Search

Showing total 6 results
Start Over Topic biology.animal
6 results

1. Migration in geographic and ecological space by a large herbivore

Author

Atle Mysterud, Nicolas Morellet, Stefano Focardi, Ferdinando Urbano, Marco Heurich, Derek B. Spitz, Wibke Peters, Francesca Cagnacci, John D. C. Linnell, Mark Hebblewhite, Petter Kjellander, Department of Ecosystem and Conservation Science, Wildlife Biology Program, University of Montana, Research and Innovation Centre, Biodiversity and Molecular Ecology Department, Edmund Mach Foundation (FEM), Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Department of Conservation and Research, Bavarian Forest National Park, Faculty of Environment and Natural Resources, Wildlife Ecology and Management, University of Freiburg, Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Norwegian Institute for Nature Research (NINA), Organismic and Evolutionary Biology Department, Harvard University [Cambridge], This paper was conceived and written within the collaborative EURODEER project (paper no. 006 of the EURODEER series, Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences (SLU), and Peters, Wibke

Subjects
0106 biological sciences, Range (biology), migration spatiotemporelle, Population, Niche, Zoology and botany: 480 [VDP], normalized difference vegetation index, capreolus capreolus, migration animale, 010603 evolutionary biology, 01 natural sciences, behavioral plasticity, Capreolus, Settore BIO/05 - ZOOLOGIA, biology.animal, Biologie animale, ungulates, Realized niche width, 10. No inequality, education, Zoologiske og botaniske fag: 480 [VDP], Ecology, Evolution, Behavior and Systematics, Animal biology, Ecological niche, animal migration, education.field_of_study, partial migration, biology, Ecology, 010604 marine biology & hydrobiology, [SDV.BA]Life Sciences [q-bio]/Animal biology, 15. Life on land, biology.organism_classification, spatiotemporal variation, faune sauvage, Roe deer, large herbivores, ecological distance, realized niche, niche switching, Spatial variability
Abstract

Partial migration, when only part of the population migrates seasonally while the other part remains resident on the shared range, is the most common form of migration in ungulates. Migration is often defined by spatial separation of seasonal ranges and consequently, classification of individuals as migrants or residents is usually only based on geographic criteria. However, the underlying mechanism for migration is hypothesized to be movement in response to spatiotemporal resource variability and thus, migrants are assumed to travel an “ecological distance” (ED) or shift their realized ecological niches. While ecological and geographic distances should be related, their relationship may depend on landscape heterogeneity. Here, we tested the utility of ecological niche theory to both classify migratory individuals and to understand the underlying ecological factors for migratory behavior. We developed an integrative approach combining measures in geographic and ecological niche space and used this to classify and explain migratory behavior of 71 annual roe deer (Capreolus capreolus) movement trajectories in five European study areas. First, to assess the utility of the ED concept for classifying migratory behavior, we tested whether roe deer sought the same ecological conditions year-round or moved to different ecological conditions by measuring the annual ED travelled and the seasonal niche overlap using multivariate statistics. Comparing methods to classify migrants and residents based on geographic and ecological niche space, we found that migratory roe deer switched between seasons both in geographic and in ecological dimensions. Second, we tested which seasonal ecological factors separated resident from migrant niches using discriminant analysis and which broad-scale determinants (e.g., spatiotemporal forage variation and population density) predicted migration probability using generalized linear models. Our results indicated that factors describing forage and topographic variability discriminated seasonal migrant from resident niches. Determinants for predicting migration probability included the temporal variation (seasonality) and also the spatial variability of forage patches. Last, we also found suggestive evidence for a positive relationship between population density and migration probability. By applying the ecological niche concept to the study of partial migration in ungulates, our work underlines that partial migration is a form of behavioral plasticity. Key words: behavioral plasticity; Capreolus capreolus; ecological distance; large herbivores; niche switching; Normalized Difference Vegetation Index; partial migration; realized niche; spatiotemporal variation; ungulates

Published
2017

2. Partial migration in roe deer: migratory and resident tactics are end points of a behavioural gradient determined by ecological factors

Author

Petter Kjellander, Atle Mysterud, Federico Ossi, Markus Neteler, Anja Stache, Luca Delucchi, John D. C. Linnell, Stefano Focardi, Marco Heurich, A. J. Mark Hewison, Francesca Cagnacci, Nicolas Morellet, Ferdinando Urbano, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Department of Research and Documentation, Bavarian Forest National Park, Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Norwegian Institute for Nature Research (NINA), University of Oslo (UiO), Independent, and This paper was conceived and written within the collaborative EURODEER project (paper no. 001 of the EURODEER series

Subjects
Capriolo, 0106 biological sciences, Ungulate, Range (biology), [SDV]Life Sciences [q-bio], partialL migration, population, Distribution (economics), 010603 evolutionary biology, 01 natural sciences, Ungulati, Capreolus, Settore BIO/07 - ECOLOGIA, biology.animal, Ecosystem, GPS location data, EURODEER, Ecology, Evolution, Behavior and Systematics, general phenomenon of migration, biology, Ecology, business.industry, Residence time, 010604 marine biology & hydrobiology, Facultative migration, 15. Life on land, biology.organism_classification, Habitat selection, Roe deer, Geography, Habitat, environmental sciences and ecology, ecological factors, Capreolus capreolus, Residence, ecology, business, Migrazione parziale
Abstract

International audience; Ungulate populations exhibiting partial migration present a unique opportunity to explore the causes of the general phenomenon of migration. The European roe deer Capreolus capreolus is particularly suited for such studies due to a wide distribution range and a high level of ecological plasticity. In this study we undertook a comparative analysis of roe deer GPS location data from a representative set of European ecosystems available within the EURODEER collaborative project. We aimed at evaluating the ecological factors affecting migration tactic (i.e. occurrence) and pattern (i.e. timing, residence time, number of migratory trips). Migration occurrence varied between and within populations and depended on winter severity and topographic variability. Spring migrations were highly synchronous, while the timing of autumn migrations varied widely between regions, individuals and sexes. Overall, roe deer were faithful to their summer ranges, especially males. In the absence of extreme and predictable winter conditions, roe deer seemed to migrate opportunistically, in response to a tradeoff between the costs of residence in spatially separated ranges and the costs of migratory movements. Animals performed numerous trips between winter and summer ranges which depended on factors influencing the costs of movement such as between-range distance, slope and habitat openness. Our results support the idea that migration encompasses a behavioural continuum, with one-trip migration and residence as its end points, while commuting and multi-trip migration with short residence times in seasonal ranges are intermediate tactics. We believe that a full understanding of the variation in tactics of temporal separation in habitat use will provide important insights on migration and the factors that influence its prevalence.

Published
2011

3. Dominance style is a key predictor of vocal use and evolution across nonhuman primates

Author

Samantha J. Green, Daria Valente, Zarin P. Machanda, Erica van de Waal, Joan B. Silk, Christopher Young, Daniela Hedwig, Klaus Zuberbühler, Oliver Schülke, Lindsey Hagberg, Sally E. Street, Anna Zanoli, Mary S. M. Pavelka, Martha M. Robbins, Martin N. Muller, Chloe Chen-Kraus, Roberta Salmi, Barbara Fruth, Cristina Giacoma, Isaac Schamberg, Michelle Brown, Louise Peckre, Fredy Quintero, Richard W. Wrangham, Andrew J. J. MacIntosh, Shreejata Gupta, Gillian King-Bailey, Felix O. Angwela, Eithne Kavanagh, Stuart Semple, Zanna Clay, Melissa Emery Thompson, Claudia Wilke, Camille Coye, Julia Ostner, Cyril C. Grueter, Marco Gamba, Raffaella Ventura, Margarita Briseño-Jaramillo, Hugh Notman, Sophie Marshall, Jérôme Micheletta, Thore J. Bergman, Bonaventura Majolo, Anna H. Weyher, Megan Petersdorf, Valérie A. M. Schoof, Gabriel Ramos-Fernández, Maryjka B. Blaszczyk, Kirsty E. Graham, Adriano R. Lameira, Morgan L. Gustison, Alban Lemasson, Karim Ouattara, Alejandro Estrada, Laura M. Bolt, David Macgregor Inglis, Peter M. Kappeler, Valeria Torti, Claudia Fichtel, Barbora Kuběnová, Stéphanie Mercier, J. Roberto Sosa-López, Katharine M. Jack, Katie E. Slocombe, University of York [York, UK], Nottingham Trent University, Durham University, University of Michigan [Ann Arbor], University of Michigan System, University of Texas at Austin [Austin], University of Waterloo [Waterloo], Universidad Nacional Autónoma de México (UNAM), University of California [Santa Barbara] (UCSB), University of California, Yale University [New Haven], University of Exeter, Ethologie animale et humaine (EthoS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), No funding was provided specifically for the current paper, but funding which supported data collection at field sites is acknowledged in electronic supplementary material, S11., University of St Andrews. School of Psychology and Neuroscience, University of St Andrews. Institute of Behavioural and Neural Sciences, University of St Andrews. Centre for Social Learning & Cognitive Evolution, Mountains of the Moon University, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), The University of New Mexico [Albuquerque], German Primate Center - Deutsches Primatenzentrum -- Leibniz Insitute for Primate Research -- [Göttingen, Allemagne] (GPC - DPZ), Liverpool John Moores University (LJMU), Max Planck Institute of Animal Behavior, Università degli studi di Torino = University of Turin (UNITO), School of Psychology and Neuroscience [University of St. Andrews], University of St Andrews [Scotland], The University of Western Australia (UWA), Harvard University, Cornell University [New York], Tulane University, Kyoto University, University of Roehampton, United Kingdom, Tufts University [Medford], University of Lincoln, Université de Neufchätel (UNIME), University of Portsmouth, Athabasca University (AU), Centre Suisse de Recherches Scientifiques en Cote d'Ivoire [Abidjan] (CSRS-CI), University of Calgary, New York University [New York] (NYU), NYU System (NYU), Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, University of Georgia [USA], Arizona State University [Tempe] (ASU), Instituto Politecnico Nacional [Mexico] (IPN), Abertay University (Abertay University), Université de Lausanne = University of Lausanne (UNIL), University of Massachusetts [Amherst] (UMass Amherst), University of Massachusetts System (UMASS), University of Pretoria [South Africa], and University of Lethbridge

Subjects
0106 biological sciences, Science, Basic Behavioral and Social Science, 010603 evolutionary biology, 01 natural sciences, Key (music), Style (sociolinguistics), social behaviour, [SCCO]Cognitive science, biology.animal, ddc:570, Behavioral and Social Science, dominance style, 0501 psychology and cognitive sciences, Animal communication, Primate, 050102 behavioral science & comparative psychology, Research Articles, Sociality, QL, Multidisciplinary, biology, communication, QH, Repertoire, 05 social sciences, DAS, QL Zoology, sociality, vocal, C800 Psychology, vocal, sociality, communication, dominance style, social behaviour, Dominance hierarchy, Dominance (ethology), communication, sociality, social behaviour, dominance style, vocal, Organismal and Evolutionary Biology, Psychology, Cognitive psychology
Abstract

Animal communication has long been thought to be subject to pressures and constraints associated with social relationships. However, our understanding of how the nature and quality of social relationships relates to the use and evolution of communication is limited by a lack of directly comparable methods across multiple levels of analysis. Here, we analysed observational data from 111 wild groups belonging to 26 non-human primate species, to test how vocal communication relates to dominance style (the strictness with which a dominance hierarchy is enforced, ranging from 'despotic' to 'tolerant'). At the individual-level, we found that dominant individuals who were more tolerant vocalized at a higher rate than their despotic counterparts. This indicates that tolerance within a relationship may place pressure on the dominant partner to communicate more during social interactions. At the species-level, however, despotic species exhibited a larger repertoire of hierarchy-related vocalizations than their tolerant counterparts. Findings suggest primate signals are used and evolve in tandem with the nature of interactions that characterize individuals' social relationships. Publisher PDF

Published
2021

4. New data for the Early Upper Paleolithic of Kostenki (Russia)

Author

Andrei Sinitsyn, Thibaut Devièse, Natasha Reynolds, Mikhail V. Sablin, Thomas Higham, Alexander Bessudnov, Rob Dinnis, Abi Pate, British Museum, Institute for the History of Material Culture [St Petersburg], the Russian Academy of Sciences [Moscow, Russia] (RAS), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), School of Archaeology [Oxford], University of Oxford, Zoological Institute, Russian Academy of Sciences [Moscow] (RAS), This research was supported by the Leverhulme Trust (RPG-2012-800). A.B.'s work was supported by grants RFBR18-39-20009 and RSF18-78-00136, and by state assignment 0184-2018-0012. NR was supported during the writing of this paper by a Postdoctoral Study Grant from the Fondation Fyssen and the European Union's Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement No 747400. A.S. acknowledges grant RFBR17-06-00319a and state assignment 0184-2018-0012, and we also acknowledge the participation of ZIN RAS (state assignment АААА-А17-117022810195-3). The research that enabled the production of HYP radiocarbon dates came from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013), ERC grant 324139 'PalaeoChron', which also supported N.R., T.D. and T.H., European Project: 324139,EC:FP7:ERC,ERC-2012-ADG_20120411,PALAEOCHRON(2013), European Project: 747400,PeOPLE, and University of Oxford [Oxford]

Subjects
Radiocarbon dating, Bladelet technology, 010506 paleontology, Neanderthal, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Archaeological record, Eastern Europe, 01 natural sciences, law.invention, law, biology.animal, Assemblage (archaeology), 0601 history and archaeology, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, 060101 anthropology, biology, Anatomically modern humans, 06 humanities and the arts, Archaeology, Geography, Early Upper Palaeolithic, Anthropology, Upper Paleolithic, Period (geology), Kostenki, Aurignacian, Chronology
Abstract

Several questions remain regarding the timing and nature of the Neanderthal-anatomically modern human (AMH) transition in Europe. The situation in Eastern Europe is generally less clear due to the relatively few sites and a dearth of reliable radiocarbon dates. Claims have been made for both notably early AMH and notably late Neanderthal presence, as well as for early AMH (Aurignacian) dispersal into the region from Central/Western Europe. The Kostenki-Borshchevo complex (European Russia) of Early Upper Paleolithic (EUP) sites offers high-quality data to address these questions. Here we revise the chronology and cultural status of the key sites of Kostenki 17 and Kostenki 14. The Kostenki 17/II lithic assemblage shares important features with Proto-Aurignacian material, strengthening an association with AMHs. New radiocarbon dates for Kostenki 17/II of ∼41–40 ka cal BP agree with new dates for the recently excavated Kostenki 14/IVw, which shows some similarities to Kostenki 17/II. Dates of ≥41 ka cal BP from other Kostenki sites cannot be linked to diagnostic archaeological material, and therefore cannot be argued to date AMH occupation. Kostenki 14's Layer in Volcanic Ash assemblage, on the other hand, compares to Early Aurignacian material. New radiocarbon dates targeting diagnostic lithics date to 39–37 ka cal BP. Overall, Kostenki's early EUP is in good agreement with the archaeological record further west. Our results are therefore consistent with models predicting interregional penecontemporaneity of diagnostic EUP assemblages. Most importantly, our work highlights ongoing challenges for reliably radiocarbon dating the period. Dates for Kostenki 14 agreed with the samples' chronostratigraphic positions, but standard pre-treatment methods consistently produced incorrect ages for Kostenki 17/II. Extraction of hydroxyproline from bone collagen using preparative high-performance liquid chromatography, however, yielded results consistent with the samples' chronostratigraphic position and with the layer's archaeological contents. This suggests that for some sites compound-specific techniques are required to build reliable radiocarbon chronologies.

Published
2019

5. Concerns about the widespread use of rodent models for human risk assessments of endocrine disruptors

Author

Gabriel Livera, René Frydman, Delphine Moison, Vincent Muczynski, Alexandra Benachi, René Habert, R. Lambrot, Abdelali Lehraiki, Virginie Rouiller-Fabre, Geraldine Delbes, Tiphany Grisin, Christine Levacher, Marie-Justine Guerquin, Sébastien Messiaen, Thierry N’Tumba-Byn, Stabilité génétique, Cellules Souches et Radiations (SCSR (U_967)), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Service de gynécologie-obstétrique, médecine de la reproduction [Béclère], Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Antoine Béclère [Clamart], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), The work of our group presented in this paper was supported byUniversité Paris Diderot-Paris 7, CEA, INSERM, the FrenchAgence pour la Santé et la Sécurité dans l’Environnement et le Travail (AFSSET), the French Agence Nationale de SécuritéSanitaire de l’Alimentation, de l’Environnement et du Travail(ANSES Contrat EST62010/2/046), the Agence Nationale de laRecherche (ANR, contrat Phtalatestis and contrat MECABPA)and the Ministère de l’Ecologie, du Développement Durable,des Transports et du Logement (Programme ANTIOPES –Storm). None of the authors received any personal financialremuneration or funding for research studies from anychemical industrial company., ANR-07-SEST-0019,PHTALATESTIS,Effets et mécanismes d'action des phtalates sur le développement et les fonctions du testicule chez la souris et l'homme(2007), ANR-11-CESA-0001,MECABPA,Effets et mécanismes d'action du bisphénol A (BPA) sur le développement et les fonctions des gonades foetales chez la souris, la brebis et l'homme(2011), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), AP-HP - Hôpital Antoine Béclère [Clamart], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11), Courcelles, Michel, Santé-environnement et Santé-travail - Effets et mécanismes d'action des phtalates sur le développement et les fonctions du testicule chez la souris et l'homme - - PHTALATESTIS2007 - ANR-07-SEST-0019 - SEST - VALID, Contaminants et Environnements : Métrologie, santé, Adaptabilité, Comportements et Usages - Effets et mécanismes d'action du bisphénol A (BPA) sur le développement et les fonctions des gonades foetales chez la souris, la brebis et l'homme - - MECABPA2011 - ANR-11-CESA-0001 - CESA - VALID, Cellules Souches et Radiations (SCSR - U 967), Université Paris-Sud - Paris 11 (UP11) - Commissariat à l'énergie atomique et aux énergies alternatives (CEA) - Université Paris Diderot - Paris 7 (UPD7) - Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris-Sud - Paris 11 (UP11) - Assistance publique - Hôpitaux de Paris (AP-HP) - Hôpital Antoine Béclère, and Institut National de la Recherche Scientifique [Québec] (INRS) - Réseau International des Instituts Pasteur (RIIP) - Institut Armand Frappier

Subjects
Animal Experimentation, Male, Embryology, medicine.medical_specialty, Cell type, Rodent, [SDV]Life Sciences [q-bio], Retinoic acid, Rodentia, Review, Endocrine Disruptors, Risk Assessment, Mice, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Endocrinology, Internal medicine, biology.animal, Testis, Toxicity Tests, medicine, Animals, Humans, Endocrine system, Animal testing, [SDV.BDLR] Life Sciences [q-bio]/Reproductive Biology, Gametogenesis, 030304 developmental biology, 0303 health sciences, Fetus, 030219 obstetrics & reproductive medicine, biology, Phthalate, Obstetrics and Gynecology, Cell Biology, Rats, 3. Good health, [SDV.TOX] Life Sciences [q-bio]/Toxicology, [SDV] Life Sciences [q-bio], Reproductive Medicine, chemistry, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Models, Animal, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract

International audience; Fetal testis is a major target of endocrine disruptors (EDs). During the last 20 years, we have developed an organotypic culture system that maintains the function of the different fetal testis cell types and have used this approach as a toxicological test to evaluate the effects of various compounds on gametogenesis and steroidogenesis in rat, mouse and human testes. We named this test rat, mouse and human fetal testis assay. With this approach, we compared the effects of six potential EDs ((mono-(2-ethylhexyl) phthalate (MEHP), cadmium, depleted uranium, diethylstilboestrol (DES), bisphenol A (BPA) and metformin) and one signalling molecule (retinoic acid (RA)) on the function of rat, mouse and human fetal testis at a comparable developmental stage. We found that the response is similar in humans and rodents for only one third of our analyses. For instance, RA and MEHP have similar negative effects on gametogenesis in the three species. For another third of our analyses, the threshold efficient concentrations that disturb gametogenesis and/or steroidogenesis differ as a function of the species. For instance, BPA and metformin have similar negative effects on steroidogenesis in human and rodents, but at different threshold doses. For the last third of our analyses, the qualitative response is species specific. For instance, MEHP and DES affect steroidogenesis in rodents, but not in human fetal testis. These species differences raise concerns about the extrapolation of data obtained in rodents to human health risk assessment and highlight the need of rigorous comparisons of the effects in human and rodent models, when assessing ED risk.

Published
2014

6. BMC Genomics

Author

Grace C. Davey, Penelope K. Lindeque, Richard Reinhardt, Christophe Klopp, Pascal Favrel, Dario Moraga, Pierre Boudry, Sylvie Lapegue, Patrick Prunet, Arnaud Huvet, Julien de Lorgeril, Jeanne Moal, Viviane Boulo, Elodie Fleury, Christophe Lelong, Christopher Sauvage, Patrick Wincker, François Moreews, Michel Mathieu, Frédérick Gavory, Arnaud Tanguy, Caroline Fabioux, Charlotte Corporeau, Evelyne Bachère, Jenny P. Shaw, Yannick Gueguen, Laboratoire Environnement Ressources Morbihan Pays de Loire (LERMPL), LITTORAL (LITTORAL), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Brest (UBO), Plymouth Marine Laboratory (PML), Max-Planck-Institut für Molekulare Genetik (MPIMG), Max-Planck-Gesellschaft, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA), Génétique fonctionnelle, agronomie et santé [IFR 140] (GFAS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Diagnostics Centre (NDC), National University of Ireland [Galway] (NUI Galway), Laboratoire de Génétique et Pathologie (LGP), Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Systèmes d'Elevage, Nutrition Animale et Humaine (SENAH), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Rennes, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Laboratoire de Physiologie des Invertébrés (LPI), Physiologie Fonctionnelle des Organismes Marins (PFOM), The research presented in this paper was performed within the framework of several research projects funded by: Genoscope (11/AP2006-2007), Marine Genomics Network of Excellence (GOCE-CT-2004-505403), the European project 'Aquafirst' (513692) in the Sixth Framework Program, ANR 'CgPhysiogène' (ANR-06-GANI-0009) and 'Gametogenes' (ANR-08-GENM-041), ANR-06-GANI-0009,CgPhysiogene,Bases moléculaires des fonctions physiologiques de l'huître Crassostrea gigas : interactions hôte/pathogène/milieu(2006), ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008), Laboratoire Laboratoire Environnement Ressources Morbihan Pays de Loire (LER/MPL), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Plymouth Marine Laboratory, Institut National de la Recherche Agronomique (INRA)-IFR140, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Ecole Nationale Supérieure Agronomique de Rennes-Institut National de la Recherche Agronomique (INRA), Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Laboratoire de Physiologie des Invertébrés [Plouzané] (LPI), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Oyster, genome annotation, génomique fonctionnelle, computer.software_genre, Genome, User-Computer Interface, single nucleotide polymorphisms, Databases, Genetic, crassostrea gigas, structure du génome, Expressed Sequence Tags, base de données, 0303 health sciences, Expressed sequence tag, biology, Database, 04 agricultural and veterinary sciences, Genomics, crustacea, Pacific oyster, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], energy-balance, factor-beta superfamily, DNA microarray, expression des gènes, Biotechnology, lcsh:QH426-470, Sequence analysis, lcsh:Biotechnology, kappa-b, Polymorphism, Single Nucleotide, génomique, 03 medical and health sciences, biology.animal, lcsh:TP248.13-248.65, Genetics, summer mortality, Animals, Crassostrea, 030304 developmental biology, Gene Library, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, huître, cell-development, génome, Gene Expression Profiling, linkage maps, Sequence Analysis, DNA, biology.organism_classification, lcsh:Genetics, coquillage, 040102 fisheries, 0401 agriculture, forestry, and fisheries, identification, marine genomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Microsatellite Repeats
Abstract

Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.

Published
2009