s) : HAL CCSD WILEY-BLACKWELL Wiley
Résumé : International audience
Connectivity among populations determines the dynamics and evolution of populations, and its assessment is essential in ecology in general and in conservation biology in particular. The robust basis of any ecological study is the accurate delimitation of evolutionary units, such as populations, metapopulations and species. Yet a disconnect still persists between the work of taxonomists describing species as working hypotheses and the use of species delimitation by molecular ecologists interested in describing patterns of gene flow. This problem is particularly acute in the marine environment where the inventory of biodiversity is relatively delayed, while for the past two decades, molecular studies have shown a high prevalence of cryptic species. In this study, we illustrate, based on marine case studies, how the failure to recognize boundaries of evolutionary-relevant unit leads to heavily biased estimates of connectivity. We review the conceptual framework within which species delimitation can be formalized as falsifiable hypotheses and show how connectivity studies can feed integrative taxonomic work and vice versa. Finally, we suggest strategies for spatial, temporal and phylogenetic sampling to reduce the probability of inadequately delimiting evolutionary units when engaging in connectivity studies.
ISSN: 0962-1083

hal-01218810
https://hal.archives-ouvertes.fr/hal-01218810
DOI : 10.1111/mec.13048

Éditeur(s) : HAL CCSD PeerJ
Résumé : International audience
Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction. How to cite this article Leray et al. (2015), Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 3:e1047
ISSN: 2167-8359

Droits : http://creativecommons.org/licenses/by/
hal-01174184
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184/file/peerj-1047.pdf
DOI : 10.7717/peerj.1047

Éditeur(s) : Elsevier
Résumé : The multi-component aspect of species diversity of groundfish assemblages was examined on the basis of a set of experimental trawl surveys conducted on the east coast of Corsica. We analysed and compared the structuration of diversity within three different bathymetric strata: the continental shelf (60-120 m depth), the upper slope (250-400 m) and the lower slope (450-570 m). For each of these three bathymetric strata, we simultaneously analysed 12 indices that are theoretically complementary and relate to 4 diversity components: (1) the number of species, (2) rarity, (3) evenness and (4) taxonomic diversity. Principal component analysis based on Spearman's correlation coefficients was carried out to investigate empirical relationships between the selected indices. Our results showed not only that a single diversity index cannot provide a complete view of the groundfish diversity along the east coast of Corsica, but also that-in some cases-one index cannot even encapsulate a complete description of a specific diversity component. We also found that the nature and the number of independent diversity components slightly varied from one bathymetric stratum to another. The main differences-which mainly occurred in the deepest bathymetric stratum-might be associated with lower density of individuals and lower dominance of some species at deeper depths. Finally, this study is the first dealing with groundfish diversity in this area, which is currently characterized by one of the lowest fishing intensity rates in the northern Mediterranean Sea. It might be considered as a first '' reference state '' with a view to monitoring the spatio-temporal changes in species diversity patterns along the east coast of Corsica in the future. (C) 2007 Elsevier B.V. All rights reserved.
Fisheries Research (0165-7836) (Elsevier), 2007-12 , Vol. 88 , N. 1-3 , P. 120-132

Droits : 2007 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2007/publication-3512.pdf
DOI:10.1016/j.fishres.2007.08.003
http://archimer.ifremer.fr/doc/00000/3512/

Éditeur(s) : HAL CCSD Magnolia Press
Résumé : International audience
A new species of wrasse, Macropharyngodon pakoko, is described from the Marquesas Islands, bringing the total number of species of the genus Macropharyngodon to 12. Macropharyngodon pakoko was found at depths from 0-42 m and is endemic to the Marquesas Islands. Macropharyngodon pakoko is similar to M. meleagris, which is widely distributed from the central and western Pacific to Cocos-Keeling in the Indian Ocean, but differs genetically and in several coloration characters: males with irregularly curved black humeral blotch with incomplete iridescent blue border; inverted irregular " U "-shaped band on the cheek; a small black spot at the upper base of the pectoral fin; and background color of the body greenish with faint bluish black spots on each scale. Females lack black pigment on the chest posterior to the ventral attachment of the gill membranes; reddish black blotches on the body are widely spaced, particularly on the head where they are more reddish and half the size of those on body; caudal fin with small, bright yellow spots arranged in narrow vertical bands with pale interspaces; pelvic fins pale with three reddish yellow cross-bands; a small black spot at the upper base of the pectoral fin; and small reddish spots along the base of the anal fin. Juveniles have irregular black blotches on the body, a small black spot instead of an ocellus posteriorly on the dorsal fin and lack large black spots and ocellus on the anal fin.
ISSN: 1175-5326

Droits : http://creativecommons.org/licenses/by/
hal-01333340
https://hal-univ-perp.archives-ouvertes.fr/hal-01333340
https://hal-univ-perp.archives-ouvertes.fr/hal-01333340/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01333340/file/7387-23089-2-PB.pdf
DOI : 10.11646/zootaxa.3857.3.6