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Auteur (up) Delrieu‐Trottin, E.; Durand, J.-D.; Limmon, G.; Sukmono, T.; Kadarusman; Sugeha, H.Y.; Chen, W.-J.; Busson, F.; Borsa, P.; Dahruddin, H.; Sauri, S.; Fitriana, Y.; Zein, M.S.A.; Hocdé, R.; Pouyaud, L.; Keith, P.; Wowor, D.; Steinke, D.; Hanner, R.; Hubert, N. url  doi
openurl 
  Titre Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods Type Article scientifique
  Année 2020 Publication Revue Abrégée Evolutionary Applications  
  Volume Numéro Pages  
  Mots-Clés Coral Triangle; cryptic diversity; DNA barcoding; reference library; taxonomic gap  
  Résumé DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.  
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  ISSN 1752-4571 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2729  
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Auteur (up) Escalle, L.; Murua, H.; Amande, J.M.; Arregui, I.; Chavance, P.; Delgado de Molina, A.; Gaertner, D.; Fraile, I.; Filmalter, J.D.; Santiago, J.; Forget, F.; Arrizabalaga, H.; Dagorn, L.; Mérigot, B. url  doi
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  Titre Post-capture survival of whale sharks encircled in tuna purse-seine nets: tagging and safe release methods Type Article scientifique
  Année 2016 Publication Revue Abrégée Aquatic Conserv: Mar. Freshw. Ecosyst.  
  Volume 25 Numéro 4 Pages 433-447  
  Mots-Clés mega fauna; post-release mortality; Psat; Rhincodon typus; tropical tuna purse-seine  
  Résumé 1. Whale shark, the world's largest fish, is believed to be particularly vulnerable owing to its biological characteristics (slow growth, late maturation, great longevity) and is listed as Vulnerable by IUCN and included in Appendix II of CITES. 2. Whale sharks are occasionally encircled in tropical tuna purse-seine nets, throughout this global fishery. Although apparent immediate survival rates following encirclement and release have recently been assessed through scientific onboard observer programmes, a more rigorous methodology is still required for studying post-released survival. 3. This work provides a method for applying pop-up satellite tags and reports an enhanced release procedure for whale sharks. The first assessment of survival after release from purse-seine nets involved six whale sharks tagged between May and September 2014 in the eastern tropical Atlantic Ocean. Five tags transmitted data: three popped up as programmed (after 30 days), while two surfaced prematurely (one after 21 and the other after 71 days (programmed to pop off after 30 and 90 days, respectively)) but showed no sign of unusual behaviour. 4. Overall, whale sharks survived at least 21 days (one at least 71 days) after release from purse-seine nets. These observations based on five large individuals (total length > 8 m), suggest that whale sharks have a good chance of survival when released with the proposed method. 5. Additional tagging in this and other oceans, especially of juveniles which may be more sensitive to encirclement and release operations, is essential to further assess whale shark post-release survival rates in tuna purse-seine fisheries. Copyright © 2016 John Wiley & Sons, Ltd.  
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  Volume de collection Numéro de collection Edition  
  ISSN 1099-0755 ISBN Médium  
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Auteur (up) Grande, M.; Murua, H.; Zudaire, I.; Arsenault-Pernet, E.J.; Pernet, F.; Bodin, N. doi  openurl
  Titre Energy allocation strategy of skipjack tuna Katsuwonus pelamis during their reproductive cycle Type Article scientifique
  Année 2016 Publication Revue Abrégée J. Fish Biol.  
  Volume 89 Numéro 5 Pages 2434-2448  
  Mots-Clés bonito euthynnus-pelamis; cod gadus-morhua; fatty-acid-composition; highly migratory fish; Income breeder; Indian Ocean; lipid classes; oocyte growth; reproduction; sarda-sarda; teleost fish; thunnus-albacares; Tropical tuna; western indian-ocean  
  Résumé The lipid composition of somatic and reproductive tissues was determined for female skipjack tuna Katsuwonus pelamis caught in the western Indian Ocean between latitude 10 degrees N and 20 degrees S and longitude 40 degrees and 70 degrees E. The highest total lipid (TL) contents were in the liver and gonads, with white muscle levels approximately three-fold lower. Three lipid classes dominated: triacylglycerols (TAG), sterol esters and wax esters (SE-WE) and phospholipids (PL). Collectively, these accounted for between 70 and 80% of TLs. Changes in lipid concentrations were evaluated over the maturation cycle. Immature fish had the lowest gonad and liver TL levels; concentrations of TL, TAG, SE-WE and PL accumulated from immature to mature (spawning-capable) phase, reflecting sustained vitellogenic activity of the liver and a transfer of lipids to developing oocytes from the onset of vitellogenesis. Gonado-somatic and hepato-somatic indices were positively correlated with each other and positively related to TL in the gonads and liver. Fulton's condition index and lipid concentrations in muscle did not vary significantly over the maturation cycle; fat content in the main storage tissues was undepleted as the ovary developed. Hence, K. pelamis apparently supports reproduction directly from food intake over the breeding season. In the gonads, reserve lipids (SE-WE and TAG) and sterols were related to batch fecundity but this was not the case for somatic and hepatic tissues. These results suggest that K. pelamis utilizes an income breeding strategy.  
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  ISSN 0022-1112 ISBN Médium  
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Auteur (up) Grzebyk, D.; Audic, S.; Lasserre, B.; Abadie, E.; de Vargas, C.; Bec, B. doi  openurl
  Titre Insights into the harmful algal flora in northwestern Mediterranean coastal lagoons revealed by pyrosequencing metabarcodes of the 28S rRNA gene Type Article scientifique
  Année 2017 Publication Revue Abrégée Harmful Algae  
  Volume 68 Numéro Pages 1-16  
  Mots-Clés Phytoplankton diversity; Harmful algae; Monitoring; alexandrium dinophyceae; dinoflagellate stoeckeria-changwonensis; domoic acid accumulation; eastern adriatic sea; Metabarcoding; partial lsu rdna; pfiesteria-piscicida dinophyceae; phylogenetic-relationships; pseudo-nitzschia bacillariophyceae; species complex dinophyceae; toxic dinoflagellate  
  Résumé This study investigated the genetic diversity of phytoplankton communities in six shallow lagoons located on the French coast of the northwestern Mediterranean Sea that represented a trophic gradient ranging from oligotrophic to hypereutrophic. The phytoplankton communities were sampled once a month from spring (May) to the beginning of autumn (September/early October) in 2012 and fractionated by size. Metabarcodes were generated from cDNAs by targeting the D1-D2 region of the 28S rRNA gene and pyrosequenced using Roche 454 technology. Examination of the annotated barcodes revealed harmful algal species not previously documented in these lagoons. Three ichthyotoxic species belonging to Pfiesteriaceae were detected: Luciella masanensis was relatively widespread and abundant in many samples, whereas Pfiesteria piscicida and Stoeckeria changwonensis were found as single barcode sequences. Furthermore, a phylogenetic analysis of barcodes annotated as belonging to Pfiesteriaceae suggested the existence of two previously undescribed clades. The other toxic or potentially harmful dinoflagellates detected through rare barcodes were Dinophysis acuminata, Vulcanodinium rugosum, Alexandrium andersonii and A. ostenfeldii. The two most abundant dinoflagellate taxa were Gymnodinium litoralis and Akashiwo sanguinea with respect to sequence numbers. Four diatom species from the genus Pseudo-nitzschia that potentially produce domoic acid were identified (P. galaxiae, P. delicatissima, P. brasiliana and P. calliantha). These observations are discussed in terms of the literature and monitoring records related to the identified taxa in this Mediterranean area. (C) 2017 Elsevier B.V. All rights reserved.  
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  ISSN 1568-9883 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2227  
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Auteur (up) Hasan, M.E.; Durand, J.-D.; Iwatsuki, Y. url  openurl
  Titre Acanthopagrus datnia (Hamilton, 1822), a senior synonym of Acanthopagrus longispinnis (Valenciennes, 1830) (Perciformes: Sparidae) Type Article scientifique
  Année 2020 Publication Revue Abrégée Zootaxa  
  Volume 4750 Numéro 2 Pages 151-181  
  Mots-Clés 16s; Acanthopagrus latus; Bangladesh; Bay of Bengal; Coi; DNA barcoding; Pisces; Rag-1; Sparidentex datnia  
  Résumé The taxonomic status of the Bay of Bengal nominal sparid species Coius datnia Hamilton, 1822 and Acanthopagrus longispinnis (Valenciennes, 1830) are reviewed and investigated both morphologically and genetically. Because of inadequate description and no type specimen, Coius datnia has recently been considered to belong to Sparidentex, a genus without molarifom teeth. Critical examination of the original description and examination of specimens from the type locality and adjacent areas reveal that Coius datnia belongs to Acanthopagrus, a genus with an inner series of molars. Furthermore, examination of specimens previously recognized as Acanthopagrus longispinnis (Valenciennes 1830), and recent collection of fresh specimens from lower Ganges estuary in Bangladesh, show that morphological differences between Acanthopagrus datnia and A. longispinnis are minor, and they are genetically identical. The longer second anal-fin spine in A. longispinnis (>21% SL) is, in fact, a feature of some younger A. datnia. Accordingly, A. datnia is regarded as a senior synonym of A. longispinnis, and is distinguished from its congeners by the presence of 12 dorsal-fin spines (rarely 11 or 13), 3½ scale rows between the fifth dorsal-fin spine base and lateral line, pelvic and anal-fins pale yellow to yellow with black streaks present in the interradial membranes of anal-fin rays, and caudal fin grey or yellowish grey. A neotype (and neogenotype) has been designated for Acanthopagrus datnia (Hamilton, 1822).  
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  ISSN 1175-5334 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2730  
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